Homo Naledi – A New Species Discovered

The Cradle of Humankind World Heritage Site near Johannesburg, South Africa has once again produced bones.  Previous finds, nearly one third of all ancient hominin fossils found, date to 3.5 million years of age.  This new find may be the bones of our ancestor, but regardless, they certainly are the bones of a new, previously unknown, species.

The announcement came this week and articles can be seen online in several locations.  The National Geographic Society is a partner in the excavation and retrieval of the bones from a very difficult cave, Rising Star, through only a very small opening following a precipitous decline.  Stated bluntly – this is a “scare the hell out of you” cave.  Not exactly convenient or inviting.

Rising Star Cave

“Dinaledi Chamber illustration” by Paul H. G. M. Dirks et al – http://elifesciences.org/content/4/e09561. Licensed under CC BY 4.0 via Commons – https://commons.wikimedia.org/wiki/File:Dinaledi_Chamber_illustration.jpg#/media/File:Dinaledi_Chamber_illustration.jpg

There was more than one skeleton present.  In this article and video from the New York Times, you can see that many bones were recovered, quite obviously from multiple individuals.  More than 1550 in total – representing at least 15 different individuals.  How did they get in this extremely remote cave with very limited access in the first place? And why?

Is this a separate species from ours, or our ancestors?  How long ago did they live, and where do they fit on the family tree?  The scientists are now referring to the ancient family tree as a braided stream – a river that divides into channels only to converge again later.

These announcements are being followed by a special on Nova/National Geographic Special titled the “Dawn of Humanity” which premieres on Sept. 16, 2015 at 9 PM ET/8 Central on PBS and is streaming online now.  This documentary details the discovery and excavation of the fossils in the cave including Homo Naledi.

In the mean time, take a look at this wonderful article, chock full of pictures of course, by National Geographic.  If you subscribe to the National Geographic magazine, guess what will be on the cover of the October issue???

This article in New Scientist has a great reconstruction of the Homo Naledi skull, and states that no attempt has yet been made to extract DNA.  I continue to remind myself that patience is a virtue.

Anzick Matching Update

In response to my article about haplogroup C3*, a regular contributor, Armando, left the following comment:

“Roberta, there was a problem with the way Felix was processing files and he had to change the Clovis Anzick file three times at Gedmatch. The last one is kit F999919 uploaded October 8, 2014. You can see his post on that at http://www.fc.id.au/2014/10/new-clovis-anzick-1-kit-in-gedmatch.html

If you do one-to-many matching on Clovis Anzick F999919 at Gedmatch there is not a single person that reports to have mtDNA M. Your extracts for Clovis Anzick are from September 24, 2014 and therefore are based on a bad file which was kit F999912. The older bad kits F999912 and F999913 have been deleted from Gedmatch. Felix mentions the updates at http://www.fc.id.au/2014/09/clovis-anzick-1-dna-match-living-people.html

This comment came in on Christmas Eve, and I replied that I would look into this after the holidays.

Given that it was Christmas Eve, I certainly wasn’t going to bother anyone over the holidays with questions, so I quickly ran a one to many compare for the current Anzick kit, F999919, and found at 5cM and below that there were 4 haplogroup M matches.

ancient match

As I did before, I sent emails to those who provided e-mail addresses asking about their matrilineal heritage.

The first thing I wanted to do, of course, was to check with Felix.  I knew that Felix had updated the kits, but my understanding was that he added SNPs from the various companies to create a single file with all the SNPs from all three testing companies, not that any file was bad, so to speak.

I asked Felix if the original files had problems or were bad, and here is his response.

“I can assure you none of the earlier/older versions uploaded to GEDmatch (kit# F999912 and F999913) of Clovis Anzick was bad.

  • F999912 – Contains only FTDNA SNPs extracted from VCF file provided by authors.
  • F999913 – Contains all SNPs used by DNA testing companies extracted from VCF file provided by authors.
  • F999919 – Contains all SNPs used by DNA testing companies processed from BAM file provided by authors.

Source files: 

I removed the earlier versions not because they are bad but only to avoid redundancy for the same sample kit, and processed BAM file (which is a 41 GB file) contains significantly more SNPs compared to VCF source. Because the latest file has more SNPs, it is possible that some missing SNPs in earlier uploads (which was assumed as matching in GEDmatch) may actually have mismatches in new file and thus, could fall below the thresholds or could break the previously matching segment.

The difference in matches between F999912 and F999919 kit for Clovis Anzick is similar to difference in matches between a 23andMe V4 kit and V3 kit for the same person.”

After thinking about this some, it occurred to me that perhaps GedMatch was treating different files from different vendors differently in their matching and sorting routines. That might account for a difference in matching. So, I asked John Olson at GedMatch.

John’s reply is as follows:

“At one time, I did use different thresholds depending on which vendor was being compared to which other vendor.  That was a holdover from when FTDNA had Affymetrix kits that were producing somewhat different results than Illumina kits.  I have since changed the one-to-many thresholds to 5cM/500 SNPs for all comparisons.  The one-to-one thresholds default to 7cm/700 SNPs.  I believe I made that change about a year ago, but it may have been longer.  At any rate, they are all the same now, and I’m pretty sure they are all the same since Felix has introduced the F9999xx kits.  Another change made within the past year is to treat A=T and C=G for all comparisons.  This was done to get rid of single SNP errors in the few cases where one vendor was reporting a different strand than another vendor.  In a few cases, I have observed that this “heals” some single-SNP breaks in otherwise continuous matching segments.

It is possible that older one-to-many comparisons may have been made under slightly different conditions than newer ones.  Older comparisons made with a 3cm/300 SNP threshold may show larger total segment match if they contained many very small matching segments.  This usually happens with endogamous populations.  Comparisons affected by the change to A=T, C=G may show a larger matching segment where 2 smaller matching segments existed previously.

Another issue to be aware of when comparing artificial kits is that there may be large gaps between the defined SNPs.  So, even if there is a gap of a million SNPs, the GEDmatch comparison algorithm will treat them as contiguous.  This works OK when everybody is using the same SNPs, but when the list of SNPs is significantly different, it may produce matches that are bogus.  This is particularly obvious when generating artificial kits that are missing large segments of data.  I have had to deal with this issue with phased kits and Lazarus kits by introducing the concept of a “hard break” that forces a break between smaller matching segments.”

I wanted to know how the three files that Felix prepared compared relative to the matches they produced.  I originally ran several comparisons with each of the first two versions, kits F999912 and F999913, and I didn’t save all of the original files, but I do have at least one file saved from each version.  Therefore, I dropped all three sets of results (F999912, F999913 and F999919) into a spreadsheet to see how matching compared between the three Anzick file versions.

Keep in mind that the first file (F999912) contained just the FTDNA SNPs, while the second (F999913) and third (F999919) files contain the SNPs from all of the testing companies.  This could potentially make the participant files appear to have missing segments when the matching routine at GedMatch sees SNPs in the Anzick file not in the participant files.  However, this shouldn’t be much different than comparing a file from two different vendors except that the Anzick file has the SNPs from all three vendors combined.

The first file from 9-23 at the default threshold had 491 matches, but I subsequently lowered the threshold so I could see as many matches as possible.

GedMatch only shows you your closest 1500 matches, although I now know that as of 12-31-2014, there were a total of 3442 Anzick matches at the 5cM threshold.

The second file from 9-29, run at 6cM had more than 1500 matches.  I ran the third kit at default settings on December 27th and it has 720 matches.

One would expect that the second and third files would have the effect of including more matches from both 23andMe and Ancestry since all of the SNPs utilized by those companies are included (if they are available in the Anzick sample.)  We also have to remember that there are new files being uploaded from all three vendor sites on a daily basis, so the total available to match is also increasing.  Of the 721 kit matches to F999919, 31 were shades of green which indicate that they have been uploaded during the last 30 days, so we could probably presume that about double that number were uploaded (and match) in two months or triple in three months, so probably about 100 new kits.  Those kits would show in the match extraction for this month but not for the first month and possibly not for the second.  However, all the kits that matched the first month at the highest threshold should still be showing in the second and third month.  Let’s see if that holds true.

I dropped all three sets of data into a spreadsheet and colorized the rows.

ancient match 1

  • Blue = F999912, first extraction, 9-23-2014
  • Yellow = F999913, second extraction, 9-29-2014
  • Pink = F999919, third extraction, 12-27-2014

Then I counted the number of blue rows, which are the first extraction, that had matches to both yellow and pink, or only yellow, the second extraction, or only pink, the third (current) extraction, or no matches at all.

You can see that the green grouping shows that all three match each other.  The match between A003479 in both the second and third extraction could be because the kit was not present when the first extraction was done.

All 3 match 1st to 2nd Only 1st  to 3rd Only No Match
Percent First Extraction Matches to Other Extractions 54% 36% 5% 5%

By percent, this is how the matching between kits worked.  About half of the kits in the first extraction continued to match kits in both subsequent extractions.  Of the remaining half, three quarters of the balance matches the second extraction only and a few match just the third extraction or no extraction at all.  For the most part, there is no evident reason upon inspection why the kits would not match the second or third extraction, so the cause has to be a result of the additional SNPs or the matching routine or both.  This is not to imply that the results are problematic, just that they are different than I would have expected.

A very low percentage of kits matched only between the first and third extracts and the same percentage had no matches in either the second or third extraction.

I took a closer look at the kits with no matches at all.  All of them had relatively low threshold total cM and largest segment size.  The smallest total cM was 7.1 and the largest was 8.2.  The smallest segment was 7.1 and the largest segment was also 8.2.  All of these entries had the total cM equal to the largest cM.  It appears that these simply slipped below the match threshold, but that doesn’t appear to be the case because in the current (pink) extract, a total of 171 entries were at or below 8.2 total cM and 8.2 largest cM and several kits had the exact same cM as the kits that didn’t show up from the first (blue) extract as a match – so obviously something truly was different in the SNPs or how the matching was done.

Is there any correlation to the kits in the original extract that didn’t match any other extract in terms of which testing company the participants utilized?

One Ancestry kit (4%), 18 23andMe kits (64%), 7 Family Tree DNA kits (25%) and 2 FN kits (7%) didn’t match anyone.  But how many kits were in the original extract from the various companies?

Original Kit Matches Second KitMatches Current Kit Matches
Ancestry Kits (A) 26 (5%) 438 (29%) 199 (28%)
FTDNA Kits (F) 94 (19%) 295 (20%) 121 (17%)
Other F+ Kits* 15 (3%) 35 (2%) 15 (2%)
23andMe Kits (M) 354 (72%) 732 (49%) 382 (53%)

*FB, FN, FE, FV

The effect of the additional SNPs in the kits seems to have been to increase the Ancestry kit matches significantly.

It was interesting to see how the same person’s kit from different vendors compared as well.  In this random example, the Family Finder kit has a higher total cM and largest segment than the 23andMe v3 kit.

ancient match 2

Here’s a kit from one person at all three vendors, but the 23andMe kit is version 4, in which 23andMe significantly reduced the number of SNPs tested by about one third, from about 900,000 to about 600,000.

ancient match 3

I wondered if there is a difference in what is reported based on the threshold selected.  Now at first glance, one would think, “well of course there is a difference,” but the difference should be on the bottom end of the list.  In other words, the top matches should be the top matches at 7cM, 6cM, 5cM, etc.  The top matches at 7cM would still be the top at 6cM, just more smaller matches appended to the end of the match list – or that is what I would expect.

Let’s see if this holds true with the current file.

I ran the “one to many” option for the current Anzick kit, F999919, at seven different levels, on the same day, one right after the other, as follows:

  • 7cM, 700 SNPs
  • 6cM, 600 SNPs
  • 5cM, 500 SNPs
  • 4cM, 400 SNPs
  • 3cM, 300 SNPs
  • 2cM, 200 SNPs
  • 1cM, 100 SNPs

The first extract produced 719 records.  The rest were all over the 1500 threshold, so we only see the first 1500.  Normally, for genealogy the 1500 threshold would certainly be adequate, but for research, the threshold is frustrating.

To make this easier let me say that the extracts from 5cM down through 1cM were exactly the same, but the extracts at 7, 6 and 5cM, respectively, were not.

Discussions with John Olson at GedMatch shed some light on why the 5cM through 1cM extracts were exactly the same.

 “For the past year or so, the database has only stored matches down to 5 cM.”

I sure wish I had known that BEFORE I did all of those extracts.

I combined and color coded all 7 extractions into a spreadsheet.

Most of the grouping look like this where blue=7cm, pink=6cM, grn=5cM, purple=4cm, teal=3cm,apricot=2cm, yellow=1cm.  Nice rainbows.

ancient match 4

All of the matches from the 7cM extraction, with the exception of a few X matches at the end, some of which have no matches on chromosomes 1-22, are included in the 6cM and 5cM extractions, but after the first several records, they are not in the same position.  In other words, they are not the top 719, in the same order, in either the 5 or 6cM extraction, but the 5cM through 1cM extractions are identical.  Of course, now we know why the 5cM through 1cM matches are exact. From here forth in the article, I won’t mention the 4cM-1cM extracts because they are the same as the 5cM extract.

For example, looking at the kit in position 712, the last non-X match in the 7cM extract – you find this same kit at row 1140 in the 6cM extract and row 1489 in the 5cM extract.

The 6cM extract appears to have some issues.  I ran this twice with the same parameters to be sure there wasn’t an error in how it was set up, and the two runs were identical.

There are about 350 individuals who show up in the 6cM extract who should  show up in the 5cM extract as well, but who don’t show in the 5cM extract.  They are under the threshold for the 7cM extract, so that is correct, but why are these 350 individuals not appearing as matches at the 5cM threshold?

ancient match 5

The kits noted above are the largest non-matching total cM and largest cM that don’t show up in the 5cM extract.  The smallest matches are 6.1 and 6.1, respectively.

Checking the 5cM extract, below, there are files with smaller total cMs and a smaller largest segment that are showing as matches.

ancient match 6

However, looking at the kits with the smallest cMs at the 5cM level, the smallest total cMs is 6.9 and it is combined with the largest segment of 6.9 as well, so that is above the 6.8 and 6.8 shown above.  The smallest individual segment is 5.1 but the total cM for that individual is 10.1.  So obviously the matching threshold at GedMatch is some combination of both the total cM and the largest segment.  This is somewhat unexpected, but doesn’t seem to be a red flag, just how this system works.

So, where are we?

I am glad to have Felix confirm that the files weren’t “bad,” only truly “new and improved,” and that the matching between the various files is pretty much as expected – and from various tests run, everything pretty much looks kosher.  The newer files with all of the SNPs utilized by the companies seem to level the playing field, allowing Ancestry kits a better chance of matching.

Aside from my intense interest due to the Native American connection, this is also how I’ve been extracting potential Native American mitochondrial haplogroups from the Anzick matches, including haplogroup M, for my research notes.  M is potentially a Native American haplogroup, but is as yet unproven.  With haplogroup M showing up in these people who are often heavily Native, and often from Mexico, Central and South America where 80% of the mitochondrial population is believed to be of Native American heritage, it seems prudent to add them to my research notes for further research and possible proof in the future.  I contact individuals and ask about their matrilineal heritage.  If they don’t have Asian or genealogically proven heritage elsewhere, and their families emerge from the areas with high Native frequencies, I include them on the research list.

In the three days between the two extracts this past week, three of the four haplogroup M individuals were pushed below the match threshold and are no longer visible at the default level.  Yes, I have confirmed hat they are still there just not visible at the 1500 match threshold.

I have contacted the individuals with e-mail addresses, asking about their matrilineal heritage.  One person said the tester’s mother’s heritage was from India, so that haplogroup M is not on the research list, of course, because it is proven to be from elsewhere – a place where haplogroup M and subgroups are quite common.

In total, there were 15 new potentially Native DNA mitochondrial DNA haplogroups listed in the 12-27 extract.  I’ll be adding those to my research notes as soon as I have the opportunity to contact these folks and ask about their known matrilineal genealogy.

I didn’t really anticipate that there would be so much change, nor so quickly, so it looks like I’m going to have to check the Anzick matches for potential Native mitochondrial haplogroups much more often.

Since it looks like there may be lots of additions over time, far more than I expected, I’ll also be going back and making better notes in my research file.  I will, for example, note the kit number and date for all of the extractions.  For this and future extractions, I’ll also be listing the number of results per haplogroup.  I think that would be valuable information as well.

I’d like to thank Armando for raising this topic.  The research into matching with a kit that has the entire spectrum of SNPs from all three of the companies has been quite interesting.  In fact, unless Felix has added all of the SNPs to the other ancient kits, this is the only kit in existence that has all of the SNPs from all of the companies included.

My thanks to Felix Immanuel (formerly Felix Chandrakumar) and John Olson for assistance with research for this article.

2014 Top Genetic Genealogy Happenings – A Baker’s Dozen +1

It’s that time again, to look over the year that has just passed and take stock of what has happened in the genetic genealogy world.  I wrote a review in both 2012 and 2013 as well.  Looking back, these momentous happenings seem quite “old hat” now.  For example, both www.GedMatch.com and www.DNAGedcom.com, once new, have become indispensable tools that we take for granted.  Please keep in mind that both of these tools (as well as others in the Tools section, below) depend on contributions, although GedMatch now has a tier 1 subscription offering for $10 per month as well.

So what was the big news in 2014?

Beyond the Tipping Point

Genetic genealogy has gone over the tipping point.  Genetic genealogy is now, unquestionably, mainstream and lots of people are taking part.  From the best I can figure, there are now approaching or have surpassed three million tests or test records, although certainly some of those are duplicates.

  • 500,000+ at 23andMe
  • 700,000+ at Ancestry
  • 700,000+ at Genographic

The organizations above represent “one-test” companies.  Family Tree DNA provides various kinds of genetic genealogy tests to the community and they have over 380,000 individuals with more than 700,000 test records.

In addition to the above mentioned mainstream firms, there are other companies that provide niche testing, often in addition to Family Tree DNA Y results.

In addition, there is what I would refer to as a secondary market for testing as well which certainly attracts people who are not necessarily genetic genealogists but who happen across their corporate information and decide the test looks interesting.  There is no way of knowing how many of those tests exist.

Additionally, there is still the Sorenson data base with Y and mtDNA tests which reportedly exceeded their 100,000 goal.

Spencer Wells spoke about the “viral spread threshold” in his talk in Houston at the International Genetic Genealogy Conference in October and terms 2013 as the year of infection.  I would certainly agree.

spencer near term

Autosomal Now the New Normal

Another change in the landscape is that now, autosomal DNA has become the “normal” test.  The big attraction to autosomal testing is that anyone can play and you get lots of matches.  Earlier in the year, one of my cousins was very disappointed in her brother’s Y DNA test because he only had a few matches, and couldn’t understand why anyone would test the Y instead of autosomal where you get lots and lots of matches.  Of course, she didn’t understand the difference in the tests or the goals of the tests – but I think as more and more people enter the playground – percentagewise – fewer and fewer do understand the differences.

Case in point is that someone contacted me about DNA and genealogy.  I asked them which tests they had taken and where and their answer was “the regular one.”  With a little more probing, I discovered that they took Ancestry’s autosomal test and had no clue there were any other types of tests available, what they could tell him about his ancestors or genetic history or that there were other vendors and pools to swim in as well.

A few years ago, we not only had to explain about DNA tests, but why the Y and mtDNA is important.  Today, we’ve come full circle in a sense – because now we don’t have to explain about DNA testing for genealogy in general but we still have to explain about those “unknown” tests, the Y and mtDNA.  One person recently asked me, “oh, are those new?”

Ancient DNA

This year has seen many ancient DNA specimens analyzed and sequenced at the full genomic level.

The year began with a paper titled, “When Populations Collide” which revealed that contemporary Europeans carry between 1-4% of Neanderthal DNA most often associated with hair and skin color, or keratin.  Africans, on the other hand, carry none or very little Neanderthal DNA.

https://dna-explained.com/2014/01/30/neanderthal-genome-further-defined-in-contemporary-eurasians/

A month later, a monumental paper was published that detailed the results of sequencing a 12,500 Clovis child, subsequently named Anzick or referred to as the Anzick Clovis child, in Montana.  That child is closely related to Native American people of today.

https://dna-explained.com/2014/02/13/clovis-people-are-native-americans-and-from-asia-not-europe/

In June, another paper emerged where the authors had analyzed 8000 year old bones from the Fertile Crescent that shed light on the Neolithic area before the expansion from the Fertile Crescent into Europe.  These would be the farmers that assimilated with or replaced the hunter-gatherers already living in Europe.

https://dna-explained.com/2014/06/09/dna-analysis-of-8000-year-old-bones-allows-peek-into-the-neolithic/

Svante Paabo is the scientist who first sequenced the Neanderthal genome.  Here is a neanderthal mangreat interview and speech.  This man is so interesting.  If you have not read his book, “Neanderthal Man, In Search of Lost Genomes,” I strongly recommend it.

https://dna-explained.com/2014/07/22/finding-your-inner-neanderthal-with-evolutionary-geneticist-svante-paabo/

In the fall, yet another paper was released that contained extremely interesting information about the peopling and migration of humans across Europe and Asia.  This was just before Michael Hammer’s presentation at the Family Tree DNA conference, so I covered the paper along with Michael’s information about European ancestral populations in one article.  The take away messages from this are two-fold.  First, there was a previously undefined “ghost population” called Ancient North Eurasian (ANE) that is found in the northern portion of Asia that contributed to both Asian populations, including those that would become the Native Americans and European populations as well.  Secondarily, the people we thought were in Europe early may not have been, based on the ancient DNA remains we have to date.  Of course, that may change when more ancient DNA is fully sequenced which seems to be happening at an ever-increasing rate.

https://dna-explained.com/2014/10/21/peopling-of-europe-2014-identifying-the-ghost-population/

Lazaridis tree

Ancient DNA Available for Citizen Scientists

If I were to give a Citizen Scientist of the Year award, this year’s award would go unquestionably to Felix Chandrakumar for his work with the ancient genome files and making them accessible to the genetic genealogy world.  Felix obtained the full genome files from the scientists involved in full genome analysis of ancient remains, reduced the files to the SNPs utilized by the autosomal testing companies in the genetic genealogy community, and has made them available at GedMatch.

https://dna-explained.com/2014/09/22/utilizing-ancient-dna-at-gedmatch/

If this topic is of interest to you, I encourage you to visit his blog and read his many posts over the past several months.

https://plus.google.com/+FelixChandrakumar/posts

The availability of these ancient results set off a sea of comparisons.  Many people with Native heritage matched Anzick’s file at some level, and many who are heavily Native American, particularly from Central and South America where there is less admixture match Anzick at what would statistically be considered within a genealogical timeframe.  Clearly, this isn’t possible, but it does speak to how endogamous populations affect DNA, even across thousands of years.

https://dna-explained.com/2014/09/23/analyzing-the-native-american-clovis-anzick-ancient-results/

Because Anzick is matching so heavily with the Mexican, Central and South American populations, it gives us the opportunity to extract mitochondrial DNA haplogroups from the matches that either are or may be Native, if they have not been recorded before.

https://dna-explained.com/2014/09/23/analyzing-the-native-american-clovis-anzick-ancient-results/

Needless to say, the matches of these ancient kits with contemporary people has left many people questioning how to interpret the results.  The answer is that we don’t really know yet, but there is a lot of study as well as speculation occurring.  In the citizen science community, this is how forward progress is made…eventually.

https://dna-explained.com/2014/09/25/ancient-dna-matches-what-do-they-mean/

https://dna-explained.com/2014/09/30/ancient-dna-matching-a-cautionary-tale/

More ancient DNA samples for comparison:

https://dna-explained.com/2014/10/04/more-ancient-dna-samples-for-comparison/

A Siberian sample that also matches the Malta Child whose remains were analyzed in late 2013.

https://dna-explained.com/2014/11/12/kostenki14-a-new-ancient-siberian-dna-sample/

Felix has prepared a list of kits that he has processed, along with their GedMatch numbers and other relevant information, like gender, haplogroup(s), age and location of sample.

http://www.y-str.org/p/ancient-dna.html

Furthermore, in a collaborative effort with Family Tree DNA, Felix formed an Ancient DNA project and uploaded the ancient autosomal files.  This is the first time that consumers can match with Ancient kits within the vendor’s data bases.

https://www.familytreedna.com/public/Ancient_DNA

Recently, GedMatch added a composite Archaic DNA Match comparison tool where your kit number is compared against all of the ancient DNA kits available.  The output is a heat map showing which samples you match most closely.

gedmatch ancient heat map

Indeed, it has been a banner year for ancient DNA and making additional discoveries about DNA and our ancestors.  Thank you Felix.

Haplogroup Definition

That SNP tsunami that we discussed last year…well, it made landfall this year and it has been storming all year long…in a good way.  At least, ultimately, it will be a good thing.  If you asked the haplogroup administrators today about that, they would probably be too tired to answer – as they’ve been quite overwhelmed with results.

The Big Y testing has been fantastically successful.  This is not from a Family Tree DNA perspective, but from a genetic genealogy perspective.  Branches have been being added to and sawed off of the haplotree on a daily basis.  This forced the renaming of the haplogroups from the old traditional R1b1a2 to R-M269 in 2012.  While there was some whimpering then, it would be nothing like the outright wailing now that would be occurring as haplogroup named reached 20 or so digits.

Alice Fairhurst discussed the SNP tsunami at the DNA Conference in Houston in October and I’m sure that the pace hasn’t slowed any between now and then.  According to Alice, in early 2014, there were 4115 individual SNPs on the ISOGG Tree, and as of the conference, there were 14,238 SNPs, with the 2014 addition total at that time standing at 10,213.  That is over 1000 per month or about 35 per day, every day.

Yes, indeed, that is the definition of a tsunami.  Every one of those additions requires one of a number of volunteers, generally haplogroup project administrators to evaluate the various Big Y results, the SNPs and novel variants included, where they need to be inserted in the tree and if branches need to be rearranged.  In some cases, naming request for previously unknown SNPs also need to be submitted.  This is all done behind the scenes and it’s not trivial.

The project I’m closest to is the R1b L-21 project because my Estes males fall into that group.  We’ve tested several, and I’ll be writing an article as soon as the final test is back.

The tree has grown unbelievably in this past year just within the L21 group.  This project includes over 700 individuals who have taken the Big Y test and shared their results which has defined about 440 branches of the L21 tree.  Currently there are almost 800 kits available if you count the ones on order and the 20 or so from another vendor.

Here is the L21 tree in January of 2014

L21 Jan 2014 crop

Compare this with today’s tree, below.

L21 dec 2014

Michael Walsh, Richard Stevens, David Stedman need to be commended for their incredible work in the R-L21 project.  Other administrators are doing equivalent work in other haplogroup projects as well.  I big thank you to everyone.  We’d be lost without you!

One of the results of this onslaught of information is that there have been fewer and fewer academic papers about haplogroups in the past few years.  In essence, by the time a paper can make it through the peer review cycle and into publication, the data in the paper is often already outdated relative to the Y chromosome.  Recently a new paper was released about haplogroup C3*.  While the data is quite valid, the authors didn’t utilize the new SNP naming nomenclature.  Before writing about the topic, I had to translate into SNPese.  Fortunately, C3* has been relatively stable.

https://dna-explained.com/2014/12/23/haplogroup-c3-previously-believed-east-asian-haplogroup-is-proven-native-american/

10th Annual International Conference on Genetic Genealogy

The Family Tree DNA International Conference on Genetic Genealogy for project administrators is always wonderful, but this year was special because it was the 10th annual.  And yes, it was my 10th year attending as well.  In all these years, I had never had a photo with both Max and Bennett.  Everyone is always so busy at the conferences.  Getting any 3 people, especially those two, in the same place at the same time takes something just short of a miracle.

roberta, max and bennett

Ten years ago, it was the first genetic genealogy conference ever held, and was the only place to obtain genetic genealogy education outside of the rootsweb genealogy DNA list, which is still in existence today.  Family Tree DNA always has a nice blend of sessions.  I always particularly appreciate the scientific sessions because those topics generally aren’t covered elsewhere.

https://dna-explained.com/2014/10/11/tenth-annual-family-tree-dna-conference-opening-reception/

https://dna-explained.com/2014/10/12/tenth-annual-family-tree-dna-conference-day-2/

https://dna-explained.com/2014/10/13/tenth-annual-family-tree-dna-conference-day-3/

https://dna-explained.com/2014/10/15/tenth-annual-family-tree-dna-conference-wrapup/

Jennifer Zinck wrote great recaps of each session and the ISOGG meeting.

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy/

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy-isogg-meeting/

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy-sunday/

I thank Family Tree DNA for sponsoring all 10 conferences and continuing the tradition.  It’s really an amazing feat when you consider that 15 years ago, this industry didn’t exist at all and wouldn’t exist today if not for Max and Bennett.

Education

Two educational venues offered classes for genetic genealogists and have made their presentations available either for free or very reasonably.  One of the problems with genetic genealogy is that the field is so fast moving that last year’s session, unless it’s the very basics, is probably out of date today.  That’s the good news and the bad news.

https://dna-explained.com/2014/11/12/genetic-genealogy-ireland-2014-presentations 

https://dna-explained.com/2014/09/26/educational-videos-from-international-genetic-genealogy-conference-now-available/

In addition, three books have been released in 2014.emily book

In January, Emily Aulicino released Genetic Genealogy, The Basics and Beyond.

richard hill book

In October, Richard Hill released “Guide to DNA Testing: How to Identify Ancestors, Confirm Relationships and Measure Ethnicity through DNA Testing.”

david dowell book

Most recently, David Dowell’s new book, NextGen Genealogy: The DNA Connection was released right after Thanksgiving.

 

Ancestor Reconstruction – Raising the Dead

This seems to be the year that genetic genealogists are beginning to reconstruct their ancestors (on paper, not in the flesh) based on the DNA that the ancestors passed on to various descendants.  Those segments are “gathered up” and reassembled in a virtual ancestor.

I utilized Kitty Cooper’s tool to do just that.

https://dna-explained.com/2014/10/03/ancestor-reconstruction/

henry bolton probablyI know it doesn’t look like much yet but this is what I’ve been able to gather of Henry Bolton, my great-great-great-grandfather.

Kitty did it herself too.

http://blog.kittycooper.com/2014/08/mapping-an-ancestral-couple-a-backwards-use-of-my-segment-mapper/

http://blog.kittycooper.com/2014/09/segment-mapper-tool-improvements-another-wold-dna-map/

Ancestry.com wrote a paper about the fact that they have figured out how to do this as well in a research environment.

http://corporate.ancestry.com/press/press-releases/2014/12/ancestrydna-reconstructs-partial-genome-of-person-living-200-years-ago/

http://www.thegeneticgenealogist.com/2014/12/16/ancestrydna-recreates-portions-genome-david-speegle-two-wives/

GedMatch has created a tool called, appropriately, Lazarus that does the same thing, gathers up the DNA of your ancestor from their descendants and reassembles it into a DNA kit.

Blaine Bettinger has been working with and writing about his experiences with Lazarus.

http://www.thegeneticgenealogist.com/2014/10/20/finally-gedmatch-announces-monetization-strategy-way-raise-dead/

http://www.thegeneticgenealogist.com/2014/12/09/recreating-grandmothers-genome-part-1/

http://www.thegeneticgenealogist.com/2014/12/14/recreating-grandmothers-genome-part-2/

Tools

Speaking of tools, we have some new tools that have been introduced this year as well.

Genome Mate is a desktop tool used to organize data collected by researching DNA comparsions and aids in identifying common ancestors.  I have not used this tool, but there are others who are quite satisfied.  It does require Microsoft Silverlight be installed on your desktop.

The Autosomal DNA Segment Analyzer is available through www.dnagedcom.com and is a tool that I have used and found very helpful.  It assists you by visually grouping your matches, by chromosome, and who you match in common with.

adsa cluster 1

Charting Companion from Progeny Software, another tool I use, allows you to colorize and print or create pdf files that includes X chromosome groupings.  This greatly facilitates seeing how the X is passed through your ancestors to you and your parents.

x fan

WikiTree is a free resource for genealogists to be able to sort through relationships involving pedigree charts.  In November, they announced Relationship Finder.

Probably the best example I can show of how WikiTree has utilized DNA is using the results of King Richard III.

wiki richard

By clicking on the DNA icon, you see the following:

wiki richard 2

And then Richard’s Y, mitochondrial and X chromosome paths.

wiki richard 3

Since Richard had no descendants, to see how descendants work, click on his mother, Cecily of York’s DNA descendants and you’re shown up to 10 generations.

wiki richard 4

While this isn’t terribly useful for Cecily of York who lived and died in the 1400s, it would be incredibly useful for finding mitochondrial descendants of my ancestor born in 1802 in Virginia.  I’d love to prove she is the daughter of a specific set of parents by comparing her DNA with that of a proven daughter of those parents!  Maybe I’ll see if I can find her parents at WikiTree.

Kitty Cooper’s blog talks about additional tools.  I have used Kitty’s Chromosome mapping tools as discussed in ancestor reconstruction.

Felix Chandrakumar has created a number of fun tools as well.  Take a look.  I have not used most of these tools, but there are several I’ll be playing with shortly.

Exits and Entrances

With very little fanfare, deCODEme discontinued their consumer testing and reminded people to download their date before year end.

https://dna-explained.com/2014/09/30/decodeme-consumer-tests-discontinued/

I find this unfortunate because at one time, deCODEme seemed like a company full of promise for genetic genealogy.  They failed to take the rope and run.

On a sad note, Lucas Martin who founded DNA Tribes unexpectedly passed away in the fall.  DNA Tribes has been a long-time player in the ethnicity field of genetic genealogy.  I have often wondered if Lucas Martin was a pseudonym, as very little information about Lucas was available, even from Lucas himself.  Neither did I find an obituary.  Regardless, it’s sad to see someone with whom the community has worked for years pass away.  The website says that they expect to resume offering services in January 2015. I would be cautious about ordering until the structure of the new company is understood.

http://www.dnatribes.com/

In the last month, a new offering has become available that may be trying to piggyback on the name and feel of DNA Tribes, but I’m very hesitant to provide a link until it can be determined if this is legitimate or bogus.  If it’s legitimate, I’ll be writing about it in the future.

However, the big news exit was Ancestry’s exit from the Y and mtDNA testing arena.  We suspected this would happen when they stopped selling kits, but we NEVER expected that they would destroy the existing data bases, especially since they maintain the Sorenson data base as part of their agreement when they obtained the Sorenson data.

https://dna-explained.com/2014/10/02/ancestry-destroys-irreplaceable-dna-database/

The community is still hopeful that Ancestry may reverse that decision.

Ancestry – The Chromosome Browser War and DNA Circles

There has been an ongoing battle between Ancestry and the more seasoned or “hard-core” genetic genealogists for some time – actually for a long time.

The current and most long-standing issue is the lack of a chromosome browser, or any similar tools, that will allow genealogists to actually compare and confirm that their DNA match is genuine.  Ancestry maintains that we don’t need it, wouldn’t know how to use it, and that they have privacy concerns.

Other than their sessions and presentations, they had remained very quiet about this and not addressed it to the community as a whole, simply saying that they were building something better, a better mousetrap.

In the fall, Ancestry invited a small group of bloggers and educators to visit with them in an all-day meeting, which came to be called DNA Day.

https://dna-explained.com/2014/10/08/dna-day-with-ancestry/

In retrospect, I think that Ancestry perceived that they were going to have a huge public relations issue on their hands when they introduced their new feature called DNA Circles and in the process, people would lose approximately 80% of their current matches.  I think they were hopeful that if they could educate, or convince us, of the utility of their new phasing techniques and resulting DNA Circles feature that it would ease the pain of people’s loss in matches.

I am grateful that they reached out to the community.  Some very useful dialogue did occur between all participants.  However, to date, nothing more has happened nor have we received any additional updates after the release of Circles.

Time will tell.

https://dna-explained.com/2014/11/18/in-anticipation-of-ancestrys-better-mousetrap/

https://dna-explained.com/2014/11/19/ancestrys-better-mousetrap-dna-circles/

DNA Circles 12-29-2014

DNA Circles, while interesting and somewhat useful, is certainly NOT a replacement for a chromosome browser, nor is it a better mousetrap.

https://dna-explained.com/2014/11/30/chromosome-browser-war/

In fact, the first thing you have to do when you find a DNA Circle that you have not verified utilizing raw data and/or chromosome browser tools from either 23andMe, Family Tree DNA or Gedmatch, is to talk your matches into transferring their DNA to Family Tree DNA or download to Gedmatch, or both.

https://dna-explained.com/2014/11/27/sarah-hickerson-c1752-lost-ancestor-found-52-ancestors-48/

I might add that the great irony of finding the Hickerson DNA Circle that led me to confirm that ancestry utilizing both Family Tree DNA and GedMatch is that today, when I checked at Ancestry, the Hickerson DNA Circle is no longer listed.  So, I guess I’ve been somehow pruned from the circle.  I wonder if that is the same as being voted off of the island.  So, word to the wise…check your circles often…they change and not always in the upwards direction.

The Seamy Side – Lies, Snake Oil Salesmen and Bullys

Unfortunately a seamy side, an underbelly that’s rather ugly has developed in and around the genetic genealogy industry.  I guess this was to be expected with the rapid acceptance and increasing popularity of DNA testing, but it’s still very unfortunate.

Some of this I expected, but I didn’t expect it to be so…well…blatant.

I don’t watch late night TV, but I’m sure there are now DNA diets and DNA dating and just about anything else that could be sold with the allure of DNA attached to the title.

I googled to see if this was true, and it is, although I’m not about to click on any of those links.

google dna dating

google dna diet

Unfortunately, within the ever-growing genetic genealogy community a rather large rift has developed over the past couple of years.  Obviously everyone can’t get along, but this goes beyond that.  When someone disagrees, a group actively “stalks” the person, trying to cost them their employment, saying hate filled and untrue things and even going so far as to create a Facebook page titled “Against<personname>.”  That page has now been removed, but the fact that a group in the community found it acceptable to create something like that, and their friends joined, is remarkable, to say the least.  That was accompanied by death threats.

Bullying behavior like this does not make others feel particularly safe in expressing their opinions either and is not conducive to free and open discussion. As one of the law enforcement officers said, relative to the events, “This is not about genealogy.  I don’t know what it is about, yet, probably money, but it’s not about genealogy.”

Another phenomenon is that DNA is now a hot topic and is obviously “selling.”  Just this week, this report was published, and it is, as best we can tell, entirely untrue.

http://worldnewsdailyreport.com/usa-archaeologists-discover-remains-of-first-british-settlers-in-north-america/

There were several tip offs, like the city (Lanford) and county (Laurens County) is not in the state where it is attributed (it’s in SC not NC), and the name of the institution is incorrect (Johns Hopkins, not John Hopkins).  Additionally, if you google the name of the magazine, you’ll see that they specialize in tabloid “faux reporting.”  It also reads a lot like the King Richard genuine press release.

http://urbanlegends.about.com/od/Fake-News/tp/A-Guide-to-Fake-News-Websites.01.htm

Earlier this year, there was a bogus institutional site created as well.

On one of the DNA forums that I frequent, people often post links to articles they find that are relevant to DNA.  There was an interesting article, which has now been removed, correlating DNA results with latitude and altitude.  I thought to myself, I’ve never heard of that…how interesting.   Here’s part of what the article said:

Researchers at Aberdeen College’s Havering Centre for Genetic Research have discovered an important connection between our DNA and where our ancestors used to live.

Tiny sequence variations in the human genome sometimes called Single Nucleotide Polymorphisms (SNPs) occur with varying frequency in our DNA.  These have been studied for decades to understand the major migrations of large human populations.  Now Aberdeen College’s Dr. Miko Laerton and a team of scientists have developed pioneering research that shows that these differences in our DNA also reveal a detailed map of where our own ancestors lived going back thousands of years.

Dr. Laerton explains:  “Certain DNA sequence variations have always been important signposts in our understanding of human evolution because their ages can be estimated.  We’ve known for years that they occur most frequently in certain regions [of DNA], and that some alleles are more common to certain geographic or ethnic groups, but we have never fully understood the underlying reasons.  What our team found is that the variations in an individual’s DNA correlate with the latitudes and altitudes where their ancestors were living at the time that those genetic variations occurred.  We’re still working towards a complete understanding, but the knowledge that sequence variations are connected to latitude and altitude is a huge breakthrough by itself because those are enough to pinpoint where our ancestors lived at critical moments in history.”

The story goes on, but at the bottom, the traditional link to the publication journal is found.

The full study by Dr. Laerton and her team was published in the September issue of the Journal of Genetic Science.

I thought to myself, that’s odd, I’ve never heard of any of these people or this journal, and then I clicked to find this.

Aberdeen College bogus site

About that time, Debbie Kennett, DNA watchdog of the UK, posted this:

April Fools Day appears to have arrived early! There is no such institution as Aberdeen College founded in 1394. The University of Aberdeen in Scotland was founded in 1495 and is divided into three colleges: http://www.abdn.ac.uk/about/colleges-schools-institutes/colleges-53.php

The picture on the masthead of the “Aberdeen College” website looks very much like a photo of Aberdeen University. This fake news item seems to be the only live page on the Aberdeen College website. If you click on any other links, including the link to the so-called “Journal of Genetic Science”, you get a message that the website is experienced “unusually high traffic”. There appears to be no such journal anyway.

We also realized that Dr. Laerton, reversed, is “not real.”

I still have no idea why someone would invest the time and effort into the fake website emulating the University of Aberdeen, but I’m absolutely positive that their motives were not beneficial to any of us.

What is the take-away of all of this?  Be aware, very aware, skeptical and vigilant.  Stick with the mainstream vendors unless you realize you’re experimenting.

King Richard

King Richard III

The much anticipated and long-awaited DNA results on the remains of King Richard III became available with a very unexpected twist.  While the science team feels that they have positively identified the remains as those of Richard, the Y DNA of Richard and another group of men supposed to have been descended from a common ancestor with Richard carry DNA that does not match.

https://dna-explained.com/2014/12/09/henry-iii-king-of-england-fox-in-the-henhouse-52-ancestors-49/

https://dna-explained.com/2014/12/05/mitochondrial-dna-mutation-rates-and-common-ancestors/

Debbie Kennett wrote a great summary article.

http://cruwys.blogspot.com/2014/12/richard-iii-and-use-of-dna-as-evidence.html

More Alike than Different

One of the life lessons that genetic genealogy has held for me is that we are more closely related that we ever knew, to more people than we ever expected, and we are far more alike than different.  A recent paper recently published by 23andMe scientists documents that people’s ethnicity reflect the historic events that took place in the part of the country where their ancestors lived, such as slavery, the Trail of Tears and immigration from various worldwide locations.

23andMe European African map

From the 23andMe blog:

The study leverages samples of unprecedented size and precise estimates of ancestry to reveal the rate of ancestry mixing among American populations, and where it has occurred geographically:

  • All three groups – African Americans, European Americans and Latinos – have ancestry from Africa, Europe and the Americas.
  • Approximately 3.5 percent of European Americans have 1 percent or more African ancestry. Many of these European Americans who describe themselves as “white” may be unaware of their African ancestry since the African ancestor may be 5-10 generations in the past.
  • European Americans with African ancestry are found at much higher frequencies in southern states than in other parts of the US.

The ancestry proportions point to the different regional impacts of slavery, immigration, migration and colonization within the United States:

  • The highest levels of African ancestry among self-reported African Americans are found in southern states, especially South Carolina and Georgia.
  • One in every 20 African Americans carries Native American ancestry.
  • More than 14 percent of African Americans from Oklahoma carry at least 2 percent Native American ancestry, likely reflecting the Trail of Tears migration following the Indian Removal Act of 1830.
  • Among self-reported Latinos in the US, those from states in the southwest, especially from states bordering Mexico, have the highest levels of Native American ancestry.

http://news.sciencemag.org/biology/2014/12/genetic-study-reveals-surprising-ancestry-many-americans?utm_campaign=email-news-weekly&utm_source=eloqua

23andMe provides a very nice summary of the graphics in the article at this link:

http://blog.23andme.com/wp-content/uploads/2014/10/Bryc_ASHG2014_textboxes.pdf

The academic article can be found here:

http://www.cell.com/ajhg/home

2015

So what does 2015 hold? I don’t know, but I can’t wait to find out. Hopefully, it holds more ancestors, whether discovered through plain old paper research, cousin DNA testing or virtually raised from the dead!

What would my wish list look like?

  • More ancient genomes sequenced, including ones from North and South America.
  • Ancestor reconstruction on a large scale.
  • The haplotree becoming fleshed out and stable.
  • Big Y sequencing combined with STR panels for enhanced genealogical research.
  • Improved ethnicity reporting.
  • Mitochondrial DNA search by ancestor for descendants who have tested.
  • More tools, always more tools….
  • More time to use the tools!

Here’s wishing you an ancestor filled 2015!

 

Kostenki14 – A New Ancient Siberian DNA Sample

k14 skeleton

This week, published in Science, we find another ancient DNA full genome sequence from Siberia in an article titled “Genomic structure in Europeans dating back at least 36,200 years” by Seguin-Orlando et al.. This sample, partially shown above, is quite old and closely related to the Mal’ta child, also found in Siberia from about 24,000 years ago. Interestingly enough, K14 carries more Neanderthal DNA than current Europeans. This skeleton was actually excavated in 1954, but was only recently genetically analyzed.

k14 mapFrom the paper, this map above shows the locations of recently analyzed ancient DNA samples.  Note that even though K14 and Mal’ta child are similar, they are not located in close geographic proximity.

k14 population clusterAlso from the paper, this chart of population clusters is quite interesting, because we can see which of these ancient samples share some heritage with today’s indigenous American populations, shown in grey. UPGH=Upper Paleolithic Hunter-Gatherer, MHG=Mesolithic Hunter Gatherer, which is later in time that Paleolithic, and NEOL=Neolithic indicating the farming population that arrived in Europe approximately 7,000-10,000 years ago from the Middle East

You can see that the Neolithic samples show no trace of ancestry with today’s Native people, but both pre-Neolithic Hunter-Gatherer cultures show some amount of shared ancestry with Native people. However, to date, MA1, the Malta child is the most closely related and carries the most DNA in common with today’s Native people.

Felix Chandrakumar is currently preparing the K14 genome for addition to the ancient DNA kits at GedMatch.  It will be interesting to see if this sample also matches currently living individuals.

Also from the K14 paper, you can see on the map below where K14 matches current worldwide and European populations, where the warmer colors, i.e. red, indicated a closer match.

K14 population matches

Of interest to genealogists and population geneticists, K14’s mitochondrial haplogroup is U2 and his Y haplogroup is C-M130, the same as LaBrana, a late Mesolithic hunter-gatherer found in northern Spain. Haplogroup C is, of course, one of the base haplogroups for the Native people of the Americas.

The K14 paper further fleshes out the new peopling of Europe diagram discussed in my Peopling of Europe article.

This map, from the Lazardis “Ancient human genomes suggest three ancestral populations for present-day Europeans” paper published in September 2014, shows the newly defined map including Ancient North Eurasian in this diagram.

Lazaridis tree

K14 adds to this diagram in the following manner, although the paths are flipped right to left.

K14 tree

Blue represent current populations, red are ancient remains and green are ancestral populations.

Dienekes wrote about this find as well, here.

Paper Abstract:

The origin of contemporary Europeans remains contentious. We obtain a genome sequence from Kostenki 14 in European Russia dating to 38,700 to 36,200 years ago, one of the oldest fossils of Anatomically Modern Humans from Europe. We find that K14 shares a close ancestry with the 24,000-year-old Mal’ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a meta-population that at times stretched from Europe to central Asia.

You can read the full paper at the two links below.

http://www.sciencemag.org/content/early/2014/11/05/science.aaa0114

http://www2.zoo.cam.ac.uk/manica/ms/2014_Seguin_Orlando_et_al_Science.pdf

It’s been a great year for ancient DNA analysis and learning about our ancestral human populations.

However, I have one observation I just have to make about this particular find.

What amazing teeth. Obviously, this culture did not consume sugar!

Peopling of Europe 2014 – Identifying the Ghost Population

Beginning with the full sequencing of the Neanderthal genome, first published in May 2010 by the Max Planck Institute with Svante Paabo at the helm, and followed shortly thereafter with a Denisovan specimen, we began to unravel our ancient history.

neanderthal reconstructed

Neanderthal man, reconstructed at the National Museum of Nature and Science in Tokyo

The photo below shows a step in the process of extracting DNA from ancient bones at Max Planck.

planck extraction

Our Y and mitochondrial DNA haplogroups take us back thousands of years in time, but at some point, where and how people were settling and intermixing becomes fuzzy. Ancient DNA can put the people of that time and place in context.  We have discovered that current populations do not necessarily represent the ancient populations of a particular locale.

Recent information discovered from ancient burials tells us that the people of Europe descend from a 3 pronged model. Until recently, it was believed that Europeans descended from Paleolithic hunter-gatherers and Neolithic farmers, a two-pronged model.

Previously, it was believed that Europe was peopled by the ancient hunter-gatherers, the Paleolithic, who originally settled in Europe beginning about 45,000 years ago. At this time, the Neanderthal were already settled in Europe but weren’t considered to be anatomically modern humans, and it was believed, incorrectly, that the two groups did not interbreed.  These hunter-gatherers were the people who settled in Europe before the last major ice age, the Younger Dryas, taking refuge in the southern portions of Europe and Eurasia, and repeopling the continent after the ice receded, about 12,000 years ago.  By that time, the Neanderthals were gone, or as we now know, at least partially assimilated.

This graphic shows Europe during the last ice age.

ice age euripe

The second settlement wave, the agriculturalist farmers from the Near East either overran or integrated with the hunter-gatherers in the Neolithic period, depending on which theory you subscribe to, about 8000-10,000 years ago.

2012 – Ancient Northern European (ANE) Hints

Beginning in 2012, we began to see hints of a third lineage that contributed to the peopling of Europe as well, from the north. Buried in the 2012 paper, Estimating admixture proportions and dates with ADMIXTOOLS by Patterson et al, was a very interesting tidbit.  This new technique showed a third population, referred to by many as a “ghost population”, because no one knew who they were, that contributed to the European population.

patterson ane

The new population was termed Ancient North Eurasian, or ANE.

Dienekes covered this paper in his blog, but without additional information, in the community in general, there wasn’t much more than a yawn.

2013 – Mal’ta Child Stirs Excitement

The first real hint of meat on the bones of ANE came in the form of ancient DNA analysis of a 24,000 year old Siberian boy that has come to be named Mal’ta (Malta) Child. In the original paper, by Raghaven et al, Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, he was referred to as MA-1.  I wrote about this in my article titled Native American Gene Flow – Europe?, Asia and the Americas.   Dienekes wrote about this paper as well.

This revelation caused quite a stir, because it was reported that the Ancestor of Native Americans in Asia was 30% Western Eurasian.  Unfortunately, in some cases, this was immediately interpreted to mean that Native Americans had come directly from Europe which is not what this paper said, nor inferred.  It was also inferred that the haplogroups of this child, R* (Y) and U (mtDNA) were Native American, which is also incorrect.  To date, there is no evidence for migration to the New World from Europe in ancient times, but that doesn’t mean we aren’t still looking for that evidence in early burials.

What this paper did show was that Europeans and Native Americans shared a common ancestor, and that the Siberian population had contributed to the European population as well as the Native American population.  In other words, descendants settled in both directions, east and west.

The most fascinating aspect of this paper was the match distribution map, below, showing which populations Malta child matched most closely.

malta child map

As you can see, MA-1, Malta Child, matches the Native American population most closely, followed by the northern European and Greenland populations. The further south in Europe and Asia, the more distant the matches and the darker the blue.

2013 – Michael Hammer and Haplogroup R

Last fall at the Family Tree DNA conference, Dr. Michael Hammer, from the Hammer Lab at the University of Arizona discussed new findings relative to ancient burials, specifically in relation to haplogroup R, or more specifically, the absence of haplogroup R in those early burials.

hammer 2013

hammer 2013-1

hammer 2013-2

hammer 2013-3

Based on the various theories and questions, ancient burials were enlightening.

hammer 2013-4

hammer 2013-5

In 2013, there were a total of 32 burials from the Neolithic period, after farmers arrived from the Near East, and haplogroup R did not appear. Instead, haplogroups G, I and E were found.

hammer 2013-7

What this tells us is that haplogroup R, as well as other haplogroup, weren’t present in Europe at this time. Having said this, these burials were in only 4 locations and, although unlikely, R could be found in other locations.

hammer 2-13-8

hammer 2013-9

hammer 2013-10

hammer 2013-11

Last year, Dr. Hammer concluded that haplogroup R was not found in the Paleolithic and likely arrived with the Neolithic farmers. That shook the community, as it had been widely believed that haplogroup R was one of the founding European haplogroups.

hammer 2013-12

While this provided tantalizing information, we still needed additional evidence. No paper has yet been published that addresses these findings.  The mass full sequencing of the Y chromosome over this past year with the introduction of the Big Y will provide extremely valuable information about the Y chromosome and eventually, the migration path into and across Europe.

2014 – Europe’s Three Ancient Tribes

In September 2014, another paper was published by Lazaridis et al that more fully defined this new ANE branch of the European human family tree.  An article in BBC News titled Europeans drawn from three ancient ‘tribes’ describes it well for the non-scientist.  Of particular interest in this article is the artistic rendering of the ancient individual, based on their genetic markers.  You’ll note that they had dark skin, dark hair and blue eyes, a rather unexpected finding.

In discussing the paper, David Reich from Harvard, one of the co-authors, said, “Prior to this paper, the models we had for European ancestry were two-way mixtures. We show that there are three groups. This also explains the recently discovered genetic connection between Europeans and Native Americans.  The same Ancient North Eurasian group contributed to both of them.”

The paper, Ancient human genomes suggest three ancestral populations for present-day Europeans, appeared as a letter in Nature and is behind a paywall, but the supplemental information is free.

The article summary states the following:

We sequenced the genomes of a ~7,000-year-old farmer from Germany and eight ~8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes1, 2, 3, 4 with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians3, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations’ deep relationships and show that early European farmers had ~44% ancestry from a ‘basal Eurasian’ population that split before the diversification of other non-African lineages.

This paper utilized ancient DNA from several sites and composed the following genetic contribution diagram that models the relationship of European to non-European populations.

Lazaridis tree

Present day samples are colored purple, ancient in red and reconstructed ancestral populations in green. Solid lines represent descent without admixture and dashed lines represent admixture.  WHG=western European hunter-gatherer, EEF=early European farmer and ANE=ancient north Eurasian

2014 – Michael Hammer on Europe’s Ancestral Population

For anyone interested in ancient DNA, 2014 has been a banner years. At the Family Tree DNA conference in Houston, Texas, Dr. Michael Hammer brought the audience up to date on Europe’s ancestral population, including the newly sequenced ancient burials and the information they are providing.

hammer 2014

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Dr. Hammer said that ancient DNA is the key to understanding the historical processes that led up to the modern. He stressed that we need to be careful inferring that the current DNA pattern is reflective of the past because so many layers of culture have occurred between then and now.

hammer 2014-2

Until recently, it was assumed that the genes of the Neolithic farmers replaced those of the Paleolithic hunter-gatherers. Ancient DNA is suggesting that this is not true, at least not on a wholesale level.

hammer 2014-3

The theory, of course, is that we should be able to see them today if they still exist. The migration and settlement pattern in the slide below was from the theory set forth in the 1990s.

hammer 2014-4

In 2013, Dr. Hammer discussed the theory that haplogroup R1b spread into Europe with the farmers from the Near East in the Neolithic. This year, he expanded upon that topic that based on the new findings from ancient burials.

hammer 2014-5

Last year, Dr. Hammer discussed 32 burials from 4 sites. Today, we have information from 15 ancient DNA sites and many of those remains have been full genome sequenced.

hammer 2014-6

Information from papers and recent research suggests that Europeans also have genes from a third source lineage, nicknamed the “ghost population of North Eurasia.”

hammer 2014-7

Scientists are finding a signal of northeast Asian related admixture in northern Europeans, first suggested in 2012.  This was confirmed with the sequencing of Malta child and then in a second sequencing of Afontova Gora2 in south central Siberia.

hammer 2014-8

We have complete genomes from nine ancient Europeans – Mesolithic hunter gatherers and Neothilic farmers. Hammer refers to the Mesolithic here, which is a time period between the Paleolithic (hunter gatherers with stone tools) and the Neolithic (farmers).

hammer 2014-9

In the PCA charts, shown above, you can see that Europeans and people from the Near East cluster separately, except for a bridge formed by a few Mediterranean and Jewish populations. On the slide below, the hunter-gatherers (WHG) and early farmers (EEF) have been overlayed onto the contemporary populations along with the MA-1 (Malta Child) and AG2 (Afontova Gora2) representing the ANE.

hammer 2014-10

When sequenced, separate groups formed including western hunter gathers and early european farmers include Otzi, the iceman.  A third group is the north south clinal variation with ANE contributing to northern European ancestry.  The groups are represented by the circles, above.

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Dr. Hammer said that the team who wrote the “Ancient Human Genomes” paper just recently published used an F3 test, results shown above, which shows whether populations are an admixture of a reference population based on their entire genome. He mentioned that this technique goes well beyond PCA.

hammer 2014-13

Mapped onto populations today, most European populations are a combination of the three early groups. However, the ANE is not found in the ancient Paleolithic or Neolithic burials.  It doesn’t arrive until later.

hammer 2014-14

This tells us that there was a migration event 45,000 years ago from the Levant, followed about 7000 years ago by farmers from the Near East, and that ANE entered the population some time after that. All Europeans today carry some amount of ANE, but ancient burials do not.

These burials also show that southern Europe has more Neolithic farmer genes and northern Europe has more Paleolithic/Mesolithic hunter-gatherer genes.

hammer 2014-15

Pigmentation for light skin came with farmers – blue eyes existed in hunter gatherers even though their skin was dark.

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Dr. Hammer created these pie charts of the Y and mitochondrial haplogroups found in the ancient burials as compared to contemporary European haplogroups.

hammer 2014-17

The pie chart on the left shows the haplogroups of the Mesolithic burials, all haplogroup I2 and subclades. Note that in the current German population today, no I2a1b and no I1 was found.  The chart on the right shows current Germans where haplogroup I is a minority.

hammer 2014-18

Therefore, we can conclude that haplogroup I is a good candidate to be identified as a Paleolithic/Mesolithic haplogroup.

This information shows that the past is very different from today.

hammer 2014-19

In 2014 we have many more burials that have been sequenced than last year, as shown on the map above.

Green represents Neolithic farmers, red are Mesolithic hunter-gatherers, brown at bottom right represents more recent samples from the Metallic age.

hammer 2014-20

There are a total of 48 Neolithic burials where haplogroup G dominates. In the Mesolithic, there are a total of six haplogroup I.

This suggests that haplogroup I is a good candidate to be the father of the Paleolithic/Mesolithic and haplogroup G, the founding father of the Neolithic.

In addition to haplogroup G in the Neolithic, one sample of both E1b1b1 (M35) and C were also found in Spain.  E1b1b1 isn’t surprising given it’s north African genesis, but C was quite interesting.

The Metal ages, which according to wiki begin about 3300BC in Europe, is where haplogroup R, along with I1, first appear.

diffusion of metallurgy

Please note that the diffusion of melallurgy map above is not part of Dr. Hammer’s presentation. I have added it for clarification.

hammer 2014-21

Nothing is constant in Europe. The Y DNA was very upheaved, as indicated on the graphic above.  Mitochondrial DNA shifted from pre-Neolithic to Neolithic which isn’t terribly different from the present day.

Dr. Hammer did not say this, but looking at the Y versus the mtDNA haplogroups, I wonder if this suggests that indeed there was more of a replacement of the males in the population, but that the females were more widely assimilated. This would certainly make sense, especially if the invaders were warriors and didn’t have females with them.  They would have taken partners from the invaded population.

Haplogroup G represents the spread of farming into Europe.

hammer 2014-22

The most surprising revelation is that haplogroup R1b appears to have emerged after the Neolithic agriculture transition. Given that just three years ago we thought that haplogroup R1b was one of the original European settlers thousands of years ago, based on the prevalence of haplogroup R in Europe today, at about 50%, this is a surprising turn of events.  Last year’s revelation that R was maybe only 7000-8000 years old in Europe was a bit of a whammy, but the age of R in Europe in essence just got halved again and the source of R1b changed from the Near East to the Asian steppes.

Obviously, something conferred an advantage to these R1b men. Given that they arrived in the early Metalic age, was it weapons and chariots that enabled the R1b men who arrived to quickly become more than half of the population?

hammer 2014-23

The Bronze Age saw the first use of metal to create weapons. Warrior identity became a standard part of daily life.  Celts ranged over Europe and were the most dominant iron age warriors.  Indo-European languages and chariots arrived from Asia about this time.

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The map above shows the Hallstadt and LaTene Celtic cultures in Europe, about 600BC. This was not a slide presented by Dr. Hammer.

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Haplogroup R1b was not found in an ancient European context prior to a Bell Beaker period burial in Germany 4.8-4.0 kya (thousand years ago, i.e. 4,800-4,000 years ago).  R1b arrives about 4.6 kya and is also found in a Corded Ware culture burial in Germany.  A late introduction of these lineages which now predominate in Europe corresponds to the autosomal signal of the entry of Asian and Eastern European steppe invaders into western Europe.

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Local expansion occurred in Europe of R1b subgroups U106, L21 and U152.

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A current haplogroup R distribution map that reflects the findings of this past year is shown above.

Haplogroup I is interesting for another reason. It looks like haplogroup I2a1b (M423) may have been replaced by I1 which expanded after the Mesolithic.

hammer 2014-31

On the slide above, the Loschbour sample from Luxembourg was mapped onto a current haplogroup I SNP map where his closest match is a current day Russian.

One of the benefits of ancient DNA genome processing is that we will be able to map current trees into maps of old SNPs and be able to tell who we match most closely.

Autosomal DNA can also be mapped to see how much of our DNA is from which ancient population.

hammer 2014-32

Dr. Hammer mapped the percentages of European Mesolithic/Paleolithic hunter-gatherers in blue, Neolithic Farmers from the Near East in magenta and Asian Steppe Invaders representing ANE in yellow, over current populations. Note the ancient DNA samples at the top of the list.  None of the burials except for Malta Child carry any yellow, indicating that the ANE entered the European population with the steppe invaders; the same group that brought us haplogroup R and possibly I1.

Dr. Hammer says that ANE was introduced to and assimilated into the European population by one or more incursions. We don’t know today if ANE in Europeans is a result of a single blast event or multiple events.  He would like to do some model simulations and see if it is related to timing and arrival of swords and chariots.

We know too that there are more recent incursions, because we’re still missing major haplogroups like J.

The further east you go, meaning the closer to the steppes and Volga region, the less well this fits the known models. In other words, we still don’t have the whole story.

At the end of the presentation, Michael was asked if the whole genomes sequenced are also obtaining Y STR data, which would allow us to compare our results on an individual versus a haplogroup level. He said he didn’t know, but he would check.

Family Tree DNA was asked if they could show a personal ancient DNA map in myOrigins, perhaps as an alternate view. Bennett took a vote and that seemed pretty popular, which he interpreted as a yes, we’d like to see that.

In Summary

The advent of and subsequent drop in the price of whole genome sequencing combined with the ability to extract ancient DNA and piece it back together have provided us with wonderful opportunities.  I think this is jut the proverbial tip of the iceberg, and I can’t wait to learn more.

If you are interested in other articles I’ve written about ancient DNA, check out these links:

Ancient DNA Matches – What Do They Mean?

The good news is that my three articles about the Anzick and other ancient DNA of the past few days have generated a lot of interest.

The bad news is that it has generated hundreds of e-mails every day – and I can’t possibly answer them all personally.  So, if you’ve written me and I don’t reply, I apologize and  I hope you’ll understand.  Many of the questions I’ve received are similar in nature and I’m going to answer them in this article.  In essence, people who have matches want to know what they mean.

Q – I had a match at GedMatch to <fill in the blank ancient DNA sample name> and I want to know if this is valid.

A – Generally, when someone asks if an autosomal match is “valid,” what they really mean is whether or not this is a genealogically relevant match or if it’s what is typically referred to as IBS, or identical by state.  Genealogically relevant samples are referred to as IBD, or identical by descent.  I wrote about that in this article with a full explanation and examples, but let me do a brief recap here.

In genealogy terms, IBD is typically used to mean matches over a particular threshold that can be or are GENEALOGICALLY RELEVANT.  Those last two words are the clue here.  In other words, we can match them with an ancestor with some genealogy work and triangulation.  If the segment is large, and by that I mean significantly over the threshold of 700 SNPs and 7cM, even if we can’t identify the common ancestor with another person, the segment is presumed to be IBD simply because of the math involved with the breakdown of segment into pieces.  In other words, a large segment match generally means a relatively recent ancestor and a smaller segment means a more distant ancestor.  You can readily see this breakdown on this ISOGG page detailing autosomal DNA transmission and breakdown.

Unfortunately, often smaller segments, or ones determined to be IBS are considered to be useless, but they aren’t, as I’ve demonstrated several times when utilizing them for matching to distant ancestors.  That aside, there are two kinds of IBS segments.

One kind of IBS segment is where you do indeed share a common ancestor, but the segment is small and you can’t necessarily connect it to the ancestor.  These are known as population matches and are interpreted to mean your common ancestor comes from a common population with the other person, back in time, but you can’t find the common ancestor.  By population, we could mean something like Amish, Jewish or Native American, or a country like Germany or the Netherlands.

In the cases where I’ve utilized segments significantly under 7cM to triangulate ancestors, those segments would have been considered IBS until I mapped them to an ancestor, and then they suddenly fell into the IBD category.

As you can see, the definitions are a bit fluid and are really defined by the genealogy involved.

The second kind of IBS is where you really DON’T share an ancestor, but your DNA and your matches DNA has managed to mutate to a common state by convergence, or, where your Mom’s and Dad’s DNA combined form a pseudo match, where you match someone on a segment run long enough to be considered a match at a low level.  I discussed how this works, with examples, in this article.  Look at example four, “a false match.”

So, in a nutshell, if you know who your common ancestor is on a segment match with someone, you are IBD, identical by descent.  If you don’t know who your common ancestor is, and the segment is below the normal threshold, then you are generally considered to be IBS – although that may or may not always be true.  There is no way to know if you are truly IBS by population or IBS by convergence, with the possible exception of phased data.

Data phasing is when you can compare your autosomal DNA with one or both parents to determine which half you obtained from whom.  If you are a match by convergence where your DNA run matches that of someone else because the combination of your parents DNA happens to match their segment, phasing will show that clearly.  Here’s an example for only one location utilizing only my mother’s data phased with mine.  My father is deceased and we have to infer his results based on my mother’s and my own.  In other words, mine minus the part I inherited from my mother = my father’s DNA.

My Result My Result Mother’s Result Mother’s Result Father’s Inferred Result Father’s Inferred Result
T A T G A

In this example of just one location, you can see that I carry a T and an A in that location.  My mother carries a T and a G, so I obviously inherited the T from her because I don’t have a G.  Therefore, my father had to have carried at least an A, but we can’t discern his second value.

This example utilized only one location.  Your autosomal data file will hold between 500,000 and 700,000 location, depending on the vendor you tested with and the version level.

You can phase your DNA with that of your parent(s) at GedMatch.  However, if both of your parents are living, an easier test would be to see if either of your parents match the individual in question.  If neither of your parents match them, then your match is a result of convergence or a data read error.

So, this long conversation about IBD and IBS is to reach this conclusion.

All of the ancient specimens are just that, ancient, so by definition, you cannot find a genealogy match to them, so they are not IBD.  Best case, they are IBS by population.  Worse case, IBS by convergence.  You may or may not be able to tell the difference.  The reason, in my example earlier this week, that I utilized my mother’s DNA and only looked at locations where we both matched the ancient specimens was because I knew those matches were not by convergence – they were in fact IBS by population because my mother and I both matched Anzick.

ancient compare5

Q – What does this ancient match mean to me?

A – Doggone if I know.  No, I’m serious.  Let’s look at a couple possibilities, but they all have to do with the research you have, or have not, done.

If you’ve done what I’ve done, and you’ve mapped your DNA segments to specific ancestors, then you can compare your ancient matching segments to your ancestral spreadsheet map, especially if you can tell unquestionably which side the ancestral DNA matches.  In my case, shown above, the Clovis Anzik matched my mother and me on the same segment and we both matched Cousin Herbie.  We know unquestionably who our common ancestor is with cousin Herbie – so we know, in our family line, which line this segment of DNA shared with Anzick descends through.

ancient compare6

If you’re not doing ancestor mapping, then I guess the Anzick match would come in the category of, “well, isn’t that interesting.”  For some, this is a spiritual connection to the past, a genetic epiphany.  For other, it’s “so what.”

Maybe this is a good reason to start ancestor mapping!  This article tells you how to get started.

Q – Does my match to Anzick mean he is my ancestor?

A – No, it means that you and Anzick share common ancestry someplace back in time, perhaps tens of thousands of years ago.

Q – I match the Anzick sample.  Does this prove that I have Native American heritage? 

A – No, and it depends.  Don’t you just hate answers like this?

No, this match alone does not prove Native American heritage, especially not at IBS levels.  In fact, many people who don’t have Native heritage match small segments?  How can this be?  Well, refer to the IBS by convergence discussion above.  In addition, Anzick child came from an Asian population when his ancestors migrated, crossing from Asia via Beringia.  That Eurasian population also settled part of Europe – so you could be matching on very small segments from a common population in Eurasia long ago.  In a paper just last year, this was discussed when Siberian ancient DNA was shown to be related to both Native Americans and Europeans.

In some cases, a match to Anzick on a segment already attributed to a Native line can confirm or help to confirm that attribution.  In my case, I found the Anzick match on segments in the Lore family who descend from the Acadians who were admixed with the Micmac.  I have several Anzick match segments that fit that criteria.

A match to Anzick alone doesn’t prove anything, except that you match Anzick, which in and of itself is pretty cool.

Q – I’m European with no ancestors from America, and I match Anzick too.  How can that be?

A – That’s really quite amazing isn’t it.  Just this week in Nature, a new article was published discussing the three “tribes” that settled or founded the European populations.  This, combined with the Siberian ancient DNA results that connect the dots between an ancient population that contributed to both Europeans and Native Americans explains a lot.

3 European Tribes

If you think about it, this isn’t a lot different than the discovery that all Europeans carry some small amount of Neanderthal and Denisovan DNA.

Well, guess what….so does Anzick.

Here are his matches to the Altai Neanderthal.

Chr Start Location End Location Centimorgans (cM) SNPs
2 241484216 242399416 1.1 138
3 19333171 21041833 2.6 132
6 31655771 32889754 1.1 133

He does not match the Caucasus Neanderthal.  He does, however, match the Denisovan individual on one location.

Chr Start Location End Location Centimorgans (cM) SNPs
3 19333171 20792925 2.1 107

Q – Maybe the scientists are just wrong and the burial is not 12,500 years old,  maybe just 100 years old and that’s why the results are matching contemporary people.

A – I’m not an archaeologist, nor do I play one…but I have been closely involved with numerous archaeological excavations over the past decade with The Lost Colony Research Group, several of which recovered human remains.  The photo below is me with Anne Poole, my co-director, sifting at one of the digs.

anne and me on dig

There are very specific protocols that are followed during and following excavation and an error of this magnitude would be almost impossible to fathom.  It would require  kindergarten level incompetence on the part of not one, but all professionals involved.

In the Montana Anzick case, in the paper itself, the findings and protocols are both discussed.  First, the burial was discovered directly beneath the Clovis layer where more than 100 tools were found, and the Clovis layer was undisturbed, meaning that this is not a contemporary burial that was buried through the Clovis layer.  Second, the DNA fragmentation that occurs as DNA degrades correlated closely to what would be expected in that type of environment at the expected age based on the Clovis layer.  Third, the bones themselves were directly dated using XAD-collagen to 12,707-12,556 calendar years ago.  Lastly, if the remains were younger, the skeletal remains would match most closely with Native Americans of that region, and that isn’t the case.  This graphic from the paper shows that the closest matches are to South Americans, not North Americans.

anzick matches

This match pattern is also confirmed independently by the recent closest GedMatch matches to South Americans.

Q – How can this match from so long ago possibly be real?

A – That’s a great question and one that was terribly perplexing to Dr. Svante Paabo, the man who is responsible for producing the full genome sequence of the first, and now several more, Neanderthals.  The expectation was, understanding autosomal DNA gets watered down by 50% in every generation though recombination, that ancient genomes would be long gone and not present in modern populations.  Imagine Svante’s surprise when he discovered that not only isn’t true, but those ancient DNA segmetns are present in all Europeans and many Asians as well.  He too agonized over the question about how this is possible, which he discussed in this great video.  In fact he repeated these tests over and over in different ways because he was convinced that modern individuals could not carry Neanderthal DNA – but all those repeated tests did was to prove him right.  (Paabo’s book, Neanderthal Man, In Search of Lost Genomes is an incredible read that I would highly recommend.)

What this means is that the population at one time, and probably at several different times, had to be very small.  In fact, it’s very likely that many times different pockets of the human race was in great jeopardy of dying out.  We know about the ones that survived.  Probably many did perish leaving no descendants today.  For example, no Neanderthal mitochondrial DNA has been found in any living or recent human.

In a small population, let’s say 5 males and 5 females who some how got separated from their family group and founded a new group, by necessity.  In fact, this could well be a description of how the Native Americans crossed Beringia.  Those 5 males and 5 females are the founding population of the new group.  If they survive, all of the males will carry the men’s haplogroups – let’s say they are Q and C, and all of the descendants will carry the mitochondrial haplogroups of the females – let’s say A, B, C, D and X.

There is a very limited amount of autosomal DNA to pass around.  If all of those 10 people are entirely unrelated, which is virtually impossible, there will be only 10 possible combinations of DNA to be selected from.  Within a few generations, everyone will carry part of those 10 ancestor’s DNA.  We all have 8 ancestors at the great-grandparent level.  By the time those original settlers’ descendants had great-great-grandparents – of which each one had 16, at least 6 of those original people would be repeated twice in their tree.

There was only so much DNA to be passed around.  In time, some of the segments would no longer be able to be recombined because when you look at phasing, the parents DNA was exactly the same, example below.  This is what happens in endogamous populations.

My Result My Result Mother’s Result Mother’s Result Father’s Result Father’s  Result
T T T T T T

Let’s say this group’s descendants lived without contact with other groups, for maybe 15,000 years in their new country.  That same DNA is still being passed around and around because there was no source for new DNA.  Mutations did occur from time to time, and those were also passed on, of course, but that was the only source of changed DNA – until they had contact with a new population.

When they had contact with a new population and admixture occurred, the normal 50% recombination/washout in every generation began – but for the previous 15,000 years, there had been no 50% shift because the DNA of the population was, in essence, all the same.  A study about the Ashkenazi Jews that suggests they had only a founding population of about 350 people 700 years ago was released this week – explaining why Ashkenazi Jewish descendants have thousands of autosomal matches and match almost everyone else who is Ashkenazi.  I hope that eventually scientists will do this same kind of study with Anzick and Native Americans.

If the “new population” we’ve been discussing was Native Americans, their males 15,000 year later would still carry haplogroups Q and C and the mitochondrial DNA would still be A, B, C, D and X.  Those haplogroups, and subgroups formed from mutations that occurred in their descendants, would come to define their population group.

In some cases, today, Anzick matches people who have virtually no non-Native admixture at the same level as if they were just a few generations removed, shown on the chart below.

anzick gedmatch one to all

Since, in essence, these people still haven’t admixed with a new population group, those same ancient DNA segments are being passed around intact, which tells us how incredibly inbred this original small population must have been.  This is known as a genetic bottleneck.

The admixture report below is for the first individual on the Anzick one to all Gedmatch compare at 700 SNPs and 7cM, above.  In essence, this currently living non-admixed individual still hasn’t met that new population group.

anzick1

If this “new population” group was Neanderthal, perhaps they lived in small groups for tens of thousands of years, until they met people exiting Africa, or Denisovans, and admixed with them.

There weren’t a lot of people anyplace on the globe, so by virtue of necessity, everyone lived in small population groups.  Looking at the odds of survival, it’s amazing that any of us are here today.

But, we are, and we carry the remains, the remnants of those precious ancestors, the Denisovans, the Neanderthals and Anzick.  Through their DNA, and ours, we reach back tens of thousands of years on the human migration path.  Their journey is also our journey.  It’s absolutely amazing and it’s no wonder people have so many questions and such a sense of enchantment.  But it’s true – and only you can determine exactly what this means to you.

Utilizing Ancient DNA at GedMatch

Mummy of 6 month old boy found in Greenland

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

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

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

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

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

1.  Montana Anzick at GedMatch

This is the only clearly Native American sample.

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

F999912

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

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

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

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

2.  Paleo Eskimo from Greenland at GedMatch

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

F999906

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

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

3.  Altai Neanderthal at GedMatch

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

F999902

One match to what is obviously another Neaderthal entry.

4.  Russian Causasus Neanderthal at GedMatch

Another contribution from the Neanderthal Genome Project.

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

F999909

No matches.

5.  Denisova at GedMatch

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

F999903

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

But now, for the fun part.

My Comparison

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

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

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

So, let’s see what we find.

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

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

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

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

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

Anzick

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

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

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

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

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

ancient compare

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

Paleo

At 200 SNP level, 2 segments.

1 26535949 27884441 1.1 258
2 127654021 128768822 1.2 228

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

Altai Neanderthal

ancient compare2

Russian Neanderthal

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

Denisovan

I have one match.

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

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

Matching to Ancestral Lines

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

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

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

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

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

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

ancient compare3

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

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

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

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

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

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

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

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

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

Let’s see what else the matches show.

ancient compare4

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

ancient compare5

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

ancient compare6

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

ancient compare7

More matching to the proven Miller line.

ancient compare8

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

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

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

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

ancient compare9

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

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

Regardless, it’s interesting, very interesting.

What Have I Learned?

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

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

My relationship level to these ancient people is as follows:

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

The Lores and the Millers

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

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

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

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

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

Bottom Line

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