Ancient DNA Matching – A Cautionary Tale

egg

I hope that all of my readers realize that you are literally watching science hatch.  We are on the leading, and sometimes bleeding edge, of this new science of genetic genealogy.  Because many of these things have never been done before, we have to learn by doing and experimenting.  Because I blog about this, these experiments are “in public,” so there is no option of a private “oops.”  Fortunately, I’m not sensitive about these kinds of things.  Plus, I think people really enjoy coming along for the ride of discovery.  I mean, where else can you do that?  It’s really difficult to get a ride-along on the space shuttle!

One of the best pieces of advice I ever got was from someone who was taken from my life far too early.  I had made a mistake of some sort…don’t even remember what…and he gave me a card that said, “The only people who don’t make mistakes are the people who don’t try.”

This isn’t an “oops” moment.  More like an “aha” moment.  Or more precisely, a “huh” moment.  It falls in the “Houston, we’ve got a problem” category.

So, this week’s new discovery is that there seems to be some inconsistency in the matching to the Anzick kit at GedMatch.  Before I go any further, I want to say very clearly that this is in no way a criticism of anyone or any tool.  Every person involved is a volunteer and we would not be making any of these steps forward, including a few backwards, without these wonderful volunteers and tools.

I have reached out to the people involved and asked for their help to unravel this mystery, and I’m sharing the story with you, partly so you can understand what is involved, and the process, partly so that you don’t inadvertently encounter the same kinds of issues and draw unrealistic or incorrect conclusions, and partly so you can help.  If there has been any common theme in all of my articles in the past week or so about the ancient DNA articles, it has been that we really don’t understand what conclusions to draw yet…and we still don’t.  So don’t.

Let’s introduce the players here.

The Players

Felix Chandrakumar has very graciously prepared the various ancient DNA files and uploaded them to GedMatch.  Felix has written a number of DNA analysis tools as well.

John Olson is one of the two volunteers who created and does everything at Gedmatch, plus works a full time job.  By the way, in case you’re not aware, this is a contribution site, meaning they depend on your financial contributions to function, purchase hardware, servers, etc.  If you use this site, periodically scroll down and click on the donate button.  We, as a community, would be lost without John and his partner.

David Pike is a long time genetic genealogist who I have had the pleasure of working with on a number of Native American and related topics over the years. He also has created several genetic genealogy tools to deal with autosomal DNA. David prepared the Anzick files for some private work we were doing several months ago, so he has experience with this DNA as well.  Dr. Pike has a great deal of experience analyzing the endogamous population of Newfoundland, which is also admixed with Native Americans.

Marie Rundquist, also a long time genetic genealogist who specializes in both technology and Acadian history along with genetic genealogy.  Acadians are proven to be admixed with Native Americans.  Marie shares my deep interest and commitment to Native American study and genetics.  Furthermore, Marie and I also share ancestors and co-administer several related projects.   As you might imagine, Marie and I took this opportunity immediately to see if she and her mother share any of Anzick’s segments with me and my mother.

So, a big thank you to all of these people.

The Mystery

When Felix originally e-mailed me about the Anzick kit being uploaded to GedMatch, as you might imagine, I stopped doing whatever I was doing and immediately went to study Anzick and the other ancient DNA kits.

I wrote about this experience in the article, “Utilizing Ancient DNA at GedMatch.”

As part of that process, I not only ran Anzick’s kit utilizing the “one to many” option, I also compared my own kit to Anzick’s.  My proven Native lines descend through my mother, so I ran her kit against Anzick’s as well, at the same thresholds, and I combined the two results to see where mother and I overlapped.

I showed these overlaps in the article, along with which genealogy lines they matched by utilizing my ancestor matching spreadsheet.

Everything was hunky dory…for then.

Day 2

The next day, I received a note from Felix that the Anzick kit may not have been fully tokenized at GedMatch previously, so I reran the Anzick “one to all” comparison and wrote about those results in the second article, “Analyzing the Native American Clovis Ancient Results.”  Because it wasn’t yet fully processed originally, the second results produced more matches, not fewer.

I wasn’t worried about the one to one comparison of Anzick to my own kit, because one to one comparisons are available immediately, while one to many comparisons are not, per the GedMatch instructions.

“Once you have loaded your data, you will be able to use some features of the site within a minute or so. Additional batch processing, which usually takes a couple of days, must complete before you can use some of the tools comparing you to everyone in the data pool.”

So, everything was stlll hunky dory.

Day 3

The next day, Marie and I had a few minutes, sometime between 2 and 3AM, and no, I’m not kidding.  We decided to compare results.  I decided it would be quicker to run the match again at GedMatch than to sort through my Master spreadsheet, into which I had copied the results and added other information.  So, I did a second download of the Anzick comparison, utilizing the exact same thresholds (200 SNPs, 2cM, and the rest left at the default,) and added them to a spreadsheet that Marie and I were passing back and forth, and sent them to Marie.  I noticed that there seemed to be fewer matches, but by then it was after 3AM and I decided to follow up on that later.

Not so hunky dory…but I didn’t know it yet.

Day 4

The following day, Dr. Ann Turner (MD), also a long-time genetic genealogist, posted the following comment on the article.

“These results, finding “what appear to be contemporary matches for the Anzick child”, seemed very counter-intuitive to me, so I asked John Olson of GEDMatch to look under the hood a bit more. It turns out the ancient DNA sequence has many no-calls, which are treated as universal matches for segment analysis. Another factor which should be examined is whether some of the matching alleles are simply the variants with the highest frequency in all populations. If so, that would also lead to spurious matching segments. It may not be appropriate to apply tools developed for genetic genealogy to ancient DNA sequences like this without a more thorough examination of the underlying data.”

I had been aware of the no-calls due to the work that Dr. David Pike did back in March with the Anzick raw data files, but according to David, that shouldn’t affect the results.

Here’s what Dr. Pike, a Professor of Mathematics, had to say:

“Yes, these forensic samples have very high No-Call rates, which may give rise to more false matches than we would normally experience.  Also, be aware that false matches are more prone to occur when using reduced thresholds (such as 100 SNPs and 1 cM) and unphased data.  In this case I don’t think there’s any way around using low thresholds, simply because we’re looking for very small blocks of DNA (probably nobody alive today will have any large matching blocks with the Anzick child).

On the assumption that there will be a nearly constant noise ratio, meaning that most people will have about the same number of false matches with the Anzick child, those who are from the same gene pool should have an increased number of real matches.  So by comparing the total amount of matching DNA, it ought to be possible to gauge people’s affinity with Anzick’s gene pool.”

Here are Felix’s comments about no-calls as well:

“Personally, no calls are fine as long as there are more SNPs matching above the threshold level because the possibility of errors occurring exactly on no-call positions for all the matches in all their matching segments is impossible.”

Courtesy of Felix, we’ll see an example of how no calls intersperse in  a few minutes.

If no-calls were causing spurious matches in the Anzick kit, you’d expect to see the same for the other ancient DNA kits.  I know that the Denisovan and Neanderthal kits also have many no-calls, and based on the nature of ancient DNA, I’m sure all of them do.  So, if no calls are the culprit, they should be affecting matches to the other kits in the same way, and they aren’t.

Hunky-doryness is being replaced by a nonspecific nagging feeling…same one I used to get when my teenagers were up to something.

Day 5

A day or so later, Felix uploaded file F999913 to replace F999912 with the complete SNPs from all of the companies.  The original 999912 kit only included the SNP locations utilized by Family Tree DNA.  Felix added the SNPs utilized by 23and Me not utilized at Family Tree DNA, and the ones from Ancestry as well.  This is great news for anyone who tested at those two companies, but I had utilized my kit from Family Tree DNA, so for me, there should be no difference at all.

I later asked Felix if he had changed anything else in the file, and he said that he had not.  He provided extensive documentation about what he had done.

I waited until kit F999912 was deleted to be sure tokenizing was complete for F999913 and re-compared the data again.  As expected, Anzick’s one to all had more matches than before, because additional people were included due to the added SNPs from 23andMe and Ancestry.

Some of Anzick’s matches are in the contemporary range, at 3.1 estimated generations, with the largest cM segment of 22.8 and total cMs of 202.8.

anzick 999913

These relatively large matches cause Felix to question whether the sample is actually ancient, based on these relatively large segments.  I addressed my feelings on this in the article, Ancient DNA Matches – What Do They Mean?

Marie and Dr. Pike, both with extensive experience with admixed populations addressed this as well.  Marie commented,

“Native DNA found in the Anzick sample hasn’t changed all of that much and may still be found in modern, Native American populations, and that if people have Native American ancestry, they’ll match to it.”

Dr. Pike says:

“I agree with Marie on this… within endogamous populations, there is an increased likelihood of blocks of DNA being preserved over lengthy time frames.  Moreover, even if a block of DNA gets cut up via recombination, within an endogamous population the odds of some parts of the block later reuniting in a person’s DNA are higher than otherwise.  And it exaggerates the closeness of [the] relationship that gets predicted when comparing people.

I have seen something similar within the Newfoundland & Labrador Family Finder Project, whereby lots of people are sharing small blocks of DNA, likely as a result of DNA from the early colonists still circulating among the modern gene pool.

As an anecdotal example, I have a semi-distant relative (with ancestry from Newfoundland) at 23andMe who shares 3 blocks of DNA with my father, 2 with my mother and 5 five me.  As you can imagine, the relative is predicted to be a closer cousin to me than she is to either of my parents!

It doesn’t take an endogamous or isolated population to see this effect.

It can also happen in families involving cousin marriages too, although that would be more pronounced and not quite the same thing as we’re discussing with respect to ancient DNA.”

This addition of other companies SNPs should not affect my matches with Anzick because my kits are both from FTDNA and won’t utilize the added SNPs.

However, I ran my and my mother’s matches again, and we had a significantly different outcome than either of the previous times.

I utilized the same threshold for all downloads and those are the only values I changed – 200 SNPs and 2cM, leaving the other values at default, for all Anzick comparisons to my mother and my kits.

I am not hunky-dory anymore.

The Heartburn

These matches, which should be the same in all three downloads, produced significantly different results.

Here are the number of matches at the same threshold comparing me and Mom to the Anzick file:

Me and Anzick

  • original download 999912 – 47 matches
  • second download 999912 – 21 matches
  • 999913 – 35 matches

Mom and Anzick

  • original download 999912 – 63
  • second download 999912 – 37
  • 999913 – 36

And no, the 36 /35 that mom and I have for 999913 are not all the same.

Kit Number Matches Between Me, Mother and Anzick
#1-F999912 original download 19
#2-F999912 second download 6
#3-F999913 11

Of those various downloads, the following grid shows which ones matched each other.

#1 to #2 #2 to #3 #1 to #3 All 3
# of Matches 6 2 3 2

So, comparing the first download to the last download, of the 19 original matches, we lost 16 matches.  In the third download, we gained 8 matches and only 3 remained as common matches. So of 30 total matches between my mother, myself and Anzick, in two downloads that should have been exactly the same, only 3 matches held, or 10%.

Obviously, something is wrong, but what, and where?  At that point, I asked Marie to download her and her mother’s results again too, and she experienced the same issue.

Clearly a problem exists someplace.  That’s the question I asked Felix, John and David to help answer.

I realize that this spreadsheet it very long, and I apologize, but I think this issue is much easier to see visually.  I’ve compiled the matches by color and shade to make looking at them relatively easy.

My matches to the Anzick kit are in shades of pink – the first match download being the lightest and the last one to kit F999913 being the darkest.  Mother is green, same shading scheme.

The three columns to the right show the matching segments for each download – shaded in green.  You can easily see which ones line up, meaning which ones match consistently across all three downloads.  There aren’t many.  They should all match.

anzick me mom problem

Obviously this led to many questions that I asked of the various players involved.

My first thought was that perhaps a matching algorithm change occurred in GedMatch, but John assured me that he had made no changes.

Next question was whether or not Felix changed something other than adding the 23andMe and Ancestry SNPs.  He had not.

Felix was kind enough to explain about bunching and to do some analysis on the files.

“When you have low thresholds, make sure you don’t allow errors. For example, at 200 SNPs, the default ‘Mismatch Evaluation window’ and in GEDMatch is same as SNP threshold and ‘Mismatch-Bunching limit’ is half of mismatch evaluation window. So, at 200 cM, you are allowing 1 error every 100 SNPs apart from no-calls.

I did some analysis on your phased mother’s kit, PF6656M1 so that at least we know that it is an IBD for one generation.  The spreadsheet (below) are segments I found at 2 cM/200 SNPs threshold without allowing any errors.”

Kit PF6656M1 is one single kit created by phasing my data against my mother’s so that we don’t have to run both kits.  I had not utilized the phased kit previously, so I was interested in his results.

felix anzick

The results above confirm chromosome matches, 2, 17, 19 and 21, but introduce a new match on chromosome 4.  This match was present in the original download, but not in the second or third download, so once again, we have disparate data, except the thresholds Felix used were at a different level.

One of the more interesting things that Felix included is the no-call match information, the three columns to the right.  I want to show what the no-calls look like.  There are not huge segments that are blank and are being called as matches because they are no-calls, when they shouldn’t be.  No calls are scattered like salt and pepper.  In fact, no calls happen in every kit and they are called as matches so they don’t in fact disrupt a valid match string, potentially making it too small to be considered a match.  Of course, ancient DNA has more no-calls that contemporary DNA kits.

Below are the first few match positions from chromosome 2 where mother, Anzick and I have a confirmed match across all downloads.  The genotype shows you that both kits match.

felix no calls

For consistency, I ran the same kits that Felix ran, PF6656M1 and F999913, with the original thresholds I had used, and found the following:

Chr Start Location End Location Centimorgans (cM) SNPs
1 31358221 33567640 2.0 261
2 218855489 220351363 2.4 253
4 1957991 3571907 2.5 209
5 2340730 2982499 2.3 200
17 53111755 56643678 3.4 293
19 46226843 48568731 2.2 250
21 35367409 36761280 3.7 215

This introduces chromosomes 1 and 5, not shown above.   The chromosome 1 match was shown in the first and second download, but not the third, and the chromosome 5 match was shown in the first download only, but not the second or third.

Can you see me beating my head against the wall yet??

In a fit of apparent insanity, I decided to try, once again, an individual download of Anzick compared to my mother and to me, but not utilizing the phased kit – the original F6656 and F9141, and at the original thresholds, for consistency.  I wanted to see if the matches were the same now as they were a day or so ago.  They should be exact.  This first one is mine.

me second 999913

What you should see are two identical downloads.  I have color coded the rows so you can see easily – and what you should see are candy-cane stripes – one red and one white for every match location.

That’s not what we’re seeing.  The kits are the same, the match parameters are the same, but the results are not.  Once again, the downloads don’t match.

I did another match on mother and Anzick, and her results were consistent between the first and second match to kit F999913.

mom second 999913

The begs the next question.  Have mother’s results always been consistent, suggesting a problem with my kit?

I sorted all of her downloads, and no, they are not consistent, except for the first and second download matches to kit F999913, shown above.  The inconsistencies show up in both mother and my kits, although not in the same locations.  Recall also that Marie had the same issue.

In Summary

Something is wrong, someplace.  I know that sounds intuitively obvious – NOW.  But it wasn’t initially and I wouldn’t even have suspected a problem without running the second and third downloads, quite unintentionally.  Most people never do that, because once you’ve done the match, you have no reason to ever match to that particular person again.  Given that, you’ll never know if a problem exists.

So, the only Anzick GedMatch matches I have any confidence in at all, at this point, are the few that are consistent between all of the downloads, and I didn’t add the fourth download into the mix.  I don’t’ see any point because I’ve pretty much concluded that until we determine where the issue resides, that I won’t have confidence in the results.

The next question that comes to mind, and that I can’t answer, is whether or not this issue is present in contemporary matching kits – or if this is somehow an ancient DNA problem – although I don’t know quite how that could be – since matching is matching.

I haven’t saved any matches that I’ve run to other people in spreadsheets, so I can’t go back and see if a GedMatch match today produces the exact same results as a previous match.

Clearly there is no diagnosis or solution in this summary.  We are not yet hunky dory.

What You Can Do

  1. Run your Anzick and ancient DNA matches multiple times, at the same exact thresholds, on different days, to see if your results are consistent or inconsistent. Same kit, same thresholds, the results should be identical.
  2. If you have some saved GedMatch matches with contemporary people, and you are positive of the match thresholds used, please run them again to see if the results are identical. They should be.
  3. No drawing of or jumping to conclusions, please, especially about ancient DNA:) It’s a journey and we are fellow pilgrims!

If your results are not consistent, please document the problem and let the appropriate person know.  I don’t want to overwhelm John at GedMatch but I’m concerned at this point that the problem may not be isolated to ancient DNA matching since the issue seems to extend to Marie’s results as well.

If your results, especially to Anzick, from previous matches to now are consistent, that’s worth knowing too.  Please add a comment to that effect.

Thoughts and ideas are welcome.

deCODEme Consumer Tests Discontinued

decodeme

I hate to see players, especially ones with good products, exit the marketplace, but sadly, that’s what deCODEme genetics is doing.  Initially, they had an excellent, albeit expensive, ethnicity product.  The company filed bankruptcy in 2008/2009 and has been twice sold since that time.  This upheaval occurred about the time that prices came down in the industry, and deCODEme never dropped their prices nor invested in the marketspace by implementing features like genealogy matching to other kits.  I’m not surprised that they have made this decision, but I wish they had been able to take a different fork in the road.  Today, as one of their customers, I received this notice.

Dear deCODEme customer,

This is to notify that the deCODEme service from deCODE genetics is being discontinued.

For this reason, all deCODEme customer accounts will be permanently closed on January 01 2015. However, user accounts will be accessible through December 31, 2014.

For logging in you will need to enter your username and password on the deCODEme login page; http://www.decodeme.com .  In case of a forgotten password, you can select the “Forgot my password” option on the login page, but for a forgotten username you will need to send an email to:

support@decodeme.com.

We encourage customers to save and/or print their results as needed.

deCODEme Customer Service

Ancient DNA Matches – What Do They Mean?

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

ancient compare5

Q – What does this ancient match mean to me?

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

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

ancient compare6

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

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

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

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

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

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

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

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

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

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

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

3 European Tribes

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

Well, guess what….so does Anzick.

Here are his matches to the Altai Neanderthal.

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

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

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

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

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

anne and me on dig

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

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

anzick matches

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

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

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

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

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

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

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

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

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

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

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

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

anzick gedmatch one to all

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

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

anzick1

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

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

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

Analyzing the Native American Clovis Anzick Ancient Results

This ancient DNA truly is the gift that keeps on giving.

Today, Felix Chandrakamur e-mailed me and told me that the Anzick results were not yet fully processed at Gedmatch when I performed a “compare to all.”  He knows this because he knows when he uploaded the results, and after they were finished, he ran the same compare and obtained vastly different results.  I am updating my original article to point to this one, so the data will be accurately reflected.

In fact, the results are utterly fascinating, take your breath away kind of fascinating.  Felix wrote an article about his findings, Clovis-Anzick-1 ancient DNA have matches with living people!

While finding what appear to be contemporary matches for the Anzick child may sound ho-hum, it’s not, and when you look at the results and the message they hold for us, it’s absolutely astounding.

Felix ran his comparison with default values of 7cM.  This is the threshold that is typically utilized as the line in the sand between “real” and IBS, matches – real meaning the results are and could be, if you could find your common ancestor, genealogically relevant.  In this case, that clearly isn’t true.

The exception to this rule is heavily admixed groups, such as Ashkenazi Jewish people who are related to every other Askhenazi Jewish person autosomally.  It seems, looking at these results, that this is the same situation we find with the 12,500 year old Anzick child and currently living people.  This population had to be painfully small for a very long time and the DNA had to exist in every person within that population group for it to be passed in segments this large to people living today.

After receiving Felix’s e-mail, of course, I had to go back and run the compares again.  In particular, I wanted to run the one to many, as he had.

I began at the 1cM level and noticed that I received exactly 1500 results, which seemed to me like a cutoff – not an actual number of matches.  So, I upped that threshold to 2, then 3, then 4, then 5, then 6, then finally to the default of 7.  It was only at 7, the IBS/IBD default, that the results were under the 1500 threshold, at 1466.

1466 current matches?????

This is absolutely amazing.  The Anzick child lived about 12,500 years ago in Montana.  How are 1466 matches to currently living people possible?

Many of these matches are to people from the southwest and Mexico today.  They are not, for the most part, from eastern Canada.

Let’s take a look at what we found.

In the 1466 results, as Felix mentioned, the closest matches match at current “cousin” levels to Anzick.  The highest 7 matches that show haplogroups are haplogroup Q1a3a.  Unfortunately, with the constant renaming of the haplogroups recently, it’s difficult to interpret the haplogroup exactly, which is why we’ve gone to SNP names.  Looking at some of the names and e-mails, several appear to carry Spanish surnames or be from Mexico or South America.

Of the 1466 results:

  • 2 were Y haplogroup C
  • 79 were Y haplogroup Q
  • 520 carried a mitochondrial DNA haplogroup of A, B, C, D, M or X
  • Of the 79 haplogroup Q carriers, 52 also carried a Native mitochondrial haplogroup.
  • A total 549 individuals out of 1466 carried at least one Native American haplogroup, or about 37.5%.  That’s amazingly high.

Of these closest matches who are Y haplogroup Q, they also all carry variant Native American mitochondrial DNA haplogroups as well, so these people may not be heavily admixed.  In other words, they may be almost “pure” Native American.

In order to test this theory, I entered the number of the kit that rated the highest in terms of total cM at 160.1 with the largest segment at 14.8.  You can click on the images to enlarge.

anzick1

As you can see, this individual is very nearly 100% Native American.

The second individual on the list, who may be from Guatemala, also carries almost no admixture.

anzick2

Of the highest 21 matches that listed any haplogroup information, all have either or both Native Y or mitochondrial DNA haplogroups.

Out of curiosity, I ran the first person on the list who had neither a Native American Y or mitochondrial haplogroup – both being European.

As you can see, below, they are still clearly heavily Native American, but clearly admixed.

anzick3

I moved to the last person of the 1466 on this list whose DNA matched at a total of 7cM, who did not carry a Native haplogroup.  This individual, below, is more heavily admixed.

anzick 3.5

Lastly, I ran the same admixture tool on the last person, who had a total of 7cM matching that did have a Native American mitochondrial haplogroup.

anzick4

Not surprisingly, the individual with almost no non-Native admixture is much more likely to carry the ancient segments in higher percentages than the individuals who are admixed.   This again strongly suggests that at one point, these segments were present in an entire group of Native people and may still be present in very high numbers in people who carry no admixture.

Out of curiosity, and assuming that these first two individuals are not known to be related to each other, I ran them against each other in a one to one comparison.

There were no matches at the default values, but by dropping them just a little, to 5cM and 500 SNPs, they match on 6 segments.

anzick5

It looks like they should match on chromosome 17 at the 700 SNP/7 cM default threshold.

At 200 SNPs and 2cM, there were 67 segments.  These are clearly ancient in nature and size, but matching just the same.  By lowering the threshold to 100 SNPs and 1cM, they share a whopping 990 segments.

Indeed, these two men very clearly share a lot of population specific DNA from the ancient people of the New World, including that of Anzick male child who lived in Montana 12,500 years ago.

Utilizing Ancient DNA at GedMatch

Mummy of 6 month old boy found in Greenland

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

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

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

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

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

1.  Montana Anzick at GedMatch

This is the only clearly Native American sample.

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

F999912

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

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

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

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

2.  Paleo Eskimo from Greenland at GedMatch

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

F999906

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

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

3.  Altai Neanderthal at GedMatch

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

F999902

One match to what is obviously another Neaderthal entry.

4.  Russian Causasus Neanderthal at GedMatch

Another contribution from the Neanderthal Genome Project.

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

F999909

No matches.

5.  Denisova at GedMatch

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

F999903

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

But now, for the fun part.

My Comparison

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

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

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

So, let’s see what we find.

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

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

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

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

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

Anzick

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

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

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

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

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

ancient compare

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

Paleo

At 200 SNP level, 2 segments.

1 26535949 27884441 1.1 258
2 127654021 128768822 1.2 228

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

Altai Neanderthal

ancient compare2

Russian Neanderthal

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

Denisovan

I have one match.

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

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

Matching to Ancestral Lines

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

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

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

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

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

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

ancient compare3

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

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

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

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

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

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

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

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

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

Let’s see what else the matches show.

ancient compare4

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

ancient compare5

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

ancient compare6

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

ancient compare7

More matching to the proven Miller line.

ancient compare8

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

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

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

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

ancient compare9

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

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

Regardless, it’s interesting, very interesting.

What Have I Learned?

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

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

My relationship level to these ancient people is as follows:

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

The Lores and the Millers

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

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

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

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

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

Bottom Line

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

Joseph B. “Dode” Bolton (1853-1920), Who’s Your Mama?, 52 Ancestors #37

bolton1

Looking down the Powell River from Cumberland Gap, we peer into the heart of the lands where the Boltons lived, near the border of Claiborne and Hancock Counties in Tennessee, just slightly south of Lee County, Virginia, along the meanders of the Powell River.

Joseph B. “Dode” Bolton was born on September 18, 1853 in Hancock County, Tennessee to Joseph Preston Bolton and his wife, Margaret Herrell (Harrell) Martin Bolton.  We don’t know what his middle initial, B., stands for, nor do we know how he obtained the nickname, Dode.  His grandson, Joseph Estes, through daughter Ollie Bolton Estes, obviously named for him, also had the same nickname.

Unfortunately, the records of Joseph Preston Bolton and Margaret Herrell Martin Bolton and their son, Joseph B. “Dode” Bolton and his wife, Margaret (Margret) Clarkson/Claxton Bolton are difficult to sort through because the names of the both couples are the same and of course, they live in very close proximity and in a burned records county.  This confirms that the genealogy Gods have a sense of humor.

Hancock County records were only partially burned, in 1885 and 1930, so we only know of Joseph Dode’s approximate marriage date/year of 1873 based on the birth of his first child and the census record in 1910 which indicates that he had been married for 37 years to wife Margaret N. Claxton (Clarkson).

Their children were:

  1. Ollie Florence Bolton, my grandmother, born May 5, 1874 in Hoop Creek, Hancock County, died April 9, 1955 in Chicago, Illinois. She married William George Estes in 1893, later divorcing about 1915.
  2. Charles Tipton Bolton born June 30, 1876, died before 1953, enrolled for the WWI Draft in Sonora, Washington Co., AK, listed his father as J.B. Bolton in Hoop, TN.
  3. Elizabeth Bolton born 1879, married E.C. Baker Dec. 20, 1901 in Claiborne Co., died before 1953.  Note:  A family member who personally knew and was friends with “Lizzie” Bolton who was married to E.C. Baker tells me that she was unquestionably the daughter of Daniel Marson Bolton.  So the Joseph’s daughter, Elizabeth, married someone else.
  4. Dudley Hickham Bolton born March 21, 1881, registered for the draft in Hoop, Hancock Co. TN for WWI, married to Matilda, known as Tilda, died in 1818 in Bell Co., KY according to the family.
  5. Dalsey Edgar Bolton born July 26, 1883, died Nov. 9, 1946, El Paso, Texas from a broken back in an auto accident in New Mexico, wife Jennie in 1940 census.
  6. Ida Ann Bolton born May 30, 1886 married Gilbert Scott Saylor, lived in London, KY, taught school, no children, died June 7, 1953 of breast cancer, buried in the Plank Cemetery.
  7. Mary Lee Bolton born June 21,1888 married Tip Richmond Sumpter, died Sept. 25, 1935 in Illinois, buried Brush Creek Cemetery, Divernon, IL.
  8. Estle Vernon Bolton born December 4, 1890, died December 1971, Truth or Consequences, Sierra Co., NM.
  9. Cerenia Elizabeth “Lizzie” Bolton, died young, before the 1900 census.
  10. Samuel Estwell H. Bolton born June 12, 1894, died October 8, 1918, France, a casualty of WWI, buried in the Plank Cemetery, Claiborne Co., TN.
  11. Henry Bolton born May 1897, probably died before 1910 as not in census.

We do have photos of a few of these people, but none of Joseph Bolton or his wife, Margaret Clarkson/Claxton Bolton.

bolton2

Ida and Elizabeth Bolton, daughters of Joseph “Dode” Bolton and Margaret Clarkson.

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Dalsey Edgar Bolton, son of Joseph “Dode” Bolton and Margaret Clarkson, above.

Ollie Bolton 1950s

Ollie Bolton, taken about 1950, daughter of Joseph “Dode” Bolton and Margaret Clarkson.

Bolton, Estle Vernon crop2

Estle Vernon Bolton

As ironic as it is, given that William George Estes, son-in-law of Joseph Bolton, was a photographer, there don’t seem to be any photographs of Joseph Bolton and Margaret Clarkson/Claxton.  I keep hoping that there really ARE some, someplace and eventually, someone will find and share one.  I can’t tell you how crazy this makes me.  Joseph didn’t die until 1920 – there SHOULD BE pictures!!!

Update:  My wish has been granted.  A wonderful cousin did in fact find a photo of Joseph B. Bolton in a box of family photos and has been kind enough to share with me.

Joseph B Bolton2

This photo identifies the men as Joseph and Dudley Bolton, Joseph’s son.  The cousin thinks that the child is Elizabeth Bolton, daughter of Matilda and Dudley Bolton who was born about 1910, putting this photo at about 1913 or 1914.  Joseph would have been about 60 years old at the time!

In 1900, the Bolton family had their first reunion in Claiborne County, and to the best of my knowledge, they still have them annually, or at least they were still holding them a few years ago.  In 1985, the family produced a book titled “Bolton Family History” and in the book, included a photo of the first reunion.

Bolton4

Given this photo above, I would think that the entire Bolton family should be in the top photo, but that family in the photo is clearly not large enough to encompass even just the Claiborne County folks.  At least six of Joseph Preston Bolton’s children were still living in 1900, and in that area.  At that time, Joseph “Dode” Bolton and Margaret would have been under 50.  James, the son of Joseph Preston Bolton and his first wife would have been about 55 here, pictured in the bottom photo.  Are Joseph “Dode” Bolton and Margaret in that top photo?  Was William Estes taking pictures?  He and Ollie were living in Claiborne County in 1900, according to the census.

Joseph B. “Dode” Bolton’s death certificate tells us that he lived in Sedalia, in Hancock County at the time of his death.  My Genealogy Hound has 1888 maps of the Tennessee Counties that include at least some place names.  You can see New Sedalia just above the headwaters of Sycamore Creek which runs along Little Sycamore Road from Springdale in Claiborne County.  The name was changed to Sedalia in the 1890s.  The Plank Cemetery, where both Joseph and Margaret Bolton are buried is found on Little Sycamore road just inside Claiborne County.  While the county line bisects this road, the people living on this road function as one community called “Little Sycamore.”

Bolton5

What do we know about Joseph Bolton’s life?  We know where Joseph was born, based on the 1850 census where his father, Joseph Bolton, and his first wife, Mary “Polly” Tankersley were living.  Joseph Sr. was still living in Hancock County in the 1860 census which shows the family living on 4 Mile Creek in Hancock County and Joseph Jr. was age 7.

Bolton6

You can see, on this map above, that Four Mile Creek intersects with the Powell River near the Atlanthis Hill area.  Rebel Hollow Road is where Rebels were hung during the Civil War, except in Hancock County, it’s called “Rebel Holler.”

The Civil War

Minnie, one of the Crazy Aunts, said Joseph fought in the Civil War for the North. She might have been talking about his father, Joseph Sr., although I checked military and other records, and there is no record of Joseph Preston Bolton or his son, Joseph, serving in the Civil War.  Joseph “Dode” Bolton would have been about 8 when the Civil War began in 1861 when 7 stated seceded from the Union and formed the Confederacy.  Tennessee was officially a southern state, but the northern-most counties which did not have the type of land that supported large plantation type of farms provided many recruits for the Union forces.  Recruits would cross over the border to neighboring Kentucky, a Union state, under the cover of night to enlist, often in groups.

To a large extent, the Civil War was fought in cities and farms of Tennessee, as only Virginia saw more battles. Tennessee was the last of the Southern states to declare secession from the Union, but saw more than its share of the devastation resulting from years of warring armies criss-crossing the state. Its rivers were key arteries to the Deep South, and, from the early days of the war, Union efforts focused on securing control of those transportation routes, as well as major roads and mountain passes such as the Cumberland Gap, just a few miles away from where the Bolton’s lived.

Family history tells us quite a bit about the Civil War in Hancock County though.  Family members said that soldiers from both sides came though, mostly looking for food, and sometimes looking for recruits, willing or otherwise, which may have something to do with the hangings in Rebel Holler, according to local lore.

The Vannoy family who lived in close proximity to the Boltons found a cave and took what livestock they could and hid in the cave in the mountains.  The Estes family, who lived down Little Sycamore Road had all of their livestock stolen.  One of their daughters snuck into the Confederate camp at night and took their milk cow back.  She was the family hero.

The Civil War was very hard on the families in this area.  Not only were their allegiances terribly torn, even within families, their lands were used as a battleground.  The 1890 veterans census for Hancock County, TN is quite unique because it recorded the Civil War veterans for both the Union and the Confederacy, later marking through the Confederate veterans.  This gives us a unique view as to how many soldiers on each side were either still living, or their widows were living, in 1890.

1890 vet census Hancock co tn1

While this doesn’t tell us directly about how the Bolton family felt about the Civil War, there is some interesting information here that suggests their allegiance.

Evaline Martin, daughter of Margaret Herrell Martin Bolton through her first husband, Anson Cook Martin, married Calvin Busic about the same time her mother married Joseph Preston Bolton.  Therefore, she was a half-sister to Joseph “Dode” Bolton.  Calvin Busic is listed on the veteran’s census along with his death in 1862.  He died of malarial fever while in the service and he fought on the side of the Union.

Samuel Clarkson, the father of Margaret Clarkson/Claxton, the future wife of Joseph Dode Bolton also fought for the Union in the war.  He died in 1876 as a result of bronchitis and pneumonia contracted during the war, about 3 years after his daughter married Joseph Dode Bolton.

Samuel Clarkson’s sister’s husband, Calvin Wolfe also served in the Union forces.

In fact, if you look at the men who lived in the Atlanthis Hill area, most of them were Union sympathizers, but not all.

Elijah Wolf, Margaret Herrell Martin Bolton’s niece’s husband fought for the Confederacy and was prisoner of war at Louisville, KY.

I imagine these families didn’t have family reunions for years following the Civil War.  The four page 1890 veteran’s census for Hancock County shows a total of 25 who fought for the Confederacy and 24 who fought for the Union.  The Atlanthis Hill area seems to be heavily Union with the more southeastern end of the county, Mulberry Gap to Sneedville, more Confederate.

In the 1970s, when I was visiting one of the old farms near Cumberland Gap, their garden was edged by civil war cannonballs found on their property while plowing.  Aunt Margaret, born in 1906, said the old-timers would put their old Civil War uniforms on when she was young, went to town, and “fought that war over and over,” especially on “Decoration Day.”

There wasn’t anyone alive during that time in Hancock County or Claiborne County, Tennessee that wasn’t directly affected by the Civil War.  It truly was the worst of times between the actual fighting, marauding troops, hunger and concerns about an uncertain future.

Church

The Bolton and Clarkson families both attended Rob Camp Church which was formed in October of 1845.  The church minutes make for very interesting reading.

rob camp

We know that Margaret Herrell Martin, Joseph “Dode” Bolton’s mother, was a member, because her first husband, Anson Cook Martin was received by experience shortly after the church was formed, and shortly before his death about 1845.

In January 1853, we find a note that Margaret Bolton was received by experience, or in today’s Baptist vernacular, was “saved” and was likely baptized.

Her son, Joseph B. “Dode” Bolton would be born that September.

Beginning in 1854, Joseph Preston Bolton was mentioned in the church minutes four times, the last time being when he was excluded from the church as his own request following accusations by another member.  In 1866, Joseph was once again received back into the flock and in 1868, he is a deacon. It’s likely that Margaret continued to attend this church, even while Joseph Sr. was excluded and that Joseph Dode Bolton grew up in this church.

Joseph Preston Bolton, Dode’s father, was also a founding member of Mt. Zion Baptist Church in Hancock County, shown below. Joseph “Dode” Bolton would have been 15 at that time.

OLYMPUS DIGITAL CAMERA

According to the Rob Camp Church minutes, on the second Saturday of April, 1869, Rob Camp Church released the following people from their fellowship to form the Mount Zion Baptist Church.  On the third Saturday of May, the following list of brothers and sisters met to officially constitute the church which would be located on a parcel of land belonging to William Mannon.  Most of these people were related to Margaret Clarkson, Joseph B. “Dode” Bolton’s future wife in some fashion.

  • E.H. Clarkson (Edward Hilton, 1st cousin once removed to Margret)
  • Mary Clarkson (Mary Martin, wife of E.H. Clarkson, half sister to Joseph Preston Bolton through his mother Mary Herrell Martin Bolton and Anson Cook Martin)
  • William Mannon
  • Elizabeth Mannon
  • Mary Muncy
  • Clarissa Hill
  • Sarah Shefley (cousin)
  • Farwix Clarkson (grandfather to Margret)
  • Agnes Clarkson (grandmother to Margret)
  • Nancy Furry (cousin)
  • Elizabeth Clarkson (mother to Margret)
  • Margret Clarkson (future wife of Joseph B. “Dode” Bolton – she was about 3 years older than he and would have been considered an adult at 18)
  • William Bolton (son of Joseph Preston Bolton)
  • James Bolton (son of Joseph Preston Bolton)
  • John Grimes
  • Catherine Grimes
  • Joseph Bolton (this would be Joseph Preston Bolton Sr., the deacon)

In the first church meeting of the new church, Joseph Bolton was made a Deacon.  One of the first things the new church did was to create a list of members and they all signed a very lengthy statement about the mission of the church.  Among those names is Joseph Bolton, noted as a Deacon, Margret Bolton and Margret Clarkson.  However, a note beside Joseph’s name, obviously added later, says “excluded” and a note beside Margaret’s name says “dis” for dismissed.  Obviously, things did not go swimmingly well at the new church.

The next page in the notes is a page titled “Dismissed by Letter.”  This meant that the church gave you a letter to take to your next church that basically stated that you had been baptized and were a member in good standing.  Joseph B. Bolton is on that list.  That would be the younger Joseph.  There is no date.

In the 1870 census, the Bolton family is living in the same location in the 14th district of Hancock County and Joseph Dode Bolton is found living with his parents.

Joseph Dode Bolton married Margaret Clarkson about 1873, and about the same time, his father, Joseph, was once again in trouble with the church.  The trouble boiled over into 1874 and eventually, Joseph Sr. was once again excluded from the church.

Given all of the family relationships, I’m presuming that Joseph Dode Bolton and his bride, Margaret were probably married in this church and continued to attend Mt. Zion until 1876 when Little Mulberry, below, was formed.

Little mulberry

Little Mulberry Baptist Church is located in the 5th Civil District of Hancock Co. in the lower Mulberry Community.  Little Mulberry Church was organized in May 1876 with 19 charter members:

  • G.W. Coleman
  • Mary and Norah Clarkson (first cousin to Margaret Clarkson)
  • Thomas and Jane Greer
  • William Pendleton
  • Lucy Skidmore
  • Jane Baker
  • Mr. and Mrs. H. Edens
  • James Fugate
  • C.K. Coleman
  • J.B. and Margaret Bolton (This is the younger Joseph Bolton.)
  • Thomas and Mollie Reed
  • Etta and Susan Sumpter

In 1879, there is a note in the Mt. Zion Baptist Church minutes that Joseph D. (sic) Bolton be charged with getting drunk and that E. H. Clarkson be sent to talk to him.  At the July meeting, Brother Joseph Bolton was present and made his acknowledgement to the church and was “restored back in fool fellowship.”  I don’t think that’s really what they meant, “fool fellowship,” but it surely is exactly what they said.

On the Hancock Co. 1880 tax list from the East Tennessee Roots Vol VI, number 4, Margret Bolton is listed with 55 acres, $350 value, 105 to county, 35 to state, 35 to school, 87.5 for special, 262.5 total taxes, no poll.  The 1880 census shows Joseph Sr. and Margaret living in Claiborne County.  Joseph Bolton Jr. lives beside Margret’s land in Hancock County, with no land, 1 poll (himself), but then under him it says 100 to school and 30 special and 130 total, paid to Edds.  Joseph Dode probably farms his mother’s land.

The 1880 census shows Joseph Bolton (Jr.), age 27 with his wife Margaret and their first 3 children, Ollie F., age 6, Charles J. or T., age 4 and Elizabeth, age 1.  Joseph shows his mother and father as born in Virginia.  They still live in the same district at Joseph’s parents did in 1860 and 1870.

In 1885, the Rob Camp church minutes have a list of “Names.”  On that list is Margret Bolton.  It’s unclear whether his is a current list as of that date, but I suspect that it is because Joseph (Sr.) is not to be found and he is still living.

In February 1887, the Mt. Zion Church notes mention that Brother Clinton Clouse and Brother Joseph B. Bolton talked and made the acknowledgement to the church “for living cold and out of duty and hoped to live a better life from this time forward.” Ironically, it was Clinton Clouse that was brought up on charges at the same time as Joseph in 1879, except Clinton was brought up for swearing as well.  Makes me wonder if they were best buds, or if the timing was simply circumstantial.  The 1880 census perhaps sheds some light on that question.

1880 hancock census

In June of 1888, Mt. Zion Church received Margret Bolton by letter.  This may have been Margret, the widow of Joseph Bolton, the elder, who died in December of 1887. According to the “Bolton Family History” book, in 1887, Joseph was living in Little Sycamore, in Claiborne County.  Perhaps after his death Margaret moved back to where she was more comfortable, in essence, going “home.”

Near the end of the Mt. Zion notes, after October 1896, there are several pages of members.  Upon them, Joseph B. Bolton is listed and by his name, “excluded.”  About half of the men were excluded.  I don’t know if he was in good company, but he certainly had a lot of it!

Of course, there is no 1890 census.  Prior to the 1900 census, the Joseph Bolton family lived in the 14th district but in 1900 and 1910 they live in the 8th district, so they have apparently moved.  None of the neighbors are the same, and Clinton Clouse or Cloth is nowhere to be found, which was probably a great relief to Joseph’s wife, Margret.  In 1900, their name was misspelled Bolting.

1900 hancock census

In 1910 they lived in Hancock County on Back Valley Road as is detailed in the article about their son, Samuel, who died in WWI.

Joseph B. “Dode” Bolton’s death certificate says his father, Joseph Bolton, was born in Washington Co., VA and his mother was Nancy Christie, which is dead wrong as far as we know.  Margret, his wife, notified the authorities of his death, and then herself died on March 11th, just two weeks later.  It appears that Joseph was buried on February 25th, so the family oral history that they put him out in the woodshed or barn and waited for her to die and had one funeral is not accurate.

Bolton7

Joseph’s death certificate says he was sick from Feb. 18th through the 24th, so died of pneumonia following the flu after being sick for only 6 days.  However, Margret’s death certificate says that she was sick from Feb. 18th through March 10th, so she got sick at the same time, but it took her another 2 weeks to die.  I wonder if she went to Joseph’s funeral – or maybe they buried the body but had a joint funeral at the church, especially if she was sick, they would probably have been waiting for her to get better.  Or maybe Joseph didn’t want a funeral at any church, given that the final note we have says that he was excluded and there is no evidence that he ever attended another church.

What a terrible blow to the family, to lose both parents within two weeks.  If they were sick, it’s very likely that many others in the community were as well.  A quick spin through the Hancock County death certificates confirms that there were several other deaths from pneumonia following the flu in the surrounding weeks.

Joseph Bolton’s death certificate is interesting.  It gives us lots of information, not all of it accurate.  Remember, death information is given by relatives, some of them quite bereaved, or perhaps distant, or maybe elderly and forgetful.  In Margret’s case, she was both bereaved and ill.  I view death certificate information as a great hint – to be proven.

In the case of Joseph, his birth location of Washington County, VA, is suspect, very suspect.  In 1850, his parents were both living in Claiborne County, TN, as they were in 1860, so unless they moved away, and back again, he was born in Hancock County, TN, not Washington Co., VA.  The portion of Hancock County where the Bolton family lived was split from Claiborne in 1845, so the family didn’t move, the county line did.

The most interesting piece of information, or in this case, misinformation, was his mother’s name.  Nancy Christie.  Joseph Bolton’s mother was Margaret Herrell.  She had previously been married to Anson Cook Martin who died about 1845 in Hancock County, leaving his widow with 9 children.  Margaret remarried to Joseph Bolton after 1850, as Joseph’s former wife, Mary Tankersley, was still living in the 1850 census which was dated in December, although it is supposed to be taken “as of” June.  I have seen cases of people on the census who have actually died, but are enumerated because they were still alive in the month the census was taken “as of.”

Margaret Martin, with her children, was enumerated in1850 as a head of household.  Margaret had two more children after marrying Joseph Bolton: Mary Ann Matilda born in 1851 and Joseph B. “Dode” Bolton born in 1853.

In the 1860 census, taken in August, daughter Mary Bolton is shown as age 9, so born in 1851, meaning she had already had her birthday for that year.  Since in the 1850 census, Joseph’s first wife was still living in December, and Mary was born in 1851, probably before August, this strongly suggests that Mary Tankersley Bolton was already dead when the census was taken in December of 1851 and Joseph married Margaret about that time.  Both people had a houseful of kids and had probably known each other for years.  Joseph’s youngest child was about 2 and Margaret’s about 6.  I’m betting their courtship lasted about a week or may simply have consisted of a visit and a chat.  I surely wish we had their marriage license.

In the 1860 census, two of her Martin children, Malinda, age 18 and Alexander, the baby at 15 are still living with Margaret Herrell Martin Bolton and Joseph Bolton.

Back to the pesky issue of the death certificate.  How can one mistake a mother’s name, or a grandmothers, especially if you knew the person well?  And not just the last name, but the first name too?  Margaret Clarkson Bolton clearly knew her mother-in-law, Margaret Herrell Martin Bolton, the grandmother to her children.  Margaret Herrell Martin Bolton didn’t die until sometime after 1880 and before 1892, so Margaret’s children, if they provided the death certificate information, would have clearly known their grandmother.  Joseph Bolton Jr. was around age 40 when his mother died.  His wife, Margaret Claxton had been a daughter-in-law to his mother for some 20 years and was a neighbor to his grandmother, Mary McDowell Harrell before that.  So these families were well known to each other their entire lives, not just after marriage.  Margaret Clarkson/Claxton was raised on the land beside her mother-in-law, Margaret Herrell Martin Bolton.  This much confusion and misinformation just makes me uneasy, especially without a marriage license, even though we clearly do find Margaret Herrell Martin’s children with Joseph Bolton’s family in 1860.

Fortunately, not all of the Hancock County records burned. Just generally the ones I want, and of course, all of the marriage licenses!

On July 1, 1878, Pleasant Smith and Serelda Smith, his wife, John Martin and Hanah Martin, his wife, sign their interest in land after the death of Marget (sic) Bolton for $100 to J.M. Martin.  That land was located in the 14th district containing 50 acres bounded by John McDaniels, Elexander Herrell and others.  That deed as also witnessed by D.M. Bolton.  The deed was registered and sworn to by D.M. Bolton on January 10, 1892. This is very likely the 50 acres that Joseph Bolton, Jr., was farming in 1880.

What this tells us is that Margaret (Herrell Martin) Bolton was still living in 1878, and that she had died before January 10, 1892.

In 1885, in Chancery Court, in Hancock County, James Spears brings suit against J. M. Martin, William Martin, Joseph Bolton and Margaret Bolton.  As interesting as the suit itself is the list of who was involved.  Cannon Herrell, Alexander Herrell and John McDowell were each paid for 2 days, likely as chainers to the surveyor.  This suit has to do with land.  James Spears is somehow connected to the Herrell family, as he testifies as to their character in other suits.  By the time this suit gets to court, the people have agreed and they survey the land.  They surveyor’s notes give us somewhat of a location for the “lands in controversy.”  Beginning at James M. Martin’s house…Spear’s line…Martin’s line…Spear’s water…bank of Powell’s River.  It should also be noted that there are Spears buried in the old McDowell Cemetery on Powell River.

Alexander Herrell is Margaret Herrells’ brother, Cannon is her half-brother and John McDowell is either her uncle or nephew.

In fact, this hand drawn representation of the Claiborne County survey book shows the McDowell, Clarkson/Claxton and Herrell land, so we can rest assured that the Boltons and Martins are living in close proximity as well.

bolton8Here’s a current topo map with the McDowell, Herrell and Clarkson land plotted.  You can see Four Mile Creek at the top to the left of McDowell and then Mulberry Creek just below the word Clarkson.

bolton9

This picture was taken on a visit to Hancock County where I was standing on the McDowell land, aptly named “Slanting Misery,” looking at the Claxton/Clarkson land.

bolton10

Joseph B. “Dode” Bolton started his life near 4 Mile Creek in Hancock County, perhaps within sight of this location.  He spent most of his life in that area.  He perhaps had a drinking problem and was excluded from the church.  He seemed to have a rabble-rousing friend in Clinton Clouse for at least a decade.

Getting oneself excluded from church seemed to be a Bolton family tradition, as his father has been excluded before him, as well, twice, although not for drinking.

Joseph’s brothers and father had moved down to Little Sycamore in the early 1880s, but Joseph “Dode” didn’t.  He apparently remained in Hancock County and farmed his mother’s land, at least until her death and the land was conveyed in 1892.

On March 31st 1902, a deed was filed in Hancock County by and between S.F. Clarkson who was appointed administrator of the estate of Fernando Clarkson decd, late of Hancock Co., Tn. by the county of Hancock on Dec. 11, 1900 and Joseph Bolton of Hancock Co.., stating:  On July 30 1896 Fernando Clarkson decd did sell to Joseph Bolton a certain tract of land and execute him a title for the said tract of land lying and being in the 8th civil district of Hancock Co and on the Sulphur Fork of Mulberry Creek and bounded as follows: with L. Overtons line to G. Overtons line and thence east with G Overton’s line to a conditional line between Thomas Reed and Bolton and then with a conditional line in H.S. Fugates line to a small oak on the top of Wallen’s ridge with H.E. Fugate and E. Overton’s line.  S.F. Clarkson does now convey to Bolton together with the right of way for a road through the land now held by Thomas Reed. Signed by S.F. Clarkson and witnessed by R.L. Parkey and Ollie Parkey.

Joseph was later reportedly living at Hoop Creek, both by the family and in official documents.

bolton11

Hoop Creek is about half way between 4 Mile Creek and the Little Sycamore Community where his father lived and died.  The Plank Cemetery is at the location of West Teller Road and Little Sycamore, below  Hoop Creek was well known for being a mixed racial area.

bolton12

The Plank Cemetery is where Joseph Presley Bolton Sr. was buried in 1887.  Twenty three years later, his son, Joseph B. “Dode” Bolton was buried there and two weeks later, to the day, his wife, Margaret Clarkson Bolton.  Fifteen months earlier, their son Samuel who was killed in WWI was buried and daughter Ida was buried there in 1953.  The cemetery can be difficult to find because it sets back a long drive into the center of a field, which is dead center in this satellite view.

bolton13

You can see the Plank Cemetery, fenced, in the center of the field above.

bolton14'

There are many unmarked graves here.  Margaret Herrell Martin Bolton may be one of them.  Or, she may be buried with her first husband, Anson Cook Martin, up near Four Mile Creek, or maybe in the Herrell family cemetery, also in that vicinity.

Bolton15

I’d really like to remove any little tiny niggling nagging doubt that I might have about who Joseph B. “Dode” Bolton’s mother really was and put it to bed once and for all, forever.  Fortunately, there is a way for me to do that.

A number of Harrell descendants have DNA tested.  If Margaret Herrell is Joseph Bolton’s mother, then I, or other Joseph Bolton descendants, should match at least one of our Harrell cousins using autosomal DNA testing.

And, as you can see, on the chromosome graph below, comparing me with a Harrell cousin, we do!

Bolton16

The orange DNA segments above range in size from 1cM to 17 cM on chromosome 17.  That is a nice beautiful chunk of Margaret Harrell’s DNA!  Proof, at last, that Margaret Herrell is Joseph “Dode” Bolton’ mother.

Bolton17

As you can see, this person descends from Margaret Herrell though a child from her first marriage.  Indeed, this match is good news and proves that yes, Margaret Herrell is indeed Joseph B. “Dode” Bolton’s mother, because the Harrell cousin I match carries no Bolton DNA, and we don’t share any other ancestors – so the matching DNA has to be Harrell.

A second cousin who also descends through Joseph Bolton Sr. and Mary Tankersley also matches.  Now this gave me pause to reflect, because, she SHOULDN’T match my Herrell cousin on any common segments, because she doesn’t descend through Joseph Bolton Jr. and Margaret Herrell.  But take a look, we three have several segments in common with each other if you drop the threshold to 1cM, specifically, chromosomes 6, 7 and 12.

Bolton18

And yes, both matches also match each other.  This is called a huge fly in the ointment. So, right about now, I’m all set to have a little meltdown because there is obviously a problem SOMEPLACE and probably in my genealogy or maybe his mother really isn’t his mother….or…or…or

So, I took both a deep breath and a closer look at the second match’s tree, and lo and behold, guess what?  She has a questionable Herrell penciled in, spelled Harrell, so it didn’t’ show on my previous surname match.  The tentative Harrell is a possible child of….yep….Margaret Herrell.  Well, guess what…it’s not tentative anymore, it’s now confirmed!  I’ll have to let her know!  Whew, what a relief!!!

Bolton19

But then, it got even better.  Looking at my cousin’s Herrell matches, she had some matches that didn’t match me directly, because for me, they are below the initial matching threshold, but we all match my cousin.  Pushing all of our data through to the chromosome browser, there were now a total of 5 Herrell cousins.  Dropping our cM to 1 shows this chromosome browser match.

The reason these folks don’t show for me, except for the pink person, is because the segments are small enough that they are under the match threshold, but because we do match someone else in common, we can see them as matches by comparing everyone to the other person we match and dropping the match  threshold.

I desperately wish we could adjust the matching threshold at FTDNA, at least in specific cases.  I realize that Family Tree DNA is worried about having too many matches, but in some cases, we’re missing the confirming data by not being able to see those smaller matches.  By utilizing the standard matching, I have only one match on chromosome 17 to the pink lady, shown in the first screen shot, above, in addition to the person being matched against.  The proof of why we need to be able to adjust the threshold to capture additional matches, is all of those colored spaces below.

Bolton20

I’m green on this comparison.  Very interesting that I match with multiple cousins on chromosomes 10, 11, and 12.  It’s also very interesting that I match on a fairly large chunk of the X chromosome with my Harrell cousin that wasn’t sure she’s a Harrell!

On chromosome 11, there is one segment that 4 of 5 cousins carry that descends from Margaret Herrell.  We know this segment comes from Margaret and not Joseph because some of these cousins are Herrell cousins who don’t also descend from Joseph Bolton.

All of the technology and genealogy data aside, just sitting for a moment and realizing that this is Margaret Harrell’s and Joseph Bolton’s DNA showing up in orange, blue, green and pink.  By comparing to people who only descend through one of those people, and not both, in the future, we can even divide those matches, just like we did on chromosome 11, so we know which pieces are Margaret’s and which are Joseph’s.

To me, and to descendants hunting for confirmation of their ancestry, these are absolutely the most beautiful, multi-colored stars shining through the inky black night sky, illuminating our ancestral path, and winking at us along the way!  They are pieces of our ancestors found in us today, lighting the path forward, or backward…or both.

 

DNA Buys the Truth

true-straight

Recently, George Doe, clearly a pseudonym, a man with a PhD in Cell and Molecular Biology, a professional stem cell and reproductive biologist, related his story to Julia Belluz.  Vox published the resulting article titled, “With Genetic Testing I Gave My Parents the Gift of a Divorce.”  The original rather unflattering and somewhat derisory article by Julia is here, titled Genetic Testing Brings Families Together and Sometimes Tears Them Apart.

In these articles, Dr. Doe tells us that last year, in a class he was teaching, he used the 23andMe test to demonstrate how to collect a spit sample.

In fact, he was so excited that he bought kits for his parents as well:

“I had spent many years looking at the genes of other animals — particularly mice — but I never looked at my own. Because I was so excited about it, I got two 23andMe kits for my mom and dad as gifts. It’s a lot more fun when you can incorporate your family because you can trace not just the chromosomes but individual alleles on the chromosome so you don’t just see them, but where they came from. Also, I felt I had a good handle on my family’s medical history so I was very interested in confirming any susceptibility to cancers that I heard had run in my family, like colon cancer. I wanted to know if I had a genetic risk.”

But Dr. Doe found more than he anticipated.  He found a half brother, an adoptee, sired by his father.

“When I saw that I share about 22 percent of my genome with a person, I thought, “That’s huge.” It took a bit of time to realize Thomas and I actually share the same genome with my father. This is how it happened: when you share around 25 percent genetic similarity with someone, that means that either it’s your grandfather, uncle, or half-sibling. 23andMe listed Thomas as a grandfather, which was confusing to me. I called my dad. All I had was his name, Thomas, and the fact that he’s male. I just asked my dad, “Does this name sound familiar?” He said no. He logged into his account, and Thomas wasn’t showing up at all. I was so confused. We figured out that at the very bottom of your profile, there’s a little box that says “check this box if you want to see close family members in this search program.”

Dad checked it, and Thomas’ name appeared in his list. 23andMe said dad was 50 percent related with Thomas and that he was a predicted son.”

Given Dr. Doe’s next comments, one can surmise that this child was not conceived before Dr. Does’ parents married, nor was Dr. Doe’s father a sperm donor.

“Years of repressed memories and emotions uncorked and resulted in tumultuous times that have torn my nuclear family apart. My parents divorced. No one is talking to my dad. We’re not anywhere close to being healed yet and I don’t know how long it will take to put the pieces back together.”

Correction Note:  CeCe Moore provides information that Doe’s half-brother was conceived prior to the marriage, as reported by Belluz.  However, we don’t know that the conception was outside of the time span of the relationship of the parents.  CeCe also states that “both Neil Schwartzman and I were misquoted/misrepresented in the article. Neil says that he never told her it was a negative experience for him. (Some of my quotes have been changed – with no correction noted interestingly, but there is still some misrepresentation of our conversation.) So, this does make me wonder if Ms. Belluz got Doe’s story exactly right as well. Ms. Belluz clearly had an agenda and twisted the “truth” to support it.”

At this point, I felt really bad for the Doe family, and I still do.  But Dr. Doe’s next paragraph bothered me when I first read it and it bothers me now.

Instead of laying the blame for this problem where it clearly resides, at the feet of his father, he is unhappy instead with the testing company, in this case, 23andMe.

“After this discovery was made, I went back to 23andMe and talked to them. I said, “I’m not sure all your customers realize that when they participate in your family finder program, they’re participating in what are essentially really advanced paternity tests.” People find out that their parents aren’t who they think they are. They have nearly a million people in the database. If there happens to be anyone in there you’re related to, they’ll find your match. This is a solid science.”

Dr. Doe goes onto say;

“I don’t want to say if I knew that I wouldn’t have participated. But I’m really devastated at the outcome. I wrestle with these emotions. I love my family. This is nothing I ever would have wished. My dream would be to introduce Thomas to dad, to incorporate a new family tradition, to merge families. We all get to broaden our horizons and live happily ever after. At least right now, that’s not what happened. I still hold out hope that in time we can resolve things. But I also worry that as these transitions happen there may have been some permanent emotional damage that may not be able to be undone.”

Dr. Doe goes on to say that 23andMe isn’t doing enough to protect the public from themselves, in essence.  23andMe did and does have a special box to click to indicate that you DO want to see close relatives.  Most people have no idea that this box even exists, let alone that they need to click it.  In fact, the mere fact that you have to click the box, and it’s not front and center, makes your results unreliable because you believe that you’re seeing all of your results, when you aren’t.  He even describes how this option confused his father and his father could not see his children.  His father isn’t the only one.  This option has caused more panic among families that “should” match until someone explains this hidden “Opt In” option and where they have to click.

Now, I’ve been quiet all week, mulling this situation over.  While I was mulling, 23andMe, who had previously announced that they were going to make seeing close relatives an “opt out” instead of an “opt in,” announced they had changed their mind.  Coincidence?  Doubtful.  In fact, Vox, who published the original two articles also published 23andMe’s announcement and stated that the announcement was a result of their original articles.

I find this stance personally abhorrent.  I believe that the people who test have the right to the truth – all of it – and not just if they happen to discover that all of their results are not being displayed.  They are adults.  They choose to take, or not take the test.  If you take the test, you have every right to expect you’re seeing all of your results.

Dr. Doe, of all people, has absolutely no right to complain.  He, of all people, a PhD in this field, knew exactly what he could discover.  The problem is that the truth is sometimes inconvenient and ugly, especially if you don’t expect to discover that your father cheated on your mother, or vice versa.

Dr. Doe – the problem is not that 23andMe did not protect you from yourself.  You, admittedly, clicked right through the options, believing of course, that it “couldn’t be me.” The problem is your family’s choices, perhaps then, and certainly now.

23andMe’s reversal on their policy will do nothing, absolutely nothing, to protect people like Dr. Doe from himself.  The only policy that will do that is the French policy of making DNA testing illegal to “protect the family unit.”  God forbid that we ever become that paranoid.

What 23andMe’s policy does it to continue to obscure the truth from unsuspecting testers.  Unfortunately, even if they put a big red box dead center in the screen today that says “If you don’t click here, you won’t see close relatives including sons, daughters……,” many people will never see it, because many people never sign on again after receiving their initial results.  In other words, many of their clients’ data would remain dark.  The only way to solve that problem is to do what 23andMe announced they would do and were preparing to do, to shift the option from “Opt In” to “Opt Out,” until Dr. Doe created a publicity nightmare because he couldn’t handle the results of his own test, AFTER, he intentionally and with full knowledge, clicked the “Opt In” option.

Furthermore, Dr. Doe could have discovered the same thing if he had found his father’s old journals, for example.  He could have discovered an old letter from a sweetheart.  He could have found the letter telling his father that the child would be put up for adoption.  What would he have done then?  Who would he complain to that no one protected him from himself?  The company that created the paper and the ink???  The post office because they might deliver a letter with disturbing information inside?

I don’t mean to be insensitive here, but it’s vastly unfair to make hundreds of thousands of people pay the price for Dr. Doe’s family issues.  The timing of this article with the much anticipated 23andMe change has created the perfect media storm.  Dr. Doe whined, loudly, and publicly, and 23andMe doesn’t want to create even more negative publicity.

If you think that I’m speaking from an ivory tower, or a vacuum, so to speak, I’m not.  Let me explain about infidelity and betrayal.  After my former husband’s massive stroke, when I was in my late 30s and he was in his late 40s, I found pictures of him with another female, with the sailboat that I bought him.  Yep, he was on vacation, with another woman, while I was staying home and working.  I felt terribly, horribly betrayed…not to mention gullible, stupid and naïve…oh yes, and angry.

I found those pictures a month or two after his stroke, when he was so terribly incapacitated that he couldn’t even speak, sit up, or eat, let alone answer any questions.  Really, there was nothing he could have said anyway – the pictures, multiple pictures, over multiple summers….were all the evidence I needed.  But I wanted them, I so wanted them to not be true.  But they were.  Staring back at me in living color.

The truth was ugly and painful and devastating.  But it was also freeing.  It freed me from the pain of loss of something I never had – a loving and loyal husband.  I only thought I did.  At the time it was horrifically painful.  Today, I’m incredibly grateful that I didn’t spend my entire married life with a cheating, lying scoundrel.

I also know about infidelity within a family when we discovered that my half-brother through my father was not my father’s child.  I lived through the pain of that too, and I can tell you that my brother, Dave, who wasn’t my biological brother, and I were far closer than many biological family members.

DNA does not tear families apart, people do.  Infidelity does.  Poor choices do.

My grandfather, about 1910, recently married to my grandmother, was present in his mother-in-law’s kitchen the day that a young man knocked on the back door.  His mother-in-law, Nora Kirsch Lore had recently been widowed after being married to Curtis Benjamin “CB” Lore for more than 20 years.  The young man asked for CB, by name.  Nora asked him to come inside and figured he was one of the young men who had worked for CB in his construction and racehorse business.  That’s not at all why the young man was looking for CB Lore.  CB Lore, according to the young man’s mother, was his father.  Let’s just say that it was a very awkward day in that kitchen as Nora asked the young man what year he was born.

In 1910, there was no way to prove, or disprove, this allegation.  Today, there is – DNA.  Nora too was devastated by her husband’s indiscretion, to put is softly, or outright betrayal to call it what it was.  But she was not without a hint – he had always been somewhat of a playboy.  Had she known specifically about this woman?  No, but it didn’t entirely surprise her either.  It only confirmed, or at least potentially confirmed, what she suspected happened when he traveled.  It certainly was not this young man’s fault for showing up to find his father.  Just like it isn’t DNA’s fault today.

Dr. Doe is not responsible for “outing” his father.  His father obviously made his own choices.  So did his mother.

Dr. Doe did not buy his parents a divorce, his parents did.  Pure and simple.  Their choice.  Sounds like that divorce was, perhaps, years overdue.

What Dr. Doe gave his mother was possibly the gift of truth and freedom.  Mrs. Doe obviously had the option of discussing things with her husband.  She didn’t.  Dr. Doe himself said it brought up repressed memories, and they obviously were not pleasant.  This was only a festering scab and he, unfortunately, was the one who bumped up against it and knocked it off.

I’m glad Dr. Doe is getting help.  I hope the entire family is getting help.

As I tell people, if you can’t stand the heat, get out of the kitchen.  If you don’t want the truth, don’t DNA test.  Period.

The culprit in this story is not Dr. Doe, is not 23andMe, but is very clearly Dr. Doe’s father’s original behavior combined with current family dynamics.

Sadly, the people that are ultimately paying the price for Dr. Does’ family turmoil are the hundreds of thousands of people that now continue to have their results obscured because of 23andMe’s abrupt change of policy.

That’s not right either.

23andMe lives and dies not on genetic genealogy or on the revenue from the tests themselves, but on their customers allowing them to use their results to compile for medical studies and to sell.  If you want to make your feelings known, you can personally opt out of allowing 23andMe to utilize your results for those types of endeavors.  In other words, 23andMe will no longer be able to make money from your DNA.

Perhaps 23andMe will hear and understand that message.  Companies understand dollars.

To remove your consent for 23andMe to utilize your DNA, or to at least review the consent form, sign on and click on the down arrow beside your name.

23andme consent

Then click on “Privacy and Consent.”

23andme consent2

Scroll down to the bottom of the page to “Basic Research Consent.”  If you have given consent, this is what you will see.

23andme consent3

Click in the green box on “view/change consent.”  You will then see the consent document.

23andMe consent4

Scroll down again.  You will see that the “give consent” box, in green, has been clicked already.

23andme consent5

Underneath that box, click on the blue “click here to change your consent.”  You will then see a green and a red box with your consent options.

23andme consent6

You can see that I’ve selected “I am this person and I don’t give consent,” in the red box.  Then click on the green “Save” button.

The change takes place imediately for any future projects or initiatives, but does not affect any studies or data sales that have previously taken place.

Furthermore, e-mail 23andMe’s Human Projects Administrator at hpa@23andMe.com and tell them why.

You have a voice in this matter.  Use it.