Mass Pre-Contact Native Grave in California Yields Disappointing Results

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.

Eerkens 2015 table

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.

Homo Naledi – A New Species Discovered

Homo naledi

“Homo naledi” by Berger et al. 2015 – http://elifesciences.org/lookup/doi/10.7554/eLife.09560.019. Licensed under CC BY 4.0 via Commons – https://commons.wikimedia.org/wiki/File:Homo_naledi.jpg#/media/File:Homo_naledi.jpg

The Cradle of Humankind World Heritage Site near Johannesburg, South Africa has once again produced bones.  Previous finds, nearly one third of all ancient hominin fossils found, date to 3.5 million years of age.  This new find may be the bones of our ancestor, but regardless, they certainly are the bones of a new, previously unknown, species.

The announcement came this week and articles can be seen online in several locations.  The National Geographic Society is a partner in the excavation and retrieval of the bones from a very difficult cave, Rising Star, through only a very small opening following a precipitous decline.  Stated bluntly – this is a “scare the hell out of you” cave.  Not exactly convenient or inviting.

Rising Star Cave

“Dinaledi Chamber illustration” by Paul H. G. M. Dirks et al – http://elifesciences.org/content/4/e09561. Licensed under CC BY 4.0 via Commons – https://commons.wikimedia.org/wiki/File:Dinaledi_Chamber_illustration.jpg#/media/File:Dinaledi_Chamber_illustration.jpg

There was more than one skeleton present.  In this article and video from the New York Times, you can see that many bones were recovered, quite obviously from multiple individuals.  More than 1550 in total – representing at least 15 different individuals.  How did they get in this extremely remote cave with very limited access in the first place? And why?

Is this a separate species from ours, or our ancestors?  How long ago did they live, and where do they fit on the family tree?  The scientists are now referring to the ancient family tree as a braided stream – a river that divides into channels only to converge again later.

These announcements are being followed by a special on Nova/National Geographic Special titled the “Dawn of Humanity” which premieres on Sept. 16, 2015 at 9 PM ET/8 Central on PBS and is streaming online now.  This documentary details the discovery and excavation of the fossils in the cave including Homo Naledi.

In the mean time, take a look at this wonderful article, chock full of pictures of course, by National Geographic.  If you subscribe to the National Geographic magazine, guess what will be on the cover of the October issue???

This article in New Scientist has a great reconstruction of the Homo Naledi skull, and states that no attempt has yet been made to extract DNA.  I continue to remind myself that patience is a virtue.

Some Native Americans Had Oceanic Ancestors

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.

Aleutians to Brazil

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.

Raghaven 2015

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.

Skoglund 2015-2

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.

Australia to Aleutians

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.

Botocudo Ancient Remains from Brazil

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’.

New Nat Geo map

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 19th 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.

ISOGG y 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.

Ray Banks C1 tree

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

Ray Banks C2 treeIn 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 Banks Z32295

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.

Botocudo not admixed

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.

Minas Gerais Brazil

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.

F999963 mito

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

F999963 Y

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.

F999963 largest

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.

F999964 mito

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

F999964 Y

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.

F999964 largest

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!

Naia – Oldest Native American Facial Reconstruction

Naia, named affectionately for the ancient water nymphs of Greek mythology is actually the face of the oldest Native American.  At least, the oldest one whose skull is complete and whose face we can reconstruct.  Naia was a teenager when she died between 12,000 and 13,000 years ago by falling into a cave in the Yukatan. In 2007, her remains were found in a submerged cavern, and history was about to be made, after waiting some 12,000+ years.

A scientific team would study her remains, sample her DNA and reconstruct her face.  The January 2015 issue of National Geographic magazine has an absolutely wonderful article and the online magazine version does as well.

nat geo naia

Start by reading the wonderful story, of course, but don’t miss the video about how they recovered the remains and the subsequent analysis.  There is also a photo gallery and several other links, across the top of the article – all worth seeing.

One of the unexpected findings was how different Naia looks than what we would have expected based on what Native people look like today.  She had a more African and Polynesian facial structure than later Native people, and she was much smaller.  Be sure to check out Nat Geo’s “clues to an ancient mystery.”

Naia’s mitochondrial DNA confirms that indeed, her matrilineal line originated in Asia, a common base haplogroup found in Native Americans todayhaplogroup D1.

The accompanying academic paper was published in the May 2014 issue of the Journal Science, titled “Late Pleistocene Human Skeleton and mtDNA Link Paleoamericans and Modern Native Americans” by James Chatters et al.

The article is behind a paywall, but the abstract is as follows:

Abstract:

Because of differences in craniofacial morphology and dentition between the earliest American skeletons and modern Native Americans, separate origins have been postulated for them, despite genetic evidence to the contrary. We describe a near-complete human skeleton with an intact cranium and preserved DNA found with extinct fauna in a submerged cave on Mexico’s Yucatan Peninsula. This skeleton dates to between 13,000 and 12,000 calendar years ago and has Paleoamerican craniofacial characteristics and a Beringian-derived mitochondrial DNA (mtDNA) haplogroup (D1). Thus, the differences between Paleoamericans and Native Americans probably resulted from in situ evolution rather than separate ancestry.

A second article, published in Science, also in May 2014, “Bones from a Watery “Black Hole” Confirm First American Origins” by Michael Balter discuss the fact that the earlier skeletons of Native people often don’t resemble contemporary Native people.

Also behind a paywall, the summary states:

Summary:

Most researchers agree that the earliest Americans came over from Asia via the Bering Strait between Siberia and Alaska, beginning at least 15,000 years ago. But many have long puzzled over findings that some of the earliest known skeletons—with long skulls and prominent foreheads—do not resemble today’s Native Americans, who tend to have rounder skulls and flatter faces. Some have even suggested that at least two migrations into the Americas were involved, one earlier and one later. But the discovery of a nearly 13,000-year-old teenage girl in an underwater cave in Mexico’s Yucatán Peninsula argues against that hypothesis. The girl had the skull features of older skeletons, but the genetic profile of some of today’s Native Americans—suggesting that the anatomical differences were the result of evolutionary changes after the first Americans left Asia, rather than evidence of separate ancestry.

Of course, the fact that Naia was found so early in such a southern location has spurred continuing debate about migration waves and paths, land versus water arrivals.  Those questions won’t be resolved until we have a lot more data to work with – but they do make for lively debate.  Dienekes wrote a short article about this topic when the paper was first released, and the comments make for more interesting reading than the article.

Kostenki14 – A New Ancient Siberian DNA Sample

k14 skeleton

This week, published in Science, we find another ancient DNA full genome sequence from Siberia in an article titled “Genomic structure in Europeans dating back at least 36,200 years” by Seguin-Orlando et al.. This sample, partially shown above, is quite old and closely related to the Mal’ta child, also found in Siberia from about 24,000 years ago. Interestingly enough, K14 carries more Neanderthal DNA than current Europeans. This skeleton was actually excavated in 1954, but was only recently genetically analyzed.

k14 mapFrom the paper, this map above shows the locations of recently analyzed ancient DNA samples.  Note that even though K14 and Mal’ta child are similar, they are not located in close geographic proximity.

k14 population clusterAlso from the paper, this chart of population clusters is quite interesting, because we can see which of these ancient samples share some heritage with today’s indigenous American populations, shown in grey. UPGH=Upper Paleolithic Hunter-Gatherer, MHG=Mesolithic Hunter Gatherer, which is later in time that Paleolithic, and NEOL=Neolithic indicating the farming population that arrived in Europe approximately 7,000-10,000 years ago from the Middle East

You can see that the Neolithic samples show no trace of ancestry with today’s Native people, but both pre-Neolithic Hunter-Gatherer cultures show some amount of shared ancestry with Native people. However, to date, MA1, the Malta child is the most closely related and carries the most DNA in common with today’s Native people.

Felix Chandrakumar is currently preparing the K14 genome for addition to the ancient DNA kits at GedMatch.  It will be interesting to see if this sample also matches currently living individuals.

Also from the K14 paper, you can see on the map below where K14 matches current worldwide and European populations, where the warmer colors, i.e. red, indicated a closer match.

K14 population matches

Of interest to genealogists and population geneticists, K14’s mitochondrial haplogroup is U2 and his Y haplogroup is C-M130, the same as LaBrana, a late Mesolithic hunter-gatherer found in northern Spain. Haplogroup C is, of course, one of the base haplogroups for the Native people of the Americas.

The K14 paper further fleshes out the new peopling of Europe diagram discussed in my Peopling of Europe article.

This map, from the Lazardis “Ancient human genomes suggest three ancestral populations for present-day Europeans” paper published in September 2014, shows the newly defined map including Ancient North Eurasian in this diagram.

Lazaridis tree

K14 adds to this diagram in the following manner, although the paths are flipped right to left.

K14 tree

Blue represent current populations, red are ancient remains and green are ancestral populations.

Dienekes wrote about this find as well, here.

Paper Abstract:

The origin of contemporary Europeans remains contentious. We obtain a genome sequence from Kostenki 14 in European Russia dating to 38,700 to 36,200 years ago, one of the oldest fossils of Anatomically Modern Humans from Europe. We find that K14 shares a close ancestry with the 24,000-year-old Mal’ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a meta-population that at times stretched from Europe to central Asia.

You can read the full paper at the two links below.

http://www.sciencemag.org/content/early/2014/11/05/science.aaa0114

http://www2.zoo.cam.ac.uk/manica/ms/2014_Seguin_Orlando_et_al_Science.pdf

It’s been a great year for ancient DNA analysis and learning about our ancestral human populations.

However, I have one observation I just have to make about this particular find.

What amazing teeth. Obviously, this culture did not consume sugar!

Peopling of Europe 2014 – Identifying the Ghost Population

Beginning with the full sequencing of the Neanderthal genome, first published in May 2010 by the Max Planck Institute with Svante Paabo at the helm, and followed shortly thereafter with a Denisovan specimen, we began to unravel our ancient history.

neanderthal reconstructed

Neanderthal man, reconstructed at the National Museum of Nature and Science in Tokyo

The photo below shows a step in the process of extracting DNA from ancient bones at Max Planck.

planck extraction

Our Y and mitochondrial DNA haplogroups take us back thousands of years in time, but at some point, where and how people were settling and intermixing becomes fuzzy. Ancient DNA can put the people of that time and place in context.  We have discovered that current populations do not necessarily represent the ancient populations of a particular locale.

Recent information discovered from ancient burials tells us that the people of Europe descend from a 3 pronged model. Until recently, it was believed that Europeans descended from Paleolithic hunter-gatherers and Neolithic farmers, a two-pronged model.

Previously, it was believed that Europe was peopled by the ancient hunter-gatherers, the Paleolithic, who originally settled in Europe beginning about 45,000 years ago. At this time, the Neanderthal were already settled in Europe but weren’t considered to be anatomically modern humans, and it was believed, incorrectly, that the two groups did not interbreed.  These hunter-gatherers were the people who settled in Europe before the last major ice age, the Younger Dryas, taking refuge in the southern portions of Europe and Eurasia, and repeopling the continent after the ice receded, about 12,000 years ago.  By that time, the Neanderthals were gone, or as we now know, at least partially assimilated.

This graphic shows Europe during the last ice age.

ice age euripe

The second settlement wave, the agriculturalist farmers from the Near East either overran or integrated with the hunter-gatherers in the Neolithic period, depending on which theory you subscribe to, about 8000-10,000 years ago.

2012 – Ancient Northern European (ANE) Hints

Beginning in 2012, we began to see hints of a third lineage that contributed to the peopling of Europe as well, from the north. Buried in the 2012 paper, Estimating admixture proportions and dates with ADMIXTOOLS by Patterson et al, was a very interesting tidbit.  This new technique showed a third population, referred to by many as a “ghost population”, because no one knew who they were, that contributed to the European population.

patterson ane

The new population was termed Ancient North Eurasian, or ANE.

Dienekes covered this paper in his blog, but without additional information, in the community in general, there wasn’t much more than a yawn.

2013 – Mal’ta Child Stirs Excitement

The first real hint of meat on the bones of ANE came in the form of ancient DNA analysis of a 24,000 year old Siberian boy that has come to be named Mal’ta (Malta) Child. In the original paper, by Raghaven et al, Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, he was referred to as MA-1.  I wrote about this in my article titled Native American Gene Flow – Europe?, Asia and the Americas.   Dienekes wrote about this paper as well.

This revelation caused quite a stir, because it was reported that the Ancestor of Native Americans in Asia was 30% Western Eurasian.  Unfortunately, in some cases, this was immediately interpreted to mean that Native Americans had come directly from Europe which is not what this paper said, nor inferred.  It was also inferred that the haplogroups of this child, R* (Y) and U (mtDNA) were Native American, which is also incorrect.  To date, there is no evidence for migration to the New World from Europe in ancient times, but that doesn’t mean we aren’t still looking for that evidence in early burials.

What this paper did show was that Europeans and Native Americans shared a common ancestor, and that the Siberian population had contributed to the European population as well as the Native American population.  In other words, descendants settled in both directions, east and west.

The most fascinating aspect of this paper was the match distribution map, below, showing which populations Malta child matched most closely.

malta child map

As you can see, MA-1, Malta Child, matches the Native American population most closely, followed by the northern European and Greenland populations. The further south in Europe and Asia, the more distant the matches and the darker the blue.

2013 – Michael Hammer and Haplogroup R

Last fall at the Family Tree DNA conference, Dr. Michael Hammer, from the Hammer Lab at the University of Arizona discussed new findings relative to ancient burials, specifically in relation to haplogroup R, or more specifically, the absence of haplogroup R in those early burials.

hammer 2013

hammer 2013-1

hammer 2013-2

hammer 2013-3

Based on the various theories and questions, ancient burials were enlightening.

hammer 2013-4

hammer 2013-5

In 2013, there were a total of 32 burials from the Neolithic period, after farmers arrived from the Near East, and haplogroup R did not appear. Instead, haplogroups G, I and E were found.

hammer 2013-7

What this tells us is that haplogroup R, as well as other haplogroup, weren’t present in Europe at this time. Having said this, these burials were in only 4 locations and, although unlikely, R could be found in other locations.

hammer 2-13-8

hammer 2013-9

hammer 2013-10

hammer 2013-11

Last year, Dr. Hammer concluded that haplogroup R was not found in the Paleolithic and likely arrived with the Neolithic farmers. That shook the community, as it had been widely believed that haplogroup R was one of the founding European haplogroups.

hammer 2013-12

While this provided tantalizing information, we still needed additional evidence. No paper has yet been published that addresses these findings.  The mass full sequencing of the Y chromosome over this past year with the introduction of the Big Y will provide extremely valuable information about the Y chromosome and eventually, the migration path into and across Europe.

2014 – Europe’s Three Ancient Tribes

In September 2014, another paper was published by Lazaridis et al that more fully defined this new ANE branch of the European human family tree.  An article in BBC News titled Europeans drawn from three ancient ‘tribes’ describes it well for the non-scientist.  Of particular interest in this article is the artistic rendering of the ancient individual, based on their genetic markers.  You’ll note that they had dark skin, dark hair and blue eyes, a rather unexpected finding.

In discussing the paper, David Reich from Harvard, one of the co-authors, said, “Prior to this paper, the models we had for European ancestry were two-way mixtures. We show that there are three groups. This also explains the recently discovered genetic connection between Europeans and Native Americans.  The same Ancient North Eurasian group contributed to both of them.”

The paper, Ancient human genomes suggest three ancestral populations for present-day Europeans, appeared as a letter in Nature and is behind a paywall, but the supplemental information is free.

The article summary states the following:

We sequenced the genomes of a ~7,000-year-old farmer from Germany and eight ~8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes1, 2, 3, 4 with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians3, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations’ deep relationships and show that early European farmers had ~44% ancestry from a ‘basal Eurasian’ population that split before the diversification of other non-African lineages.

This paper utilized ancient DNA from several sites and composed the following genetic contribution diagram that models the relationship of European to non-European populations.

Lazaridis tree

Present day samples are colored purple, ancient in red and reconstructed ancestral populations in green. Solid lines represent descent without admixture and dashed lines represent admixture.  WHG=western European hunter-gatherer, EEF=early European farmer and ANE=ancient north Eurasian

2014 – Michael Hammer on Europe’s Ancestral Population

For anyone interested in ancient DNA, 2014 has been a banner years. At the Family Tree DNA conference in Houston, Texas, Dr. Michael Hammer brought the audience up to date on Europe’s ancestral population, including the newly sequenced ancient burials and the information they are providing.

hammer 2014

hammer 2014-1

Dr. Hammer said that ancient DNA is the key to understanding the historical processes that led up to the modern. He stressed that we need to be careful inferring that the current DNA pattern is reflective of the past because so many layers of culture have occurred between then and now.

hammer 2014-2

Until recently, it was assumed that the genes of the Neolithic farmers replaced those of the Paleolithic hunter-gatherers. Ancient DNA is suggesting that this is not true, at least not on a wholesale level.

hammer 2014-3

The theory, of course, is that we should be able to see them today if they still exist. The migration and settlement pattern in the slide below was from the theory set forth in the 1990s.

hammer 2014-4

In 2013, Dr. Hammer discussed the theory that haplogroup R1b spread into Europe with the farmers from the Near East in the Neolithic. This year, he expanded upon that topic that based on the new findings from ancient burials.

hammer 2014-5

Last year, Dr. Hammer discussed 32 burials from 4 sites. Today, we have information from 15 ancient DNA sites and many of those remains have been full genome sequenced.

hammer 2014-6

Information from papers and recent research suggests that Europeans also have genes from a third source lineage, nicknamed the “ghost population of North Eurasia.”

hammer 2014-7

Scientists are finding a signal of northeast Asian related admixture in northern Europeans, first suggested in 2012.  This was confirmed with the sequencing of Malta child and then in a second sequencing of Afontova Gora2 in south central Siberia.

hammer 2014-8

We have complete genomes from nine ancient Europeans – Mesolithic hunter gatherers and Neothilic farmers. Hammer refers to the Mesolithic here, which is a time period between the Paleolithic (hunter gatherers with stone tools) and the Neolithic (farmers).

hammer 2014-9

In the PCA charts, shown above, you can see that Europeans and people from the Near East cluster separately, except for a bridge formed by a few Mediterranean and Jewish populations. On the slide below, the hunter-gatherers (WHG) and early farmers (EEF) have been overlayed onto the contemporary populations along with the MA-1 (Malta Child) and AG2 (Afontova Gora2) representing the ANE.

hammer 2014-10

When sequenced, separate groups formed including western hunter gathers and early european farmers include Otzi, the iceman.  A third group is the north south clinal variation with ANE contributing to northern European ancestry.  The groups are represented by the circles, above.

hammer 2014-11

hammer 2014-12

Dr. Hammer said that the team who wrote the “Ancient Human Genomes” paper just recently published used an F3 test, results shown above, which shows whether populations are an admixture of a reference population based on their entire genome. He mentioned that this technique goes well beyond PCA.

hammer 2014-13

Mapped onto populations today, most European populations are a combination of the three early groups. However, the ANE is not found in the ancient Paleolithic or Neolithic burials.  It doesn’t arrive until later.

hammer 2014-14

This tells us that there was a migration event 45,000 years ago from the Levant, followed about 7000 years ago by farmers from the Near East, and that ANE entered the population some time after that. All Europeans today carry some amount of ANE, but ancient burials do not.

These burials also show that southern Europe has more Neolithic farmer genes and northern Europe has more Paleolithic/Mesolithic hunter-gatherer genes.

hammer 2014-15

Pigmentation for light skin came with farmers – blue eyes existed in hunter gatherers even though their skin was dark.

hammer 2014-16

Dr. Hammer created these pie charts of the Y and mitochondrial haplogroups found in the ancient burials as compared to contemporary European haplogroups.

hammer 2014-17

The pie chart on the left shows the haplogroups of the Mesolithic burials, all haplogroup I2 and subclades. Note that in the current German population today, no I2a1b and no I1 was found.  The chart on the right shows current Germans where haplogroup I is a minority.

hammer 2014-18

Therefore, we can conclude that haplogroup I is a good candidate to be identified as a Paleolithic/Mesolithic haplogroup.

This information shows that the past is very different from today.

hammer 2014-19

In 2014 we have many more burials that have been sequenced than last year, as shown on the map above.

Green represents Neolithic farmers, red are Mesolithic hunter-gatherers, brown at bottom right represents more recent samples from the Metallic age.

hammer 2014-20

There are a total of 48 Neolithic burials where haplogroup G dominates. In the Mesolithic, there are a total of six haplogroup I.

This suggests that haplogroup I is a good candidate to be the father of the Paleolithic/Mesolithic and haplogroup G, the founding father of the Neolithic.

In addition to haplogroup G in the Neolithic, one sample of both E1b1b1 (M35) and C were also found in Spain.  E1b1b1 isn’t surprising given it’s north African genesis, but C was quite interesting.

The Metal ages, which according to wiki begin about 3300BC in Europe, is where haplogroup R, along with I1, first appear.

diffusion of metallurgy

Please note that the diffusion of melallurgy map above is not part of Dr. Hammer’s presentation. I have added it for clarification.

hammer 2014-21

Nothing is constant in Europe. The Y DNA was very upheaved, as indicated on the graphic above.  Mitochondrial DNA shifted from pre-Neolithic to Neolithic which isn’t terribly different from the present day.

Dr. Hammer did not say this, but looking at the Y versus the mtDNA haplogroups, I wonder if this suggests that indeed there was more of a replacement of the males in the population, but that the females were more widely assimilated. This would certainly make sense, especially if the invaders were warriors and didn’t have females with them.  They would have taken partners from the invaded population.

Haplogroup G represents the spread of farming into Europe.

hammer 2014-22

The most surprising revelation is that haplogroup R1b appears to have emerged after the Neolithic agriculture transition. Given that just three years ago we thought that haplogroup R1b was one of the original European settlers thousands of years ago, based on the prevalence of haplogroup R in Europe today, at about 50%, this is a surprising turn of events.  Last year’s revelation that R was maybe only 7000-8000 years old in Europe was a bit of a whammy, but the age of R in Europe in essence just got halved again and the source of R1b changed from the Near East to the Asian steppes.

Obviously, something conferred an advantage to these R1b men. Given that they arrived in the early Metalic age, was it weapons and chariots that enabled the R1b men who arrived to quickly become more than half of the population?

hammer 2014-23

The Bronze Age saw the first use of metal to create weapons. Warrior identity became a standard part of daily life.  Celts ranged over Europe and were the most dominant iron age warriors.  Indo-European languages and chariots arrived from Asia about this time.

hammer 2014-24

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The map above shows the Hallstadt and LaTene Celtic cultures in Europe, about 600BC. This was not a slide presented by Dr. Hammer.

hammer 2014-27

Haplogroup R1b was not found in an ancient European context prior to a Bell Beaker period burial in Germany 4.8-4.0 kya (thousand years ago, i.e. 4,800-4,000 years ago).  R1b arrives about 4.6 kya and is also found in a Corded Ware culture burial in Germany.  A late introduction of these lineages which now predominate in Europe corresponds to the autosomal signal of the entry of Asian and Eastern European steppe invaders into western Europe.

hammer 2014-28

Local expansion occurred in Europe of R1b subgroups U106, L21 and U152.

hammer 2014-29

hammer 2014-30

A current haplogroup R distribution map that reflects the findings of this past year is shown above.

Haplogroup I is interesting for another reason. It looks like haplogroup I2a1b (M423) may have been replaced by I1 which expanded after the Mesolithic.

hammer 2014-31

On the slide above, the Loschbour sample from Luxembourg was mapped onto a current haplogroup I SNP map where his closest match is a current day Russian.

One of the benefits of ancient DNA genome processing is that we will be able to map current trees into maps of old SNPs and be able to tell who we match most closely.

Autosomal DNA can also be mapped to see how much of our DNA is from which ancient population.

hammer 2014-32

Dr. Hammer mapped the percentages of European Mesolithic/Paleolithic hunter-gatherers in blue, Neolithic Farmers from the Near East in magenta and Asian Steppe Invaders representing ANE in yellow, over current populations. Note the ancient DNA samples at the top of the list.  None of the burials except for Malta Child carry any yellow, indicating that the ANE entered the European population with the steppe invaders; the same group that brought us haplogroup R and possibly I1.

Dr. Hammer says that ANE was introduced to and assimilated into the European population by one or more incursions. We don’t know today if ANE in Europeans is a result of a single blast event or multiple events.  He would like to do some model simulations and see if it is related to timing and arrival of swords and chariots.

We know too that there are more recent incursions, because we’re still missing major haplogroups like J.

The further east you go, meaning the closer to the steppes and Volga region, the less well this fits the known models. In other words, we still don’t have the whole story.

At the end of the presentation, Michael was asked if the whole genomes sequenced are also obtaining Y STR data, which would allow us to compare our results on an individual versus a haplogroup level. He said he didn’t know, but he would check.

Family Tree DNA was asked if they could show a personal ancient DNA map in myOrigins, perhaps as an alternate view. Bennett took a vote and that seemed pretty popular, which he interpreted as a yes, we’d like to see that.

In Summary

The advent of and subsequent drop in the price of whole genome sequencing combined with the ability to extract ancient DNA and piece it back together have provided us with wonderful opportunities.  I think this is jut the proverbial tip of the iceberg, and I can’t wait to learn more.

If you are interested in other articles I’ve written about ancient DNA, check out these links:

Anzick (12,707-12,556), Ancient One, 52 Ancestors #42

anzick burial location

His name is Anzick, named for the family land, above, where his remains were found, and he is 12,500 years old, or more precisely, born between 12,707 and 12,556 years before the present.  Unfortunately, my genealogy software is not prepared for a birth year with that many digits.  That’s because, until just recently, we had no way to know that we were related to anyone of that age….but now….everything has changed ….thanks to DNA.

Actually, Anzick himself is not my direct ancestor.  We know that definitively, because Anzick was a child when he died, in present day Montana.

anzick on us map

Anzick was loved and cherished, because he was smeared with red ochre before he was buried in a cave, where he would be found more than 12,000 years later, in 1968, just beneath a layer of approximately 100 Clovis stone tools, shown below.  I’m sure his parents then, just as parents today, stood and cried as the laid their son to rest….never suspecting just how important their son would be some 12,500 years later.

anzick clovis tools

From 1968 until 2013, the Anzick family looked after Anzick’s bones, and in 2013, Anzick’s DNA was analyzed.

DNA analysis of Anzick provided us with his mitochondrial haplogroup,  D4h3a, a known Native American grouping, and his Y haplogroup was Q-L54, another known Native American haplogroup.  Haplogroup Q-L54 itself is estimated to be about 16,900 years old, so this finding is certainly within the expected range.  I’m not related to Anzick through Y or mitochondrial DNA.

Utilizing the admixture tools at GedMatch, we can see that Anzick shows most closely with Native American and Arctic with a bit of east Siberian.  This all makes sense.

Anzick MDLP K23b

Full genome sequencing was performed on Anzick, and from that data, it was discovered that Anzick was related to Native Americans, closely related to Mexican, Central and South Americans, and not closely related to Europeans or Africans.  This was an important discovery, because it in essence disproves the Solutrean hypothesis that Clovis predecessors emigrated from Southwest Europe during the last glacial maximum, about 20,000 years ago.

anzick matches

The distribution of these matches was a bit surprising, in that I would have expected the closest matches to be from North America, in particular, near to where Anzick was found, but his closest matches are south of the US border.  Although, in all fairness, few people in Native tribes in the US have DNA tested and many are admixed.

This match distribution tells us a lot about population migration and distribution of the Native people after they left Asia, crossed Beringia on the land bridge, now submerged, into present day Alaska.

This map of Beriginia, from the 2008 paper by Tamm et all, shows the migration of Native people into (and back from) the new world.

beringia map

Anzick’s ancestors crossed Beringia during this time, and over the next several thousand years, found their way to Montana.  Some of Anzick’s relatives found their way to Mexico, Central and South America.  The two groups may have split when Anzick’s family group headed east instead of south, possibly following the edges of glaciers, while the south-moving group followed the coastline.

Recently, from Anzick’s full genome data, another citizen scientist extracted the DNA locations that the testing companies use for autosomal DNA results, created an Anzick file, and uploaded the file to the public autosomal matching site, GedMatch.  This allowed everyone to see if they matched Anzick.  We expected no, or few, matches, because after all, Anzick was more than 12,000 years old and all of his DNA would have washed out long ago due to the 50% replacement in every generation….right?  Wrong!!!

What a surprise to discover fairly large segments of DNA matching Anzick in living people, and we’ve spent the past couple of weeks analyzing and discussing just how this has happened and why.  In spite of some technical glitches in terms of just how much individual people carry of the same DNA Anzick carried, one thing is for sure, the GedMatch matches confirm, in spades, the findings of the scientists who wrote the recent paper that describes the Anzick burial and excavation, the subsequent DNA processing and results.

For people who carry known Native heritage, matches, especially relatively large matches to Anzick, confirm not only their Native heritage, but his too.

For people who suspect Native heritage, but can’t yet prove it, an Anzick match provides what amounts to a clue – and it may be a very important clue.

In my case, I have proven Native heritage through the Micmac who intermarried with the Acadians in the 1600s in Nova Scotia.  Given that Anzick’s people were clearly on a west to east movement, from Beringia to wherever they eventually wound up, one might wonder if the Micmac were descended from or otherwise related to Anzick’s people.  Clearly, based on the genetic affinity map, the answer is yes, but not as closely related to Anzick as Mexican, Central and South Americans.

After several attempts utilizing various files, thresholds and factors that produced varying levels of matching to Anzick, one thing is clear – there is a match on several chromosomes.  Someplace, sometime in the past, Anzick and I shared a common ancestor – and it was likely on this continent, or Beringia, since the current school of thought is that all Native people entered the New World through this avenue.  The school of thought is not united in an opinion about whether there was a single migration event, or multiple migrations to the new word.  Regardless, the people came from the same base population in far northeast Asia and intermingled after arriving here if they were in the same location with other immigrants.

In other words, there probably wasn’t much DNA to pass around.  In addition, it’s unlikely that the founding population was a large group – probably just a few people – so in very short order their DNA would be all the same, being passed around and around until they met a new population, which wouldn’t happen until the Europeans arrived on the east side of the continent in the 1400s.  The tribes least admixed today are found south of the US border, not in the US.  So it makes sense that today the least admixed people would match Anzick the most closely – because they carry the most common DNA, which is still the same DNA that was being passed around and around back then.

Many of us with Native ancestors do carry bits and pieces of the same DNA as Anzick.  Anzick can’t be our ancestor, but he is certainly our cousin, about 500 generations ago, using a 25 year generation, so roughly our 500th cousin.  I had to laugh at someone this week, an adoptee who said, “Great, I can’t find my parents but now I have a 12,500 year old cousin.”  Yep, you do!  The ironies of life, and of genealogy, never fail to amaze me.

Utilizing the most conservative matching routine possible, on a phased kit, meaning one that combines the DNA shared by my mother and myself, and only that DNA, we show the following segment matches with Anzick.

Chr Start Location End Location Centimorgans (cM) SNPs
2 218855489 220351363 2.4 253
4 1957991 3571907 2.5 209
17 53111755 56643678 3.4 293
19 46226843 48568731 2.2 250
21 35367409 36761280 3.7 215

Being less conservative produces many more matches, some of which are questionable as to whether they are simply convergence, so I haven’t utilized the less restrictive match thresholds.

Of those matches above, the one on chromosomes 17 matches to a known Micmac segment from my Acadian lines and the match on chromosome 2 also matches an Acadian line, but I share so many common ancestors with this person that I can’t tell which family line the DNA comes from.

There are also Anzick autosomal matches on my father’s side.  My Native ancestry on his side reaches back to colonial America, in either Virginia or North Carolina, or both, and is unproven as to the precise ancestor and/or tribe, so I can’t correlate the Anzick DNA with proven Native DNA on that side.  Neither can I associate it with a particular family, as most of the Anzick matches aren’t to areas on my chromosome that I’ve mapped positively to a specific ancestor.

Running a special utility at GedMatch that compared Anzick’s X chromosome to mine, I find that we share a startlingly large X segment.  Sometimes, the X chromosome is passed for generations intact.

Interestingly enough, the segment 100,479,869-103,154,989 matches a segment from my mother exactly, but the large 6cM segment does not match my mother, so I’ve inherited that piece of my X from my father’s line.

Chr Start Location End Location Centimorgans (cM) SNPs
X 100479869 103154989 1.4 114
X 109322285 113215103 6.0 123

This tells me immediately that this segment comes from one of the pink or blue lines on the fan chart below that my father inherited from his mother, Ollie Bolton, since men don’t inherit an X chromosome from their father.  Utilizing the X pedigree chart reduces the possible lines of inheritance quite a bit, and is very suggestive of some of those unknown wives.

olliex

It’s rather amazing, if you think about it, that anyone today matches Anzick, or that we can map any of our ancestral DNA that both we and Anzick carry to a specific ancestor.

Indeed, we do live in exciting times.

Honoring Anzick

On a rainy Saturday in June, 2014, on a sagebrush hillside in Montana, in Native parlance, our “grandfather,” Anzick was reburied, bringing his journey full circle.  Sarah Anzick, a molecular biologist, the daughter of the family that owns the land where the bones were found, and who did part of the genetic discovery work on Anzick, returns the box with his bones for reburial.

anzick bones

More than 50 people, including scientists, members of the Anzick family and representatives of six Native American tribes, gathered for the nearly two-hour reburial ceremony. Tribe members said prayers, sang songs, played drums and rang bells to honor the ancient child. The bones were placed in the grave and sprinkled with red ocher, just like when his parents buried him some 12,500 years before.

Participants at the reburial ceremony filled in the grave with handfuls, then shovelfuls of dirt and covered it with stones. A stick tied with feathers marks Anzick’s final resting place.

Sarah Anzick tells us that, “At that point, it stopped raining. The clouds opened up and the sun came out. It was an amazing day.”

I wish I could have been there.  I would have, had I known.  After all, he is part of me, and I of him.

anzick grave'

Welcome to the family, Anzick, and thank you, thank you oh so much, for your priceless, unparalleled gift!!!

tobacco

If you want to read about the Anzick matching journey of DNA discovery, here are the articles I’ve written in the past two weeks.  It has been quite a roller coaster ride, but I’m honored and privileged to be doing this research.  And it’s all thanks to an ancient child named Anzick.

Utilizing Ancient DNA at Gedmatch

Analyzing the Native American Anzick Clovis Native American Results

New Native American Mitochondrial DNA Haplogroups Extrapolated from Anzick Match Results

Ancient DNA Matching, A Cautionary Tale

More Ancient DNA Samples for Comparison

Ancient DNA Matches – What Do They Mean?

The good news is that my three articles about the Anzick and other ancient DNA of the past few days have generated a lot of interest.

The bad news is that it has generated hundreds of e-mails every day – and I can’t possibly answer them all personally.  So, if you’ve written me and I don’t reply, I apologize and  I hope you’ll understand.  Many of the questions I’ve received are similar in nature and I’m going to answer them in this article.  In essence, people who have matches want to know what they mean.

Q – I had a match at GedMatch to <fill in the blank ancient DNA sample name> and I want to know if this is valid.

A – Generally, when someone asks if an autosomal match is “valid,” what they really mean is whether or not this is a genealogically relevant match or if it’s what is typically referred to as IBS, or identical by state.  Genealogically relevant samples are referred to as IBD, or identical by descent.  I wrote about that in this article with a full explanation and examples, but let me do a brief recap here.

In genealogy terms, IBD is typically used to mean matches over a particular threshold that can be or are GENEALOGICALLY RELEVANT.  Those last two words are the clue here.  In other words, we can match them with an ancestor with some genealogy work and triangulation.  If the segment is large, and by that I mean significantly over the threshold of 700 SNPs and 7cM, even if we can’t identify the common ancestor with another person, the segment is presumed to be IBD simply because of the math involved with the breakdown of segment into pieces.  In other words, a large segment match generally means a relatively recent ancestor and a smaller segment means a more distant ancestor.  You can readily see this breakdown on this ISOGG page detailing autosomal DNA transmission and breakdown.

Unfortunately, often smaller segments, or ones determined to be IBS are considered to be useless, but they aren’t, as I’ve demonstrated several times when utilizing them for matching to distant ancestors.  That aside, there are two kinds of IBS segments.

One kind of IBS segment is where you do indeed share a common ancestor, but the segment is small and you can’t necessarily connect it to the ancestor.  These are known as population matches and are interpreted to mean your common ancestor comes from a common population with the other person, back in time, but you can’t find the common ancestor.  By population, we could mean something like Amish, Jewish or Native American, or a country like Germany or the Netherlands.

In the cases where I’ve utilized segments significantly under 7cM to triangulate ancestors, those segments would have been considered IBS until I mapped them to an ancestor, and then they suddenly fell into the IBD category.

As you can see, the definitions are a bit fluid and are really defined by the genealogy involved.

The second kind of IBS is where you really DON’T share an ancestor, but your DNA and your matches DNA has managed to mutate to a common state by convergence, or, where your Mom’s and Dad’s DNA combined form a pseudo match, where you match someone on a segment run long enough to be considered a match at a low level.  I discussed how this works, with examples, in this article.  Look at example four, “a false match.”

So, in a nutshell, if you know who your common ancestor is on a segment match with someone, you are IBD, identical by descent.  If you don’t know who your common ancestor is, and the segment is below the normal threshold, then you are generally considered to be IBS – although that may or may not always be true.  There is no way to know if you are truly IBS by population or IBS by convergence, with the possible exception of phased data.

Data phasing is when you can compare your autosomal DNA with one or both parents to determine which half you obtained from whom.  If you are a match by convergence where your DNA run matches that of someone else because the combination of your parents DNA happens to match their segment, phasing will show that clearly.  Here’s an example for only one location utilizing only my mother’s data phased with mine.  My father is deceased and we have to infer his results based on my mother’s and my own.  In other words, mine minus the part I inherited from my mother = my father’s DNA.

My Result My Result Mother’s Result Mother’s Result Father’s Inferred Result Father’s Inferred Result
T A T G A

In this example of just one location, you can see that I carry a T and an A in that location.  My mother carries a T and a G, so I obviously inherited the T from her because I don’t have a G.  Therefore, my father had to have carried at least an A, but we can’t discern his second value.

This example utilized only one location.  Your autosomal data file will hold between 500,000 and 700,000 location, depending on the vendor you tested with and the version level.

You can phase your DNA with that of your parent(s) at GedMatch.  However, if both of your parents are living, an easier test would be to see if either of your parents match the individual in question.  If neither of your parents match them, then your match is a result of convergence or a data read error.

So, this long conversation about IBD and IBS is to reach this conclusion.

All of the ancient specimens are just that, ancient, so by definition, you cannot find a genealogy match to them, so they are not IBD.  Best case, they are IBS by population.  Worse case, IBS by convergence.  You may or may not be able to tell the difference.  The reason, in my example earlier this week, that I utilized my mother’s DNA and only looked at locations where we both matched the ancient specimens was because I knew those matches were not by convergence – they were in fact IBS by population because my mother and I both matched Anzick.

ancient compare5

Q – What does this ancient match mean to me?

A – Doggone if I know.  No, I’m serious.  Let’s look at a couple possibilities, but they all have to do with the research you have, or have not, done.

If you’ve done what I’ve done, and you’ve mapped your DNA segments to specific ancestors, then you can compare your ancient matching segments to your ancestral spreadsheet map, especially if you can tell unquestionably which side the ancestral DNA matches.  In my case, shown above, the Clovis Anzik matched my mother and me on the same segment and we both matched Cousin Herbie.  We know unquestionably who our common ancestor is with cousin Herbie – so we know, in our family line, which line this segment of DNA shared with Anzick descends through.

ancient compare6

If you’re not doing ancestor mapping, then I guess the Anzick match would come in the category of, “well, isn’t that interesting.”  For some, this is a spiritual connection to the past, a genetic epiphany.  For other, it’s “so what.”

Maybe this is a good reason to start ancestor mapping!  This article tells you how to get started.

Q – Does my match to Anzick mean he is my ancestor?

A – No, it means that you and Anzick share common ancestry someplace back in time, perhaps tens of thousands of years ago.

Q – I match the Anzick sample.  Does this prove that I have Native American heritage? 

A – No, and it depends.  Don’t you just hate answers like this?

No, this match alone does not prove Native American heritage, especially not at IBS levels.  In fact, many people who don’t have Native heritage match small segments?  How can this be?  Well, refer to the IBS by convergence discussion above.  In addition, Anzick child came from an Asian population when his ancestors migrated, crossing from Asia via Beringia.  That Eurasian population also settled part of Europe – so you could be matching on very small segments from a common population in Eurasia long ago.  In a paper just last year, this was discussed when Siberian ancient DNA was shown to be related to both Native Americans and Europeans.

In some cases, a match to Anzick on a segment already attributed to a Native line can confirm or help to confirm that attribution.  In my case, I found the Anzick match on segments in the Lore family who descend from the Acadians who were admixed with the Micmac.  I have several Anzick match segments that fit that criteria.

A match to Anzick alone doesn’t prove anything, except that you match Anzick, which in and of itself is pretty cool.

Q – I’m European with no ancestors from America, and I match Anzick too.  How can that be?

A – That’s really quite amazing isn’t it.  Just this week in Nature, a new article was published discussing the three “tribes” that settled or founded the European populations.  This, combined with the Siberian ancient DNA results that connect the dots between an ancient population that contributed to both Europeans and Native Americans explains a lot.

3 European Tribes

If you think about it, this isn’t a lot different than the discovery that all Europeans carry some small amount of Neanderthal and Denisovan DNA.

Well, guess what….so does Anzick.

Here are his matches to the Altai Neanderthal.

Chr Start Location End Location Centimorgans (cM) SNPs
2 241484216 242399416 1.1 138
3 19333171 21041833 2.6 132
6 31655771 32889754 1.1 133

He does not match the Caucasus Neanderthal.  He does, however, match the Denisovan individual on one location.

Chr Start Location End Location Centimorgans (cM) SNPs
3 19333171 20792925 2.1 107

Q – Maybe the scientists are just wrong and the burial is not 12,500 years old,  maybe just 100 years old and that’s why the results are matching contemporary people.

A – I’m not an archaeologist, nor do I play one…but I have been closely involved with numerous archaeological excavations over the past decade with The Lost Colony Research Group, several of which recovered human remains.  The photo below is me with Anne Poole, my co-director, sifting at one of the digs.

anne and me on dig

There are very specific protocols that are followed during and following excavation and an error of this magnitude would be almost impossible to fathom.  It would require  kindergarten level incompetence on the part of not one, but all professionals involved.

In the Montana Anzick case, in the paper itself, the findings and protocols are both discussed.  First, the burial was discovered directly beneath the Clovis layer where more than 100 tools were found, and the Clovis layer was undisturbed, meaning that this is not a contemporary burial that was buried through the Clovis layer.  Second, the DNA fragmentation that occurs as DNA degrades correlated closely to what would be expected in that type of environment at the expected age based on the Clovis layer.  Third, the bones themselves were directly dated using XAD-collagen to 12,707-12,556 calendar years ago.  Lastly, if the remains were younger, the skeletal remains would match most closely with Native Americans of that region, and that isn’t the case.  This graphic from the paper shows that the closest matches are to South Americans, not North Americans.

anzick matches

This match pattern is also confirmed independently by the recent closest GedMatch matches to South Americans.

Q – How can this match from so long ago possibly be real?

A – That’s a great question and one that was terribly perplexing to Dr. Svante Paabo, the man who is responsible for producing the full genome sequence of the first, and now several more, Neanderthals.  The expectation was, understanding autosomal DNA gets watered down by 50% in every generation though recombination, that ancient genomes would be long gone and not present in modern populations.  Imagine Svante’s surprise when he discovered that not only isn’t true, but those ancient DNA segmetns are present in all Europeans and many Asians as well.  He too agonized over the question about how this is possible, which he discussed in this great video.  In fact he repeated these tests over and over in different ways because he was convinced that modern individuals could not carry Neanderthal DNA – but all those repeated tests did was to prove him right.  (Paabo’s book, Neanderthal Man, In Search of Lost Genomes is an incredible read that I would highly recommend.)

What this means is that the population at one time, and probably at several different times, had to be very small.  In fact, it’s very likely that many times different pockets of the human race was in great jeopardy of dying out.  We know about the ones that survived.  Probably many did perish leaving no descendants today.  For example, no Neanderthal mitochondrial DNA has been found in any living or recent human.

In a small population, let’s say 5 males and 5 females who some how got separated from their family group and founded a new group, by necessity.  In fact, this could well be a description of how the Native Americans crossed Beringia.  Those 5 males and 5 females are the founding population of the new group.  If they survive, all of the males will carry the men’s haplogroups – let’s say they are Q and C, and all of the descendants will carry the mitochondrial haplogroups of the females – let’s say A, B, C, D and X.

There is a very limited amount of autosomal DNA to pass around.  If all of those 10 people are entirely unrelated, which is virtually impossible, there will be only 10 possible combinations of DNA to be selected from.  Within a few generations, everyone will carry part of those 10 ancestor’s DNA.  We all have 8 ancestors at the great-grandparent level.  By the time those original settlers’ descendants had great-great-grandparents – of which each one had 16, at least 6 of those original people would be repeated twice in their tree.

There was only so much DNA to be passed around.  In time, some of the segments would no longer be able to be recombined because when you look at phasing, the parents DNA was exactly the same, example below.  This is what happens in endogamous populations.

My Result My Result Mother’s Result Mother’s Result Father’s Result Father’s  Result
T T T T T T

Let’s say this group’s descendants lived without contact with other groups, for maybe 15,000 years in their new country.  That same DNA is still being passed around and around because there was no source for new DNA.  Mutations did occur from time to time, and those were also passed on, of course, but that was the only source of changed DNA – until they had contact with a new population.

When they had contact with a new population and admixture occurred, the normal 50% recombination/washout in every generation began – but for the previous 15,000 years, there had been no 50% shift because the DNA of the population was, in essence, all the same.  A study about the Ashkenazi Jews that suggests they had only a founding population of about 350 people 700 years ago was released this week – explaining why Ashkenazi Jewish descendants have thousands of autosomal matches and match almost everyone else who is Ashkenazi.  I hope that eventually scientists will do this same kind of study with Anzick and Native Americans.

If the “new population” we’ve been discussing was Native Americans, their males 15,000 year later would still carry haplogroups Q and C and the mitochondrial DNA would still be A, B, C, D and X.  Those haplogroups, and subgroups formed from mutations that occurred in their descendants, would come to define their population group.

In some cases, today, Anzick matches people who have virtually no non-Native admixture at the same level as if they were just a few generations removed, shown on the chart below.

anzick gedmatch one to all

Since, in essence, these people still haven’t admixed with a new population group, those same ancient DNA segments are being passed around intact, which tells us how incredibly inbred this original small population must have been.  This is known as a genetic bottleneck.

The admixture report below is for the first individual on the Anzick one to all Gedmatch compare at 700 SNPs and 7cM, above.  In essence, this currently living non-admixed individual still hasn’t met that new population group.

anzick1

If this “new population” group was Neanderthal, perhaps they lived in small groups for tens of thousands of years, until they met people exiting Africa, or Denisovans, and admixed with them.

There weren’t a lot of people anyplace on the globe, so by virtue of necessity, everyone lived in small population groups.  Looking at the odds of survival, it’s amazing that any of us are here today.

But, we are, and we carry the remains, the remnants of those precious ancestors, the Denisovans, the Neanderthals and Anzick.  Through their DNA, and ours, we reach back tens of thousands of years on the human migration path.  Their journey is also our journey.  It’s absolutely amazing and it’s no wonder people have so many questions and such a sense of enchantment.  But it’s true – and only you can determine exactly what this means to you.

Analyzing the Native American Clovis Anzick Ancient Results

This ancient DNA truly is the gift that keeps on giving.

Today, Felix Chandrakamur e-mailed me and told me that the Anzick results were not yet fully processed at Gedmatch when I performed a “compare to all.”  He knows this because he knows when he uploaded the results, and after they were finished, he ran the same compare and obtained vastly different results.  I am updating my original article to point to this one, so the data will be accurately reflected.

In fact, the results are utterly fascinating, take your breath away kind of fascinating.  Felix wrote an article about his findings, Clovis-Anzick-1 ancient DNA have matches with living people!

While finding what appear to be contemporary matches for the Anzick child may sound ho-hum, it’s not, and when you look at the results and the message they hold for us, it’s absolutely astounding.

Felix ran his comparison with default values of 7cM.  This is the threshold that is typically utilized as the line in the sand between “real” and IBS, matches – real meaning the results are and could be, if you could find your common ancestor, genealogically relevant.  In this case, that clearly isn’t true.

The exception to this rule is heavily admixed groups, such as Ashkenazi Jewish people who are related to every other Askhenazi Jewish person autosomally.  It seems, looking at these results, that this is the same situation we find with the 12,500 year old Anzick child and currently living people.  This population had to be painfully small for a very long time and the DNA had to exist in every person within that population group for it to be passed in segments this large to people living today.

After receiving Felix’s e-mail, of course, I had to go back and run the compares again.  In particular, I wanted to run the one to many, as he had.

I began at the 1cM level and noticed that I received exactly 1500 results, which seemed to me like a cutoff – not an actual number of matches.  So, I upped that threshold to 2, then 3, then 4, then 5, then 6, then finally to the default of 7.  It was only at 7, the IBS/IBD default, that the results were under the 1500 threshold, at 1466.

1466 current matches?????

This is absolutely amazing.  The Anzick child lived about 12,500 years ago in Montana.  How are 1466 matches to currently living people possible?

Many of these matches are to people from the southwest and Mexico today.  They are not, for the most part, from eastern Canada.

Let’s take a look at what we found.

In the 1466 results, as Felix mentioned, the closest matches match at current “cousin” levels to Anzick.  The highest 7 matches that show haplogroups are haplogroup Q1a3a.  Unfortunately, with the constant renaming of the haplogroups recently, it’s difficult to interpret the haplogroup exactly, which is why we’ve gone to SNP names.  Looking at some of the names and e-mails, several appear to carry Spanish surnames or be from Mexico or South America.

Of the 1466 results:

  • 2 were Y haplogroup C
  • 79 were Y haplogroup Q
  • 520 carried a mitochondrial DNA haplogroup of A, B, C, D, M or X
  • Of the 79 haplogroup Q carriers, 52 also carried a Native mitochondrial haplogroup.
  • A total 549 individuals out of 1466 carried at least one Native American haplogroup, or about 37.5%.  That’s amazingly high.

Of these closest matches who are Y haplogroup Q, they also all carry variant Native American mitochondrial DNA haplogroups as well, so these people may not be heavily admixed.  In other words, they may be almost “pure” Native American.

In order to test this theory, I entered the number of the kit that rated the highest in terms of total cM at 160.1 with the largest segment at 14.8.  You can click on the images to enlarge.

anzick1

As you can see, this individual is very nearly 100% Native American.

The second individual on the list, who may be from Guatemala, also carries almost no admixture.

anzick2

Of the highest 21 matches that listed any haplogroup information, all have either or both Native Y or mitochondrial DNA haplogroups.

Out of curiosity, I ran the first person on the list who had neither a Native American Y or mitochondrial haplogroup – both being European.

As you can see, below, they are still clearly heavily Native American, but clearly admixed.

anzick3

I moved to the last person of the 1466 on this list whose DNA matched at a total of 7cM, who did not carry a Native haplogroup.  This individual, below, is more heavily admixed.

anzick 3.5

Lastly, I ran the same admixture tool on the last person, who had a total of 7cM matching that did have a Native American mitochondrial haplogroup.

anzick4

Not surprisingly, the individual with almost no non-Native admixture is much more likely to carry the ancient segments in higher percentages than the individuals who are admixed.   This again strongly suggests that at one point, these segments were present in an entire group of Native people and may still be present in very high numbers in people who carry no admixture.

Out of curiosity, and assuming that these first two individuals are not known to be related to each other, I ran them against each other in a one to one comparison.

There were no matches at the default values, but by dropping them just a little, to 5cM and 500 SNPs, they match on 6 segments.

anzick5

It looks like they should match on chromosome 17 at the 700 SNP/7 cM default threshold.

At 200 SNPs and 2cM, there were 67 segments.  These are clearly ancient in nature and size, but matching just the same.  By lowering the threshold to 100 SNPs and 1cM, they share a whopping 990 segments.

Indeed, these two men very clearly share a lot of population specific DNA from the ancient people of the New World, including that of Anzick male child who lived in Montana 12,500 years ago.