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….

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Native Americans, Neanderthal and Denisova Admixture

Denisova cave

Recently, a Neanderthal toe bone yielded enough DNA to sequence the full genome of the woman whose remains were found in the Denisova Cave in the Altai Mountains, shown above.  This information was published in the Journal Nature in an article titled “The complete genome sequence of a Neanderthal from the Altai Mountains” by Prufer et al.  I wrote about what was found here, but it wasn’t until I really read the 200+ pages of supplemental information that I found additional buried information.

The article itself talks about some of the findings relative to Native Americans, but the supplemental information provides additional detail and the supporting charts.

In the paper, the Mixe and the Karitiana people of Mexico and Brazil, respectively were most often used to represent Native Americans.  There are about 90,000 Mixe language speakers alive today, so their population is not small.  However, the Karitiana are just the opposite, with only about 320 people in a very remote region of Brazil.  The Karitiana shun contact with outsiders.  In some parts of this study, additional population groups were used for additional Native samples.

Here’s what the article itself has to say about Neanderthals, Denisovans and Native Americans.

Denisovan gene flow in mainland Asia

We used the two high-coverage archaic genomes and a hidden Markov model (HMM) to identify regions of specifically Neanderthal and specifically Denisovan ancestry in 13 experimentally phased present-day human genomes (Supplementary Information sections 4 and 13). In the Sardinian and French genomes from Europe we find genomic regions of Neanderthal origin and few or no regions of Denisovan origin. In contrast, in the Han Chinese, the Dai in southern China, and the Karitiana and Mixe in the Americas, we find, in addition to regions of Neanderthal origin, regions that are consistent with being of Denisovan origin (Zscore54.3 excess relative to the Europeans) (Supplementary Information section 13), in agreement with previous analysis based on low-coverage archaic genomes. These regions are also more closely related to the Denisova genome than the few regions identified in Europeans (Supplementary Information section 13). We estimate that the Denisovan contribution to mainland Asian and Native American populations is ,0.2% and thus about 25 times smaller than the Denisovan contribution to populations in Papua New Guinea and Australia. The failure to detect any larger Denisovan contribution in the genome of a 40,000-year-old modern human from the Beijing area suggests that any Denisovan contribution to modern humans in mainland Asia was always quantitatively small. In fact, we cannot, at the moment, exclude that the Denisovan contribution to people across mainland Asia is owing to gene flow from ancestors of present-day people in Oceania after they mixed with Denisovans. We also note that in addition to this Denisovan contribution, the genomes of the populations in Asia and America appear to contain more regions of Neanderthal origin than populations in Europe (Supplementary Information sections 13 and 14).

The fascinating part of this, aside from the fact that Native people also carry both Denisovan and Neanderthal DNA, and that they carry more than Europeans, is that the Denisovan and Neanderthal DNA that they carry is different than that carried by Europeans.  In fact, it appears that not all Europeans carry Denisovan DNA and this paper lowers the estimated percentage of Neanderthal for all Europeans.

This difference in the Neanderthal and Denisovan DNA might be able to help solve a long-standing mystery, and that’s whether or not part of the Native population of the Eastern seaboard, and in particular, the far Northeast part of that region, was populated by or admixed with Europeans long before the time of Columbus and other European pre-colonial explorers.  This information, of course would have to come from pre-contact burials, but they do exist and with this new information in hand, they might just yield answers never before available.

Dr. Ricki Lewis, in her DNA Science Blog, mentioned something else quite interesting culled from a Christmas Day issue of Nature titled “Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico.”  In a nutshell, from article introduction, we find this commentary:

“The risk haplotype carries four amino acid substitutions, all in SLC16A11; it is present at ~50% frequency in Native American samples and ~10% in east Asian, but is rare in European and African samples. Analysis of an archaic genome sequence indicated that the risk haplotype introgressed into modern humans via admixture with Neanderthals.”

Ricki extrapolated on this further:

“Researchers determine the degree to which a mutant gene differs from the most common sequence (wild type), then impose a time scale in the form of  known mutation rates. The SLC16A11 five-site haplotype is so divergent that it goes back to nearly 800,000 years ago — before our ancestors expanded out of Africa.

The most plausible explanation, unexpected I suspect, seemed to be that the haplotype came from an archaic human – a Neanderthal or Denisovan or their as-yet unnamed contemporaries. And the haplotype indeed shows up in the skeleton of a Neanderthal found in the Denisovan cave in Siberia.”

And so, it seems that the Native American people today indeed inherited their propensity for type 2 diabetes from their ancient Neanderthal ancestors who lived in the Altai Mountains.  It also appears that this genetic predisposition did not carry forward to Europe, if indeed this group of Neanderthals was ancestral to Europeans at all.

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I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

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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.”

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

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400,000 Year Old DNA from Spain Sequenced

Atapuerca Cave Remains

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

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

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

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

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

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

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

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

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

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

malta boy map

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

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

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

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

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

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

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

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

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

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I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

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Ethnicity Results – True or Not?

I can’t even begin to tell you how many questions I receive that go something like this:

“I received my ethnicity results from XYZ.  I’m confused.  The results don’t seem to align with my research and I don’t know what to make of them?”

In the above question, the vendors who are currently offering these types of results among their autosomal tests are Family Tree DNA, 23andMe and Ancestry along with National Geographic who is a nonprofit.  Of those four, by far, Ancestry is the worst at results matching reality and who I receive the most complaints and comments about.  I wrote an article about Ancestry’s results and Judy Russell recently wrote an article about their new updated results as did Debbie Kennett.  My Ancestry results have not been updated yet, so I can’t comment personally.

Let’s take a look at the results from the four players and my own analysis.

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 at Ancestry.

Here are my current ethnicity results from the three major testing companies plus Genographic.

Ancestry

80% British Isles

12% Scandinavian

8% Uncertain

Family Tree DNA

75% Western Europe

25% Europe – Romanian, Russian, Tuscan, Finnish

23andMe (Standard Estimate)

99.2% European

0.5% East Asian and Native American

0.3% Unassigned

Genographic 2.0

Northern European – 43%

Mediterranean – 36%

Southwest Asian – 18%

Why Don’t The Results Match?

Why don’t the results match either my work or each other?

1. The first answer I always think of when asked this question is that perhaps some of the genealogy is incorrect.  That is certainly a possibility via either poor genealogy research or undocumented adoptions.  However, as time has marched forward, I’ve proven that I’m descended from most of these lines through either Y-line, mitochondrial DNA or autosomal matches.  This confirms my genealogy research.  For example, Acadians were originally French and I definitely descend from Acadian lines.

2. The second answer is time.  The vendors may well be using different measures of time, meaning more recent versus deep ancestry.  Geno 2.0 looks back the furthest.  Their information says that “your percentages reflect both recent influences and ancient genetic patterns in your DNA due to migrations as groups from different regions mixed over thousands of years.  Your ancestors also mixed with ancient, now extinct hominid cousins like Neanderthals in Europe and the Middle East of the Denisovans in Asia.”

It’s difficult to determine which of the matching populations are more recent and which are less recent.  By way of example, many Germans and others in eastern Europe are descendants of Genghis Khan’s Mongols who invaded portions of Europe in the 13th century.  So, do we recognize and count their DNA when found as “German,” “Polish,” “Russian,” or “Asian?”  The map below shows the invasions of Genghis Khan.  Based on this, Germans who descend from Genghis’s Mongols could match Koreans on those segments of DNA. Both of those people would probably find that confusing.

genghis khan map

3. The third answer is the reference populations.  Here is what National Geographic has to say: “Modern day indigenous populations around the world carry particular blends of these regions. We compared your DNA results to the reference populations we currently have in our database and estimated which of these were most similar to you in terms of the genetic markers you carry. This doesn’t necessarily mean that you belong to these groups or are directly from these regions, but that these groups were a similar genetic match and can be used as a guide to help determine why you have a certain result. Remember, this is a mixture of both recent (past six generations) and ancient patterns established over thousands of years, so you may see surprising regional percentages.”

Each of the vendors has compiled their own list of reference populations from published material, and in the case of National Geographic, as yet unpublished material as well.

If you read the fine print, some of these results that at first glance appear to not match actually do, or could.  For example, Southwest Asia (Geno 2.0) could be Russia (Family Tree DNA) or at least pointing to the same genetic base.

This video map of Europe through the ages from 1000AD to present will show the ever changing country boundaries and will quickly explain why coming up with labels for ethnicity is so difficult.  I mean, what exactly does “France” or “Germany” mean, and when?

4. The fourth answer is focus.  Each of these organizations comes to us as a consumer with a particular focus.  Of them, one and only one must make their way on their own merits alone.  That one is Family Tree DNA.  Unlike the Genographic Project, Family Tree DNA doesn’t have a large nonprofit behind them.  Unlike 23andMe, they are not subsidized by the medical community and venture capital.  And unlike Ancestry.com, Family Tree DNA is not interested in selling you a subscription.  In fact, the DNA market could dry up and go away for any of those three, meaning 23andMe, National Geographic and Ancestry, and their business would simply continue with their other products.  To them, DNA testing is only a blip on a spreadsheet.  Not true for Family Tree DNA.  Their business IS genetic genealogy and DNA testing.  So of all these vendors, they can least afford to have upset clients and are therefore the most likely to be the most vigilant about the accuracy of their testing, the quality of the tools and results provided to customers.

My Opinion

So what is my personal opinion on all of this?

I think these ethnicity results are very interesting.  I think in some way all of them are probably correct, excluding Ancestry.  I have absolutely no confidence in Ancestry’s results based on their track record and historylack of tools, lack of transparency and frustratingly poor quality.

I think that as more academic papers are published and we learn more about these reference populations and where their genes are found in various populations, all of these organizations will have an opportunity to “tighten up” their results.  If you’ll notice, both Ancestry and Family Tree DNA still include the words “beta.”  The vendors know that these results are not the end all and be all in the ethnicity world.

Am I upset with these vendors?  Aside from Ancestry who has to know they have a significant problem and has yet to admit to or fix it, no, I’m not.  Frustrated, as a consumer, yes, because like all genealogists, I want it NOW please and thank you!!!

Without these kinds of baby steps, we will never as a community crawl, walk, or run.  I dream of the day when we will be able to be tested, obtain our results, and along with that, maybe a list of ancestors we descend from and where their ancestors originated as well.  So, in essence, current genealogy (today Y-line and mtdna), older genealogy (autosomal lines) and population genetics (ethnicity of each line).

So what should we as consumers do today?  Personally, I think we should file this information away in the “that’s interesting” folder and use it when and where it benefits us.  I think we should look at it as a display of possibilities.  We should not over-interpret these results.

There is perhaps one area of exception, and that is when dealing with majority ethnic groups.  By this, I mean African, Asian, Native American and European.  For those groups, this type of ethnicity breakdown, the presence or absence of a particular group is more correct than incorrect, generally.  Very small amounts of any admixture are difficult to discern for any vendor.  For an example of that, look at my Native percentages and some of those are proven lines.  For the individual who wants more information, and more detail into the possibilities, I wrote about how to use the raw autosomal data outside of the vendors tools, at GedMatch, to sort out minority admixture in The Autosomal Me series.

Perhaps the Genographic Project page sums it up best with their statement that, “If you have a very mixed background, the pattern can get complicated quickly!”  Not only is that true, it can be complicated by any and probably all of the factors above.  When you think about it, it’s rather amazing that we can tell as much as we can.

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

The Autosomal Me – Testing Company Results

This is Part 4 of a multi-part series, The Autosomal Me.

Part 1 was “The Autosomal Me – Unraveling Minority Admixture” and Part 2 was “The Autosomal Me – The Ancestors Speak.”  Part 1 discussed the technique we are going to use to unravel minority ancestry, and why it works.  Part 2 gave an example of the power of fragmented chromosomal mapping and the raw beauty of the results.  Part 3, “The Autosomal Me – Who Am I?,” discussed how to use our pedigree charts to gauge expected results and how autosomal results are grouped into population buckets.  We also named this technique, Minority Admixture Mapping, or MAP for short.

In this segment, Part 4, let’s take a look at what the testing company autosomal results look like.  The results are presented in timeline order, with the oldest results first and the latest, and presumably most accurate results, last.

23andMe Version 1

23andMe was the first company to offer this type of testing affordably.  They initially only offered 3 population groups, and one inferred that Asian was actually Native American.  Of course, that wasn’t a valid assumption for everyone, but it was the best that could be done under the circumstances.  This was my ethnicity results display at 23andMe until December 2012 went their updated version was released.

Autosomal test 1

DeCode Genetics

DeCode Genetics initially offered autosomal tests for ancestry.  Unfortunately, under the pressure of financial issues, they stepped away from the genetic genealogy marketspace and have since been sold.

Their test showed the following ethnic breakdown, picking up both my Native and African heritage:

autosomal test 2

I particularly like these results because the X chromosome is included, and seeing Native on the X chromosome, which has a unique inheritance path is a very important piece of data.

Family Tree DNA Version 1

Family Tree DNA’s first version of their Family Finder product produced results stating that I am 100% European, split between western and northern, shown below (minus the map.)

autosomal test 3

Dr. Doug McDonald

Doug McDonald, a retired physical chemistry professor, compiles contributed raw data and compares the raw data locations with both reference populations and the contributor results.  This is not a commercial endeavor but a private research project which has been ongoing for years.  His analysis of my raw data results from 23andMe and Family Tree DNA showed that they are primarily European.  His first analysis was without Middle Eastern populations and the results showed European except for a total of about 3% East Asian, Oceana and American.   However, in a second run including the Pakistan and Middle Eastern populations, the results now showed 88% European, about 1% Oceanic and American and the balance Middle Eastern and Pakistani.

A small amount of Middle Eastern heritage is not unexpected since I do have confirmed Turkish ancestors.

Dr. McDonald indicated that this was slightly more, 1-2%, than most Europeans, and that I was generally planted firmly in the middle of the “English” area in his data.  His results showed no African.

Standard deviation (statistical noise) is about 1%.  He can achieve these low deviation numbers by using such a large number of markers (536,904 to be exact)[1] for his comparison.  I am grateful to Dr. McDonald for his contribution, not only to me, but to this field.

The graph below shows that my primary ancestry falls in the English/French region.

autosomal test 4

The second graph maps these results on my chromosomes. The American, bright green, is found on chromosomes 1 and 2, and the X chromosome shows South Asian.

autosomal test 5

Doug indicates that the Native American is found at about the .5% level.  Interestingly, on my mother’s graphs and charts (below), the Native segments are nearly identical, but my first grey South Asian segment on my X is Mideast on her chart.

autosomal test 6

It’s also interesting to note that my Native American on chromosome 2 is larger than my mother’s which may well reflect Native heritage on my father’s side.  Ironically, the oral history of Native ancestry was on my father’s side, not my mothers.

Doug’s analysis has been updated several times over the years and these results are the most current.  The vendors have made upgrades too.  In 2012, both 23andMe and Family Tree DNA underwent upgrades to their ethnicity software and the Genographic Project version 2.0 test was released.

23andMe 2012 Updated Version

The new 23andMe software offers different confidence levels.

The standard estimate, or confidence level, shows that I have about .5% Native American.  This is consistent with Dr. McDonald’s findings.

autosomal test 7

A second view is available which paints the chromosomes.  A split view is also available if one of your parents has been tested at 23andMe as well.  That is not an option for me.

autosomal test 8

The conservative estimate, below, shows less Native at .2%.

autosomal test 9

The speculative level below shows the Native back to .5% but adjusts the European regions significantly.

autosomal test 10

Although 23andMe does not provide participants with the start and stop locations, through alternative means, meaning a very smart friend, Rebekah Canada, who is a Java programmer, start and stop locations can be discerned.

CeCe Moore documented Rebekah’s technique for those who will be following along with their own results through this process.

In a future segment of this series, we’ll look at alternative ways to discern Native segments.  Thanks to Rebekah’s technique, I can tell you that 23andMe shows my Native segments as follows:

Chromosome 1 – 165,658,091 to 175,711,116

Chromosome 2 – 86,316,174 to103,145,426

23andMe also provides a Neanderthal percentage.  What fun!!!

autosomal test 11

Family Tree DNA Updated 2012 Version

My mother was deceased before chip based autosomal testing was available, but I ordered the Family Finder test for her as soon as it was available.  Thankfully her DNA was stored at Family Tree DNA and was still viable.

autosomal test 12

Mother’s original results are shown above and her most recent results are shown below.  Her results shifted within Europe and her margin of error doubled.

autosomal test 13

My current results from Family Tree DNA’s updated software are shown below.

 autosomal test 14

National Geographic Genographic 2.0

I was very surprised to see my National Geographic results.  They were very unexpected, in particular the high percentages of Mediterranean and Southwest Asian, totaling 54%.

autosomal test 15

It made more sense when I read the information.  It’s true, reading is fundamental.

autosomal test 16

These results are, in essence, more anthropological in nature.

autosomal test 17

autosomal test 18

Of course, one of the fun parts of the Genographic results are the Neanderthal and Denisovan percentages.

autosomal test 19

These are somewhat different than the 23andMe results, although if you add the Neanderthal and Denisovan values together, the resultant 2.2% is very close to 23andMe’s 2.5%.

Ancestry.com

In 2012, Ancestry introduced an autosomal DNA test as well.  What it provides is very limited, with limited tools, but it does provide percentages of ethnicity in addition to matches.  Recently, Ancestry announced that the percentages may change over time.  They have been severely beaten within the genetic genealogy community for quality issues with this product, including percentages of ethnicity that are highly erroneous.  Their stated time reference is 500 years ago.

Recently this new page was added before you can see your detailed results.

autosomal test 20

Ancestry shows my heritage as only British and Scandinavian.

autosomal test 21

Ironically, Ancestry has mapped the birth locations of my ancestors in Europe on the map above, based on my family tree submitted.  Interesting that Germany doesn’t show in Ancestry’s ethnicity list but many of my family lines originated in Germany and Holland, and none in Scandinavia.

Testing Provider Summary

Where do we stand now?

A summary of the various test results is shown below compared to my pedigree analysis.

Test Results Chart

autosomal test 22

I have included Dr. McDonald’s analysis here, not because he’s a testing provider in the sense of the testing companies, but because his offering was available in this timeframe, and because he worked with Family Tree DNA to develop their Population Finder code.

You can see that the results are relatively consistent between testing companies.  There is certainly no question about majority ancestry, but the minority admixture which hovers someplace near 1%, give or take 5% in either direction, is much less consistent and not always reported.  If I were to have tested with only one company and taken the results as gospel, I could certainly have been left believing that I had no Native or African admixture.  For many people, it’s this small amount of minority admixture that they are seeking.  So in answer to the question of which testing company is “best,” the answer is, if you’re looking for trace amounts of anything, the compendium of all the testing companies (minus Ancestry) would provide the best set of results.  We will be using the match information as well in the next sections, so certainly nothing has been “wasted” testing with multiple companies, again, except Ancestry.  I am hopeful that Ancestry will in the future release our raw data (which they have promised to do) in a useable format, fix their misleading ethnicity results and add chromosome painting tools so that we can fully utilize our data.

In Part 5 of the series, we’ll take a look at third party tools and how they can continue to refine and add to our knowledge of our admixture.


1.  Genealogy-DNA Rootsweb posting by Doug McDonald on 7-26-09 and personal correspondence.

2.  71.5% western European, 28.4% Northeastern European

3.  Inferred that Asian is actually Native in an American with no history of Asian ancestry.

4.  No category, inferred.

5.  78.6% Northern European, 1.8% Southern European, 18.7% Nonspecific European

6.  54.6% Northern European, .3% Southern European, 43% Nonspecific European

7.  91.7% Northern European, 3% Southern European, 3.3% Nonspecific European

8.  75.18% West Europe (French and Orcadian), 24.82 Europe (Romanian, Russian, Tuscan and Finnish).  Note that my mother’s results are almost identical except the Finnish is missing from hers.

9.  43% North Europe and 36% Mediterranean

10.  80% British, 12% Scandinavian

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

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Genealogy Services

Genealogy Research

Decoding and Rethinking Neanderthals

decod neanderthal 1

On January 9, 2013, PBS ran a wonderful documentary, Decoding Neanderthals, about Neanderthals, what we have recently discovered about them, and what it means to us as humans. There has been a lot of discussion about this topic spurred by both the 23andMe and the Geno2.0 tests that provide a percentage of Neanderthal to participants. Geno2.0 also provides a percentage of Denisovan.

Program Description:
Over 60,000 years ago, the first modern humans—people physically identical to us today—left their African homeland and entered Europe, then a bleak and inhospitable continent in the grip of the Ice Age. But when they arrived, they were not alone: the stocky, powerfully built Neanderthals had already been living there for hundreds of thousands of years. So what happened when the first modern humans encountered the Neanderthals? Did we make love or war? That question has tantalized generations of scholars and seized the popular imagination. Then, in 2010, a team led by geneticist Svante Paabo announced stunning news. Not only had they reconstructed much of the Neanderthal genome—an extraordinary technical feat that would have seemed impossible only a decade ago—but their analysis showed that “we” modern humans had interbred with Neanderthals, leaving a small but consistent signature of Neanderthal genes behind in everyone outside Africa today. In “Decoding Neanderthals,” NOVA explores the implications of this exciting discovery. In the traditional view, Neanderthals differed from “us” in behavior and capabilities as well as anatomy. But were they really mentally inferior, as inexpressive and clumsy as the cartoon caveman they inspired? NOVA explores a range of intriguing new evidence for Neanderthal self-expression and language, all pointing to the fact that we may have seriously underestimated our mysterious, long-vanished human cousins.

I’m going to share some of the highlights of the program, but this is in no way a spoiler, as the program contains lots of visual information that just can’t be conveyed by a review.

Chris Stringer from the Natural History Museum in London introduced us to the Neanderthals. It turns out that our perception of what a Neanderthal looks like is a result in large part of skeleton that was reconstructed improperly due to advanced arthritis, causing the individual to appear to walk hunched over, much like, well, our stereotypical view of a caveman. Just goes to show what bad PR can cause.

neanderthal skull

Neanderthal skeletons can be positively identified. Their facial structure is different than that of modern man, with an identifiable brow ridge and bones that push forward in the nose and mouth region, as compared to our flatter faces today.

Neanderthals lived a short life, most were dead by age 30. They were large and strong. They participated in up-close and personal hunting, using spears, which meant they had to come in close contact with their prey.

Neanderthals began living in Europe about 300,000 years ago, having exited from Africa. They evolved to fit the European, colder, climate. It had been thought up until recently that they lacked the brainpower of humans, had no spoken language, or the ability for such, no personal ornamentation, art or evidence of ritual or religion. These are the functions that make us uniquely human and separate us from the non-human world, and we fully believed that Neanderthals lacked these defining characteristics.

We have learned differently, much as a result of genetic discoveries that tell a different story of Neanderthals.

Homo sapiens left African about 40,000 years ago, and within 10,000 years, Neanderthals, who had spread throughout most of Europe and much of Asia were gone. The map below shows the locations where fossilized Neanderthal remains have been found.

decod neanderthal 3

The assumption has been made that Homo Sapiens were responsible for the Neanderthals demise, either by killing them off or providing too much competition for scarce resources, outnumbering them 10 to 1.

decod neanderthal 4

Svante Paabo, a Swedish geneticist now at the Max Planck Institute for Evolutionary Anthropology forever changed the genetic world, how we perceive Neanderthals, and paradoxically, how we think of ourselves.

Pääbo is known as one of the founders of paleogenetics, a discipline that uses the methods of genetics to study early humans and other ancient populations.

In August 2002, Paabo published findings about the “language gene”, FOXP2, which is lacking or damaged in some individuals with language disabilities. This research would prove critical, later, in the humanization of the Neanderthal.

In 2006, he announced a plan to reconstruct the entire genome of Neanderthals. In 2007, Pääbo was named one of TIME Magazine’s 100 most influential people of the year.

In February 2009, at the Annual Meeting of the American Association for the Advancement of Science (AAAS), it was announced that the Max Planck Institute for Evolutionary Anthropology had completed the first draft version of the Neanderthal genome. Over 3 billion base pairs were sequenced in collaboration with the 454 Life Sciences Corporation. This project, led by Pääbo, shed and will continue to shed new light on the recent evolutionary history of modern humans.

In March 2010, Pääbo and his coworkers published a report about the DNA analysis of a finger bone found in the Denisova Cave in Siberia; the results suggest that the bone belonged to an extinct member of the genus Homo that had not yet been recognized, the Denisova hominin.

In May 2010, Pääbo and his colleagues published a draft sequence of the Neanderthal genome in the journal Science. Below, a scientist at Max Plank extracting Neanderthal DNA.

decod neanderthal 5

Paabo shared in the program that many times during the Neanderthal sequencing project, he himself “despaired many times of being able to do it”, doubting that it could be done. It took a total of 4 years. The team found good candidates, 3 well-preserved female bone fragments from the Vindija Cave in Croatia.

decod neanderthal 6

Because of the age of the fragments, and because they had been in the ground for so long, much of the DNA recovered wasn’t Neanderthal, but that of bacterial organisms and fungus. The team developed a method to eliminate the bacteria, leaving only Neanderthal DNA. However, those genetic fragments still had to be reassembled, piece by piece, like a huge jigsaw puzzle with no picture on the box, into the Neanderthal genome.

Four long years later, the puzzle was finished. I hope the team had a very big celebratory party!

Ed Green, a scientist on Paabo’s team said that the first thing the scientists looked for was to determine whether or not Neanderthals had the FOXP2 gene for language, and if so, is it identical to the human version, or is it different. The answer was that it was identical to the language gene carried by Homo Sapiens, modern humans. This tells us not only that Neanderthals had the capabilities for language, but that this gene evolved in Africa, before Neanderthals left, 300,000 years ago.

The next question, of course, was whether or not modern humans carried any DNA that could be labeled as Neanderthal. In other words, the question of inter-species breeding arose. It was believed that this was impossible, because two different species cannot have fertile offspring. This was proven to be an inaccurate assumption relative to Neanderthal and Homo Sapiens.

Paabo’s team sequenced the DNA of 5 individuals from different parts of the world. They isolated parts of the Neanderthal DNA that were measurably different from that of modern humans. In other words, those sequences could be positively identified as Neanderthal. Compared against the DNA of the 5 contemporary individuals, only the person from Africa had none of the Neanderthal DNA.

Paabo didn’t believe the results, thought they might be an artifact of statistical error or the result of not enough data, so he had his team repeat the exercise with different people, again, and again, and again, and every time, the results came back the same. Neanderthals and humans inbred, and to the degree that there is Neanderthal DNA in every population on every continent outside of Africa today.

John Hawks, an anthropologist at the University of Wisconsin used jelly beans to illustrate Neanderthal DNA in worldwide populations today. It turns out that the Chinese have the least amount, with about 1% and the people of Tuscany have the most, with about 4%. So the mountainous areas of Europe and Italy were a hotbed of Neanderthal activity and human interbreeding.

This caused other experts to think again about the Neanderthals in what could be called a radical shift in perspective. All of a sudden, when we realized that they were part of us, they became more human to us. They could and probably did have speech, so they could and probably did other “human” things too.

Joao Zilhao, a paleolithic archaeologist at the University of Bristol, also a flintknapper, spent years reconstructing the process of making Neanderthal tools, what were once believed to be scraps of flint with sharp edges. He proved, among other things, that obtaining these “scraps” involved a complex process of very specific flintknapping strokes. This skill was far from the previously perceived unintelligent caveman, and furthermore, it likely required language instruction.

neanderthal tools

Another early technology, in use 250,000 years ago, involved a complex process to create a type of pitch to secure spearheads to spear shafts.

The Neanderthals began evolving before our very eyes.

Michael Walker, a professor of Zoology and Physical Anthropology at the University of Murcia, discovered indeed that Neanderthals likely did have ceremony and ritual, the hallmarks of religion, which involved the ability for complex thought and reasoning. Shells and bones, drilled or punched to be worn as ornaments have been identified, along with pigments believed to have been used as body paints.

We still do this today; look at the fans at any football game.

In addition, it appears that a burial may have been found in Spain, along with two panther paws. Michael mentioned them as a trophy, I thought more in terms of spiritual significance.

John Hawks discussed what the Neanderthal parts of our genome have done for humans. Many of the Neanderthal genes have no known purpose, but there is one significant exception. It’s somehow ironic that we may indeed have survived as a species in a foreign environment, colder Europe, thanks to inbreeding with the Neanderthals. Humans carry a very specific Neanderthal piece of DNA that is essential to the immune system’s ability to attack viruses and bacteria, the HLA or Human Leukocyte Antigen. Because individuals who carried HLA might well have survived when others didn’t, the HLA became naturally selected for, and therefore present in the descendant population, us, “saving lives to this day.’

As John said, we are just beginning to understand our debt to the Neanderthals. Not only that, we also are rethinking what extinction really meant. We have presumed that Neanderthals went extinct, or died out, because we could no longer find their remains in fossil evidence. Perhaps, as Mark Twain said “reports of my demise have been greatly exaggerated.”

Is the reason we could no longer find separate Neanderthals because they interbred and assimilated into the Homo Sapiens population who were probably the dominant species, outnumbering them ten to one? Was their extinction not a dying out at all, but an absorption? Perhaps that was simply the natural progression of things, or maybe they realized that their recipe for success, for long-term survival, was not to remain separate, but to become part of the larger population. In fact they do survive today in just that way, as a part of all of us outside of Africa.

Decoding Neanderthals is available to watch online at http://www.pbs.org/wgbh/nova/evolution/decoding-neanderthals.html

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I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

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2012 Top 10 Genetic Genealogy Happenings

2012 has been a very busy year for genetic genealogists.  There have been lots of discoveries and announcements that affect everyone, now and in the future.  The watchwords for 2012 would be “churn” and “explosive growth.”  Let’s take a look at the 10 most important events, why they are important and what they mean for the future of genetic genealogy.

These items are in what I think are relatively good order, ranked by their importance, although I had a very difficult time deciding between number 1 and 2.

1. The New Root – Haplogroup A00

At the Family Tree DNA conference in November, Michael Hammer, Bonnie Schrack and Thomas Krahn announced that they had made a monumental discovery in the age of modern man known as Y-line Adam.  The discovery of Haplogroup A00 pushes the “birth” of mankind back from about 140,000 years ago to an amazing 338,000 years ago.  Utterly amazing.  The DNA came from an American family from South Carolina.  This discovery highlights the importance of citizen science.  Bonnie is a haplogroup administrator who recognized the potential importance of one of her participants’ DNA.  Thomas Krahn of course is with Family Tree DNA and ran the WTY test, and Michael Hammer is at the University of Arizona.  So you have the perfect blend here of participant, citizen scientist, commercial lab and academia.  What was never thought possible a decade or so ago is not only working, it’s working well and changing the face of both science and humanity.

http://dna-explained.com/2012/11/16/the-new-root-haplogroup-a00/

http://www.haplogroup-a.com./

2. Geno 2.0

Geno 2.0 is the Nickname for the National Geographic Society’s Genographic Project version 2.0.  That mouthful is why it has a nickname.

This amazing project has leveraged the results of the past 7 years of research from the original Genographic project into a new groundbreaking product.  Geno 2.0, utilizing the GenoChip, a sequencing chip created specifically for Nat Geo, offers the most complete Y tree in the world today, expanding the SNP tree from just over 800 SNPs to over 12,000.  They are in essence redrawing the Y chromosome tree as I write this.  In addition, the person who purchases Geno 2.0 will receive a mitochondrial DNA haplogroup assignment.  Over 3300 new mitochondrial mutations were discovered. A brand new anthropological “percentages of ethnicity” report is featured based on over 75,000 Ancestry Informative Markers, many only recently discovered by the Genographic project.  Additionally, participants will receive their percentage of both Neanderthal and Denisovan ancestry based on 30,000 SNPs identified that signal interbreeding between the hominids.  A new website will also facilitate social networking and uploading information to Family Tree DNA.

The wonderful news is that there is a massive amount of new information here that will change the landscape of genetic genealogy.  The difficulty is that we are struggling a bit under the load of that massive amount of information that is just beginning to descend upon us.  It’s a great problem to have!

http://dna-explained.com/2012/07/25/national-geographic-geno-2-0-announcement-the-human-story/

http://dna-explained.com/2012/07/26/geno-2-0-qa-with-bennett-greenspan/

http://dna-explained.com/2012/07/30/geno-2-0-answers-from-spencer-wells/

http://dna-explained.com/2012/07/31/geno-2-0-wty-mtdna-full-sequence-participants-and-more/

http://dna-explained.com/2012/10/14/what-to-order-geno-2-0-vs-family-tree-dna-products/

http://dna-explained.com/2012/10/16/geno-2-0-the-kit-arrives/

http://dna-explained.com/2012/12/11/geno-2-0-results-first-peek/

http://dna-explained.com/2012/12/12/geno-2-0-results-kicking-the-tires/

3. Reconstructed Sapiens Reference Sequence (RSRS)

In July, Family Tree DNA implemented the RSRS that in effect reconstructs the genetic profile of Mitochondrial Eve and bases the comparison of our DNA today against the RSRS sequence as opposed to the Cambridge Reference Sequence (rCRS) created in 1981 that is or was the current standard.  The RSRS is a result of the watershed paper published in April 2012 by Dr. Doron Behar and 8 other authors titled “A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root.”  A complementary research website, www.mtdnacommunity.org, accompanies the paper.

http://dna-explained.com/2012/07/14/what-happened-to-my-mitochondrial-dna/

http://dna-explained.com/2012/07/15/the-crs-and-the-rsrs/

http://dna-explained.com/2012/07/16/the-mtdna-community/

http://dna-explained.com/2012/12/02/little-a-big-a-mitochondrial-dna/

4. Full Genome and Exome Sequence Offered Commercially by Gene by Gene

It was announced at the November DNA conference that Gene by Gene, the parent company of Family Tree DNA, through their division titled DNA DTC is offering full genomic sequencing for the amazing price of $5495 for the full genome and $695 for the exome.  This is a first in the consumer marketspace.  Today, this doesn’t have a lot of application for genetic genealogy, but as the price continues to drop, and utilities are built to process the full genomic data, certainly a market and applications will emerge.  This is an important step forward in the industry with a product that still cost 3 million dollars in 2007.

http://dna-explained.com/2012/11/30/gene-by-gene-announces-landmark-dna-dtc-full-genome-sequence/

5. Neanderthal and Denisovan DNA

It’s official – they did it.  Yep, they interbred and well, they are not them anymore, they are us.  Given that everyone in Asia and Europe carries a part of them, but not people from Africa, it would appear that two populations admixed rather thoroughly in Eurasia and/or the populations were small.  The amount of Neanderthal and Denisovan DNA will continue at approximately the proportions seen today in Europe (2% Neanderthal) and Asia unless a significant amount of admixture from a population (Africa) that does not carry this admixture is introduced.  So if you’re European, you carry both Neanderthal and Denisovan DNA.  They are your ancestors.  The good news is that you can find how much of each through  the Geno 2.0 test.  23andMe results give you the percentage of Neanderthal, but not Denisovan.

http://dna-explained.com/2012/08/31/denisovan-dna-tells-a-story/

http://dna-explained.com/2012/12/12/geno-2-0-results-kicking-the-tires/

6. Ancestral Genome Reconstruction Begins,  Led by Falling Autosomal Prices and the Ability to Fish in Multiple Ponds

2012 has been the year of autosomal testing price reductions and a great deal of churn in this marketspace.  Companies are playing leap-frog with one another.  However, sometimes things are not all that they seem.

Initially, 23andMe opted for an initial payment plus monthly subscription model, which they abandoned for a one time payment price of $299 in early 2012.  Family Tree DNA was slightly less, at $289.

Ancestry led the price war by giving away kits, then selling them for $99, then $129 plus a subscription as an entrance into this market.  However, looking at the Ancestry consent form hints at possible reasons why they were selling below the cost of the tests.  You are in essence giving them permission to sell your DNA and associated information.  In addition, to gain full access to your results and matches, you must maintain some level of subscription to Ancestry.com, increasing the total effective price.

Next came Family Tree DNA’s sale where they dropped their autosomal price to $199, but they were shortly upstaged by 23andMe whose price has now dropped to $99 permanently, apparently, a result of a 50 million dollar investment in order to reach 1 million customers.  They currently have about 180,000.  23andMe has always been in the medical/health business, so their clients have always understood what they were consenting to and for.

Not to be outdone, Family Tree DNA introduced the ability earlier in 2012 to upload your data files from 23andMe to FamilyTree DNA for $89, far less than a second test, which allows you to fish in a second pond where genealogists live for matches.  The challenge at 23andMe is that most of their clients test for the health traits and either don’t answer inquiries or match requests, or know little about their genealogy if they do.  At Family Tree DNA, matches don’t have to answer and allow a match, testers are automatically matched with all participants who take the Family Finder test (or upload their 23andMe results) and testers are provided with their matches’ e-mail address.

Of course, Geno 2.0 was also introduced in the midst of this, in July, for $199 with the additional lollipop of new SNPS, lots of them, that others simply don’t have access to yet.

The good news is that consumers have benefitted from this leapfrogging, I think.  Let’s hope that the subsidized tests at Ancestry and 23andMe don’t serve long term to water down the demand to the point where unsubsidized companies (who don’t selling participants genetic results to others) have problems remaining viable.

Personally, I’ve tested at all of these companies.  I’ll be evaluating the results shortly in detail on my blog at www.dna-explained.com.

The tools provided by most testing companies, plus GedMatch, and multiple ponds to fish in are allowing the serious genetic genealogist to “reconstruct” their genome, attributing segments to specific ancestors.  Conversely, we will also be able to “reconstruct” specific ancestral family lines as well by identifying autosomal segments in multiple descendants.  This new vision of autosomal genetic genealogy will allow much more accurate ancestral line matching, and ancestor identification in the not-so-distant future.

http://www.yourgeneticgenealogist.com/2012/01/family-tree-dna-now-accepting-23andme.html

http://www.yourgeneticgenealogist.com/2012/05/23andme-eliminates-subscription-model.html

http://www.yourgeneticgenealogist.com/2012/10/clarification-of-what-is-available-to.html

http://www.yourgeneticgenealogist.com/2012/12/23andme-receives-50-million-and-drops.html

http://www.thegeneticgenealogist.com/2012/12/26/23andme-and-labcorp-sued-for-patent-infringement/

7. Ethnicity Tests Mature – Minus 1

The good news is that the various ethnicity tests (known as BGA or biogeographical ancestry tests) that provide participants with their percentages of various world populations are improving.  The bad news is that there is currently one bad apple in the card with very misleading percentages – and that is Ancestry.com.

23andMe introduced a new version of their ethnicity product in December, expanding from only 3 geographic categories to several.  The Geno 2.0 test results are just beginning to be returned which include ethnicity predictions and references to several base populations.

Family Tree DNA finally has some competition in this arena where for years they have been the only serious player, although opinions differ widely about which of these three organizations results are the most accurate.  All four are Illumina chip based, using hundreds of thousands of locations, as compared with the previous CODIS type tests which used between 15 and 300 markers and are now outdated.  All companies use different reference populations which, of course, provide somewhat different results to participants.  All companies, except Ancestry, have documented and shared their reference population information.

Outside of these companies, Doug McDonald offers a private analysis and Gedmatch offers a series of BGA comparisons written by third parties.

While this industry continues to grow and mature, I’m thinking about just averaging the autosomal ethnic results and calling it good:)

http://dna-explained.com/2012/07/21/ethnicity-finders/

http://dna-explained.com/2012/10/24/ancestrys-mythical-admixture-percentages/

http://dna-explained.com/2012/12/07/new-worldview-at-23andme/

http://dna-explained.com/2012/09/09/doug-mcdonald-on-biogeograpical-analysis/

http://dna-explained.com/2012/12/11/geno-2-0-results-first-peek/

http://www.yourgeneticgenealogist.com/2012_12_01_archive.html

8. Finding Your Roots PBS Series with Henry Louis Gates

PBS sponsored a wonderful series in the spring of 2012 hosted by Henry Louis “Skip” Gates, the chair of African American Studies at Harvard.  This series followed a lesser known 2010 series.  The 2012 inspirational series reached tens of thousands of people and increased awareness of genetic genealogy as well as sparked an interest in genealogy itself, especially for mixed race and African American people.  I was disappointed that the series did not pursue the Native American results unexpectedly obtained for one participant.  It seemed like a missed opportunity.  Series like this bring DNA testing for genealogy into the mainstream, making it less “strange” and frightening and more desirable for the average person.  These stories were both inspirational and heartwarming.  I hope we can look forward to similar programs in the future.

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

CeCe Moore covered this series in March and April on her blog.

http://www.yourgeneticgenealogist.com/2012/03/finding-your-roots-with-henry-louis.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis_09.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis_16.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis_23.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis_30.html

9. Ancestry, GeneTree and Sorenson

GeneTree, a for profit company and Sorenson, a non-profit company were both purchased by Ancestry.com.  This was about the same time as Ancestry introduced their autosomal AncestryDNA product.  Speculation was that the autosomal results at Sorenson might be the foundation for the new autosomal test comparisons, although there has been no subsequent evidence of this.

Ancestry initially gave away several thousand kits in order to build their data base, then sold thousands more for $99 before raising the price to what appears to be a normalized price of $129 plus an annual ancestry subscription.

While GeneTree was never a major player in the DNA testing marketspace, Sorenson Molecular Genealogical Foundation played an important role for many years as a nonprofit research institute.  There was significant distress in the genetic genealogy community related to the DNA contributed to Sorenson for research being absorbed by Ancestry as a “for profit” company.  Ancestry is maintaining the www.smgf.org website, but no additional results will be added.  Sorenson has been entirely shuttered.  Many of the Sorenson/GeneTree employees appear to have moved over to Ancestry.

The initial AncestryDNA autosomal product offering is poor, lacks tools and the ethnicity portion has significant issues. It’s strength is that many people who test are already Ancestry subscribers and have attached their trees.  So you can’t see how you connect genetically to your matches (lack of tools), but you can see the trees, if they are attached and not marked as private, of those with whom you match.  Ancestry provides “hints” relative to matching individuals or surnames.

Eventually, if Ancestry improves its products, provides tools and releases the raw data to consumers, this may be a good thing.  It’s an important event in 2012 because of the massive size of Ancestry, but the product is mediocre at best.  Ancestry seems unwilling to acknowledge issues unless their feet are held to the fire publicly as illustrated with a “lab error” erroneous match for an adoptee caught by the consuming public and ignored by Ancestry until CeCe Moore exposed them in her blog.  Whether Ancestry ultimately helps or hurts the genetic genealogy industry is a story yet to be told.  There is very little positive press in the genetic genealogy community surrounding the Ancestry product, but with their captive audience, they are clearly going to be a player.

http://www.yourgeneticgenealogist.com/2012/05/ancestrycom-buys-genetree-and-launches.html

http://dna-explained.com/2012/07/12/did-you-test-at-genetree/

http://dna-explained.com/2012/08/30/is-history-repeating-itself-at-ancestry/

http://dna-explained.com/2012/07/18/the-trouble-with-ancestry-com-matches/

http://dna-explained.com/2012/08/14/y-dna-family-tree-dna-vs-ancestry/

http://dna-explained.com/2012/08/16/ancestrys-consent-form-for-ancestrydna-autosomal-test/

http://dna-explained.com/2012/09/10/ancestry-autosomal-results-are-back/

http://dna-explained.com/2012/10/15/ancestrys-dna-survey/

http://dna-explained.com/2012/10/23/ancestry-to-release-array-data-in-2013/

http://dna-explained.com/2012/10/24/ancestrys-mythical-admixture-percentages/

http://www.thegeneticgenealogist.com/2012/06/19/problems-with-ancestrydnas-genetic-ethnicity-prediction/

http://www.yourgeneticgenealogist.com/2012/08/ancestrydna-confusing-relationship.html

http://www.yourgeneticgenealogist.com/2012/08/follow-up-on-ancestrydna-and-adoptees.html

http://www.yourgeneticgenealogist.com/2012/09/23andme-says-no-match-for-adoptees.html

10. GedMatch

GedMatch, www.gedmatch.com, created by John Olson and Curtis Rogers, isn’t new in 2012, but it’s maturing into a tool that is becoming the defacto workhorse of the serious autosomal community.  People who test at either 23andMe or Family Tree DNA download their raw results and other match information and then use a variety of tools at GedMatch to look at results in different ways and using different thresholds. GedMatch is currently working to accept the newly arriving Geno 2.0 data files.  Ancestry does not at this time allow their customers access to their raw data files, so there is nothing to upload. The bad news is that not everyone downloads/uploads their information.  Only the most savvy users, and the download/upload is not always a smooth process, often necessitating several attempts, a magic wand and some fairy dust for luck.

GedMatch is a volunteer effort funded by donations on the GedMatch site.  The magnitude of this project came to light when they needed new servers this year because the amount of traffic disabled their internet service provider.  It may be a volunteer effort, but it has mainstream requirements.  Therefore, while occasionally frustrating, it’s easy to understand why it’s light on documentation and one has to poke around a bit to figure things out.  I would actually prefer that they make it a subscription site, clean up the bugs, add the documentation and take it to the next level.  It would also be very nice if they could arrange something with the major players in terms of a seamless data transfer for clients.  All told, it’s an amazing contribution as a volunteer site.  Hats off to Curtis and John for their ongoing contribution to genetic genealogists!!!

www.gedmatch.com

http://www.legalgenealogist.com/blog/2012/08/12/gedmatch-a-dna-geeks-dream-site/

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research