Analyzing the Native American Clovis Anzick Ancient Results

Posted on September 23, 2014 by Roberta Estes

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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.

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.

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.

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.

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.

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.

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.

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Utilizing Ancient DNA at GedMatch

Posted on September 22, 2014 by Roberta Estes

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Mummy of 6 month old boy found in Greenland

It has been a wonderful week for those of us following ancient DNA full genome sequencing, because now we can compare our own results to those of the ancient people found whose DNA has been fully sequenced, including one Native American.

Felix Chandrakumar has uploaded the autosomal files of five ancient DNA specimens that have been fully sequenced to GedMatch. Thanks Felix.

When news of these sequences first hit the academic presses, I was wishing for a way to compare our genomes – and now my wish has come true.

Utilizing GedMatch’s compare one to all function, I ran all of the sequences individually and found, surprisingly, that there are, in some cases, matches to contemporary people today. I dropped the cM measure to 1 for both autosomal and X.

Please note that because these are ancient DNA sequences, they will all have some segments missing and none can be expected to be entirely complete. Still, these sequences are far better than nothing.

1. Montana Anzick at GedMatch

This is the only clearly Native American sample.

http://www.y-str.org/2014/09/clovis-anzick-dna.html

F999912

9-27-2014 – Please note that kit F999912 has been replaced by kit F999913.

10-23-2014 – Please note that kit F999913 has been replaced by kit F999919.

No matches at 1cM in the compare to all. This must be because the SNP count is still at default thresholds, in light of information discovered later in this article.

Update – as it turns out, this kit was not finished processing when I did the one to one compare. After it finished, the results were vastly different. See this article for results.

2. Paleo Eskimo from Greenland at GedMatch

http://www.y-str.org/2013/12/palaeo-eskimo-2000-bc-dna.html

F999906

Thirty-nine matches with segments as large at 3.8. One group of matches appears to be a family. One of these matches is my cousin’s wife. That should lead to some interesting conversation around the table this holiday season! All of these matches, except 1, are on the X chromosome. This must be a function of these segments being passed intact for many generations.

I wrote about some unusual properties of X chromosomal inheritance and this seems to confirm that tendency in the X chromosome, or the matching thresholds are different at GedMatch for the X.

3. Altai Neanderthal at GedMatch

http://www.y-str.org/2013/08/neanderthal-dna.html

F999902

One match to what is obviously another Neaderthal entry.

4. Russian Causasus Neanderthal at GedMatch

Another contribution from the Neanderthal Genome Project.

http://www.y-str.org/2014/09/mezmaiskaya-neanderthal-dna.html

F999909

No matches.

5. Denisova at GedMatch

http://www.y-str.org/2013/08/denisova-dna.html

F999903

Two matches, one to yet another ancient entry and one to a contemporary individual on the X chromosome.

But now, for the fun part.

My Comparison

Before I start this section, I want to take a moment to remind everyone just how old these ancient segments are.

Anzick – about 12,500 years old
Paleo-Eskimo – about 4,000 years old
Altai Neanderthal – about 50,000 years old
Russian Caucasus Neanderthal – about 29,000 years old
Denisova – about 30,000 years old

In essence, the only way for these segments to survive intact to today would have been for them to enter the population of certain groups, as a whole, to be present in all of the members of that group, so that segment would no longer be divided and would be passed intact for many generation, until that group interbred with another group who did not carry that segment. This is exactly what we see in endogamous populations today, such as the Askenazi Jewish population who is believed, based on their common shared DNA, to have descended from about 350 ancestors about 700 years ago. Their descendants today number in the millions.

So, let’s see what we find.

I compared by own kit at GedMatch utilizing the one to one comparison feature, beginning with 500 SNPs and 1cM, dropping the SNP values to 400, then 300, then 200, until I obtained a match of some sort, if I obtained a match at all.

Typically in genetic genealogy, we’re looking for genealogy matches, so the default matching thresholds are set relatively high. In this case, I’m looking for deep ancestral connections, if they exist, so I was intentionally forcing the thresholds low. I’m particularly interested in the Anzick comparison, in light of my Native American and First Nations heritage.

The definition of IBS, identical by state, vs IBD, identical by descent segments varies by who is talking and in what context, but in essence, IBD means that there is a genealogy connection in the past several generations.

IBS means that the genealogy connection cannot be found and the IBS match can be a function of coming from a common population at some time in the past, or it can be a match by convergence, meaning that your DNA just happened to mutate to the same state as someone else’s. If this is the case, then you wouldn’t expect to see multiple segments matching the same person and you would expect the matching segments to be quite short. The chances of hundreds of SNPs just happening to align becomes increasingly unlikely the longer the matching SNP run.

So, having said that, here are my match results.

Anzick

I had 2 matches at 400 SNPs, several at 300 and an entire list at 200, shown below.

Chr	Start Location	End Location	Centimorgans (cM)	SNPs
1	6769350	7734985	1.7	232
1	26552555	29390880	1.9	264
1	31145273	33730360	2.7	300
1	55655110	57069976	1.9	204
1	71908934	76517614	2.8	265
1	164064635	165878596	2.8	264
1	167817718	171330902	3.3	466
1	186083870	192208998	4.2	250
2	98606363	100815734	1.4	256
2	171132725	173388331	2.0	229
2	218855489	220373983	2.5	261
3	128892631	131141396	1.7	263
3	141794591	143848459	2.5	207
4	1767539	3571907	2.7	235
4	70345811	73405268	2.5	223
5	2340730	2982499	2.3	200
5	55899022	57881001	2.3	231
5	132734528	134538202	1.9	275
5	137986213	140659207	1.7	241
6	34390761	36370969	1.8	293
8	17594903	18464321	1.9	200
8	23758017	25732105	1.7	240
8	109589884	115297391	1.9	203
9	122177526	124032492	1.6	229
10	101195132	102661955	1.2	264
10	103040561	105596277	1.3	304
10	106135611	108371247	1.5	226
12	38689229	41184500	1.6	247
13	58543514	60988948	1.6	220
13	94528801	95252127	1.0	277
14	60929984	62997711	1.8	255
14	63724184	65357663	1.7	201
14	72345879	74206753	1.7	263
15	36850933	38329491	2.7	238
16	1631282	2985328	2.5	273
16	11917282	13220406	3.7	276
16	15619825	17324720	3.1	305
16	29085336	31390250	1.3	263
16	51215026	52902771	3.4	224
17	52582669	56643678	4.7	438
19	11527683	13235913	1.7	203
19	15613137	16316773	1.2	204
19	46195917	49338412	3.3	397
20	17126434	18288231	2.1	225
21	35367409	36969215	4.1	254
21	42399499	42951171	1.6	233
22	33988022	35626259	5.0	289

In my case, I’m particularly fortunate, because my mother tested her DNA as well. By process of elimination, I can figure out which of my matches are through her, and then by inference, which are through my father or are truly IBS by convergence.

I carry Native heritage on both sides, but my mother’s is proven to specific Native ancestors where my father’s is only proven to certain lines and not yet confirmed through genealogy records to specific ancestors.

Because I had so many matches, quite to my surprise, I also compared my mother’s DNA to the Anzick sample, combined the two results and put them in a common spreadsheet, shown below. White are my matches. Pink are Mom’s matches, and the green markers are on the segments where we both match the Anzick sample, confirming that my match is indeed through mother.

We’ll work with this information more in a few minutes.

Paleo

At 200 SNP level, 2 segments.

1	26535949	27884441	1.1	258
2	127654021	128768822	1.2	228

My mother matches on 9 segments, but neither of the two above, so they are either from my father’s side or truly IBS by convergence.

Altai Neanderthal

Russian Neanderthal

Neither my mother nor I have any matches at 100SNPs and 1cM.

Denisovan

I have one match.

Chr	Start Location	End Location	Centimorgans (cM)	SNPs
4	8782230	9610959	1.2	100

My mother matches 2 segments at 100 SNPs but neither match is the same as my segment.

Matching to Ancestral Lines

I’ve been mapping my DNA to specific ancestors utilizing the genealogy information of matches and triangulation for some time. This consists of finding common ancestors with your matches. Finding one person who matches you and maps to a common ancestor on a particular segment consists of a hint. Finding two that share the same ancestral line and match you and each other on the same segment is confirmation – hence, the three of you triangulate. More than three is extra gravy:)

I have also recorded other relevant information in my matches file, like the GedMatch Native chromosomal comparisons when I wrote “The Autosomal Me” series about hunting for my Native chromosomal segments.

So, after looking at the information above, it occurred to me that I should add this ancestral match information to my matches spreadsheet, just for fun, if nothing else.

I added these matches, noted the source as GedMatch and then sorted the results, anxious to see what we might find. Would at least one of these segments fall into the proven Native segments or the matches to people who also descend from those lines?

What I found was both astonishing and confusing….and true to form to genealogy, introduced new questions.

I have extracted relevant matching groups from my spreadsheet and will discuss them and why they are relevant. You can click on any of the images to see a larger image.

This first set of matches is intensely interesting, and equally as confusing.

First, these matches are to both me and mother, so they are confirmed through my mother’s lines. In case anyone notices, yes, I did switch my mother’s line color to white and mine to pink to be consistent with my master match spreadsheet coloration.

Second, both mother and I match the Anzick line on the matches I’ve utilized as examples.

Third, both 23andMe and Dr. Doug McDonald confirmed the segments in red as Native which includes the entire Anzick segment.

Fourth, utilizing the Gedmatch admixture tools, mother and I had this range in common. I described this technique in “The Autosomal Me” series.

Fifth, these segments show up for two distinct genealogy lines that do not intersect until my grandparents, the Johann Michael Miller line AND the Acadian Lore line.

Sixth, the Acadian Lore line is the line with proven Native ancestors.

Seventh, the Miller line has no Native ancestors and only one opportunity for a Native ancestor, which is the unknown wife of Philip Jacob Miller who married about 1750 to a women rumored to be Magdalena Rochette, but research shows absolutely no source for that information, nor any Rochette family anyplace in any proximity in the same or surrounding counties to the Miller family. The Miller’s were Brethren. Furthermore, there is no oral history of a Native ancestor in this line, but there have been other hints along the way, such as the matching segments of some of the “cousins” who show as Native as well.

Eighth, this makes my head hurt, because this looks, for all the world, like Philip Jacob Miller who was living in Bedford County, PA when he married about 1750 may have married someone related to the Acadian lines who had intermarried with the Micmac. While this is certainly possible, it’s not a possibility I would ever have suspected.

Let’s see what else the matches show.

In this matching segment Mom and I both match Emma, who descends from Marie, a MicMac woman. Mom’s Anzik match is part of this same segment.

In this matching segment, Mom and I both match cousin Denny who descends from the Lore line who is Acadian and confirmed to have MicMac ancestry. Mom’s Anzik segments all fit in this range as well.

In this matching segment, cousin Herbie’s match to Mom and I falls inside the Anzick segments of both Mom and I.

More matching to the proven Miller line.

This last grouping with Mom is equally as confusing at the first. Mom and I both match cousin Denny on the Lore side, proven Acadian.

Mom and I both match the Miller side too, and the Anzik for both of us falls dead center in these matches.

There are more, several more matches, that also indicate these same families, but I’m not including them because they don’t add anything not shown in these examples. Interestingly enough, there are no pointers to other families, so this isn’t something random. Furthermore, on my father’s side, as frustrating as it is, here are no Anzick matches that correlate with proven family lines. ARGGHHHHHH……

On matches that I don’t share with mother, there is one of particular interest.

You’ll notice that the Anzik and the Paleo-Greenland samples match each other, as well as me. This is my match, and by inference, not through mother. Unfortunately, the other people in this match group don’t know their ancestors or we can’t identify a common ancestor.

Given the genetic genealogy gold standard of checking to see if your autosomal matches match each other, I went back to GedMatch to see if the Paleo-Greenland kit matched the Clovis Anzik kit on this segment, and indeed, they do, plus many more segments as well. So, at some time, in some place, the ancestors of these two people separated by thousands of miles were related to each other. Their common ancestor would have either been in Asia or in the Northern part of Canada if the Paleo people from Greenland entered from that direction.

Regardless, it’s interesting, very interesting.

What Have I Learned?

Always do experiments. You never know what you’ll find.

I’m much more closely related to the Anzick individual than I am to the others. This isn’t surprising given my Native heritage along with the endogamous culture of the Acadians.

My relationship level to these ancient people is as follows:

	Lived Years Ago	Relatedness	Comments
Montana Anzick	12,500	107.4cM at 200 SNP level	Confirmed to Lore (Acadian) and Miller, but not other lines
Greenland Paleo	4,000	2.3cM at 200 SNP level	No family line matches, does match to Anzick in one location
Altai Neanderthal	50,000	2.1cM at 200 SNP level	No family line matches
Russian Neanderthal	29,000	0
Denisovan	30,000	1.2cM at 200 SNP	No family line matches

The Lores and the Millers

Looking further at the Lore and Miller lines, there are only two options for how these matching segments could have occurred. There are too many for them all to be convergence, so we’ll have to assume that they are indeed because we shared a common population at some time and place.

The nature of how small the segments are testify that this is not a relatively recent common ancestor, but how “unrecent” is open to debate. Given that Neanderthal and Denisovan ancient segments are found in all Europeans today, it’s certainly possible for these segments to be passed intact, even after thousands of years.

The confirmations to the Lore line come through proven Lore cousins and also through other proven Acadian non-specific matches. This means that the Acadian population is highly endogamous and when I find an Acadian match, it often means that I’m related through many ancestors many times. This, of course, increases the opportunity for the DNA to be passed forward, and decreases the opportunity for it to be lost in transmission, but it also complicates the genealogy greatly and makes determining which ancestor the DNA segment came from almost impossible.

However, I think we are safe to say the segments are from the Acadian population, although my assumption would be that they are from the Native Ancestors and not the French, given the high number of Anzick matches, Anzick being proven to be Native. Having said that, that assumption may not be entirely correct.

The Miller line is relatively well documented and entirely from Germany/Switzerland, immigrating in the early 1700s, with the exception of the one unknown wife in the first generation married in the US. Further examination would have to be done to discover if any of the matches came through Johann Michael Miller’s sons other than Philip Jacob Miller, my ancestor. There are only three confirmed children, all sons. If this segment shows up in Johann Michael Miller’s line not associated with son Philip Jacob Miller, then we would confirm that indeed the segment came from Europe and not a previously unknown Native or mixed wife of Philip Jacob.

Bottom Line

So, what’s the bottom line here? I know far more than I did. The information confirms, yet again, the Acadian Native lines, but it introduces difficult questions about the Miller line. I have even more tantalizing questions for which I have no answers today, but I tell you what, I wouldn’t trade this journey along the genetic pathway with all of its unexpected bumps, rocks, slippery slopes and crevices for anything!! That’s why it’s called an adventure!

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DNA Analysis of 8000 Year Old Bones Allows Peek Into the Neolithic

Posted on June 9, 2014 by Roberta Estes

In the paper, “Ancient DNA Analysis of 8000 B.C. Near Eastern Farmers Supports an Early Neolithic Pioneer Maritime Colonization of Mainland Europe through Cyprus and the Aegean Islands,” by Fernandez et al, published June 5, 2014, we find a report on the analysis of ancient skeletal remains that sheds light on the Neolithic area before expansion from the Fertile Crescent into Europe.

It was about 8000 years ago, give or take 1000 years, when 63 people died in what is now Syria. They were buried in three separate locations, and recently their skeletal remains were exhumed and DNA tested. Of those, 15 yielded mitochondrial DNA results.

Haplogroups revealed were:

R0 (3)
K (6)
L3
U*
N*
H (2)
HV

Of course, there were only 15 skeletons with viable DNA, but conspicuously missing is haplogroup J, long believed to have diffused to Europe in the Neolithic.

Haplogroups I, T and V are also missing, but are much less prevalent in Europe than haplogroup J.

The authors also provided an updated map of the Neolithic diffusion into Europe, with projected dates, indicating they believe the expansion was initially through the Mediterranean via Cyprus, Crete and the Aegean Sea.

The author abstract and summary are provided below and you can read the entire article at PLOS Genetics.

Abstract

The genetic impact associated to the Neolithic spread in Europe has been widely debated over the last 20 years. Within this context, ancient DNA studies have provided a more reliable picture by directly analyzing the protagonist populations at different regions in Europe. However, the lack of available data from the original Near Eastern farmers has limited the achieved conclusions, preventing the formulation of continental models of Neolithic expansion. Here we address this issue by presenting mitochondrial DNA data of the original Near-Eastern Neolithic communities with the aim of providing the adequate background for the interpretation of Neolithic genetic data from European samples. Sixty-three skeletons from the Pre Pottery Neolithic B (PPNB) sites of Tell Halula, Tell Ramad and Dja’de El Mughara dating between 8,700–6,600 cal. B.C. were analyzed, and 15 validated mitochondrial DNA profiles were recovered. In order to estimate the demographic contribution of the first farmers to both Central European and Western Mediterranean Neolithic cultures, haplotype and haplogroup diversities in the PPNB sample were compared using phylogeographic and population genetic analyses to available ancient DNA data from human remains belonging to the Linearbandkeramik-Alföldi Vonaldiszes Kerámia and Cardial/Epicardial cultures. We also searched for possible signatures of the original Neolithic expansion over the modern Near Eastern and South European genetic pools, and tried to infer possible routes of expansion by comparing the obtained results to a database of 60 modern populations from both regions. Comparisons performed among the 3 ancient datasets allowed us to identify K and N-derived mitochondrial DNA haplogroups as potential markers of the Neolithic expansion, whose genetic signature would have reached both the Iberian coasts and the Central European plain. Moreover, the observed genetic affinities between the PPNB samples and the modern populations of Cyprus and Crete seem to suggest that the Neolithic was first introduced into Europe through pioneer seafaring colonization.

Author Summary

Since the original human expansions out of Africa 200,000 years ago, different prehistoric and historic migration events have taken place in Europe. Considering that the movement of the people implies a consequent movement of their genes, it is possible to estimate the impact of these migrations through the genetic analysis of human populations. Agricultural and husbandry practices originated 10,000 years ago in a region of the Near East known as the Fertile Crescent. According to the archaeological record this phenomenon, known as “Neolithic”, rapidly expanded from these territories into Europe. However, whether this diffusion was accompanied or not by human migrations is greatly debated. In the present work, mitochondrial DNA –a type of maternally inherited DNA located in the cell cytoplasm- from the first Near Eastern Neolithic populations was recovered and compared to available data from other Neolithic populations in Europe and also to modern populations from South Eastern Europe and the Near East. The obtained results show that substantial human migrations were involved in the Neolithic spread and suggest that the first Neolithic farmers entered Europe following a maritime route through Cyprus and the Aegean Islands.

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Finding Native American Ethnic Results in Germanic People

Posted on May 21, 2014 by Roberta Estes

I’m often asked about the significance of small percentages of autosomal DNA in results. Specifically, the small percentages are often of Native American or results that would suggest Native admixture. One of the first questions I always ask is whether or not the individual has Germanic or eastern European admixture.

Why?

Take a look at this map of the Invasion of the Roman Empire. See the Huns and their path?

It’s no wonder we’re so admixed.

Here’s a map of the Hunnic empire at its peak under Attila between the years 420-469.

But that wasn’t the end of the Asian invasions. The Magyars, who settled in Hungary arrived from Asia as well, in the 800s and 900s, as shown on this map from LaSalle University.

Since both the Hungarians and some Germanic people descend from Asian populations, as do Native Americans, albeit thousands of years apart, it’s not unrealistic to expect that, as populations, they share a genetic connection.

Therefore, when people who carry heritage from this region of the world show small amounts of Native or Asian origin, I’m not surprised. However, for Americans, trying to sort out their Native ethnic heritage, this is most unhelpful.

Let’s take a look at the perfect example candidate. This man is exactly half Hungarian and half German. Let’s see what his DNA results say, relative to any Asian or Native heritage, utilizing the testing companies and the free admixture tools at www.gedmatch.com.

He has not tested at Ancestry, but at Family Tree DNA, his myOrigins report 96% European, 4% Middle Eastern. At 23andMe in speculative view, he shows 99.7 European and .2 sub-saharan African.

Moving to the admixture tools at GedMatch, MDLP is not recommended for Asian or Native ancestry, so I have excluded that tool.

Eurogenes K13 is the most recently updated admixture tool, so let’s take a look at that one first.

Eurogenes K13

Eurogenes K13 showed 7% West Asian, which makes perfect sense considering his heritage, but it might be counted as “Native” in other circumstances, although I would certainly be very skeptical about counting it as such.

However, East Asian, Siberian and Amerindian would all be amalgamated into the Native American category, for a combined percentage of 1.31.

However, selecting the “admixture proportions by chromosome” view shows something a bit different. The cumulative percentages, by chromosome equate to 10.10%. Some researchers mistakenly add this amount and use that as their percentage of Native ancestry. This is not the case, because those are the portions of 100% of each individual chromosome, and the total would need to be divided by 22 to obtain the average value across all chromosomes. The total is irrelevant, and the average may not reflect how the developer determines the amount of admixture because chromosomes are not the same size nor carry the same number of SNPs. Questions relative to the functional underpinnings of each tool should be addressed to the developers.

Dodecad

I understand that there is a newer version of Dodecad, but that it has not been submitted to GedMatch for inclusion, per a discussion with GedMatch. I can’t tell which of the Dodecad versions on GedMatch is the most current, so I ran the results utilizing both v3 and 12b.

I hope v3 is not the most current, because it does not include any Native American category or pseudocategory – although there is a smattering of Northeast Asian at .27% and Southwest Asian at 1%.

Dodecad 12b below

The 12b version does show .52% Siberian and 2.6% Southwest Asian, although I’m not at all sure the Southwest Asian should be included.

HarappaWorld

Harappaworld shows .09 Siberian, .27% American (Native American), .23% Beringian and 1.8% Southwest Asian, although I would not include Southwest Asian in the Native calculation.

In Summary

Neither Family Tree DNA nor 23andMe find Native ancestry in our German/Hungarian tester, but all 3 of the admixture tools at Gedmatch find either small amounts of Native or Asian ancestry that could certainly be interpreted as Native, such as Siberian or Beringian.

Does this mean this German/Hungarian man has Native American ancestry? Of course not, but it does probably mean that the Native population and his ancestral populations did share some genes from the same gene pool thousands of years ago.

While you might think this is improbable, or impossible, consider for a minute that every person outside of Africa today carries some percentage of Neanderthal DNA, and all Europeans also carry Denisovan DNA. Our DNA does indeed have staying power over the millennia, especially once an entire population or group of people is involved. We’ve recently seen this same type of scenarios in the full genome sequencing of a 24,000 year old Siberian male skeleton.

Our German/Hungarian man carries 2.4% Neanderthal DNA according to 23andMe and 2.7% according to the Genographic Project, which also reports that he carries 3.9% Denisovan. The European average is about 2% for Neanderthal.

The net-net of this is that minority admixture is not always what it seems to be, especially when utilizing autosomal DNA to detect small amounts of Native American admixture. The big picture needs to be taken into consideration. Caution is advised.

When searching for Native admixture, when possible, both Y DNA and mitochondrial DNA give specific answers for specific pedigree lines relative to ancestry. Of course, to utilize Y or mtDNA, the tester must descend from the Native ancestor either directly paternally to test the male Y chromosome, or directly matrilineally to test the mitochondrial line. You can read about this type of testing, and how it works, in my article, Proving Native American Ancestry Using DNA. You can also read about other ways to prove Native ancestry using autosomal DNA, including how to unravel which pedigree line the Native ancestry descends from, utilizing admixture tools, in the article, “The Autosomal Me.”

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Clovis People Are Native Americans, and from Asia, not Europe

Posted on February 13, 2014 by Roberta Estes

In a paper published in Nature today, titled “The genome of a Late Pleistocene human from a Clovis burial site in western Montana,” by Rasmussen et al, the authors conclude that the DNA of a Clovis child is ancestral to Native Americans. Said another way, this Clovis child was a descendant, along with Native people today, of the original migrants from Asia who crossed the Bering Strait.

This paper, over 50 pages including supplemental material, is behind a paywall but it is very worthwhile for anyone who is specifically interested in either Native American or ancient burials. This paper is full of graphics and extremely interesting for a number of reasons.

First, it marks what I hope is perhaps a spirit of cooperation between genetic research and several Native tribes.

Second, it utilized new techniques to provide details about the individual and who in world populations today they most resemble.

Third, it utilized full genome sequencing and the analysis is extremely thorough.

Let’s talk about these findings in more detail, concentrating on information provided within the paper.

The Clovis are defined as the oldest widespread complex in North America dating from about 13,000 to 12,600 calendar years before present. The Clovis culture is often characterized by the distinctive Clovis style projectile point. Until this paper, the origins and genetic legacy of the Clovis people have been debated.

These remains were recovered from the only known Clovis site that is both archaeological and funerary, the Anzick site, on private land in western Montana. Therefore, the NAGPRA Act does not apply to these remains, but the authors of the paper were very careful to work with a number of Native American tribes in the region in the process of the scientific research. Sarah L. Anzick, a geneticist and one of the authors of the paper, is a member of the Anzick family whose land the remains were found upon. The tribes did not object to the research but have requested to rebury the bones.

The bones found were those of a male infant child and were located directly below the Clovis materials and covered in red ochre. They have been dated to about 12,707-12,556 years of age and are the oldest North or South American remains to be genetically sequenced.

All 4 types of DNA were recovered from bone fragment shavings: mitochondrial, Y chromosome, autosomal and X chromosome.

Mitochondrial DNA

The mitochondrial haplogroup of the child was D4h3a, a rather rare Native American haplogroup. Today, subgroups exist, but this D4h3a sample has none of those mutations so has been placed at the base of the D4h3a tree branch, as shown below in a grapic from the paper. Therefore, D4h3a itself must be older than this skeleton, and they estimate the age of D4h3a to be 13,000 plus or minus 2,600 years, or older.

Today D4h3a is found along the Pacific coast in both North and South America (Chile, Peru, Ecuador, Bolivia, Brazil) and has been found in ancient populations. The highest percentage of D4h3a is found at 22% of the Cayapa population in Equador. An ancient sample has been found in British Columbia, along with current members of the Metlakatla First Nation Community near Prince Rupert, BC.

Much younger remains have been found in Tierra del Fuego in South America, dating from 100-400 years ago and from the Klunk Mound cemetery site in West-Central Illinois dating from 1800 years ago.

It’s sister branch, D4h3b consists of only one D4h3 lineage found in Eastern China.

Y Chromosomal DNA

The Y chromosome was determined to be haplogroup Q-L54. Haplogroup Q and subgroup Q-L54 originated in Asia and two Q-L54 descendants predominate in the Americas: Q-M3 which has been observed exclusively in Native-Americans and Northeastern Siberians and Q-L54.

The tree researchers constructed is shown below.

They estimate the divergence between haplogroups Q-L54 and Q-M3, the two major haplogroup Q Native lines, to be about 16,900 years ago, or from between 13,000 – 19,700.

The researchers shared with us the methodology they used to determine when their most common recent ancestor (MCRA) lived.

“The modern samples have accumulated an average of 48.7 transversions [basic mutations] since their MCRA lived and we observed 12 in Anzick. We infer an average of approximately 36.7 (48.7-12) transversions to have accumulated in the past 12.6 thousands years and therefore estimate the divergence time of Q-M3 and Q-L54 to be approximately 16.8 thousands years (12.6ky x 48.7/36.7).”

Autosomal

They termed their autosomal analysis “genome-wide genetic affinity.” They compared the Anzick individual with 52 Native populations for which known European and African genetic segments have been “masked,” or excluded. This analysis showed that the Anzick individual showed a closer affinity to all 52 Native American populations than to any extant or ancient Eurasian population using several different, and some innovative and new, analysis techniques.

Surprisingly, the Anzick infant showed less shared genetic history with 7 northern Native American tribes from Canada and the Artic including 3 Northern Amerind-speaking groups. Those 7 most distant groups are: Aleutians, East Greenlanders, West Greenlanders, Chipewyan, Algonquin, Cree and Ojibwa.

They were closer to 44 Native populations from Central and South America, shown on the map below by the red dots. In fact, South American populations all share a closer genetic affinity with the Anzick individual than they do with modern day North American Native American individuals.

The researchers proposed three migration models that might be plausible to support these findings, and utilized different types of analysis to eliminate two of the three. The resulting analysis suggests that the split between the North and South American lines happened either before or at the time the Anzick individual lived, and the Anzick individual falls into the South American group, not the North American group. In other words, the structural split pre-dates the Anzick child. They conclude on this matter that “the North American and South American groups became isolated with little or no gene flow between the two groups following the death of the Anzick individual.” This model also implies an early divergence between these two groups.

In Eurasia, genetic affinity with the Anzick individual decreases with distance from the Bering Strait.

The researchers then utilized the genetic sequence of the 24,000 year old MA-1 individual from Mal’ta, Siberia, a 40,000 year old individual “Tianyuan” from China and the 4000 year old Saqqaq Palaeo-Eskimo from Greenland.

Again, the Anzick child showed a closer genetic affinity to all Native groups than to either MA-1 or the Saqqaq individual. The Saqqaq individual is closest to the Greenland Inuit populations and the Siberian populations close to the Bering Strait. Compared to MA-1, Anzick is closer to both East Asian and Native American populations, while MA-1 is closer to European populations. This is consistent with earlier conclusions stating that “the Native American lineage absorbed gene flow from an East Asian lineage as well as a lineage related to the MA-1 individual.” They also found that Anzick is closer to the Native population and the East Asian population than to the Tianyuan individual who seems equally related to a geographically wide range of Eurasian populations. For additional information, you can see their charts in figure 5 in their supplementary data file.

I have constructed the table below to summarize who matches who, generally speaking.

In addition, a French population was compared and only showed an affiliation with the Mal’ta individual and generically, Tianyuan who matches all Eurasians at some level.

Conclusions

The researchers concluded that the Clovis infant belonged to a meta-population from which many contemporary Native Americans are descended and is closely related to all indigenous American populations. In essence, contemporary Native Americans are “effectively direct descendants of the people who made and used Clovis tools and buried this child,” covering it with red ochre.

Furthermore, the data refutes the possibility that Clovis originated via a European, Solutrean, migration to the Americas.

I would certainly be interested to see this same type of analysis performed on remains from the eastern Canadian or eastern seaboard United States on the earliest burials. Pre-contact European admixture has been a hotly contested question, especially in the Hudson Bay region, for a very long time, but we have yet to see any pre-Columbus era contact burials that produce any genetic evidence of such.

Additionally, the Ohio burial suggests that perhaps the mitochondrial DNA haplogroup is or was more widespread geographically in North American than is known today. A wider comparison to Native American DNA would be beneficial, were it possible. A quick look at various Native DNA and haplogroup projects at Family Tree DNA doesn’t show this haplogroup in locations outside of the ones discussed here. Haplogroup Q, of course, is ubiquitous in the Native population.

National Geographic article about this revelation including photos of where the remains were found. They can make a tuft of grass look great!

Another article can be found at Voice of America News.

Science has a bit more.

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Neanderthal Genome Further Defined in Contemporary Eurasians

Posted on January 30, 2014 by Roberta Estes

A new study released by Howard Hughes Medical Institute at Harvard Medical School on January 29^th titled “When Populations Collide” provides some interesting insights about Neanderthal DNA in modern humans. This study compared the full Neanderthal genome to that of 1004 living individuals.

In general, people in East Asia carry more Neanderthal than Europeans who carry 1-3%, and Africans carry none or very little. It appears, according to David Reich, that Neanderthal DNA is not proportionately represented in contemporary humans, meaning that some areas of Neanderthal DNA are commonly found and others not at all. Some Neanderthal genes are carried by more than 60% of Europeans or Asians, most often associated with skin and hair color, or keratin. Reich’s thought is that people exiting Africa assimilated with Neanderthals and selected for these genes that gave them an adaptive and survival advantage in the cooler non-African climate.

One particularly big Neanderthal genetic desert is the X chromosome, a phenomenon called hybrid sterility. Reich suggests that this means that when Neanderthals and humans exiting from Africa interbred, they were on the cusp of being unable to reproduce successfully. Reich explains that “when two populations are distantly related, genes related to fertility inherited on the X chromosome can interact poorly with genes elsewhere in the genome and that interference can render males, who carry only one X, sterile.”

Given the recent discussions about the X chromosome and the possibility that it may be inherited in an all-or-nothing manner more often than the other chromosomes, I had to wonder how they determined that this was hybrid sterility and not an case of absence of recombination.

Reich’s team apparently had the same question, so they evaluated the genes related to the function of the testes, confirming they too had a particularly low inheritance frequency of Neanderthal DNA. These, combined, would eventually cause the X to be present in very small quantities in the genome of descendants since the Neanderthal X could only be inherited from women and then would cause the resulting males to be sterile. So in essence, only females could pass the X on and only their daughters would pass it further. Males carrying that X not only wouldn’t pass the X, they wouldn’t pass anything at all due to sterility.

If, in addition to this, the X has unusual recombination features, that could exacerbate the situation. Conversely, if the X is inherited intact more often than not at all, it could increase the likelihood of the X being brought forward in the population.

Reich says his team is now focused on looking at Neanderthal DNA and human disease genes. He says that his new study revealed that lupus, diabetes and Crohn’s Disease likely originate from Neanderthals.

Another study, published the same day in Science titled “Resurrecting Surviving Neandertal Lineages from Modern Human Genomes,” reaches the same conclusions about the Neanderthal inherited traits related to skin color. This study compared the full genomes of 379 East Asians and 286 Europeans to Neanderthal genomes and discovered that they could map about 20% of the Neanderthal DNA in those individuals today. This, conversely, means that 80% of the Neanderthal genome is missing, so either truly missing or simply missing in the people whose DNA they sequenced. It will be interesting to see what is found as more contemporary genetic sequences are compared against Neanderthal, and as more Neanderthal DNA is found and sequenced.

Fortunately, recent advances in dealing with contaminated ancient DNA hold a great deal of promise in terms of increasing our ability to sequence DNA that was previously thought to be useless. This report is described in the article “Separating endogenous ancient DNA from modern day contamination in a Siberian Neanderthal” and was used in the sequencing and analysis of the Neanderthal toe bone found in Siberia.

To better understand the legacy of Neanderthals, Dr. Reich and his colleagues are collaborating with the UK Biobank, which collects genetic information from hundreds of thousands of volunteers. The scientists will search for Neanderthal genetic markers, and investigate whether Neanderthal genes cause any noticeable differences in anything from weight to blood pressure to scores on memory tests.

“This experiment of nature has been done,” says Dr. Reich, “and we can study it.”

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Stonehenge

Posted on January 16, 2014 by Roberta Estes

You know, there are just some things in this world that defy words. Some things are stunning in photos, but in person, they are absolutely unspeakable – there are no words adequate to describe them. Overwhelming, majestic, none of those words are “enough.”

Stonehenge is one of those places. Maybe that’s why people have been attracted here for thousands of years. It’s a magnet calling to our human spirit.

This was my second day in London. Jim and I had just spent a rather sleepless night in the Kenner’s Easy Bake Oven, a very small hotel room with no air conditioning, in a heat wave. However, nothing was going to keep us from visiting Stonehenge, so off we went to find the tour company, something much easier said than done, it turns out.

We wanted to sign up for a bus tour, but the company said we had to come down to their office to physically make those arrangements, in person. So, we took a subway tour by accident to get to the bus tour. Thank Heavens we left lots of time. To get to Stonehenge from London, you ride about 2 hours each way on the bus through what I would term nondescript farmland for the hour and a half visit at Stonehenge, but it was worth every minute of that ride and even being lost on the subway too.

But Jim and I had a special treat. Our breakfast was included in our hotel room. It was a real breakfast too, not just cereal and milk. I think it’s because they felt guilty about that Kenner’s Easy Bake Oven thing. In any case, the breakfast was really wonderful. It included several kinds of fresh baked breads, cheeses including brie and freshly made raspberry jelly sitting in little jelly cups in icewater so they would set up quickly.

They also had normal breakfast things like eggs and “bacon” which was really good and not bacon as we know it in the US, and baked beans, which is a breakfast staple in England. This rather unique combination, complete with tomatoes and mushrooms, is known as the English Full Breakfast and you can see some pictures here. And yes, it does include “blood pudding” also known as black pudding which isn’t pudding at all. There is a picture of me trying that…but I won’t publish it. I will try almost anything once, and I did, and guaranteed, there will not be a second time.

I decided that the freshly baked bread was calling to me and so was the cheese. Not only is that my farm upbringing, but it’s also the result of living in Switzerland as a student. It’s all coming back now and I have this indescribable urge to have some wine with my bread and cheese:)

I noticed that the tour description said nothing about food, nor about stopping anyplace, so I presumed we needed to be prepared. Let me translate – go to the bathroom just before leaving and take food or water or anything you’re going to need.

So, I made us a picnic lunch. It was the best lunch ever, with petit pain and brie and jelly (in packets, not the homemade raspberry – no way to transport that) and a banana and a pear and a tomato slice. Yepper, a killer picnic lunch and we had it sitting on the grass at Stonehenge. It was really squishy, but it was really, really good. And yes, we had to lick our fingers. Welcome to our picnic at Stonehenge. After we ate, we took pictures from our picnic site. I mean, how many times in your life do you get to picnic at Stonehenge?

Jim, by the way, refuses to smile in photos. Still, I think this one is very cool. He’s thinking about smiling and trying hard not to! BTW – this photo is now on the cover of Jim’s iphone – a nifty Christmas gift!

There are lots of theories and myths about Stonehenge, the why and how, including aliens and Merlin, but the truth is that no one really knows why it was created, or how, or by whom. However, no culture would invest so much time and labor into something that wasn’t sacred to them in some way.

Below, the oldest known depiction of Stonehenge.

From a manuscript of the Roman de Brut by Wace in the British Library (Egerton 3028), a giant helps Merlin build Stonehenge.

You can’t sit in the beauty and majesty of his incredible monument without pondering and thinking, about Stonehenge itself, and also about the people who created this megalithic structure. And I wondered of course, if I was related to them. Are they my ancestors? I certainly have several British Isles ancestors. Were some of them here then? Did they participate in some way, either in building the monument or whatever form of worship followed? What do we know about Stonehenge?

Stonehenge is a prehistoric monument in Wiltshire, England, about 2 miles (3.2 km) west of Amesbury and 8 miles (13 km) north of Salisbury. One of the most famous sites in the world, Stonehenge is the remains of a ring of standing stones set within earthworks. It is in the middle of the most dense complex of Neolithic and Bronze Age monuments in England, including several hundred burial mounds. It sits simply in the middle of a plain. In fact, while driving through that area, there are little burial mounds everyplace. This is through the bus window, so pardon the glare on the glass. The mounds are to the right and also in the distance mid-photo.

Archaeologists believe Stonehenge was built anywhere from 3000 BC to 2000 BC. Radiocarbon dating in 2008 suggested that the first stones were raised between 2400 and 2200 BC, whilst another theory suggests that the bluestones, from Wales, may have been raised at the site as early as 3000 BC

Stonehenge was built in three phases between 3000 B.C. and 1600 B.C. Archaeologists agree it was a temple — but to what god or gods, and exactly how it was used, remains unclear.

Archaeological evidence found by the Stonehenge Riverside Project in 2008 indicates that Stonehenge could have been a burial ground from its earliest beginnings for elite families. The dating of cremated remains found on the site indicate that deposits contain human bone from as early as 3000 BC, when the ditch and bank were first dug. These burials locations are marked by bluestones. The Stonehenge stones may be the largest headstones ever! Such deposits continued at Stonehenge for at least another 500 years.

Stones for Stonehenge, much of which still stands, were brought from up to 175 miles (280 kilometers) away. Construction continued for centuries, and the site may have been a temple for Druid worship, a giant astronomical calendar, a place of healing, or maybe all of the above.

Evidence suggests large crowds gathered at Stonehenge for the summer and winter solstices, a tradition that continues today.

Senior curator Sara Lunt says there are still major discoveries to be made — more than half the site remains unexcavated. But the original purpose of Stonehenge may remain a mystery.

“We know there was a big idea” behind Stonehenge and other stone circles built across the British Isles in the Neolithic period, she said. But “what the spiritual dimension of this idea is — that is the key, and that is what we can’t get.”

The surrounding circular earth bank and ditch, which constitute the earliest phase of the monument, have been dated to about 3100 BC. The site and its surroundings were added to the UNESCO’s list of World Heritage Sites in 1986 in a co-listing with Avebury Henge. Stonehenge is owned by the Crown and managed by English Heritage, while the surrounding land is owned by the National Trust.

When we were visiting, they were in the process of completing a new visitor’s center. We didn’t see the new center, as it is about a mile and a half away and completely out of view. The then-current center is just out of sight of Stonehenge itself. The idea of the new center is to remove all of the modern day trappings and distractions, including motor noise, so that visitors can enjoy the monument in a more pristine and natural environment. That seemed to be a very volatile subject and not everyone is happy about the changes.

Recently the new facility was opened.

Among the exhibits in the new facility is the reconstructed face of one 5,000-year-old local resident from his skull. Oscar Nilsson, a forensic sculptor, created the bust and says that he had good teeth and handsome features, in a shaggy, prehistoric kind of way. Actually, I think he looks uncannily like my x-husband on a good day….which kind of gives me the creeps and makes me desperately want to know about his haplogroup.

I was very disappointed to discover that they have not, to date, performed DNA testing. My inquiry to English Heritage about DNA testing on these and other remains found in close proximity received the following reply:

Dear Ms Estes,

Many thanks for your email regarding the human remains on display at the new Stonehenge visitor and exhibition centre. I have been asked to respond on behalf of the Project team.

Dr Simon Mays, Senior Osteologist for English Heritage has provided the Interpretation and Curatorial team with some information regarding further testing following the recent sampling carried out on the Winterbourne Stoke 1 human remains that he guided. He advises that analysis of DNA is destructive and we would only consider using such a technique on ancient material if the results would help to answer compelling questions about the human remains that could not be answered in any other way: only then would the destruction of a piece of human bone be ethically justifiable. In this case, DNA analysis was not relevant to the questions that we considered important, which included the man’s place of origin and early development, his mobility and his age at death.

Although a fairly common procedure nowadays for historic and recent material, attempts to extract DNA from ancient skeletons fails in the majority of cases because of, inter alia, poor preservation of the relevant molecule. When DNA does survive from ancient material, it is often in very poor condition, so the information it can supply is strictly limited.

Any destructive analysis that English Heritage might wish to carry out in the future on the human remains in the Visitor Centre would be subject to the agreement of the institutions which have loaned them to English Heritage.

I hope this goes some way to answer your query, but please let me know if you need further information.
Kind regards,

Rebecca Thomas

Stonehenge Programme & Finance Co-ordinator
29 Queen Square | Bristol | BS1 4ND
Tel: 0117 975 1301 (internal 2301)
Rebecca.Thomas@english-heritage.org.uk

Let’s hope they reconsider in the future. If you have feedback for them about how DNA won’t answer questions about the history of this man…their contact information is listed above. I encourage you to share your opinion with them and perhaps ask some pointed questions. I have to wonder if any of the cremains might be a possibility. They are already “destroyed,” so to speak, and the heat of the cremation fire might not have been hot enough to destroy all of the DNA. I know that contemporary cremations are at much higher temperatures and do destroy the DNA. It might be worth having Dr. King or another individual who has successfully extracted ancient DNA do an evaluation. Furthermore, while they are accurate, the process is destructive – it is minimally so. A small piece of bone needs to be drilled – significantly smaller than a tooth. It seems a shame not to utilize the tools available to us.

I have to wonder just who this reconstructed man is, in terms of ancient ancestry and clans. Were these people from Europe or Scandinavia, perhaps? Were they haplogroup R, like about half of Europe is today, or would they carry a different haplotype?

Recent work by Dr. Michael Hammer and first presented at the Family Tree DNA Administrators Conference in November of 2013 indicated that there was no early haplogroup R yet found in early burials. Initially, haplogroup R1b had been thought to have overwintered the ice ace about 12,000 years ago in Anatolia and Iberia, repopulating Europe after the ice melted. However, if that is true, then were are the R1b burials? Instead, we are finding haplogroup G and I and some E, but not any R. The first site to show any haplogroup R is R1b from a German Bell Beaker site dated to the third millennium BCE, or about 5,000 years ago.

The Neolithic timeframe covers the expansion of agriculture from the Middle East across Europe beginning about 10,000 BC and continuing across Europe to about 5,000 BC. Haplogroup R, it appears, did not accompany this expansion, but arrived later, post-Neolithic, potentially with the Bell Beaker Culture between 2,000 and 3,000 BC.

This culture is named after its distinctly shaped drinking vessels.

3,500 years old, 40 cm (16 in) high “Giant Beaker of Pavenstädt”, Gütersloh town museum, Germany. Other Beaker culture items, below.

It’s also believed that mitochondrial haplogroup H spread into Europe with the Bell Beaker culture as well.

Beakers arrived in Britain around 2500 BC, declined in use around 2200-2100 BC with the emergence of food vessels and cinerary urns and finally fell out of use around 1700 BC. The earliest British beakers were similar to those from the Rhine but later styles are most similar to those from Ireland In Britain, domestic assemblages from this period are very rare, making it hard to draw conclusions about many aspects of society. Most British beakers come from funerary contexts.

From Wiki, this map shows the generalized movement of the Bell Baker culture.

The most famous site in Britain from this period is…drum roll please…Stonehenge. Many barrows surround it and an unusual number of ‘rich’ burials can be found nearby, such as the Amesbury Archer who lived contemporarily with the construction of portions of Stonehenge.

The Amesbury Archer is an early Bronze Age man whose grave was discovered during excavations at the site of a new housing development in Amesbury near Stonehenge. The grave was uncovered in May 2002, and the man is believed to date from about 2300 BC. He is nicknamed the “archer” because of the many arrowheads that were among the artifacts buried with him. Had he lived near the Stones, the calibrated radiocarbon dates for his grave and dating of Stonehenge suggest the sarsens and trilithons at Stonehenge may have been raised by the time he was born, although a new bluestone circle may have been raised at the same time as his birth.

In spite of what English Heritage said, DNA testing could help answer many of these questions about who these early people were, where they came from and who they were descended from and related to.

When we visited Stonehenge, the guide suggested that historically there may have been processions from Avesbury, across the Salisbury plain, following the Avon River and then up the hill to Stonehenge. The Avon River, 2 miles distant, and with parallel ditches leading from Stonehenge to the River, is theorized to be how the stones were transported to the Salisbury Plain from their origins in Wales, hundreds of miles distant.

Evidence on the banks of the river of huge fires between two avenues connecting Stonehenge with another nearby Neolithic site, Durrington Walls, shown below, suggests that both sites were linked.

I discovered, with a little googling, that indeed, contemporary visitors have been retracing this exact trail and are attempting to establish a historical walk, of sorts, shown below.

I can’t help but think how wonderful this would be, to retrace the steps of the original people of Avesbury and the Salisbury plains, whoever they were. Hugh Thomson, the author of the “Magic Circles” article hyperlinked above, probably sums it up the best with this commentary:

“I can’t help thinking how much better it is to arrive at Stonehenge on foot. The comparison that comes to mind, and which I know well, is the Inca Trail to Machu Picchu. The experience of trekking to both sites is immeasurably richer, not just because you’ve “earned it”, but because both sets of ruins are only properly understood in the context of the sacred landscape that surrounds them.”

It’s probably much different that arriving on a tour bus after being lost on the subway.

If I ever return to England, I’ll have to come back to Stonehenge. I would very much like to visit at sunrise and now, I’d like to retrace the walk of the original inhabitants, whoever they were. And yes, I’d like to know if I might be distantly related to one of these people buried in these barrows, shown below, surrounding Stonehenge. Think how you’d feel standing here if you knew your ancestors did as well. It could only enhance the visitor experience and the science would, of course, help resolve the many unknowns in the history of Stonehenge. I hope English Heritage gets their curiosity peaked and reconsiders DNA testing, as they seem a bit behind the curve. After all, they have Dr. Turi King, with the University of Leicester, of King Richard fame, quite nearby.

Truly, we had a wonderful day at Stonehenge. The weather was perfect, no rain and sunny. Beautiful photos. Just a few people here, no large crowds, and our lovely picnic.

After our visit, on the bus on the way back to London, I thought, “guess I can check this off of my bucket list,” but then I realized, I really don’t have a bucket list. My life has provided me with so many rich opportunities that I never dreamed that I would have. I never imagined that I would ever have the opportunity to visit Stonehenge, so it actually wasn’t ON my bucket list. However, now that I’ve been here, I’d love to come back.

You know, there’s something wrong with this picture. I thought you visited places to check them off the list, not to add them to the list as a return visit! But Stonehenge, well, it’s a magical place, and it will do that to you…consider this fair warning!

Resources:

http://www.independent.co.uk/news/science/archaeology/before-stonehenge–did-this-man-lord-it-over-wiltshires-sacred-landscape-9008683.html

http://www.theguardian.com/science/2013/mar/09/archaeology-stonehenge-bones-burial-ground

http://finance.yahoo.com/news/ancient-stonehenge-gets-modern-day-092304265.html

http://www.english-heritage.org.uk/daysout/properties/stonehenge/

http://en.wikipedia.org/wiki/Amesbury_Archer

http://en.wikipedia.org/wiki/Beaker_culture

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2013’s Dynamic Dozen – Top Genetic Genealogy Happenings

Posted on December 28, 2013 by Roberta Estes

Last year I wrote a column at the end of the year titled “2012 Top 10 Genetic Genealogy Happenings.” It’s amazing the changes in this industry in just one year. It certainly makes me wonder what the landscape a year from now will look like.

I’ve done the same thing this year, except we have a dozen. I couldn’t whittle it down to 10, partly because there has been so much more going on and so much change – or in the case of Ancestry, who is noteworthy because they had so little positive movement.

If I were to characterize this year of genetic genealogy, I would call it The Year of the SNP, because that applies to both Y DNA and autosomal. Maybe I’d call it The Legal SNP, because it is also the year of law, court decisions, lawsuits and FDA intervention. To say it has been interesting is like calling the Eiffel Tower an oversized coat hanger.

I’ll say one thing…it has kept those of us who work and play in this industry hopping busy! I guarantee you, the words “I’m bored” have come out of the mouth of no one in this industry this past year.

I’ve put these events in what I consider to be relatively accurate order. We could debate all day about whether the SNP Tsunami or the 23andMe mess is more important or relevant – and there would be lots of arguing points and counterpoints…see…I told you lawyers were involved….but in reality, we don’t know yet, and in the end….it doesn’t matter what order they are in on the list:)

Y Chromosome SNP Tsunami Begins

The SNP tsumani began as a ripple a few years ago with the introduction at Family Tree DNA of the Walk the Y program in 2007. This was an intensively manual process of SNP discovery, but it was effective.

By the time that the Geno 2.0 chip was introduced in 2012, 12,000+ SNPs would be included on that chip, including many that were always presumed to be equivalent and not regularly tested. However, the Nat Geo chip tested them and indeed, the Y tree became massively shuffled. The resolution to this tree shuffling hasn’t yet come out in the wash. Family Tree DNA can’t really update their Y tree until a publication comes out with the new tree defined. That publication has been discussed and anticipated for some time now, but it has yet to materialize. In the mean time, the volunteers who maintain the ISOGG tree are swamped, to say the least.

Another similar test is the Chromo2 introduced this year by Britain’s DNA which scans 15,000 SNPs, many of them S SNPs not on the tree nor academically published, adding to the difficulty of figuring out where they fit on the Y tree. While there are some very happy campers with their Chromo2 results, there is also a great deal of sloppy science, reporting and interpretation of “facts” through this company. Kind of like Jekyll and Hyde. See the Sloppy Science section.

But Walk the Y, Chromo2 and Geno 2.0, are only the tip of the iceburg. The new “full Y” sequencing tests brought into the marketspace quietly in early 2013 by Full Genomes and then with a bang by Family Tree DNA with the their Big Y in November promise to revolutionize what we know about the Y chromosome by discovering thousands of previously unknown SNPs. This will in effect swamp the Y tree whose branches we thought were already pretty robust, with thousands and thousands of leaves.

In essence, the promise of the “fully” sequenced Y is that what we might term personal or family SNPs will make SNP testing as useful as STR testing and give us yet another genealogy tool with which to separate various lines of one genetic family and to ratchet down on the time that the most common recent ancestor lived.

http://dna-explained.com/2013/03/31/new-y-dna-haplogroup-naming-convention/

http://dna-explained.com/2013/11/10/family-tree-dna-announces-the-big-y/

http://dna-explained.com/2013/11/16/what-about-the-big-y/

http://www.yourgeneticgenealogist.com/2013/11/first-look-at-full-genomes-y-sequencing.html

http://cruwys.blogspot.com/2013/12/a-first-look-at-britainsdna-chromo-2-y.html

http://cruwys.blogspot.com/2013/11/yseqnet-new-company-offering-single-snp.html

http://cruwys.blogspot.com/2013/11/the-y-chromosome-sequence.html

http://cruwys.blogspot.com/2013/11/a-confusion-of-snps.html

http://cruwys.blogspot.com/2013/11/a-simplified-y-tree-and-common-standard.html

23andMe Comes Unraveled

The story of 23andMe began as the consummate American dotcom fairy tale, but sadly, has deteriorated into a saga with all of the components of a soap opera. A wealthy wife starts what could be viewed as an upscale hobby business, followed by a messy divorce and a mystery run-in with the powerful overlording evil-step-mother FDA. One of the founders of 23andMe is/was married to the founder of Google, so funding, at least initially wasn’t an issue, giving 23andMe the opportunity to make an unprecedented contribution in the genetic, health care and genetic genealogy world.

Another way of looking at this is that 23andMe is the epitome of the American Dream business, a startup, with altruism and good health, both thrown in for good measure, well intentioned, but poorly managed. And as customers, be it for health or genealogy or both, we all bought into the altruistic “feel good” culture of helping find cures for dread diseases, like Parkinson’s, Alzheimer’s and cancer by contributing our DNA and responding to surveys.

The genetic genealogy community’s love affair with 23andMe began in 2009 when 23andMe started focusing on genealogy reporting for their tests, meaning cousin matches. We, as a community, suddenly woke up and started ordering these tests in droves. A few months later, Family Tree DNA also began offering this type of testing as well. The defining difference being that 23andMe’s primary focus has always been on health and medical information with Family Tree DNA focused on genetic genealogy. To 23andMe, the genetic genealogy community was an afterthought and genetic genealogy was just another marketing avenue to obtain more people for their health research data base. For us, that wasn’t necessarily a bad thing.

For awhile, this love affair went along swimmingly, but then, in 2012, 23andMe obtained a patent for Parkinson’s Disease. That act caused a lot of people to begin to question the corporate focus of 23andMe in the larger quagmire of the ethics of patenting genes as a whole. Judy Russell, the Legal Genealogist, discussed this here. It’s difficult to defend 23andMe’s Parkinson’s patent while flaying alive Myriad for their BRCA patent. Was 23andMe really as altruistic as they would have us believe?

Personally, this event made me very nervous, but I withheld judgment. But clearly, that was not the purpose for which I thought my DNA, and others, was being used.

But then came the Designer Baby patent in 2013. This made me decidedly uncomfortable. Yes, I know, some people said this really can’t be done, today, while others said that it’s being done anyway in some aspects…but the fact that this has been the corporate focus of 23andMe with their research, using our data, bothered me a great deal. I have absolutely no issue with using this information to assure or select for healthy offspring – but I have a personal issue with technology to enable parents who would select a “beauty child,” one with blonde hair and blue eyes and who has the correct muscles to be a star athlete, or cheerleader, or whatever their vision of their as-yet-unconceived “perfect” child would be. And clearly, based on 23andMe’s own patent submission, that is the focus of their patent.

Upon the issuance of the patent, 23andMe then said they have no intention of using it. They did not say they won’t sell it. This also makes absolutely no business sense, to focus valuable corporate resources on something you have no intention of using? So either they weren’t being truthful, they lack effective management or they’ve changed their mind, but didn’t state such.

What came next, in late 2013 certainly points towards a lack of responsible management.

23andMe had been working with the FDA for approval the health and medical aspect of their product (which they were already providing to consumers prior to the November 22^nd cease and desist order) for several years. The FDA wants assurances that what 23andMe is telling consumers is accurate. Based on the letter issued to 23andMe on November 22^nd, and subsequent commentary, it appears that both entities were jointly working towards that common goal…until earlier this year when 23andMe mysteriously “somehow forgot” about the FDA, the information they owed them, their submissions, etc. They also forgot their phone number and their e-mail addresses apparently as well, because the FDA said they had heard nothing from them in 6 months, which backdates to May of 2013.

It may be relevant that 23andMe added the executive position of President and filled it in June of 2013, and there was a lot of corporate housecleaning that went on at that time. However, regardless of who got housecleaned, the responsibility for working with the FDA falls squarely on the shoulders of the founders, owners and executives of the company. Period. No excuses. Something that critically important should be on the agenda of every executive management meeting. Why? In terms of corporate risk, this was obviously a very high risk item, perhaps the highest risk item, because the FDA can literally shut their doors and destroy them. There is little they can do to control or affect the FDA situation, except to work with the FDA, meet deadlines and engender goodwill and a spirit of cooperation. The risk of not doing that is exactly what happened.

It’s unknown at this time if 23andMe is really that corporately arrogant to think they could simply ignore the FDA, or blatantly corporately negligent or maybe simply corporately stupid, but they surely betrayed the trust and confidence of their customers by failing to meet their commitments with and to the FDA, or even communicate with them. I mean, really, what were they thinking?

There has been an outpouring of sympathy for 23andme and negative backlash towards the FDA for their letter forcing 23andMe to stop selling their offending medical product, meaning the health portion of their testing. However, in reality, the FDA was only meting out the consequences that 23andMe asked for. My teenage kids knew this would happen. If you do what you’re not supposed to….X, Y and Z will, or won’t, happen. It’s called accountability. Just ask my son about his prom….he remembers vividly. Now why my kids, or 23andMe, would push an authority figure to that point, knowing full well the consequences, utterly mystifies me. It did when my son was a teenager and it does with 23andMe as well.

Some people think that the FDA is trying to stand between consumers and their health information. I don’t think so, at least not in this case. Why I think that is because the FDA left the raw data files alone and they left the genetic genealogy aspect alone. The FDA knows full well you can download your raw data and for $5 process it at a third party site, obtaining health related genetic information. The difference is that Promethease is not interpreting any data for you, only providing information.

There is some good news in this and that is that from a genetic genealogy perspective, we seem to be safe, at least for now, from government interference with the testing that has been so productive for genetic genealogy. The FDA had the perfect opportunity to squish us like a bug (thanks to the opening provided by 23andMe,) and they didn’t.

The really frustrating aspect of this is that 23andMe was a company who, with their deep pockets in Silicon Valley and other investors, could actually afford to wage a fight with the FDA, if need be. The other companies who received the original 2010 FDA letter all went elsewhere and focused on something else. But 23andMe didn’t, they decided to fight the fight, and we all supported their decision. But they let us all down. The fight they are fighting now is not the battle we anticipated, but one brought upon themselves by their own negligence. This battle didn’t have to happen, and it may impair them financially to such a degree that if they need to fight the big fight, they won’t be able to.

Right now, 23andMe is selling their kits, but only as an ancestry product as they work through whatever process they are working through with the FDA. Unfortunately, 23andMe is currently having some difficulties where the majority of matches are disappearing from some testers records. In other cases, segments that previously matched are disappearing. One would think, with their only revenue stream for now being the genetic genealogy marketspace that they would be wearing kid gloves and being extremely careful, but apparently not. They might even consider making some of the changes and enhancements we’ve requested for so long that have fallen on deaf ears.

One thing is for sure, it will be extremely interesting to see where 23andMe is this time next year. The soap opera continues.

I hope for the sake of all of the health consumers, both current and (potentially) future, that this dotcom fairy tale has a happy ending.

Also, see the Autosomal DNA Comes of Age section.

http://dna-explained.com/2013/10/05/23andme-patents-technology-for-designer-babies/

http://www.thegeneticgenealogist.com/2013/10/07/a-new-patent-for-23andme-creates-controversy/

http://dna-explained.com/2013/11/13/genomics-law-review-discusses-designing-children/

http://www.thegeneticgenealogist.com/2013/06/11/andy-page-fills-new-president-position-at-23andme/

http://dna-explained.com/2013/11/25/fda-orders-23andme-to-discontinue-testing/

http://dna-explained.com/2013/11/26/now-what-23andme-and-the-fda/

http://dna-explained.com/2013/12/06/23andme-suspends-health-related-genetic-tests/

http://www.legalgenealogist.com/blog/2013/11/26/fooling-with-fda/

Supreme Court Decision – Genes Can’t Be Patented – Followed by Lawsuits

In a landmark decision, the Supreme Court determined that genes cannot be patented. Myriad Genetics held patents on two BRCA genes that predisposed people to cancer. The cost for the tests through Myriad was about $3000. Six hours after the Supreme Court decision, Gene By Gene announced that same test for $995. Other firms followed suit, and all were subsequently sued by Myriad for patent infringement. I was shocked by this, but as one of my lawyer friends clearly pointed out, you can sue anyone for anything. Making it stick is yet another matter. Many firms settle to avoid long and very expensive legal battles. Clearly, this issue is not yet resolved, although one would think a Supreme Court decision would be pretty definitive. It potentially won’t be settled for a long time.

http://dna-explained.com/2013/06/13/supreme-court-decision-genes-cant-be-patented/

http://www.legalgenealogist.com/blog/2013/06/14/our-dna-cant-be-patented/

http://dna-explained.com/2013/09/07/message-from-bennett-greenspan-free-my-genes/

http://www.thegeneticgenealogist.com/2013/06/13/new-press-release-from-dnatraits-regarding-the-supreme-courts-holding-in-myriad/

http://www.legalgenealogist.com/blog/2013/08/18/testing-firms-land-counterpunch/

http://www.legalgenealogist.com/blog/2013/07/11/myriad-sues-genetic-testing-firms/

Gene By Gene Steps Up, Ramps Up and Produces

As 23andMe comes unraveled and Ancestry languishes in its mediocrity, Gene by Gene, the parent company of Family Tree DNA has stepped up to the plate, committed to do “whatever it takes,” ramped up the staff both through hiring and acquisitions, and is producing results. This is, indeed, a breath of fresh air for genetic genealogists, as well as a welcome relief.

http://dna-explained.com/2013/08/07/gene-by-gene-acquires-arpeggi/

http://dna-explained.com/2013/12/05/family-tree-dna-listens-and-acts/

http://dna-explained.com/2013/12/10/family-tree-dnas-family-finder-match-matrix-released/

http://www.haplogroup.org/ftdna-family-finder-matches-get-new-look/

http://www.haplogroup.org/ftdna-family-finder-new-look-2/

http://www.haplogroup.org/ftdna-family-finder-matches-new-look-3/

Autosomal DNA Comes of Age

Autosomal DNA testing and analysis has simply exploded this past year. More and more people are testing, in part, because Ancestry.com has a captive audience in their subscription data base and more than a quarter million of those subscribers have purchased autosomal DNA tests. That’s a good thing, in general, but there are some negative aspects relative to Ancestry, which are in the Ancestry section.

Another boon to autosomal testing was the 23andMe push to obtain a million records. Of course, the operative word here is “was” but that may revive when the FDA issue is resolved. One of the down sides to the 23andMe data base, aside from the fact that it’s not genealogist friendly, is that so many people, about 90%, don’t communicate. They aren’t interested in genealogy.

A third factor is that Family Tree DNA has provided transfer ability for files from both 23andMe and Ancestry into their data base.

Fourth is the site, GedMatch, at www.gedmatch.com which provides additional matching and admixture tools and the ability to match below thresholds set by the testing companies. This is sometimes critically important, especially when comparing to known cousins who just don’t happen to match at the higher thresholds, for example. Unfortunately, not enough people know about GedMatch, or are willing to download their files. Also unfortunate is that GedMatch has struggled for the past few months to keep up with the demand placed on their site and resources.

A great deal of time this year has been spent by those of us in the education aspect of genetic genealogy, in whatever our capacity, teaching about how to utilize autosomal results. It’s not necessarily straightforward. For example, I wrote a 9 part series titled “The Autosomal Me” which detailed how to utilize chromosome mapping for finding minority ethnic admixture, which was, in my case, both Native and African American.

As the year ends, we have Family Tree DNA, 23andMe and Ancestry who offer the autosomal test which includes the relative-matching aspect. Fortunately, we also have third party tools like www.GedMatch.com and www.DNAGedcom.com, without which we would be significantly hamstrung. In the case of DNAGedcom, we would be unable to perform chromosome segment matching and triangulation with 23andMe data without Rob Warthen’s invaluable tool.

http://dna-explained.com/2013/06/21/triangulation-for-autosomal-dna/

http://dna-explained.com/2013/07/13/combining-tools-autosomal-plus-y-dna-mtdna-and-the-x-chromosome/

http://dna-explained.com/2013/07/26/family-tree-dna-levels-the-playing-field-sort-of/

http://dna-explained.com/2013/08/03/kitty-coopers-chromsome-mapping-tool-released/

http://dna-explained.com/2013/09/29/why-dont-i-match-my-cousin/

http://dna-explained.com/2013/10/03/family-tree-dna-updates-family-finder-and-adds-triangulation/

http://dna-explained.com/2013/10/21/why-are-my-predicted-cousin-relationships-wrong/

http://dna-explained.com/2013/12/05/family-tree-dna-listens-and-acts/

http://dna-explained.com/2013/12/09/chromosome-mapping-aka-ancestor-mapping/

http://dna-explained.com/2013/12/10/family-tree-dnas-family-finder-match-matrix-released/

http://dna-explained.com/2013/12/15/one-chromosome-two-sides-no-zipper-icw-and-the-matrix/

http://dna-explained.com/2013/06/02/the-autosomal-me-summary-and-pdf-file/

DNAGedcom – Indispensable Third Party Tool

While this tool, www.dnagedcom.com, falls into the Autosomal grouping, I have separated it out for individual mention because without this tool, the progress made this year in autosomal DNA ancestor and chromosomal mapping would have been impossible. Family Tree DNA has always provided segment matching boundaries through their chromosome browser tool, but until recently, you could only download 5 matches at a time. This is no longer the case, but for most of the year, Rob’s tool saved us massive amounts of time.

23andMe does not provide those chromosome boundaries, but utilizing Rob’s tool, you can obtain each of your matches in one download, and then you can obtain the list of who your matches match that is also on your match list by requesting each of those files separately. Multiple steps? Yes, but it’s the only way to obtain this information, and chromosome mapping without the segment data is impossible

A special hats off to Rob. Please remember that Rob’s site is free, meaning it’s donation based. So, please donate if you use the tool.

http://www.yourgeneticgenealogist.com/2013/01/brought-to-you-by-adoptiondna.html

I covered www.Gedmatch.com in the “Best of 2012” list, but they have struggled this year, beginning when Ancestry announced that raw data file downloads were available. GedMatch consists of two individuals, volunteers, who are still struggling to keep up with the required processing and the tools. They too are donation based, so don’t forget about them if you utilize their tools.

Ancestry – How Great Thou Aren’t

Ancestry is only on this list because of what they haven’t done. When they initially introduced their autosomal product, they didn’t have any search capability, they didn’t have a chromosome browser and they didn’t have raw data file download capability, all of which their competitors had upon first release. All they did have was a list of your matches, with their trees listed, with shakey leaves if you shared a common ancestor on your tree. The implication, was, and is, of course, that if you have a DNA match and a shakey leaf, that IS your link, your genetic link, to each other. Unfortunately, that is NOT the case, as CeCe Moore documented in her blog from Rootstech (starting just below the pictures) as an illustration of WHY we so desperately need a chromosome browser tool.

In a nutshell, Ancestry showed the wrong shakey leaf as the DNA connection – as proven by the fact that both of CeCe’s parents have tested at Ancestry and the shakey leaf person doesn’t match the requisite parent. And there wasn’t just one, not two, but three instances of this. What this means is, of course, that the DNA match and the shakey leaf match are entirely independent of each other. In fact, you could have several common ancestors, but the DNA at any particular location comes only from one on either Mom or Dad’s side – any maybe not even the shakey leaf person.

So what Ancestry customers are receiving is a list of people they match and possible links, but most of them have no idea that this is the case, and blissfully believe they have found their genetic connection. They have found a genealogical cousin, and it MIGHT be the genetic connection. But then again, they could have found that cousin simply by searching for the same ancestor in Ancestry’s data base. No DNA needed.

Ancestry has added a search feature, allowed raw data file downloads (thank you) and they have updated their ethnicity predictions. The ethnicity predictions are certainly different, dramatically different, but equally as unrealistic. See the Ethnicity Makeovers section for more on this. The search function helps, but what we really need is the chromosome browser, which they have steadfastly avoided promising. Instead, they have said that they will give us “something better,” but nothing has materialized.

I want to take this opportunity, to say, as loudly as possible, that TRUST ME IS NOT ACCEPTABLE in any way, shape or form when it comes to genetic matching. I’m not sure what Ancestry has in mind by the way of “better,” but it if it’s anything like the mediocrity with which their existing DNA products have been rolled out, neither I nor any other serious genetic genealogist will be interested, satisfied or placated.

Regardless, it’s been nearly 2 years now. Ancestry has the funds to do development. They are not a small company. This is obviously not a priority because they don’t need to develop this feature. Why is this? Because they can continue to sell tests and to give shakey leaves to customers, most of whom don’t understand the subtle “untruth” inherent in that leaf match – so are quite blissfully happy.

In years past, I worked in the computer industry when IBM was the Big Dog against whom everyone else competed. I’m reminded of an old joke. The IBM sales rep got married, and on his wedding night, he sat on the edge of the bed all night long regaling his bride in glorious detail with stories about just how good it was going to be….

You can sign a petition asking Ancestry to provide a chromosome browser here, and you can submit your request directly to Ancestry as well, although to date, this has not been effective.

The most frustrating aspect of this situation is that Ancestry, with their plethora of trees, savvy marketing and captive audience testers really was positioned to “do it right,” and hasn’t, at least not yet. They seem to be more interested in selling kits and providing shakey leaves that are misleading in terms of what they mean than providing true tools. One wonders if they are afraid that their customers will be “less happy” when they discover the truth and not developing a chromosome browser is a way to keep their customers blissfully in the dark.

http://dna-explained.com/2013/03/21/downloading-ancestrys-autosomal-dna-raw-data-file/

http://dna-explained.com/2013/03/24/ancestry-needs-another-push-chromosome-browser/

http://dna-explained.com/2013/10/17/ancestrys-updated-v2-ethnicity-summary/

http://www.thegeneticgenealogist.com/2013/06/21/new-search-features-at-ancestrydna-and-a-sneak-peek-at-new-ethnicity-estimates/

http://www.yourgeneticgenealogist.com/2013/03/ancestrydna-raw-data-and-rootstech.html

http://www.legalgenealogist.com/blog/2013/09/15/dna-disappointment/

http://www.legalgenealogist.com/blog/2013/09/13/ancestrydna-begins-rollout-of-update/

Ancient DNA

This has been a huge year for advances in sequencing ancient DNA, something once thought unachievable. We have learned a great deal, and there are many more skeletal remains just begging to be sequenced. One absolutely fascinating find is that all people not African (and some who are African through backmigration) carry Neanderthal and Denisovan DNA. Just this week, evidence of yet another archaic hominid line has been found in Neanderthal DNA and on Christmas Day, yet another article stating that type 2 Diabetes found in Native Americans has roots in their Neanderthal ancestors. Wow!

Closer to home, by several thousand years is the suggestion that haplogroup R did not exist in Europe after the ice age, and only later, replaced most of the population which, for males, appears to have been primarily haplogroup G. It will be very interesting as the data bases of fully sequenced skeletons are built and compared. The history of our ancestors is held in those precious bones.

http://dna-explained.com/2013/01/10/decoding-and-rethinking-neanderthals/

http://dna-explained.com/2013/07/04/ancient-dna-analysis-from-canada/

http://dna-explained.com/2013/07/10/5500-year-old-grandmother-found-using-dna/

http://dna-explained.com/2013/10/25/ancestor-of-native-americans-in-asia-was-30-western-eurasian/

http://dna-explained.com/2013/11/12/2013-family-tree-dna-conference-day-2/

http://dna-explained.com/2013/11/22/native-american-gene-flow-europe-asia-and-the-americas/

http://dna-explained.com/2013/12/05/400000-year-old-dna-from-spain-sequenced/

http://www.thegeneticgenealogist.com/2013/10/16/identifying-otzi-the-icemans-relatives/

http://cruwys.blogspot.com/2013/12/recordings-of-royal-societys-ancient.html

http://cruwys.blogspot.com/2013/02/richard-iii-king-is-found.html

http://dna-explained.com/2013/12/22/sequencing-of-neanderthal-toe-bone-reveals-unknown-hominin-line/

http://dna-explained.com/2013/12/26/native-americans-neanderthal-and-denisova-admixture/

http://dienekes.blogspot.com/2013/12/ancient-dna-what-2013-has-brought.html

Sloppy Science and Sensationalist Reporting

Unfortunately, as DNA becomes more mainstream, it becomes a target for both sloppy science or intentional misinterpretation, and possibly both. Unfortunately, without academic publication, we can’t see results or have the sense of security that comes from the peer review process, so we don’t know if the science and conclusions stand up to muster.

The race to the buck in some instances is the catalyst for this. In other cases, and not in the links below, some people intentionally skew interpretations and results in order to either fulfill their own belief agenda or to sell “products and services” that invariably report specific findings.

It’s equally as unfortunate that much of these misconstrued and sensationalized results are coming from a testing company that goes by the names of BritainsDNA, ScotlandsDNA, IrelandsDNA and YorkshiresDNA. It certainly does nothing for their credibility in the eyes of people who are familiar with the topics at hand, but it does garner a lot of press and probably sells a lot of kits to the unwary.

I hope they publish their findings so we can remove the “sloppy science” aspect of this. Sensationalist reporting, while irritating, can be dealt with if the science is sound. However, until the results are published in a peer-reviewed academic journal, we have no way of knowing.

Thankfully, Debbie Kennett has been keeping her thumb on this situation, occurring primarily in the British Isles.

http://dna-explained.com/2013/08/24/you-might-be-a-pict-if/

http://cruwys.blogspot.com/2013/12/the-british-genetic-muddle-by-alistair.html

http://cruwys.blogspot.com/2013/12/setting-record-straight-about-sara.html

http://cruwys.blogspot.com/2013/09/private-eye-on-britainsdna.html

http://cruwys.blogspot.com/2013/07/private-eye-on-prince-williams-indian.html

http://cruwys.blogspot.com/2013/06/britainsdna-times-and-prince-william.html

http://cruwys.blogspot.com/2013/03/sense-about-genealogical-dna-testing.html

http://cruwys.blogspot.com/2013/03/sense-about-genetic-ancestry-testing.html

Citizen Science is Coming of Age

Citizen science has been slowing coming of age over the past few years. By this, I mean when citizen scientists work as part of a team on a significant discovery or paper. Bill Hurst comes to mind with his work with Dr. Doron Behar on his paper, A Copernican Reassessment of the Human Mitochondrial DNA from its Root or what know as the RSRS model. As the years have progressed, more and more discoveries have been made or assisted by citizen scientists, sometimes through our projects and other times through individual research. JOGG, the Journal of Genetic Genealogy, which is currently on hiatus waiting for Dr. Turi King, the new editor, to become available, was a great avenue for peer reviewed publication. Recently, research projects have been set up by citizen scientists, sometimes crowd-funded, for specific areas of research. This is a very new aspect to scientific research, and one not before utilized.

The first paper below includes the Family Tree DNA Lab, Thomas and Astrid Krahn, then with Family Tree DNA and Bonnie Schrack, genetic genealogist and citizen scientist, along with Dr. Michael Hammer from the University of Arizona and others.

http://dna-explained.com/2013/03/26/family-tree-dna-research-center-facilitates-discovery-of-ancient-root-to-y-tree/

http://dna-explained.com/2013/04/10/diy-dna-analysis-genomeweb-and-citizen-scientist-2-0/

http://dna-explained.com/2013/06/27/big-news-probable-native-american-haplogroup-breakthrough/

http://dna-explained.com/2013/07/22/citizen-science-strikes-again-this-time-in-cameroon/

http://dna-explained.com/2013/11/30/native-american-haplogroups-q-c-and-the-big-y-test/

http://www.yourgeneticgenealogist.com/2013/03/citizen-science-helps-to-rewrite-y.html

Ethnicity Makeovers – Still Not Soup

Unfortunately, ethnicity percentages, as provided by the major testing companies still disappoint more than thrill, at least for those who have either tested at more than one lab or who pretty well know their ethnicity via an extensive pedigree chart.

Ancestry.com is by far the worse example, swinging like a pendulum from one extreme to the other. But I have to hand it to them, their marketing is amazing. When I signed in, about to discover that my results had literally almost reversed, I was greeted with the banner “a new you.” Yea, a new me, based on Ancestry’s erroneous interpretation. And by reversed, I’m serious. I went from 80% British Isles to 6% and then from 0% Western Europe to 79%. So now, I have an old wrong one and a new wrong one – and indeed they are very different. Of course, neither one is correct…..but those are just pesky details…

23andMe updated their ethnicity product this year as well, and fine tuned it yet another time. My results at 23andMe are relatively accurate. I saw very little change, but others saw more. Some were pleased, some not.

The bottom line is that ethnicity tools are not well understood by consumers in terms of the timeframe that is being revealed, and it’s not consistent between vendors, nor are the results. In some cases, they are flat out wrong, as with Ancestry, and can be proven. This does not engender a great deal of confidence. I only view these results as “interesting” or utilize them in very specific situations and then only using the individual admixture tools at www.Gedmatch.com on individual chromosome segments.

As Judy Russell says, “it’s not soup yet.” That doesn’t mean it’s not interesting though, so long as you understand the difference between interesting and gospel.

http://dna-explained.com/2013/08/05/autosomal-dna-ancient-ancestors-ethnicity-and-the-dandelion/

http://dna-explained.com/2013/10/04/ethnicity-results-true-or-not/

http://www.legalgenealogist.com/blog/2013/09/15/dna-disappointment/

http://cruwys.blogspot.com/2013/09/my-updated-ethnicity-results-from.html?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+Cruwysnews+%28Cruwys+news%29

http://dna-explained.com/2013/10/17/ancestrys-updated-v2-ethnicity-summary/

http://dna-explained.com/2013/10/19/determining-ethnicity-percentages/

http://www.thegeneticgenealogist.com/2013/09/12/ancestrydna-launches-new-ethnicity-estimate/

http://cruwys.blogspot.com/2013/12/a-first-look-at-chromo-2-all-my.html

Genetic Genealogy Education Goes Mainstream

With the explosion of genetic genealogy testing, as one might expect, the demand for education, and in particular, basic education has exploded as well.

I’ve written a 101 series, Kelly Wheaton wrote a series of lessons and CeCe Moore did as well. Recently Family Tree DNA has also sponsored a series of free Webinars. I know that at least one book is in process and very near publication, hopefully right after the first of the year. We saw several conferences this year that provided a focus on Genetic Genealogy and I know several are planned for 2014. Genetic genealogy is going mainstream!!! Let’s hope that 2014 is equally as successful and that all these folks asking for training and education become avid genetic genealogists.

http://dna-explained.com/2013/08/10/ngs-series-on-dna-basics-all-4-parts/

https://sites.google.com/site/wheatonsurname/home

http://www.yourgeneticgenealogist.com/2012/08/getting-started-in-dna-testing-for.html

http://dna-explained.com/2013/12/17/free-webinars-from-family-tree-dna/

http://www.thegeneticgenealogist.com/2013/06/09/the-first-dna-day-at-the-southern-california-genealogy-society-jamboree/

http://www.yourgeneticgenealogist.com/2013/06/the-first-ever-independent-genetic.html

http://cruwys.blogspot.com/2013/10/genetic-genealogy-comes-to-ireland.html

http://cruwys.blogspot.com/2013/03/wdytya-live-day-3-part-2-new-ancient.html

http://cruwys.blogspot.com/2013/03/who-do-you-think-you-are-live-day-3.html

http://cruwys.blogspot.com/2013/03/who-do-you-think-you-are-live-2013-days.html

http://genealem-geneticgenealogy.blogspot.com/2013/03/the-surnames-handbook-guide-to-family.html

http://www.isogg.org/wiki/Beginners%27_guides_to_genetic_genealogy

A Thank You in Closing

I want to close by taking a minute to thank the thousands of volunteers who make such a difference. All of the project administrators at Family Tree DNA are volunteers, and according to their website, there are 7829 projects, all of which have at least one administrator, and many have multiple administrators. In addition, everyone who answers questions on a list or board or on Facebook is a volunteer. Many donate their time to coordinate events, groups, or moderate online facilities. Many speak at events or for groups. Many more write articles for publications from blogs to family newsletters. Additionally, there are countless websites today that include DNA results…all created and run by volunteers, not the least of which is the ISOGG site with the invaluable ISOGG wiki. Without our volunteer army, there would be no genetic genealogy community. Thank you, one and all.

2013 has been a banner year, and 2014 holds a great deal of promise, even without any surprises. And if there is one thing this industry is well known for….it’s surprises. I can’t wait to see what 2014 has in store for us!!! All I can say is hold on tight….

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Sequencing of Neanderthal Toe Bone Reveals Unknown Hominin Line

Posted on December 22, 2013 by Roberta Estes

This week, in the journal Nature, scientists reported on the full sequencing of a Neanderthal toe bone found in the Denisova Cave in the Altai Mountains, the location where the Denisovan skeleton found in 2008 and sequenced earlier this year was also found.

The abstract of the paper, which is behind a paywall, says:

We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.

The abstract also includes this graphic from the paper

This sequence is significant because of a number of unique findings.

The skeleton showed physical traits of both Neanderthals and modern humans and is thought to be about 50,000 years old.
Genetic sequencing revealed that this bone belonged to a Neanderthal woman, not a Denisovan, although other Denisovan remains, including one previously sequenced, have been found in this cave.
The closest genetic relative is found in the Mezmaiskaya Cave in the Caucasus Mountains, some 2000+ miles distant. Admittedly, we don’t have a lot of sequenced remains for comparison.
Sequencing revealed a heretofore unknown genetic line of archaic humans. This person obtained from between 2.7 to 5.8 percent of their genome from this unknown line. That percentage is equal to someplace between a great-great-great-grandparent and a great-great-great-great-great-grandparent, assuming only one ancestor was involved. If this unknown human lineage was admixed into the population in multiple individuals, then the trace amounts could be passed around forever, just like the Neanderthal and Denisovan lineages are in Europeans today.
This unknown line could be homo erectus.
There is no evidence that this unknown human lineage interbred with either modern humans or Neanderthals. I would presume this means that this unknown line then bred with the Denisovan group which did not manifest itself in contemporary humans.
This individual was inbred with their parents being closely related, possibly half-siblings or an uncle and niece, or an aunt and nephew or a grandfather and granddaughter or grandmother and grandson. Inbreeding was also common among the woman’s recent ancestors. Another article headline this week pronounced that “Neanderthals Liked Incest” which I found to be offensive. Incest is a highly negatively charged cultural word. In the not so recent past, the practice of inbreeding was perfectly acceptable in European royalty. Furthermore, we have no idea how these people felt about inbreeding, hence the word “liked” is misleading. It could well be that they lived in a small nuclear family group and there were no other choices for partners. There could also be other cultural and selection factors at play here of which we are unaware. For example, perhaps males were more protective of mothers and children to whom they were related than ones where they had no family or group ties – increasing the likelihood of survival of offspring of women to whom the males were related.
At least half of a percent of the Denisovan genome came from Neanderthals, but none of the Denisovan genome has yet been detected in Neanderthals. If this holds, it would imply that our ancestors either bred with Neanderthals and Denisovans separately, or with Denisovans who carried Neanderthal DNA. Given that most Europeans carry more Neanderthal DNA than Denisovan, the second scenario alone is unlikely. It’s also possible that we simply haven’t found Neanderthal’s who did carry Denisovan DNA.
More than 31,000 differences were found between modern humans and Neanderthals and Denisovans, many having to do with brain development.

Dienekes discussed this research in his blog as well. Note his “family tree.”

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400,000 Year Old DNA from Spain Sequenced

Posted on December 5, 2013 by Roberta Estes

Talk about record shattering. 400,000 year old DNA has now been sequenced, and that quite handily breaks the previous 100,000 year old record. The only problem is that these ancient and archaic people weren’t staying where they were supposed to. Well, that’s “supposed to” according to the story we thought we knew. Obviously, we didn’t know, and ancient DNA is only beginning to tell the story, which isn’t at all like we thought it would be.

Before now, Neanderthals were thought to have settled in the west, meaning Europe primarily, and Denisovans in the East, in Siberia. This is due to where bones have been found and the DNA sequenced from just a few. However, this new find from a cave in Atapuerca, Spain changes all of that. These people were not closely related to Neanderthal, who were later found in Germany, but instead are related to the Denisovans, their remains found some 4000 miles east, per mitochondrial DNA, meaning their direct matrilineal line. However, even though they are related, they are distantly related.

Yesterday the mitochondrial sequence appeared on GenBank, after the release of the paper. According to Ian Logan, this new sequence has just over 500 mutations, about half of which can be matched with Denisovan and the other half are unique. So while the Denisovan and this new sequence do share a maternal ancestor, they are many, many generations distant. Of course, that would be expected, because they are about 350,000 years apart too in terms of time, or a meager 14,000 generations.

What does this mean? The scientists don’t know for sure. Perhaps these Atapuerca Cave people were the ancestors of Denisovans and Neanderthals. Perhaps the Denisovan mitochondrial DNA “washed out” over generations in the Neanderthal or maybe not enough Neanderthal remains have been located and sequenced. Neither Neanderthal nor Denisovan mitochondrial DNA has been found in any living humans or relatively contemporary burials, meaning not outside of Neanderthals and Denisovans. In short, we need more skeletons and more DNA to reveal more information about our ancient ancestors. It opens the possibility that modern humans are but a small sprig on the larger and quite ancient Denisovan/Neanderthal Eurasian tree. We don’t know where modern humans fit in all of this, but according to autosomal genetic results, everyone with either European or Asian heritage carries some of them in all of us, just not the mitochondrial line. We are just beginning this journey of discovery.

For more, access the Science article, Dienekes Anthrolpology Blog and John Hawks blog. The academic article in Nature, A mitochondrial genome sequence of a hominin from Sima de los Huesos, by Meyer et all is behind a paywall.

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