Anzick Matching Update

Posted on January 5, 2015 by Roberta Estes

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.

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:

VCF Source: http://www.cbs.dtu.dk/suppl/clovis/data/Anzick-1/genotypes/
BAM Source: http://www.cbs.dtu.dk/suppl/clovis/data/Anzick-1/bams/

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 27^th 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.

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.

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.

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.

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?

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.

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.

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

Posted on December 30, 2014 by Roberta Estes

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.

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.

http://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.

http://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.

http://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 great 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.

http://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.

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

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.

http://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.

http://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.

http://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.

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

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

More ancient DNA samples for comparison:

http://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.

http://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.

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

Compare this with today’s tree, below.

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.

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

10^th 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 10^th annual. And yes, it was my 10^th 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.

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.

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

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

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

http://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.

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

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

In addition, three books have been released in 2014.

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

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

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.

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

I 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.

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.

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.

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

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

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.

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.

http://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.

http://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.

http://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.

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

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

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

http://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.

http://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.

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.

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

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.

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

http://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.

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!

______________________________________________________________

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Henry III, King of England, Fox in the Henhouse, 52 Ancestors #49

Posted on December 9, 2014 by Roberta Estes

I had been so looking forward to the results of the DNA processing of King Richard the III. Richard was killed in the Battle of Bosworth in 1485 and was reportedly buried in the “choir of the church” at the Greyfriars friary in Leicester. The friary was dissolved in 1538, following the orders of King Henry VIII who ordered all monasteries destroyed. The building was later destroyed, and over the years, the exact location of the cemetery was lost. In 2012, the friary location was found again, quite by accident and remains believed to be King Richard III were discovered buried under the car park, or what is known as a parking lot in the US.

Richard had a very distinctive trait – scoliosis to the point where his right shoulder was higher than his left. He was also described, at age 32, as a fine-boned hunchback with a withered arm and a limp. This, in addition to his slim build and his battle injuries led investigators to believe, and later confirm through mitochondrial DNA matching, that it was indeed Richard. At least they are 99% sure that it is Richard using archaeological, osteological and radiocarbon dating, in addition to DNA and good old genealogy.

Mitochondrial DNA testing was initially used to identify Richard the III by comparing his mitochondrial to that of current individuals matrilineally descended from his sister, Anne of York. That DNA was rare, and matched exactly in one case, and with only one difference in a second descendant, so either the skeleton is Richard or another individual who is matrilineally related. Fortunately, Richard’s mtDNA was quite unusual, with no other individuals matching in more than 26,000 other European sequences. The scientists estimated that the chances of a random match were about 1 in 10,000. The scientific team has utilized other evidence as well and feel certain that they have identified King Richard III himself.

King Richard III did not have any surviving descendants, so why was I so excited?

As it turns out, his Y DNA is representative of the Plantagenet family line which includes King Richard III’s great-great-great-great-grandfather, King Edward I, who is also my 19^th great-grandfather, which would make King Richard III my 5^th cousin, 16 times removed, I think. Maybe.

According to a paper released this week by Turi King, et al, “Identification of the remains of King Richard III”, it seems that there is a bit of a fly in the ointment. It’s no wonder this paper was in peer review forever. The authors knew that when it was released, it would be the shot heard round the world. For one thing, a tiny trivial matter, one of the possible outcomes could call into question the legitimacy of the current English monarchy. Only a detail for an American, but I’m thinking this is probably important to many people in England, especially those who think they should be the ruling monarch, and in particular, to the ruling monarch herself.

I wonder if Dr. Turi King rang up the Queen in advance with the news. I mean, what would you say to her??? How, exactly, would one begin that conversation? “Um, Your Highness, um, I think there has been a fox in the henhouse…”

In order to confirm the Y DNA line of King Richard III, his Y DNA was compared to that of another descendant of King Edward III, the great-grandson of my ancestor, Edward I. Edward III had two sons, Edmund, Duke of York from whom King Richard III descended and John of Gaunt, from whom the other Y DNA testers descend. Five male descendants of Henry Somerset were tested for comparison. Of those five, four matched each other, and one did not, indicating an NPE (nonparental event) or undocumented adoption in that line. The pedigree chart provided in the paper, below, shows the line of descent for both the Y and mitochondrial DNA participants.

Now, what we have is an uncertain situation. We know that Richard’s mitochondrial DNA matches that of his sister’s descendants, Michael Ibsen and Wendy Duldig, shown at right, above.

We know that the Y DNA of Richard does not match with the Y DNA of the Somerset line. We know that in the Somerset line, there were two illegitimate births, according to the paper, in the 13 generations between John of Gaunt and Henry Somerset, which were later legitimized. The first illegitimate birth is John Beaufort, the oldest illegitimate child of John of Gaunt and his mistress, Katherine Swynford, who later became John’s third wife. Katherine was previously married to a knight in the service of John of Gaunt, who is believed to have died, and was governess to John of Gaunt’s daughters.

The second illegitimate birth is Charles Somerset (1460-1526) who was the illegitimate son of Henry Beaufort and Joan Hill, about whom little is known.

The Somerset line proves to be downstream of haplogroup R1b-U152 (x L2, Z36, Z56, M160, M126 and Z192) with STR markers confirming their relationship to each other. King Richard III’s haplogroup is G-P287.

In this case, we don’t even need to scrutinize the STR markers, because the haplogroups don’t match, as you can see, above, in a haplotree provided in the paper.

The paper goes on to say that given a conservative false paternity rate of between 1 and 2% per generation, that there is a 16% probability of a false paternity in the number of generations separating King Richard III and the Somerset men.

What does this really mean?

According to the paper:

“One can speculate that a false-paternity event (or events) at some point(s) in this genealogy could be of key historical significance, particularly if it occurred in the five generations between John of Gaunt (1340–1399) and Richard III). A false-paternity between Edward III (1312–1377) and John would mean that John’s son, Henry IV (1367–1413), and Henry’s direct descendants (Henry V and Henry VI) would have had no legitimate claim to the crown. This would also hold true, indirectly, for the entire Tudor dynasty (Henry VII, Henry VIII, Edward VI, Mary I and Elizabeth I) since their claim to the crown also rested, in part, on their descent from John of Gaunt. The claim of the Tudor dynasty would also be brought into question if the false paternity occurred between John of Gaunt and his son, John Beaufort, Earl of Somerset. If the false paternity occurred in either of the three generations between Edward III and Richard, Duke of York, the father of Edward IV and Richard III, then neither of their claims to the crown would have been legitimate.”

While the known illegitimate births in the Somerset line lead us to look at those generations with scrutiny, the break in the Y chromosome inheritance could have happened in any generation, on either side of the tree.

According to the BBC article announcing the DNA results:

“Henry’s ancestor John of Gaunt was plagued by rumors of illegitimacy throughout his life, apparently prompted by the absence of Edward III at his birth. He was reportedly enraged by gossip suggesting he was the son of a Flemish butcher.

“Hypothetically speaking, if John of Gaunt wasn’t Edward III’s son, it would have meant that (his son) Henry IV had no legitimate claim to the throne, nor Henry V, nor Henry VI,” said Prof Schurer.”

So where does this leave us? I wonder if anyone has the name of that Flemish butcher????

Will the real Plantagenet, please stand up…or maybe be dug up.

What we need is a tie-breaker. Although the paper did not state this explicitly, I’m sure that the scientists also knew that they needed a tie-breaker – a male that descends through all males from someone upstream of Edward III. It appears that the Plantagenet line may well be a dead end, other than the Somerset line. I’m sure, with all of the resources brought to bear by the authors of this paper, that if there was another Plantagenet Y DNA male to be found, they would have done so.

So, the bottom line is that we don’t know what the real Plantagenet Y DNA line looks like, short of exhuming one of the Plantagenet Kings. They are mostly buried in Westminster Abbey in crypts. The Plantagenet line could be a subgroup of haplogroup R1b-U152. It could be haplogroup G. And, it could be yet something else. How? There could have been a NPE in both lines. I have seen it happen before.

Purely looking at the number of generations, meaning the number of opportunities for the genetic break to occur, there were 3 opportunities between King Richard the III and his great-great-grandfather, King Edward III, and there were 14 opportunities between Henry Somerset and King Edward III, so it’s more likely to have occurred in the Somerset line.

But that is small comfort, because all it took was one event, and there clearly was one. We don’t know which one, where. In this case, probabilities don’t matter – only actualities matter.

Back to my ancestor, King Henry III, father of King Edward I….

Dear Grandpa King Henry III,

I was just writing to catch you up on the news. This is your 20 times great-granddaughter….you do remember me…right?

I am sorry to report that there seems to have been a fox in the henhouse. Yes, that would be the Plantagenet henhouse. No, I don’t know when, or where. We just have fox DNA. Yes, we probably also have hen DNA, which would be your DNA, but you see, we can’t tell the difference between fox DNA and hen DNA.

By the way, would you mind trying that Houdini message thing and sending me a message about which DNA is fox and which is hen?

Thanks a million….

Your 20 times great-granddaughter

Even though we will probably never know what the Plantagenet DNA line looks like, we do know a lot about King Henry III, the father of King Edward I. We also have some idea what King Henry himself looked like. The effigy on his coffin in Westminster Abbey is shown below.

King Henry III was born on October 1, 1207 in Winchester Castle, shown below, the son of King John and Isabella of Angouleme, and died on November 16, 1272. He was known as Henry of Winchester and was King of England, Lord of Ireland and Duke of Aquitaine from 1216 until his death.

He ascended the throne at age 9, on October 28^th, 1216, at Gloucester Cathedral, and ruled under a guardian, council of 13 executors and the tutelage of his mother until he became of age. He assumed formal control of the government in January 1227, although he didn’t turn 21 until the following year. He ruled for a total of 56 years. A 13^th century depiction of his coronation is shown below.

Henry took the cross, declaring himself a crusader, which entitled him to special protections from Rome. While Henry never did actually go on Crusade, he might well have joined the Seventh Crusade in 1248 had he not been engaged in such a negative rivalry with the King of France. After Louis’s defeat at the Battle of Al Mansurah in 1250, Henry announced that he would be undertaking his own crusade to the Levant, but that Crusade never happened. Henry was aging by that time, at 43. It would he Henry’s son, Edward, who would represent the family in the Crusades, leaving in 1270 for the Eighth Crusade.

Henry was also crowned a second time, after the first Baron’s War, on May 17, 1220, at Westminster Abbey, in an effort to affirm the authority of the King, and with the Pope’s blessing. The medieval manuscript by Matthew Paris depicts the second coronation.

While the first coronation was hurried after his father’s death and with, in essence, a borrowed crown from Queen Isabella, since the royal crown had been either lost or sold during the war, the second coronation used a new set of royal regalia.

Engravings of Henry’s great seal.

Henry married Eleanor of Provence, daughter of Raymond-Berengar, the Count of Provene and Beatrice of Savoy, whose sisters all married Kings as well. Eleanor had never seen Henry before their marriage at Canterbury cathedral on January 14, 1236. At the time of their marriage, she was age 12 and he was 28. It was feared she was barren at first, but they went on to have 5 children, including Henry’s successor to the crown, Edward I. Her first child was born when she was age 15.

This medieval manuscript chronology from the early 1300s shows Henry III at the top, with his children left to right, the future King Edward I, Margaret, Beatrice, Edmund and Katherine.

In 1239 when Eleanor gave birth to their first child, Edward, named after Henry’s patron saint and ancestor, Edward the Confessor, Henry was overjoyed and held huge celebrations, giving lavishly to the Church and to the poor to encourage God to protect his young son. Their first daughter, Margaret, named after Eleanor’s sister, followed in 1240, her birth also accompanied by celebrations and donations to the poor.

Eleanor accompanied Henry to Poitrou on a military campaign, and their third child, Beatrice, named after Eleanor’s mother, and born in Poitou, France in1242.

This manuscript by Matthew Paris depicts Henry and Eleanor returning to England from Poitou in 1243.

Their fourth child, Edmund, arrived in 1245 and was named after the 9th-century saint. Concerned about Eleanor’s health, Henry donated large amounts of money to the Church throughout the pregnancy. A third daughter, Katherine, was born in 1253 but soon fell ill, possibly the result of a degenerative disorder such as Rett syndrome, and was unable to speak. She died in 1257 and Henry was distraught.

Henry’s children spent most of their childhood at Windsor Castle and he appears to have been extremely close to his family, rarely spending extended periods apart from them. King Henry III and Eleanor had the following children:

Edward, eventually King Edward I, was born on June 17, 1239 and died on July 7, 1307. He married Eleanor of Castile in 1254 and Margaret of France in 1299.
Margaret was born on September 29, 1240 and died on February 26, 1275, at age 35. She was the Queen of Scots and married King Alexander III, the King of Scotland at age 11. She had three children; Margaret born in 1261 who married King Eric II of Norway, Alexander born in 1264 who died at age 20 and David born in 1272 who died at age 9.
Beatrice was born on June 25, 1242 and died on March 24, 1275 at the age of 33. She married John II, Duke of Brittany, a love match, and had 6 children. Two of her descendant females would marry kings.
Edmund, known as Edmund Crouchback, was born on January 16, 1245 and died on June 5, 1296, at the age of 51. Crouchback reportedly refers to “crossed-back” and refers to his participation in the Ninth Crusade, although with King Richard III’s scoliosis, I have to wonder. He married Lady Aveline de Forz in 1269 at age 11. She died 4 years later, at age 15, possibly related to childbirth. He then married Blanche de Artois in 1276, in Paris, widow of Henri I, King of Navarre, with whom he had three sons, two of whom revolted against King Edward II.
The story of Katherine is sad indeed. She was born either deaf or a deaf-mute at Westminster Palace on November 25, 1253 and died on Mary 3. 1257, before her 4^th birthday. It was obvious at her birth, that in spite of her beauty, something was wrong. As she aged a bit, it also became evident that she was mentally challenged. Matthew Paris, chronicler of King Henry III, described her as “the most beautiful girl, but dumb and useless.” She was therefore not a political asset and was never betrothed. Her parents, however, loved her devotedly.

A few days after her christening, on the day of Saint Edward the Confessor’s death, January 5,1254, the King held a massive banquet, to which he invited all the nobility. The provisions for this banquet included “fourteen wild boars, twenty-four swans, one hundred and thirty-five rabbits, two hundred and fifty partridges, fifty hares, two hundred and fifty wild ducks, sixteen hundred and fifty fowls, thirty-six female geese and sixty-one thousand eggs”.

After Katherine’s death, both Henry and Eleanor were heartbroken.

Although the marriage of Henry III and Eleanor was clearly political in nature, Henry was kind and generous and they apparently came to love each other. Henry, unusual as compared to other English Kings, had no illegitimate children.

Henry was reported to have a drooping eyelid and an occasional fierce temper, but was generally known to be “amiable, easy-going and sympathetic,” as reported by historian David Carpenter.

The sketch above is from Cassell’s History of England published in 1902 but it does not reflect a drooping eyelid. The painting, below, from an unknown artist in 1620 is titled simply “Edward,” but it does depict the drooping eyelid. King Edward I was the son of Henry III. Now, if Richard III had only been reported with a droopy eyelid, we’d have another clue. Interestingly enough, the National Portrait Gallery has a discussion about the “crooked eye group” of kings, the latest of which is Edward II.

Henry III was known for his piety, celebrating mass at least once a day, holding lavish religious ceremonies and giving generously to charities. He fed 500 paupers each day, fasted before the feast days of Edward the Confessor and may have washed the feet of lepers. He was often moved to tears during religious ceremonies. The King was particularly devoted to the figure of Edward the Confessor, whom he adopted as his patron saint. Edward the Confessor was an early English King who lived a very pious life and who was also Henry III’s 6 times great-grandfather.

Henry reformed the system of silver coins in England in 1247, replacing the older Short Cross silver pennies with a new Long Cross design, shown below. Between 1243 and 1258, the King assembled two great hoards, or stockpiles, of gold. In 1257, Henry needed to spend the second of these hoards urgently and, rather than selling the gold quickly and depressing its value, Henry decided to introduce gold pennies into England, following the popular trend in Italy. The gold pennies resembled the gold coins issued by Edward the Confessor, but the overvalued currency attracted complaints from the City of London and was ultimately abandoned.

In 1247, Henry was sent the “Relic of the Holy Blood” by the Patriarch of Jerusalem, said to contain some of the blood of Christ. He carried the Relic through the streets of London from its storage location at the Church of the Holy Sepulchre in a procession to Westminster Abbey, shown below, by Matthew Paris. He then promoted the relic as a focus for pilgrimages, but it never became popular.

Henry III’s reign in England was marked by multiple insurrections and allegations of ineffective government at best and improprieties at worst.

Henry started out at a disadvantage due to his age and of course, inexperience as a child. The first problem happened before Henry was of age.

Taking advantage of the child-king, Louis VIII of France allied himself with Hugh de Lusignan and invaded first Poitou and then Gascony, lands held by the English monarchy. Henry III’s army in Poitou was under-resourced and lacked support from the French barons, many of whom had felt abandoned during the years of Henry’s minority and as a result, the province quickly fell. It became clear that Gascony would also fall unless reinforcements were sent from England.

In early 1225 a great council approved a tax of £40,000 to dispatch an army, which quickly retook Gascony. In exchange for agreeing to support Henry III, the English barons demanded that the King reissue the Magna Carta, originally issued by King John in 1215. Henry complied, declared that the charter was issued of his own “spontaneous and free will” and confirmed the new with the royal seal. This gave the new Great Charter and the Charter of the Forest of 1225, shown below from the UK National Archives, much more authority than any previous versions. The barons anticipated that the King would act in accordance with these definitive charters, subject to the law and moderated by the advice of the nobility.

Henry invaded France in 1230, in an attempt to reclaim family lands lost since the reign of King John, but his attempts were both unsuccessful and very expensive. As you can see, most of the Plantagenet family holdings in France had been lost, except for Gascony.

The drawing below depicts Henry travelling to Brittany in 1230, by Matthew Paris.

The English people paid for military actions as well as Henry’s expensive lifestyle, carrying out major remodeling of royal properties, through increased taxes, which caused Henry, over time, to become very unpopular.

In 1258, a group of Barons seized power in a coup, reforming English government through a process called the Provisions of Oxford, which is regarded at England’s first constitution. This document was the first to be published in English since the Norman Conquest 200 years previously. As a result, Henry ruled in conjunction with a council of 24 members, 12 selected by the crown and 12 by the barons. Those 24 then selected 2 men to oversee decisions. This certainly wasn’t what Henry wanted, but he had little choice at the time.

However, in 1261, Henry overthrew the Provisions of Oxford and the superceeding Provisions of Westminster, with assistance from the Pope in the form of a papal bull which started the second Baron’s War. In 1264, Henry was defeated and taken prisoner at the battle of Lewes, but his oldest son, the eventual King Edward I, escaped from captivity and freed his father the following year.

This time, Henry won and was restored to power, initially reacted harshly, confiscating all of the land and titles of the revolting Barons. In an effort to bring eventual peace, the Dictum of Kenilworth was issued to reconcile the rebels of the Baron’s War with the King.

Their rebel leader, Simon de Montfort, Henry’s brother-in-law who had married his sister, Eleanor, was now dead at the Battle of Evesham in 1265, shown above. The Dictum pardoned the revolting Barons and restored their previously confiscated lands to them, contingent on payment of penalties equal to their level of involvement in the rebellion, typically 5 times the value of the annual yield of the land.

The spirit of peace and reconciliation established by the Dictum of Kenilworth lasted for the remainder of Henry III’s reign and into the 1290s, although reconstruction was slow. Henry died in 1272, succeeded by his son, Edward, who became King Edward I, who was on crusade in the Holy Lands at the time of his father’s death.

Although unpopular due to his spending habits, Henry invested significantly in many properties still enjoyed by people today, improving their defenses and adding facilities, including rebuilding Westminster Abbey and his favorite palatial complex by the same name in London.

The Tower of London was extended to form a concentric fortress with extensive living quarters, although Henry primarily used the castle as a secure retreat in the event of war or civil strife.

Tower of London as it appears today from the Thames.

Henry also kept a menagerie at the Tower, a tradition begun by his father, and his exotic specimens included an elephant, a leopard and a camel.

Henry was given an elephant, above, as a gift by King Louis IX of France.

King Henry III visiting Louis IX of France.

Among other projects, Henry built the Great Hall of Winchester Castle, shown above.

Perhaps Henry’s legacy contribution is the creation of what would become the English Parliament. The term “parliament” first appeared in the 1230s and 1240s to describe large gatherings of the royal court, and parliamentary gatherings were held periodically throughout Henry’s reign. They were used to agree to the raising of taxes which, in the 13th century, were single, one-off levies, typically on movable property, intended to supplement the King’s normal revenues for particular projects. During Henry’s reign, the counties began to send regular delegations to these parliaments, and came to represent a broader cross-section of the community than simply the major barons.

In Henry’s last years, he was increasingly ill. He continued to invest in Westminster Abbey, which became a replacement for the Angevin mausoleum at Fontevraud Abbey in Anjou, France, In 1269 Henry oversaw a grand ceremony to rebury Edward the Confessor in a lavish new shrine, personally helping to carry the body to its new resting place in the rebuilt Westminster Abbey. Edward the Confessor has built the original Westminster Abbey in 1065 which was demolished by Henry III to construct the new Westminster Abbey in its place.

In 1270, Henry’s son, Edward left on the Eighth Crusade and at one time, Henry voiced his intention to join Edward. That never happened, and Henry III died at Westminster Palace on the evening of November 16, 1272. Eleanor was probably at his side.

At his request, Henry was buried in Westminster Abbey in front of the church’s high altar, in the former resting place of Edward the Confessor. A few years later, work began on a grander tomb for King Henry III and in 1290, Edward moved his father’s body to its current location in Westminster Abbey.

See, it wouldn’t be difficult at all to access the remains of King Henry III…no digging involved!!! For that matter, we could just skip to the beginning and start with the remains of Edward the Confessor.

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Kostenki14 – A New Ancient Siberian DNA Sample

Posted on November 12, 2014 by Roberta Estes

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.

From 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.

Also 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.

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.

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

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!

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Peopling of Europe 2014 – Identifying the Ghost Population

Posted on October 21, 2014 by Roberta Estes

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 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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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).

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.

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.

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.

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.

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.

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

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

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.

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.

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.

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.

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

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.

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?

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.

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

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.

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

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.

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.

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:

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Anzick (12,707-12,556), Ancient One, 52 Ancestors #42

Posted on October 18, 2014 by Roberta Estes

His name is Anzick, named for the family land, above, where his remains were found, and he is 12,500 years old, or more precisely, born between 12,707 and 12,556 years before the present. Unfortunately, my genealogy software is not prepared for a birth year with that many digits. That’s because, until just recently, we had no way to know that we were related to anyone of that age….but now….everything has changed ….thanks to DNA.

Actually, Anzick himself is not my direct ancestor. We know that definitively, because Anzick was a child when he died, in present day Montana.

Anzick was loved and cherished, because he was smeared with red ochre before he was buried in a cave, where he would be found more than 12,000 years later, in 1968, just beneath a layer of approximately 100 Clovis stone tools, shown below. I’m sure his parents then, just as parents today, stood and cried as the laid their son to rest….never suspecting just how important their son would be some 12,500 years later.

From 1968 until 2013, the Anzick family looked after Anzick’s bones, and in 2013, Anzick’s DNA was analyzed.

DNA analysis of Anzick provided us with his mitochondrial haplogroup, D4h3a, a known Native American grouping, and his Y haplogroup was Q-L54, another known Native American haplogroup. Haplogroup Q-L54 itself is estimated to be about 16,900 years old, so this finding is certainly within the expected range. I’m not related to Anzick through Y or mitochondrial DNA.

Utilizing the admixture tools at GedMatch, we can see that Anzick shows most closely with Native American and Arctic with a bit of east Siberian. This all makes sense.

Full genome sequencing was performed on Anzick, and from that data, it was discovered that Anzick was related to Native Americans, closely related to Mexican, Central and South Americans, and not closely related to Europeans or Africans. This was an important discovery, because it in essence disproves the Solutrean hypothesis that Clovis predecessors emigrated from Southwest Europe during the last glacial maximum, about 20,000 years ago.

The distribution of these matches was a bit surprising, in that I would have expected the closest matches to be from North America, in particular, near to where Anzick was found, but his closest matches are south of the US border. Although, in all fairness, few people in Native tribes in the US have DNA tested and many are admixed.

This match distribution tells us a lot about population migration and distribution of the Native people after they left Asia, crossed Beringia on the land bridge, now submerged, into present day Alaska.

This map of Beriginia, from the 2008 paper by Tamm et all, shows the migration of Native people into (and back from) the new world.

Anzick’s ancestors crossed Beringia during this time, and over the next several thousand years, found their way to Montana. Some of Anzick’s relatives found their way to Mexico, Central and South America. The two groups may have split when Anzick’s family group headed east instead of south, possibly following the edges of glaciers, while the south-moving group followed the coastline.

Recently, from Anzick’s full genome data, another citizen scientist extracted the DNA locations that the testing companies use for autosomal DNA results, created an Anzick file, and uploaded the file to the public autosomal matching site, GedMatch. This allowed everyone to see if they matched Anzick. We expected no, or few, matches, because after all, Anzick was more than 12,000 years old and all of his DNA would have washed out long ago due to the 50% replacement in every generation….right? Wrong!!!

What a surprise to discover fairly large segments of DNA matching Anzick in living people, and we’ve spent the past couple of weeks analyzing and discussing just how this has happened and why. In spite of some technical glitches in terms of just how much individual people carry of the same DNA Anzick carried, one thing is for sure, the GedMatch matches confirm, in spades, the findings of the scientists who wrote the recent paper that describes the Anzick burial and excavation, the subsequent DNA processing and results.

For people who carry known Native heritage, matches, especially relatively large matches to Anzick, confirm not only their Native heritage, but his too.

For people who suspect Native heritage, but can’t yet prove it, an Anzick match provides what amounts to a clue – and it may be a very important clue.

In my case, I have proven Native heritage through the Micmac who intermarried with the Acadians in the 1600s in Nova Scotia. Given that Anzick’s people were clearly on a west to east movement, from Beringia to wherever they eventually wound up, one might wonder if the Micmac were descended from or otherwise related to Anzick’s people. Clearly, based on the genetic affinity map, the answer is yes, but not as closely related to Anzick as Mexican, Central and South Americans.

After several attempts utilizing various files, thresholds and factors that produced varying levels of matching to Anzick, one thing is clear – there is a match on several chromosomes. Someplace, sometime in the past, Anzick and I shared a common ancestor – and it was likely on this continent, or Beringia, since the current school of thought is that all Native people entered the New World through this avenue. The school of thought is not united in an opinion about whether there was a single migration event, or multiple migrations to the new word. Regardless, the people came from the same base population in far northeast Asia and intermingled after arriving here if they were in the same location with other immigrants.

In other words, there probably wasn’t much DNA to pass around. In addition, it’s unlikely that the founding population was a large group – probably just a few people – so in very short order their DNA would be all the same, being passed around and around until they met a new population, which wouldn’t happen until the Europeans arrived on the east side of the continent in the 1400s. The tribes least admixed today are found south of the US border, not in the US. So it makes sense that today the least admixed people would match Anzick the most closely – because they carry the most common DNA, which is still the same DNA that was being passed around and around back then.

Many of us with Native ancestors do carry bits and pieces of the same DNA as Anzick. Anzick can’t be our ancestor, but he is certainly our cousin, about 500 generations ago, using a 25 year generation, so roughly our 500^th cousin. I had to laugh at someone this week, an adoptee who said, “Great, I can’t find my parents but now I have a 12,500 year old cousin.” Yep, you do! The ironies of life, and of genealogy, never fail to amaze me.

Utilizing the most conservative matching routine possible, on a phased kit, meaning one that combines the DNA shared by my mother and myself, and only that DNA, we show the following segment matches with Anzick.

Chr	Start Location	End Location	Centimorgans (cM)	SNPs
2	218855489	220351363	2.4	253
4	1957991	3571907	2.5	209
17	53111755	56643678	3.4	293
19	46226843	48568731	2.2	250
21	35367409	36761280	3.7	215

Being less conservative produces many more matches, some of which are questionable as to whether they are simply convergence, so I haven’t utilized the less restrictive match thresholds.

Of those matches above, the one on chromosomes 17 matches to a known Micmac segment from my Acadian lines and the match on chromosome 2 also matches an Acadian line, but I share so many common ancestors with this person that I can’t tell which family line the DNA comes from.

There are also Anzick autosomal matches on my father’s side. My Native ancestry on his side reaches back to colonial America, in either Virginia or North Carolina, or both, and is unproven as to the precise ancestor and/or tribe, so I can’t correlate the Anzick DNA with proven Native DNA on that side. Neither can I associate it with a particular family, as most of the Anzick matches aren’t to areas on my chromosome that I’ve mapped positively to a specific ancestor.

Running a special utility at GedMatch that compared Anzick’s X chromosome to mine, I find that we share a startlingly large X segment. Sometimes, the X chromosome is passed for generations intact.

Interestingly enough, the segment 100,479,869-103,154,989 matches a segment from my mother exactly, but the large 6cM segment does not match my mother, so I’ve inherited that piece of my X from my father’s line.

Chr	Start Location	End Location	Centimorgans (cM)	SNPs
X	100479869	103154989	1.4	114
X	109322285	113215103	6.0	123

This tells me immediately that this segment comes from one of the pink or blue lines on the fan chart below that my father inherited from his mother, Ollie Bolton, since men don’t inherit an X chromosome from their father. Utilizing the X pedigree chart reduces the possible lines of inheritance quite a bit, and is very suggestive of some of those unknown wives.

It’s rather amazing, if you think about it, that anyone today matches Anzick, or that we can map any of our ancestral DNA that both we and Anzick carry to a specific ancestor.

Indeed, we do live in exciting times.

Honoring Anzick

On a rainy Saturday in June, 2014, on a sagebrush hillside in Montana, in Native parlance, our “grandfather,” Anzick was reburied, bringing his journey full circle. Sarah Anzick, a molecular biologist, the daughter of the family that owns the land where the bones were found, and who did part of the genetic discovery work on Anzick, returns the box with his bones for reburial.

More than 50 people, including scientists, members of the Anzick family and representatives of six Native American tribes, gathered for the nearly two-hour reburial ceremony. Tribe members said prayers, sang songs, played drums and rang bells to honor the ancient child. The bones were placed in the grave and sprinkled with red ocher, just like when his parents buried him some 12,500 years before.

Participants at the reburial ceremony filled in the grave with handfuls, then shovelfuls of dirt and covered it with stones. A stick tied with feathers marks Anzick’s final resting place.

Sarah Anzick tells us that, “At that point, it stopped raining. The clouds opened up and the sun came out. It was an amazing day.”

I wish I could have been there. I would have, had I known. After all, he is part of me, and I of him.

Welcome to the family, Anzick, and thank you, thank you oh so much, for your priceless, unparalleled gift!!!

If you want to read about the Anzick matching journey of DNA discovery, here are the articles I’ve written in the past two weeks. It has been quite a roller coaster ride, but I’m honored and privileged to be doing this research. And it’s all thanks to an ancient child named Anzick.

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Tenth Annual Family Tree DNA Conference Wrapup

Posted on October 15, 2014 by Roberta Estes

This slide, by Robert Baber, pretty well sums up our group obsession and what we focus on every year at the Family Tree DNA administrator’s conference in Houston, Texas.

Getting to Houston, this year, was a whole lot easier than getting out of Houston. They had storms yesterday and many of us spent the entire day becoming intimately familiar with the airport. Jennifer Zinck, of Ancestor Central, is still there today and doesn’t have a flight until late.

And this is how my day ended, after I finally got out of Houston and into my home airport. This isn’t at the airport, by the way. Everything was fine there, but I made the apparent error of stopping at a Starbucks on the way home. This is the parking lot outside an hour or so later. What can I say? At least I had my coffee, and AAA rocks, as did the tow truck driver and my daughter for getting out of bed to come and rescue me!!! Hmmm, I think maybe things have gone full circle. I remember when I used to go and rescue her:)

So far, today hasn’t improved any, so let’s talk about something much more pleasant…the conference itself.

Resources

One of the reasons I mentioned Jennifer Zinck, aside from the fact that she’s still stuck in the airport, is because she did a great job actually covering the conference as it happened. Since I had some time yesterday to visit with her since our gates weren’t terribly far apart, I asked her how she got that done. I took notes too, and photos, but she turned out a prodigious amount of work in a very short time. While I took a lightweight MacBook Air, she took her regular PC that she is used to typing on, and she literally transcribed as the sessions were occurring. She just added her photos later, and since she was working on a platform that she was familiar with, she could crop and make the other adjustments you never see but we perform behind the scenes before publishing a photo.

On the other hand, I struggled with a keyboard that works differently and is a different size than I’m used to as well as not being familiar with the photo tools to reduce the size of pictures, so I just took rough notes and wrote the balance later. Having familiar tools make such a difference. I think I’ll carry my laptop from now on, even though it is much heavier. Kudos to Jennifer!

I was initially going to summarize each session, but since Jen did such a good job, I’m posting her links. No need to recreate a wheel that doesn’t need to be recreated.

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

ISOGG, the International Society of Genetic Genealogy is not affiliated with Family Tree DNA or any testing company, but Family Tree DNA is generous enough to allow an ISOGG meeting on Sunday before the first conference session.

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

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

You can find my conference postings here:

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

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

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

Several people were also posting on a twitter feed as well.

https://twitter.com/search?q=%23FTDNA2014&src=tyah

Those of you where are members of the ISOGG Yahoo group for project administrators can view photos posted by Katherine Borges in that group and there are also some postings on the Facebook ISOGG group as well.

Now that you have the links for the summaries, what I’d like to do is to discuss some of the aspects I found the most interesting.

The Mix

When I attended my first conference 10 years ago, I somehow thought that for the most part, the same group of people would be at the conferences every year. Some were, and in fact, a handful of the 160+ people attending this conference have attended all 10 conferences. I know of two others for certain, but there were maybe another 3 or so who stood up when Bennett asked for everyone who had been present at all 10 conferences to stand.

Doug Mumma, the very first project administrator was with us this weekend, and still going strong. Now, if Doug and I could just figure out how we’re related…

Some of the original conference group has passed on to the other side where I’m firmly convinced that one of your rewards is that you get to see all of those dead ends of your tree. If we’re lucky, we get to meet them as well and ask all of those questions we have on this side. We remember our friends fondly, and their departure sadly, but they enriched us while they were here and their memories make us smile. I’m thinking specifically of Kenny Hedgepath and Leon Little as I write this, but there have been others as well.

The definition of a community is that people come and go, births, deaths and moves.

This year, about half of the attendees had never attended a conference before. I was very pleased to see this turn of events – because in order to survive, we do need new people who are as crazy as we are…er….I mean as dedicated as we are.

ISOGG traditionally hosts a potluck reception on Saturday evening. Lots of putting names with faces going on here.

Collaboration

I asked people about their favorite part of the conference or their favorite session. I was surprised at the number of people who said lunches and dinners. Trust me, the food wasn’t that wonderful, so I asked them to elaborate. In essence, the most valuable aspect of the conference was working with and talking to other administrators.

It’s not like we don’t talk online, but there is somehow a difference between online communications and having a group discussion, or a one-on-one discussion. Laptops were out and in use everyplace, along with iPads and other tools. It was so much fun to walk by tables and hear snippets of conversations like “the mutation at location 309.1….” and “null marker at 425” and “I ordered a kit for my great uncle…..”

I agree, as well. I had pre-arranged two dinners before arriving in order to talk with people with whom I share specific interests. At lunches, I either tried to sit with someone I specifically needed to talk to, or I tried to meet someone new.

I also asked people about their specific goals for the next year. Some people had a particular goal in mind, such as a specific brick wall that needs focus. Some, given that we are administrators, had wider-ranging project based goals, like Big Y testing certain family groups, and a surprising number had the goal of better utilizing the autosomal results.

Perhaps that’s why there were two autosomal sessions, an introduction by Jim Bartlett and then Tim Janzen’s more advanced session.

Autosomal DNA Results

Note the cool double helix light fixture behind the speakers.

Tim specifically mentioned two misconceptions which I run across constantly.

Misconception 1 – A common surname means that’s how you match. Just because you find a common surname doesn’t mean that’s your DNA match. This belief is particularly prevalent in the group of people who test at Ancestry.com.

Misconception 2 – Your common ancestor has to be within the past 6 generations. Not true, many matches can be 6-10^th cousins because there are so many descendants of those early ancestors, even as many as 15 generations back.

Tim also mentioned that endogamous relationships are a tough problem with no easy answer. Polynesians, Ashkenazi Jews, Low German Mennonites, Acadians, Amish, and island populations. Do I ever agree with him! I have Brethren, Mennonite and Acadian in the same parent’s line.

Tim has been working with the Mennonite DNA project now for many years.

Tim included a great resource slide.

Tim has graciously made his entire presentation available for download.

There are probably a dozen or so of us that are actively mapping our ancestors, and a huge backlog of people who would like to. As Tim pointed out with one of his slides, this is not an easy task nor is it for the people who simply want to receive “an answer.”

I will also add that we “mappers” are working with and actively encouraging Family Tree DNA to develop tools so that the mapping is less spreadsheet manual work and more automated, because it certainly can be.

Upload GEDCOM Files

If you haven’t already, upload your GEDCOM to Family Tree DNA. This is becoming an essential part of autosomal matching. Furthermore, Family Tree DNA will utilize this file to construct your surname list and that will help immensely determining common surnames and your common ancestor with your Family Finder matches. If you have sponsored tests for cousins, then upload a GEDCOM file for them or at least construct a basic tree on their Family Tree DNA page.

Ethics

Family Tree DNA always tries to provide a speaker about ethics, and the only speakers I’ve ever felt understood anything about what we want to do are Judy Russell and Blaine Bettinger. I was glad to see Blaine presenting this year.

The essence of Blaine’s speech is that ethics isn’t about law. Law is cut and dried. Ethics isn’t, and there are no ethics police.

Sometimes our decisions are colored necessarily by right and wrong. Sometimes those decisions are more about the difference between a better and a worse way.

As a community, we want to reduce negative press coverage and increase positive coverage. We want to be proactive, not reactive.

Blaine stresses that while informed consent is crucial, that DNA doesn’t reveal secrets that aren’t also revealed by other genealogical forms of research. DNA often reveals more recent secrets, such as adoptions and NPEs, so it’s possibly more sensitive.

Two things need to govern our behavior. First, we need to do only things that we would be comfortable seeing above the fold in the New York Times. Second, understand that we can’t make promises about topics like anonymity or about the absence of medical information, because we don’t know what we don’t know.

The SNP Tsunami

One of my concerns has been and remains the huge number of new SNPs that have been discovered over the past year or so with the Big Y by Family Tree DNA and corresponding tests from other vendors.

When I say concern, I’m thrilled about this new technology and the advances it is allowing us to make as a community to discover and define the evolution of haplogroups. My concern is that the amount of data is overwhelming. However, we are working through that, thanks to the hours and hours of volunteer work by haplogroup administrators and others.

Alice Fairhurst, who volunteers to maintain the ISOGG haplotree, mentioned that she has added over 10,000 SNPs to the Y tree this year alone, bringing the total to over 14,000. Those SNPs are fully vetted and placed. There are many more in process and yet more still being discovered. On the first page of the Y SNP tree, the list of SNP sources and other critical information, such as the criteria for a SNP to be listed, is provided.

So, if you’re waiting for that next haplotree poster, give it up because there isn’t a printing press that big, unless you want wallpaper.

These slides are from Alice’s presentation. The ISOGG tree provides an invaluable resource for not only the genetic genealogy community, but also researchers world-wide.

As one example of how the SNP tsunami has affected the Y tree, Alice provided the following summary of R-U106, one of the two major branches of haplogroup R.

From the ISOGG 2006 Y tree, this was the entire haplogroup R Y tree. You can see U106 near the bottom with 3 sub-branches. While this probably makes you chuckle today, remember that 2006 was only 8 years ago and that this tree didn’t change much for several years.

2007 was the same.

2008 shows 5 subclades and one of the subclades had 2 subclades.

2009 showed a total of 12 sub-branches and 2010 added one more.

2011 however, showed a large change. U106 in 2011 had 44 subgroups total and became too large to show on one screen shot. 2012 shows 99 subclades, if I counted accurately. The 2014 U106 tree is shown below.

There’s another slide too, but I didn’t manage to get the picture. You get the idea though…

As you can imagine, for Family Tree DNA, trying to keep up with all of the haplogroups, not just one subgroup like U106 is a gargantuan task that is constantly changing, like hourly. Their Y tree is currently the National Geographic tree, and while they would like to update it, I’m sure, the definition of “current tree” is in a constant state of flux. Literally, Mike Walsh, one of the admins in the R-L21 group uploads a new tree spreadsheet several times every day.

In order to deal attempt to deal with this, and to encourage people who don’t want to do a Big Y discovery type test, but do want to ferret out their location on their assigned portion of the tree, Family Tree DNA is reintroducing the Backbone tests.

They are starting with M222, also known as the Niall of the 9 Hostages haplogroup which is their beta for the new product and new process. You can see the provisional tree and results in the two slides they provided, below. I apologize for the quality, but it was the best I could do.

Haplogroup administrators are going to be heavily involved in this process. Family Tree DNA is putting SNP panels together that will help further define the tree and where various SNPs that have been recently discovered, and continue to be discovered, will fall on the tree.

As Big Y tests arrive, haplogroup project administrators typically assemble a spreadsheet of the SNPS and provisionally where they fall on the tree, based on the Big Y results.

What Bennett asked is for the admins to work with Family Tree DNA to assemble a testing panel based on those results. The goal is for the cost to be between $1.50 and $2 (US) for each SNP in the panel, which will reduce the one-off SNP testing and provide a much more complete and productive result at a far reduced price as compared to the current $29 or $39 per individual SNP.

If you are a haplogroup administrator, get in touch with Family Tree DNA to discuss your desired backbone panels. New panels, when it’s your turn, will take about 2 weeks to develop.

Keep in mind that the following SNPs, according to Bennett, are not optimal for panels:

Palindromic regions
Often mutating regions designated as .1, .2, etc.
SNPs in STRs

Nir Leibovich, the Chief Business Officer, also addressed the future and the Big Y to some extent in his presentation.

Utilizing the Big Y for Genealogy

In my case, during the last sale, I ordered several Big Y tests for my Estes family line because I have several genealogically documented lines from the original Estes family in Kent, England through our common ancestor, Robert Estes born in 1555 and his wife Anne Woodward. The participants also agreed to extend their markers to 111 markers as well. When the results are back, we’ll be able to compare them on a full STR marker set, and also their SNPs. Hopefully, they will match on their known SNPs and there will be some new novel variants that will be able to suffice as line marker mutations.

We need more BIG Y tests of these types of genealogically confirmed trees that have different sons’ lines from a distant common ancestor to test descendant lines. This will help immensely to determine the actual, not imputed, SNP mutation rate and allow us to extrapolate the ages of haplogroups more accurately. Of course, it also goes without saying that it helps to flesh out the trees.

I personally expect the next couple of years will be major years of discovery. Yes, the SNP tsumani has hit land, but it’s far from over.

Research and Development

David Mittleman, Chief Scientific Officer, mentioned that Family Tree DNA now has their own R&D division where they are focused on how to best analyze data. They have been collaborating with other scientists. A haplogroup G1 paper will be published shortly which states that SNP mutation rates equate to Sanger data.

FTDNA wants to get Big Y data into the public domain. They have set up consent for this to be done by uploading into NCBI. Initially they sent a survey to a few people that sampled the interest level. Those who were interested received a release document. If you are interested in allowing FTDNA to utilize your DNA for research, be it mitochondrial, Y or autosomal, please send them an e-mail stating such.

Don’t Forget About Y Genealogy Research

It’s very easy for us to get excited about the research and discovery aspect of DNA – and the new SNPs and extending haplotrees back in time as far as possible, but sometimes I get concerned that we are forgetting about the reason we began doing genetic genealogy in the first place.

Robert Baber’s presentation discussed the process of how to reconstruct a tree utilizing both genealogy and DNA results. It’s important to remember that the reason most of our participants test is to find their ancestors, not, primarily, to participate in the scientific process.

Robert has succeeded in reconstructing 110 or 111 markers of the oldest known Baber ancestor, shown above. I wrote about how to do this in my article titled, Triangulation for Y DNA.

Not only does this allow us to compare everyone with the ancestor’s DNA, it also provides us with a tool to fit individuals who don’t know specific genealogical line into the tree relatively accurately. When I say relatively, the accuracy is based on line marker mutations that have, or haven’t, happened within that particular family.

Jim illustrated how to do this as well, and his methodology is available at the link on his slide, below.

I had to laugh. I’ve often wondered what our ancestors would think of us today. Robert said that that 11 generations after Edward Baber died, he flew over church where Edward was buried and wondered what Edward would have thought about what we know and do today – cars, airplanes, DNA, radio, TV etc.. If someone looked in a crystal ball and told Edward what the future held 11 generations later, he would have thought that they were stark raving mad.

Eleven generations from my birth is roughly the year 2280. I’m betting we won’t be trying to figure out who our ancestors were through this type of DNA analysis then. This is only a tiny stepping stone to an unknown world, as different to us as our world is to Edward Baber and all of our ancestors who lived in a time where we know their names but their lives and culture are entirely foreign to ours.

Publications

When the Journal of Genetic Genealogy was active, I, along with other citizen scientists published regularly. The benefit of the journal was that it was peer reviewed and that assured some level of accuracy and because of that, credibility, and it was viewed by the scientific community as such. My co-authored works published in JOGG as well as others have been cited by experts in the academic community. It other words, it was a very valuable journal. Sadly, it has fallen by the wayside and nothing has been published since 2011. A new editor was recruited, but given their academic load, they have not stepped up to the plate. For the record, I am still hopeful for a resurrection, but in the mean time, another opportunity has become available for genetic genealogists.

Brad Larkin has founded the Surname DNA Journal, which, like JOGG, is free to both authors and subscribers. In case you weren’t aware, most academic journal’s aren’t. While this isn’t a large burden for a university, fees ranging from just over $1000 to $5000 are beyond the budget of genetic genealogists. Just think of how many DNA tests one could purchase with that money.

Brad has issued a call for papers. These papers will be peer reviewed, similarly to how they were reviewed for JOGG.

Take a look at the articles published in this past year, since the founding of Surname DNA Journal.

The History, Adoption, and Regulation of Jewish Surnames in the Russian Empire, A Reviewby Dr. Jeffrey Mark Paull and Dr Jeffrey Briskman
Preliminary Phylogenetic Analysis of Briese Family Relationships by David Briese
Differences in Autosomal DNA Characteristics between Jewish and Non-Jewish Populations by Dr. Jeffrey Mark Paull, Gaye Sherman Tannenbaum, and Dr Jeffrey Briskman
Using STRs for Intra-Family Y-DNA Comparisons: Segmenting Markers by Joe Flood, PhD
Y-DNA of the British Monarchy by Brad Larkin
The Irish Septs by David Austin Larkin
Using Y Chromosome DNA Testing to Pinpoint a Genetic Homeland in Ireland by Dr. Tyrone Bowes, PhD
Ancestral Parish Sampling in Ulster and Wexford for the Larkin DNA Project by Brad Larkin

The citizen science community needs an avenue to publish and share. Peer reviewed journals provide us with another level of credibility for our work. Sharing is clearly the lynchpin of genetic genealogy, as it is with traditional genealogy. Give some thought about what you might be able to contribute.

Brad Larkin solicited nominations prior to the conference and awarded a Genetic Genealogist of the Year award. This year’s award was dually presented to Ian Kennedy in Australia, who, unfortunately, was not present, and to CeCe Moore, who just happened to follow Brad’s presentation with her own.

Don’t Forget about Mitochondrial DNA Either

I believe that mitochondrial DNA the most underutilized DNA tool that we have, often because how to use mitochondrial DNA, and what it can tell you, is poorly understood. I wrote about this in an article titled, Mitochondrial, The Maligned DNA.

Given that I work with mitochondrial DNA daily when I’m preparing client’s Personalized DNA Reports (orderable from your personal page at Family Tree DNA or directly from my website), I know just how useful mitochondrial can be and see those examples regularly. Unfortunately, because these are client reports, I can’t write about them publicly.

CeCe Moore, however, isn’t constrained by this problem, because one of the ways she contributes to genetic genealogy is by working with the television community, in particular Genealogy Roadshow and the PBS series, Finding Your Roots. Now, I must admit, I was very surprised to see CeCe scheduled to speak about mitochondrial DNA, because the area of expertise where she is best known is autosomal DNA, especially in conjunction with adoptee research.

During the research for the production of these shows, CeCe has utilized mitochondrial DNA with multiple celebrities to provide information such as the ethnic identification of the ancestor who provided the mitochondrial DNA as Native American.

Autosomal DNA testing has a broad but shallow reach, across all of your lines, but just back a few generations. Both Y and mitochondrial DNA have a very deep reach, but only on one specific line, which makes them excellent for identifying a common ancestor on that line, as well as the ethnicity of that individual.

I have seen other cases, where researchers connected the dots between people where no paper trail existed, but a relationship between women was suspected.

CeCe mentioned that currently there are only 44,000 full sequence results in the Family Tree DNA data base and and 185K total HVR1, HVR2 and full sequence tests. Y has half a million. We need to increase the data base, which, of course increases matches and makes everyone happier. If you haven’t tested your mitochondrial DNA to the full sequence level, this would be a great time!

There are several lessons on how to utilize mitochondrial DNA at this ISOGG link.

I’m very hopeful that CeCe’s presentation will be made available as I think her examples are quite powerful and will serve to inspire people. Actually, since CeCe is in the “movie business,” perhaps a short video clip could be made available on the FTDNA website for anyone who hasn’t tested their mitochondrial DNA so they can see an example of why they should!

myOrigins

I would be fibbing to you if I told you I am happy with myOrigins. I don’t feel that it is as sensitive as other methods for picking up minority admixture, in particular, Native American, especially in small amounts. Unfortunately, those small amounts are exactly what many people are looking for.

If someone has a great-great-great-great grandparent that is Native, they carry about 1%, more or less, of the Native ancestor’s DNA today. A 4X great grandparent puts their birth year in the range of 1800-1825 – or just before the Trail of Tears. People whose colonial American families intermarried with Native families did so, generally, before the Trail of Tears. By that time, many tribes were already culturally extinct and those east of the Mississippi that weren’t extinct were fighting for their lives, both literally and figuratively.

We really need the ability to develop the most sensitive testing to report even the smallest amounts of Native DNA and map those segments to our chromosomes so that we can determine who, and what line in our family, was Native.

I know that Family Tree DNA is looking to improve their products, and I provided this feedback to them. Many people test autosomally only for their ethnicity results and I surely would love to have those people’s results available as matches in the FTDNA data base.

Razib Khan has been working with Family Tree DNA on their myOrigins product and spoke about how the myOrigins data is obtained.

Given that all humans are related, one way or another, far enough back in time, myOrigins has to be able to differentiate between groups that may not be terribly different. Furthermore, even groups that appear different today may not have been historically. His own family, from India, has no oral history of coming from the East, but the genetic data clearly indicates that they did, along with a larger group, about 1000 years ago. This may well be a result of the adage that history is written by the victors, or maybe whatever happened was simply too long ago or unremarkable to be recorded.

Razib mentioned that depending on the cluster and the reference samples, that these clusters and groups that we see on our myOrigins maps can range from 1000-10,000 years in age.

The good news is that genetics is blind to any preconceived notions. The bad news is that the software has to fit your results to the best population, even though it may not be directly a fit. Hopefully, as we have more and better reference populations, the results will improve as well.

Razib showed a PCA (principal components analysis) graph, above. These graphs chart reference populations in different quadrants. Where the different populations overlap is where they share common historic ancestors. As you can see, on this graph with these reference populations, there is a lot of overlap in some cases, and none in others.

Your personal results would then be plotted on top of the reference populations. The graph below shows me, as the white “target” on a PCA graph created by Doug McDonald.

The Changing Landscape

A topic discussed privately among the group, and primarily among the bloggers, is the changing landscape of genetic genealogy over the past year or so. In many ways I think the bloggers are the canaries in the mine.

One thing that clearly happened is that the proverbial tipping point occurred, and we’re past it. DNA someplace along the line became mainstream. Today, DNA is a household word. At gatherings, at least someone has tested, and most people have heard about DNA testing for genealogy or at least consumer based DNA testing.

The good news in all of this is that more and more people are testing. The bad news is that they are typically less informed and are often impulse purchasers. This gives us the opportunity for many more matches and to work with new people. It also means there is a steep learning curve and those new testers often know little about their genealogy. Those of us in the “public eye,” so to speak, have seen an exponential spike in questions and communications in the past several months. Unfortunately, many of the new people don’t even attempt to help themselves before asking questions.

Sometimes opportunity comes with work clothes – for them and us both.

I was talking with Spencer about this at the reception and he told me I was stealing his presentation. He didn’t seem too upset by this:)

I had to laugh, because this falls clearly into the “be careful what you wish for, you may get it” category. The Genographic project through National Geographic is clearly, very clearly, a critical component of the tipping point, and this was reflected in Spencer’s presentation. Although I covered quite a bit of Spencer’s presentation in my day 2 summary, I want to close with Spencer here. I also want to say that if you ever have the opportunity to hear Spencer speak, please do yourself the favor and be sure to take that opportunity. Not only is he brilliant, he’s interesting, likeable and very approachable. Of course, it probably doesn’t hurt that I’ve know him now for 9 years! I’ve never thought to have my picture taken with Spencer before, but this time, one of my friends did me the favor.

I have to admit, I love talking to Spencer, and listening to him. He is the adventurer through whom we all live vicariously. In the photo below, Spencer along with his crew, drove from London to Mongolia. Not sure why he is standing on the top of the Land Rover, but I’m sure he will tell us in his upcoming book about that journey,

I’m warning you all now, if I win the lottery, I’m going on the world tour that he hosts with National Geographic, and of course, you’ll all be coming with me via the blog!

Spencer talked about the consumer genomics market and where we are today.

Spencer mentioned that genetic genealogy was a cottage industry originally. It was, and it was even smaller than that, if possible. It actually was started by Bennett and his cell phone. I managed to snap a picture of Bennett this weekend on the stage looking at his cell, and I thought to myself, “this is how it all started 14 years ago.” Just look where we are today. Thank you Michael Hammer for telling Bennett that you received “lots of phone calls from crazy genealogists like you.”

So, where exactly are we today? In 2013, the industry crossed the millionth kit line. The second millionth kit was sold in early summer 2014 and the third million will be sold in 2015. No wonder we feel like a tidal wave has hit. It has.

Why now?

DNA has become part of national consciousness. Businesses advertise that “it’s in our DNA.” People are now comfortable sharing via social media like facebook and twitter. What DNA can do and show you, the secrets it can unlock is spreading by word of mouth. Spencer termed this the “viral spread threshold” and we’ve crossed that invisible line in the sand. He terms 2013 as the year of infection and based on my blog postings, subscriptions, hits, reach and the number of e-mails I receive, I would completely agree. Hold on tight for the ride!

Spencer talked about predictions for near term future and said a 5 year plan is impossible and that an 18 month plan is more realistic. He predicts that we will continue to see exponential growth over the next several years. He feels that genetic genealogy testing will be primary driver of growth because medical or health testing is subject to the clinical utility trap being experienced currently by 23andMe. The Big 4 testing companies control 99% of consumer market in US (Ancestry, 23andMe, Family Tree DNA and National Geographic.)

Spencer sees a huge international market potential that is not currently being tapped. I do agree with him, but many in European countries are hesitant, and in some places, like France, DNA testing that might expose paternity is illegal. When Europeans see DNA testing as a genealogical tool, he feels they will become more interested. Most Europeans know where their ancestral village is, or they think they do, so it doesn’t have the draw for them that it does for some of us.

Ancestry testing (aka genetic genealogy as opposed to health testing) is now a mature industry with 100% growth rate.

Spencer also mentioned that while the Genographic data base is not open access, that affiliate researchers can send Nat Geo a proposal and thereby gain research access to the data base if their proposal is approved. This extends to citizen scientists as well.

Michael Hammer

You’ll notice that Michael Hammer’s presentation, “Ancient and Modern DNA Update, How Many Ancestral Populations for Europe,” is missing from this wrapup. It was absolutely outstanding, and fascinating, which is why I’m writing a separate article about his presentation in conjunction with some additional information. So, stay tuned.

Testing, More Testing

It’s becoming quite obvious that the people who are doing the best with genetic genealogy are the ones who are testing the most family members, both close and distant. That provides them with a solid foundation for comparison and better ways to “drop matches” into the right ancestor box. For example, if someone matches you and your mother’s sister, Aunt Margaret, especially if your mother is not available to test, that’s a very important hint that your match is likely from your mother’s line.

So, in essence, while initially we would advise people to test the oldest person in a generational line, now we’ve moved to the “test everyone” mentality. Instead of a survey, now we need a census. The exception might be that the “child” does not necessarily need to be tested because both parents have tested. However, having said that, I would perhaps not make that child’s test a priority, but I would eventually test that child anyway. Why? Because that’s how we learn. Let me give you an example.

I was sitting at lunch with David Pike. were discussing autosomal DNA generational transmission and inheritance. He pulled out his iPad, passed it to me, and showed me a chromosome (not the X) that has been passed entirely intact from one generation to the next. Had the child not been tested, we would never have known that. Now, of course, if you’ll remember the 50% rule, by statistical prediction, the child should get half of the mother’s chromosome and half of the father’s, but that’s not how it worked. So, because we don’t know what we don’t know, I’m now testing everyone I can find and convince in my family. Unfortunately, my family is small.

Full genome testing is in the future, but we’re not ready yet. Several presenters mentioned full genome testing in some context. Here’s the bottom line. It’s not truly full genome testing today, only 95-96%. The technology isn’t there yet, and we’re still learning. In a couple of years, we will have the entire genome available for testing, and over time, the prices will fall. Keep in mind that most of our genome is identical to that of all humans, and the autosomal tests today have been developed in order to measure what is different and therefore useful genealogially. I don’t expect big breakthroughs due to full genome testing for genetic genealogy, although I could be wrong. You can, however, count me in, because I’m a DNA junkie. When the full genome test is below $1000, when we have comparison tools and when the coverage won’t necessitate doing a second or upgrade test a few years later, I’ll be there.

Thank you

I want to offer a heartfelt thank you to Max Blankfeld and Bennett Grenspan, founders of Family Tree DNA, shown with me in the photo below, for hosting and subsidizing the administrator’s conference – now for a decade. I look forward to seeing them, and all of the other attendees, next year.

I anticipate that this next decade will see many new discoveries resulting in tools that make our genealogy walls fall. I can’t help but wonder what the article I’ll be writing on the 20^th anniversary looking back at nearly a quarter century of genetic genealogy will say!

______________________________________________________________

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Tenth Annual Family Tree DNA Conference Day 3

Posted on October 13, 2014 by Roberta Estes

The internet in the hotel hasn’t gotten any faster, so I’ll just be providing highlights and today’s new announcements. More info, plus pictures, when I get home.

Sunday always begins with the ISOGG meeting hosted by Director, Katherine Borges.

This year’s meeting was especially touching, because Max Blankfeld and Bennett Greenspan, founders of Family Tree DNA, received plaques for their 10 years of investment and dedication and as a thank you for hosting the conferences for administrators.

Much of today’s agenda was focused on research, technical updates and new products and features.

This next year, Family Tree DNA’s focus is on three initiatives:

Customer service and feedback
Features – listen to citizen scientists and group administrators
New products and features to make genetic genealogy better for genealogists

Family Tree DNA is actively soliciting your feedback and has set up a special address for suggestions. This takes you to a google docs file where you enter your name, e-mail and 1000 characters maximum.

http://www.familytreedna.com/suggestions

Free Ancestry and 23andMe Uploads

In order to attract more uploads, which will, of course, give us more matches, Family Tree DNA is announcing free uploads from Ancestry and 23andMe, the v3 chip only, but with a string attached. The transferee can do the actual transfer for free, but they will only see their top 20 matches, only an initial and a last name, and will not be able to communicate with them unless they decide to pay $39 to join, or perhaps stated more accurately, to active all of the features of a paid transfer. However, in lieu of the $39 fee, you can also recruit 4 other people to upload their data, whether or not they actually pay the fee or not.

Search Feature

One of the reasons Family Tree DNA implemented the new trees was so that they could implement new search functionality. Soon, one will be able to search all public trees. I think this will benefit the community immensely, because it will allow people to see if people from their family lines are present in the data base, which will, hopefully, encourage testing.

Facilitating Communication

A new social media function called myGroups is being implemented to facilitate contact within groups. Today, projects and outside mailing lists and groups don’t fully overlap.

The example shown correlated to about 25% of a project group that was subscribed to an outside Yahoo group for discussion. MyGroups is designed to facilitate discussions that include all project members.

Furthermore, Ancestry’s My Family product became obsolete on September 30th, leaving many people with no place to discuss family lines and groups and share pictures and documents. The new myGroups is designed to replace some of that functionality within the context of a project. A project could be defined as an ancestral couple, for example or a surname project, or a haplogroup project. Of course, the discussions would be quite different for each type of myGroup. They are ready to launch this in an alpha state and if someone is excited about this and wants to volunteer, and can deal with a few bugs…then please drop Family Tree DNA a note.

News in the Field

We had many wonderful presentations, but my personal favorite was by Michael Hammer.

I can’t begin to do this topic justice without a real keyboard and a decent internet connection so I can upload lots of pictures. We now have 18 fully genome sequenced ancient DNA samples, which is, admittedly, just a smattering. However, if they are representative of the hunter-gatherer (Paleolithic) and early farmer (Neolithic) populations, then what we thought we knew about Y haplogroup R, J and others has just been turned upside down. And then, there is the teaser, like what is haplogroup C doing in Spain???

Oh, and want to know how much of your European DNA is ancestrally neolithic, hunter-gatherer, ancient northern european or later from the metallic age? That’s one of the features Family Tree DNA was asked about and I believe they said that was something they could probably do. I’m not positive if that means they will implement that feature, but I do know they’ll evaluate how difficult and accurate this would be to implement.

Join me in a few days, after I get home, when I promise, I’ll do Michael’s presentation justice. I’m so excited about ancient DNA and the secrets it’s unlocking!!!

Fun times ahead!

______________________________________________________________

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DNA Day with Ancestry

Posted on October 8, 2014 by Roberta Estes

For quite some time now, the genetic genealogy community has been beating the living tar out of Ancestry.com for not listening, among other things. Well, I’m here to say, they are listening. Now, what I can’t say is how much they are hearing. The jury is out and we will see. However, we are hopeful.

Ancestry invited a few of the leaders in the genetic genealogy field to come and meet with them this week. They dedicated the resources of eighteen of their scientists and executives to this meeting and they spent the day with us, sharing information about the science underlying their upcoming product changes and having frank discussions with the group.

This was a very cordial, informative and I think, team-building, experience, but there was far from uniform agreement. There was a great deal of discussion which I think helps everyone understand the position and reasoning of the other parties involved. Like anything else, it’s not as simple as one might hope.

Another important aspect of these meeting is that they serve to put faces with names and humanize the other people involved.

I also found it encouraging that most of the people at Ancestry are genealogists and utilize their own tools.

Tim Sullivan, CEO of Ancestry stopped by and talked with us for a few minutes. He asked us what we wanted, why and if we had any questions for him. He told us about his own genealogy experiences. And, we discovered, he does read our blogs. Tim is very actively engaged as is Ken Chahine, Senior Vice President and General Manager DNA, who is in many of the photographs because he was sitting at the end of the screen and was with us for the entire day.

I will be covering different aspects of the content of these meetings as time moves forward and as Ancestry’s new software version is implemented, but for now, I wanted to update you on the two burning questions in the genetic genealogy community.

These, as you might guess, were also the most contentious aspects of the entire meeting.

Will We Receive a Chromosome Brower?

I want to share with you readers that there is absolutely no question that Ancestry heard the message that we need a chromosome browser, loud, clear and uniformly from us. Ancestry is equally as adamant, it appears, as we are, that we don’t need one.

So, the short answer is no.

The longer answer is probably not.

Judy Russell, in comments to her article, “when less is more,” which I strongly encourage you to read, says about the chromosome browser:

“In my personal opinion, speaking only for myself and based solely on my own perceptions of the attitudes of some folks at AncestryDNA and not on any specific representations by anyone else, my judgment is that we may get a chromosome browser at AncestryDNA when hell freezes over.”

This was also followed by a comment about pigs flying…..plus, she took all the good phrases…not much left for me to say.

I think this pretty well sums it up.

I do want to discuss why Ancestry does not feel a chromosome browser is warranted. This topic was discussed directly and indirectly several times throughout the day. These concerns listed below are not necessarily in priority order based on discussions, because I couldn’t really discern a priority.

1. Given that Ancestry will hit the million kit DNA mark sometime in the first quarter of 2015, they feel that very few, a small percentage, of those people would ever utilize, or understand the results of a chromosome browser. Given that, they don’t feel it is a good investment of their engineering time to invest in something that few people, or a small percentage of the whole, will utilize.

2. Since Ancestry did not begin utilizing chromosome browsing in the beginning, they are concerned about privacy issues having to do with now introducing the feature to people who did not expect to have that to begin with.

3. Ancestry is concerned about unexpectedly and unintentionally revealing health information. For example, let’s say that today, a particular SNP is included in their information and is not known to be medically relevant. Next year, someone discovers that a particular SNP on chromosome 7 is connected to the genetic propensity for erectile dysfunction. Remember, a genetic propensity does NOT mean you have or will get the particular disease. In this case, of course, that would not apply to women.

Ancestry’s concern is that since they would have already been displaying that match on chromosome 7 between several people for months/years, the cow is proverbially out of the barn and closing the door at that point it a bit late, if possible at all.

Of course, as we pointed out to Ancestry, that’s the entire point of having testers sign a release, and both Family Tree DNA and 23andMe both deal with the same issue.

4. Ancestry feels that a chromosome browser would provide information to people that they should not be drawing conclusions from, and they are.

For example, as they showed us, there are areas in each person’s chromosome and their matches chromosomes that are what they call “pile up” areas. These are areas that we would call IBS, identical by state as opposed to IBD, identical by descent. Some of these pileup areas are so old that they could potentially be considered AIMs, or Ancestrally Informative Markers that harken back to continents like Africa, Asia or Europe.

This slide shows Cathy Ball, VP Genomics and Bioinformatics, showing me my own pileup areas. The two screens are a TV screen to the right where the colors resolved much better, and the larger screen where the display was larger.

What this shows you is that on the chart at left, I have one area that has a very large number of pileups, probably about 800 matches (out of my 12,500 total matches), two areas that have 400 each, two that have about 200. On the chart at right, the top of the chart is 25 match segments, so you can see that most of my matches fall below that. Ancestry feels that the higher matched segments are less relevant because they match to so many people, that they aren’t really indicative of shared ancestry in a genealogical timeframe.

And no, they did not tell me which chromosome these pileup segments are found on, and I’m DYING to know so that I can relate that to my ancestral chromosome mapping….but no cigar. It’s so frustrating that they know, they have the info, our info, but they won’t share it with us. I’m not referring here to the slide and my pileup, but the lack of segment information in general. I don’t know how that’s any worse that allowing customers to infer that a shakey leaf tree match is equivalent to a DNA match…..

Everyone has these pileup areas, which also means that they show up on your chromosome browser as matches. Ancestry is concerned that you will see three people, whether from a common genealogy line or not, who match on one segment and you will presume that they are genealogically related, when perhaps they aren’t, because their match is IBS from a pileup area.

Clearly, those of us who work in this field daily deal with IBS issues routinely, but Ancestry is concerned about the general consumer who doesn’t.

I suggested that the chromosome browser could be even more useful if they had a way to show but “grey out” those pileup areas, so we would be aware that their confidence is low, and to highlight the areas where the rarest alleles match, because those matches are most likely to indicate true genealogical matches. That suggestion met with polite silence.

Roberta’s Opinion

I do agree that many people won’t utilize the chromosome browser, but many people won’t utilize many of their services. That doesn’t prevent Ancestry from providing those services for those who want to utilize them. I’m fine with Ancestry making the Chromosome Browser part of a subscription kit so only subscribers have access, just like many of their data bases.

Unfortunately, without a chromosome browser, we are left with nothing concrete to base any matches on, nor the ability to utilize that information in conjunction with chromosome segment information from other companies to map our segments to various ancestors. The problem of incorrect ancestor attribution remains and will remain present in their matches.

They are changing their matching algorithm and in some ways, it will be improved, but in one way, I am gravely concerned that it will be worse. Ancestry will begin weighting various factors in calculating the match strength, and one of those factors will be the number of trees that list a particular ancestor. If you’ve just had a coronary…so did we. I thought one of the genetic genealogists was going to have the big one right there – they turned so red in the face.

A second confidence weighting factor will be the amount of source information for a particular tree which Ancestry feels helps judge the quality of the tree. In a sense, I agree, but attaching source information, perhaps incorrectly, to the wrong family, or having the wrong ancestor you’ve just attached source information to, is still the same large problem. Clearly, quality is not a matter of quantity, but just as clearly Ancestry cannot look at each tree individually and render an opinion, so they have to develop some automated methodology if they are going down this path.

Ancestry is trying to find ways to improve their matching and predictions of common ancestry. As time moves forward, I’ll be covering these developments. As someone in the meeting said, first steps first.

But back to the chromosome browser, my gut reaction to this is, and this is my opinion alone, that they don’t want to invest the development effort into something that will make the user experience more complex and may increase their customer support staff load to support and explain matching on a chromosome browser. I don’t think they believe the genealogy community has the ability to utilize and understand this type of tool. Ancestry is a genealogy marketing company. They want the user’s experience to be pleasant, easy and fulfilling…not difficult and certainly not upsetting.

Our message did not waiver, we need a chromosome browser and “trust me” simply won’t work.

The Y DNA and mtDNA Data Base

When Ancestry sent the invitation to this meeting, I had to wonder if they really thought through the fact that this meeting would occur less than a week after they decommissioned their Y and mtDNA data base.

Did they really want a group of people that were mad as wet hens arriving to meet with them? I fully expected to receive an “un-invitation” after my article and before the meeting, but I didn’t.

Without going into nitty-gritty detail, Ancestry indicates that the data base that held those results was literally on its last leg and they did not want to invest any money into something they was not bringing in any revenue and for a product they were no longer selling. I do believe that data base was indeed in its death throes because after the denial of service attack in June, it was no longer searchable.

In the ensuing discussion, the genetic genealogy community provided a number of alternative scenarios both within and outside of Ancestry as a way to salvage the information in that database. Ancestry has agreed to take the matter under consideration internally and discuss the various options. They made no promises, but I personally find it very encouraging that they are willing to discuss the matter and reconsider.

I told them I’d like nothing more than to write a retraction article that says that Ancestry did not, after all, burn the DNA courthouse.

In the same vein, I asked if they had any plans to decommission the Sorenson data base at www.smgf.org and they indicated that they do not have any plans at this point to do that. Obviously, nothing is forever, and they could reconsider in the future but at least it appears that resource is safe for now and adding the Y and mtDNA records from Ancestry into that data base was one option discussed.

In Conclusion

I do feel this was a productive meeting. The scientific aspects of having a large data base to draw from are quite interesting and I’ll be sharing some those in upcoming articles. Some of the best conversations took place beside the proverbial “water cooler.” I am hopeful that we made progress, or at least thawed the ice a little on the issues so critical for the genetic genealogy community, but time will tell. In a way, I felt like this was a United Nations type of meeting where everyone leaves with a better understanding.

______________________________________________________________

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More Ancient DNA Samples For Comparison

Posted on October 4, 2014 by Roberta Estes

Felix Chandrakumar has prepared and added three additional ancient DNA kits to GedMatch. Thanks Felix! This is a wonderful service you’re performing for the genetic genealogy community!

The Linearbandkeramik (LBK) sample, also referenced as “Stuttgart,” reflecting where it was discovered in Germany. This individual was an early farmer dating from about 7,500 years ago and was one of the samples analyzed for the paper, Ancient genomes suggest three ancestral populations for present-day Europeans. Kit F999916
The La Brana-Arintero sample from Leon, Spain, about 7000 years old, represents a pre-agricultural European human genome – in other words, before the agriculturists from the Near East arrived. In an article at Science Daily, they have reconstructed his face. Original academic article available here. Kit F999915
The Mal’ta sample, from Siberia, about 24,000 years of age. The results were discussed in article, Native American Gene Flow – Europe?, Asia and the Americas, and the original article is available here. Kit F999914

These kits, along with the ones listed earlier, give us the opportunity to compare our own DNA with that of ancient people in specific populations. It’s like taking a step back in time and seeing if we carry any of the same small segments as these people did – suggesting of course that we descend from the same population.

This Ancient European DNA map by Richard Stevens shows the European locations where ancient DNA has been retrieved.

Recent discussion has focused on determining what matches to these specimens actually mean to genetic genealogists today. We obviously don’t have that answer at this point. We know that, due to their age, these samples are not close relatives in terms of genealogy generations, but in some cases, we find that we have matches far larger than one would expect to be found utilizing the 50% washout per generation math.

Endogamy, especially in a closed population such as Native Americans is certainly one explanation. That doesn’t explain the European matches however – either to Anzick, the Native American specimen, nor Europeans to the European samples. The higher no-call rate in the autosomal files can contribute as well, but wouldn’t account for all matches. In some cases, maybe everyone carries the same DNA because the population carries that DNA in very high rates – but the population carries the DNA in very high rates because the ancient ancestors did as well…so this is a bit of circular logic. All that said, we’re still left wondering what is real and what is Memorex, so to speak?

Ancient DNA is changing our understanding of the human past, and that of our ancestors. It allows us a connection to the ancient people that is tangible, parts of them found in us today, as unbelievable as it seems.

When Svante Paabo discovered that modern Europeans all carry pieces of Neanderthal DNA, he too was struck by what I’ll call “the disbelief factor,” thinking, of course, that it can’t possibly be true. He discussed this at length in his book, Neanderthal Man, In Search of Lost Genomes, and the steps taken by his team to prove that the matches weren’t in error or due to some problem with the ancient genome reconstruction process. Indeed, all Europeans and Asians carry both Neanderthal and Denisovan DNA, and by the same process of the DNA being carried by the entire population at one point, which must be the avenue for contemporary humans to carry other ancient DNA as well. As we find individual matches to small pieces of DNA with these matches, how much of that is “real” versus convergence or a result of no-calls in the ancient files?

In that vein, I find this article from Dienekes Anthropology Blog quite interesting, found in the ASHG Titles of Interest from the upcoming Conference in October in San Diego, CA.

Reducing pervasive false positive identical-by-descent segments detected by large-scale pedigree analysis. E. Y. Durand, N. Eriksson, C. Y. McLean.

“Analysis of genomic segments shared identical-by-descent (IBD) between individuals is fundamental to many genetic applications, from demographic inference to estimating the heritability of diseases. A large number of methods to detect IBD segments have been developed recently. However, IBD detection accuracy in non-simulated data is largely unknown. In principle, it can be evaluated using known pedigrees, as IBD segments are by definition inherited without recombination down a family tree. We extracted 25,432 genotyped European individuals containing 2,952 father-mother-child trios from the 23andMe, Inc. dataset. We then used GERMLINE, a widely used IBD detection method, to detect IBD segments within this cohort. Exploiting known familial relationships, we identified a false positive rate over 67% for 2-4 centiMorgan (cM) segments, in sharp contrast with accuracies reported in simulated data at these sizes. We show that nearly all false positives arise due to allowing switch errors between haplotypes when detecting IBD, a necessity for retrieving long (> 6 cM) segments in the presence of imperfect phasing. We introduce HaploScore, a novel, computationally efficient metric that enables detection and filtering of false positive IBD segments on population-scale datasets. HaploScore scores IBD segments proportional to the number of switch errors they contain. Thus, it enables filtering of spurious segments reported due to GERMLINE being overly permissive to imperfect phasing. We replicate the false IBD findings and demonstrate the generalizability of HaploScore to alternative genotyping arrays using an independent cohort of 555 European individuals from the 1000 Genomes project. HaploScore can be readily adapted to improve the accuracy of segments reported by any IBD detection method, provided that estimates of the genotyping error rate and switch error rate are available.”

I’m pleased to see that they are addressing smaller segments, in the 2cM-4cM range, because those are the ranges some are finding in matches to these ancient genomes. A few matches are even larger.

Of course, all of this ancient matching has caused an upsurge in interest in the cultures and populations of these ancient people whose DNA we carry.

I find this graphic very interesting from the paper, Toward a new history and geography of human genes informed by ancient DNA, just published this month, by Joseph Pickrell and David Reich. This map, which shows the population movement into and out of geographic regions of the world in the past, is especially interesting in that several back migrations are shown into Africa. I’ve never seen the “history of the world in population migration” summed up quite so succinctly before, but it helps us understand why certain DNA is found in specific locations.

As we find and fully sequence additional ancient DNA specimens, we’ll be able to better understand how the ancient populations were related to each other, and then, how we descend from each of them.

This is a fascinating age of personal discovery!

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