Mass Pre-Contact Native Grave in California Yields Disappointing Results

Posted on October 20, 2015 by Roberta Estes

In 2012 during excavation for a shopping mall near San Francisco, a mass grave containing 7 men was unearthed. The manner in which they were buried led archaeologists to believe that they had been murdered, and quickly buried, not ceremonially buried as tribal members would be. They were found among more than 200 other burials.

The victims ages ranged from about 18 to about 40 and scientists concentrated on analyzing the wounds, cause of death and DNA of these men. In part, they wanted to see if they were related to each other and if they originated in this area or came from elsewhere. In other words, were they unsuccessful invaders as suggested by the circumstances of their burials?

This article tells more about the excavations and includes some photos.

Analysis suggests the men lived about 1200 years ago, clearly before European contact. Analysis of the men’s teeth provided information about their history. These men had spent their lives together, but their isotope signatures were clearly different than the individuals in the balance of the burials. Indeed, they look to have been invaders.

An academic paper titled “Isotopic and genetic analysis of a mass grave in central California: Implications for precontact hunter-gatherer warfare” was published a few weeks ago in the American Journal of Physical Anthropology. The article itself is behind a paywall available here. The abstract is provided below:

Abstract

OBJECTIVES:

Analysis of a mass burial of seven males at CA-ALA-554, a prehistoric site in the Amador Valley, CA, was undertaken to determine if the individuals were “locals” or “non-locals,” and how they were genetically related to one another.

METHODS:

The study includes osteological, genetic (mtDNA), and stable (C, N, O, S) and radiogenic (Sr) isotope analyses of bone and tooth (first and third molars) samples.

RESULTS:

Isotopes in first molars, third molars, and bone show they spent the majority of their lives living together. They are not locals to the Amador Valley, but were recently living to the east in the San Joaquin Valley, suggesting intergroup warfare as the cause of death. The men were not maternally related, but represent at least four different matrilines. The men also changed residence as a group between age 16 and adult years.

CONCLUSIONS:

Isotope data suggest intergroup warfare accounts for the mass burial. Genetic data suggest the raiding party included sets of unrelated men, perhaps from different households. Generalizing from this case and others like it, we hypothesize that competition over territory was a major factor behind ancient warfare in Central California. We present a testable model of demographic expansion, wherein villages in high-population-density areas frequently fissioned, with groups of individuals moving to lower-population-density areas to establish new villages. This model is consistent with previous models of linguistic expansion. Am J Phys Anthropol, 2015. © 2015 Wiley Periodicals, Inc.

http://www.ncbi.nlm.nih.gov/pubmed/26331533

Genetic Information

I was extremely disappointed with the genetic information. Working with the local Ohlone community, the scientists did attempt to extract DNA from the 7 individuals in the mass grave, with 6 extractions being successful.

They only analyzed the HVR1 region of the mitochondrial DNA.

In the paper, the authors indicate that nuclear DNA which would include the Y chromosome as well as autosomal DNA was too degraded to recover. While disappointing, there is nothing they can do about that.

However, only analyzing the mitochondrial DNA, which they clearly were able to amplify, at the HVR1 level is an incredible lost opportunity. They obtained enough resolution in 6 of the individuals to obtain general haplogroup assignments. However, the HVR2 and coding regions would have provided the defining information about extended haplogroups and individual mutations, including, perhaps, haplogroups rarely or never seen previously in the Americas.

Furthermore, given the information above, we can’t tell if the D1 individuals are related to each other matrilineally or not. The B2 individuals are clearly not related in a recent timeframe nor are the A2, B2 and D1 people related to each other on their matrilineal line. What a shame more information wasn’t obtained.

While I’m grateful that DNA testing was undertaken, I’m saddened by the partial results, especially in this day of full genomic sequencing for ancient DNA specimens. I’m perplexed as to why they would not have obtained as much information as was possible, given the significant effort expended in recovering any ancient DNA specimen.

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Some Native Americans Had Oceanic Ancestors

Posted on July 22, 2015 by Roberta Estes

This week has seen a flurry of new scientific and news articles. What has been causing such a stir? It appears that Australian or more accurately, Australo-Melanese DNA has been found in South America’s Native American population. In addition, it has also been found in Aleutian Islanders off the coast of Alaska. In case you aren’t aware, that’s about 8,500 miles as the crow flies. That’s one tired crow. As the person paddles or walks along the shoreline, it’s even further, probably about 12,000 miles.

Whatever the story, it was quite a journey and it certainly wasn’t all over flat land.

This isn’t the first inkling we’ve had. Just a couple weeks ago, it was revealed that the Botocudo remains from Brazil were Polynesian and not admixed with either Native, European or African. This admixture was first discovered via mitochondrial DNA, but full genome sequencing confirmed their ancestry and added the twist that they were not admixed – an extremely unexpected finding. This is admittedly a bit confusing, because it implies that there were new Polynesian arrivals in the 1600s or 1700s.

Unlikely as it seems, it obviously happened, so we set that aside as relatively contemporary.

The findings in the papers just released are anything but contemporary.

The First Article

The first article in Science, “Genomic evidence for the Pleistocene and recent population history of Native Americans” by Raghaven et al published this week provides the following summary (bolding is mine):

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Following their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 KYA, one that is now dispersed across North and South America and the other is restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative ‘Paleoamerican’ relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

This article in EurekAlert and a second one here discuss the Science paper.

Migration map from the Raghaven paper.

The paper included the gene flow and population migration map, above, along with dates.

The scientists sequenced the DNA of 31 living individuals from the Americas, Siberia and Oceana as follows:

Siberian:

Altai – 2
Buryat – 2
Ket – 2
Kiryak – 2
Sakha – 2
Siberian Yupik – 2

North American Native:

Tsimshian (number not stated, but by subtraction, it’s 1)

Southern North American, Central and South American Native:

Pima – 1
Huichol -1
Aymara – 1
Yakpa – 1

Oceana:

Papuan – 14

The researchers also state that they utilized 17 specimens from relict groups such as the Pericues from Mexico and Fuego-Patagonians from the southernmost tip of South America. They also sequenced two pre-Columbian mummies from the Sierra Tarahumara in northern Mexico. In total, 23 ancient samples from the Americas were utilized.

They then compared these results with a reference panel of 3053 individuals from 169 populations which included the ancient Saqqaq Greenland individual at 400 years of age as well as the Anzick child from Montana from about 12,500 years ago and the Mal’ta child from Siberia at 24,000 years of age.

Not surprisingly, all of the contemporary samples with the exception of the Tsimshian genome showed recent western Eurasian admixture.

As expected, the results confirm that the Yupik and Koryak are the closest Eurasian population to the Americas. They indicate that there is a “clean split” between the Native American population and the Koryak about 20,000 years ago.

They found that “Athabascans and Anzick-1, but not the Greenlandis Inuit and Saqqaq belong to the same initial migration wave that gave rise to present-day Amerindians from southern North America and Central and South America, and that this migration likely followed a coastal route, given our current understanding of the glacial geological and paleoenvironmental parameters of the Late Pleistocene.”

Evidence of gene flow between the two groups was also found, meaning between the Athabascans and the Inuit. Additionally, they found evidence of post-split gene flow between Siberians and Native Americans which seems to have stopped about 12,000 years ago, which meshes with the time that the Beringia land bridge was flooded by rising seas, cutting off land access between the two land masses.

They state that the results support all Native migration from Siberia, contradicting claims of an early migration from Europe.

The researchers then studied the Karitiana people of South America and determined that the two groups, Athabascans and Karitiana diverged about 13,000 years ago, probably not in current day Alaska, but in lower North America. This makes sense, because the Clovis Anzick child, found in Montana, most closely matches people in South America.

By the Clovis period of about 12,500 years ago, the Native American population had already split into two branches, the northern and southern, with the northern including Athabascan and other groups such as the Chippewa, Cree and Ojibwa. The Southern group included people from southern North America and Central and South America.

Interestingly, while admixture with the Inuit was found with the Athabascan, Inuit admixture was not found among the Cree, Ojibwa and Chippewa. The researchers suggest that this may be why the southern branch, such as the Karitiana are genetically closer to the northern Amerindians located further east than to northwest coast Amerindians and Athabascans.

Finally, we get to the Australian part. The researchers when trying to sort through the “who is closer to whom” puzzle found unexpected results. They found that some Native American populations including Aleutian Islanders, Surui (Brazil) and Athabascans are closer to Australo-Melanesians compared to other Native Americans, such as Ojibwa, Cree and Algonquian and South American Purepecha (Mexico), Arhuaco (Colombia) and Wayuu (Colombia, Venezuela). In fact, the Surui are one of the closest populations to East Asians and Australo-Melanese, the latter including Papuans, non-Papuan Melanesians, Solomon Islanders and hunter-gatherers such as Aeta. The researchers acknowledge these are weak trends, but they are nonetheless consistently present.

Dr. David Reich, from Harvard, a co-author of another paper, also published this past week, says that 2% of the DNA of Amazonians is from Oceana. If that is consistent, it speaks to a founder population in isolation, such that the 2% just keeps getting passed around in the isolated population, never being diluted by outside DNA. I would suggest that is not a weak signal.

The researchers suggest that the variance in the strength of this Oceanic signal suggests that the introduction of the Australo-Melanese occurred after the initial peopling of the Americas. The ancient samples cluster with the Native American groups and do not show the Oceanic markers and show no evidence of gene flow from Oceana.

The researchers also included cranial morphology analysis, which I am omitting since cranial morphology seems to have led researchers astray in the past, specifically in the case of Kennewick man.

One of the reasons cranial morphology is such a hotly debated topic is because of the very high degree of cranial variance found in early skeletal remains. One of the theories evolving from the cranial differences involving the populating of the Americans has been that the Australo-Melanese were part of a separate and earlier migration that gave rise to the earliest Americans who were then later replaced by the Asian ancestors of current day Native Americans. If this were the case, then the now-extinct Fuego-Patagonains samples from the location furthest south on the South American land mass should have included DNA from Oceana, but it didn’t.

The Second Article

A second article published this week, titled “’Ghost population’ hints at long lost migration to the Americas” by Ellen Callaway discusses similar findings, presented in a draft letter to Nature titled “Genetic evidence for two founding populations of the Americas” by Skoglund et al. This second group discovers the same artifact Australo-Melanesian DNA in Native American populations but suggests that it may be from the original migration and settlement event or that there may have been two distinct founding populations that settled at the same time or that there were two founding events.

EurekAlert discusses the article as well.

It’s good to have confirmation and agreement between the two labs who happened across these results independently that the Australo-Melanesian DNA is present in some Native populations today.

Their interpretations and theories about how this Oceanic DNA arrived in some of the Native populations vary a bit, but if you read the details, it’s really not quite as different as it first appears from the headlines. Neither group claims to know for sure, and both discuss possibilities.

Questions remain. For example, if the founding group was small, why, then, don’t all of the Native people and populations have at least some Oceanic markers? The Anzick Child from 12,500 years ago does not. He is most closely related to the tribes in South America, where the Oceanic markers appear with the highest frequencies.

In the Harvard study, the scientists fully genome sequenced 63 individuals without discernable evidence of European or African ancestors in 21 Native American populations, restricting their study to individuals from Central and South America that have the strongest evidence of being entirely derived from a homogenous First American ancestral population.

Their results show that the two Amazonian groups, Surui and Karitians are closest to the “Australasian populations, the Onge from the Andaman Island in the Bay of Bengal (a so-called ‘Negrito’ group), New Guineans, Papuans and indigenous Australians.” Within those groups, the Australasian populations are the only outliers – meaning no Africans, Europeans or East Asian DNA found in the Native American people.

When repeating these tests, utilizing blood instead of saliva, a third group was shown to also carry these Oceanic markers – the Xavante, a population from the Brazilian plateau that speaks a language of the Ge group that is different from the Tupi language group spoke by the Karitians and Surui.

The closest populations that these Native people matched in Oceana, shown above on the map from the draft Skoglund letter, were, in order, New Guineans, Papuans and Andamanese. The researchers further state that populations from west of the Andes or north of the Panama isthmus show no significant evidence of an affinity to the Onge from the Andaman Islands with the exception of the Cabecar (Costa Rica).

That’s a very surprising finding, given that one would expect more admixture on the west, which is the side of the continent where the migration occurred.

The researchers then compared the results with other individuals, such as Mal’ta child who is known to have contributed DNA to the Native people today, and found no correlation with Oceanic DNA. Therefore, they surmised that the Oceanic admixture cannot be explained by a previously known admixture event.

They propose that a mystery population they have labeled as “Population Y” (after Ypykuera which means ancestor in the Tupi language family) contributed the Australasian lineage to the First Americans and that is was already mixed into the lineage by the time it arrived in Brazil.

According to their work, Population Y may itself have been admixed, and the 2% of Oceanic DNA found in the Brazilian Natives may be an artifact of between 2 and 85% of the DNA of the Surui, Karitiana and Xavante that may have come from Population Y. They mention that this result is striking in that the majority of the craniums that are more Oceanic in Nature than Asiatic, as would be expected from people who migrated from Siberia, are found in Brazil.

They conclude that the variance in the presence or absence of DNA in Native people and remains, and the differing percentages argue for more than one migration event and that “the genetic ancestry of Native Americans from Central and South America cannot be due to a single pulse of migration south of the Late Pleistocene ice sheets from a homogenous source population, and instead must reflect at least two streams of migration or alternatively a long drawn out period of gene flow from a structured Beringian or Northeast Asian source.”

Perhaps even more interesting is the following statement:

“The arrival of population Y ancestry in the Americas must in any scenario have been ancient: while Population Y shows a distant genetic affinity to Andamanese, Australian and New Guinean populations, it is not particularly closely related to any of them, suggesting that the source of population Y in Eurasia no longer exists.”

They further state they find no admixture indication that would suggest that Population Y arrived in the last few thousand years.

So, it appears that perhaps the Neanderthals and Denisovans were not the only people who were our ancestors, but no longer exist as a separate people, only as an admixed part of us today. We are their legacy.

The Take Away

When I did the Anzick extractions, we had hints that something of this sort might have been occurring. For example, I found surprising instances of haplogroup M, which is neither European, African nor Native American, so far as we know today. This may have been a foreshadowing of this Oceanic admixture. It may also be a mitochondrial artifact. Time will tell. Perhaps haplogroup M will turn out to be Native by virtue of being Oceanic and admixed thousands of years ago. There is still a great deal to learn. Regardless of how these haplogroups and Oceanic DNA arrived in Brazil in South America and in the Aleutian Islands off of Alaska, one thing is for sure, it did.

We know that the Oceanic DNA found in the Brazilian people studied for these articles is not contemporary and is ancient. This means that it is not related to the Oceanic DNA found in the Botocudo people, who, by the way, also sport mitochondrial haplogroups that are within the range of Native people, meaning haplogroup B, but have not been found in other Native people. Specifically, haplogroups B4a1a1 and B4a1a1a. Additionally, there are other B4a1a, B4a1b and B4a1b1 results found in the Anzick extract which could also be Oceanic. You can see all of the potential and confirmed Native American mitochondrial DNA results in my article “Native American Mitochondrial Haplogroups” that I update regularly.

We don’t know how or when the Botocudo arrived, but the when has been narrowed to the 1600s or 1700s. We don’t know how or when the Oceanic DNA in the Brazilian people arrived either, but the when was ancient. This means that Oceanic DNA has arrived in South America at least twice and is found among the Native peoples both times.

We know that some Native groups have some Oceanic admixture, and others seem to have none, in particular the Northern split group that became the Cree, Ojibwa, Algonquian, and Chippewa.

We know that the Brazilian Native groups are most closely related to Oceanic groups, but that the first paper also found Oceanic admixture in the Aleutian Islands. The second paper focused on the Central and South American tribes.

We know that the eastern American tribes, specifically the Algonquian tribes are closely related to the South Americans, but they don’t share the Oceanic DNA and neither do the mid-continent tribes like the Cree, Ojibwa and Chippewa. The only Paleolithic skeleton that has been sequenced, Anzick, from 12,500 years ago in Montana also does not carry the Oceanic signature.

In my opinion, the disparity between who does and does not carry the Oceanic signature suggests that the source of the Oceanic DNA in the Native population could not have been a member of the first party to exit out of Beringia and settle in what is now the Americas. Given that this had to be a small party, all of the individuals would have been thoroughly admixed with each other’s ancestral DNA within just a couple of generations. It would have been impossible for one ancestor’s DNA to only be found in some people. To me, this argues for one of two scenarios.

First, a second immigration wave that joined the first wave but did not admix with some groups that might have already split off from the original group such as the Anzick/Montana group.

Second, multiple Oceanic immigration events. We still have to consider the possibility that there were multiple events that introduced Oceanic DNA into the Native population. In other words, perhaps the Aleutian Islands Oceanic DNA is not from the same migration event as the Brazilian DNA which we know is not from the same event as the Botocudo. I would very much like to see the Oceanic DNA appear in a migration path of people, not just in one place and then the other. We need to connect the dots.

What this new information does is to rule out the possibility that there truly was only one wave of migration – one group of people who settled the Americas at one time. More likely, at least until the land bridge submerged, is that there were multiple small groups that exited Beringia over the 8,000 or so years it was inhabitable. Maybe one of those groups included people from Oceana. Someplace, sometime, as unlikely as it seems, it happened.

The amazing thing is that it’s more than 10,000 miles from Australia to the Aleutian Islands, directly across the Pacific. Early adventurers would have likely followed a coastal route to be sustainable, which would have been significantly longer. The fact that they survived and sent their DNA on a long adventure from Australia to Alaska to South America – and it’s still present today is absolutely amazing.

We know we still have a lot to learn and this is the tip of a very exciting iceberg. As more contemporary and ancient Native people have their full genomes sequenced, we’ll learn more answers. The answer is in the DNA. We just have to sequence enough of it and learn how to understand the message being delivered.

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Botocudo Ancient Remains from Brazil

Posted on July 2, 2015 by Roberta Estes

Update: Please note that I am leaving this article because the scientific information is accurate, BUT, it was subsequently discovered that the remains were mislabeled in the museum and were not Native.

One thing you can always count on in the infant science of population genetics… whatever you think you know, for sure, for a fact…well….you don’t. So don’t say too much, too strongly or you’ll wind up having to decide if you’d like catsup with your crow! Well, not literally, of course. It’s an exciting adventure that we’re on together and it just keeps getting better and better. And the times…they are a changin’.

Courtesy National Geographic https://natgeoeducationblog.files.wordpress.com/2015/04/world_map_of_y-dna_haplogroups.png

We have some very interesting news to report. Fortunately, or unfortunately – the news weaves a new, but extremely interesting, mystery.

Ancient Mitochondrial DNA

Back in 2013, a paper, Identification of Polynesian mtdNA haplogroups in remains of Botocudo Amerindians from Brazil, was published that identified both Native American and Polynesian haplogroups in a group of 14 skeletal remains of Botocudo Indians from Brazil whose remains arrived at a Museum in August of 1890 and who, the scientists felt, died in the second half of the 19^th century.

Twelve of their mitochondrial haplogroups were the traditional Native haplogroup of C1.

However, two of the skulls carried Polynesian haplogroups, downstream of haplogroup B, specifically B4a1a1a and B4a1a1, that compare to contemporary individuals from Polynesian, Solomon Island and Fijian populations. These haplotypes had not been found in Native people or previous remains.

Those haplogroups include what is known as the Polynesian motif and are found in Indonesian populations and also in Madagascar, according to the paper, but the time to the most common recent ancestor for that motif was calculated at 9,300 years plus or minus 2000 years. This suggests that the motif arose after the Asian people who would become the Native Americans had already entered North and South America through Beringia, assuming there were no later migration waves.

The paper discusses several possible scenarios as to how a Polynesian haplotype found its way to central Brazil among a now extinct Native people. Of course, the two options are either pre-Columbian (pre-1500) contact or post-Columbian contact which would infer from the 1500s to current and suggests that the founders who carried the Polynesian motif were perhaps either slaves or sailors.

In the first half of the 1800s, the Botocudo Indians had been pacified and worked side by side with African slaves on plantations.

Beyond that, without full genome sequencing there was no more that could be determined from the remains at that time. We know they carried a Polynesian motif, were found among Native American remains and at some point in history, intermingled with the Native people because of where they were found. Initial contact could have been 9,000 years ago or 200. There was no way to tell. They did have some exact HVR1 and HVR2 matches, so they could have been “current,” but I’ve also seen HVR1 and HVR2 matches that reach back to a common ancestor thousands of years ago…so an HVR1/HVR2 match is nothing you can take to the bank, certainly not in this case.

Full Genome Sequencing and Y DNA

This week, one on my subscribers, Kalani, mentioned that Felix Immanuel had uploaded another two kits to GedMatch of ancient remains. Those two kits are indeed two of the Botocudo remains – the two with the Polynesian mitochondrial motif which have now been fully sequenced. A corresponding paper has been published as well, “Two ancient genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil” by Malaspinas et al with supplemental information here.

There are two revelations which are absolutely fascinating in this paper and citizen scientist’s subsequent work.

First, their Y haplogroups are C-P3092 and C-Z31878, both equivalent to C-B477 which identifies former haplogroup C1b2. The Y haplogroups aren’t identified in the paper, but Felix identified them in the raw data files that are available (for those of you who are gluttons for punishment) at the google drive links in Felix’s article Two Ancient DNA from indigenous Botocudos of Brazil.

I’ve never seen haplogroup C1b2 as Native American, but I wanted to be sure I hadn’t missed a bus, so I contacted Ray Banks who is one of the administrators for the main haplogroup C project at Family Tree DNA and also is the coordinator for the haplogroup C portion of the ISOGG tree.

You can see the position of C1b2, C-B477 in yellow on the ISOGG (2015) tree relative to the position of C-P39 in blue, the Native American SNP shown several branches below, both as branches of haplogroup C.

Ray maintains a much more descriptive tree of haplogroup C1 at this link and of C2 at this link.

The branch above is the Polynesian (B477) branch and below, the Native American (P39) branch of haplogroup C.

In addition to confirming the haplogroup that Felix identified, when Ray downloaded the BAM files and analyzed the contents, he found that both samples were also positive for M38 and M208, which moves them downstream two branches from C1b2 (B477).

Furthermore, one of the samples had a mutation at Z32295 which Ray has included as a new branch of the C tree, shown below.

Ray indicated that the second sample had a “no read” at Z32295, so we don’t know if he carried this mutation. Ray mentions that both men are negative for many of the B459 equivalents, which would move them down one more branch. He also mentioned that about half of the Y DNA sites are missing, meaning they had no calls in the sequence read. This is common in ancient DNA results. It would be very interesting to have a Big Y or equivalent test on contemporary individuals with this haplogroup from the Pacific Island region.

Ray notes that all Pacific Islanders may be downstream of Z33295.

Not Admixed

The second interesting aspect of the genomic sequencing is that the remains did not show any evidence of admixture with European, Native American nor African individuals. More than 97% of their genome fits exactly with the Polynesian motifs. In other words, they appear to be first generation Polynesians. They carry Polynesian mitochondrial, Y and autosomal (nuclear) DNA, exclusively.

In total, 25 Botocudo remains have been analyzed and of those, two have Polynesian ancestry and those two, BOT15 and BOT17, have exclusively Polynesian ancestry as indicated in the graphic above from the paper.

When did they live? Accelerator mass spectrometry radiocarbon dating with marine correction gives us dates of 1479-1708 AD and 1730-1804 for specimen BOT15 and 1496-1842 for BOT17.

The paper goes on to discuss four possible scenarios for how this situation occurred and the pros and cons of each.

The Polynesian Peru Slave Trade

This occurred between 1862-1864 and can be ruled out because the dates for the skulls predate this trade period, significantly.

The Madagascar-Brazil Slave Trade

The researchers state that Madagascar is known to have been peopled by Southeast Asians and not by Polynesians. Another factor excluding this option is that it’s known that the Malagasy ancestors admixed with African populations prior to the slave trade. No such ancestry was detected in the samples, so these individuals were not brought as a result of the Madagascar-Brazil slave trade – contrary to what has been erroneously inferred and concluded.

Voyaging on European Ships as Crew, Passengers or StowAways

Trade on Euroamerican ships in the Pacific only began after 1760 AD and by 1760, Bot15 and Bot17 were already deceased with a probability of .92 and .81, respectively, making this scenario unlikely, but not entirely impossible.

Polynesian Voyaging

Polynesian ancestors originated from East Asia and migrated eastwards, interacting with New Guineans before colonizing the Pacific. These people did colonize the Pacific, as unlikely as it seems, traveling thousands of miles, reaching New Zealand, Hawaii and Easter Island between 1200 and 1300 AD. Clearly they did not reach Brazil in this timeframe, at least not as related to these skeletal remains, but that does not preclude a later voyage.

Of the four options, the first two appear to be firmly eliminated which leaves only the second two options.

One of the puzzling aspects of this analysis it the “pure” Polynesian genome, eliminating admixture which precludes earlier arrival.

The second puzzling aspect is how the individuals, and there were at least two, came to find themselves in Minas Gerais, Brazil, and why we have not found this type of DNA on the more likely western coastal areas of South America.

Regardless of how they arrived, they did, and now we know at least a little more of their story.

GedMatch

At GedMatch, it’s interesting to view the results of the one-to-one matching.

Both kits have several matches. At 5cM and 500 SNPs, kit F999963 has 86 matches. Of those, the mitochondrial haplogroup distribution is overwhelmingly haplogroup B, specifically B4a1a1 with a couple of interesting haplogroup Ms.

Y haplogroups are primarily C2, C3 and O. C3 and O are found exclusively in Asia – meaning they are not Native.

Kit F999963 matches a couple of people at over 30cM with a generation match estimate just under 5 generations. Clearly, this isn’t possible given that this person had died by about 1760, according to the paper, which is 255 years or about 8.5-10 generations ago, but it says something about the staying power of DNA segments and probably about endogamy and a very limited gene pool as well. All matches over 15cM are shown below.

Kit F999964 matches 97 people, many who are different people that kit F999963 matched. So these ancient Polynesian people, F999963 and F999964 don’t appear to be immediate relatives.

Again, a lot of haplogroup B mitochondrial DNA, but less haplogroup C Y DNA and no haplogroup O individuals.

Kit F999964 doesn’t match anyone quite as closely as kit F999963 did in terms of total cM, but the largest segment is 12cM, so the generational estimate is still at 4.6, All matches over 15cM are shown below.

Who are these individuals that these ancient kits are matching? Many of these individuals know each other because they are of Hawaiian or Polynesian heritage and have already been working together. Several of the Hawaiian folks are upwards of 80%, one at 94% and one believed to be 100% Hawaiian. Some of these matches are to Maori, a Polynesian people from New Zealand, with one believed to be 100% Maori in addition to several admixed Maori. So obviously, these ancient remains are matching contemporary people with Polynesian ancestry.

The Unasked Question

Sooner or later, we as a community are going to have to face the question of exactly what is Native or aboriginal. In this case, because we do have the definitive autosomal full genome testing that eliminates admixture, these two individuals are clearly NOT Native. Without full genomic testing, we would have never known.

But what if they had arrived 200 years earlier, around 1500 AD, one way or another, possibly on an early European ship, and had intermixed with the Native people for 10 generations? What if they carried a Polynesian mitochondrial (or Y) DNA motif, but they were nearly entirely Native, or so much Native that the Polynesian could no longer be found autosomally? Are they Native? Is their mitochondrial or Y DNA now also considered to be Native? Or is it still Polynesian? Is it Polynesian if it’s found in the Cook Islands or on Hawaii and Native if found in South America? How would we differentiate?

What if they arrived, not in 1500 AD, but about the year 500 AD, or 1000 BCE or 2000 BCE or 3000 BCE – after the Native people from Asia arrived but unquestionably before European contact? Does that make a difference in how we classify their DNA?

We don’t have to answer this yet today, but something tells me that we will, sooner or later…and we might want to start pondering the question.

Acknowledgements:

I want to thank all of the people involved whose individual work makes this type of comparative analysis possible. After all, the power of genetic genealogy, contemporary or ancient, is in collaboration. Without sharing, we have nothing. We learn nothing. We make no progress.

In addition to the various scientists and papers already noted, special thanks to Felix Immanual for preparing and uploading the ancient files. This is no small task and the files often take a month of prep each. Thanks to Kalani for bringing this to my attention. Thanks to Ray Banks for his untiring work with haplogroup C and for maintaining his haplogroup webpage with specifics about where the various subgroups are found. Thanks to ISOGG’s volunteers for the haplotree. Thanks to GedMatch for providing this wonderful platform and tools. Thanks to everyone who uploads their DNA, and that of their relatives and works on specific types of projects – like Hawaiian and Maori. Thanks to my haplogroup C-P39 co-administrators, Dr. David Pike and Marie Rundquist, for their contributions to this discussion and for working together on the Native American Haplogroup C-P39 Project. It’s important to have other people who are passionate about the same subjects to bounce things off of and to work with. This is the perfect example of the power of collaboration!

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Kennewick Man is Native American

Posted on June 18, 2015 by Roberta Estes

Finally, an answer, after almost 20 years and very nearly losing the opportunity of ever knowing.

Today, in Nature, a team of scientists released information about the full genomic sequencing of Kennewick Man who was discovered in 1996 in Washington state. Previous DNA sequencing attempts had failed, and 8000 year old Kennewick Man was then embroiled in years of legal battles. Ironically, the only reason DNA testing was allowed is because, based on cranial morphology it was determined that he was likely more closely associated with Asian people or the Auni than the Native American population, and therefore NAGPRA did not apply. However, subsequent DNA testing has removed all question about Kennewick Man’s history. He truly is the Ancient One.

Kennewick man is Native American. His Y haplogroup is Q-M3 and his mitochondrial DNA is X2a. This autosomal DNA was analyzed as well, and compared to some current tribes, where available.

From the paper:

We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man. We revisit the cranial analyses and find that, as opposed to genomic-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia.

Interestingly enough, the Colville Tribe, located near where Kennewick Man was found, decided to participate in the testing by submitting DNA for comparison.

The ancestry and affiliations of Kennewick Man by Rasmussen, et al, Nature (2015) doi:10.1038/nature14625

Also from the paper:

Our results are in agreement with a basal divergence of Northern and Central/Southern Native American lineages as suggested from the analysis of the Anzick-1 genome¹². However, the genetic affinities of Kennewick Man reveal additional complexity in the population history of the Northern lineage. The finding that Kennewick is more closely related to Southern than many Northern Native Americans (Extended Data Fig. 4) suggests the presence of an additional Northern lineage that diverged from the common ancestral population of Anzick-1 and Southern Native Americans (Fig. 3). This branch would include both Colville and other tribes of the Pacific Northwest such as the Stswecem’c, who also appear symmetric to Kennewick with Southern Native Americans (Extended Data Fig. 4). We also find evidence for additional gene flow into the Pacific Northwest related to Asian populations (Extended Data Fig. 5), which is likely to post-date Kennewick Man. We note that this gene flow could originate from within the Americas, for example in association with the migration of paleo-Eskimos or Inuit ancestors within the past 5 thousand years²⁵, or the gene flow could be post colonial¹⁹.

The authors go on to say that Kennewick Man is significiantly different than Anzick Child, which matches closely with many Meso and South American samples. Kennewick on the other hand, is closely related to the Chippewa and Anzick was not.

This divergence may suggest a population substructure and migration path within the Americas, although I would think significantly more testing of Native people would be in order before a migration path would be able to be determined or even suggested. It is very interesting that Anzick from Montana, 12,500 years ago, would match Meso American samples so closely. I would have expected Kennewick to perhaps match Meso Americans more closely because I would have expected the migration pathway to be down the coastline. Perhaps that migration had already happened by the time Kennewick man came onto the scene some 8000 years ago.

You can read the entire paper at this link.

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Yamnaya, Light Skinned, Brown Eyed….Ancestors???

Posted on June 15, 2015 by Roberta Estes

Late last fall, I reported that scientists had discovered a European ghost population. This group of people then referred to as the ANE, Ancient Northern Europeans, was a previously unknown population from the north that had mixed into the known European populations, the Hunter-Gatherers and the farmers from the Middle East, the Neolithic.

That discovery came as a result of the full genome sequencing of a few ancient specimens, including one from the Altai.

Recently, several papers have been published as a result of ongoing sequencing efforts of another 200 or so ancient specimens. As a result, scientists now believe that this ghost population has been identified as the Yamnaya and that they began a mass migration in different directions, including Europe, about 5,000 years ago. Along with their light skin and brown eyes, they brought along with them their gene(s) for lactose tolerance. So, if you have European heritage and are lactose tolerant, then maybe you can thank your Yamnaya ancestors.

1.Haak et al. http://doi.org/z9d (2015) from Feb. 18, 2015 “Steppe migration rekindles debate on language origin” by Ellen Callaway

For those of us who avidly follow these types of discoveries, this is not only amazing, it’s wonderful news. It helps to continue to explain how and why some haplogroups are found in the Native American population and in the Northern European population as well. For example, haplogroup Q is found in both places – not exact duplicates, but certainly close enough for us to know they were at one time related. It also explains how people from Germany, for example, are showing small percentages of Native American ancestry. Their common ancestors were indeed from central Asia, thousands of years ago, and we can still see vestiges of that population today in both groups of people.

So, if the Yamnaya people are the ghost people, the ANE, who are they?

The Yamna culture was primarily nomadic and was found in Russia in the Ural Region, the Pontic Steppe, dating to the 36^th-23^rd century BC. It is also known as the Pit Grave Culture, the Ochre Grave Culture and feeds into the Corded Ware Culture.

“Corded Ware culture” by User:Dbachmann – Own work based based on Image:Europe 34 62 -12 54 blank map.png. Licensed under CC BY-SA 3.0 via Wikimedia Commons – https://commons.wikimedia.org/wiki/File:Corded_Ware_culture.png#/media/File:Corded_Ware_culture.png

Characteristics for the culture are burials in kurgans (tumuli) in pit graves with the dead body placed in a supine position with bent knees. The bodies were covered in ochre. Multiple graves have been found in these kurgans, often as later insertions. The first known cart burial is also found in a kurgan grave. A kurgan often appears as a hill, example shown below, and have been found in locations throughout eastern and northern Europe..

Hallstatt-era tumulus in the Sulm valley necropolis in Austria, photo by Hermann A. M. Mucke.

Additionally, some scientists believe that the Yamna culture was responsible for the introduction of PIE, Proto-Indo-European-Language, the now defunct mother-tongue of European languages. Others think it’s way too soon to tell, and that suggestion is jumping the gun a bit.

Why might these recent discoveries be important to many genetic genealogists? Primarily, because Y haplogroup R has been identified in ancient Russian remains dating from 2700-3400 BCE. Haplogroup R and subgroups had not been found in the ancient European remains sequenced as of last fall. In addition, subgroups of mitochondrial haplogroups U, W, H, T and W have been identified as well.

Keep in mind that we are still dealing with less than 300 skeletal remains that have been fully sequenced. This trend may hold, or a new discovery may well cause the thought pattern to be “reconfigured” slightly or significantly. Regardless, it’s exciting to be part of the learning and discovery process.

Oh yes, and before I forget to mention it…it seems that your Neanderthal ancestors may not be as far back in your tree as you thought. They have now found 40,000 year old skeletal remains that suggest that person’s great-great-grandfather was in fact, full Neanderthal. That’s significantly later than previously thought, by 10,000 or 20,000 years, and in Europe, not the Near East…and who knows what is just waiting to be found. The new field of ancient DNA is literally bursting open as we watch.

I’ve accumulated several recent articles and some abstracts so that you can read about these interesting developments, in summary, and not have to do a lot of searching. Enjoy!

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Modern Europe was formed by milk-drinking Russians: Mass migration brought new genetic makeup to continent 5,000 years ago
http://www.dailymail.co.uk/news/article-3119310/How-white-Europeans-arrived-5-000-years-ago-Mass-migration-southern-Russia-brought-new-technology-dairy-farming-continent.html

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DNA Deciphers Roots of Modern Europeans
http://www.nytimes.com/2015/06/16/science/dna-deciphers-roots-of-modern-europeans.html?smid=fb-nytimes&smtyp=cur&_r=1

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Science – Nomadic Herders Left a Strong Genetic Mark on Europeans and Asians
http://news.sciencemag.org/archaeology/2015/06/nomadic-herders-left-strong-genetic-mark-europeans-and-asians

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Nature – DNA Data Explosion Light Up the Bronze Age
http://www.nature.com/news/dna-data-explosion-lights-up-the-bronze-age-1.17723

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From the European Nucleotide Archive. http://www.ebi.ac.uk/ena/data/view/PRJEB9021

Investigation of Bronze Age in Eurasia by sequencing from 101 ancient human remains. We show that around 3 ka BC, Central and Northern Europe and Central Asia receive genetic input through people related to the Yamnaya Culture from the Pontic-Caspian Steppe, resulting in the formation of the Corded Ware Culture in Europe and the Afanasievo Culture in Central Asia. A thousand years later, genetic input from North-Central Europe into Central Asia gives rise to the Sintashta and Andronovo Cultures. During the late BA and Iron Age, the European-derived populations in Asia are gradually replaced by multi-ethnic cultures, of which some relate to contemporary Asian groups, while others share recent ancestry with Native American

Description

The Bronze Age (BA) of Eurasia (c. 3,000-1,000 years BC, 3-1 ka BC) was a period of major cultural changes. Earlier hunter-gathering and farming cultures in Europe and Asia were replaced by cultures associated with completely new perceptions and technologies inspired by early urban civilization. It remains debated if these cultural shifts simply represented the circulation of ideas or resulted from large-scale human migrations, potentially also facilitating the spread of Indo-European languages and certain phenotypic traits. To investigate this and the role of BA in the formation of Eurasian genetic structure, we used new methodological improvements to sequence low coverage genomes from 101 ancient humans (19 > 1X average depth) covering 3 ka BC to 600 AD from across Eurasia. We show that around 3 ka BC, Central and Northern Europe and Central Asia receive genetic input through people related to the Yamnaya Culture from the Pontic-Caspian Steppe, resulting in the formation of the Corded Ware Culture in Europe and the Afanasievo Culture in Central Asia. A thousand years later, genetic input from North-Central Europe into Central Asia gives rise to the Sintashta and Andronovo Cultures. During the late BA and Iron Age, the European-derived populations in Asia are gradually replaced by multi-ethnic cultures, of which some relate to contemporary Asian groups, while others share recent ancestry with Native Americans. Our findings are consistent with the hypothesised spread of Indo-European languages during early BA and reveal that major parts of the demographic structure of present-day Eurasian populations were shaped during this period. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency during the BA, contrary to lactose tolerance, indicating a more recent onset of positive selection in the latter than previously believed.

Abstract

The findings echo those of a team that sequenced 69 ancient Europeans ³. Both groups speculate that the Yamnaya migration was at least partly responsible for the spread of the Indo-European languages into Western Europe.

The report on the 69 ancient remains sequenced is below.

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Steppe migration rekindles debate on language origin
http://www.nature.com/news/steppe-migration-rekindles-debate-on-language-origin-1.16935

The Harvard team collected DNA from 69 human remains dating back 8,000 years and cataloged the genetic variations at almost 400,000 different points. The Copenhagen team collected DNA from 101 skeletons dating back about 3,400 years and sequenced the entire genomes.

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Population genetics of Bronze Age Eurasia
http://www.nature.com/nature/journal/v522/n7555/full/nature14507.html

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Dienekes Anthropology Blog
http://dienekes.blogspot.com/2014/06/ancient-dna-from-bronze-age-altai.html

Forensic Science International: Genetics Received 2 January 2014; received in revised form 21 May 2014; accepted 25 May 2014. published online 04 June 2014.

The Altai Mountains have been a long term boundary zone between the Eurasian Steppe populations and South and East Asian populations. Mitochondrial DNA analyses revealed that the ancient Altaians studied carried both Western (H, U, T) and Eastern (A, C, D) Eurasian lineages. In the same way, the patrilineal gene pool revealed the presence of different haplogroups (Q1a2a1-L54, R1a1a1b2-Z93 and C), probably marking different origins for the male paternal lineages.

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Dienekes Anthropology Blog
http://dienekes.blogspot.com/2013/06/mtdna-from-late-bronze-age-west-siberia.html

Includes mitochondrial haplogroups C, U2e, T, U5a, T1, A10.

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Population Genetics copper and Bronze Age populations of Eastern Steppe, thesis by Sandra Wilde
http://ubm.opus.hbz-nrw.de/volltexte/2015/3975/ (in German)

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Eurogenes blog discusses
http://eurogenes.blogspot.com/2015/03/population-genetics-of-copper-and.html

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Polish Genes Blog
http://polishgenes.blogspot.com/2015/05/r1a1a-from-early-bronze-age-warrior.html

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Early European May Have Had Neanderthal Great-Great-Greandparent
http://www.nature.com/news/early-european-may-have-had-neanderthal-great-great-grandparent-1.17534

40,000 year old Romanian skeleton with 5 – 11% Neanderthal, including large parts of some chromosomes – as close as a great-grandparent. Previously thought that interbreeding was in the Middle East and 10,000 or 20,000 years earlier.

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How is this all happening?

The Scientist Magazine has a great overview in the June 1, 2015 edition, in “What’s Old is New Again.”
http://www.the-scientist.com/?articles.view/articleNo/43069/title/What-s-Old-Is-New-Again/

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George Estes (1763-1859), 3 Times Revolutionary War Veteran, 52 Ancestors #66

Posted on April 6, 2015 by Roberta Estes

George Estes was born in Amelia County, Virginia to Moses Estes and Luremia Combs on February 3, 1763. He tells us his birth date and his father’s name, among several other very interesting things, in his application for a Revolutionary War pension.

In 1832, Congress passed an act making men who served in the Revolution eligible for a pension. Thank goodness they did, because it caused records to be created documenting the service and lives of these men that would otherwise never have existed.

George applied for his pension on September 14, 1833. In his owns words, he tells us about his 3 tours of duty. Yes, three separate tours of duty.

“I entered the service in January 1781 as a substitute for my father Moses Estes and marched from Halifax County where I then lived under Captain Wall through the counties of Charlotte, Lunenburg, Dinwiddie and Petersburg to Cabin Point on the James River.”

I would think the word “marched” implies on foot. And there is a lot of marching going on.

“At that place I was transferred to Capt. Long’s company of infantry and marched with him to Suffolk on the Nansemond River where I was stationed for some time under Colonel Dick and Gen. Michlenburg. From there we marched to Portsmouth and many other places and arrived at Barrett’s Neck where I was discharged by Capt. Lewis in the month of April 1781 having served 3 months on this tour. My discharge is lost and cannot be found but the service record is proved by Elias Palmer who was a soldier with me during the whole time.

In the month of May 1781 I was drafted to serve my own tour and marched from Halifax County in Capt. Clark’s company through Richmond to New Kent Courthouse where we joined General Mechlenburg’s Company. I was then attached to Capt. Read’s company of cavalry and continued with him marching in various directions until our time of service for 3 months expired. I was discharged by General Waine in the County of Charles City in the month of August 1781. My discharge is lost and cannot be found and I do not know any person living who was in that service with me.

In the fall of 1781 I moved a family of people to the state of Tennessee staid in that country upwards of a year and in the month of October 1782 I entered the service of the United States as a volunteer and marched from the county of Washington in state of North Carolina in Capt. Cox’s company of mounted horsemen under Col. Campbell and Col. Shelby into the Cherokee Nation of Indians. We marched in various directions in the said nation until we arrived at the shoemake town. At that place we received information that a treaty had been reached with the indians and we were discharged. The whole time of service on this term was 2 months and 20 days. I was discharged by Capt. Cox about the end of December and came to Virginia where I have lived in the county of Halifax ever since. My discharge is lost and cannot be found and no person [is] in this country that was in that service with me.

I was born in the county of Amelia on the third day of February 1763. My age was recorded in a family bible that was in my father’s possession but I don’t know what became of it. I lived in the county of Halifax when I entered the service in the said county when the war ended and have lived in the county ever since. Christopher White, Thomas Conner and Peter F. Kent and many others can testify as to my character for veracity and their belief of my service as a soldier of the Revolution. There is no clergyman living in my neighborhood.”

George (X) Estes

(his mark)

Sept. 14, 1833

So George served three times in total, twice by obligation, when his father and his numbers came due, and once as a volunteer. He served in place of his father. War is difficult enough for a young man.

When George filed for his pension, he was 70 years old. While he signed with an X in 1833, in earlier documents, he signed his name, so he was capable of writing.

George’s signature is shown on a petition dated Dec. 10, 1785, above, for an assessment for religious teachers. Note that his name appears very near that of William Younger who lived adjacent his father Moses Estes. George would marry Mary Younger a year later, although a connection between the two Younger families has never been proven.

This petition dated November 17, 1795 shows Moses and his son George Estes both of whom are opposed to the sale of the church glebe lands, in addition to the signature of their neighbor William Younger. Note that George actually spells his own name in two different ways, Estes and Eastis. And we wonder why we are confused today.

Documenting George’s first two tour service records in Virginia was difficult, but finding the third one was next to impossible. Then, quite by accident, when looking for my Dodson family records, I stumbled across the documentation for George’s third tour, where he is listed as George Eastis, in the North Carolina archives, of all places.

From the Book “Tennessee Soldiers in the Revolution” by Penelope Johnson Allen, now digitized at Ancestry.com.

Look at this, George is right across the page, directly from Lazarus Dodson, the man I was looking for. Talk about serendipity.

My cousin, Debbie, wrote to the NC archives and was sent the following document that tells us that George Estes was paid in a specie certificate, a type of credit voucher, on June 12, 1783. His name appears on the 10th line in the third column. Ironically, Lazarus Dodson, whose name appears two entries below George’s is the father of Lazarus Dodson, whose daughter, Rutha or Ruthy, would marry George’s grandson John Y. Estes in Claiborne County, Tennessee in January 1841, 58 years after their grandfathers served together in the Revolutionary War. I wonder if they ever figured that out.

I called the North Carolina archives and asked if the original pay rosters and additional information were available. They said they were, but they did not do “lookup work.” A week later, I was standing at the research desk in the archives in Raleigh, with these papers in hand, and an amazed librarian kind of stuttered and stammered around when I introduced myself and told her where I came from (Michigan) and why I was there. I think they are far more used to people “going away” when told the archives doesn’t do “lookup work” than showing up 1000 miles and a week later. Sadly, that trip was for naught, because while they did have additional records for some soldiers, there was nothing more for George. Don’t even ask how upset I was.

Why, I was then forced to do research on some of my NC lines since I was there in the archives with nothing else to do. I mean…you can’t waste a trip like that!

George’s certificate was issued by the auditors, Bledsoe and Williams, and by referencing the attached documents, you can determine the location where the soldiers served. In this case, exactly as described by George Estes, he served in the Morgan District which included the Washington and Sullivan County areas which eventually became Tennessee.

By putting these three pieces of information together, George’s pay list, which includes the auditor, the auditor and their districts – we can confirm where George was when he served his third service term.

In 1833, from Jasper Co., GA, Clarissa C. Boyd declares that her brother, George Easters, a resident of Halifax Co., VA in 1781, served 6 months in the Virginia militia. On January 15, 1784. George Estes, infantry, Continental Line, was issued a certificate for the balance of his pay.

George was placed on Virginia pension roll at $31.38 per annum, certificate 16886 issued on Oct. 12, 1833.

On April 5, 1855 in Halifax Co., George (X) Estes of said county, age 92, applies for bounty land. He obtains the land and signs the bounty certificate over to his daughter Susannah immediately.

What do we know about what happened to George during his Revolutionary War service?

In his first term of service, serving in place of his father, Moses, George spent time at Cabin Point on the James River about which we discover the following:

By late summer 1780 with South Carolina under their control, the British were ready to push into Virginia and Maryland and deal Washington a final blow. In Virginia, Governor Thomas Jefferson had placed General Steuben in charge of the state’s defense. By January 1, 1781, the British were in Chesapeake Bay and Jefferson was calling up county militiamen to repel the impending attack. Benedict Arnold, now in charge of the British fleet, sailed up the James River and burned Richmond then moved back downriver to settle in at Portsmouth on the Chesapeake Bay. The Halifax County Militia and was sent to Cabin Point on the James River to watch for Arnold’s next anticipated raid up the river. The militia had little to do but sit and wait and worry about the news coming in daily of Cornwallis’ raids in the Carolinas and his impending threat to Virginia.

It seems that all was not well at home in Halifax County during this time. Boyd’s Ferry is the present city of South Boston and the Boyd’s Ferry crossing was very close to the Estes homestead, which was located just above the crossing on the main road.

In a letter to Governor Jefferson dated February 15th, 1781, camped at Boyd’s Ferry on the Dan River, Greene called for reinforcement of militia:

“We have crossed the Dan, and I am apprehensive they will cross it above us…If they should they will oblige us to cross the Stanton branch of the Roanoke…It is by no means certain, that Lord Cornwallis will not push through Virginia.”

Jefferson dispatched letters on February 17 and 18 to a long list of county Lieutenants and Baron von Steuben asking for militia to join General Greene who had “crossed the Dan at Boyd’s Ferry and was retreating before the enemy.” News of the alarming activities of Greene and Cornwallis aligned along either side of the Dan near Boyd’s Ferry must have reached the Halifax County Militiamen shortly after February 18. While they sat on the James River waiting for Arnold to make a move, Cornwallis and his army was camped at the doorstep of their homes in Halifax County.

The record is dated February 23, 1781 Cabin Point, Virginia and states:

“A list of the mens names belonging to Major Jones Battalion of Militia who have deserted. Distinguishing those who carried off their arms from those who did not. Also those who deserted from their post.”

The list of names does not include George Estes. He had a decision to make, and he chose to remain at his post, although one could scarcely have blamed him had he returned home to protect and defend his home place and family. Perhaps the knowledge that his father and siblings were there relieved his mind somewhat.

Now let’s turn to George’s third tour of duty from what would become eastern Tennessee, but was at that time western North Carolina..

In 1782, the Cherokee, who had sided with the British continued to raid. John Sevier banded together a group of men in western North Carolina, now eastern Tennessee, and with Colonels Campbell and Shelby marched on the Cherokee towns. Shoemake town, as it was called by whites, was located in upper Georgia and had previously been burned in May of 1781. The Indians allied with the British because the British assured them that they would stop the encroachment of the Europeans into their traditional territory. The Indians did not fare well in the Revolutionary War, nor afterwards. This “march on the Cherokee” appears to have been one last final grandstand that gave the Cherokee the final nudge to end their part in the war.

Rather miraculously, George does not seem to have engaged in any actual battles during his 3 tours of duty. By this late date in the war, most of the actual fighting was in North and South Carolina.

Back Home in Halifax County

After returning to Halifax County, George Estes spent most of his life on his father’s original land. His father Moses died in 1813, but the estate was contested and not settled until 1837, long after many of Moses’s children had died as well.

That land is located in the city of South Boston at the intersection of Estes and Main Street. The following photo is standing in the Oak Ridge cemetery, originally part of the Estes land, looking down Estes Street. Note the blue water tower. It’s a landmark we’ll reference later.

The Estes farm used to be beyond the blue tank on the left and the houses on the right. Today Estes Street is gated, not because it’s an upscale gated community, but because that land is now the landfill. This was heartbreaking to me, until I learned that the graves had been moved. It still makes me sad.

Below is what’s left of the Estes land taken from behind the area (yes, I was in the landfill but I cropped that portion from the photo.) We are looking at the original Estes woods.

In the above photo, for perspective, notice the blue water tower in the upper right corner. In the photo below, you can see the ‘other end” of the now gated “Estes Street” emerging that originates near the blue water tower that can also be seen in the left upper corner of the photo.

The Estes family in Halifax County, Virginia tells the story of when the family moved the graves from the old Estes land shown above to the Estes plot in the Oak Ridge cemetery. This apparently happened in the early 1900s and the only graves not moved were those of two unrelated people, one being an unrelated child whose parents had no place to bury the child and the second, an “in-law” of a descendant whose family did not want them moved.

It turns out that when Moses Estes’ children fought so bitterly over his land, they also apparently established separate cemeteries. One cemetery was the “original” Estes cemetery where Ezekiel, Susannah, Ezekiel’s mother who is George’s daughter, George and probably old Moses himself are buried. The other cemetery was located behind the houses, apparently, down Estes street. I believe that the Oak Ridge Estes plot is the original Estes cemetery, but I cannot definitively prove this through records still in existence today, although an early cemetery history states that this is the case. Oral history says that when they moved Moses’s grave, only a collar bone and a casket hinge were left. Whether this is accurate or a tall tale, we’ll never know, but indeed, whatever remains of the elder Estes clan is buried in the Oak Ridge cemetery directly across the street from the old Estes homestead and at the end of Estes Street. The rest, well, it’s under the landfill or dispersed.

Today Main Street is paved. When they removed the cobblestones to pave Main Street, they used them to construct the beautiful stone wall around the cemetery. George Estes served on many “road crews” as documented in court records and it is entirely possible that he laid these very cobblestones, shaped from the stones found on the Estes land. George was probably glad to get rid of them as they would have made plowing difficult.

The bright white monuments in the cemetery are the Estes family stones, made of marble apparently, after they were cleaned by family members about 2006. Ezekiel who died in 1885 has a stone that proclaims him “an honorable man,” but none of the earlier family members have stones. Ezekiel’s mother Susannah died in 1870 and his grandfather George died in July of 1859, an amazing 96 years of age.

The Halifax County Estes family has a clearly remembered oral history of “Granpappy George who lived to be 108 (or 106 or 115).” Sometimes stories grow with time, and that one certainly did, but he was quite elderly when he passed and obviously legendary.

George lived far from a sedentary lifestyle. He was obviously not afraid of adventure or danger, serving three separate terms in the Revolutionary War, one as a substitute for his father and one as a volunteer. George returned home and married Mary Younger on December 19, 1786 the same day that his brother Bartlett Estes married Rachel Pounds. I wonder if they were married in a double ceremony.

When I first started researching this couple, everyone in the family said that George Estes and Mary Younger could not have been the father of John R. Estes because they only had one child, Susannah. As a novice, I figured those researchers had a lot more information and years of experience, but as one by one, I worked through and eliminated many of the alternative parents, the options became fewer and fewer and I began to wonder how “they” knew that George only had one child. I certainly hadn’t found anything that said he had only one child. And having found only one child doesn’t mean there was only one child. In fact, I’ve become very suspicious of any record before the days of modern birth control that suggests that someone had only one or two children, unless the wife or husband died.

As it turns out, Susannah was the only child that was easily evident. And “they” didn’t know how “they” knew – trying to find the source of that information was like trying to find the elusive fountain of youth. And that was before the days of quick-click trees on Ancestry. If the researchers had looked at the few census records we do have, they would have seen a discrepancy that screamed for an explanation – multiple children living with George and Mary.

George and Mary positively had 7 children who survived to adulthood and probably at least two who didn’t, based on a combination of records, including the 1820 and 1830 census.

It seems that several of George’s children regularly pushed the envelope of the day and would have brushes with the law or, perhaps better stated, the court system and “polite society.” It’s thanks to those records that we can add color to our family portrait. I love lawsuits – well – historical lawsuits anyway. I extracted probably 75-100 years worth of court, deed and tax records from Halifax County and reassembled them, like a big puzzle, into family groups.

Of particular interest was the information from the “Younger, Marcus Chancery Suit 1842-057, Halifax Co. Va.” In the documents from that suit, I found the payments made to the various heirs of Marcus Younger, who had died in 1816. In the case of Mary Younger Estes, her heirs are listed in 1842 because she is deceased. This suit was filed almost 30 years after Marcus’s death. Normally would never think to look that far out – but chancery suits are often quite different. It’s not at all unusual for chancery suits to reach back 2 generations, to a grandparent’s will, especially if unmarried children are involved, as was the case with Marcus’s will. When the unmarried child dies, Mary’s sister in this case, sometimes the assets revert to the other children or their heirs.

In the suit papers, it is noted that Mary Younger Estes’s children will receive one sixth of her one quarter share of the 83 acres to be sold following the death of Mary’s unmarried sister.

The children of Mary Younger Estes were listed as: John, William, Susannah, Sally wife of T. Estes, Polly wife of James Smith and a grandchild name Mark Estes. This means that Mary had 6 children either living or who had died but who have heirs. In this case, one child has died leaving one heir, Mark.

Of course, I found this list AFTER I had reassembled what I believed to be the family of Mary Younger and George Estes. You know it didn’t match up perfectly, or I wouldn’t even be mentioning it.

I had all of those children listed, but in addition, I had a Bartlett and Rebecca.

There is no son Bartlett listed in the 1842 document, but there is instead a grandchild named Mark Estes. This implies that Mark’s parent is of the Estes surname, the parent is dead and Mark is the only living child. We know through various records that daughter Susannah has a son, Mark, but this cannot be that Mark because Susannah is very clearly included as living. We also know that George’s son, Marcus, died in 1815 leaving a widow and no children. The Bartlett I have attributed as the son of Mary and George had 7 children, and none known to be Mark, although one male name is unknown.

There are several Bartletts living in this vicinity and I could have the various Bartlett’s confused. However, if daughter Rebecca died and left a son Mark, this would fit perfectly. But, if it is the same Rebecca, she is prosecuted in 1844 for living with a black man, which precludes her from being dead in 1842, so Rebecca is not the child of George Estes, but more likely George’s niece.

This family makes me pull my hair out.

Thankfully, it seems that several of George’s children have lived a bit of a colorful life, meaning they have records that remain about them having had brushes with the law or, perhaps better stated, the court system and running afoul of “polite society.” Here is what is known about the children of George Estes and Mary Younger.

John R. Estes whose photo we believe is shown below was probably the oldest child and was born sometime between March and June of 1787. He married Ann Moore in 1811 and was on the way to Claiborne Co., TN by 1820 where he died in 1885, like his father, nearly reaching 100 years of age. Obviously, there is a longevity gene in the Estes family. John R.’s great grandson, William George Estes lived to be 98 years of age and William George’s two daughter both lived to be just shy of 100. There’s hope that I’ll live long enough to finish my genealogy research:)

Marcus Estes was born about 1788 as well and is shown on tax lists in Halifax County from 1811-1814 when he dies, leaving a widow with the beautiful name of Quintinney. In 1815, his estate is assigned to the sheriff to administer. There is also a War of 1812 record for Marcus, but there may be no further service records since no one applied for either bounty land or a pension based on his service. He served in the same unit as his brother, John R. Estes and I have to wonder if he died during that time.
William Y. Estes was also born sometime in this timeframe. The census says 1785 or 1786, but the census is also often notoriously wrong. In 1815, William married Rebecca Miller and drank to the point where his wife’s father commented on his behavior in his will in a very unflattering manner, forbidding William to ever have any control over Rebecca’s inheritance. William died in Halifax County between 1860 and 1870.
Susannah Y. Estes was born about 1800 and never married. She had 5 illegitimate children between 1814 and 1835, 2 males and three females. She lived on the old home place and cared for her elderly father, George, until his death in 1859.
Polly Estes, born between 1801 and 1808 married in 1824 to James Smith. She died in Halifax County after 1880, having had 4 children. We know very little about Polly, because, she was apparently one of the few well-behaved Estes’s. You know that old saying about “well behaved women seldom make history.” I relish my ill-behaved ancestors and their family members because that is often the only way we learn about their lives and put meat on their bones. Below, George’s signature along with James Smith when Polly marries.

This photo is of George’s grandchild, J. E. and wife Mary Anne Smith, the youngest child of Polly Estes Smith.

I’m dying to know about that eye patch.

Sally Estes was born sometime around 1800 and married her first cousin, Thomas Estes, son of Bartlett Estes and Rachel Pounds. Marrying cousins was a common practice of the time. They removed to Tennessee shortly after their marriage. George and Thomas both sign the marriage bond, below.

I initially thought Rebecca Estes was George’s child because of her proximity in the census where in 1830, a Rebecca Estridge with 3 daughters is living near George Estes and Susan Estes, all living in separate households. In 1835, a Rebecca Estes is in the court notes with Robert Rickman for support of her child, and in 1844, Rebecca is “indicted for felony, report of grand jury – a white woman living together in open adultery with a negro man, James Bird, free man of color, as presented by Jacob W. Farguson and William Ingram.” I cannot find Rebecca nor James Bird after this time. If this is the same Rebecca in 1844 as in 1830 and 1835, then she cannot be the child of George Estes because in 1842, Rebecca would have been dead.

It’s very unlikely that either Bartlett or Rebecca are George’s children and we are simply missing one child who had son Mark. It is certainly possible that this Marcus was born posthumously to George’s son Marcus. Given that Marcus’s estate went entirely to debt, there would have been nothing left to leave to a child, so no guardian would have been appointed. We’ll likely never know, but this is the most likely explanation. There is no Mark or Marcus Estes in the 1840 or 1850 census.

Life in Halifax County with Daughter Susannah

We don’t have a lot of information about life as George knew it, but thanks to Susannah, we do have a couple of glimpses into what their life was like.

Susannah Estes never married, lived on the old homeplace and wound up with all of George’s assets which caused problems with his other children. By the time George Estes died in 1859, there was nothing left, so he had no will. He had already deeded his land to Susannah, plus anything left from his pension or his Revolutionary War service.

On February 12, 1833, George Estes grants to Susan Y. Eastes, “my daughter, all my right, title, claim and interest which I have for military services rendered during the War of the Revolution.”

Much to my shock, in early 1837, Susannah brings suit against her father forcing him to answer to the court why he, as executor, has not distributed his father, Moses’s estate.

On March 25, 1837, George Estes deeds to Susannah Y. Estes “for $100 land on both sides of road from Halifax to S. Boston on Dan River adjoining Adam Toot, John Ransom, John Jinnett, tract of land that my father Moses died seized of.” This occurs immediately after George’s father’s estate was settled.

If you look at a map of South Boston plotting the locations we know, this is a huge tract of land.

We know the land went as far north at present day Waddell Woods (top arrow) because Waddell spring is mentioned in deeds. The Oak Ridge Cemetery is the green area pointed out by the second arrow from the top. The blue water tower is across the street, to the right of that arrow. The main road is 129 and is pointed to by the third arrow from the top, running from the Dan River (at the bottom) through the Estes land and on North. Today, this land includes most of South Boston, then Boyd’s Ferry.

We get a glimpse of their possessions, when, in 1842, Susannah, who now owns her parents land, takes a mortgage which is void if it is paid. Apparently, the mortgage is paid, because nothing more is ever mentioned in any of the deed or court books.

“Tract of land where we now live, one three-horse wagon and gear, 1 bay mare, 1 grey horse, hogs and sheep, all of our present crop of corn and fodder, tobacco, 4 feather beds and furniture, household and kitchen furniture, plantation tools for debt of $50.16.”

In addition to the land George inherited from Moses, George continues to assist Susannah.

On April 15, 1857, George Estes deeds to Susan Y. Estes the bounty lands he is entitled to “by late acts of Congress and a part of proceeds being in the hands of Easley Holt and Co. In consideration of natural love and affection and value received…all right and interest to any balance that is remaining at my death after paying my debts with him.”

When she died on August 23, 1870, Susannah was not a poor woman and left a nontrivial estate, including land. Her personal property inventory probably included many items inherited from her father and mother:

Appraisement of property of Susan Estes:

cow
yearling
loom
potatoes
walnut chest
barrels
flax wheel
3 pots
2 skillets
oven
brass kettle
tea kettle
4 jars
4 jugs
2 water buckets
3 axes
lot tin
2 pitchers and bottles
1 jar vinegar
lot tableware
hoes
wedges
pot rack
candlesticks
1 press
1 desk
1 looking glass
7 chairs
1 bed
bolster
pillar
1 blanket
1 counterpin and sheet
1 quilt
1 barrell cider
small chest
basket
2 bee hives

I can’t help but wonder what the quilt looked like and who made it. Was it from a time when she and her mother and sisters perhaps gathered around a quilting frame?

After Susan’s death, a lawsuit followed regarding a debt incurred before her death and the validity of the debt based on her mental state. She was deemed competent. Aside from the depositions, which were in themselves very enlightening as to Susannah’s life, and death, the list of items she purchased at the store, on account, I found very interesting as well:

The following are items appearing on the store account of “Miss Susan Estes”:

Coffee
Sugar
Bucket
Linen shirt
2 linen collars
5 yards calico (total 1.06)
3 yard gingham
1 bottle ? oil
20 yards oznaburg
75 yard pant goods
Weeding hoe
Shelves for buster
Coffee pot
Tin bucket
Sugar
Rice
Candles
Molasses
Coffee
Bacon
Molasses
Coffee
Nails
Shoes
1 oz indigo
1 # soda
Coffee
Sole leather
2 oz indigo
Pale cotton
Sugar
Copperons?
Rubber tuck combs
2 yd cambric
Flex thread
6 8×10 window glass
Bacon
Seed oats
Bags
Frt and drayage
Paid on acct with bacon from house
Goods box
Plow point
Coffee
Fine iron
Goods box
Molasses
Hat for Buster
Pants for Buster
Coat for Buster
Vest for Buster
Bacon sides
Pole exe
Pale Box
Stamped envelope (.04)
Bacon sides
2 doz henning??
Paid with Reg. 162 old casting

Obviously, Buster is a nickname for someone, but who? Whoever, he was, he had a vest, hat, coat, pants and shelves.

In addition, Ezekiel Estes submitted a bill to the estate for $21.18 for shingling the house and Susannah’s doctor bill was $51. She died a slow death of a heart ailment.

Above, George Estes’s granddaughter, Susannah’s daughter, Mary Mildred Estes born April 3, 1828 and died Jan. 20, 1917 in Lynchburg, VA., married William Greenwood and second, Jesse Jacobs..

Susannah’s son, Ezekiel Estes, below, born in 1814 and died in 1885 in Halifax County, married Martha Barley.

A few years after I published this original article, Jerry, one of Ezekiel’s descendants contacted me and provided this amazing watch case that was owned by Ezekiel.

Ezekiel Estes watch case 2.jpg

Ezekiel Estes watch case

This beautiful pocket-watch case is made of Iroquoian beadwork, causing me to wonder how he obtained it, and if there is more significance than a simple watch case. Regardless, it’s beautiful and a huge thank you to Jerry for sharing so that everyone can enjoy this treasure.

The Court

George Estes himself had a few encounters with the legal system. People at that time seemed to be quite litigious, and George was involved with no fewer than 14 nonfamily cases, generally as a defendant, and went to court even more often as a witness.

Court days, which initially happened quarterly, then monthly, were quite the social event in the 1700s and 1800s in Virginia. Anyone who was anyone attended, and much business was transacted outside the courthouse and in the taverns. It was also one of the best ways to hear the news as well as see the news being made. The original reality TV!

I recall that when my daughter and I first went to Halifax County, we visited the clerk’s office asking asked about the various record books and such. My daughter had the book of court notes out, and was looking in the plaintiff’s index. We told the lady that we were looking for Estes and she said “Oh, well then, your people are in this book”, and retrieved the defendants ledger. Things haven’t changed much over the years apparently. The Estes family is legendary, or at least infamous!

George’s first court appearance was in 1786 when he was prosecuted for “profane swearing.” In one case, George and his father Moses were involved as witnesses in a lawsuit where someone signed a document they later regretted after partaking of the fruit brandy at the Estes home. The Estes family was well known for its fine orchards. The fruit brandies were kept cool in a special compartment under the foundation of the house.

In 1802, George put a mortgage on his household items which included 2 feather beds and furniture for 9 pounds, 2 shillings and 2 pence. You can tell that of their household goods, the coveted items were the feather beds.

In 1837, George gave a deposition in the chancery case of Light vs Yuonger wherein the descendants of Thomas Younger battled, for years, over the estate of Thomas Younger after his daughter Rachel Younger died. Thomas was likely the great-uncle of George’s wife, Mary Younger. While the outcome of the case actually doesn’t involve our family directly, we do find a deposition given by George in 1837 over the value of a slave named Peter who in 1812 had been disabled with elephantitis. George, age 74 at that time, signed his deposition.

George Estes 1837 deposition in Light vs Younger.jpg

Moses’s Land

Most of the court cases, not included in the 15 non-family cases mentioned above, involved years and years of appearances having to do with Moses estate settlement which was finally settled in 1837, 24 years after Moses’s death. George, the eldest son, was 74 years old when his father’s estate was settled and he immediately deeded his portion of the land to Susannah.

This family battled over land and inheritance for generations, beginning in 1813 with Moses’ death, followed by George’s children and then Susannah’s and continuing into the present generations whose parents were still involved with that land until the county took the land by eminent domain. At least one person refused to sell the land and instead has a ‘long-term lease”, although what they think they’ll do with a stinky landfill is beyond me. I suspect it was a matter of principle.

When I visited Halifax County, two elderly living cousins, Doug and Shirley, both now deceased, remembered the land from their childhood. Shirley told me that the original home burned in about 1933, complete with all of the family photos, Bibles, etc. She remembers that someone on the school bus told her that her grandparents’ house burned the night before.

Shirley explained that the original home had 8 rooms with 2 fireplaces. Photos of “all the family” hung there – but of course burned in the fire which is why none exist today, according to Shirley. The home had a cellar – which is reflected in a chancery suit where it’s mentioned that Moses Estes stored his fruit brandy in the cellar. Apparently, one night, someone drank too much and signed something they regretted at Moses’s house. Although Moses wasn’t the signer, Shirley mentioned that the Estes men liked their alcohol a bit too much and alcoholism ran in the family.

Shirley said there were blackberries, raspberries, huge mulberry trees “three foot through,” grapes and 5 cherry trees. I suspect there were apple and peach trees too back when Moses planted his orchard.

Shirley said that there were three springs, making this property quite desirable for homesteading. The Walker spring is about half a mile away, the Waddell spring, and a small spring by the house which had a spring-house built over it to cool things like milk. They grew gourds, and there were always “dipping gourds” by the springs so anyone could get a cool drink of water.

The Estes family used to haul ice, cut from the river, hoping it would last until at least partway through the summer. One time Ezekiel Estes, Moses’s great-grandson through granddaughter Susannah was hauling ice for one Mr. Willingham using steers instead of oxen. When asked if he couldn’t make those steers go faster, Zeke said “no, cause I need them tomorrow.”

The man who bulldozed the property after the city purchased it told me there were 3 houses “back there,” all “farm type” homes. Apparently the first home built was a log cabin, probably about 1782 when the family first arrived from Amelia County, and it was later used for the young couples after they were first married.

The home that burned was described as a large 2 story home with upper and lower porches all around. Porches are important in the south.

There has been a great deal of speculation about why George provided only for his daughter Susannah. It could be because she was not married and he felt protective towards her, wanting to provide for her and his grandchildren after his passing. She was very young, 13 or 14 when she became pregnant, and it would be easy to see how he could have been especially protective of her and her children whom he had lived with for their entire lives. In essence, George raised her children as his own, especially Ezekiel who was the eldest. Ezekiel was born right about the time that George and Mary stopped having children, so Ezekiel probably just fit perfectly into the stair-steps of children.

It could also be that George gave his worldly good to Susannah because she took care of George in his old age – although that wouldn’t explain the 1830s deeds. George’s wife Mary probably died sometime between 1820 and 1830, and certainly before George started deeding to Susannah in 1833, because Mary signed no release of dower rights.

Others have suggested that perhaps Susannah might have been an opportunist and perhaps manipulative or devious. Some have questioned the propriety of the situation. Susannah had only two male children. Her oldest, Ezekiel, has descendants who have DNA tested and they match a Moore family that lived in the area, although not the same Moore family that Susannah’s brother, John R. Estes married into.

I think it suffices to say that George, Susannah and Ezekiel were extremely close and given the social stigma attached to illegitimate birth in that era, let alone 5 illegitimate children, the family was probably increasingly subject to harsh scrutiny, discrimination, criticism and were socially marginalized. One hint may be held in George’s 1833 Revolutionary War pension application where he states there is no clergy in his neighborhood, but the oldest church in the county is but a few blocks down the street from his home, within walking distance. One can certainly understand why and how George could and would feel a great deal of affection for his grandchildren in particular, as he apparently lived with them as they grew up. There are several records that involve both George and Ezekiel who probably looked up to his grandfather as a role model.

In fact, it was Ezekiel Estes who reported the death of George Estes and said that he was 100 years and 4 months old, born in Amelia County. I hope, for George’s sake, that the family had a bang up 100 year old birthday celebration where everyone came to visit and eat that fine southern food, even if we know today they were a few years early. Or maybe George really was 100 years old in 1859 and simply misstated his birth year in 1833. Regardless, I hope they had a wonderful celebration and he had many guests who sat and visited and imbibed some of that fine Estes brandy! I wish I could hear the stories of his hundred years of life. What a gift that would be.

George is reportedly buried here in the Estes section of the Oak Ridge Cemetery immediately to the right just inside the entrance. The Estes family markers are all bright white here after being cleaned by now deceased cousin Nancy Osborne. We don’t know exactly where Susannah, George with his wife Mary Younger and Moses with his wife Luremia Combs are buried, but rest assured that they are here among their descendants and family members.

It’s believed that George and Mary are buried in the unmarked area, below.

In the following photograph, the picture is taken from behind the stones, before they were cleaned and restored, with the original Estes land showing across the street. The Estes homestead was behind these houses which stand on part of Moses’ land that was sold off by descendants. The original homestead is now the landfill, although some forest was preserved as a barrier between these homes and the landfill the last time I in visited in 2006 or so. The cobblestones showing in the wall below are the original road cobblestones that George probably helped to lay.

I would like to have a Revolutionary War marker placed for George Estes in the cemetery so that he will be honored and his grave will be marked for future generations.

George certainly lived an amazing life. He was born in Amelia County during the French and Indian war, as his father and uncles serving in that conflict. About 1770, the Moses Estes family migrated in mass, it seems, to Halifax County where his father and grandfather, both named Moses, established homes, albeit a few miles apart.

About the time George came of age, he volunteered to take his father’s place in the Revolutionary War. After returning home, just a month later, his own “slot” came up, so he then served for himself.

Many Estes men were pushing the new frontier. In fact, George moved an Estes family to Hawkins County, TN, probably offering to help in order to see a bit of the world. He stayed for almost a year, and it was from there in October of 1782 that he enlisted as a volunteer to serve his third stint in the military in the Revolutionary War. George obviously saw a lot and probably talked about that part of the country to his children when telling tales about his great adventure. He’s one of the very few men I’ve ever heard of going BACK home from the frontier, and staying there. His son, John R. Estes would eventually settle in Claiborne County, TN himself, some 30+ years later, near where his father was in what would become Eastern Tennessee.

We don’t know much about George’s religious leanings. When he was young and first married, church attendance was required in the Anglican church. That’s also about the time he was prosecuted for “profane swearing.”

We know that his wife, Mary Younger’s family was probably Methodist, a dissenting religion, but one that was “legal” by the 1780s. Given that his son, John R. Estes married the minister’s daughter, in all likelihood, this family was Methodist. Whether George was enthusiastically Methodist too, “went along” begrudgingly and slept through services in the back row or simply stayed at home, we’ll never know. We do know, per a deposition, that George Estes was with the Reverend William Moore’s family on Christmas Day, 1811. George’s son, John R. Estes was married to Reverend William Moore’s daughter, Ann Moore.

At least two of George’s children ran badly afoul of either the law of the social norms of the time. Son William drank to excess and daughter Susannah had five children out of wedlock, as a pattern occurrence. This would have made it difficult for the rest of George’s children to “marry well” because something like that paints the entire family with the same brush.

Today, it’s inconceivable to us, but at that time, people who were born “out-of-wedlock” really could only marry others of their same social status. Interracial marriages were outlawed and the choices people had, both legally and in reality were much more limited than today. Remember, I told you that the county clerk still knew that the Estes’s would be found in the “defendants” book??? Maybe this is part of why so many descendants left for lands where there was less judgment waiting and one could start anew, without stigma already attached from the behavior of others.

George’s wife Mary would pass away sometime between about 1820 and 1830. George would have been between 60 and 70 years old at that time, and would live almost another 30-40 years.

After Mary’s death, it appears that Susannah took care of George. Given that by this time, Susannah had 5 illegitimate children she had to provide for, George’s pension probably took care of Susannah as well. I wonder how military pensions were figured at that time. I would have thought they would all have been relatively equal for the same rank (private), and if unequal, perhaps George received something for each of his three stints in the military. By way of contrast, his son, John R. Estes who served in the War of 1812 was collecting a pension at the same time received $8 a month as compared to George’s $31 year, which breaks down to $2.58 per month. In the end, Susannah wound up with all of George’s assets although, clearly, his pension stopped when he died.

By the time George died, his son Marcus had passed away, possibly in the War of 1812, and there are a couple of children I lose in the records, but as far as we know, most of George’s children outlived him. Some had moved west but George still had Polly, Susannah and William Y. nearby, although William Y. seemed unable to even help himself, due to his drinking, based on numerous court records.

The good news is that because of where Moses’s land was located, and the ability to locate the Oak Ridge Cemetery today, then track through the landfill deeds and family records, we were able to find the original Estes land.

Furthermore, we know that graves were moved from the Estes cemetery, now under the landfill, to the Estes plot in the Oak Ridge Cemetery, which may have been the original Estes cemetery in the first place.

All I know is that when cousin Nancy started talking about having moved the graves and finding the collar bone of Moses Estes, I just couldn’t stop myself from thinking about DNA. I know fully well that today, even with enough money, that the retrieval of ancient DNA for consumer purposes really isn’t a viable option. But I also know that in another decade, with the advances in technology and the associated drop in prices, combined with what has been able to be accomplished with sequencing ancient genomes – that eventually – that collarbone would have been useful.

I know, bad genealogist, bad genealogist. Bad, bad, bad. I can’t help it. It’s that nonconformant Estes side coming out! It’s in my genes. I can’t help it. In fact, I know where there’s a bone we can dig up to prove it….

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A Study Utilizing Small Segment Matching

Posted on January 21, 2015 by Roberta Estes

There has been quite a bit of discussion in the last several weeks, both pro and con, about how to use small matching DNA segments in genetic genealogy. A couple of people are even of the opinion that small segments can’t be used at all, ever. Others are less certain and many of us are working our way through various scenarios. Evidence certainly exists that these segments can be utilized.

I’ve been writing foundation articles, in preparation for this article, for several weeks now. Recently, I wrote about how phasing works and determining IBD versus IBS matches and included guidelines for telling the difference between the different kinds of matches. If you haven’t read that article, it’s essential to understanding this article, so now would be a good time to read or review that article.

I followed that with a step by step article, Demystifying Autosomal DNA Matching, on how to do phasing and matching in combination with the guidelines about how to determine IBD (identical by descent) versus IBS (identical by chance) and identical by population matches when evaluating your own matches.

Now that we understand IBS, IBD, Phasing and how matching actually works on a case by case basis, let’s look at applying those same matching and IBS vs IBD guidelines to small data segments as well.

A Little History

So those of you who haven’t been following the discussion on various blogs and social media don’t feel like you’ve been dropped into the middle of a conversation with no context, let me catch you up.

On Thanksgiving Day, I published an article about identifying one of my ancestors, after many years of trying, Sarah Hickerson.

That article spurred debate, which is just fine when the debate is about the science, but it subsequently devolved into something less pleasant. There are some individuals with very strong opinions that utilizing small segments of DNA data can “never be done.”

I do not agree with that position. In fact, I strongly disagree and there are multiple cases with evidence to support small segments being both accurate and useful in specific types of genealogical situations. We’ll take a look at several.

I do agree that looking at small segment data out of context is useless. To the best of my knowledge, no genealogist begins with their smallest segments and tries to assemble them, working from the bottom up. We all begin with the largest segments, because they are the most useful and the closest connections in our tree, and work our way down. Generally, we only work with small segments when we have to – and there are times that’s all we have. So we need to establish guidelines and ways to know if those small segments are reliable or not. In other words, how can we draw conclusions and how much confidence can we put in those conclusions?

Ultimately, whether you choose to use or work with small segment data will be your own decision, based on your own circumstances. I simply wanted to understand what is possible and what is reasonable, both for my own genealogy and for my readers.

In my projects, I haven’t been using small segment data out of context, or randomly. In other words, I don’t just pick any two small segment matches and infer or decide that they are valid matches. Fortunately, by utilizing the IBD vs IBS guidelines, we have tools to differentiate IBD (Identical by Descent) segments from IBS (Identical by State) by chance segments and IBD/IBS by population for matching segments, both large and small.

Studying small segment data is the key to determining exactly how small segments can reasonably be utilized. This topic probably isn’t black or white, but shades of gray – and assuming the position that something can’t be done simply assures that it won’t be.

I would strongly encourage those involved and interested in this type of research to retain those small segments, work with them and begin to look for patterns. The only way we, as a community, are ever going to figure out how to work with small segments successfully and reliably is to, well, work with them.

Discussing the science and scenarios surrounding the usage of small data segments in various different situations is critical to seeing our way through the forest. If the answers were cast in concrete about how to do this, we wouldn’t be working through this publicly today.

Negative personal comments and inferences have no place in the scientific community. It discourages others from participating, and serves to stifle research and cooperation, not encourage it. I hope that civil scientific discussions and comparisons involving small segment data can move forward, with decorum, because they are critically needed in order to enhance our understanding, under varying circumstances, of how to utilize small segment data. As Judy Russell said, disagreeing doesn’t have to be disagreeable.

Two bloggers, Blaine Bettinger and CeCe Moore wrote articles following my Hickerson article. Blaine subsequently wrote a second article here. Felix Immanuel wrote articles here and here.

A few others have weighed in, in writing, as well although most commentary has been on Facebook. Israel Pickholtz, a professional genealogist and genetic consultant, stated on his blog, All My Foreparents, the following:

It is my nature to distrust rules that put everything into a single category and that’s how I feel about small segments. Sometimes they are meaningful and useful, sometimes not.

When I reconstructed my father’s DNA using Lazerus (described last week in Genes From My Father), I happily accepted all small segments of whatever size because those small segments were in the DNA of at least one of his children and at least one of his brother/sister/first cousin. If I have a particular small segment, I must have received it from my parents. If my father’s brother (or sister) has it as well, then it is eminently clear to me that I got it from my father and that it came to him and his brother from my grandfather. And it is not reasonable to say that a sliver of that small segment might have come from my mother, because my father’s people share it.

After seeing Israel’s commentary about Lazarus, I reconstructed the genome of both Roscoe and John Ferverda, brothers, which includes both large and small segments. Working with the Ferverda DNA further, I wrote an article, Just One Cousin, about matching between two siblings and a first cousin, which includes lots of small data segments, some of which were proven to triangulate, meaning they are genuine, and some which did not. There are lots more examples in the demystifying article, as well.

What Not To Do

Before we begin, I want to make it very clear that am not now, and never have, advocated that people utilize small data segments out of context of larger matching segments and/or at least suspected matching genealogy. For example, I have never implied or even hinted that anyone should go to GedMatch, do a “one to many” compare at 1 cM and then contact people informing them that they are related. Anyone who has extrapolated what I’ve written to mean that either simply did not understand or intentionally misinterpreted the articles.

Sarah Hickerson Revisited

If I thought Sarah Hickerson caused me a lot of heartburn in the decades before I found her, little did I know how much heartburn that discovery would cause.

Let’s go back to the Sarah Hickerson article that started the uproar over whether small data segments are useful at all.

In that article, I found I was a member of a new Ancestry DNA Circle for Charles Hickerson and Mary Lytle, the parents of Sarah Hickerson.

Because there are no tools at Ancestry to prove DNA connections, I hurried over to Family Tree DNA looking for any matches to Hickersons for myself and for my Vannoy cousins who also (potentially) descended from this couple. Much to my delight, I found several matches to Hickersons, in fact, more than 20 – a total of 614 rows of spreadsheet matches when I included all of my Vannoy cousins who potentially descend from this couple to their Hickerson matches. There were 64 matching clusters of segments, both small and large. Some matches were as large as 20cM with 6000 SNPs and more than 20 were over 10cM with from 1500 to 6000 SNPs. There were also hundreds of small segments that matched (and triangulated) as well.

By the time I added in a few more Vannoy cousins that we’ve since recruited, the spreadsheet is now up to 1093 rows and we have 52 Vannoy-Hickerson TRIANGULATED CLUSTERS utilizing only Family Tree DNA tools.

Triangulated DNA, found in 3 or more people at the same location who share a common ancestor is proven to be from that ancestor (or ancestral couple.) This is the commonly accepted gold standard of autosomal DNA triangulation within the industry.

Here’s just one example of a cluster of three people. Charlene and Buster are known (proven, triangulated) cousins and Barbara is a descendant of Charles Hickerson and Mary Lytle.

What more could you want?

Yes, I called this a match. As far as I’m concerned, it’s a confirmed ancestor. How much more confirmed can you get?

Some clusters have as many as 25 confirmed triangulated members.

Others took issue with this conclusion because it included small segment data. This seems like the perfect opportunity in which to take a look at how small segments do, or don’t stand up to scrutiny. So, let’s do just that. I also did the same type of matching comparison in a situation with 2 siblings and a known cousin, here.

To Trash…or Not To Trash

Some genetic genealogists discard small segments entirely, generally under either 5 or 7cM, which I find unfortunate for several reasons.

If a person doesn’t work with small segments, they really can’t comment on the lack of results, and they’ll never have a success because the small segments will have been discarded.
If a person doesn’t work with small segments, they will never notice any trends or matches that may have implications for their ancestry.
If a person doesn’t work with small segments, they can’t contribute to the body of evidence for how to reasonably utilize these segments.
If a person doesn’t work with small segments, they may well be throwing the baby out with the bathwater, but they’ll never know.
They encourage others to do the same.

The Sarah Hickerson article was not meant as a proof article for anything – it was meant to be an article encouraging people to utilize genetic genealogy for not only finding their ancestor and proving known connections, but breaking down brick walls. It was pointing the way to how I found Sarah Hickerson. It was one of my 52 Ancestors Series, documenting my ancestors, not one of the specifically educational articles. This article is different.

If you are only interested in the low hanging fruit, meaning within the past 5 or 6 generations, and only proving your known pedigree, not finding new ancestors beyond that 5-6 generation level, then you can just stop reading now – and you can throw away your small segments. But if you want more, then keep reading, because we as a community need to work with small segment data in order to establish guidelines that work relative to utilizing small segments and identifying the small segments that can be useful, versus the ones that aren’t.

I do not believe for one minute that small segments are universally useless. As Israel said, if his family did not receive those segments from a common family member, then where did they all get those matching segments?

In fact, utilizing triangulated and proven DNA relationships within families is how adoptees piece together their family trees, piggybacking off of the work of people with known pedigrees that they match genetically. My assumption had been that the adoptee community utilized only large DNA segments, because the larger the matching segments, generally the closer in time the genealogy match – and theoretically the easier to find.

However, I discovered that I was wrong, and the adoptee community does in fact utilize small segments as well. Here’s one of the comments posted on my Chromosome Browser War blog article.

“Thanks for the well thought out article, Roberta, I have something to add from the folks at DNAadoption. Adoptees are not just interested in the large segments, the small segments also build the proof of the numerous lines involved. In addition, the accumulation of surnames from all the matches provides a way to evaluate new lines that join into the tree.”

Diane Harman-Hoog (on behalf of the 6 million adoptees in this country, many of who are looking for information on medical records and family heritage).

Diane isn’t the only person who is working with small segment data. Tim Janzen works with small segments, in particular on his Mennonite project, and discusses small segments on the ISOGG WIKI Phasing page. Here is what Tim has to say:

“One advantage of Family Finder is that FF has a 1 cM threshold for matching segments. If a parent and a child both have a matching segment that is in the 2 to 5 cM range and if the number of matching SNPs is 500 or more then there is a reasonably high likelihood that the matching segment is IBD (identical by descent) and not IBS (identical by state).”

The same rules for utilizing larger segment data need to be applied to small segment data to begin with.

Are more guidelines needed for small segments? I don’t know, but we’ll never know if we don’t work with many individual situations and find the common methods for success and identify any problematic areas.

Why Do Small Segments Matter?

In some cases, especially as we work beyond the 6 generation level, small segments may be all we have left of a specific ancestor. If we don’t learn to recognize and utilize the small segments available to us, those ancestors, genetically speaking, will be lost to us forever.

As we move back in time, the DNA from more distant ancestors will be divided into smaller and smaller segments, so if we ever want the ability to identify and track those segments back in time to a specific ancestor, we have to learn how to utilize small segment data – and if we have deleted that data, then we can’t use it.

In my case, I have identified all of my 5^th generation ancestors except one, and I have a strong lead on her. In my 6^th generation, however, I have lots of walls that need to be broken through – and DNA may be the only way I’ll ever do that.

Let’s take a look at what I can expect when trying to match people who also descend from an ancestor 5 generations back in time. If they are my same generation, they would be my fourth cousins.

Based on the autosomal statistics chart at ISOGG, 4^th cousins, on the average, would expect to share about 13.28 cM of DNA from their common ancestor. This would not be over the match threshold at FTDNA of approximately 20 cM total, and if those segments were broken into three pieces, for example, that cousin would not show as a match at either FTDNA or 23andMe, based on the vendors’ respective thresholds.

% Shared DNA	Expected Shared cM	Relationship
0.781%	53.13	Third cousins, common ancestor is 4 generations back in time
0.391%	26.56	Third cousins once removed
	20 cm	Family Tree DNA total cM Threshold
0.195%	13.28	Fourth cousins, common ancestor is 5 generations back in time
	7 cM	23andMe individual segment cM match threshold
0.0977%	6.64	Fourth cousins once removed
0.0488%	3.32	Fifth cousins, common ancestor is 6 generations back in time
0.0244	1.66	Fifth cousins once removed

If you’re lucky, as I was with Hickerson, you’ll match at least some relative who carries that ancestral DNA line above the threshold, and then they’ll match other cousins above the threshold, and you can build a comparison network, linking people together, in that fashion. And yes you may well have to utilize GedMatch for people testing at various different vendors and for those smaller segment comparisons.

For clarification, I have never “called” a genealogy match without supporting large segment data. At the vendors, you can’t even see matches if they don’t have larger segments – so there is no way to even know you would match below the threshold.

I do think that we may be able to make calls based on small segments, at least in some instances, in the future. In fact, we have to figure out how to do this or we will rarely be able to move past the 5^th or 6^th generation utilizing genetics.

At the 5^th generation, or third cousins, one expects to see approximately 26 cM of matching DNA, still over the threshold (if divided correctly), but from that point further back in time, the expected shared amount of DNA is under the current day threshold. For those who wonder why the vendors state that autosomal matches are reliable to about the 5^th or 6^th generation, this is the answer.

I do not discount small segments without cause. In other words, I don’t discount small segments unless there is a reason. Unless they are positively IBS by chance, meaning false, and I can prove it, I don’t disregard them. I do label them and make appropriate notes. You can’t learn from what’s not there.

Let me give you an example. I have one area of my spreadsheet where I have a whole lot of segments, large and small, labeled Acadian. Why? Because the Acadians are so intermarried that I can’t begin to sort out the actual ancestor that DNA came from, at least not yet…so today, I just label them “Acadian.”

This example row is from my master spreadsheet. I have my Mom’s results in my spreadsheet, so I can see easily if someone matches me and Mom both. My rows are pink. The match is on Mom’s side, which I’ve color coded purple. I don’t know which ancestor is the most recent common ancestor, but based on the surnames involved, I know they are Acadian. In some cases, on Acadian matches, I can tell the MRCA and if so, that field is completed as well.

As a note of interest, I inherited my mother’s segment intact, so there was no 50% division in this generation.

I also have segments labeled Mennonite and Brethren. Perhaps in the future I’ll sort through these matches and actually be able to assign DNA segments to specific ancestors. Those segments aren’t useless, they just aren’t yet fully analyzed. As more people test, hopefully, patterns will emerge in many of these DNA groupings, both small and large.

In fact, I talked about DNA patterns and endogamous populations in my recent article, Just One Cousin.

For me, today, some small segment matches appear to be central European matches. I say “appear to be,” because they are not triangulated. For me this is rather boring and nondescript – but if this were my African American client who is trying to figure out which line her European ancestry came from, this could be very important. Maybe she can map these segments to at least a specific ancestral line, which she would find very exciting.

Learning to use small segments effectively has the potential to benefit the following groups of people:

People with colonial ancestry, because all that may be left today of colonial ancestors is small segments.
People looking to break down brick walls, not just confirm currently known ancestors.
People looking for minority ancestors more than 5 or 6 generations back in their trees.
Adoptees – although very clearly, they want to work with the largest matches first.
People working with ethnic identification of ancestors, because you will eventually be able to track ethnicity identifying segments back in time to the originating ancestor(s).

Conversely, people from highly endogamous groups may not be helped much, if at all, by small segments because they are so likely to be widely shared within that population as a group from a common ancestor much further back in time. In fact, the definition of a “small segment” for people with fully endogamous families might be much larger than for someone with no known endogamy.

However, if we can identify segments to specific populations, that may help the future accuracy of ethnicity testing.

Let’s go back and take a look at the Hickerson data using the same format we have been using for the comparisons so far.

Small Segment Examples

These Hickerson/Vannoy examples do not utilize random small segment matches, but are utilizing the same matching rules used for larger matches in conjunction with known, triangulated cousin groups from a known ancestor. Many cousins, including 2 brothers and their uncle all carry this same DNA. Like in Israel’s case, where did they get that same DNA if not from a common ancestor?

In the following examples, I want to stress that all of the people involved DO HAVE LARGER SEGMENT MATCHES on other chromosomes, which is how we knew they matched in the first place, so we aren’t trying to prove they are a match. We know they are. Our goal is to determine if small segments are useful in the same situation, proving matches, as with larger segments. In other words, do the rules hold true? And how do we work with the data? Could we utilize these small segment matches if we didn’t have larger matching segments, and if so, how reliable would they be?

There is a difference between a single match and a triangulated group:

Matches between two people are suggestive of a common ancestor but could be IBS by chance or population..
Multiple matches, such as with the 6 different Hickersons who descend from Charles Hickerson and Mary Lytle, both in the Ancestry DNA Circle and at Family Tree DNA, are extremely suggestive of a specific common ancestor.
Only triangulated groups are proof of a common ancestor, unless the people are closely related known relatives.

In our Hickerson/Vannoy study, all participants match at least to one other (but not to all other) group members at Family Tree DNA which means they match over the FTDNA threshold of approximately 20 cM total and at least one segment over 7.7cM and 500 SNPs or more.

In the example below, from the Hickerson article, the known Vannoy cousins are on the left side and the Hickerson matches to the Vannoy cousins are across the top. We have several more now, but this gives you an idea of how the matching stacked up initially. The two green individuals were proven descendants from Charles Hickerson and Mary Lytle.

The goal here is to see how small data segments stack up in a situation where the relationship is distant. Can small segments be utilized to prove triangulation? This is slightly different than in the Just One Cousin article, where the relationship between the individuals was close and previously known. We can contrast the results of that close relationship and small segments with this more distant connection and small segments.

Sarah Hickerson and Daniel Vannoy

The Vannoy project has a group of about a dozen cousins who descend from Elijah Vannoy who have worked together to discover the identify of Elijah’s parents. Elijah’s father is one of 4 Vannoy men, all sons of the same man, found in Wilkes County, NC. in the late 1700s. Elijah Vannoy is 5 generations upstream from me.

What kind of evidence do we have? In the paper genealogy world, I have ruled out one candidate via a Bible record, and probably a second via census and tax records, but we have little information about the third and fourth candidates – in spite of thoroughly perusing all existent records. So, if we’re ever going to solve the mystery, short of that much-wished-for Vannoy Bible showing up on e-Bay, it’s going to have to be via genetic genealogy.

In addition to the dozen or so Vannoy cousins who have DNA tested, we found 6 individuals who descend from Sarah Hickerson’s parents, Charles Hickerson and Mary Lytle who match various Vannoy cousins. Additionally, those cousins match another 21 individuals who carry the Hickerson or derivative surnames, but since we have not proven their Hickerson lineage on paper, I have not utilized any of those additional matches in this analysis. Of those 26 total matches, at Family Tree DNA, one Hickerson individual matches 3 Vannoy cousins, nine Hickerson descendants match 2 Vannoy cousins and sixteen Hickerson descendants match 1 Vannoy cousin.

Our group of Vannoy cousins matching to the 6 Charles Hickerson/Mary Lytle descendants contains over 60 different clusters of matching DNA data across the 22 chromosomes. Those 6 individuals are included in 43 different triangulated groups, proving the entire triangulation group shares a common ancestor. And that is BEFORE we add any GedMatch information.

If that sounds like a lot, it’s not. Another recent article found 31 clusters among siblings and their first cousin, so 60 clusters among a dozen known Vannoy cousins and half a dozen potential Hickerson cousins isn’t unusual at all.

To be very clear, Sarah Hickerson and Daniel Vannoy were not “declared” to be the parents of Elijah Vannoy, born in 1784, based on small segment matches alone. Larger segment matches were involved, which is how we saw the matches in the first place. Furthermore, the matches triangulated. However, small segments certainly are involved and are more prevalent, of course, than large segments. Some cousins are only connected by small segments. Are they valid, and how do we tell? Sometimes it’s all we have.

Let me give you the classic example of when small segments are needed.

We have four people. Person A and B are known Vannoy cousins and person C and D are potential Hickerson cousins. Potential means, in this case, potential cousins to the Vannoys. The Hickersons already know they both descend from Charles Hickerson and Mary Lytle.

Person A matches person C on chromosome 1 over the matching threshold.
Person B matches person D on chromosome 2 over the matching threshold.

Both Vannoy cousins match Hickerson cousins, but not the same cousin and not on the same segments at the vendor. If these were same segment matches, there would be no question because they would be triangulated, but they aren’t.

So, what do we do? We don’t have access to see if person C and D match each other, and even if we did, they don’t match on the same segments where they match persons A and B, because if they did we’d see them as a match too when we view A and B.

If person A and B don’t match each other at the vendor, we’re flat out of luck and have to move this entire operation to GedMatch, assuming all 4 people have or are willing to download their data.

If person A and B match each other at the vendor, we can see their small segment data as compared to each other and to persons C and D, respectively which then gives us the ability to see if A matches C on the same small segment as B matches D.

If we are lucky, they will all show a common match on a small segment – meaning that A will match B on a small segment of chromosome 3, for example, and A will match C on that same segment. In a perfect world, B will also match D on that same segment, and you will have 4 way triangulation – but I’m happy with the required 3 way match to triangulate.

This is exactly what happened in the article, Be Still My H(e)art. As you can see, three people match on chromosomes 1 and 8, below – two of whom are proven cousins and the third was the wife surname candidate line.

The example I showed of chromosome 2 in the Hickerson article was where all participants of the 5 individuals shown on the chromosome browser were matching to the Vannoy participant. I thought it was a good visual example. It was just one example of the 60+ clusters of cousin matches between the dozen Vannoy cousins and 6 Hickerson descendants.

This example was criticized by some because it was a small segment match. I should probably have utilized chromosome 15 or searched for a better long segment example, but the point in my article was only to show how people that match stack up together on the chromosome browser – nothing more. Here’s the entire chromosome, for clarity.

Certainly, I don’t want to mislead anyone, including myself. Furthermore, I dislike being publicly characterized as “wrong” and worse yet, labeled “irresponsible,” so I decided to delve into the depths of the data and work through several different examples to see if small segment data matching holds in various situations. Let’s see what we found.

Chromosome 15

I selected chromosome 15 to work with because it is a region where a lot of Vannoy descendants match – and because it is a relatively large segment. If the Hickersons do match the Vannoys, there’s a fairly good change they might match on at least part of that segment. In other words, it appears to be my best bet due to sheer size and the number of Elijah Vannoy’s descendants who carry this segment. In addition to the 6 individuals above who matched on chromosome 15, here are an additional 4. As you can see, chromosome 15 has a lot of potential.

The spreadsheet below shows the sections of chromosome 15 where cousins match. Green individuals in the Match column are descendants of Charles Hickerson and Mary Lytle, the parents of Sarah Hickerson. The balance are Vannoys who match on chromosome 15.

As you can see, there are several segments that are quite large, shown in yellow, but there are also many that are under the threshold of 7cM, which are all segments that would be deleted if you are deleting small segments. Please also note that if you were deleting small segments, all of the Hickerson matches would be gone from chromosome 15.

Those of you with an eagle eye will already notice that we have two separate segments that have triangulated between the Vannoy cousins and the Hickerson descendants, noted in the left column by yellow and beige. So really, we could stop right here, because we’ve proven the relationship, but there’s a lot more to learn, so let’s go on.

You Can’t Use What You Can’t See

I need to point something out at this point that is extremely important.

The only reason we see any segment data below the match threshold is because once you match someone on a larger segment at Family Tree DNA, over the threshold, you also get to view the small segment data down to 1cM for your match with that person.

What this means is that if one person or two people match a Hickerson descendant, for example you will see the small segment data for their individual matches, but not for anyone that doesn’t match the participant over the matching threshold.

What that means in the spreadsheet above, is that the only Hickerson that matches more than one Vannoy (on this segment) is Barbara – so we can see her segment data (down to 1cM ) as compared to Polly and Buster, but not to anyone else.

If we could see the smaller segment data of the other participants as compared to the Hickerson participants, even though they don’t match on a larger segment over the matching threshold, there could potentially be a lot of small segment data that would match – and therefore triangulate on this segment.

This is the perfect example of why I’ve suggested to Family Tree DNA that within projects or in individuals situations, that we be allowed to reduce the match threshold – especially when a specific family line match is suspected.

This is also one of the reasons why people turn to GedMatch, and we’ll do that as well.

What this means, relative to the spreadsheet is that it is, unfortunately, woefully incomplete – and it’s not apples to apples because in some cases we have data under the match threshold, and in some, we don’t. So, matches DO count, but nonmatches where small segment data is not available do NOT count as a non-match, or as disproof. It’s only negative proof IF you have the data AND it doesn’t match.

The Vannoys match and triangulate on many segments, so those are irrelevant to this discussion other than when they match to Hickerson DNA. William (H), descends from two sons of Charles Hickerson and Mary Lytle. Unfortunately, he only matches one Vannoy, so we can only see his small segments for that one Vannoy individual, William (V). We don’t know what we are missing as compared to the rest of the Vannoy cousins.

To see William (H)’s and William (V)’s DNA as compared to the rest of the Vannoy cousins, we had to move to GedMatch.

Matching Options

Since we are working with segments that are proven to be Vannoy, and we are trying to prove/disprove if Daniel Vannoy and Sarah Hickerson are the parents of Elijah through multiple Hickerson matches, there are only a few matching options, which are:

The Hickerson individuals will not triangulate with any of the Vannoy DNA, on chromosome 15 or on other chromosomes, meaning that Sarah Hickerson is probably not the mother of Elijah Vannoy, or the common ancestor is too far back in time to discern that match at vendor thresholds.
The Hickerson individuals will not triangulate on this segment, but do triangulate on other segments, meaning that this segment came entirely from the Vannoy side of the family and not the Hickerson side of the family. Therefore, if chromosome 15 does not triangulate, we need to look at other chromosomes.
The Hickerson individuals triangulate with the Vannoy individuals, confirming that Sarah Hickerson is the mother of Elijah Vannoy, or that there is a different common unknown ancestor someplace upstream of several Hickersons and Vannoys.

All of the Vannoy cousins descend from Elijah Vannoy and Lois McNiel, except one, William (V), who descends from the proven son of Sarah Hickerson and Daniel Vannoy, so he would be expected to match at least some Hickerson descendants. The 6 Hickerson cousins descend from Charles Hickerson and Mary Lytle, Sarah’s parents.

William (H), the Hickerson cousin who descends from David, brother to Sarah Hickerson, is descended through two of David Hickerson’s sons.

I decided to utilize the same segment “mapping comparison” technique with a spreadsheet that I utilized in the phasing article, because it’s easy to see and visualize.

I have created a matching spreadsheet and labeled the locations on the spreadsheet from 25-100 based on the beginning of the start location of the cluster of matches and the end location of the cluster.

Each individual being compared on the spreadsheet below has a column across the top. On the chart below, all Hickerson individuals are to the right and are shown with their cells highlighted yellow in the top row.

Below, the entire colorized chart of chromosome 15 is shown, beginning with location 25 and ending with 100, in the left hand column, the area of the Vannoy overlap. Remember, you can double click on the graphics to enlarge. The columns in this spreadsheet are not fully expanded below, but they are in the individual examples.

I am going to step through this spreadsheet, and point out several aspects.

First, I selected Buster, the individual in the group to begin the comparison, because he was one of the closest to the common ancestor, Elijah Vannoy, genealogically, at 4 generations. So he is the person at Family Tree DNA that everyone is initially compared against.

Everyone who matches Buster has their matching segments shown in blue. Buster is shown furthest left.

When participants match someone other than Buster, who they match on that segment is typed into their column. You can tell who Buster matches because their columns are blue on matching locations. Here’s an example.

You can see that in my column, it’s blue on all segments which means I match Buster on this entire region. In addition, there are names of Carl, Dean, William Gedmatch and Billie Gedmatch typed into the cell in the first row which means at that location, in addition to Buster, I also match Carl and Dean at Family Tree DNA and William (descended from the son of Daniel Vannoy and Sarah Hickerson) at Gedmatch and Billie (a Hickerson) at Gedmatch. Their name is typed into my column, and mine into theirs. Please note that I did not run everyone against everyone at GedMatch. I only needed enough data to prove the point and running many comparisons is a long, arduous process even when GedMatch isn’t experiencing problems.

On cells that aren’t colorized blue, the person doesn’t match Buster, but may still match other Vannoy cousin segments. For example, Dean, below, matches Buster on location 25-29, along with some other cousins. However, he does not match Buster on location 30 where he instead matches Harold and Carl who also don’t match Buster at that location. Harold, Carl and Dean do, however, all descend from the same son of Elijah so they may well be sharing DNA from a Vannoy wife at this location, especially since no one who doesn’t share that specific wife’s line matches those three at this location.

Remember, we are not working with random small data segments, but with a proven matching segment to a common Vannoy ancestor, with a group of descendants from a possible/probable Hickerson ancestor that we are trying to prove/disprove. In other words, you would expect either a lot of Hickerson matches on the same segments, if Hickerson is indeed a Vannoy ancestral family, or virtually none of them to match, if not.

The next thing I’d like to point out is that these are small segments of people who also have larger matching segments, many of whom do triangulate on larger segments on other chromosomes. What we are trying to discern is whether small segment matches can be utilized by employing the same matching criteria as large segment matching. In other words, is small segment data valid and useful if it meets the criteria for an IBD match?

For example, let’s look at Daniel. Daniel’s segments on chromosome 15, were it not for the fact that he matches on larger segments on other chromosomes, would not be shown as matches, because they are not individually over the match threshold.

Look at Daniel’s column for Polly and Warren.

The segments in red show a triangulated group where Daniel and Warren, or Daniel, Warren and Polly match. The segments where all 3 match are triangulated.

This proves, unquestionably, that small segments DO match utilizing the normal prescribed IBD matching criteria. This spreadsheet, just for chromosome 15, is full of these examples.

Is there any reason to think that these triangulated matches are not identical by descent? If they are not IBD, how do all of these people match the same DNA? Chance alone? How would that be possible? Two people, yes, maybe, but 3 or more? In some cases, 5 or 6 on the same segment? That is simply not possible, or we have disproven the entire foundation that autosomal DNA matching is based upon.

The question will soon be asked if small segments that triangulate can be useful when there are no larger matching segments to put the match over the initial vendor threshold.

Triangulated Groups

As you can see, most of the people and segments on the spreadsheet, certainly the Elijah descendants, are heavily triangulated, meaning that three or more people match each other on the same locations. Most of this matching is over the vendor threshold at Family Tree DNA.

You can see that Buster, Me, Dean, Carl and Harold all match each other on the same segments, on the left half of the spreadsheet where our names are in each other’s columns.

Remember when I said that the spreadsheet was incomplete? This is an example. David and Warren don’t match each other at a high enough total of segments to get them over the matching threshold when compared to each other, so we can’t see their small segment data as compared to each other. David matches Buster, but Warren doesn’t, so I can’t even see them both in relationship to a common match. There are several people who fall into this category.

Let’s select one individual to use as an example.

I’ve chosen the Vannoy cousin, William(V), because his kit has been uploaded to Gedmatch, he has Vannoy matches and because William is proven to descend from Sarah Hickerson and Daniel Vannoy through their son Joel – so we expect some Hickerson DNA to match William(V).

If William (V) matches the Hickersons on the same DNA locations as he matches to Elijah’s descendants, then that proves that Elijah’s descendant’s DNA in that location is Hickerson DNA.

At GedMatch, I compared William(V) with me and then with Dean using a “one to one” comparison at a low threshold, simply because I wanted as much data as I could get. Family Tree DNA allows for 1 cM and I did the same, allowing 100 SNPs at GedMatch. Family Tree DNA’s lowest SNP threshold is 500.

In case you were wondering, even though I did lower the GedMatch threshold below the FTDNA minimum, there were 45 segments that were above 1cM and above 500 SNPs when matching me to William(V), which would have been above the lowest match threshold at FTDNA (assuming we were over the initial match threshold.) In other words, had we not been below the original match threshold (20cM total, one segment over 7.7cM), these segments would have been included at FTDNA as small segments. As you can see in the chart below, many triangulated.

I colorized the GedMatch matches, where there were no FTDNA matches, in dark red text. This illustrates graphically just how much is missed when the small segments are ignored in cases with known or probable cousins. In the green area, the entry that says “Me GedMatch” could not be colorized red (because you can’t colorize only part of the text of a cell) so I added the Gedmatch designation to differentiate between a match through FTDNA and one from GedMatch. I did the same with all Gedmatch matches, whether colorized or not.

Let’s take a look and see how small segments from GedMatch affect our Hickerson matching. Note that in the green area, William (V) matches William (H), the Hickerson descendant, and William (V) matches to me and Dean as well. This triangulates William (V)’s Hickerson DNA and proves that Elijah’s descendants DNA includes proven Hickerson segments.

In this next example, I matched William (H), the Hickerson cousin (with no Vannoy heritage) against both Buster and me.

Without Gedmatch data, only two segments of chromosome 15 are triangulated between Vannoy and Hickerson cousins, because we can’t see the small data segments of the rest of the cousins who don’t match over the threshold.

You can see here that nearly the entire chromosome is triangulated using small segments. In the chart below, you can see both William(V) and William (H) as they match various Vannoy cousins. Both triangulate with me.

I did the same thing with the Hickerson descendant, Billie, as compared to both me and Dean, with the same type of results.

The next question would be if chromosome 15 is a pileup area where I have a lot of IBS matches that are really population based matches. It does not appear to be. I have identified an area of my chromosomes that may be a pileup area, but chromosome 15 does not carry any of those characteristics.

So by utilizing the small segments at GedMatch for chromosome 15 that we can’t otherwise see, we can triangulate at least some of the Hickerson matches. I can’t complete this chart, because several individuals have not uploaded to GedMatch.

Why would the Hickerson descendant match so many of the Vannoy segments on chromosome 15? Because this is not a random sample. This is a proven Vannoy segment and we are trying to see which parts of this segment are from a potential Hickerson mother or the Vannoy father. If from the Hickerson mother, then this level of matching is not unexpected. In fact, it would be expected. Since we cheated and saw that chromosome 15 was already triangulated at Family Tree DNA, we already knew what to expect.

In the spreadsheet below, I’ve added the 2 GedMatch comparisons, William (V) to me and Dean, and William (H) to me and Buster. You can see the segments that triangulate, on the left. We could also build “triangulated groups,” like GedMatch does. I started to do this, but then stopped because I realized most cells would be colored and you’d have a hard time seeing the individual triangulated segments. I shifted to triangulating only the individuals who triangulate directly with the Hickerson descendant, William(H), shown in green. GedMatch data is shown in red.

I would like to make three points.

1. This still is not a complete spreadsheet where everyone is compared to everyone. This was selectively compared for two known Hickerson cousins, William (V) who descends from both Vannoys and Hickersos and William (H) who descends only from Hickersons.

2. There are 25 individually triangulated segments to the Hickerson descendant on just this chromosome to the various Vannoy cousins. That’s proof times 25 to just one Hickerson cousin.

3. I would NEVER suggest that you select one set of small segments and base a decision on that alone. This entire exercise has assembled cumulative evidence. By the same token, if the rules for segment matching hold up under the worst circumstances, where we have an unknown but suspected relationship and the small segments appear to continue to follow the triangulation rules, they could be expected to remain true in much more favorable circumstances.

Might any of these people have random DNA matches that are truly IBS by chance on chromosome 15? Of course, but the matching rules, just like for larger segments, eliminates them. According to triangulation rules, if they are IBS by chance, they won’t triangulate. If they do triangulate, that would confirm that they received the same DNA from a common ancestor.

If this is not true, and they did not receive their common DNA from a common ancestor, then it disproves the fundamental matching rule upon which all autosomal DNA genetic genealogy is based and we all need to throw in the towel and just go and do something else.

Is there some grey area someplace? I would presume so, but at this point, I don’t know how to discern or define it, if there is. I’ve done three in-depth studies on three different families over the past 6 weeks or so, and I’ve yet to find an area (except for endogamous populations that have matches by population) where the guidelines are problematic. Other researchers may certainly make different discoveries as they do the same kind of studies. There is always more to be discovered, so we need to keep an open mind.

In this situation, it helps a lot that the Hickerson/Vannoy descendants match and triangulate on larger segments on other chromosomes. This study was specifically to see if smaller segments would triangulate and obey the rules. We were fortunate to have such a large, apparently “sticky” segment of Vannoy DNA on chromosome 15 to work with.

Does small segment matching matter in most cases, especially when you have larger segments to utilize? Probably not. Use the largest segments first. But in some cases, like where you are trying to prove an ancestor who was born in the 1700s, you may desperately need that small segment data in order to triangulate between three people.

Why is this important – critically important? Because if small segments obey all of the triangulation rules when larger segments are available to “prove” the match, then there is no reason that they couldn’t be utilized, using the same rules of IBD/IBS, when larger segments are not available. We saw this in Just One Cousin as well.

However, in terms of proof of concept, I don’t know what better proof could possibly be offered, within the standard genetic genealogy proofs where IBD/IBS guidelines are utilized as described in the Phasing article. Additional examples of small segment proof by triangulation are offered in Just One Cousin, Lazarus – Putting Humpty Dumpty Together Again, and in Demystifying Autosomal DNA Matching.

Raising Elijah Vannoy and Sarah Hickerson from the Dead

As I thought more about this situation, I realized that I was doing an awful lot of spreadsheet heavy lifting when a tool might already be available. In fact, Israel’s mention of Lazarus made me wonder if there was a way to apply this tool to the situation at hand.

I decided to take a look at the Lazarus tool and here is what the intro said:

Generate ‘pseudo-DNA kits’ based on segments in common with your matches. These ‘pseudo-DNA kits’ can then be used as a surrogate for a common ancestor in other tests on this site. Segments are included for every combination where a match occurs between a kit in group1 and group2.

It’s obvious from further instructions that this is really meant for a parent or grandparent, but the technique should work just the same for more distant relatives.

I decided to try it first just with the descendants of Elijah Vannoy. At first, I thought that recreated Elijah would include the following DNA:

DNA segments from Elijah Vannoy
DNA segments from Elijah Vannoy’s wife, Lois McNiel
DNA segments that match from Elijah’s descendants spouse’s lines when individuals come from the same descendant line. This means that if three people descend from Joel Vannoy and Phoebe Crumley, Elijah’s son and his wife, that they would match on some DNA from Phoebe, and that there was no way to subtract Phoebe’s DNA.

After working with the Lazarus tool, I realized this is not the case because Lazarus is designed to utilize a group of direct descendants and then compare the DNA of that group to a second group of know relatives, but not descendants.

In other words, if you have a grandson of a man, and his brother. The DNA shared by the brother and the grandson HAS to be the DNA contributed to that grandson by his grandfather, from their common ancestor, the great grandfather. So, in our situation above, Phoebe’s DNA is excluded.

The chart below shows the inheritance path for Lazarus matching.

Because Lazarus is comparing the DNA of Son Doe with Brother Doe – that eliminates any DNA from the brother’s wives, Sarah Spoon or Mary – because those lines are not shared between Brother Doe and Son Doe. The only shared ancestors that can contribute DNA to both are Father Doe and Methusaleh Fisher.

The Lazarus instructions allow you to enter the direct descendants of the person/couple that you are reconstructing, then a second set of instructions asks for remaining relatives not directly descended, like siblings, parents, cousins, etc. In other words, those that should share DNA through the common ancestor of the person you are recreating.

To recreate Elijah, I entered all of the Vannoy cousins and then entered William (V) as a sibling since he is the proven son of Daniel Vannoy and Sarah Hickerson.

Here is what Lazarus produced.

Lazarus includes segments of 4cM and 500 SNPs.

The first thing I thought was, “Holy Moly, what happened to chromosome 15?” I went back and looked, and sure enough, while almost all of the Elijah descendants do match on chromosome 15, William (V), kit 156020, does not match above the Lazarus threshold I selected. So chromosome 15 is not included. Finding additional people who are known to be from this Vannoy line and adding them to the “nondescendant” group would probably result in a more complete Elijah.

Next, to recreate Sarah Hickerson, I added all of the Vannoy cousins plus William (V) as descendants of Sarah Hickerson and then I added just the one Hickerson descendant, William, as a sibling. William’s ancestor is proven to be the sibling of Sarah.

I didn’t know quite what to expect.

Clearly if the DNA from the Hickerson descendant didn’t match or triangulate with DNA from any of the Vannoy cousins at this higher level, then Sarah Hickerson wasn’t likely Elijah’s mother. I wanted to see matching, but more, I wanted to see triangulation.

I was stunned. Every kit except two had matches, some of significant size.

Please note that locations on chromosomes 3, 4 and 13, above, are triangulated in addition to matching between two individuals, which constitutes proof of a common ancestor. Please also note that if you were throwing away segments below 7cM, you would lose all of the triangulated matches and all but two matches altogether.

Clearly, comparing the Vannoy DNA with the Hickerson DNA produced a significant number of matches including three triangulated segments.

Where Are We?

I never have, and I never would recommend attempting to utilize random small match segments out of context. By out of context, I mean simply looking at all of your 1cM segments and suggesting that they are all relevant to your genealogy. Nope, never have. Never would.

There is no question that many small segments are IBS by chance or identical by population. Furthermore, working with small segments in endogamous populations may not be fruitful.

Those are the caveats. Small segments in the right circumstances are useful. And we’ve seen several examples of the right circumstances.

Over the past few weeks, we have identified guidelines and tools to work with small segments, and they are the same tools and guidelines we utilize to work with larger segments as well. The difference is size. When working with large segments, the fact that they are large serves an a filter for us and we don’t question their authenticity. With all small segments, we must do the matching and analysis work to prove validity. Probably not worthwhile if you have larger segments for the same group of people.

Working with the Vannoy data on chromosome 15 is not random, nor is the family from an endogamous population. That segment was proven to be Vannoy prior to attempts to confirm or disprove the Hickerson connection. And we’ve gone beyond just matching, we’ve proven the ancestral link by triangulation, including small segments. We’ve now proven the Hickerson connection about 7 ways to Sunday. Ok, maybe 7 is an exaggeration, but here is the evidence summed up for the Vannoy/Hickerson study from multiple vendors and tools:

Ancestry DNA Circle indicating that multiple Hickerson descendants match me and some that don’t match me, match each other. Not proof, but certainly suggestive of a common ancestor.
A total of 26 Hickerson or derivative family name matches to Vannoy cousins at Family Tree DNA. Not proof, but again, very suggestive.
6 Charles Hickerson/Mary Lytle descendants match to Vannoy cousins at Family Tree DNA. Extremely suggestive, needs triangulation.
Triangulation of segments between Vannoy and Hickerson cousins at Family Tree DNA. Proof, but in this study we were only looking to determine whether small segment matches constituted proof.
Triangulation of multiple Hickerson/Vannoy cousins on chromosome 15 at GedMatch utilizing small segments and one to one matching. More proof.
Lazarus, at higher thresholds than the triangulation matching, when creating Sarah Hickerson, still matched 19 segments and triangulated three for a total of 73.2cM when comparing the Hickerson descendant against the Vannoy cousins. Further proof.

So, can small segment matching data be useful? Is there any reason NOT to accept this evidence as valid?

With proper usage, small segment data certainly looks to provide value by judiciously applying exactly the same rules that apply to all DNA matching. The difference of course being that you don’t really have to think about utilizing those tools with large segment matches. It’s pretty well a given that a 20cM match is valid, but you can never assume anything about those small segment matches without supporting evidence. So are larger segments easier to use? Absolutely.

Does that automatically make small segments invalid? Absolutely not.

In some cases, especially when attempting to break down brick walls more than 5 or 6 generations in the past, small segment data may be all we have available. We must use it effectively. How small is too small? I don’t know. It appears that size is really not a factor if you strictly adhere to the IBD/IBS guidelines, but at some point, I would think the segments would be so small that just about everyone would match everyone because we are all humans – so the ultimate identical by population scenario.

Segments that don’t match an individual and either or both parents, assuming you have both parents to test, can safely be disregarded unless they are large and then a look at the raw data is in order to see if there is a problem in that area. These are IBS by chance. IBS segments by chance also won’t triangulate further up the tree. They can’t, because they don’t match your parents so they cannot come from an ancestor. If they don’t come from an ancestor, they can’t possibly match two other people whose DNA comes from that ancestor on that segment.

If both parents aren’t available, or your small segments do match with your parents, I would suggest that you retain your small segments and map them.

You can’t recognize patterns if the data isn’t present and you won’t be able to find that proverbial needle in the haystack that we are all looking for.

Based on what we’ve seen in multiple case studies, I would conclude that small segment data is certainly valid and can play a valid role in a situation where there is a known or suspected relationship.

I would agree that attempting to utilize small segment data outside the context of a larger data match is not optimal, at least not today, although I wish the vendors would provide a way for us to selectively lower our thresholds. A larger segment match can point the way to smaller segment matches between multiple people that can be triangulated. In some situations, like the person A, B, C, D Hickerson-Vannoy situation I described earlier in this article, I would like to be able to drop the match threshold to reveal the small segment data when other matches are suggestive of a family relationship.

In the Hickerson situation, having the ability to drop the matching thresholds would have been the key to positively confirming this relationship within the vendor’s data base and not having to utilize third party tools like GedMatch – which require the cooperation of all parties involved to download their raw data files. Not everyone transferred their data to Gedmatch in my Vannoy group, but enough did that we were able to do what we needed to do. That isn’t always the case. In fact, I have an nearly identical situation in another line but my two matches at Ancestry have declined to download their data to Gedmatch.

This not the first time that small segment data has played a successful role in finding genealogy solutions, or confirming what we thought we knew – although in all cases to date, larger segments matched as well – and those larger segment matches were key and what pointed me to the potential match that ultimately involved the usage of the small segments for triangulation.

Using larger data segments as pointers probably won’t be the case forever, especially if we can gain confidence that we can reliably utilize small segments, at least in certain situations. Specifically, a small segment match may be nothing, but a small segment triangulated match in the context of a genealogical situation seems to abide by all of the genetic genealogy DNA rules.

In fact, a situation just arose in the past couple weeks that does not include larger segments matching at a vendor.

Let’s close this article by discussing this recent scenario.

The Adoptee

An adoptee approached me with matching data from GedMatch which included matches to me, Dean, Carl and Harold on chromosome 15, on segments that overlap, as follows.

On the spreadsheet above, sent to me by the adoptee, we can see some matches but not all matches. I ran the balance of these 4 people at GedMatch and below is the matching chart for the segment of chromosome 15 where the adoptee matches the 4 Vannoy cousins plus William(H), the Hickerson cousin.

	Me	Carl	Dean	Harold	Adoptee
Me	NA	FTDNA	FTDNA	GedMatch	GedMatch
Carl	FTDNA	NA	FTDNA	FTDNA	GedMatch
Dean	FTDNA	FTDNA	NA	FTDNA	GedMatch
Harold	GedMatch	FTDNA	FTDNA	NA	GedMatch
Adoptee	GedMatch	GedMatch	GedMatch	GedMatch	NA
William (H)	GedMatch	GedMatch	GedMatch	GedMatch	GedMatch

I decided to take the easy route and just utilize Lazarus again, so I added all of the known Vannoy and Hickerson cousins I utilized in earlier Lazarus calculations at Gedmatch as siblings to our adoptee. This means that each kit will be compared to the adoptees DNA and matching segments will be reported. At a threshold of 300 SNPs and 4cM, our adoptee matches at 140cM of common DNA between the various cousins.

Please note that in addition to matching several of the cousins, our adoptee also triangulates on chromosomes 1, 11, 15, 18, 19 and 21. The triangulation on chromosome 21 is to two proven Hickerson descendants, so he matches on this line as well.

I reduced the threshold to 4cM and 200 SNPs to see what kind of difference that would make.

Our adoptee picked up another triangulation on chromosome 1 and added additional cousins in the chromosome 15 “sticky Vannoy” cluster and the chromosome 18 cluster.

Given what we just showed about chromosome 15, and the discussions about IBD and IBS guidelines and small matching segments, what conclusions would you draw and what would you do?

Tell the adoptee this is invalid because there are no qualifying large match segments that match at the vendors.
Tell the adoptee to throw all of those small segments away, or at least all of the ones below 7cM because they are only small matching segments and utilizing small matching segments is only a folly and the adoptee is only seeing what he wants to see – even though the Vannoy cousins with whom he triangulates are proven, triangulated cousins.
Check to see if the adoptee also matches the other cousins involved, although he does clearly already exceeds the triangulation criteria to declare a common ancestor of 3 proven cousins on a matching segment. This is actually what I did utilizing Lazarus and you just saw the outcome.

If this is a valid match, based on who he does and doesn’t match in terms of the rest of the family, you could very well narrow his line substantially – perhaps by utilizing the various Vannoy wives’ DNA, to an ancestral couple. Given that our adoptee matches both the Vannoys and the Hickersons, I suspect he is somehow descended from Daniel Vannoy and Sarah Hickerson.

In Conclusion

What is the acceptable level to utilize small segments in a known or suspected match situation?

Rather than look for a magic threshold number, we are much better served to look at reliable methods to determine the difference between DNA passed from our ancestors to us, IBD, and matches by chance. This helps us to establish the reliability of DNA segments in individual situations we are likely to encounter in our genealogy. In other words, rather that throw the entire pile of wheat away because there is some percentage of chaff in the wheat, let’s figure out how to sort the wheat from the chaff.

Fortunately, both parental phasing and triangulation eliminate the identical by chance segments.

Clearly, the smaller the segments, even in a known match situation, the more likely they are identical by population, given that they triangulate. In fact, this is exactly how the Neanderthal and Denisovan genomes have been reconstructed.

Furthermore, given that the Anzick DNA sample is over 12,000 years old, Identical by population must be how Anzick is matching to contemporary humans, because at least some of these people do clearly share a common ancestor with Anzick at some point, long ago – more than 12,000 years ago. In my case, at least some of the Anzick segments triangulate with my mother’s DNA, so they are not IBS by chance. That only leaves identical by population or identical by descent, meaning within a genealogical timeframe, and we know that isn’t possible.

There are yet other situations where small segment matches are not IBS by chance nor identical by population. For example, I have a very hard time believing that the adoptee situation is nothing but chance. It’s not a folly. It’s identical by descent as proven by triangulation with 10 different cousins – all on segments below the vendor matching thresholds.

In fact, it’s impossible to match the Vannoy cousins, who are already triangulated individually, by chance. While the adoptee match is not over the vendor threshold, the segments are not terribly small and they do all triangulate with multiple individuals who also triangulate with larger segments, at the vendors and on different chromosomes.

This adoptee triangulated match, even without the Hickerson-Vannoy study disproves the blanket statement that small segments below 5cM cannot be used for genealogy. All of these segments are 7.1cM or below and most are below 5.

This small segment match between my mother and her first cousins also disproves that segments under 5cM can never be used for genealogy.

This small segment passed from my mother to me disproves that statement too – clearly matching with our cousin, Cheryl. If I did not receive this from my mother, and she from her parent, then how do we match a common cousin???

More small segment proof, below, between my mother and her second cousin when Lazarus was reconstructing my mother’s father.

And this Vannoy Hickerson 4 cousin triangulated segment also disproves that 5cM and below cannot be used for genealogy.

Where did these small segments come from if not a common ancestor, either one or several generations ago? If you look at the small segment I inherited from my mother and say, “well, of course that’s valid, you got it from your mother” then the same logic has to apply that she inherited it from her parent. The same logic then applies that the same small segment, when shared by my mother’s cousin, also came from the their common grandparents. One cannot be true without the others being true. It’s the same DNA. I got it from my mother. And it’s only a 1.46cM segment, shown in the examples above.

Here are my observations and conclusions:

As proven with hundreds of examples in this and other articles cited, small segments can be and are inherited from our ancestors and can be utilized for genetic genealogy.
There is no line in the sand at 7cM or 5cM at which a segment is viable and useful at 5.1cM and not at 4.9cM.
All small segment matches need to be evaluated utilizing the guidelines set forth for IBD versus IBS by chance versus identical by population set forth in the articles titled How Phasing Works and Determining IBD Versus IBS Matches and Demystifying Autosomal DNA Matching.
When given a choice, large segment matches are always easier to use because they are seldom IBS by chance and most often IBD.
Small segment matches are more likely to be IBS by chance than larger matches, which is why we need to judiciously apply the IBD/IBS Guidelines when attempting to utilize small segment matches.
All DNA matches, not just small segments, must be triangulated to prove a common ancestor, unless they are known close relatives, like siblings, first cousins, etc.
When working in genetic genealogy, always glean the information from larger matches and assemble that information. However, when the time comes that you need those small segments because you are working 5, 6 or 7 generations back in time, remember that tools and guidelines exist to use small segments reliably.
Do not attempt to use small segments out of context. This means that if you were to look only at your 1cM matches to unknown people, and you have the ability to triangulate against your parents, most would prove to be IBS by chance. This is the basis of the argument for why some people delete their small segments. However, by utilizing parental phasing, phasing against known family members (like uncles, aunts and first cousins) and triangulation, you can identify and salvage the useable small segments – and these segments may be the only remnants of your ancestors more than 5 or 6 generations back that you’ll ever have to work with. You do not have to throw all of them away simply because some or many small segments, out of context, are IBS by chance. It doesn’t hurt anything to leave them just sit in your spreadsheet untouched until the day that you need them.

Ultimately, the decision is yours whether you will use small segments or not – and either decision is fine. However, don’t make the decision based on the belief that small segments under some magic number, like 5cM or 7cM are universally useless. They aren’t.

Whether small segments are too much work and effort in your individual situation depends on your personal goals for genetic genealogy and on factors like whether or not you descend from an endogamous population. People’s individual goals and circumstances vary widely. Some people test at Ancestry and are happy with inferential matching circles and nothing more. Some people want to wring every tidbit possible out of genealogy, genetic or otherwise.

I hope everyone will begin to look at how they can use small segment data reliably instead of simply discarding all the small segments on the premise that all small segment data is useless because some small segments are not useful. All unstudied and discarded data is indeed useless, so discarding becomes a self-fulfilling prophecy.

But by far, the worst outcome of throwing perfectly good data away is that you’ll never know what genetic secrets it held for you about your ancestors. Maybe the DNA of your own Sarah Hickerson is lurking there, just waiting for the right circumstances to be found.

______________________________________________________________

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Anzick Matching Update

Posted on January 5, 2015 by Roberta Estes

In response to my article about haplogroup C3*, a regular contributor, Armando, left the following comment:

“Roberta, there was a problem with the way Felix was processing files and he had to change the Clovis Anzick file three times at Gedmatch. The last one is kit F999919 uploaded October 8, 2014. You can see his post on that at http://www.fc.id.au/2014/10/new-clovis-anzick-1-kit-in-gedmatch.html

If you do one-to-many matching on Clovis Anzick F999919 at Gedmatch there is not a single person that reports to have mtDNA M. Your extracts for Clovis Anzick are from September 24, 2014 and therefore are based on a bad file which was kit F999912. The older bad kits F999912 and F999913 have been deleted from Gedmatch. Felix mentions the updates at http://www.fc.id.au/2014/09/clovis-anzick-1-dna-match-living-people.html“

This comment came in on Christmas Eve, and I replied that I would look into this after the holidays.

Given that it was Christmas Eve, I certainly wasn’t going to bother anyone over the holidays with questions, so I quickly ran a one to many compare for the current Anzick kit, F999919, and found at 5cM and below that there were 4 haplogroup M matches.

As I did before, I sent emails to those who provided e-mail addresses asking about their matrilineal heritage.

The first thing I wanted to do, of course, was to check with Felix. I knew that Felix had updated the kits, but my understanding was that he added SNPs from the various companies to create a single file with all the SNPs from all three testing companies, not that any file was bad, so to speak.

I asked Felix if the original files had problems or were bad, and here is his response.

“I can assure you none of the earlier/older versions uploaded to GEDmatch (kit# F999912 and F999913) of Clovis Anzick was bad.

F999912 – Contains only FTDNA SNPs extracted from VCF file provided by authors.
F999913 – Contains all SNPs used by DNA testing companies extracted from VCF file provided by authors.
F999919 – Contains all SNPs used by DNA testing companies processed from BAM file provided by authors.

Source files:

VCF Source: http://www.cbs.dtu.dk/suppl/clovis/data/Anzick-1/genotypes/
BAM Source: http://www.cbs.dtu.dk/suppl/clovis/data/Anzick-1/bams/

I removed the earlier versions not because they are bad but only to avoid redundancy for the same sample kit, and processed BAM file (which is a 41 GB file) contains significantly more SNPs compared to VCF source. Because the latest file has more SNPs, it is possible that some missing SNPs in earlier uploads (which was assumed as matching in GEDmatch) may actually have mismatches in new file and thus, could fall below the thresholds or could break the previously matching segment.

The difference in matches between F999912 and F999919 kit for Clovis Anzick is similar to difference in matches between a 23andMe V4 kit and V3 kit for the same person.”

After thinking about this some, it occurred to me that perhaps GedMatch was treating different files from different vendors differently in their matching and sorting routines. That might account for a difference in matching. So, I asked John Olson at GedMatch.

John’s reply is as follows:

“At one time, I did use different thresholds depending on which vendor was being compared to which other vendor. That was a holdover from when FTDNA had Affymetrix kits that were producing somewhat different results than Illumina kits. I have since changed the one-to-many thresholds to 5cM/500 SNPs for all comparisons. The one-to-one thresholds default to 7cm/700 SNPs. I believe I made that change about a year ago, but it may have been longer. At any rate, they are all the same now, and I’m pretty sure they are all the same since Felix has introduced the F9999xx kits. Another change made within the past year is to treat A=T and C=G for all comparisons. This was done to get rid of single SNP errors in the few cases where one vendor was reporting a different strand than another vendor. In a few cases, I have observed that this “heals” some single-SNP breaks in otherwise continuous matching segments.

It is possible that older one-to-many comparisons may have been made under slightly different conditions than newer ones. Older comparisons made with a 3cm/300 SNP threshold may show larger total segment match if they contained many very small matching segments. This usually happens with endogamous populations. Comparisons affected by the change to A=T, C=G may show a larger matching segment where 2 smaller matching segments existed previously.

Another issue to be aware of when comparing artificial kits is that there may be large gaps between the defined SNPs. So, even if there is a gap of a million SNPs, the GEDmatch comparison algorithm will treat them as contiguous. This works OK when everybody is using the same SNPs, but when the list of SNPs is significantly different, it may produce matches that are bogus. This is particularly obvious when generating artificial kits that are missing large segments of data. I have had to deal with this issue with phased kits and Lazarus kits by introducing the concept of a “hard break” that forces a break between smaller matching segments.”

I wanted to know how the three files that Felix prepared compared relative to the matches they produced. I originally ran several comparisons with each of the first two versions, kits F999912 and F999913, and I didn’t save all of the original files, but I do have at least one file saved from each version. Therefore, I dropped all three sets of results (F999912, F999913 and F999919) into a spreadsheet to see how matching compared between the three Anzick file versions.

Keep in mind that the first file (F999912) contained just the FTDNA SNPs, while the second (F999913) and third (F999919) files contain the SNPs from all of the testing companies. This could potentially make the participant files appear to have missing segments when the matching routine at GedMatch sees SNPs in the Anzick file not in the participant files. However, this shouldn’t be much different than comparing a file from two different vendors except that the Anzick file has the SNPs from all three vendors combined.

The first file from 9-23 at the default threshold had 491 matches, but I subsequently lowered the threshold so I could see as many matches as possible.

GedMatch only shows you your closest 1500 matches, although I now know that as of 12-31-2014, there were a total of 3442 Anzick matches at the 5cM threshold.

The second file from 9-29, run at 6cM had more than 1500 matches. I ran the third kit at default settings on December 27^th and it has 720 matches.

One would expect that the second and third files would have the effect of including more matches from both 23andMe and Ancestry since all of the SNPs utilized by those companies are included (if they are available in the Anzick sample.) We also have to remember that there are new files being uploaded from all three vendor sites on a daily basis, so the total available to match is also increasing. Of the 721 kit matches to F999919, 31 were shades of green which indicate that they have been uploaded during the last 30 days, so we could probably presume that about double that number were uploaded (and match) in two months or triple in three months, so probably about 100 new kits. Those kits would show in the match extraction for this month but not for the first month and possibly not for the second. However, all the kits that matched the first month at the highest threshold should still be showing in the second and third month. Let’s see if that holds true.

I dropped all three sets of data into a spreadsheet and colorized the rows.

Blue = F999912, first extraction, 9-23-2014
Yellow = F999913, second extraction, 9-29-2014
Pink = F999919, third extraction, 12-27-2014

Then I counted the number of blue rows, which are the first extraction, that had matches to both yellow and pink, or only yellow, the second extraction, or only pink, the third (current) extraction, or no matches at all.

You can see that the green grouping shows that all three match each other. The match between A003479 in both the second and third extraction could be because the kit was not present when the first extraction was done.

	All 3 match	1st to 2nd Only	1st to 3rd Only	No Match
Percent First Extraction Matches to Other Extractions	54%	36%	5%	5%

By percent, this is how the matching between kits worked. About half of the kits in the first extraction continued to match kits in both subsequent extractions. Of the remaining half, three quarters of the balance matches the second extraction only and a few match just the third extraction or no extraction at all. For the most part, there is no evident reason upon inspection why the kits would not match the second or third extraction, so the cause has to be a result of the additional SNPs or the matching routine or both. This is not to imply that the results are problematic, just that they are different than I would have expected.

A very low percentage of kits matched only between the first and third extracts and the same percentage had no matches in either the second or third extraction.

I took a closer look at the kits with no matches at all. All of them had relatively low threshold total cM and largest segment size. The smallest total cM was 7.1 and the largest was 8.2. The smallest segment was 7.1 and the largest segment was also 8.2. All of these entries had the total cM equal to the largest cM. It appears that these simply slipped below the match threshold, but that doesn’t appear to be the case because in the current (pink) extract, a total of 171 entries were at or below 8.2 total cM and 8.2 largest cM and several kits had the exact same cM as the kits that didn’t show up from the first (blue) extract as a match – so obviously something truly was different in the SNPs or how the matching was done.

Is there any correlation to the kits in the original extract that didn’t match any other extract in terms of which testing company the participants utilized?

One Ancestry kit (4%), 18 23andMe kits (64%), 7 Family Tree DNA kits (25%) and 2 FN kits (7%) didn’t match anyone. But how many kits were in the original extract from the various companies?

	Original Kit Matches	Second KitMatches	Current Kit Matches
Ancestry Kits (A)	26 (5%)	438 (29%)	199 (28%)
FTDNA Kits (F)	94 (19%)	295 (20%)	121 (17%)
Other F+ Kits*	15 (3%)	35 (2%)	15 (2%)
23andMe Kits (M)	354 (72%)	732 (49%)	382 (53%)

*FB, FN, FE, FV

The effect of the additional SNPs in the kits seems to have been to increase the Ancestry kit matches significantly.

It was interesting to see how the same person’s kit from different vendors compared as well. In this random example, the Family Finder kit has a higher total cM and largest segment than the 23andMe v3 kit.

Here’s a kit from one person at all three vendors, but the 23andMe kit is version 4, in which 23andMe significantly reduced the number of SNPs tested by about one third, from about 900,000 to about 600,000.

I wondered if there is a difference in what is reported based on the threshold selected. Now at first glance, one would think, “well of course there is a difference,” but the difference should be on the bottom end of the list. In other words, the top matches should be the top matches at 7cM, 6cM, 5cM, etc. The top matches at 7cM would still be the top at 6cM, just more smaller matches appended to the end of the match list – or that is what I would expect.

Let’s see if this holds true with the current file.

I ran the “one to many” option for the current Anzick kit, F999919, at seven different levels, on the same day, one right after the other, as follows:

7cM, 700 SNPs
6cM, 600 SNPs
5cM, 500 SNPs
4cM, 400 SNPs
3cM, 300 SNPs
2cM, 200 SNPs
1cM, 100 SNPs

The first extract produced 719 records. The rest were all over the 1500 threshold, so we only see the first 1500. Normally, for genealogy the 1500 threshold would certainly be adequate, but for research, the threshold is frustrating.

To make this easier let me say that the extracts from 5cM down through 1cM were exactly the same, but the extracts at 7, 6 and 5cM, respectively, were not.

Discussions with John Olson at GedMatch shed some light on why the 5cM through 1cM extracts were exactly the same.

“For the past year or so, the database has only stored matches down to 5 cM.”

I sure wish I had known that BEFORE I did all of those extracts.

I combined and color coded all 7 extractions into a spreadsheet.

Most of the grouping look like this where blue=7cm, pink=6cM, grn=5cM, purple=4cm, teal=3cm,apricot=2cm, yellow=1cm. Nice rainbows.

All of the matches from the 7cM extraction, with the exception of a few X matches at the end, some of which have no matches on chromosomes 1-22, are included in the 6cM and 5cM extractions, but after the first several records, they are not in the same position. In other words, they are not the top 719, in the same order, in either the 5 or 6cM extraction, but the 5cM through 1cM extractions are identical. Of course, now we know why the 5cM through 1cM matches are exact. From here forth in the article, I won’t mention the 4cM-1cM extracts because they are the same as the 5cM extract.

For example, looking at the kit in position 712, the last non-X match in the 7cM extract – you find this same kit at row 1140 in the 6cM extract and row 1489 in the 5cM extract.

The 6cM extract appears to have some issues. I ran this twice with the same parameters to be sure there wasn’t an error in how it was set up, and the two runs were identical.

There are about 350 individuals who show up in the 6cM extract who should show up in the 5cM extract as well, but who don’t show in the 5cM extract. They are under the threshold for the 7cM extract, so that is correct, but why are these 350 individuals not appearing as matches at the 5cM threshold?

The kits noted above are the largest non-matching total cM and largest cM that don’t show up in the 5cM extract. The smallest matches are 6.1 and 6.1, respectively.

Checking the 5cM extract, below, there are files with smaller total cMs and a smaller largest segment that are showing as matches.

However, looking at the kits with the smallest cMs at the 5cM level, the smallest total cMs is 6.9 and it is combined with the largest segment of 6.9 as well, so that is above the 6.8 and 6.8 shown above. The smallest individual segment is 5.1 but the total cM for that individual is 10.1. So obviously the matching threshold at GedMatch is some combination of both the total cM and the largest segment. This is somewhat unexpected, but doesn’t seem to be a red flag, just how this system works.

So, where are we?

I am glad to have Felix confirm that the files weren’t “bad,” only truly “new and improved,” and that the matching between the various files is pretty much as expected – and from various tests run, everything pretty much looks kosher. The newer files with all of the SNPs utilized by the companies seem to level the playing field, allowing Ancestry kits a better chance of matching.

Aside from my intense interest due to the Native American connection, this is also how I’ve been extracting potential Native American mitochondrial haplogroups from the Anzick matches, including haplogroup M, for my research notes. M is potentially a Native American haplogroup, but is as yet unproven. With haplogroup M showing up in these people who are often heavily Native, and often from Mexico, Central and South America where 80% of the mitochondrial population is believed to be of Native American heritage, it seems prudent to add them to my research notes for further research and possible proof in the future. I contact individuals and ask about their matrilineal heritage. If they don’t have Asian or genealogically proven heritage elsewhere, and their families emerge from the areas with high Native frequencies, I include them on the research list.

In the three days between the two extracts this past week, three of the four haplogroup M individuals were pushed below the match threshold and are no longer visible at the default level. Yes, I have confirmed hat they are still there just not visible at the 1500 match threshold.

I have contacted the individuals with e-mail addresses, asking about their matrilineal heritage. One person said the tester’s mother’s heritage was from India, so that haplogroup M is not on the research list, of course, because it is proven to be from elsewhere – a place where haplogroup M and subgroups are quite common.

In total, there were 15 new potentially Native DNA mitochondrial DNA haplogroups listed in the 12-27 extract. I’ll be adding those to my research notes as soon as I have the opportunity to contact these folks and ask about their known matrilineal genealogy.

I didn’t really anticipate that there would be so much change, nor so quickly, so it looks like I’m going to have to check the Anzick matches for potential Native mitochondrial haplogroups much more often.

Since it looks like there may be lots of additions over time, far more than I expected, I’ll also be going back and making better notes in my research file. I will, for example, note the kit number and date for all of the extractions. For this and future extractions, I’ll also be listing the number of results per haplogroup. I think that would be valuable information as well.

I’d like to thank Armando for raising this topic. The research into matching with a kit that has the entire spectrum of SNPs from all three of the companies has been quite interesting. In fact, unless Felix has added all of the SNPs to the other ancient kits, this is the only kit in existence that has all of the SNPs from all of the companies included.

My thanks to Felix Immanuel (formerly Felix Chandrakumar) and John Olson for assistance with research for this article.

______________________________________________________________

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2014 Top Genetic Genealogy Happenings – A Baker’s Dozen +1

Posted on December 30, 2014 by Roberta Estes

It’s that time again, to look over the year that has just passed and take stock of what has happened in the genetic genealogy world. I wrote a review in both 2012 and 2013 as well. Looking back, these momentous happenings seem quite “old hat” now. For example, both www.GedMatch.com and www.DNAGedcom.com, once new, have become indispensable tools that we take for granted. Please keep in mind that both of these tools (as well as others in the Tools section, below) depend on contributions, although GedMatch now has a tier 1 subscription offering for $10 per month as well.

So what was the big news in 2014?

Beyond the Tipping Point

Genetic genealogy has gone over the tipping point. Genetic genealogy is now, unquestionably, mainstream and lots of people are taking part. From the best I can figure, there are now approaching or have surpassed three million tests or test records, although certainly some of those are duplicates.

500,000+ at 23andMe
700,000+ at Ancestry
700,000+ at Genographic

The organizations above represent “one-test” companies. Family Tree DNA provides various kinds of genetic genealogy tests to the community and they have over 380,000 individuals with more than 700,000 test records.

In addition to the above mentioned mainstream firms, there are other companies that provide niche testing, often in addition to Family Tree DNA Y results.

In addition, there is what I would refer to as a secondary market for testing as well which certainly attracts people who are not necessarily genetic genealogists but who happen across their corporate information and decide the test looks interesting. There is no way of knowing how many of those tests exist.

Additionally, there is still the Sorenson data base with Y and mtDNA tests which reportedly exceeded their 100,000 goal.

Spencer Wells spoke about the “viral spread threshold” in his talk in Houston at the International Genetic Genealogy Conference in October and terms 2013 as the year of infection. I would certainly agree.

Autosomal Now the New Normal

Another change in the landscape is that now, autosomal DNA has become the “normal” test. The big attraction to autosomal testing is that anyone can play and you get lots of matches. Earlier in the year, one of my cousins was very disappointed in her brother’s Y DNA test because he only had a few matches, and couldn’t understand why anyone would test the Y instead of autosomal where you get lots and lots of matches. Of course, she didn’t understand the difference in the tests or the goals of the tests – but I think as more and more people enter the playground – percentagewise – fewer and fewer do understand the differences.

Case in point is that someone contacted me about DNA and genealogy. I asked them which tests they had taken and where and their answer was “the regular one.” With a little more probing, I discovered that they took Ancestry’s autosomal test and had no clue there were any other types of tests available, what they could tell him about his ancestors or genetic history or that there were other vendors and pools to swim in as well.

A few years ago, we not only had to explain about DNA tests, but why the Y and mtDNA is important. Today, we’ve come full circle in a sense – because now we don’t have to explain about DNA testing for genealogy in general but we still have to explain about those “unknown” tests, the Y and mtDNA. One person recently asked me, “oh, are those new?”

Ancient DNA

This year has seen many ancient DNA specimens analyzed and sequenced at the full genomic level.

The year began with a paper titled, “When Populations Collide” which revealed that contemporary Europeans carry between 1-4% of Neanderthal DNA most often associated with hair and skin color, or keratin. Africans, on the other hand, carry none or very little Neanderthal DNA.

http://dna-explained.com/2014/01/30/neanderthal-genome-further-defined-in-contemporary-eurasians/

A month later, a monumental paper was published that detailed the results of sequencing a 12,500 Clovis child, subsequently named Anzick or referred to as the Anzick Clovis child, in Montana. That child is closely related to Native American people of today.

http://dna-explained.com/2014/02/13/clovis-people-are-native-americans-and-from-asia-not-europe/

In June, another paper emerged where the authors had analyzed 8000 year old bones from the Fertile Crescent that shed light on the Neolithic area before the expansion from the Fertile Crescent into Europe. These would be the farmers that assimilated with or replaced the hunter-gatherers already living in Europe.

http://dna-explained.com/2014/06/09/dna-analysis-of-8000-year-old-bones-allows-peek-into-the-neolithic/

Svante Paabo is the scientist who first sequenced the Neanderthal genome. Here is a great interview and speech. This man is so interesting. If you have not read his book, “Neanderthal Man, In Search of Lost Genomes,” I strongly recommend it.

http://dna-explained.com/2014/07/22/finding-your-inner-neanderthal-with-evolutionary-geneticist-svante-paabo/

In the fall, yet another paper was released that contained extremely interesting information about the peopling and migration of humans across Europe and Asia. This was just before Michael Hammer’s presentation at the Family Tree DNA conference, so I covered the paper along with Michael’s information about European ancestral populations in one article. The take away messages from this are two-fold. First, there was a previously undefined “ghost population” called Ancient North Eurasian (ANE) that is found in the northern portion of Asia that contributed to both Asian populations, including those that would become the Native Americans and European populations as well. Secondarily, the people we thought were in Europe early may not have been, based on the ancient DNA remains we have to date. Of course, that may change when more ancient DNA is fully sequenced which seems to be happening at an ever-increasing rate.

http://dna-explained.com/2014/10/21/peopling-of-europe-2014-identifying-the-ghost-population/

Ancient DNA Available for Citizen Scientists

If I were to give a Citizen Scientist of the Year award, this year’s award would go unquestionably to Felix Chandrakumar for his work with the ancient genome files and making them accessible to the genetic genealogy world. Felix obtained the full genome files from the scientists involved in full genome analysis of ancient remains, reduced the files to the SNPs utilized by the autosomal testing companies in the genetic genealogy community, and has made them available at GedMatch.

http://dna-explained.com/2014/09/22/utilizing-ancient-dna-at-gedmatch/

If this topic is of interest to you, I encourage you to visit his blog and read his many posts over the past several months.

https://plus.google.com/+FelixChandrakumar/posts

The availability of these ancient results set off a sea of comparisons. Many people with Native heritage matched Anzick’s file at some level, and many who are heavily Native American, particularly from Central and South America where there is less admixture match Anzick at what would statistically be considered within a genealogical timeframe. Clearly, this isn’t possible, but it does speak to how endogamous populations affect DNA, even across thousands of years.

http://dna-explained.com/2014/09/23/analyzing-the-native-american-clovis-anzick-ancient-results/

Because Anzick is matching so heavily with the Mexican, Central and South American populations, it gives us the opportunity to extract mitochondrial DNA haplogroups from the matches that either are or may be Native, if they have not been recorded before.

http://dna-explained.com/2014/09/23/analyzing-the-native-american-clovis-anzick-ancient-results/

Needless to say, the matches of these ancient kits with contemporary people has left many people questioning how to interpret the results. The answer is that we don’t really know yet, but there is a lot of study as well as speculation occurring. In the citizen science community, this is how forward progress is made…eventually.

http://dna-explained.com/2014/09/25/ancient-dna-matches-what-do-they-mean/

http://dna-explained.com/2014/09/30/ancient-dna-matching-a-cautionary-tale/

More ancient DNA samples for comparison:

http://dna-explained.com/2014/10/04/more-ancient-dna-samples-for-comparison/

A Siberian sample that also matches the Malta Child whose remains were analyzed in late 2013.

http://dna-explained.com/2014/11/12/kostenki14-a-new-ancient-siberian-dna-sample/

Felix has prepared a list of kits that he has processed, along with their GedMatch numbers and other relevant information, like gender, haplogroup(s), age and location of sample.

http://www.y-str.org/p/ancient-dna.html

Furthermore, in a collaborative effort with Family Tree DNA, Felix formed an Ancient DNA project and uploaded the ancient autosomal files. This is the first time that consumers can match with Ancient kits within the vendor’s data bases.

https://www.familytreedna.com/public/Ancient_DNA

Recently, GedMatch added a composite Archaic DNA Match comparison tool where your kit number is compared against all of the ancient DNA kits available. The output is a heat map showing which samples you match most closely.

Indeed, it has been a banner year for ancient DNA and making additional discoveries about DNA and our ancestors. Thank you Felix.

Haplogroup Definition

That SNP tsunami that we discussed last year…well, it made landfall this year and it has been storming all year long…in a good way. At least, ultimately, it will be a good thing. If you asked the haplogroup administrators today about that, they would probably be too tired to answer – as they’ve been quite overwhelmed with results.

The Big Y testing has been fantastically successful. This is not from a Family Tree DNA perspective, but from a genetic genealogy perspective. Branches have been being added to and sawed off of the haplotree on a daily basis. This forced the renaming of the haplogroups from the old traditional R1b1a2 to R-M269 in 2012. While there was some whimpering then, it would be nothing like the outright wailing now that would be occurring as haplogroup named reached 20 or so digits.

Alice Fairhurst discussed the SNP tsunami at the DNA Conference in Houston in October and I’m sure that the pace hasn’t slowed any between now and then. According to Alice, in early 2014, there were 4115 individual SNPs on the ISOGG Tree, and as of the conference, there were 14,238 SNPs, with the 2014 addition total at that time standing at 10,213. That is over 1000 per month or about 35 per day, every day.

Yes, indeed, that is the definition of a tsunami. Every one of those additions requires one of a number of volunteers, generally haplogroup project administrators to evaluate the various Big Y results, the SNPs and novel variants included, where they need to be inserted in the tree and if branches need to be rearranged. In some cases, naming request for previously unknown SNPs also need to be submitted. This is all done behind the scenes and it’s not trivial.

The project I’m closest to is the R1b L-21 project because my Estes males fall into that group. We’ve tested several, and I’ll be writing an article as soon as the final test is back.

The tree has grown unbelievably in this past year just within the L21 group. This project includes over 700 individuals who have taken the Big Y test and shared their results which has defined about 440 branches of the L21 tree. Currently there are almost 800 kits available if you count the ones on order and the 20 or so from another vendor.

Here is the L21 tree in January of 2014

Compare this with today’s tree, below.

Michael Walsh, Richard Stevens, David Stedman need to be commended for their incredible work in the R-L21 project. Other administrators are doing equivalent work in other haplogroup projects as well. I big thank you to everyone. We’d be lost without you!

One of the results of this onslaught of information is that there have been fewer and fewer academic papers about haplogroups in the past few years. In essence, by the time a paper can make it through the peer review cycle and into publication, the data in the paper is often already outdated relative to the Y chromosome. Recently a new paper was released about haplogroup C3*. While the data is quite valid, the authors didn’t utilize the new SNP naming nomenclature. Before writing about the topic, I had to translate into SNPese. Fortunately, C3* has been relatively stable.

http://dna-explained.com/2014/12/23/haplogroup-c3-previously-believed-east-asian-haplogroup-is-proven-native-american/

10^th Annual International Conference on Genetic Genealogy

The Family Tree DNA International Conference on Genetic Genealogy for project administrators is always wonderful, but this year was special because it was the 10^th annual. And yes, it was my 10^th year attending as well. In all these years, I had never had a photo with both Max and Bennett. Everyone is always so busy at the conferences. Getting any 3 people, especially those two, in the same place at the same time takes something just short of a miracle.

Ten years ago, it was the first genetic genealogy conference ever held, and was the only place to obtain genetic genealogy education outside of the rootsweb genealogy DNA list, which is still in existence today. Family Tree DNA always has a nice blend of sessions. I always particularly appreciate the scientific sessions because those topics generally aren’t covered elsewhere.

http://dna-explained.com/2014/10/11/tenth-annual-family-tree-dna-conference-opening-reception/

http://dna-explained.com/2014/10/12/tenth-annual-family-tree-dna-conference-day-2/

http://dna-explained.com/2014/10/13/tenth-annual-family-tree-dna-conference-day-3/

http://dna-explained.com/2014/10/15/tenth-annual-family-tree-dna-conference-wrapup/

Jennifer Zinck wrote great recaps of each session and the ISOGG meeting.

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy/

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy-isogg-meeting/

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy-sunday/

I thank Family Tree DNA for sponsoring all 10 conferences and continuing the tradition. It’s really an amazing feat when you consider that 15 years ago, this industry didn’t exist at all and wouldn’t exist today if not for Max and Bennett.

Education

Two educational venues offered classes for genetic genealogists and have made their presentations available either for free or very reasonably. One of the problems with genetic genealogy is that the field is so fast moving that last year’s session, unless it’s the very basics, is probably out of date today. That’s the good news and the bad news.

http://dna-explained.com/2014/11/12/genetic-genealogy-ireland-2014-presentations

http://dna-explained.com/2014/09/26/educational-videos-from-international-genetic-genealogy-conference-now-available/

In addition, three books have been released in 2014.

In January, Emily Aulicino released Genetic Genealogy, The Basics and Beyond.

In October, Richard Hill released “Guide to DNA Testing: How to Identify Ancestors, Confirm Relationships and Measure Ethnicity through DNA Testing.”

Most recently, David Dowell’s new book, NextGen Genealogy: The DNA Connection was released right after Thanksgiving.

Ancestor Reconstruction – Raising the Dead

This seems to be the year that genetic genealogists are beginning to reconstruct their ancestors (on paper, not in the flesh) based on the DNA that the ancestors passed on to various descendants. Those segments are “gathered up” and reassembled in a virtual ancestor.

I utilized Kitty Cooper’s tool to do just that.

http://dna-explained.com/2014/10/03/ancestor-reconstruction/

I know it doesn’t look like much yet but this is what I’ve been able to gather of Henry Bolton, my great-great-great-grandfather.

Kitty did it herself too.

http://blog.kittycooper.com/2014/08/mapping-an-ancestral-couple-a-backwards-use-of-my-segment-mapper/

http://blog.kittycooper.com/2014/09/segment-mapper-tool-improvements-another-wold-dna-map/

Ancestry.com wrote a paper about the fact that they have figured out how to do this as well in a research environment.

http://corporate.ancestry.com/press/press-releases/2014/12/ancestrydna-reconstructs-partial-genome-of-person-living-200-years-ago/

http://www.thegeneticgenealogist.com/2014/12/16/ancestrydna-recreates-portions-genome-david-speegle-two-wives/

GedMatch has created a tool called, appropriately, Lazarus that does the same thing, gathers up the DNA of your ancestor from their descendants and reassembles it into a DNA kit.

Blaine Bettinger has been working with and writing about his experiences with Lazarus.

http://www.thegeneticgenealogist.com/2014/10/20/finally-gedmatch-announces-monetization-strategy-way-raise-dead/

http://www.thegeneticgenealogist.com/2014/12/09/recreating-grandmothers-genome-part-1/

http://www.thegeneticgenealogist.com/2014/12/14/recreating-grandmothers-genome-part-2/

Tools

Speaking of tools, we have some new tools that have been introduced this year as well.

Genome Mate is a desktop tool used to organize data collected by researching DNA comparsions and aids in identifying common ancestors. I have not used this tool, but there are others who are quite satisfied. It does require Microsoft Silverlight be installed on your desktop.

The Autosomal DNA Segment Analyzer is available through www.dnagedcom.com and is a tool that I have used and found very helpful. It assists you by visually grouping your matches, by chromosome, and who you match in common with.

Charting Companion from Progeny Software, another tool I use, allows you to colorize and print or create pdf files that includes X chromosome groupings. This greatly facilitates seeing how the X is passed through your ancestors to you and your parents.

WikiTree is a free resource for genealogists to be able to sort through relationships involving pedigree charts. In November, they announced Relationship Finder.

Probably the best example I can show of how WikiTree has utilized DNA is using the results of King Richard III.

By clicking on the DNA icon, you see the following:

And then Richard’s Y, mitochondrial and X chromosome paths.

Since Richard had no descendants, to see how descendants work, click on his mother, Cecily of York’s DNA descendants and you’re shown up to 10 generations.

While this isn’t terribly useful for Cecily of York who lived and died in the 1400s, it would be incredibly useful for finding mitochondrial descendants of my ancestor born in 1802 in Virginia. I’d love to prove she is the daughter of a specific set of parents by comparing her DNA with that of a proven daughter of those parents! Maybe I’ll see if I can find her parents at WikiTree.

Kitty Cooper’s blog talks about additional tools. I have used Kitty’s Chromosome mapping tools as discussed in ancestor reconstruction.

Felix Chandrakumar has created a number of fun tools as well. Take a look. I have not used most of these tools, but there are several I’ll be playing with shortly.

Exits and Entrances

With very little fanfare, deCODEme discontinued their consumer testing and reminded people to download their date before year end.

http://dna-explained.com/2014/09/30/decodeme-consumer-tests-discontinued/

I find this unfortunate because at one time, deCODEme seemed like a company full of promise for genetic genealogy. They failed to take the rope and run.

On a sad note, Lucas Martin who founded DNA Tribes unexpectedly passed away in the fall. DNA Tribes has been a long-time player in the ethnicity field of genetic genealogy. I have often wondered if Lucas Martin was a pseudonym, as very little information about Lucas was available, even from Lucas himself. Neither did I find an obituary. Regardless, it’s sad to see someone with whom the community has worked for years pass away. The website says that they expect to resume offering services in January 2015. I would be cautious about ordering until the structure of the new company is understood.

http://www.dnatribes.com/

In the last month, a new offering has become available that may be trying to piggyback on the name and feel of DNA Tribes, but I’m very hesitant to provide a link until it can be determined if this is legitimate or bogus. If it’s legitimate, I’ll be writing about it in the future.

However, the big news exit was Ancestry’s exit from the Y and mtDNA testing arena. We suspected this would happen when they stopped selling kits, but we NEVER expected that they would destroy the existing data bases, especially since they maintain the Sorenson data base as part of their agreement when they obtained the Sorenson data.

http://dna-explained.com/2014/10/02/ancestry-destroys-irreplaceable-dna-database/

The community is still hopeful that Ancestry may reverse that decision.

Ancestry – The Chromosome Browser War and DNA Circles

There has been an ongoing battle between Ancestry and the more seasoned or “hard-core” genetic genealogists for some time – actually for a long time.

The current and most long-standing issue is the lack of a chromosome browser, or any similar tools, that will allow genealogists to actually compare and confirm that their DNA match is genuine. Ancestry maintains that we don’t need it, wouldn’t know how to use it, and that they have privacy concerns.

Other than their sessions and presentations, they had remained very quiet about this and not addressed it to the community as a whole, simply saying that they were building something better, a better mousetrap.

In the fall, Ancestry invited a small group of bloggers and educators to visit with them in an all-day meeting, which came to be called DNA Day.

http://dna-explained.com/2014/10/08/dna-day-with-ancestry/

In retrospect, I think that Ancestry perceived that they were going to have a huge public relations issue on their hands when they introduced their new feature called DNA Circles and in the process, people would lose approximately 80% of their current matches. I think they were hopeful that if they could educate, or convince us, of the utility of their new phasing techniques and resulting DNA Circles feature that it would ease the pain of people’s loss in matches.

I am grateful that they reached out to the community. Some very useful dialogue did occur between all participants. However, to date, nothing more has happened nor have we received any additional updates after the release of Circles.

Time will tell.

http://dna-explained.com/2014/11/18/in-anticipation-of-ancestrys-better-mousetrap/

http://dna-explained.com/2014/11/19/ancestrys-better-mousetrap-dna-circles/

DNA Circles, while interesting and somewhat useful, is certainly NOT a replacement for a chromosome browser, nor is it a better mousetrap.

http://dna-explained.com/2014/11/30/chromosome-browser-war/

In fact, the first thing you have to do when you find a DNA Circle that you have not verified utilizing raw data and/or chromosome browser tools from either 23andMe, Family Tree DNA or Gedmatch, is to talk your matches into transferring their DNA to Family Tree DNA or download to Gedmatch, or both.

http://dna-explained.com/2014/11/27/sarah-hickerson-c1752-lost-ancestor-found-52-ancestors-48/

I might add that the great irony of finding the Hickerson DNA Circle that led me to confirm that ancestry utilizing both Family Tree DNA and GedMatch is that today, when I checked at Ancestry, the Hickerson DNA Circle is no longer listed. So, I guess I’ve been somehow pruned from the circle. I wonder if that is the same as being voted off of the island. So, word to the wise…check your circles often…they change and not always in the upwards direction.

The Seamy Side – Lies, Snake Oil Salesmen and Bullys

Unfortunately a seamy side, an underbelly that’s rather ugly has developed in and around the genetic genealogy industry. I guess this was to be expected with the rapid acceptance and increasing popularity of DNA testing, but it’s still very unfortunate.

Some of this I expected, but I didn’t expect it to be so…well…blatant.

I don’t watch late night TV, but I’m sure there are now DNA diets and DNA dating and just about anything else that could be sold with the allure of DNA attached to the title.

I googled to see if this was true, and it is, although I’m not about to click on any of those links.

Unfortunately, within the ever-growing genetic genealogy community a rather large rift has developed over the past couple of years. Obviously everyone can’t get along, but this goes beyond that. When someone disagrees, a group actively “stalks” the person, trying to cost them their employment, saying hate filled and untrue things and even going so far as to create a Facebook page titled “Against<personname>.” That page has now been removed, but the fact that a group in the community found it acceptable to create something like that, and their friends joined, is remarkable, to say the least. That was accompanied by death threats.

Bullying behavior like this does not make others feel particularly safe in expressing their opinions either and is not conducive to free and open discussion. As one of the law enforcement officers said, relative to the events, “This is not about genealogy. I don’t know what it is about, yet, probably money, but it’s not about genealogy.”

Another phenomenon is that DNA is now a hot topic and is obviously “selling.” Just this week, this report was published, and it is, as best we can tell, entirely untrue.

http://worldnewsdailyreport.com/usa-archaeologists-discover-remains-of-first-british-settlers-in-north-america/

There were several tip offs, like the city (Lanford) and county (Laurens County) is not in the state where it is attributed (it’s in SC not NC), and the name of the institution is incorrect (Johns Hopkins, not John Hopkins). Additionally, if you google the name of the magazine, you’ll see that they specialize in tabloid “faux reporting.” It also reads a lot like the King Richard genuine press release.

http://urbanlegends.about.com/od/Fake-News/tp/A-Guide-to-Fake-News-Websites.01.htm

Earlier this year, there was a bogus institutional site created as well.

On one of the DNA forums that I frequent, people often post links to articles they find that are relevant to DNA. There was an interesting article, which has now been removed, correlating DNA results with latitude and altitude. I thought to myself, I’ve never heard of that…how interesting. Here’s part of what the article said:

Researchers at Aberdeen College’s Havering Centre for Genetic Research have discovered an important connection between our DNA and where our ancestors used to live.

Tiny sequence variations in the human genome sometimes called Single Nucleotide Polymorphisms (SNPs) occur with varying frequency in our DNA. These have been studied for decades to understand the major migrations of large human populations. Now Aberdeen College’s Dr. Miko Laerton and a team of scientists have developed pioneering research that shows that these differences in our DNA also reveal a detailed map of where our own ancestors lived going back thousands of years.

Dr. Laerton explains: “Certain DNA sequence variations have always been important signposts in our understanding of human evolution because their ages can be estimated. We’ve known for years that they occur most frequently in certain regions [of DNA], and that some alleles are more common to certain geographic or ethnic groups, but we have never fully understood the underlying reasons. What our team found is that the variations in an individual’s DNA correlate with the latitudes and altitudes where their ancestors were living at the time that those genetic variations occurred. We’re still working towards a complete understanding, but the knowledge that sequence variations are connected to latitude and altitude is a huge breakthrough by itself because those are enough to pinpoint where our ancestors lived at critical moments in history.”

The story goes on, but at the bottom, the traditional link to the publication journal is found.

The full study by Dr. Laerton and her team was published in the September issue of the Journal of Genetic Science.

I thought to myself, that’s odd, I’ve never heard of any of these people or this journal, and then I clicked to find this.

About that time, Debbie Kennett, DNA watchdog of the UK, posted this:

April Fools Day appears to have arrived early! There is no such institution as Aberdeen College founded in 1394. The University of Aberdeen in Scotland was founded in 1495 and is divided into three colleges: http://www.abdn.ac.uk/about/colleges-schools-institutes/colleges-53.php

The picture on the masthead of the “Aberdeen College” website looks very much like a photo of Aberdeen University. This fake news item seems to be the only live page on the Aberdeen College website. If you click on any other links, including the link to the so-called “Journal of Genetic Science”, you get a message that the website is experienced “unusually high traffic”. There appears to be no such journal anyway.

We also realized that Dr. Laerton, reversed, is “not real.”

I still have no idea why someone would invest the time and effort into the fake website emulating the University of Aberdeen, but I’m absolutely positive that their motives were not beneficial to any of us.

What is the take-away of all of this? Be aware, very aware, skeptical and vigilant. Stick with the mainstream vendors unless you realize you’re experimenting.

King Richard

The much anticipated and long-awaited DNA results on the remains of King Richard III became available with a very unexpected twist. While the science team feels that they have positively identified the remains as those of Richard, the Y DNA of Richard and another group of men supposed to have been descended from a common ancestor with Richard carry DNA that does not match.

http://dna-explained.com/2014/12/09/henry-iii-king-of-england-fox-in-the-henhouse-52-ancestors-49/

http://dna-explained.com/2014/12/05/mitochondrial-dna-mutation-rates-and-common-ancestors/

Debbie Kennett wrote a great summary article.

http://cruwys.blogspot.com/2014/12/richard-iii-and-use-of-dna-as-evidence.html

More Alike than Different

One of the life lessons that genetic genealogy has held for me is that we are more closely related that we ever knew, to more people than we ever expected, and we are far more alike than different. A recent paper recently published by 23andMe scientists documents that people’s ethnicity reflect the historic events that took place in the part of the country where their ancestors lived, such as slavery, the Trail of Tears and immigration from various worldwide locations.

From the 23andMe blog:

The study leverages samples of unprecedented size and precise estimates of ancestry to reveal the rate of ancestry mixing among American populations, and where it has occurred geographically:

All three groups – African Americans, European Americans and Latinos – have ancestry from Africa, Europe and the Americas.
Approximately 3.5 percent of European Americans have 1 percent or more African ancestry. Many of these European Americans who describe themselves as “white” may be unaware of their African ancestry since the African ancestor may be 5-10 generations in the past.
European Americans with African ancestry are found at much higher frequencies in southern states than in other parts of the US.

The ancestry proportions point to the different regional impacts of slavery, immigration, migration and colonization within the United States:

The highest levels of African ancestry among self-reported African Americans are found in southern states, especially South Carolina and Georgia.
One in every 20 African Americans carries Native American ancestry.
More than 14 percent of African Americans from Oklahoma carry at least 2 percent Native American ancestry, likely reflecting the Trail of Tears migration following the Indian Removal Act of 1830.
Among self-reported Latinos in the US, those from states in the southwest, especially from states bordering Mexico, have the highest levels of Native American ancestry.

http://news.sciencemag.org/biology/2014/12/genetic-study-reveals-surprising-ancestry-many-americans?utm_campaign=email-news-weekly&utm_source=eloqua

23andMe provides a very nice summary of the graphics in the article at this link:

http://blog.23andme.com/wp-content/uploads/2014/10/Bryc_ASHG2014_textboxes.pdf

The academic article can be found here:

http://www.cell.com/ajhg/home

2015

So what does 2015 hold? I don’t know, but I can’t wait to find out. Hopefully, it holds more ancestors, whether discovered through plain old paper research, cousin DNA testing or virtually raised from the dead!

What would my wish list look like?

More ancient genomes sequenced, including ones from North and South America.
Ancestor reconstruction on a large scale.
The haplotree becoming fleshed out and stable.
Big Y sequencing combined with STR panels for enhanced genealogical research.
Improved ethnicity reporting.
Mitochondrial DNA search by ancestor for descendants who have tested.
More tools, always more tools….
More time to use the tools!

Here’s wishing you an ancestor filled 2015!

______________________________________________________________

Disclosure

Thank you so much.

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Henry III, King of England, Fox in the Henhouse, 52 Ancestors #49

Posted on December 9, 2014 by Roberta Estes

I had been so looking forward to the results of the DNA processing of King Richard the III. Richard was killed in the Battle of Bosworth in 1485 and was reportedly buried in the “choir of the church” at the Greyfriars friary in Leicester. The friary was dissolved in 1538, following the orders of King Henry VIII who ordered all monasteries destroyed. The building was later destroyed, and over the years, the exact location of the cemetery was lost. In 2012, the friary location was found again, quite by accident and remains believed to be King Richard III were discovered buried under the car park, or what is known as a parking lot in the US.

Richard had a very distinctive trait – scoliosis to the point where his right shoulder was higher than his left. He was also described, at age 32, as a fine-boned hunchback with a withered arm and a limp. This, in addition to his slim build and his battle injuries led investigators to believe, and later confirm through mitochondrial DNA matching, that it was indeed Richard. At least they are 99% sure that it is Richard using archaeological, osteological and radiocarbon dating, in addition to DNA and good old genealogy.

Mitochondrial DNA testing was initially used to identify Richard the III by comparing his mitochondrial to that of current individuals matrilineally descended from his sister, Anne of York. That DNA was rare, and matched exactly in one case, and with only one difference in a second descendant, so either the skeleton is Richard or another individual who is matrilineally related. Fortunately, Richard’s mtDNA was quite unusual, with no other individuals matching in more than 26,000 other European sequences. The scientists estimated that the chances of a random match were about 1 in 10,000. The scientific team has utilized other evidence as well and feel certain that they have identified King Richard III himself.

King Richard III did not have any surviving descendants, so why was I so excited?

As it turns out, his Y DNA is representative of the Plantagenet family line which includes King Richard III’s great-great-great-great-grandfather, King Edward I, who is also my 19^th great-grandfather, which would make King Richard III my 5^th cousin, 16 times removed, I think. Maybe.

According to a paper released this week by Turi King, et al, “Identification of the remains of King Richard III”, it seems that there is a bit of a fly in the ointment. It’s no wonder this paper was in peer review forever. The authors knew that when it was released, it would be the shot heard round the world. For one thing, a tiny trivial matter, one of the possible outcomes could call into question the legitimacy of the current English monarchy. Only a detail for an American, but I’m thinking this is probably important to many people in England, especially those who think they should be the ruling monarch, and in particular, to the ruling monarch herself.

I wonder if Dr. Turi King rang up the Queen in advance with the news. I mean, what would you say to her??? How, exactly, would one begin that conversation? “Um, Your Highness, um, I think there has been a fox in the henhouse…”

In order to confirm the Y DNA line of King Richard III, his Y DNA was compared to that of another descendant of King Edward III, the great-grandson of my ancestor, Edward I. Edward III had two sons, Edmund, Duke of York from whom King Richard III descended and John of Gaunt, from whom the other Y DNA testers descend. Five male descendants of Henry Somerset were tested for comparison. Of those five, four matched each other, and one did not, indicating an NPE (nonparental event) or undocumented adoption in that line. The pedigree chart provided in the paper, below, shows the line of descent for both the Y and mitochondrial DNA participants.

Now, what we have is an uncertain situation. We know that Richard’s mitochondrial DNA matches that of his sister’s descendants, Michael Ibsen and Wendy Duldig, shown at right, above.

We know that the Y DNA of Richard does not match with the Y DNA of the Somerset line. We know that in the Somerset line, there were two illegitimate births, according to the paper, in the 13 generations between John of Gaunt and Henry Somerset, which were later legitimized. The first illegitimate birth is John Beaufort, the oldest illegitimate child of John of Gaunt and his mistress, Katherine Swynford, who later became John’s third wife. Katherine was previously married to a knight in the service of John of Gaunt, who is believed to have died, and was governess to John of Gaunt’s daughters.

The second illegitimate birth is Charles Somerset (1460-1526) who was the illegitimate son of Henry Beaufort and Joan Hill, about whom little is known.

The Somerset line proves to be downstream of haplogroup R1b-U152 (x L2, Z36, Z56, M160, M126 and Z192) with STR markers confirming their relationship to each other. King Richard III’s haplogroup is G-P287.

In this case, we don’t even need to scrutinize the STR markers, because the haplogroups don’t match, as you can see, above, in a haplotree provided in the paper.

The paper goes on to say that given a conservative false paternity rate of between 1 and 2% per generation, that there is a 16% probability of a false paternity in the number of generations separating King Richard III and the Somerset men.

What does this really mean?

According to the paper:

“One can speculate that a false-paternity event (or events) at some point(s) in this genealogy could be of key historical significance, particularly if it occurred in the five generations between John of Gaunt (1340–1399) and Richard III). A false-paternity between Edward III (1312–1377) and John would mean that John’s son, Henry IV (1367–1413), and Henry’s direct descendants (Henry V and Henry VI) would have had no legitimate claim to the crown. This would also hold true, indirectly, for the entire Tudor dynasty (Henry VII, Henry VIII, Edward VI, Mary I and Elizabeth I) since their claim to the crown also rested, in part, on their descent from John of Gaunt. The claim of the Tudor dynasty would also be brought into question if the false paternity occurred between John of Gaunt and his son, John Beaufort, Earl of Somerset. If the false paternity occurred in either of the three generations between Edward III and Richard, Duke of York, the father of Edward IV and Richard III, then neither of their claims to the crown would have been legitimate.”

While the known illegitimate births in the Somerset line lead us to look at those generations with scrutiny, the break in the Y chromosome inheritance could have happened in any generation, on either side of the tree.

According to the BBC article announcing the DNA results:

“Henry’s ancestor John of Gaunt was plagued by rumors of illegitimacy throughout his life, apparently prompted by the absence of Edward III at his birth. He was reportedly enraged by gossip suggesting he was the son of a Flemish butcher.

“Hypothetically speaking, if John of Gaunt wasn’t Edward III’s son, it would have meant that (his son) Henry IV had no legitimate claim to the throne, nor Henry V, nor Henry VI,” said Prof Schurer.”

So where does this leave us? I wonder if anyone has the name of that Flemish butcher????

Will the real Plantagenet, please stand up…or maybe be dug up.

What we need is a tie-breaker. Although the paper did not state this explicitly, I’m sure that the scientists also knew that they needed a tie-breaker – a male that descends through all males from someone upstream of Edward III. It appears that the Plantagenet line may well be a dead end, other than the Somerset line. I’m sure, with all of the resources brought to bear by the authors of this paper, that if there was another Plantagenet Y DNA male to be found, they would have done so.

So, the bottom line is that we don’t know what the real Plantagenet Y DNA line looks like, short of exhuming one of the Plantagenet Kings. They are mostly buried in Westminster Abbey in crypts. The Plantagenet line could be a subgroup of haplogroup R1b-U152. It could be haplogroup G. And, it could be yet something else. How? There could have been a NPE in both lines. I have seen it happen before.

Purely looking at the number of generations, meaning the number of opportunities for the genetic break to occur, there were 3 opportunities between King Richard the III and his great-great-grandfather, King Edward III, and there were 14 opportunities between Henry Somerset and King Edward III, so it’s more likely to have occurred in the Somerset line.

But that is small comfort, because all it took was one event, and there clearly was one. We don’t know which one, where. In this case, probabilities don’t matter – only actualities matter.

Back to my ancestor, King Henry III, father of King Edward I….

Dear Grandpa King Henry III,

I was just writing to catch you up on the news. This is your 20 times great-granddaughter….you do remember me…right?

I am sorry to report that there seems to have been a fox in the henhouse. Yes, that would be the Plantagenet henhouse. No, I don’t know when, or where. We just have fox DNA. Yes, we probably also have hen DNA, which would be your DNA, but you see, we can’t tell the difference between fox DNA and hen DNA.

By the way, would you mind trying that Houdini message thing and sending me a message about which DNA is fox and which is hen?

Thanks a million….

Your 20 times great-granddaughter

Even though we will probably never know what the Plantagenet DNA line looks like, we do know a lot about King Henry III, the father of King Edward I. We also have some idea what King Henry himself looked like. The effigy on his coffin in Westminster Abbey is shown below.

King Henry III was born on October 1, 1207 in Winchester Castle, shown below, the son of King John and Isabella of Angouleme, and died on November 16, 1272. He was known as Henry of Winchester and was King of England, Lord of Ireland and Duke of Aquitaine from 1216 until his death.

He ascended the throne at age 9, on October 28^th, 1216, at Gloucester Cathedral, and ruled under a guardian, council of 13 executors and the tutelage of his mother until he became of age. He assumed formal control of the government in January 1227, although he didn’t turn 21 until the following year. He ruled for a total of 56 years. A 13^th century depiction of his coronation is shown below.

Henry took the cross, declaring himself a crusader, which entitled him to special protections from Rome. While Henry never did actually go on Crusade, he might well have joined the Seventh Crusade in 1248 had he not been engaged in such a negative rivalry with the King of France. After Louis’s defeat at the Battle of Al Mansurah in 1250, Henry announced that he would be undertaking his own crusade to the Levant, but that Crusade never happened. Henry was aging by that time, at 43. It would he Henry’s son, Edward, who would represent the family in the Crusades, leaving in 1270 for the Eighth Crusade.

Henry was also crowned a second time, after the first Baron’s War, on May 17, 1220, at Westminster Abbey, in an effort to affirm the authority of the King, and with the Pope’s blessing. The medieval manuscript by Matthew Paris depicts the second coronation.

While the first coronation was hurried after his father’s death and with, in essence, a borrowed crown from Queen Isabella, since the royal crown had been either lost or sold during the war, the second coronation used a new set of royal regalia.

Engravings of Henry’s great seal.

Henry married Eleanor of Provence, daughter of Raymond-Berengar, the Count of Provene and Beatrice of Savoy, whose sisters all married Kings as well. Eleanor had never seen Henry before their marriage at Canterbury cathedral on January 14, 1236. At the time of their marriage, she was age 12 and he was 28. It was feared she was barren at first, but they went on to have 5 children, including Henry’s successor to the crown, Edward I. Her first child was born when she was age 15.

This medieval manuscript chronology from the early 1300s shows Henry III at the top, with his children left to right, the future King Edward I, Margaret, Beatrice, Edmund and Katherine.

In 1239 when Eleanor gave birth to their first child, Edward, named after Henry’s patron saint and ancestor, Edward the Confessor, Henry was overjoyed and held huge celebrations, giving lavishly to the Church and to the poor to encourage God to protect his young son. Their first daughter, Margaret, named after Eleanor’s sister, followed in 1240, her birth also accompanied by celebrations and donations to the poor.

Eleanor accompanied Henry to Poitrou on a military campaign, and their third child, Beatrice, named after Eleanor’s mother, and born in Poitou, France in1242.

This manuscript by Matthew Paris depicts Henry and Eleanor returning to England from Poitou in 1243.

Their fourth child, Edmund, arrived in 1245 and was named after the 9th-century saint. Concerned about Eleanor’s health, Henry donated large amounts of money to the Church throughout the pregnancy. A third daughter, Katherine, was born in 1253 but soon fell ill, possibly the result of a degenerative disorder such as Rett syndrome, and was unable to speak. She died in 1257 and Henry was distraught.

Henry’s children spent most of their childhood at Windsor Castle and he appears to have been extremely close to his family, rarely spending extended periods apart from them. King Henry III and Eleanor had the following children:

Edward, eventually King Edward I, was born on June 17, 1239 and died on July 7, 1307. He married Eleanor of Castile in 1254 and Margaret of France in 1299.
Margaret was born on September 29, 1240 and died on February 26, 1275, at age 35. She was the Queen of Scots and married King Alexander III, the King of Scotland at age 11. She had three children; Margaret born in 1261 who married King Eric II of Norway, Alexander born in 1264 who died at age 20 and David born in 1272 who died at age 9.
Beatrice was born on June 25, 1242 and died on March 24, 1275 at the age of 33. She married John II, Duke of Brittany, a love match, and had 6 children. Two of her descendant females would marry kings.
Edmund, known as Edmund Crouchback, was born on January 16, 1245 and died on June 5, 1296, at the age of 51. Crouchback reportedly refers to “crossed-back” and refers to his participation in the Ninth Crusade, although with King Richard III’s scoliosis, I have to wonder. He married Lady Aveline de Forz in 1269 at age 11. She died 4 years later, at age 15, possibly related to childbirth. He then married Blanche de Artois in 1276, in Paris, widow of Henri I, King of Navarre, with whom he had three sons, two of whom revolted against King Edward II.
The story of Katherine is sad indeed. She was born either deaf or a deaf-mute at Westminster Palace on November 25, 1253 and died on Mary 3. 1257, before her 4^th birthday. It was obvious at her birth, that in spite of her beauty, something was wrong. As she aged a bit, it also became evident that she was mentally challenged. Matthew Paris, chronicler of King Henry III, described her as “the most beautiful girl, but dumb and useless.” She was therefore not a political asset and was never betrothed. Her parents, however, loved her devotedly.

A few days after her christening, on the day of Saint Edward the Confessor’s death, January 5,1254, the King held a massive banquet, to which he invited all the nobility. The provisions for this banquet included “fourteen wild boars, twenty-four swans, one hundred and thirty-five rabbits, two hundred and fifty partridges, fifty hares, two hundred and fifty wild ducks, sixteen hundred and fifty fowls, thirty-six female geese and sixty-one thousand eggs”.

After Katherine’s death, both Henry and Eleanor were heartbroken.

Although the marriage of Henry III and Eleanor was clearly political in nature, Henry was kind and generous and they apparently came to love each other. Henry, unusual as compared to other English Kings, had no illegitimate children.

Henry was reported to have a drooping eyelid and an occasional fierce temper, but was generally known to be “amiable, easy-going and sympathetic,” as reported by historian David Carpenter.

The sketch above is from Cassell’s History of England published in 1902 but it does not reflect a drooping eyelid. The painting, below, from an unknown artist in 1620 is titled simply “Edward,” but it does depict the drooping eyelid. King Edward I was the son of Henry III. Now, if Richard III had only been reported with a droopy eyelid, we’d have another clue. Interestingly enough, the National Portrait Gallery has a discussion about the “crooked eye group” of kings, the latest of which is Edward II.

Henry III was known for his piety, celebrating mass at least once a day, holding lavish religious ceremonies and giving generously to charities. He fed 500 paupers each day, fasted before the feast days of Edward the Confessor and may have washed the feet of lepers. He was often moved to tears during religious ceremonies. The King was particularly devoted to the figure of Edward the Confessor, whom he adopted as his patron saint. Edward the Confessor was an early English King who lived a very pious life and who was also Henry III’s 6 times great-grandfather.

Henry reformed the system of silver coins in England in 1247, replacing the older Short Cross silver pennies with a new Long Cross design, shown below. Between 1243 and 1258, the King assembled two great hoards, or stockpiles, of gold. In 1257, Henry needed to spend the second of these hoards urgently and, rather than selling the gold quickly and depressing its value, Henry decided to introduce gold pennies into England, following the popular trend in Italy. The gold pennies resembled the gold coins issued by Edward the Confessor, but the overvalued currency attracted complaints from the City of London and was ultimately abandoned.

In 1247, Henry was sent the “Relic of the Holy Blood” by the Patriarch of Jerusalem, said to contain some of the blood of Christ. He carried the Relic through the streets of London from its storage location at the Church of the Holy Sepulchre in a procession to Westminster Abbey, shown below, by Matthew Paris. He then promoted the relic as a focus for pilgrimages, but it never became popular.

Henry III’s reign in England was marked by multiple insurrections and allegations of ineffective government at best and improprieties at worst.

Henry started out at a disadvantage due to his age and of course, inexperience as a child. The first problem happened before Henry was of age.

Taking advantage of the child-king, Louis VIII of France allied himself with Hugh de Lusignan and invaded first Poitou and then Gascony, lands held by the English monarchy. Henry III’s army in Poitou was under-resourced and lacked support from the French barons, many of whom had felt abandoned during the years of Henry’s minority and as a result, the province quickly fell. It became clear that Gascony would also fall unless reinforcements were sent from England.

In early 1225 a great council approved a tax of £40,000 to dispatch an army, which quickly retook Gascony. In exchange for agreeing to support Henry III, the English barons demanded that the King reissue the Magna Carta, originally issued by King John in 1215. Henry complied, declared that the charter was issued of his own “spontaneous and free will” and confirmed the new with the royal seal. This gave the new Great Charter and the Charter of the Forest of 1225, shown below from the UK National Archives, much more authority than any previous versions. The barons anticipated that the King would act in accordance with these definitive charters, subject to the law and moderated by the advice of the nobility.

Henry invaded France in 1230, in an attempt to reclaim family lands lost since the reign of King John, but his attempts were both unsuccessful and very expensive. As you can see, most of the Plantagenet family holdings in France had been lost, except for Gascony.

The drawing below depicts Henry travelling to Brittany in 1230, by Matthew Paris.

The English people paid for military actions as well as Henry’s expensive lifestyle, carrying out major remodeling of royal properties, through increased taxes, which caused Henry, over time, to become very unpopular.

In 1258, a group of Barons seized power in a coup, reforming English government through a process called the Provisions of Oxford, which is regarded at England’s first constitution. This document was the first to be published in English since the Norman Conquest 200 years previously. As a result, Henry ruled in conjunction with a council of 24 members, 12 selected by the crown and 12 by the barons. Those 24 then selected 2 men to oversee decisions. This certainly wasn’t what Henry wanted, but he had little choice at the time.

However, in 1261, Henry overthrew the Provisions of Oxford and the superceeding Provisions of Westminster, with assistance from the Pope in the form of a papal bull which started the second Baron’s War. In 1264, Henry was defeated and taken prisoner at the battle of Lewes, but his oldest son, the eventual King Edward I, escaped from captivity and freed his father the following year.

This time, Henry won and was restored to power, initially reacted harshly, confiscating all of the land and titles of the revolting Barons. In an effort to bring eventual peace, the Dictum of Kenilworth was issued to reconcile the rebels of the Baron’s War with the King.

Their rebel leader, Simon de Montfort, Henry’s brother-in-law who had married his sister, Eleanor, was now dead at the Battle of Evesham in 1265, shown above. The Dictum pardoned the revolting Barons and restored their previously confiscated lands to them, contingent on payment of penalties equal to their level of involvement in the rebellion, typically 5 times the value of the annual yield of the land.

The spirit of peace and reconciliation established by the Dictum of Kenilworth lasted for the remainder of Henry III’s reign and into the 1290s, although reconstruction was slow. Henry died in 1272, succeeded by his son, Edward, who became King Edward I, who was on crusade in the Holy Lands at the time of his father’s death.

Although unpopular due to his spending habits, Henry invested significantly in many properties still enjoyed by people today, improving their defenses and adding facilities, including rebuilding Westminster Abbey and his favorite palatial complex by the same name in London.

The Tower of London was extended to form a concentric fortress with extensive living quarters, although Henry primarily used the castle as a secure retreat in the event of war or civil strife.

Tower of London as it appears today from the Thames.

Henry also kept a menagerie at the Tower, a tradition begun by his father, and his exotic specimens included an elephant, a leopard and a camel.

Henry was given an elephant, above, as a gift by King Louis IX of France.

King Henry III visiting Louis IX of France.

Among other projects, Henry built the Great Hall of Winchester Castle, shown above.

Perhaps Henry’s legacy contribution is the creation of what would become the English Parliament. The term “parliament” first appeared in the 1230s and 1240s to describe large gatherings of the royal court, and parliamentary gatherings were held periodically throughout Henry’s reign. They were used to agree to the raising of taxes which, in the 13th century, were single, one-off levies, typically on movable property, intended to supplement the King’s normal revenues for particular projects. During Henry’s reign, the counties began to send regular delegations to these parliaments, and came to represent a broader cross-section of the community than simply the major barons.

In Henry’s last years, he was increasingly ill. He continued to invest in Westminster Abbey, which became a replacement for the Angevin mausoleum at Fontevraud Abbey in Anjou, France, In 1269 Henry oversaw a grand ceremony to rebury Edward the Confessor in a lavish new shrine, personally helping to carry the body to its new resting place in the rebuilt Westminster Abbey. Edward the Confessor has built the original Westminster Abbey in 1065 which was demolished by Henry III to construct the new Westminster Abbey in its place.

In 1270, Henry’s son, Edward left on the Eighth Crusade and at one time, Henry voiced his intention to join Edward. That never happened, and Henry III died at Westminster Palace on the evening of November 16, 1272. Eleanor was probably at his side.

At his request, Henry was buried in Westminster Abbey in front of the church’s high altar, in the former resting place of Edward the Confessor. A few years later, work began on a grander tomb for King Henry III and in 1290, Edward moved his father’s body to its current location in Westminster Abbey.

See, it wouldn’t be difficult at all to access the remains of King Henry III…no digging involved!!! For that matter, we could just skip to the beginning and start with the remains of Edward the Confessor.

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