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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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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Neuroarchaeologists Uncover Iberian Origin of Unusual Alzheimer’s Gene Mutation

Posted on December 13, 2013 by Roberta Estes

Neuroarchaeologists, a term I haven’t heard before, but one we’ll likely hear into the future. Genetics, neurology, genealogy, population genetics….they are all becoming intermixed today solving puzzles that are so complex that just a few years ago, there would have been no prayer of solving them at all.

Take early onset Alzheimers, for example. Keep in mind that this type of Alzheimer’s is only one of several, and much about this disease remains unknown, but for this particular kind of Alzheimer’s disease, this breakthrough is monumental, as is the fact that they can trace it to the Iberian peninsula in the 16^th century.

The history of our ancestors truly is in our genes.

This research was performed at the University of California at Santa Barbara and published this month in Alzheimer’s and Dementia, the Journal of the Alzheimer’s Association. Unfortunately, the academic article is behind a paywall.

Researchers tested more than 100 family members who have the disease. While many predictably showed onset signs of the disease as expected about age 45, some appeared to be protected by as much as a decade. The question was what was protecting these people and does that protective mechanism have relevance for the rest of the people afflicted by Alzheimer’s disease. The answer isn’t yet evident, and research continues, but the process they used to identify this mutation is fascinating.

The team worked with historians and genealogists and using records as old as 1540, managed to track this family, along with their mutation, to a single individual from the Iberian peninsula about the time that Spanish Conquistadors were colonizing Columbia in the early 1500s.

They may call this new field neuroarchaeology, but I think it’s more neurogenealogy, unless they’re excavating graves someplace. But I bet they think neuroarchaeology just sounds more scientific. So, want to get assistance with your genealogy….having a dread disease, or being a politician….either one will help immensely.

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Native American Gene Flow – Europe?, Asia and the Americas

Posted on November 22, 2013 by Roberta Estes

Pre-release information from the paper, “Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans” which included results and analysis of DNA sequencing of 24,000 year old skeletal remains of a 4 year old Siberian boy caused quite a stir. Unfortunately, it was also misconstrued and incorrectly extrapolated in some articles. Some people misunderstood, either unintentionally or intentionally, and suggested that people with haplogroups U and R are Native American. That is not what either the prerelease or the paper itself says. Not only is that information and interpretation incorrect, the paper itself with the detailed information wasn’t published until November 20^th, in Nature.

The paper is currently behind a paywall, so I’m going to discuss parts of it here, along with some additional information from other sources. To help with geography, the following google map shows the following locations: A=the Altai Republic, in Russia, B=Mal’ta, the location of the 24,000 year old skeletal remains and C=Lake Baikal, the region from where the Native American population originated in Asia.

Nature did publish an article preview. That information is in bold, italics and I will be commenting in nonbold, nonitalics.

The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians^{1, 2, 3}, there is no consensus with regard to which specific Old World populations they are closest to^{4, 5, 6, 7, 8}. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia⁹, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date.

Within the paper, the authors also compare the MA-1 sequence to that of another 40,000 year old individual from Tianyuan Cave, China whose genome has been partially sequenced. This Chinese individual has been shown to be ancestral to both modern-day Asians and Native Americans. This comparison was particularly useful, because it showed that MA-1 is not closely related to the Tianyuan Cave individual, and is more closely related to Native Americans. This means that MA-1’s line and Tianyuan Cave’s line had not yet met and admixed into the population that would become the Native Americans. That occurred sometime later than 24,000 years ago and probably before crossing Beringia into North America sometime between about 18,000 and 20,000 years ago.

The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers^{10, 11, 12}, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages⁵.

The paper goes on to say that MA-1 is a member of mitochondrial (maternal) haplogroup U, very near the base of that haplogroup, but without affiliation to any known subclade, implying either that the subclade is rare or extinct in modern populations. In other words, this particular line of haplogroup U has NOT been found in any population, anyplace. According to the landmark paper, “A ‘‘Copernican’’ Reassessment of the Human Mitochondrial DNA Tree from its Root,” by Behar et al, 2012, haplogroup U itself was born about 46,500 years ago (plus or minus 3.200 years) and today has 9 major subclades (plus haplogroup K) and about 300 branching clades from those 9 subclades, excluding haplogroup K.

The map below, from the supplemental material included with the paper shows the distribution of haplogroup U, the black dots showing locations of haplogroup U comparison DNA.

In a recent paper, “Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity” by Brandt et al (including the National Geographic Consortium) released in October 2013, the authors report that in the 198 ancient DNA samples collected from 25 German sites and compared to almost 68,000 current results, all of the ancient Hunter-Gatherer cultural results were haplogroup U, U4, U5 and U8. No other haplogroups were represented. In addition, those haplogroups disappeared from the region entirely with the advent of farming, shown on the chart below.

So, if someone who carries haplogroup U wants to say that they are distantly related to MA-1 who lived 24,000 years ago who was also related to their common ancestor who lived sometime prior to that, between 24,000 and 50,000 years ago, probably someplace between the Middle East where U was born, Mal’ta, Siberia and Western Europe, they would be correct. They are also distantly related to every other person in the world who carries haplogroup U, and many much more closely that MA-1 whose mitochondrial DNA line is either rare as chicken’s teeth (i.e. never found) or has gone extinct.

Let me be very clear about this, there is no evidence, none, that mitochondrial haplogroup U is found in the Native American population today that is NOT a result of post-contact admixture. In other words, in the burials that have been DNA tested, there is not one example in either North or South America of a burial carrying mitochondrial haplogroup U, or for that matter, male Y haplogroup R. Native American haplogroups found in the Americas remain subsets of mitochondrial haplogroups A, B, C, D and X and Y DNA haplogroups C and Q. Mitochondrial haplogroup M has potentially been found in one Canadian burial. No other haplogroups have been found. Until pre-contact remains are found with base haplogroups other than the ones listed above, no one can ethically claim that other haplogroups are of Native American origin. Finding any haplogroup in a contemporary Native population does not mean that it was originally Native, or that it should be counted as such. Admixture and adoption have been commonplace since Europeans first set foot on the soil of the Americas.

Now let’s talk about the Y DNA of MA-1.

The authors state that MA-1’s results are found very near the base of haplogroup R. They note that the sister lineage of haplogroup R, haplogroup Q, is the most common haplogroup in Native Americans and that the closest Eurasian Q results to Native Americans come from the Altai region.

The testing of the MA-1 Y chromosome was much more extensive than the typical STR genealogy tests taken by consumers today. MA-1’s Y chromosome was sequenced at 5.8 million base pairs at a coverage of 1.5X.

The resulting haplotree is shown below, again from the supplementary material.

The current haplogroup distribution range for haplogroup R is shown below, again with comparison points as black dots.

The current distribution range for Eurasian haplogroup Q is shown on the map below. Haplogroup Q is the most common haplogroup in Native Americans.

Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians^{2, 13}.

Kennewick Man is probably the most famous of the skeletal remains that don’t neatly fit into their preconceived box. Kennewick man was discovered on the bank of the Columbia River in Kennewick, Washington in 1996 and is believed to be from 7300 to 7600 years old. His anatomical features were quite different from today’s Native Americans and his relationship to ancient people is unknown. An initial evaluation and a 2010 reevaluation of Kennewick Man let to the conclusion by Doug Owsley, a forensic anthropologist, that Kennewick Man most closely resembles the Ainu people of Japan who themselves are a bit of an enigma, appearing much more Caucasoid than Asian. Unfortunately, DNA sequencing of Kennewick Man originally was ussuccessful and now, due to ongoing legal issues, more technologically advanced DNA testing has not been allowed. Nova sponsored a facial reconstruction of Kennewick Man which you can see here.

Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago¹⁴, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.

In addition to the sequencing they set forth above, the authors compared the phenotype information obtainable from MA-1 to the Tyrolean Iceman, typically called Otzi. You can see Otzi’s facial reconstruction along with more information here. This is particularly interesting in light of the pigmentation change from darker skin in Africa to lighter skin in Eurasia, and the question of when this appearance change occurred. MA-1 shows a genetic affinity with the contemporary people of northern Europe, the population today with the highest frequency of light pigmentation phenotypes. The authors compared the DNA of MA-1 with a set of 124 SNPs identified in 2001 by Cerquira as informative on skin, hair and eye pigmentation color, although they also caution that this method has limited prediction accuracy. Given that, they say that MA-1 had dark hair, skin and eyes, but they were not able to sequence the full set of SNPs. MA-1 also had the SNP value associated with a high risk of male pattern baldness, a trait seldom found in Native American people and was not lactose tolerant, a trait found in western Eurasians. MA-1 also does not carry the mutation associated with hair thickness and shovel shaped incisors in Asians.

The chart below from the supplemental material shows the comparison with MA-1 and the Tyrolean Iceman.

The Tarim Mummies, found in the Tarim Basin in present-day Xinjiang, China are another example of remains that seem out of place. The earliest Tarim mummies, found at Qäwrighul and dated to 1800 BCE, are of a Europoid physical type whose closest affiliation is to the Bronze Age populations of southern Siberia, Kazakhstan, Central Asia, and the Lower Volga.

The cemetery at Yanbulaq contained 29 mummies which date from 1100–500 BCE, 21 of which are Mongoloid—the earliest Mongoloid mummies found in the Tarim Basin—and eight of which are of the same Europoid physical type found at Qäwrighul.

Notable mummies are the tall, red-haired “Chärchän man” or the “Ur-David” (1000 BCE); his son (1000 BCE), a small 1-year-old baby with brown hair protruding from under a red and blue felt cap, with two stones positioned over its eyes; the “Hami Mummy” (c. 1400–800 BCE), a “red-headed beauty” found in Qizilchoqa; and the “Witches of Subeshi” (4th or 3rd century BCE), who wore 2-foot-long (0.61 m) black felt conical hats with a flat brim. Also found at Subeshi was a man with traces of a surgical operation on his neck; the incision is sewn up with sutures made of horsehair.

Their costumes, and especially textiles, may indicate a common origin with Indo-European neolithic clothing techniques or a common low-level textile technology. Chärchän man wore a red twill tunic and tartan leggings. Textile expert Elizabeth Wayland Barber, who examined the tartan-style cloth, discusses similarities between it and fragments recovered from salt mines associated with the Hallstatt culture.

DNA testing revealed that the maternal lineages were predominantly East Eurasian haplogroup C with smaller numbers of H and K, while the paternal lines were all R1a1a. The geographic location of where this admixing took place is unknown, although south Siberia is likely. You can view some photographs of the mummies here.

In closing, the authors of the MA-1 paper state that the study has four important implications.

First, we find evidence that contemporary Native Americans and western Eurasians shareancestry through gene flow from a Siberian Upper Palaeolithic population into First Americans.

Second, our findings may provide an explanation for the presence of mtDNA haplogroup X in Native Americans, which is related to western Eurasians but not found in east Asian populations.

Third, such an easterly presence in Asia of a population related to contemporary western Eurasians provides a possibility that non-east Asian cranial characteristics of the First Americans derived from the Old World via migration through Beringia, rather than by a trans-Atlantic voyage from Iberia as proposed by the Solutrean hypothesis.

Fourth, the presence of an ancient western Eurasian genomic signature in the Baikal area before and after the LGM suggests that parts of south-central Siberia were occupied by humans throughout the coldest stages of the last ice age.

The times, they are a changin’.

Dr. Michael Hammer’s presentation at the 9^th Annual International Conference on Genetic Genealogy may shed some light on all of this seeming confusing and somewhat conflicting information.

The graphic below shows the Y haplogroup base tree as documented by van Oven.

You can see, in the lower right corner, that Y haplogroup K (not to be confused with mtDNA haplogroup K discussed in conjunction with mtDNA haplogroup U) was the parent of haplogroup P which is the parent of both haplogroups Q and R.

It has always been believed that haplogroup R made its way into Europe before the arrival of Neolithic farmers about 10,000 years ago. However, that conclusion has been called into question, also by the use of Ancient DNA results. You can view additional information about Hammer’s presentation here, but in a nutshell, he said that there is no early evidence in burials, at all, for haplogroup R being in Europe at an early age. In about 40 burials from several location, haplogroup R has never been found. If it were present, especially in the numbers expected given that it represents more than half of the haplogroups of the men of Europe today, it should be represented in these burials, but it is not. Hammer concludes that evidence supports a recent spread of haplogroup R into Europe about 5000 years ago. Where was haplogroup R before spreading into Europe? In Asia.

It appears that haplogroup K diversified in Southeast Asian, giving birth to haplogroups P, Q and R. Dr. Hammer said that this new information, combined with new cluster information and newly discovered SNP information over the past two years requires that haplogroup K be significantly revised. Between the revision of haplogroup K, the parent of both haplogroup R, previously believed to be European, and haplogroup Q, known to be Asian, European and Native, we may be in for a paradigm shift in terms of what we know about ancient migrations and who is whom. This path for haplogroup R into Europe really shouldn’t be surprising. It’s the exact same distribution as haplogroup Q, except haplogroup Q is much less frequently found in Europe than haplogroup R.

What Can We Say About MA-1?

In essence, we can’t label MA-1 as paternally European because of Y haplogroup R which now looks to have had an Asian genesis and was not known to have been in Europe 24,000 years ago, only arriving about 5,000 years ago. We can’t label haplogroup R as Native American, because it has never been found in a pre-Columbian New World burial.

We can say that mitochondrial haplogroup U is found in Europe in Hunter-Gatherer groups six thousand years ago (R was not) but we really don’t know if haplogroup U was in Europe 24,000 years ago. We cannot label haplogroup U as Native because it has never been found in a pre-Columbian New World burial.

We can determine that MA-1 did have ancestors who eventually became European due to autosomal analysis, but we don’t know that those people lived in what is now Europe 24,000 years ago. So the migration might have been into Europe, not out of Europe. MA-1, his ancestors and descendants, may have lived in Asia and subsequently settled in Europe or lived someplace inbetween. We can determine that MA-1’s line of people eventually admixed with people from East Asia, probably in Siberia, and became today’s First People of North and South America.

We can say that MA-1 appears to have been about 30% what is today Western Eurasian and that he is closely related to modern day Native Americans, but not eastern Asians. The authors estimate that between 14% and 38% of Native American ancestry comes from MA-1’s ancient population.

Whoever thought we could learn so much from a 4 year old?

For anyone seriously interested in Native American population genetics, “Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans” is a must read.

It’s been a great month for ancient DNA. Additional recent articles which pertain to this topic include:

http://www.nytimes.com/2013/11/21/science/two-surprises-in-dna-of-boy-found-buried-in-siberia.html?src=me&ref=general&_r=0

http://www.sciencedaily.com/releases/2013/11/131120143631.htm

http://dienekes.blogspot.com/2013/11/ancient-dna-from-upper-paleolithic-lake.html

http://blogs.discovermagazine.com/gnxp/2013/11/long-first-age-mankind/#.Uo0eOcSkrIU

http://cruwys.blogspot.com/2013/11/day-1-at-royal-societys-2013-ancient.html

http://cruwys.blogspot.co.uk/2013/11/day-2-at-royal-societys-2013-ancient.html

http://www.sciencedaily.com/releases/2013/11/131118081251.htm

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2013 Family Tree DNA Conference Day 2

Posted on November 12, 2013 by Roberta Estes

ISOGG Meeting

The International Society of Genetic Genealogy always meets at 8 AM on Sunday morning. I personally think that 8AM meeting should be illegal, but then I generally work till 2 or 3 AM (it’s 1:51 AM now), so 8 is the middle of my night.

Katherine Borges, the Director speaks about current and future activities, and Alice Fairhurst spoke about the many updates to the Y tree that have happened and those coming as well. It has been a huge challenge to her group to keep things even remotely current and they deserve a huge round of virtual applause from all of us for the Y tree and their efforts.

Bennett opened the second day after the ISOGG meeting.

“The fact that you are here is a testament to citizen science” and that we are pushing or sometimes pulling academia along to where we are.

Bennett told the story of the beginning of Family Tree DNA. “Fourteen years ago when the hair that I have wasn’t grey,” he began, “I was unemployed and tried to reorganize my wife’s kitchen and she sent me away to do genealogy.” Smart woman, and thankfully for us, he went. But he had a roadblock. He felt there was a possibility that he could use the Y chromosome to solve the roadblock. Bennett called the author of one of the two papers published at that time, Michael Hammer. He called Michael Hammer on Sunday morning at his home, but Michael was running out the door to the airport. He declined Bennett’s request, told him that’s not what universities do, and that he didn’t know of anyplace a Y test could be commercially be done. Bennett, having run out of persuasive arguments, started mumbling about “us little people providing money for universities.” Michael said to him, “Someone should start a company to do that because I get phone calls from crazy genealogists like you all the time.” Let’s just say Bennett was no longer unemployed and the rest, as they say, is history. With that, Bennett introduced one of our favorite speakers, Dr. Michael Hammer from the Hammer Lab at the University of Arizona.

Session 1 – Michael Hammer – Origins of R-M269 Diversity in Europe

Michael has been at all of the conferences. He says he doesn’t think we’re crazy. I personally think we’ve confirmed it for him, several times over, so he KNOWS we’re crazy. But it obviously has rubbed off on him, because today, he had a real shocker for us.

I want to preface this by saying that I was frantically taking notes and photos, and I may have missed something. He will have his slides posted and they will be available through a link on the GAP page at FTDNA by the end of the week, according to Elliott.

Michael started by saying that he is really exciting opportunity to begin breaking family groups up with SNPs which are coming faster than we can type them.

Michael rolled out the Y tree for R and the new tree looks like a vellum scroll.

Today, he is going to focus on the basic branches of the Y tree because the history of R is held there.

The first anatomically modern humans migrated from Africa about 45,000 years ago.

After last glacial maximum 17,000 years ago, there was a significant expansion into Europe.

Neolithic farmers arrived from the near east beginning 10,000 years ago.

Farmers had an advantage over hunter gatherers in terms of population density. People moved into Northwestern Europe about 5,000 years ago.

What did the various expansions contribute to the population today?

Previous studies indicate that haplogroup R has a Paleolithic origin, but 2 recent studies agree that this haplogroup has a more recent origin in Europe – the Neolithic but disagree about the timing of the expansion.

The first study, Joblin’s study in 2010, argued that geographic diversity is explained by single Near East source via Anaotolia.

It conclude that the Y of Mesololithic hunger-gatherers were nearly replaced by those of incoming farmers.

In the most recent study by Busby in 2012 is the largest study and concludes that there is no diversity in the mapping of R SNP markers so they could not date lineage and expansion. They did find that most basic structure of R tree did come from the near east. They looked at P311 as marker for expansion into Europe, wherever it was. Here is a summary page of Neolithic Europe that includes these studies.

Hammer says that in his opinion, he thought that if P311 is so frequent and widespread in Europe it must have been there a long time. However, it appears that he and most everyone else, was wrong.

The hypothesis to be tested is if P311 originated prior to the Neolithic wave, it would predict higher diversity it the near east, closer to the origins of agriculture. If P311 originated after the expansion, would be able to see it migrate across Europe and it would have had to replace an existing population.

Because we now have sequences the DNA of about 40 ancient DNA specimens, Michael turned to the ancient DNA literature. There were 4 primary locations with skeletal remains. There were caves in France, Spain, Germany and then there’s Otzi, found in the Alps.

All of these remains are between 6000-7000 years old, so prior to the agricultural expansion into Europe.

In France, the study of 22 remains produced, 20 that were G2a and 2 that were I2a.

In Spain, 5 G2a and 1 E1b.

In Germany, 1I G2a and 2 F*.

Otzi is haplogroup G2a2b.

There was absolutely 0, no, haplogroup R of any flavor.

In modern samples, of 172 samples, 94 are R1b.

To evaluate this, he is dropping back to the backbone of haplogroup R.

This evidence supports a recent spread of haplogroup R lineages in western Europe about 5K years ago. This also supports evidence that P311 moved into Europe after the Neolithic agricultural transition and nearly displaced the previously existing western European Neolithic Y, which appears to be G2a.

This same pattern does not extrapolate to mitochondrial DNA where there is continuity.

What conferred advantage to these post Neolithic men? What was that advantage?

Dr. Hammer then grouped the major subgroups of haplogroup R-P3111 and found the following clusters.

U106 is clustered in Germany
L21 clustered in the British Isles
U152 has an Alps epicenter

This suggests multiple centers of re-expansion for subgroups of haplogroup R, a stepwise process leading to different pockets of subhaplogroup density.

Archaeological studies produce patterns similar to the hap epicenters.

What kind of model is going on for this expansion?

Ancestral origin of haplogroup R is in the near east, with U106, P312 and L21 which are then found in 3 European locations.

This research also suggests thatG2a is the Neolithic version of R1b – it was the most commonly found haplogroup before the R invasion.

To make things even more interesting, the base tree that includes R has also been shifted, dramatically.

Haplogroup K has been significantly revised and is the parent of haplogroups P, R and Q.

It has been broken into 4 major branches from several individual lineages – widely shifted clades.

Haps R and Q are the only groups that are not restricted to Oceana and Southeast Asia.

Rapid splitting of lineages in Southeast Asia to P, R and Q, the last two of which then appear in western Europe.

R then, populated Europe in the last 4000 years.

How did these Asians get to Europe and why?

Asian R1b overtook Neolithic G2a about 4000 years ago in Europe which means that R1b, after migrating from Africa, went to Asia as haplogroup K and then divided into P, Q and R before R and Q returned westward and entered Europe. If you are shaking your head right about now and saying “huh?”…so were we.

Here is Dr. Hammer’s revised map of haplogroup dispersion.

Moving away from the base tree and looking at more recent SNPs, Dr. Hammer started talking about some of the findings from the advanced SNP testing done through the Nat Geo project and some of what it looks like and what it is telling us.

For example, the R1bs of the British Isles.

There are many clades under L 21. For example, there is something going on in Scotland with one particular SNP (CTS11722?) as it comprises one third of the population in Scotland, but very rare in Ireland, England and Wales.

New Geno 2.0 SNP data is being utilized to learn more about these downstream SNPs and what they had to say about the populations in certain geographies.

For example, there are 32 new SNPs under M222 which will help at a genealogical level.

These SNPs must have arisen in the past couple thousand years.

Michael wants to work with people who have significant numbers of individuals who can’t be broken out with STRs any further and would like to test the group to break down further with SNPs. The Big Y is one option but so is Nat Geo and traditional SNP testing, depending on the circumstance.

G2a is currently 4-5% of the population in Europe today and R is more than 40%.

Therefore, P312 split in western Eurasia and very rapidly came to dominate Europe

Session 2 – Dr. Marja Pirttivaara – Bridging Social Media and DNA

Dr. Pirttivaara has her PhD in Physics and is passionate about genetic genealogy, history and maps. She is an administrator for DNA projects related to Finland and haplogroup N1c1, found in Finland, of course.

Finland has the population of Minnesota and is the size of New Mexico.

There are 3750 Finland project members and of them 614 are haplogroup N1c1.

Combining the N1c1 and the Uralic map, we find a correlation between the distribution of the two.

Turku, the old capital, was full or foreigners, in Medieval times which is today reflected in the far reaching DNA matches to Finnish people.

Some of the interest in Finland’s DNA comes from migration which occurred to the United States.

Facebook and other social media has changed the rules of communication and allows the people from wide geographies to collaborate. The administrator’s role has also changed on social media as opposed to just a FTDNA project admin. Now, the administrator becomes a negotiator and a moderator as well as the DNA “expert.”

Marja has done an excellent job of motivating her project members. They are very active within the project but also on Facebook, comparing notes, posting historical information and more.

Session 3 – Jason Wang – Engineering Roadmap and IT Update

Jason is the Chief Technology Officer at Family Tree DNA and recently joined with the Arpeggi merger and has a MS in Computer Engineering.

Regarding the Gene by Gene/FTDNA partnership, “The sum of the parts is greater than the whole.” He notes that they have added people since last year in addition to the Arpeggi acquisition.

Jason introduced Elliott Greenspan, who, to most of us, needed no introduction at all.

Elliott began manually scoring mitochondrial DNA tests at age 15. He joined FTDNA in 2006 officially.

Year in review and What’s Coming

4 times the data processed in the past year.

Uploads run 10 times faster. With 23andMe and Ancestry autosomal uploads, processing will start in about 5 minutes, and matches will start then.

FTDNA reinvented Family Finder with the goal of making the user experience easier and more modern. They added photos, profiles and the new comparison bars along with an advanced section and added push to chromosome browser.

Focus on users uploading the family tree. Tools don’t matter if the data isn’t there. In order to utilize the genealogy aspect, the genealogy info needs to be there. Will be enhancing the GEDCOM viewer. New GEDCOMs replace old GEDCOMs so as you update yours, upload it again.

They are now adding a SNP request form so that you can request a SNP not currently available. This is not to be confused with ordering an existing SNP.

They currently utilize build 14 for mitochondrial DNA. They are skipping build 15 entirely and moving forward with 16.

They added steps to the full sequence matches so that you can see your step-wise mutations and decide whether and if you are related in a genealogical timeframe.

New Y tree will be released shortly as a result of the Geno 2.0 testing. Some of the SNPs have mutated as much as 7 times, and what does that mean in terms of the tree and in terms of genealogical usefulness. This tree has taken much longer to produce than they expected due to these types of issues which had to be revised individually.

New 2014 tree has 6200 SNPS and 1000 branches.

Commitment to take genetic genealogy to the next level
Y draft tree
Constant updates to official tree
Commitment to accurate science

If a single sample comes back as positive for a SNP, they will put it on the tree and will constantly update this.

If 3 or 4 people have the same SNP that are not related it will go directly to the tree. This is the reason for the new SNP request form.

Part of the reason that the tree has taken so long is that not every SNP is public and it has been a huge problem.

When they find a new SNP, where does it go on the tree? When one SNP is found or a SNP fails, they have run over 6000 individual SNPs on Nat Geo samples to vet to verify the accuracy of the placement. For example, if a new SNP is found in a particular location, or one is found not to be equivalent that was believe to be so previously, they will then test other samples to see where the SNP actually belongs.

X Matching

Matching differential is huge in early testing. One child may inherit as little as 20% of the X and another 90%. Some first cousins carry none.

X matching will be an advanced feature and will have their own chromosome browser.

End of the year – January 1. Happy New Year!!!

Population Finder

It’s definitely in need of an upgrade and have assigned one person full time to this product.

There are a few contention points that can be explained through standard history.

It’s going to get a new look as well and will be easily upgradeable in the future.

They cannot utilize the National Geographic data because it’s private to Nat Geo.

Bennett – “Committed to an engineering team of any size it takes to get it done. New things will be rolling out in first and second quarter of next year.” Then Bennett kind of sighed and said “I can’t believe I just said that.”

Session 4 – Dr. Connie Bormans – Laboratory Update

The Gene by Gene lab, which of course processes all of the FTDNA samples is now a regulated lab which allows them to offer certain regulated medical tests.

CLIA
CAP
AABB
NYSDOH

Between these various accreditations, they are inspected and accredited once yearly.

Working to decrease turn-around time.

SNP request pipeline is an online form and is in place to request a new SNP be added to their testing menu.

Raised the bar for all of their tests even though genetic genealogy isn’t medical testing because it’s good for customers and increases quality and throughput.

New customer support software and new procedures to triage customer requests.

Implement new scoring software that can score twice as many tests in half the time. This decreases turn-around time to the customer as well.

New projects include improved method of mtDNA analysis, new lab techniques and equipment and there are also new products in development.

Ancient DNA (meaning DNA from deceased people) is being considered as an offering if there is enough demand.

Session 5 – Maurice Gleeson – Back to Our Past, Ireland

Maurice Gleeson coordinated a world class genealogy event in Dublin, Ireland Oct. 18-20, 2013. Family Tree DNA and ISOGG volunteers attended to educate attendees about genetic genealogy and DNA. It was a great success and the DNA kits from the conference were checked in last week and are in process now. Hopefully this will help people with Irish ancestry.

12% of the Americans have Irish ancestry, but a show of hands here was nearly 100% – so maybe Irish descendants carry the crazy genealogist gene!

They developed a website titled Genetic Genealogy Ireland 2013. Their target audience was twofold, genetic genealogy in general and also the Irish people. They posted things periodically to keep people interested. They also created a Facebook page. They announced free (sponsored) DNA tests and the traffic increased a great deal. Today ISOGG has a free DNA wiki page too. They also had a prize draw sponsored by the Ireland DNA and mtdna projects. Maurice said that the sessions and the booth proximity were quite symbiotic because when y ou came out of the DNA session, the booth was right there.

2000-5000 people passed by the booth

500 people in the booth

Sold 99 kits – 119 tests

45 took Y 37 marker tests

56 FF, 20 male, 36 female

18 mito tests

They passed out a lot of educational material the first two days. It appeared that the attendees were thinking about things and they came back the last day which is when half of the kits were sold, literally up until they threatened to turn the lights out on them.

They have uploaded all of the lectures to a YouTube channel and they have had over 2000 views. Of all of the presentation, which looked to be a list of maybe 10-15, the autosomal DNA lecture has received 25% of the total hits for all of the videos.

This is a wonderful resource, so be sure to watch these videos and publicize them in your projects.

Session 6 – Brad Larkin – Introducing Surname DNA Journal

Brad Larkin is the FTDNA video link to the “how to appropriately” scrape for a DNA test. That’s his minute or two of fame! I knew he looked familiar.

Brad began a peer reviewed genetic genealogy journal in order to help people get their project stories published. It’s free, open access, web based and the author retains the copyright.. www.surnamedna.com

Conceived in 2012, the first article was published in January 2013. Three papers published to date.

Encourage administrators to write and publish their research. This helps the publication withstand the test of time.

Most other journals are not free, except for JOGG which is now inactive. Author fees typically are $1320 (PLOS) to $5000 (Nature) and some also have subscription or reader fees.

Peer review is important. It is a critical review, a keen eye and an encouraging tone. This insures that the information is evidence based, correct and replicable.

Session 7 – mtdna Roundtable – Roberta Estes and Marie Rundquist

This roundtable was a much smaller group than yesterday’s Y DNA and SNP session, but much more productive for the attendees since we could give individual attention to each person. We discussed how to effectively use mtdna results and what they really mean. And you just never know what you’re going to discover. Marie was using one of her ancestors whose mtDNA was not the haplogroup expected and when she mentioned the name, I realized that Marie and I share yet another ancestral line. WooHoo!!

Q&A

FTDNA kits can now be tested for the Nat Geo test without having to submit a new sample.

After the new Y tree is defined, FTDNA will offer another version of the Deep Clade test.

Illumina chip, most of the time, does not cover STRs because it measures DNA in very small fragments. As they work with the Big Y chip, if the STRs are there, then they will be reported.

80% of FTDNA orders are from the US.

Microalleles from the Houston lab are being added to results as produced, but they do not have the data from the older tests at the University of Arizona.

Holiday sale starts now, runs through December 31 and includes a restaurant.com $100 gift card for anyone who purchases any test or combination of tests that includes Family Finder.

That’s it folks. We took a few more photos with our friends and left looking forward to next year’s conference. Below, left to right in rear, Marja Pirttivaara, Marie Rundquist and David Pike. Front row, left to right, me and Bennett Greenspan.

See y’all next year!!!

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2013 Family Tree DNA Conference Day 1

Posted on November 11, 2013 by Roberta Estes

This article is probably less polished than my normal articles. I’d like to get this information out and to you sooner rather than later, and I’m still on the road the rest of this week with little time to write. So you’re getting a spruced up version of my notes. There are some articles here I’d like to write about more indepth later, after I’m back at home and have recovered a bit.

Max Blankfield and Bennett Greenspan, founders, opened the conference on the first day as they always do. Max began with a bit of a story.

13 years ago Bennett started on a quest….

Indeed he did, and later, Bennett will be relating his own story of that journey.

Someone mentioned to Max that this must be a tough time in this industry. Max thought about this and said, really, not. Competition validates what you are doing.

For competition it’s just a business opportunity – it was not and is not approached with the passion and commitment that Family Tree DNA has and has always had.

He said this has been their best year ever and great things in the pipeline.

One of the big moves is that Arpeggi merged into Family Tree DNA.

10^th Anniversary Pioneer Awards

Quite unexpectedly, Max noted and thanked the early adopters and pioneers, some of which who are gone now but remain with us in spirit.

Max and Bennett recognized the administrators who have been with Family Tree DNA for more than 10 years. The list included about 20 or so early adopters. They provided plaques for us and many of us took a photo with Max as the plaques were handed out.

I am always impressed by the personal humility and gratitude of Max and Bennett, both, to their administrators. A good part of their success is attributed, I’m sure, to their personal commitment not only to this industry, but to the individual people involved. When Max noted the admins who were leaders and are no longer with us, he could barely speak. There were a lot of teary eyes in the room, because they were friends to all of us and we all have good memories.

Thank you, Max and Bennett.

The second day, we took a group photo of all of the recipients along with Max and Bennett.

With that, it was Bennett’s turn for a few remarks.

Bennett says that having their own lab provides a wonderful environment and allows them to benchmark and respond to an ever changing business environment.

Today, they are a College of American Pathologists certified lab and tomorrow, we will find out more about what is coming. Tomorrow, David Mittleman will speak about next generation sequencing.

The handout booklet includes the information that Family Tree DNA now includes over 656,898 records in more than 8,700 group projects. These projects are all managed by volunteer administrators, which in and of itself, is a rather daunting number and amount of volunteer crowd-sourcing.

Session 1 – Amy McGuire, PhD, JD – Am I My Brother’s Keeper?

Dr. McGuire went to college for a very long time. Her list of degrees would take a page or so. She is the Director of the Center for Medical Ethics and Health Policy at Baylor College of Medicine.

Thirteen years ago, Amy’s husband was sitting next to Bennett’s wife on an airplane and she gave him a business card. Then two months ago, Amy wound up sitting next to Max on another airplane. It’s a very small world.

I will tell you that Amy said that her job is asking the difficult questions, not providing the answers. You’ll see from what follows that she is quite good at that.

How is genetic genealogy different from clinical genetics in terms of ethics and privacy? How responsible are we to other family members who share our DNA?

What obligations do we have to relatives in all areas of genetics – both clinical, direct to consumer that related to medical information and then for genetic genealogy.

She referenced the article below, which I blogged about here. There was unfortunately, a lot of fallout in the media.

Identifying Personal Genomes by Surname Inference – Science magazine in January 2013. I blogged about this at the time.

She spoke a bit about the history of this issue.

In 2004, a paper was published that stated that it took only 30 to 80 specifically selected SNPS to identify a person.

2008 – Can you identify an individual from pooled or aggregated or DNA? This is relevant to situations like 911 where the DNA of multiple individuals has been mixed together. Can you identify individuals from that brew?

2005 – 15 year old boy identifies his biological father who was a sperm donor. Is this a good thing or a bad thing? Some feel that it’s unethical and an invasion of the privacy of the father. But others feel that if the donor is concerned about that, they shouldn’t be selling their sperm.

Today, for children conceived from sperm donors, there are now websites available to identify half-siblings.

The movement today is towards making sure that people are informed that their anonymity may not be able to be preserved. DNA is the ultimate identifier.

Genetic Privacy – individual perspectives vary widely. Some individuals are quite concerned and some are not the least bit concerned.

Some of the concern is based in the eugenics movement stemming from the forced sterilization (against their will) of more than 60,000 Americans beginning in 1907. These people were considered to be of no value or injurious to the general population – meaning those institutionalized for mental illness or in prison.

1927 – Buck vs Bell – The Supreme court upheld forced sterilization of a woman who was the third generation institutionalized female for retardation. “Three generations of imbeciles is enough.” I must say, the question this leaves me with is how institutionalized retarded women got pregnant in what was supposed to be a “protected” environment.

Hitler, of course, followed and we all know about the Holocaust.

I will also note here that in my experience, concern is not rooted in Eugenics, but she deals more with medical testing and I deal with genetic genealogy.

The issues of privacy and informed consent have become more important because the technology has improved dramatically and the prices have fallen exponentially.

In 2012, the Nonopore OSB Sequencer was introduced that can sequence an entire genome for about $1000.

Originally, DNA data was provided in open access data bases and was anonymized by removing names. The data base from which the 2013 individuals were identified removed names, but included other identifying information including ages and where the individuals lived. Therefore, using Y-STRs, you could identify these families just like an adoptee utilizes data bases like Y-Search to find their biological father.

Today, research data bases have moved to controlled access, meaning other researchers must apply to have access so that their motivations and purposes can be evaluated.

In a recent medical study, a group of people in a research study were informed and educated about the utility of public data bases and why they are needed versus the tradeoffs, and then they were given a release form providing various options. 53% wanted their info in public domain, 33 in restricted access data bases and 13% wanted no data release. She notes that these were highly motivated people enrolled in a clinical study. Other groups such as Native Americans are much more skeptical.

People who did not release their data were concerned with uncertainly of what might occur in the future.

People want to be respected as a research participant. Most people said they would participate if they were simply asked. So often it’s less about the data and more about how they are treated.

I would concur with Dr. McGuire on this. I know several people who refused to participate in a research study because their results would not be returned to them personally. All they wanted was information and to be treated respectfully.

What the new genetic privacy issues are really all about is whether or not you are releasing data not just about yourself, but about your family as well. What rights or issues do the other family members have relative to your DNA?

Jim Watson, one of the discoverers of DNA, wanted to release his data publicly…except for his inherited Alzheimer’s status. It was redacted, but, you can infer the “answer” from surrounding (flanking regions) DNA. He has two children. How does this affect his children? Should his children sign a consent and release before their father’s genome is published, since part of it is their sequence as well? The academic community was concerned and did not publish this information. Jim Watson published his own.

There is no concrete policy about this within the academic community.

Dr McGuire then referenced the book, “The Immortal Life of Henrietta Lacks”. Henrietta Lacks was a poor African-American woman with ovarian cancer. At that time, in the 1950s, her cancer was considered “waste” and no release was needed as waste could be utilized for research. She was never informed or released anything, but then they were following the protocols of the time. From her cell line, the HeLa cell line, the first immortal cell line was created which ultimately generated a great deal of revenue for research institutes. The family however, remained impoverished. The genome was eventually fully sequenced and published. Henrietta Lacks granddaughter said that this was private family information and should never have been published without permission, even though all of the institutions followed all of the protocols in place.

So, aside from the original ethics issues stemming from the 1950s – who is relevant family? And how does or should this affect policy?

How does this affect genetic genealogy? Should the rules be different for genetic genealogy, assuming there are (will be) standard policies in place for medical genetics? Should you have to talk to family members before anyone DNA tests? Is genetic information different than other types of information?

Should biological relatives be consulted before someone participates in a medical research study as opposed to genetic genealogy? How about when the original tester dies? Who has what rights and interests? What about the unborn? What about when people need DNA sequencing due to cancer or another immediate and severe health condition which have hereditary components. Whose rights trump whose?

Today, the data protections are primarily via data base access restrictions.

Dr. Mcguire feels the way to protect people is through laws like GINA (Genomic Information Nondiscrimination Act) which protects people from discrimination, but does not reach to all industries like life insurance.

Is this different than people posting photos of family members or other private information without permission on public sites?

While much of Dr. McGuire’s focus in on medical testing and ethics, the topic surely is applicable to genetic genealogy as well and will eventually spill over. However, I shudder to think that someone would have to get permission from their relatives before they can have a Y-line DNA test. Yes, there is information that becomes available from these tests, including haplogroup information which has the potential to make people uncomfortable if they expected a different ethnicity than what they receive or an undocumented adoption is involved. However, doesn’t the DNA carrier have the right to know, and does their right to know what is in their body override the concerns about relatives who should (but might not) share the same haplogroup and paternal line information?

And as one person submitted as a question at the end of the session, isn’t that cat already out of the bag?

Session 2 – Dr. Miguel Vilar – Geno 2.0 Update and 2014 Tree

Dr. Vilar is the Science manager for the National Geographic’s Genographic Project.

“The greatest book written is inside of us.”

Miguel is a molecular anthropologist and science writer at the University of Pennsylvania. He has a special interest in Puerto Rico which has 60% Native mitochondrial DNA – the highest percentage of Native American DNA of any Caribbean Island.

The Genographic project has 3 parts, the indigenous population testing, the Legacy project which provides grants back to the indigenous community and the public participation portion which is the part where we purchase kits and test.

Below, Dr. Vilars discussed the Legacy portion of the project.

The indigenous population aspect focuses both on modern indigenous and ancient DNA as well. This information, cumulatively, is used to reconstruct human population migratory routes.

These include 72,000 samples collected 2005-2012 in 12 research centers on 6 continents. Many of these are working with indigenous samples, including Africa and Australia.

42 academic manuscripts and >80 conference presentations have come forth from the project. More are in the pipeline.

Most recently, a Science paper was published about the spread of mtDNA throughout Europe across the past 5000 years. More than 360 ancient samples were collected across several different time periods. There seems to be a divide in the record about 7000 years ago when several disappear and some of the more well known haplogroups today appear on the scene.

Nat Geo has funded 7 new scientific grants since the Geno 2.0 portion began for autosomal including locations in Australia, Puerto Rico and others.

Public participants – Geno 1.0 went over 500,000 participants, Geno 2.0 has over 80,000 participants to date.

Dr. Vilar mentioned that between 2008 and today, the Y tree has grown exponentially. That’s for sure. “We are reshaping the tree in an enormous way.” What was once believed to very homogenous, but in reality, as it drills down to the tips, it’s very heterogenous – a great deal of diversity.

As anyone who works with this information on a daily basis knows, that is probably the understatement of the year. The Geno 2.0 project, the Walk the Y along with various other private labs are discovering new SNPs more rapidly than they can be placed on the Y tree. Unfortunately, this has led to multiple trees, none of which are either “official” or “up to date.” This isn’t meant as a criticism, but more a testimony of just how fast this part of the field is emerging. I’m hopeful that we will see a tree in 2014, even if it is an interim tree. In fact, Dr. Vilars referred to the 2014 tree.

Next week, the Nat Geo team goes to Ireland and will be looking for the first migrants and settlers in Ireland – both for Y DNA and mitochondrial DNA. Dr. Vilars says “something happened” about 4000 years ago that changed the frequency of the various haplogroups found in the population. This “something” is not well understood today but he feels it may be a cultural movement of some sort and is still being studied.

Nat Geo is also focused on haplogroup Q in regions from the Arctic to South America. Q-M3 has also been found in the Caribbean for the first time, marking a migration up the chain of islands from Mexico and South America within the past 5,000 years. Papers are coming within the next year about this.

They anticipate that interest will double within the next year. They expect that based on recent discoveries, the 2015 Y tree will be much larger yet. Dr. Michael Hammer will speak tomorrow on the Y tree.

Nat Geo will introduce a “new chip by next year.” The new Ireland data should be available on the National Geographic website within a couple of weeks.

They are also in the process up updating the website with new heat maps and stories.

Session 3 – Matt Dexter – Autosomal Analyses

Matt is a surname administrator, an adoptee and has a BS in Computer Science. Matt is a relatively new admin, as these things go, beginning his adoptive search in 2008.

Matt found out as a child that he was adopted through a family arrangement. He contacted his birth mother as an adult. She told him who his father was who subsequently took a paternity test which disclosed that the man believed to be his biological father, was not. Unfortunately, his ‘father’ had been very excited to be contacted by Matt, and then, of course, was very disappointed to discover that Matt was not his biological child.

Matt asked his mother about this, and she indicated that yes, “there was another guy, but I told him that the other guy was your father.’ With that, Matt began the search for his biological father.

In order to narrow the candidates, his mother agreed to test, so by process of elimination, Matt now knows which side of his family his autosomal results are from.

Matt covers how autosomal DNA works.

This search has led Matt to an interest in how DNA is passed in general, and specifically from grandparents to grandchildren.

One advantage he has is that he has five children whose DNA he can then compare to his wife and three of their grandparents, inferring of course, the 4^th grandparent by process of elimination. While his children’s DNA doesn’t help him identify his father, it did give him a lot of data to work with to learn about how to use and interpret autosomal DNA. Here, Matt is discussing his children’s inheritance.

Session 4 – Jeffrey Mark Paul – Differences in Autosomal DNA Characteristics between Jewish and Non-Jewish Populations and Implications for the Family Finder Test

Dr.Jeffrey Paul, who has a doctorate in Public Health from John Hopkins, noticed that his and his wife’s Family Finder results were quite different, and he wanted to know why. Why did he, Jewish, have so many more?

There are 84 participants in the Jewish project that he used for the autosomal comparison.

What factors make Ashkenazi Jews endogamous. The Ashkenazi represent 80%of world’sJewish population.

Arranged marriages based on family backgrounds. Rabbinical lineages are highly esteemed and they became very inbred with cousins marrying cousins for generations.

Cultural and legal restrictions restrict Jewish movements and who they could marry.

Overprediction, meaning people being listed as being cousins more closely than they are, is one of the problems resulting from the endogamous population issue. Some labs “correct” for this issue, but the actual accuracy of the correction is unknown.

Jeffrey compared his FTDNA Family Finder test with the expected results for known relatives and he finds the results linear – meaning that the results line up with the expected match percentages for unrelated relatives. This means that FTDNA’s Jewish “correction” seems to be working quite well. Of course, they do have a great family group with which to calibrate their product. Bennett’s family is Jewish.

Jeffrey has downloaded the results of group participants into MSAccess and generates queries to test the hypothesis that Jewish participants have more matches than a non-Jewish control group.

The Jewish group had approximately a total of 7% total non-Ashkenazi Jewish in their Population Finder results, meaning European and Middle Eastern Jewish. The non-Jewish group had almost exactly the opposite results.

Jewish people have from 1500-2100 matches.
Interfaith 700-1100 (Jewish and non)
NonJewish 60-616

Jewish people match almost 33% of the other Jewish people in the project. Jewish people match both Jewish and Interfaith families. NonJewish families match NonJewish and interfaith matches.

Jeffrey mentioned that many people have Jewish ancestry that they are unaware of.

This session was quite interesting. This study while conducted on the Jewish population, still applies to other endogamous populations that are heavily intermarried. One of the differences between Jewish populations and other groups, such as Amish, Brethren, Mennonite and Native American groups is that there are many Jewish populations that are still unmixed, where most of these other groups are currently intermixed, although of course there are some exceptions. Furthermore, the Jewish community has been endogamous longer than some of the other groups. Between both of those factors, length of endogamy and current mixture level, the Jewish population is probably much more highly admixed than any other group that could be readily studied.

Due to this constant redistribution of Jewish DNA within the same population, many Jewish people have a very high percentage of distant cousin relationships.

For non-Jewish people, if you are finding match number is the endogamous range, and a very high number of distant cousins, proportionally, you might want to consider the possibility that some of your ancestors descend from an endogamous population.

Unfortunately, the photo of Dr. Paul was unuseable. I knew I should have taken my “real camera.”

Session 5 – Finding Your Indian Prince(ss) Without Having to Kiss Too Many Frogs

This was my session, and I’ll write about it later.

Someone did get a photo, which I’ve lifted from Jennifer Zinck’s great blog (thank you Jennifer), Ancestor Central. In fact, you can see her writeup for Day 1 here and she is probably writing Day 2’s article as I type this, so watch for it too.

Session 6 – Roundtable – Y-SNPs, hosted by Roberta Estes, Rebekah Canada and Marie Rundquist

At the end of the day, after the breakout sessions, roundtable discussions were held. There were several topics. Rebekah Canada, Marie Rundquist and I together “hostessed” the Y DNA and SNP discussion group, which was quite well attended. We had a wide range of expertise in the group and answered many questions. One really good aspect of these types of arrangements is that they are really set up for the participants to interact as well. In our group, for example, we got the question about what is a public versus a private SNP, and Terry Barton who was attending the session answered the question by telling about his “private” Barton SNPs which are no longer considered private because they have now been found in three other surname individuals/groups. This means they are listed on the “tree.” So sometimes public and private can simply be a matter of timing and discovery.

Here’s Bennett leading another roundtable discussion.

Session 7 – Dr. David Mittleman

Dr. Mittleman has a PhD in genetics, is a professor as well as an entrepreneur. He was one of the partners in Arpeggi and came along to Gene by Gene with the acquisition. He seems to be the perfect mixture of techie geek, scientist and businessman.

He began his session by talking a bit about the history of DNA sequencing, next generation sequencing and a discussion about the expectation of privacy and how that has changed in the past few years with Google which was launched in 2006 and Facebook in 2010.

David also discussed how the prices have dropped exponentially in the past few years based on the increase in the sophistication of technology. Today, Y SNPs individually cost $39 to test, but for $199 at Nat Geo you can test 12,000 Y SNPs.

The WTY test, now discontinued tsted about 300,000 SNPs on the Y. It cost between $950 (if you were willing to make your results public) and $1500 (if the results were private,)

Today, the Y chromosome can be sequenced on the Illumina chip which is the same chip that Nat Geo used and that the autosomal testing uses as well. Family Tree DNA announced their new Big Y product that will sequence 10 million positions and 25,000 known SNPs for an introductory sale price of $495 for existing customers. This is not a test that a new customer would ever order. The test will normally cost $695.

Candid Shots

Tech row in the back of the room – Elliott Greenspan at left seated at the table.

ISOGG Reception

The ISOGG reception is one of my favorite parts of the conference because everyone comes together, can sit in groups and chat, and the “arrival” adrenaline has worn off a bit. We tend to strategize, share success stories, help each other with sticky problems and otherwise have a great time. We all bring food or drink and sometimes pitch in to rent the room. We also spill out into the hallways where our impromptu “meetings” generally happen. And we do terribly, terribly geeky things like passing our iPhones around with our chromosome painting for everyone to see. Do we know how to party or what???

Here’s Linda Magellan working hard during the reception. I think she’s ordering the Big Y actually. We had several orders placed by admins during the conference.

We stayed up way too late visiting and the ISOGG meeting starts at 8 AM tomorrow!

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Ancestor of Native Americans in Asia was 30% “Western Eurasian”

Posted on October 25, 2013 by Roberta Estes

The complete genome has recently been sequenced from 4 year old Russian boy who died 24,000 years ago near Lake Baikal in a location called Mal’ta, the area in Asia believed to be the origin of the Native Americans based on Y DNA and mitochondrial chromosome similarities. The map below, from Science News, shows the location.

This represents the oldest complete genome ever sequenced, except for the Neanderthal (38,000 years old) and Denisovan (41,000 years old).

This child’s genome shows that he is related closely to Native Americans, and, surprisingly, to western Asians/eastern Europeans, but not to eastern Asians, to whom Native Americans are closely related. This implies that this child was a member of part of a “tribe” that had not yet merged or intermarried with the Eastern Asians (Japan, China, etc.) that then became the original Native Americans who migrated across the Beringian land bridge between about 15,000 and 20,000 years ago.

One of the most surprising results is that about 30% of this child’s genome is Eurasian, meaning from Europe and western Asia, including his Y haplogroup which was R and his mitochondrial haplogroup which was U, both today considered European.

This does not imply that R and U are Native American haplogroups or that they are found among Native American tribes before European admixture in the past several hundred years. There is still absolutely no evidence in the Americas, in burials, for any haplogroups other than subgroups of Q and C for males and A, B, C, D, X and M (1 instance) for females. However, that doesn’t mean that additional evidence won’t be found in the future.

While this is certainly new information, it’s not unprecedented. Last year, in the journal Genetics, an article titled “Ancient Admixture in Human History” reported something similar, albeit gene flow in a different direction. This paper indicated gene flow from the Lake Baikal area to Europe. It certainly could have been bidirectional, and this new paper certainly suggests that it was.

So in essence, maybe there is a little bit of Native American in Europeans and a little bit of European in Native Americans that occurred in their deep ancestry, not in the past 500-1000 years.

What’s next? Work continues. The team is now attempting to sequence genomes from other skeletons from west of Mal’ta, East Asia and from the Americas as well.

You can read the article in Science Magazine. An academic article presenting their findings in detail will be published shortly in Nature.

A Podcast with Michael Balter can be heard here discussing the recent discovery.

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Determining Ethnicity Percentages

Posted on October 19, 2013 by Roberta Estes

Recently, as a comment to one of my blog postings, someone asked how the testing companies can reach so far back in time and tell you about your ancestors. Great question.

The tests that reliably reach the furthest back, of course, are the direct line Y-Line and mitochondrial DNA tests, but the commenter was really asking about the ethnicity predictions. Those tests are known as BGA, or biogeographical ancestry tests, but most people just think of them or refer to them as the ethnicity tests.

Currently, Family Tree DNA, 23andMe and Ancestry.com all provide this function as a part of their autosomal product along with the Genographic 2.0 test. In addition, third party tools available at www.gedmatch.com don’t provide testing, but allow you to expand what you can learn with their admixture tools if you upload your raw data files to their site. I wrote about how to use these ethnicity tools in “The Autosomal Me” series. I’ve also written about how accurate ethnicity predictions from testing companies are, or aren’t, here, here and here.

But today, I’d like to just briefly review the 3 steps in ethnicity prediction, and how those steps are accomplished. It’s simple, really, in concept, but like everything else, the devil is in the details.

There are three fundamental steps.

Creation of the underlying population data base.
Individual DNA extraction.
Comparison to the underlying population data base.

Step 1: Creation of the underlying population data base.

Don’t we wish this was as simple as it sounds. It isn’t. In fact, this step is the underpinnings of the accuracy of the ethnicity predictions. The old GIGO (garbage in, garbage out) concept applies here.

How do researchers today obtain samples of what ancestral populations looked like, genetically? Of course, the evident answer is through burials, but burials are not only few and far between, the DNA often does not amplify, or isn’t obtainable at all, and when it is, we really don’t have any way to know if we have a representative sample of the indigenous population (at that point in time) or a group of travelers passing through. So, by and large, with few exceptions, ancient DNA isn’t a readily available option.

The second way to obtain this type of information is to sample current populations, preferably ones in isolated regions, not prone to in-movement, like small villages in mountain valleys, for example, that have been stable “forever.” This is the approach the National Geographic Society takes and a good part of what the Genograpic Geno 2.0 project funding does. Indigenous populations are in most cases our most reliable link to the past. These resources, combined with what we know about population movement and history are very telling. In fact, National Geographic included over 75,000 AIMs (Ancestrally Informative Markers) on the Geno 2.0 chip when it was released.

The third way to obtain this type of information is by inference. Both Ancestry.com and 23andMe do some of this. Ancestry released its V2 ethnicity updates this week, and as a part of that update, they included a white paper available to DNA participants. In that paper, Ancestry discusses their process for utilizing contributed pedigree charts and states that, aside from immigrant locations, such as the United States and Canada, a common location for 4 grandparents is sufficient information to include that individuals DNA as “native” to that location. Ancestry used 3000 samples in their new ethnicity predictions to cover 26 geographic locations. That’s only 115 samples, on average, per location to represent all of that population. That’s pretty slim pickins. Their most highly represented area is Eastern Europe with 432 samples and the least represented is Mali with 16. The regions they cover are shown below.

Survey Monkey, a widely utilized web survey company, in their FAQ about Survey Size For Accuracy provides guidelines for obtaining a representative sample. Take a look. No matter which calculations you use relative to acceptable Margin of Error and Confidence Level, Ancestry’s sample size is extremely light.

23andMe states in their FAQ that their ethnicity prediction, called Ancestry Composition covers 22 reference populations and that they utilize public reference datasets in addition to their clients’ with known ancestry.

23andMe asks geographic ancestry questions of their customers in the “where are you from” survey, then incorporates the results of individuals with all 4 grandparents from a particular country. One of the ways they utilize this data is to show you where on your chromosomes you match people whose 4 grandparents are from the same country. In their tutorial, they do caution that just because a grandparent was born in a particular location doesn’t necessarily mean that they were originally from that location. This is particularly true in the past few generations, since the industrial revolution. However, it may still be a useful tool, when taken with the requisite grain of salt.

The third way of creating the underlying population data base is to utilize academically published information or information otherwise available. For example, the Human Genome Diversity Project (HGDP) information which represents 1050 individuals from 52 world populations is available for scrutiny. Ancestry, in their paper, states that they utilized the HGDP data in addition to their own customer database as well as the Sorenson data, which they recently purchased.

Academically published articles are available as well. Family Tree DNA utilizes 52 different populations in their reference data base. They utilize published academic papers and the specific list is provided in their FAQ.

As you can see, there are different approaches and tools. Depending on which of these tools are utilized, the underlying data base may look dramatically different, and the information held in the underlying data base will assuredly affect the results.

Step 2: Your Individual DNA Extraction

This is actually the easy part – where you send your swab or spit off to the lab and have it processed. All three of the main players utilize chip technology today. For example, 23andMe focuses on and therefore utilizes medical SNPs, where Family Tree DNA actively avoids anything that reports medical information, and does not utilize those SNPs.

In Ancestry’s white paper, they provide an excellent graphic of how, at the molecular level, your DNA begins to provide information about the geographic location of your ancestors. At each DNA location, or address, you have two alleles, one from each parent. These alleles can have one of 4 values, or nucleotides, at each location, represented by the abbreviations T, A, C and G, short for Thymine, Adenine, Cytosine and Guanine. Based on their values, and how frequently those values are found in comparison populations, we begin to fine correlations in geography, which takes us to the next step.

Step 3: Comparison to Underlying Population Data Base

Now that we have the two individual components in our recipe for ethnicity, a population reference set and your DNA results, we need to combine them.

After DNA extraction, your individual results are compared to the underlying data base. Of course, the accuracy will depend on the quality, diversity, coverage and quantity of the underlying data base, and it will also depend on how many markers are being utilized or compared.

For example, Family Tree DNA utilizes about 295,000 out of 710,000 autosomal SNPs tested for ethnicity prediction. Ancestry’s V1 product utilized about 30,000, but that has increased now to about 300,000 in the 2.0 version.

When comparing your alleles to the underlying data set one by one, patterns emerge, and it’s the patterns that are important. To begin with, T, A, C and G are not absent entirely in any population, so looking at the results, it then becomes a statistics game. This means that, as Ancestry’s graphic, above, shows, it becomes a matter of relativity (pardon the pun), and a matter of percentages.

For example, if the A allele above is shown is high frequencies in Eastern Europe, but in lower frequencies elsewhere, that’s good data, but may not by itself be relevant. However if an entire segment of locations, like a street of DNA addresses, are found in high percentages in Eastern Europe, then that begins to be a pattern. If you have several streets in the city of You that are from Eastern Europe, then that suggests strongly that some of your ancestors were from that region.

To show this in more detailed format, I’m shifting to the third party tool, GedMatch and one of their admixture tools. I utilized this when writing the series, “The Autosomal Me” and in Part 2, “The Ancestor’s Speak,” I showed this example segment of DNA.

On the graph below, which is my chromosome painting of one a small part of one of my chromosomes on the top, and my mother’s showing the exact same segment on the bottom, the various types of ethnicity are colored, or painted.

The grid shows location, or address, 120 on the chromosome and each tick mark is another number, so 121, 122, etc. It’s numbered so we can keep track of where we are on the chromosome.

You can readily see that both of us have a primary ethnicity of North European, shown by the teal. This means that for this entire segment, the results are that our alleles are found in the highest frequencies in that region.

However, notice the South Asian, East Asian, Caucus, and North Amerindian. The important part to notice here, other than I didn’t inherit much of that segment at 123-127 from her, except for a small part of East Asian, is that these minority ethnicities tend to nest together. Of course, this makes sense if you think about it. Native Americans would carry Asian DNA, because that is where their ancestors lived. By the same token, so would Germans and Polish people, given the history of invasion by the Mongols. Well, now, that’s kind of a monkey-wrench isn’t it???

This illustrates why the results may sometimes be confusing as well as how difficult it is to “identify” an ethnicity. Furthermore, small segments such as this are often “not reported” by the testing companies because they fall under the “noise” threshold of between about 5 and 7cM, depending on the company, unless there are a lot of them and together they add up to be substantial.

In Summary

In an ideal world, we would have one resource that combines all of these tools. Of course, these companies are “for profit,” except for National Geographic, and they are not going to be sharing their resources anytime soon.

I think it’s clear that the underlying data bases need to be expanded substantially. The reliability of utilizing contributed pedigrees as representative of a population indigenous to an area is also questionable, especially pedigrees that only reach back two generations.

All of these tools are still in their infancy. Both Ancestry and Family Tree DNA’s ethnicity tools are labeled as Beta. There is useful information to be gleaned, but don’t take the results too seriously. Look at them more as establishing a pattern. If you want to take a deeper dive by utilizing your raw data and downloading it to GedMatch, you can certainly do so. The Autosomal Me series shows you how.

Just keep in mind that with ethnicity predictions, with all of the vendors, as is particularly evident when comparing results from multiple vendors, “your mileage may vary.” Now you know why!

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