It has been a wonderful week for those of us following ancient DNA full genome sequencing, because now we can compare our own results to those of the ancient people found whose DNA has been fully sequenced, including one Native American.
Felix Chandrakumar has uploaded the autosomal files of five ancient DNA specimens that have been fully sequenced to GedMatch. Thanks Felix.
When news of these sequences first hit the academic presses, I was wishing for a way to compare our genomes – and now my wish has come true.
Utilizing GedMatch’s compare one to all function, I ran all of the sequences individually and found, surprisingly, that there are, in some cases, matches to contemporary people today. I dropped the cM measure to 1 for both autosomal and X.
Please note that because these are ancient DNA sequences, they will all have some segments missing and none can be expected to be entirely complete. Still, these sequences are far better than nothing.
1. Montana Anzick at GedMatch
This is the only clearly Native American sample.
9-27-2014 – Please note that kit F999912 has been replaced by kit F999913.
10-23-2014 – Please note that kit F999913 has been replaced by kit F999919.
No matches at 1cM in the compare to all. This must be because the SNP count is still at default thresholds, in light of information discovered later in this article.
Update – as it turns out, this kit was not finished processing when I did the one to one compare. After it finished, the results were vastly different. See this article for results.
2. Paleo Eskimo from Greenland at GedMatch
Thirty-nine matches with segments as large at 3.8. One group of matches appears to be a family. One of these matches is my cousin’s wife. That should lead to some interesting conversation around the table this holiday season! All of these matches, except 1, are on the X chromosome. This must be a function of these segments being passed intact for many generations.
I wrote about some unusual properties of X chromosomal inheritance and this seems to confirm that tendency in the X chromosome, or the matching thresholds are different at GedMatch for the X.
3. Altai Neanderthal at GedMatch
One match to what is obviously another Neaderthal entry.
4. Russian Causasus Neanderthal at GedMatch
Another contribution from the Neanderthal Genome Project.
5. Denisova at GedMatch
Two matches, one to yet another ancient entry and one to a contemporary individual on the X chromosome.
But now, for the fun part.
Before I start this section, I want to take a moment to remind everyone just how old these ancient segments are.
- Anzick – about 12,500 years old
- Paleo-Eskimo – about 4,000 years old
- Altai Neanderthal – about 50,000 years old
- Russian Caucasus Neanderthal – about 29,000 years old
- Denisova – about 30,000 years old
In essence, the only way for these segments to survive intact to today would have been for them to enter the population of certain groups, as a whole, to be present in all of the members of that group, so that segment would no longer be divided and would be passed intact for many generation, until that group interbred with another group who did not carry that segment. This is exactly what we see in endogamous populations today, such as the Askenazi Jewish population who is believed, based on their common shared DNA, to have descended from about 350 ancestors about 700 years ago. Their descendants today number in the millions.
So, let’s see what we find.
I compared by own kit at GedMatch utilizing the one to one comparison feature, beginning with 500 SNPs and 1cM, dropping the SNP values to 400, then 300, then 200, until I obtained a match of some sort, if I obtained a match at all.
Typically in genetic genealogy, we’re looking for genealogy matches, so the default matching thresholds are set relatively high. In this case, I’m looking for deep ancestral connections, if they exist, so I was intentionally forcing the thresholds low. I’m particularly interested in the Anzick comparison, in light of my Native American and First Nations heritage.
The definition of IBS, identical by state, vs IBD, identical by descent segments varies by who is talking and in what context, but in essence, IBD means that there is a genealogy connection in the past several generations.
IBS means that the genealogy connection cannot be found and the IBS match can be a function of coming from a common population at some time in the past, or it can be a match by convergence, meaning that your DNA just happened to mutate to the same state as someone else’s. If this is the case, then you wouldn’t expect to see multiple segments matching the same person and you would expect the matching segments to be quite short. The chances of hundreds of SNPs just happening to align becomes increasingly unlikely the longer the matching SNP run.
So, having said that, here are my match results.
I had 2 matches at 400 SNPs, several at 300 and an entire list at 200, shown below.
|Chr||Start Location||End Location||Centimorgans (cM)||SNPs|
In my case, I’m particularly fortunate, because my mother tested her DNA as well. By process of elimination, I can figure out which of my matches are through her, and then by inference, which are through my father or are truly IBS by convergence.
I carry Native heritage on both sides, but my mother’s is proven to specific Native ancestors where my father’s is only proven to certain lines and not yet confirmed through genealogy records to specific ancestors.
Because I had so many matches, quite to my surprise, I also compared my mother’s DNA to the Anzick sample, combined the two results and put them in a common spreadsheet, shown below. White are my matches. Pink are Mom’s matches, and the green markers are on the segments where we both match the Anzick sample, confirming that my match is indeed through mother.
We’ll work with this information more in a few minutes.
At 200 SNP level, 2 segments.
My mother matches on 9 segments, but neither of the two above, so they are either from my father’s side or truly IBS by convergence.
Neither my mother nor I have any matches at 100SNPs and 1cM.
I have one match.
|Chr||Start Location||End Location||Centimorgans (cM)||SNPs|
My mother matches 2 segments at 100 SNPs but neither match is the same as my segment.
Matching to Ancestral Lines
I’ve been mapping my DNA to specific ancestors utilizing the genealogy information of matches and triangulation for some time. This consists of finding common ancestors with your matches. Finding one person who matches you and maps to a common ancestor on a particular segment consists of a hint. Finding two that share the same ancestral line and match you and each other on the same segment is confirmation – hence, the three of you triangulate. More than three is extra gravy:)
I have also recorded other relevant information in my matches file, like the GedMatch Native chromosomal comparisons when I wrote “The Autosomal Me” series about hunting for my Native chromosomal segments.
So, after looking at the information above, it occurred to me that I should add this ancestral match information to my matches spreadsheet, just for fun, if nothing else.
I added these matches, noted the source as GedMatch and then sorted the results, anxious to see what we might find. Would at least one of these segments fall into the proven Native segments or the matches to people who also descend from those lines?
What I found was both astonishing and confusing….and true to form to genealogy, introduced new questions.
I have extracted relevant matching groups from my spreadsheet and will discuss them and why they are relevant. You can click on any of the images to see a larger image.
This first set of matches is intensely interesting, and equally as confusing.
First, these matches are to both me and mother, so they are confirmed through my mother’s lines. In case anyone notices, yes, I did switch my mother’s line color to white and mine to pink to be consistent with my master match spreadsheet coloration.
Second, both mother and I match the Anzick line on the matches I’ve utilized as examples.
Third, both 23andMe and Dr. Doug McDonald confirmed the segments in red as Native which includes the entire Anzick segment.
Fourth, utilizing the Gedmatch admixture tools, mother and I had this range in common. I described this technique in “The Autosomal Me” series.
Fifth, these segments show up for two distinct genealogy lines that do not intersect until my grandparents, the Johann Michael Miller line AND the Acadian Lore line.
Sixth, the Acadian Lore line is the line with proven Native ancestors.
Seventh, the Miller line has no Native ancestors and only one opportunity for a Native ancestor, which is the unknown wife of Philip Jacob Miller who married about 1750 to a women rumored to be Magdalena Rochette, but research shows absolutely no source for that information, nor any Rochette family anyplace in any proximity in the same or surrounding counties to the Miller family. The Miller’s were Brethren. Furthermore, there is no oral history of a Native ancestor in this line, but there have been other hints along the way, such as the matching segments of some of the “cousins” who show as Native as well.
Eighth, this makes my head hurt, because this looks, for all the world, like Philip Jacob Miller who was living in Bedford County, PA when he married about 1750 may have married someone related to the Acadian lines who had intermarried with the Micmac. While this is certainly possible, it’s not a possibility I would ever have suspected.
Let’s see what else the matches show.
In this matching segment Mom and I both match Emma, who descends from Marie, a MicMac woman. Mom’s Anzik match is part of this same segment.
In this matching segment, Mom and I both match cousin Denny who descends from the Lore line who is Acadian and confirmed to have MicMac ancestry. Mom’s Anzik segments all fit in this range as well.
In this matching segment, cousin Herbie’s match to Mom and I falls inside the Anzick segments of both Mom and I.
More matching to the proven Miller line.
This last grouping with Mom is equally as confusing at the first. Mom and I both match cousin Denny on the Lore side, proven Acadian.
Mom and I both match the Miller side too, and the Anzik for both of us falls dead center in these matches.
There are more, several more matches, that also indicate these same families, but I’m not including them because they don’t add anything not shown in these examples. Interestingly enough, there are no pointers to other families, so this isn’t something random. Furthermore, on my father’s side, as frustrating as it is, here are no Anzick matches that correlate with proven family lines. ARGGHHHHHH……
On matches that I don’t share with mother, there is one of particular interest.
You’ll notice that the Anzik and the Paleo-Greenland samples match each other, as well as me. This is my match, and by inference, not through mother. Unfortunately, the other people in this match group don’t know their ancestors or we can’t identify a common ancestor.
Given the genetic genealogy gold standard of checking to see if your autosomal matches match each other, I went back to GedMatch to see if the Paleo-Greenland kit matched the Clovis Anzik kit on this segment, and indeed, they do, plus many more segments as well. So, at some time, in some place, the ancestors of these two people separated by thousands of miles were related to each other. Their common ancestor would have either been in Asia or in the Northern part of Canada if the Paleo people from Greenland entered from that direction.
Regardless, it’s interesting, very interesting.
What Have I Learned?
Always do experiments. You never know what you’ll find.
I’m much more closely related to the Anzick individual than I am to the others. This isn’t surprising given my Native heritage along with the endogamous culture of the Acadians.
My relationship level to these ancient people is as follows:
|Lived Years Ago||Relatedness||Comments|
|Montana Anzick||12,500||107.4cM at 200 SNP level||Confirmed to Lore (Acadian) and Miller, but not other lines|
|Greenland Paleo||4,000||2.3cM at 200 SNP level||No family line matches, does match to Anzick in one location|
|Altai Neanderthal||50,000||2.1cM at 200 SNP level||No family line matches|
|Denisovan||30,000||1.2cM at 200 SNP||No family line matches|
The Lores and the Millers
Looking further at the Lore and Miller lines, there are only two options for how these matching segments could have occurred. There are too many for them all to be convergence, so we’ll have to assume that they are indeed because we shared a common population at some time and place.
The nature of how small the segments are testify that this is not a relatively recent common ancestor, but how “unrecent” is open to debate. Given that Neanderthal and Denisovan ancient segments are found in all Europeans today, it’s certainly possible for these segments to be passed intact, even after thousands of years.
The confirmations to the Lore line come through proven Lore cousins and also through other proven Acadian non-specific matches. This means that the Acadian population is highly endogamous and when I find an Acadian match, it often means that I’m related through many ancestors many times. This, of course, increases the opportunity for the DNA to be passed forward, and decreases the opportunity for it to be lost in transmission, but it also complicates the genealogy greatly and makes determining which ancestor the DNA segment came from almost impossible.
However, I think we are safe to say the segments are from the Acadian population, although my assumption would be that they are from the Native Ancestors and not the French, given the high number of Anzick matches, Anzick being proven to be Native. Having said that, that assumption may not be entirely correct.
The Miller line is relatively well documented and entirely from Germany/Switzerland, immigrating in the early 1700s, with the exception of the one unknown wife in the first generation married in the US. Further examination would have to be done to discover if any of the matches came through Johann Michael Miller’s sons other than Philip Jacob Miller, my ancestor. There are only three confirmed children, all sons. If this segment shows up in Johann Michael Miller’s line not associated with son Philip Jacob Miller, then we would confirm that indeed the segment came from Europe and not a previously unknown Native or mixed wife of Philip Jacob.
So, what’s the bottom line here? I know far more than I did. The information confirms, yet again, the Acadian Native lines, but it introduces difficult questions about the Miller line. I have even more tantalizing questions for which I have no answers today, but I tell you what, I wouldn’t trade this journey along the genetic pathway with all of its unexpected bumps, rocks, slippery slopes and crevices for anything!! That’s why it’s called an adventure!