10 Things to Do With Your DNAPrint, renamed AncestrybyDNA, Test

birdcage

Please note, AncestrybyDNA is NOT the same as the AncestryDNA test sold by Ancestry.com.  Both CeCe Moore and David Dowell have written about this in their respective blogs.

Back in 2002 (no, that is not a typo,) a new product called DNAPrint was introduced by a company then called DNAPrint Genomics.  It provided you, in percentages, your percentages of 4 ethnic groups: Indo-European, East-Asian, Native American and African.  Family Tree DNA remarketed this test for just over a year but ceased when they realized there were issues.

It was the first of its kind of test ever to be offered commercially, and version 2.0 utilized a whopping 71 ancestrally informative markers, according to the user’s guide delivered with the product.  The next version of the test, 2.5, titled AncestrybyDNA included 175 markers, and a third version, which I don’t believe was ever released, was to include just over 300 markers.

In 2002, this was a baby step in a brand new world.  We, as a community, were thrilled to be able to obtain this type of information.  And of course, we believed it was accurate, or relatively so.  However, the questions and ensuing debate started almost immediately and became very heated.

The company’s representatives indicated that East-Asian and Native American could be combined for those without a “Chinese grandpa” and that would have given me a whopping 25% Native American.  Even then, before pedigree analysis, I thought this was a little high.  My East Asian was shown as 15%, Native American at 10% and Indo-European at 75%.  For reference, my real Native results are probably in the 1-3% range.  Keep in mind that we were all babes in the woods, kind of stumbling around, learning, in 2002 and 2003.

Interestingly enough, I found the answer recently, quite by accident, to one of the burning questions about Native American ancestry that was asked repeatedly of Tony Frudakis during that timeframe, then a corporate officer of DNAPrint, and left unanswered.  In Carolyn Abraham’s book, The Juggler’s Children, which is a wonderful read, on page 55, the answer to the forever-hanging question was answered:

“When I finally reached Frudakis, that’s how he explained the confusion over our Native ancestry result – semantics.  The Florida company had pegged its markers as being Native American to appeal to the American market, he told me.  But it was accurate to consider them Central Asian markers, he said, that had been carried to different regions by those who migrated from that part of the globe long ago – into the Americas, into East Asia, South Asia and even southern Europe – finding their way into today’s Greeks, Italians and Turks.  ‘We may do ourselves a favour and change the name of this ancestry [component] in the test,’ he said, since apparently I wasn’t the only one baffled by it.”

So, now we know, straight from the horses mouth, via Carolyn.

Of course, since that time, many advances have occurred in this field.  Today, Family Tree DNA, 23andMe, Ancestry.com and the Genographic Project utilize chip based technology and utilize over half a million markers to achieve ethnicity predictions.  If DNAPrint, renamed AncestybyDNA was the first baby step, today we are teenagers – trying to refine our identity.  Today’s tests, although not totally accurate, are, by far, more accurate than this first baby step.  Give us another dozen years in this industry, and they’ll be spot on!

For 2003, when I ordered mine, DNAPrint was an adventure – it was exciting – it was a first step – and we learned a lot.  Unfortunately, DNAPrint under the name AncestrybyDNA is still being sold today, currently owned by the DNA Diagnostics Center.  If you are even thinking about ordering this product, take a look first at the Yelp reviews and the Better Business Bureau complaints.

I don’t regret spending the money in 2003.  Spending money on this outdated test today would be another story entirely – a total waste.  The results are entirely irrelevant today in light of the newer and more refined technology.  Unfortunately, seldom a week goes by that I don’t receive an e-mail from someone who bought this test and are quite confused and unhappy.  The test has been marketed and remarketed by a number of companies over the years.

So, here are some suggestions about what might be appropriate to do with your DNAPrint or AncestybyDNA results if you don’t want to just throw them away:

  1. Line the bottom of the birdcage.
  2. Use to light the BBQ grill or camp fire.
  3. Use under boots in the hallway in the winter.
  4. Shred, then use as confetti.
  5. Cut into strips and use as bookmarks.
  6. Use as scratch paper.
  7. Use in the garden between rows to minimize weeds.
  8. Make into a paper airplane.
  9. Roll, along with other excess paper, into logs for the fireplace.
  10. Frame, and display along with your other antiques.

Yes, it’s really that old and outdated!

Finding Native American Ethnic Results in Germanic People

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

Why?

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

Hun map

It’s no wonder we’re so admixed.

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

Hun emplire

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

magyar map

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

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

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

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

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

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

Eurogenes K13

 JK Eurogenes K13 v2

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

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

jk eurogenes k13 chart

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

Dodecad

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

jk dodecad v3

jk dodecad v3 chart

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

Dodecad 12b below

jk dodecad 12b

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

HarappaWorld

jk harappaworld

jk harappaworld chart

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

In Summary

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

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

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

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

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

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

Ethnicity Percentages – Second Generation Report Card

Recently, Family Tree DNA introduced their new ethnicity tool, myOrigins as part of their autosomal Family Finder product.  This means that all of the major players in this arena using chip based technology (except for the Genographic project) have now updated their tools.  Both 23andMe and Ancestry introduced updated versions of their tools in the fall of 2013.  In essence, this is the second generation of these biogeographical or ethnicity products.  So lets take a look and see how the vendors are doing.

In a recent article, I discussed the process for determining ethnicity percentages using biogeographical ancestry, or BGA, tools.  The process is pretty much the same, regardless of which vendor’s results you are looking at.  The variant is, of course, the underlying population data base, it’s quality and quantity, and the way the vendors choose to construct and name their regions.

I’ve been comparing my own known and proven genealogy pedigree breakdown to the vendors results for some time now.  Let’s see how the new versions stack up to a known pedigree.

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 Pedigree Percent
Germany 23.8041
British Isles 22.6104
Holland 14.5511
European by DNA 6.8362
France 6.6113
Switzerland 0.7813
Native American 0.2933
Turkish 0.0031

This leaves about 25% unknown.

Let’s look at each vendor’s results one by one.

23andMe

23andme v2

My results using the speculative comparison mode at 23andMe are shown in a chart, below.

23andMe Category 23andMe Percentage
British and Irish 39.2
French/German 15.6
Scandinavian 7.9
Nonspecific North European 27.9
Italian 0.5
Nonspecific South European 1.6
Eastern European 1.8
Nonspecific European 4.9
Native American 0.3
Nonspecific East Asian/Native American 0.1
Middle East/North Africa 0.1

At 23andMe, if you have questions about what exact population makes up each category, just click on the arrow beside the category when you hover over it.

For example, I wasn’t sure exactly what comprises Eastern European, so I clicked.

23andme eastern europe

The first thing I see is sample size and where the samples come from, public data bases or the 23andMe data base.  Their samples, across all categories, are most prevalently from their own data base.  A rough add shows about 14,000 samples in total.

Clicking on “show details” provides me with the following information about the specific locations of included populations.

23andme pop

Using this information, and reorganizing my results a bit, the chart below shows the comparison between my pedigree chart and the 23andMe results.  In cases where the vendor’s categories spanned several of mine, I have added mine together to match the vendor category.  A perfect example is shown in row 1, below, where I added France, Holland, Germany and Switzerland together to equal the 23andMe French and German category.  Checking their reference populations shows that all 4 of these countries are included in their French and German group.

Geography Pedigree Percent 23andMe %
Germany, Holland, Switzerland & France 45.7451 15.6
France 6.6113 (above) Combined
Germany 23.8014 (above) Combined
Holland 14.5511 (above) Combined
Switzerland 0.7813 (above) Combined
British Isles 22.6104 39.2
Native American 0.2933 0.4 (Native/East Asian)
Turkish 0.0031 0.1 (Middle East/North Africa)
Scandinavian 7.9
Italian 0.5
South European 1.6
East European 1.8
European by DNA 6.8362 4.9 (nonspecific European)
Unknown 25 27.9 (North European)

I can also change to the Chromosome view to see the results mapped onto my chromosomes.

23andme chromosome view

The 23andMe Reference Population

According to the 23andMe customer care pages, “Ancestry Composition uses 31 reference populations, based on public reference datasets as well as a significant number of 23andMe members with known ancestry. The public reference datasets we’ve drawn from include the Human Genome Diversity ProjectHapMap, and the 1000 Genomes project. For these datasets as well as the data from 23andMe, we perform filtering to ensure accuracy.

Populations are selected for Ancestry Composition by studying the cluster plots of the reference individuals, choosing candidate populations that appear to cluster together, and then evaluating whether we can distinguish the groups in practice. The population labels refer to genetically similar groups, rather than nationalities.”

Additional detailed information about Ancestry Composition is available here.

Ancestry.com

ancestry v2

Ancestry is a bit more difficult to categorize, because their map regions are vastly overlapping.  For example, the west Europe category is shown above, and the Scandinavian is shown below.

ancestry scandinavia

Both categories cover the Netherlands, Germany and part of the UK.

My Ancestry percentages are:

Ancestry Category Ancestry Percentage
North Africa 1
America <1
East Asia <1
West Europe 79
Scandinavia 10
Great Britain 4
Ireland 2
Italy/Greece 2

Below, my pedigree percentages as compared to Ancestry’s categories, with category adjustments.

Geography Pedigree Percent Ancestry %
West European 52.584 (combined from below) 79
Germany 23.8041 Combined
Holland 14.5511 Combined
European by DNA 6.8362 Combined
France 6.6113 Combined
Switzerland 0.7813 Combined
British Isles 22.6104 6
Native American 0.2933 ~1 incl East Asian
Turkish 0.0031 1 (North Africa)
Unknown 25
Italy/Greece 2
Scandinavian 10

Ancestry’s European populations and regions are so broadly overlapping that almost any interpretation is possible.  For example, the Netherlands could be included in several categories – and based up on the history of the country, that’s probably legitimate.

At Ancestry, clicking on a region, then scrolling down will provide additional information about that region of the world, both their population and history.

The Ancestry Reference Population

Just below your ethnicity map is a section titled “Get the Most Out of Your Ethnicity Estimate.”  It’s worth clicking, reading and watching the video.  Ancestry states that they utilized about 3000 reference samples, pared from 4245 samples taken from people whose ethnicity seems to be entirely from that specific location in the world.

ancestry populations

You can read more in their white paper about ethnicity prediction.

Family Tree DNA’s myOrigins

I wrote about the release of my Origins recently, so I won’t repeat the information about reference populations and such found in that article.

myorigins v2

Family Tree DNA shows matches by region.  Clicking on the major regions, European and Middle Eastern, shown above, display the clusters within regions.  In addition, your Family Finder matches that match your ethnicity are shown in highest match order in the bottom left corner of your match page.

Clicking on a particular cluster, such as Trans-Ural Peneplain, highlights that cluster on the map and then shows a description in the lower left hand corner of the page.

myorigins trans-ural

Family Tree DNA shows my ethnicity results as follows.

Family Tree DNA Category Family Tree DNA Percentage
European Coastal Plain 68
European Northlands 12
Trans-Ural Peneplain 11
European Coastal Islands 7
Anatolia and Caucus 3

Below, my pedigree results reorganized a bit and compared to Family Tree DNA’s categories.

Geography Pedigree Percent Family Tree DNA %
European Coastal Plain 45.7478 68
Germany 23.8041 Combined above
Holland 14.5511 Combined above
France 6.6113 Combined above
Switzerland 0.7813 Combined above
British Isles 22.6104 7 (Coastal Islands)
Turkish 0.0031 3 (Anatolia and Caucus)
European by DNA 6.8362
Native American 0.2933
Unknown 25
Trans-Ural Peneplain 11
European Northlands 12

Third Party Admixture Tools

www.GedMatch.com is kind enough to include 4 different admixture utilities, contributed by different developers, in their toolbox.  Remember, GedMatch is a free, meaning a contribution site – so if you utilize and enjoy their tools – please contribute.

On their main page, after signing in and transferring your raw data files from either 23andMe, Family Tree DNA or Ancestry, you will see your list of options.  Among them is “admixture.”  Click there.

gedmatch admixture

Of the 4 tools shown, MDLP is not recommended for populations outside of Europe, such as Asian, African or Native American, so I’ve skipped that one entirely.

gedmatch admix utilities

I selected Admixture Proportions for the part of this exercise that includes the pie chart.

The next option is Eurogenes K13 Admixture Proportions.  My results are shown below.

Eurogenes K13

Eurogenes K13

Of course, there is no guide in terms of label definition, so we’re guessing a bit.

Geography Pedigree Percent Eurogenes K13%
North Atlantic 75.19 44.16
Germany 23.8041 Combined above
British Isles 22.6104 Combined above
Holland 14.5511 Combined above
European by DNA 6.8362 Combined above
France 6.6113 Combined above
Switzerland 0.7813 Combined above
Native American 0.2933 2.74 combined East Asian, Siberian, Amerindian and South Asian
Turkish 0.0031 1.78 Red Sea
Unknown 25
Baltic 24.36
West Med 14.78
West Asian 6.85
Oceanian 0.86

Dodecad K12b

Next is Dodecad K12b

According to John at GedMatch, there is a more current version of Dodecad, but the developer has opted not to contribute the current or future versions.

Dodecad K12b

By the way, in case you’re wondering, Gedrosia is an area along the Indian Ocean – I had to look it up!

Geography Pedigree Percent Dodecad K12b
North European 75.19 43.50
Germany 23.8041 Combined above
British Isles 22.6104 Combined above
Holland 14.5511 Combined above
European by DNA 6.8362 Combined above
France 6.6113 Combined above
Switzerland 0.7813 Combined above
Native American 0.2933 3.02 Siberian, South Asia, SW Asia, East Asia
Turkish 0.0031 10.93 Caucus
Gedrosia 7.75
Northwest African 1.22
Atlantic Med 33.56
Unknown 25

Third is Harappaworld.

Harappaworld

harappaworld

Baloch is an area in the Iranian plateau.

Geography Pedigree Percent Harappaworld %
Northeast Euro 75.19 46.58
Germany 23.8041 Combined above
British Isles 22.6104 Combined above
Holland 14.5511 Combined above
European by DNA 6.8362 Combined above
France 6.6113 Combined above
Switzerland 0.7813 Combined above
Native American 0.2933 2.81 SE Asia, Siberia, NE Asian, American, Beringian
Turkish 0.0031 10.27
Unknown 25
S Indian 0.21
Baloch 9.05
Papuan 0.38
Mediterranean 28.71

The wide variety found in these results makes me curious about how my European results would be categorized using the MDLP tool, understanding that it will not pick up Native, Asian or African.

MDLP K12

mdlp k12

The Celto-Germanic category is very close to my mainland European total – but of course, many Germanic people settled in the British Isles.

Second Generation Report Card

Many of these tools picked up my Native American heritage, along with the African.  Yes, these are very small amounts, but I do have several proven lines.  By proven, I mean both by paper trail (Acadian church and other records) and genetics, meaning Yline and mtDNA.  There is no arguing with that combination.  I also have other Native lines that are less well proven.  So I’m very glad to see the improvements in that area.

Recent developments in historical research and my mitochondrial DNA matches show that my most distant maternal ancestral line in Germany have some type of a Scandinavian connection.  How did this happen, and when?  I just don’t know yet – but looking at the map below, which are my mtDNA full sequence matches, the pattern is clear.

mitomatches

Could the gene flow have potentially gone the other direction – from Germany to Scandinavia?  Yes, it’s possible.  But my relatively consistent Scandinavian ethnicity at around 10% seems unlikely if that were the case.

Actually, there is a second possibility for additional Scandinavian heritage and that’s my heavy Frisian heritage.  In fact, most of my Dutch ancestors in Frisia were either on or very near the coast on the northernmost part of Holland and many were merchants.

I also have additional autosomal matches with people from Scandinavia – not huge matches – but matches just the same – all unexplained.  The most notable of which, and the first I might add, is with my friend, Marja.

It’s extremely difficult to determine how distant the ancestry is that these tests are picking up.  It could be anyplace from a generation ago to hundreds of generations ago.  It all depends on how the DNA was passed, how isolated the population was, who tested today and which data bases are being utilized for comparison purposes along with their size and accuracy.  In most cases, even though the vendors are being quite transparent, we still don’t know exactly who the population is that we match, or how representative it is of the entire population of that region.  In some cases, when contributed data is being used, like testers at 23andMe, we don’t know if they understood or answered the questions about their ancestry correctly – and 23andMe is basing ethnicity results on their cumulative answers.  In other words, we can’t see beneath the blanket – and even if we could – I don’t know that we’d understand how to interpret the components.

So Where Am I With This?

I knew already, through confirmed paper sources that most of my ancestry is in the European heartland – Germany, Holland, France as well as in the British Isles.  Most of the companies and tools confirm this one way or another.  That’s not a surprise.  My 35 years of genealogical research has given me an extremely strong pedigree baseline that is invaluable for comparing vendor ethnicity results.

The Scandinavian results were somewhat of a surprise – especially at the level in which they are found.  If this is accurate, and I tend to believe it is present at some level, then it must be a combined effect of many ancestors, because I have no missing or unknown ancestors in the first 5 generations and only 11 of 64 missing or without a surname in generation 6.  Those missing ancestors in generation 6 only contribute about 1.5% of my DNA each, assuming they contribute an average of 50% of their DNA to offspring in each subsequent generation.

Clearly, to reach 10%, nearly all of my missing ancestors, in the US and Germany, England and the Netherlands would have to be 100% Scandinavian – or, alternately, I have quite a bit scattered around in many ancestors, which is a more likely scenario.  Still, I’m having a difficult time with that 10% number in any scenario, but I will accept that there is some Scandinavian heritage one way or another.  Finding it, however, genealogically is quite another matter.

However, I’m at a total loss as to the genesis of the South European and Mediterranean.  This must be quite ancient.  There are only two known possible ancestors from these regions and they are many generations back in time – and both are only inferred with clearly enough room to be disproven.  One is a possible Jewish family who went to France from Spain in 1492 and the other is possibly a Roman soldier whose descendants are found within a few miles of a Roman fort site today in Lancashire.  Neither of these ancestors could have contributed enough DNA to influence the outcome to the levels shown, so the South European/Mediterranean is either incorrect, or very deep ancestry.

The Eastern European makes more sense, given my amount of German heritage.  The Germans are well known to be admixed with the Magyars and Huns, so while I can’t track it or prove it, it also doesn’t surprise me one bit given the history of the people and regions where my ancestors are found.

What’s the Net-Net of This?

This is interesting, very interesting.  There are tips and clues buried here, especially when all of the various tools, including autosomal matching, Y and mtDNA, are utilized together for a larger picture.  Alone, none of these tools are as powerful as they are combined.

I look forward to the day when the reference populations are in the tens of thousands, not hundreds.  All of the tools will be far more accurate as the data base is built, refined and utilized.

Until then, I’ll continue to follow each release and watch for more tips and clues – and will compare the various tools.  For example, I’m very pleased to see Family Tree DNA’s new ethnicity matching tool incorporated into myOrigins.

I’ve taken the basic approach that my proven pedigree chart is the most accurate, by far, followed by the general consensus of the combined results of all of the vendors.  It’s particularly relevant when vendors who don’t use the same reference populations arrive at the same or similar results.  For example, 23andMe uses primarily their own clients and Nat Geo of course, although I did not include them above because they haven’t released a new tool recently, uses their own population sample results.

National Geographic’s Geno2

Nat Geo took a bit of a different approach and it’s more difficult to compare to the others.  They showed my ethnicity as 43% North European, 36% Mediterranean and 18% Southwest Asian.

nat geo results

While this initially looks very skewed, they then compared me to my two closest populations, genetically, which were the British and the Germans, which is absolutely correct, according to my pedigree chart.  Both of these populations are within a few percent of my exact same ethnicity profile, shown below.

Nat geo british 2

The description makes a lot of sense too.  “The dominant 49% European component likely reflects the earliest settlers in Europe, hunter-gatherers who arrived there more than 35,000 years ago.  The 44% Mediterranean and the 17% Southwest Asian percentages arrived later, with the spread of agriculture from the Fertile Crescent in the middle East, over the past 10,000 years.  As these early farmers moved into Europe, they spread their genetic patterns as well.”

nat geo german

So while individually, and compared to my pedigree chart, these results appear questionable, especially the Mediterranean and Southwest Asian portions, in the context of the populations I know I descend from and most resemble, the results make perfect sense when compared to my closest matching populations.  Those populations themselves include a significant amount of both Mediterranean and Southwest Asian.  Looking at this, I feel a lot better about the accuracy of my results.  Sometimes, perspective makes a world of difference.

It’s A Wrap

Just because we can’t exactly map the ethnicity results to our pedigree charts today doesn’t mean the results are entirely incorrect.  It doesn’t mean they are entirely correct, either.  The results may, in some cases, be showing where population groups descend from, not where our specific ancestors are found more recently.  The more ancestors we have from a particular region, the more that region’s profile will show up in our own personal results.  This explains why Mediterranean shows up, for example, from long ago but our one Native ancestor from 7 or 8 generations ago doesn’t.  In my case, it would be because I have many British/German/Dutch lines that combine to show the ancient Mediterranean ancestry of these groups – where I have many fewer Native ancestors.

Vendors may be picking up deep ancestry that we can’t possible know about today – population migration.  It’s not like our ancestors left a guidebook of their travels for us – at least – not outside of our DNA – and we, as a community, are still learning exactly how to read that!  We are, after all, participants on the pioneering, leading edge of science.

Having said that, I’ll personally feel a lot better about these kinds of results when the underlying technology, data bases and different vendors’ tools mature to the point where there the differences between their results are minor.

For today, these are extremely interesting tools, just don’t try to overanalyze the results, especially if you’re looking for minority admixture.  And if you don’t like your results, try a different vendor or tool, you’ll get an entirely new set to ponder!

Family Tree DNA Releases myOrigins

my origins

On May 6th, Family Tree DNA released myOrigins as a free feature of their Family Finder autosomal DNA test.  This autosomal biogeographic feature was previously called Population Finder.  It has not just been renamed, but entirely reworked.

Currently, 22 population clusters in 7 major geographic groups are utilized to evaluate your biogeographic ethnicity or ancestry as compared to these groups, many of which are quite ancient.

my origins regions

Primary Population Clusters

  • Anatolia & Caucasus
  • Asian Northeast
  • Bering Expansion
  • East Africa Pastoralist
  • East Asian Coastal Islands
  • Eastern Afroasiatic
  • Eurasian Heartland
  • European Coastal Islands
  • European Coastal Plain
  • European Northlands
  • Indian Tectonic
  • Jewish Diaspora
  • Kalahari Basin
  • Niger-Congo Genesis
  • North African Coastlands
  • North Circumpolar
  • North Mediterranean
  • Trans-Ural Peneplain

Blended Population Clusters

  • Coastal Islands & Central Plain
  • Northlands & Coastal Plain
  • North Mediterranean & Coastal Plain
  • Trans-Euro Peneplain & Coastal Plain

Each of these groups has an explanation which can be found here.

Matching

Prior to release, Family Tree DNA sent out a notification about new matching options.  One of the new features is that you will be able to see the matching regions of the people you match – meaning your populations in common.  This powerful feature lets you see matches who are similar which can be extremely useful when searching for minority admixture, for example.  However, some participants don’t want their matches to be able to see their ethnicity, so everyone was given an ‘opt out’ option.  Fortunately, few people have opted out, less than 1%.

Be aware that only your primary matches are shown.  This means that your 4-5th cousins or more distant are not shown as ethnicity matches.

Here’s what the FTDNA notification said:

With myOrigins, you’ll be able compare your ethnicity with your Family Finder matches. If you want to share your ethnic origins with your matches, you don’t need to take any action.  You’ll automatically be able to compare your ethnicity with your matches when myOrigins becomes available.  This is the recommended option. However, we do understand that sharing your ethnicity with your matches is your choice so we’re sending you this reminder in case you want to not take part (opt-out). To opt-out, please follow the instructions below. *

  1. Click this link.
  2. If you are not logged in, do so.
  3. Select the “Do not share my ethnic breakdown with my matches. This will not let me compare my ethnicity with my matches.” radio button.
  4. Click the Save button.

You can get more details about what will be shared here.  You may also join our forums for discussion* You can change your privacy settings at any time. Thus, you may opt-out of or opt back into ethnic sharing at a later date if you change your mind.

What’s New?

Let’s take a look at the My Origins results.  You can see your results by clicking on “My Origins” on the Family Finder tab on your personal page at Family Tree DNA.

Ethnicity and Matches

Your population ethnicity is shown on the main page, as well as up to three shared regions that you share with your matches.  This means that if you share more than 3 regions with these people, the 4th one (or 5th or 6th, etc.) won’t show.  This also means that if your match has an ethnicity you don’t have, that won’t show either.

my origins ethnicity

Above, you see my main results page.  Please note that this map is what is known as a heat map.  This means that the darkest, or hottest, areas are where my highest percentages are found.

Each region has a breakdown that can be seen by clicking on the region bar.  My European region bar population cluster breakdown is shown below along with my ethnicity match to my mother.

my origins euro breakdown

And my Middle Eastern breakdown is shown below.

my origins middle east breakdown

Ethnicity Mapping

A great new feature is the mapping of the maternal and paternal ethnicity of your Family Finder matches, when known.  How does Family Tree DNA know?  The location data entered in the “Matches Map” location field.  Can’t remember if you completed these fields?  It’s easy to take a look and see.  On either the Y DNA or the mtDNA tabs, click on Matches Map and you’ll see your white balloon.  If the white balloon is in the location of your most distant ancestor in your paternal line (for Y) or your matrilineal line for mtDNA (your mother’s mother’s mother’s line on up the tree until you run out of mothers), then you’ve entered the location data and you’re good to go.  If your white balloon is on the equator, click on the tab at the bottom of the map that says “update ancestor’s location” and step through the questions.

ancestor location

If you haven’t completed this information, please do.  It makes the experience much more robust for everyone.

How Does This Tool Work?

my origins paternal matches

The buttons to the far right of the page show the mapped locations of the oldest paternal lines and the oldest matrilineal (mtDNA) lines of your matches.  Direct paternal matches would of course be surname matches, but only to their direct paternal lines. This does not take into account all of their “most distant ancestors,” just the direct paternal ones.  This is the yellow button.

The green button provides the direct maternal matches.

my origins maternal matches

Do not confuse this with your Matches Map for your own paternal (if you’re a male) or mitochondrial matches.  Just to illustrate the difference, here is my own direct maternal full sequence matches map, available on my mtDNA tab.  As you can see, they are very different and convey very different information for you.

my mito match map

Comparisons

By way of comparison, here are my mother’s myOrigins results.

my origins mother

Let’s say I want to see who else matches her from Germany where our most distant mitochondrial DNA ancestor is located.

I can expand the map by scrolling or using the + and – keys, and click on any of the balloons.

my origins individual match

Indeed, here is my balloon, right where it should be, and the 97% European match to my mother pops up right beside my balloon.  The matches are not broken down beyond region.

This is full screen, so just hit the back button or the link in the upper right hand corner that says “back to FTDNA” to return to your personal page.

Walk Through

Family Tree DNA has provided a walk-through of the new features.

Methodology

How did Family Tree DNA come up with these new regional and population cluster matches?

As we know, all of humanity came originally from Africa, and all of humanity that settled outside of Africa came through the Middle East.  People left the Middle East in groups, it would appear, and lived as isolated populations for some time in different parts of the world.  As they did, they developed mutations that are found only in that region, or are found much more frequently in that region as opposed to elsewhere.  Patterns of mutations like this are established, and when one of us matches those patterns, it’s determined that we have ancestry, either recent or perhaps ancient, from that region of the world.

The key to this puzzle is to find enough differentiation to be able to isolate or identify one group from another.  Of course, the groups eventually interbred, at least most of them did, which makes this even more challenging.

Family Tree DNA says in their paper describing the population clusters:

MyOrigins attempts to reduce the wild complexity of your genealogy to the major historical-genetic themes which arc through the life of our species since its emergence 100,000 years ago on the plains of Africa. Each of our 22 clusters describe a vivid and critical color on the palette from which history has drawn the brushstrokes which form the complexity that is your own genome. Though we are all different and distinct, we are also drawn from the same fundamental elements.

The explanatory narratives in myOrigins attempt to shed some detailed light upon each of the threads which we have highlighted in your genetic code. Though the discrete elements are common to all humans, the weight you give to each element is unique to you. Each individual therefore receives a narrative fabric tailored to their own personal history, a story stitched together from bits of DNA.

They have also provided a white paper about their methodology that provides more information.

After reading both of these documents, I much prefer the explanations provided for each cluster in the white paper over the shorter population cluster paper.  The longer version breaks the history down into relevant pieces and describes the earliest history and migrations of the various groups.

I was pleased to see the methodology that they used and that four different reference data bases were utilized.

  • GeneByGene DNA customer database
  • Human Genome Diversity Project
  • International HapMap Project
  • Estonian Biocentre

Given this wealth of resources, I was very surprised to see how few members of some references populations were utilized.

Population N Population N
Armenian 46 Lithuanian 6
Ashkenazi 60 Masai 140
British 39 Mbuti 15
Burmese 8 Moroccan 7
Cambodian 26 Mozabite 24
Danish 13 Norwegian 17
Filipino 20 Pashtun 33
Finnish 49 Polish 35
French 17 Portuguese 25
German 17 Russian 41
Gujarati 31 Saudi 19
Iraqi 12 Scottish 43
Irish 45 Slovakian 12
Italian 30 Spanish 124
Japanese 147 Surui 21
Karitiana 23 Swedish 33
Korean 15 Ukrainian 10
Kuwaiti 14 Yoruba 136

In particular, the areas of France, Germany, Norway, Slovakia, Denmark and the Ukraine appear to be very under-represented, especially given Family Tree DNA’s very heavy European-origin customer base .  I would hope that one of the priorities would be to expand this reference data base substantially.  Furthermore, I don’t see any New World references included here which calls into question Native American ancestry.

Webinar

Family Tree DNA typically provides a webinar for new products as well as general education.  The myOrigins webinar can be found in the archives at this link.  It can be viewed any time.  https://www.familytreedna.com/learn/ftdna/webinars/

Accuracy

How did they do?  Certainly, Family Tree DNA has a great new interface with wonderful new maps and comparison features.  Let’s take a look at accuracy and see if everything makes sense.

I am fortunate to have the DNA of one of my parents, my mother.  In the chart below, I’m comparing that result and inferring my father’s results by subtracting mine from my mother’s.  This may not be entirely accurate, because this presumes I received the full amount of that ethnicity from my mother, and that is probably not accurate – but – it’s the best I can do under the circumstances.  It’s safe to say that my father has a minimum of this amount of that particular population category and may have more.

Region Me Mom Dad Inferred Minimum
European Coastal Plain 68 17 51
European Northlands 12 7 5
Trans Ural Peneplain 11 10 1
European Coastal Islands 7 34 0
Anatolia and Caucus 3 0 3
North Mediterranean 0 34 0
Circumpolar 0 1 0
Undetermined* 0 0 40

*The Undetermined category is not from Family Tree DNA, but is the percentage of my father not accounted for by inference.  This 40% is DNA that I did not inherit if it falls into a different category.

Based on these results alone, I have the following observations.

    1. I find it odd that my mother has 34% North Mediterranean and I have none. We have no known ancestry from this region.
    2. My mother does have one distant line of Turkish DNA via France. I have presumed that my Middle Eastern (now Anatolia and Caucus) was through that line, but these results suggest otherwise.
    3. My mother’s Circumpolar may be Native American. She does have proven Native lines (Micmac) through the Acadian families.
    4. These results have missed both my Native lines (through both parents) and my African admixture although both are small percentages.
    5. The European Coastal Plain is one of the groups that covers nearly all of Europe. Given that my mother is 3/4th Dutch/German, with the balance being Acadian, Native and English, one would expect her to have significantly more, especially given my high percentage.
    6. The European Coastal Island percentages are very different for me and my mother, with me carrying much less than my mother.  This is curious, because she is 3/4th German/Dutch with between 1/8th and 3/16th English while my father’s lines are heavily UK.  My father’s ancestry may well be reflected in European Coastal Plain which covers a great deal of territory.

What We Need to Remember

All of the biogeographic tools, from Family Tree DNA, 23andMe and Ancestry, are “estimates” and each of the tools from the three major vendors rend different results.  Each one is using different combinations of reference populations, so this really isn’t surprising.  Hopefully, as the various companies increase their population references and the size of their reference data bases, the results will increasingly mesh from company to company.  These results are only as good as the back end tools and the DNA that you randomly inherited from your ancestors.

Furthermore, we all carry far more similar DNA than different DNA, so it’s extremely difficult to make judgment calls based on ranges.  Europe, for example, is extremely admixed and the US is moreso.  The British Isles were a destination location for many groups over thousands of years.  Some of the DNA being picked up by these tests may indeed be very ancient and may cause us to wonder where it came from.  In future test versions, this may be more perfectly refined.

There is no way to gauge “ancient” DNA, like from the Middle East Diaspora, from more contemporary DNA, only a thousand years or so old, once it’s in very small segments.  In other words, it’s all very individual and personal and pretty much cast in warm jello.  We’ve come a long way, but we aren’t “there” yet.  However, without these tools and the vendors working to make them better, we’ll never get “there,” so keep that in mind.

While this makes great conversation today, and there is no question about accuracy in terms of majority ancestry/ethnicity, no one should make any sweeping conclusions based on this information.  This is not “cast in concrete” in the same way as Y DNA and mitochondrial haplogroups and STR markers.  Those are irrefutable – while biogeographical ethnicity remains a bit ethereal.

In summary, I would simply say that this tool can provide great hints and tips, especially the matching, which is unique, but it can’t disprove anything.  The absence of minority admixture, which is what so many people are hunting for, may be the result of the various data bases and the infancy of the science itself, and not the absence of admixture.

My recommendation would be to utilize all three biogeographic admixture products as well as the free tools in the Admixture category at GedMatch.  Look for consistency in results between the tools.  I discussed this methodology in “The Autosomal Me” series.

What Next?

I asked Dr. David Mittelman, Chief Scientific Officer, at Family Tree DNA about the reference populations.  He indicated that he agreed that some of their reference populations are small and they are actively working to increase them.  He also stated that it is important to note that Family Tree DNA prioritized accuracy over false positives so they definitely took a conservative approach.

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

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

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

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

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

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

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

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

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

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

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

Mitochondrial DNA

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

Clovis mtDNA

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

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

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

Y Chromosomal DNA

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

The tree researchers constructed is shown below.

Clovis Y

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

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

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

Autosomal

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

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

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

Clovis autosomal cropped

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

Clovis branch

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

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

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

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

who matches who

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

Conclusions

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

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

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

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

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

Another article can be found at Voice of America News.

Science has a bit more.

Neanderthal Genome Further Defined in Contemporary Eurasians

DNA X

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

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

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

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

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

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

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

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

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

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

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

2013’s Dynamic Dozen – Top Genetic Genealogy Happenings

dna 8 ball

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

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

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

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

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

Y Chromosome SNP Tsunami Begins

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

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

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

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

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

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

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

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

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

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

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

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

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

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

23andMe Comes Unraveled

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Also, see the Autosomal DNA Comes of Age section.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Gene By Gene Steps Up, Ramps Up and Produces

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

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

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

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

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

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

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

Autosomal DNA Comes of Age

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

DNAGedcom – Indispensable Third Party Tool

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

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

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

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

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

Ancestry – How Great Thou Aren’t

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Ancient DNA

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Sloppy Science and Sensationalist Reporting

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

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

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

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

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

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

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

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

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

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

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

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

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

Citizen Science is Coming of Age

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

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

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

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

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

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

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

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

Ethnicity Makeovers – Still Not Soup

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

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

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

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

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

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

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

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

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

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

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

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

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

Genetic Genealogy Education Goes Mainstream

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

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

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

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

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

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

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

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

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

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

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

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

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

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

A Thank You in Closing

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

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

Sequencing of Neanderthal Toe Bone Reveals Unknown Hominin Line

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

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

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

The abstract also includes this graphic from the paper

Neanderthal 12-22-2013 cropped

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

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

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

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

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

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

native flow map

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

The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians1, 2, 3, there is no consensus with regard to which specific Old World populations they are closest to4, 5, 6, 7, 8. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia9, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date.

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

The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers10, 11, 12, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages5.

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

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

Native flow Hap U map

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

Native flow Brandt map

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

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

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

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

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

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

Native flow R tree

 native flow r tree text

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

Native flow R map

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

Native flow Q map

Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians2, 13.

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

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

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

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

Native flow Otzi table

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

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

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

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

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

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

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

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

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

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

The times, they are a changin’.

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

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

Native flow basic Y

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

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

Native flow hammer dist

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

What Can We Say About MA-1?

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2013 Family Tree DNA Conference Day 2

ISOGG Meeting

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

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

Bennett opened the second day after the ISOGG meeting.

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

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

Bennett day 2 intro

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

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

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

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

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

Hammer scroll

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

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

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

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

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

What did the various expansions contribute to the population today?

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

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

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

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

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

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

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

hammer ancient y

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

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

In Spain, 5 G2a and 1 E1b.

In Germany, 1I G2a and 2 F*.

Otzi is haplogroup G2a2b.

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

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

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

hammer backbone

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

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

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

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

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

hammer post neolithic epicenters

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

Archaeological studies produce patterns similar to the hap epicenters.

What kind of model is going on for this expansion?

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

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

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

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

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

hammer hap k

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

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

hammer r and q in europe

R then, populated Europe in the last 4000 years.

How did these Asians get to Europe and why?

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

Hammer hap r dist

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

hammer haplogroup dispersion map

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

For example, the R1bs of the British Isles.

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

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

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

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

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

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

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

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

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

marja

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

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

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

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

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

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

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

Session 3 – Jason Wang – Engineering Roadmap and IT Update

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

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

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

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

Year in review and What’s Coming

4 times the data processed in the past year.

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

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

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

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

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

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

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

New 2014 tree has 6200 SNPS and 1000 branches.

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

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

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

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

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

X Matching

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

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

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

Population Finder

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

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

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

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

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

Session 4 – Dr. Connie Bormans – Laboratory Update

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

  • CLIA
  • CAP
  • AABB
  • NYSDOH

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

Working to decrease turn-around time.

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

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

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

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

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

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

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

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

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

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

2000-5000 people passed by the booth

500 people in the booth

Sold 99 kits – 119 tests

45 took Y 37 marker tests

56 FF, 20 male, 36 female

18 mito tests

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

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

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

Session 6 – Brad Larkin – Introducing Surname DNA Journal

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

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

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

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

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

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

Session 7 – mtdna Roundtable – Roberta Estes and Marie Rundquist

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

Q&A

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

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

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

80% of FTDNA orders are from the US.

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

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

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

Goodbyes

See y’all next year!!!