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

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 fromClovis point 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.

Clovis mtDNA

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.

Clovis Y

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.

Clovis autosomal cropped

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.

Clovis branch

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.

who matches who

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.

Neanderthal Genome Further Defined in Contemporary Eurasians

DNA X

A new study released by Howard Hughes Medical Institute at Harvard Medical School on January 29th 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.”

2013’s Dynamic Dozen – Top Genetic Genealogy Happenings

dna 8 ball

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 22nd 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 22nd, 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….

Sequencing of Neanderthal Toe Bone Reveals Unknown Hominin Line

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

Neanderthal 12-22-2013 cropped

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

  1. The skeleton showed physical traits of both Neanderthals and modern humans and is thought to be about 50,000 years old.
  2. 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.
  3. 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.
  4. 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.
  5. This unknown line could be homo erectus.
  6. 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.
  7. 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.
  8. 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.
  9. 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.”

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

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 20th, 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.

native flow map

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 Asians1, 2, 3, there is no consensus with regard to which specific Old World populations they are closest to4, 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-gatherers10, 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.

Native flow Hap U map

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.

Native flow Brandt map

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.

Native flow R tree

 native flow r tree text

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

Native flow R map

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

Native flow Q map

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 Asians2, 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.

Native flow Otzi table

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 9th 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.

Native flow basic Y

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.

Native flow hammer dist

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

2013 Family Tree DNA Conference Day 2

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.

Bennett day 2 intro

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.

Hammer 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.

hammer ancient y

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.

hammer backbone

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

hammer post neolithic epicenters

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.

hammer hap k

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.

hammer r and q in 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.

Hammer hap r dist

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

hammer haplogroup dispersion map

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.

marja

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.

Goodbyes

See y’all next year!!!

2013 Family Tree DNA Conference Day 1

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.

10th 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.

Plaque Max and Me 2013

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 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.

Mcguire

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.

Villars

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 4th 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.

Matt dexter

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.

 Estes Indian Princess photo

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.

FTDNA roundtable 2013

Here’s Bennett leading another roundtable discussion.

roundtable bennett

Session 7 – Dr. David Mittleman

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.

tech row

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.

Magellan

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

Ancestry’s Updated V2 Ethnicity Summary

Today when I signed onto Ancestry.com, I was greated with a message that my new Ethnicity Estimate Preview was ready for viewing.  Yippee!

Ancestry v2 1

Ancestry announced some time back that they were updating this function.  Release 1 was so poor that it should never have been released.  However, V2 is somewhat improved.  In any case, it’s different. Let’s take a look.

The graphic below shows my initial, V1 results, which bore very little resemblance to my ancestry.  My V1 results are shown below, and they are still shown on my page at Ancestry.  I was pleased so see that so I have a reference for comparison.

ancestry v2 2

Some years back, I did a pedigree analysis of my genealogy in an attempt to make sense of autosomal results from other companies.

The paper, “Revealing American Indian and Minority Heritage using Y-line, Mitochondrial, Autosomal and X Chromosomal Testing Data Combined with Pedigree Analysis” was published in the Fall 2010 issue of JoGG, Vol. 6 issue 1.

The pedigree analysis portion of this document begins about page 8.  My ancestral breakdown is as follows:

Geography Percent
Germany 23.8041
British Isles 22.6104
Holland 14.5511
European by DNA 6.8362
France 6.6113
Switzerland .7813
Native American .2933
Turkish .0031

This leaves about 25% unknown.  However, this looks nothing like the 80% British Isles and the 12% Scandinavian in Ancestry’s V1 product.

In an article titled, “Ethnicity Results, True or Not” I compared my pedigree information with the results from all the testing vendors, including Ancestry’s V1 information.  Needless to say, they didn’t fare very well.

The next screen you see talks about what’s new, but being very anxious to see the results, I bypassed that for the moment to see my new results shown below.

ancestry v2 3

My initial reaction was that I was very excited to see both my Native and African admixture shown.  I thought maybe Ancestry had actually hit a home run.  Then I looked down and saw the rest.  Uh, no home run I’m afraid.  Shucks.  Clicking on the little plus signs provide this view.

ancestry v2 4

I noticed the little box at the bottom that says “show all regions,” so I clicked there.  The only difference between that display and the one above is that the regions with zero displayed as well.

My updated V2 results show primarily Western European and Scandinavian.  I certainly won’t argue with the western European, although the percentage seems quite high, but there is absolutely NO indication that I have any Scandinavian heritage, let alone 10%, and my British Isles is dramatically reduced.

Here are the two results side by side, in percentages, with my commentary.

Location Ancestry V1 Ancestry V2 My Pedigree Comments
British Isles 80 Great Britain 4, Ireland 2 22 Great Britain includes Scotland
Scandinavia 12 10 0
Italy/Greece 0 2 Turkish <1
North Africa 0 <1 0
Native American 0 <1 <1
East Asian 0 <1 0 Probably Native American
Western Europe 0 79 51
Uncertain 8 0 25

I am not going to take issue with any of the small percentages.  I fully understand how difficult trace ethnicity is to decipher.  My concern here is with the “big chunks,” because if the big chunks aren’t correct, there is also no confidence in the small ones.

I’m left wondering about the following:

  • I went from 80% British Isles in V1, which we knew was incorrect, to 6% in V2, which is also incorrect.  I have at least 22% British Isles.
  • I went from being 0% Western European in V1 to 79% in V2, which is also incorrect.  Now granted, I do have 25% uncertain in my own pedigree, and given that I’m a cultural mixture, some of that certainly could be western European.  But all of it?  Given where my ancestor were found in colonial America, and when, it’s much more likely that the majority of the 25% that is uncertain in my pedigree chart would be British Isles.
  • Would you look at the V1 results and the V2 results, side by side, and believe for one minute they were describing the same person?  This is not a minor revision and there is very little consistency between the two – only 16%.  That means that 84% changed between the two versions.  And in that 16% is that pesky, unexplained Scandinavian, not found, by the way, by any other testing company.  Yes, I know about the Vikings, but still, 10 or 12%?  That’s equivalent to a great-grandparent, not trace amounts from centuries ago.

So V2 seems to be somewhat better, I think, but still no place close to what is known to be correct.  Based on the V2 results, which seem to have very little resemblance to the V1 results, I can’t help but wonder why Ancestry would have published such highly incorrect results for V1, and then adamantly defended those results, publishing videos, etc.  Doesn’t a corporation have some responsibility to their customers to provide correct information, and if they can’t, to be smart enough to know that and to not publish anything?  And if it’s the same technical team behind the scenes, how do we know that V2 isn’t equally as flawed, given that the results still don’t seem to jive with my known (and for the most part, DNA proven) pedigree chart?

One thing Ancestry has done that is an improvement is to provide additional information about their process for determining admixture and what has changed in the V2 version.  I went back and looked at the “What’s New” information that I skipped in my excitement to see my new results.  In that information, they provide the following bullets:

  • They increased the number of markers used for comparison from 30,000 to 300,000.
  • They increased the analysis passes from 1 to 40.  This is further explained in their white paper.
  • They broke Europe into 4 regions.
  • They broke West Africa into 6 regions.

ancestry v2 6

  • They updated the regions covered.  The V2 reference panel contains 3,000 samples that represent 26 distinct overlapping global regions (Table 3.1, below, from their white paper).  V1 covered 22 regions.

Region

# Samples

Great Britain 111
Ireland 138
Europe East 432
Iberian Peninsula 81
European Jewish 189
Europe North 232
Europe South 171
Europe West 166
Finnish/Northern Russian 59
Africa Southeastern Bantu 18
Africa North 26
Africa Southcentral Hunter Gatherers 35
Benin/Togo 60
Cameroon/Congo 115
Ivory/Ghana 99
Mali 16
Nigeria 67
Senegal 28
Native American 131
Asia Central 26
Asia East 394
Asia South 161
Melanesia 28
Polynesia 18
Caucasus 58
Near East 141
Total
  • Ancestry provided a white paper on their methods which explains how these ethnicity estimates are created.  This is very important and I applaud them for their transparency.  Unfortunately, you can’t see the white paper unless you are a subscriber and have taken their autosomal DNA test.  If you have, to see the white paper, click on the little question mark in the upper right hand corner of the ethnicity results page, then on the “whitepaper” icon.

ancestry v2 7

How Are Ethnicity Percentages Created?

Wanting to understand the process they are using, I moved to their educational maternal and Ethnicity Estimate white paper, which, unfortunately I can’t link to.  You must be a subscriber to see this document.

The first thing I discovered is that they utilized 3000 DNA samples as a reference data base, including the Humane Genome Diversity Project data utilized by all researchers in this field.

ancestry v2 8

From their white paper:

“In developing the AncestryDNA ethnicity estimation V2 reference panel, we begin with a candidate set of 4,245 individuals. First, we examine over 800 samples from 52 worldwide populations from a public project called the Human Genome Diversity Project (HGDP) (Cann et al. 2002; Cavalli-Sforza 2005). Second, we examine samples from a proprietary AncestryDNA reference collection as well as AncestryDNA samples from customers consenting to participate in research. To obtain candidate reference panel candidates from these two sets, family trees are first consulted, and a sample is included in the candidate set if all lineages trace back to the same geographic region. Although this was not possible for HGDP samples, this dataset was explicitly designed to sample a large set of populations representing a global picture of human genetic variation.

In total, our reference panel candidates include over 800 HGDP samples, over 1,500 samples from the proprietary AncestryDNA reference collection, and over 1,800 AncestryDNA customers who have explicitly consented to be included in the reference panel.”

I’m assuming that the proprietary reference collection they mention is the Sorenson data they purchased in July 2012.  The Sorenson data base was compiled from individual donors who contributed the DNA samples and pedigree charts but without any supporting documentation.

So in addition to the publicly available data, Ancestry has utilized both the Sorenson and their own data bases.  That makes sense.  It may also be the root of the problem.

There’s another quote from their paper:

“Fortunately, knowing where your grandparents are born is often a sufficient proxy for much deeper ancestry. In the recent past, it was much more difficult and thus less common for people to migrate large distances. Because of this, it is frequently the case that the birthplace of your grandparents represents a much more ancient ancestral origin for your DNA.”

They do say that this does not apply to people in America, for example.

However, how many of you have confidence in the Ancestry trees, or any trees submitted, for that matter, in public data bases.  Ancestry only allows you to attach “facts” found in their data base.  This means, for example, if you want to upload your Gedcom file that has pages and pages of documentation including wills, tax lists, and other primary sorts of documentation, you can’t.  Well, you can, but only if you copy it off into a word document and attach it separately to that person one page at a time.  In other words, Ancestry isn’t interested in any documentation or research that you’ve done elsewhere.  This also means that they have few tools themselves to determine whether your tree is accurate, especially once you get beyond the census years with family enumeration – meaning 1850 in the US.  What this means is that the only reliable references they have are their own data bases, excluding Rootsweb trees.  Ancestry owns Rootsweb too and Rootsweb has always allowed uploads of limited notes attached to people.  Some are exceedingly useful.

If Ancestry is utilizing large numbers of user submitted pedigree charts by which to calibrate or measure ethnicity, that could be a problem.

Let’s run a little experiment.  I am very familiar with the original records pertaining to Abraham Estes, born in 1647 in Nonington, Kent, England and who died in 1720 in King and Queen County, Virginia.  I have been a primary records researcher on this man for 25 years.  Not only are his records documented, but so are those of several preceding generations through church records in England.  In other words, we know what we know and what we don’t know.  We do NOT know his second wife’s surname, although there is a pervasive myth as to what it was, which is entirely unsubstantiated.

I entered his name/birth year into Ancestry’s search tool and I looked at the first 20 records show in their “Family Trees.”  I wanted to see how many displayed correct or incorrect information.  Ancestry displays these trees in order, based, apparently, on the number of source or attached records, implying records with more sources would be better to utilize.  That would generally be quite true.  Unfortunately, sources are often the IGI or Family Data Collection, which are also “unsourced,” creating a vicious cycle of undocumented rumors cited as sources.  Let’s take a look at what we have.

Record # Incorrect Info Listed Correct Info Listed Grandparents Info Present/Correct
1 First wife’s name entirely incorrect, but linked to correct original record.  Second wife’s surname entirely undocumented.  Multiple family crests listed but family was not armorial.  Children listed multiple times.  Son, Abraham’s records attached to father. Birth year and location. Death date and location. No
2 First wife entirely missing. Second wife’s surname entirely undocumented. Marriage date entirely undocumented.  Third, unknown spouse listed with the same children given to spouse 2 and 3. Birth year and location.    Death date and location. No
3 Abraham was given fictitious middle name.  Second wife’s surname entirely undocumented.  Most children missing and the two that are on the list are given fictitious middle names.  Marriage date for second wife is entirely undocumented. Birth year and location, first marriage, death date and   location. No
4 First wife’s surname missing.  Second wife’s surname entirely   undocumented.  Have land transaction attached to him 13 years after he died.  Incorrect childen. Birth date and location, first wife’s first name and date   of marriage, death date and location. No
5 Shows marriage for first and second wife on same   day/place.  First wife’s name entirely wrong.  Shows a second marriage date to second wife.  Second wife’s surname  entirely undocumented.  No burial   location known, but burial location given.  Incorrect children. Birth year and location. No

After these first 5 records, I became discouraged and did not type the balance of the 15 records.  Not one displayed only correct information, nor did any have the man’s parents and grandparents names and birth locations documented correctly.  So much for using family trees as sources.

If Ancestry is assuming that where your grandfather was born is representative of where your family was originally from, if you are from a non-immigrant location (i.e. not the US, not Canada, not Australia, etc.), that too might be a problem.  There has been a lot of movement in the British Isles, for example, since the industrial revolution, particularly in the 1800s.  Where Abraham’s grandfather was born in 1555 is probably relevant, but the grandfather of someone living today is much less predictive.

So, where does this leave us? 

Apparently Ancestry’s V1 was worse than we thought, given that my 80% majority ancestry turned into 6 and my 0% western Europe turned into 79%.  Neither of these are correct.

Ancestry’s V2 seems to be somewhat better, but raises the same types of questions about the results.

Ancestry’s white paper may indeed answer some of those questions, based on their use of contributed pedigree charts.  However, having said that, you would think that they could utilize families with a deep history of ancestry in a specific area, proven by various non-contributed (such as parish or will) records, in a non-urban environment.

Ironically, Ancestry did pick up on both my Native and African minority admixture, but they are still missing the boat on the majority factors, which calls the entire concoction into question.

So the net-net of all of this….it’s still not soup yet.  I’m disappointed and beginning to wonder if it ever will be.

Correlating Historical Facts to DNA Test Results

Sometimes DNA tests hold surprising results, results that the individual didn’t expect.  That’s what happened to Jack Goins, Hawkins County, Tn. Archivist and founder of the Melungeon Core DNA project.  Jack, a Melungeon descendant through several ancestors, expected that his Y paternal haplogroup would be either European or Native American, based on oral family history, but it wasn’t, it was E1b1a, African.

Jack’s family and ancestors were key members of the Melungeon families found in Hawkins and Hancock Counties in Tennessee beginning in the early 1800s.  In order to discover more about this group of people, which included but was not limited to his own ancestors, Jack founded the Melungeon DNA projects.

Over time, descendants of most of the family lines had representatives test within both a Y-line and mitochondrial DNA project.  The results were a paper, Melungeons: A Multi-Ethnic Population, published in JOGG, the Journal of Genetic Genealogy, in April 2012.

Many people expected to discover that the Melungeons were primarily Native American, but this was not the outcome of the DNA project.  In fact, many of the direct paternal male lines were African and all of the direct maternal female lines tested were European.  While there are paper records, in one case, that state that one of the ancestors of the Melungeons was Native American (Riddle), and there is DNA testing of another line that married into the Melungeon families that proves that indirect line is Native American (Sizemore), there is no direct line testing that indicates Native ancestry.

Aside from the uproar the results caused among researchers who were hopeful of a different outcome, it also begs the question of whether the documents we do have of those families support the DNA results.  What did the contemporary people who knew them during their lifetime think about their race?  Census takers, tax men and county clerks?  Are there patterns that emerge?  Sometimes, when we receive new information, be it genetic or otherwise, we need to revisit our documentation and look with a new set of eyes.

It’s common practice in genetic genealogy circles when “undocumented adoptions” are discovered, for example, to revisit the census and look for things like a child’s birthdate being before the parents’ marriage.  Something that went unnoticed during initial data gathering or was assumed to be in error suddenly becomes extremely important, perhaps the key to unraveling what happened to those long-ago ancestors.  Like in all projects, some descendant lines we expected to match, didn’t.

Recently Jack Goins undertook such an analysis of the documentary records collected over the years in the various counties where the Melungeon families or their direct ancestors lived.  We know that today, and in the 1900s, most of these families appear physically primarily European, an observation supported by autosomal DNA testing.  So we’re looking for records that indicate minority admixture.

Do the records indicate that these people were black, Native, European, mixed or something else, like Portuguese?  Was the African admixture recent, so recent that their descendants were viewed as mixed-race, or were the African haplogroups introduced long ago, hundreds or thousands of years ago perhaps, maybe in Mediterranean Europe?  If that was the case, then the Melungeon ancestors in America would have been considered “European,” meaning they looked white.  What do the records say about these families?  Were they uniformly considered white, black, mixed or Native in all of the locations where family members moved as they dispersed out of colonial Virginia?

If these men were Native Americans, would they have likely fought against the Indians in the French and Indian War in 1754?  Melungeon ancestors did just that and they are specifically noted as fighting “against the Shawnee.”  Their families were found in census records as “free people of color” and “mulatto” countless times which indicates they were not slaves and were not white.  On one later census record, below, in 1880, Portugee was overstricken and W for white entered.

1880 census
1880 census 2

Melungeon families and their ancestors were listed on tax records and other records as mulattoes, never as mustee and only once as Indian.  Mulattoes are typically mixed black and white, although it can be Native and white, while mustee generally means mixed Indian with something else.  On one 1767 tax list, Moses Riddle, a maternal ancestor of a Melungeon family is listed as Indian, but this is the only instance found in the hundreds of records searched.  The Riddle family paternal haplogroup reflects European ancestry so apparently the Indian ancestor originated in a maternal line.

Court records identify Melungeon families as “colored” and “black” and “African” and “free negroes and mulattoes” as well as white.  In the 1840s, a group of Melungeon men, descendants of these individuals classified as mulattoes and free people of color were prosecuted for voting, a civil liberty forbidden to those “not white,” and probably as a political move to make examples of them.  Some of these men were found not guilty, one simply paid the fine, probably to avoid prosecution due to his advanced age, and the cases were dismissed against the rest.  Some were also prosecuted for bi-racial marriage when it was illegal for anyone of mixed heritage to marry a white person.  In earlier cases, in the 1700s in Virginia, these families were prosecuted for “concealing tithables” specifically for not listing their wives, “being mulattoes.”  In another case, the records indicate an individual being referred to as ‘yellow complected,’ a term often used for a light skinned mulatto.  And yet another case states that while the men were “mulattos,” their fathers were free and their wives were white.

There are many records, more than 1600 in total that we indexed and cataloged when writing the paper, and more have surfaced since.  In all of those records, only one contemporaneous record, the 1767 Riddle tax list, states the person was an Indian.  None, other than the 1880 census record, state that they were Portuguese.  There are many that indicate African or mixed heritage, of some description, and there are also many that don’t indicate any admixture.  Especially in later census, as the families outmarried to some extent, they were nearly uniformly listed as white.  Still, this group of people looked “different” enough from their neighbors to be labeled with the derisive name of Melungeon.

While this group, based on mitochondrial DNA testing, did initially marry European women, generations of intermarriage would have caused the entire group to be darker than the nonadmixed European population in the 1700s and 1800s.  By this time, neither they nor their neighbors were sure what they were, so they claimed Portuguese and Indian.  No one claimed to have black ancestors, in fact, most denied it vehemently.  By this time, so many generations had passed that they may not have known the whole truth, and there is indeed evidence of two Indian lines within the Melungeon community.

In light of these records, the DNA results should not have been as surprising as they were.  However, this body of research had never been analyzed as a whole before.

Since the original paper was published, four additional paternal lines documented as Melungeon but without DNA representation/confirmation in the original paper have tested, and all four of them, Nichols, Perkins, Shoemake/Shumach and Bolin/Bolton carry haplogroup E1b1a.  They are not matches to each other or other Melungeon paternal lines, so it’s not a matter of undocumented adoptions within a community.

The DNA project administrators certainly welcome additional participants who descend from the Melungeon families.  Y-line DNA requires a male who descends from a patriarch via all males, given that males pass their Y chromosome to only sons.

There may indeed be Native American lines yet undiscovered within the female or ancestral lines, and we are actively seeking people descended from the wives of these Melungeon families through all women. Mitochondrial DNA, which tests the maternal line, is passed to both genders of children, but only females pass it on.  So to represent your Melungeon maternal ancestor, you must descend from her through all females, but you yourself can be either male or female.

While the primary focus is still to document the various direct family lines utilizing Y-line and mitochondrial DNA, the advent of autosomal testing has opened the door for other Melungeon descendants to test as well.  In fact, the project administrators have organized a separate project for all descendants who have taken the autosomal Family Finder test at Family Tree DNA called the Melungeon Families project.

The list of eligible Melungeon surnames is Bell, Bolton, Bowling, Bolin, Bowlin, Breedlove, Bunch, Collins, Denham, Gibson, Gipson, Goins, Goodman, Minor, Moore, Menley, Morning, Mullins, Nichols, Perkins, Riddle, Sizemore, Shumake, Sullivan, Trent and Williams.  For specifics about the paternal lines, patriarchs and where these families are historically located, please refer to the paper.

Furthermore, anyone with documented proof of additional Melungeon families or surnames is encouraged to provide that as well.  Surnames are only added to the list with proof that the family was referenced as Melungeon from a documented historical record or is ancestral to a documented Melungeon family.  For example, the Sizemore family was never directly referred to as Melungeon in documented sources, but Aggy Sizemore (haplogroup H/European), daughter of George Sizemore (haplogroup Q/Native) married Zachariah Minor (haplogroup E1b1a/African).  The Minor family is one of the Melungeon family names.  So while Sizemore itself is not Melungeon, it is certainly an ancestral name to the Melungeon group.

For more information, read Jack Goins’ article, Written Records Agree with Melungeon DNA Results.

Modern Faces and Ancient Migrations

Navajo - abroad in the Yard

Our friends at Abroad in the Yard wrote an interesting article back in December 2011 about Modern Faces and Ancient Migrations.

As you’re probably aware, the migration of people, their ethnicity and how they came to be where they are today is hotly debated among people who are not warm and friendly, at least not to each other.  There are into and out of Africa theories.  There are debates about the origins of the Aboriginal people of Australia, and there are several debates about the arrival of the Native Americans from Asia.

One of the questions about Native Americans is whether there was one wave or more.  Another question is whether or not the people who populated South America had a different genesis from those who populated North America.  It’s widely accepted that the people who populated North American, at least, arrived via the Bering Strait, although these is still some question about some arrivals from the east, from Europe, via Greenland.  But assuming the Beringia migration path, were these the only people to populate South America?   Were other Asians, Africans, Australians or Patagonians involved?  Did seafaring people settle parts of South America before the Indians arrived?

Looking at the pictures of these people and where they live today is quite interesting, especially when looking at the progression of migration and how their phenotype changes, or doesn’t.  In other words, how they resemble each other and their closest neighbors.

So take a look for yourself.  What do you think?

http://www.abroadintheyard.com/modern-faces-ancient-migration/