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

Margaret N. Clarkson/Claxton (1851-1920), Baptist Church Founder, 52 Ancestors #39

Is Margaret’s surname Claxton, Claxson, Clarkson or Clarkston?  I know one thing for sure, it’s pronounced like Claxton in Claiborne and Hancock County, Tennessee.  There’s no debate about how to say it, only how to spell it.

It’s typically spelled Clarkson, today, but historically I believe the name was Claxton, for two reasons.  First, James Lee Claxton/Clarkson’s widow, Margaret’s great-grandmother, applied for a pension due to James Lee Clarkson’s death in the War of 1812.  After denial, she reapplied and said he was sometimes known as James Lee Claxton which was, in fact, how his records were recorded.

Y DNA testing of his male descendants finds that the Claxton/Clarkson line matches several other Claxton men, so the original surname appears to be Claxton – but it can be, and was, spelled various ways and today is typically Clarkson in Hancock County, Tennessee where the family has lived for generations.  We’ll refer to Margaret with her Clarkson surname.

Margaret N. Clarkson was born to Samuel Clarkson and Elizabeth “Bettie” Ann Speaks on July 28, 1851 on the old home place in Hancock County, Tennessee.  We don’t know what her middle initial, N., stood for.

The Clarkson land bordered the north side of Powell River on River Road.

powell river

These next photos are standing on the McDowell family land looking towards the Clarkson land.  This is a panoramic series from left to right.

clarkson1

clarkson2

clarkson3

The Clarkson land is shown in this hand drawn map of the Parkey survey.

bolton8

I found this land some years ago during a visit and plotted it on a current map.

bolton9

It was here, on the land her ancestors had owned for three generations that Margaret was born.  The farmyard is shown below.  The original house is gone but was probably in this clearing.

clarkson land

The 1860 census shows Margaret, age 8, living with her family in the Alanthus Hill section of Hancock County.  The surname is spelled Claxton.

samuel clarkson 1860 census

Margaret’s life changed dramatically when she was about 11 years old, when the Civil War broke out and Tennessee became involved.  On the night of March 30, 1863, her father, Samuel Clarkson, under cover of darkness, left home and crossed the mountains into Kentucky to enlist in the Union Army.  Did she know he was leaving?  Did the family gather to say a tearful goodbye?  Margaret would have been just 4 months shy of 12 years old.

In addition, Margaret’s first cousin, Fernando Clarkson served in the Union forces as did her uncle, Henry Clarkson who died in the service of his country February 2, 1864.  William Clarkson, another first cousin died  at Camp Dennison, Ohio on May 4th, 1863 and a John Clarkson, relationship if any, unknown, who enlisted the same day as William died on March 22nd, 1863 at Nashville.  The Clarkson family paid a heavy price, all fighting for the Union.  It had to be a sad and frightening time, especially for a little girl.

Margaret’s father, Samuel served for 2 years and 2 months, but became very sick with pneumonia and bronchitis.  He nearly died, and was dismissed in May 1865 when it appeared he would not recover.  Samuel returned home, but his service records show that he was ill for the duration of his life and died of bronchitis or pneumonia resulting from his Civil War service in 1876.  He was never physically able to support his family following the war and the family struggled, along with Samuel’s elderly parents and children, to maintain the family farm.

In September 1868, Samuel Clarkson was excluded from Rob Camp church for getting drunk and not being willing to make acknowledgement.  In other words, he refused to fess up and apologize publicly.  However, his family is still clearly very closely associated with the church, because his wife, mother and father, along with his daughter, Margaret, are all on a list of people who were dismissed from Rob Camp church in 1869 for the purpose of forming Mt. Zion Church.

The 1870 census misspells the surname as Caxton, even though living next door is Fairwik Claxton, Margaret’s grandfather.

samuel clarkson 1870 census

In or about 1873, Margaret married Joseph B. “Dode” Bolton, the son of a family who attended the same church that her family did, according to Mount Zion Baptist Church records.  The Bolton family was also near neighbors on Powell River.

Their first child, Ollie, my grandmother, was born on May 5th, 1874 and in June of 1876, their first son, Charles Tipton Bolton was born.

On December 5, 1876, with two small children on a cold, bleak day, Margaret buried her father, Samuel (not Saluel, no matter what the headstone says) Clarkson, here in the Clarkson family cemetery, beside her grandparents and in all likelihood, her great-grandparents as well, although their graves are unmarked.  We know that Nancy Workman Muncy, Margaret’s great-grandmother, in the 1860 census, at age 99, was living with her daughter and husband, Agnes Muncy Clarkson and Fairwick Clarkson, so she is assuredly buried here as well as Fairwick’s mother, Sarah Cook Clarkson who died in 1863.

???????????????????????????????

Margaret would have stood in this cemetery two years earlier too, probably beside this exact same barn, in February 1874, heavily pregnant with my grandmother Ollie when her grandfather, Fairwix Clarkson died and was buried here.  The cemetery is called the Cavin Cemetery today, but it’s really the original Clarkson cemetery.

Clarkson Homesite

In May of 1876, Margaret (often spelled Margret in the church records) and Joseph Bolton were among the 18 people listed as founders of the Little Mulberry Church in Hancock County.

Little mulberry

In 1877, in the Rob Camp Church minutes, Margaret’s two sisters, Clementine and Catharine are baptized with a group of other people, probably during or following a revival.  However, in July 1880, Clementine is cited and then excluded by the church for the horrible infraction of…..dancing.  Now, I bet that was the talk of the neighborhood!!!

But Clementine is not alone.  In 1879, and again in 1887, Joseph Bolton is in trouble at Mt. Zion for drinking and swearing, so they apparently did not remain members at Little Mulberry long.

In 1880, Margaret and Joseph appear to be farming Joseph’s mother’s Herrell land in Hancock County, near the Clarkson land on near the Powell River.  They have three children.

Hancock County was actually a rather small community of sparsely populated mountain valleys.  Word traveled much faster than one would think.  In 1885, the Hancock County courthouse burned.  That must have been the talk of the county for months.  Goodspeed’s History in 1886 says that all records were burned and there were no plans “of yet” to replace the courthouse.  In 1930, the new courthouse burned as well.  Amazingly, some records do remain, mostly chancery suits after the first fire.

The 1890 census is missing of course, but we know that in 1892, Joseph Bolton’s mother had died and the heirs conveyed her land, so it’s very unlikely that Joseph continued to farm that land.

In the 1900 census, Margaret and Joseph appear to have moved as they are found in the 8th District and in 1910, they reportedly live on Back Valley Road as detailed in the article about Samuel Bolton, their son killed in WWI.

In 1907, Margaret’s mother, Elizabeth “Bettie” Speaks Clarkson, died on the old Clarkson home place at 75 years of age.  She outlived her husband by 31 years and never remarried.

Elizabeth Speaks 1896

This is the only family picture known of Bettie Speaks. It’s thought to have been taken about 1896 and it’s possible that Margaret Clarkson Bolton is in this photo.  If so, she would be the eldest child, possibly the person to the furthest left in the middle row or the furthest right in the rear.  Bettie Speaks is in the center of the middle row in the black dress.  If anyone can further identify these people, I’d surely appreciate it!

Margaret Clarkson and Joseph Dode Bolton had 11 children from 1874-1897, of which, at least 2 died young.  They could be buried in the Clarkson cemetery.

  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 Tilda, died before 1953.
  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.

Of these children, only two females lived to have children, other than Ollie.  Ollie has no living descendants who carry her mitochondrial DNA.  I have a DNA testing scholarship for anyone, male or female, who descends from either daughter, Elizabeth or Mary Lee through all females to the current generation.  Mitochondrial DNA is passed from mother to all of their children, but only females pass it on.  Margaret’s mitochondrial DNA would tell us a great deal about her ancestry.

Land

We only know of one parcel of land that was actually owned by Margaret Clarkson and Joseph Bolton.

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 deceased, 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.

As you can see on the map below, Sulphur Hollow connects directly with Hoop Creek Road to the southwest and to Mulberry Creek to the northeast which follows 63 and then dumps directly in the Powell River.

sulphur hollow

If you look carefully at the map below, you can clearly see the loop of “Slanting Misery” at the top of the map.  The Clarkson land is just to the right of where Mulberry Creek empties into Powell River, so Joseph Bolton and Margaret Clarkson Bolton moved about a mile from the land where she was born.

sulphur hollow mulberry creek

You can see in this satellite view that this land is quite mountainous.  On the map below, you can see the original Clarkson land where the cemetery is located at the red arrow.

sulphur hollow and clarkson land

It’s uncertain whether Margaret and Joseph owned land in 1918 when their son died, or in 1920 when both Margaret and Joseph died of the flu.  Typically, if people owned land, they would be buried in a family cemetery on their own land.  I did not find a deed for the sale of their land in Sulphur Hollow, and it’s possible that their residence in Back Valley and Hoop Creek was actually this same land, but we don’t know for sure.

Passing Over

Margaret and Joseph both died in 1920, within days of each other, during the last part of the Spanish flu epidemic that began in 1918.  Family rumor was that he died and the family put the body in the barn or woodshed and waited for her to die before burying both of them.  According to Joseph’s death certificate, he was buried relatively quickly, so the “double funeral” rumor, although quite romantic, isn’t true.

margaret clarkson bolton death

Margaret is buried beside Joseph Bolton in the Plank Cemetery, in Claiborne County, just across the county line from Hancock County, where Joseph’s father is also buried as well as their son, Samuel, who died in 1918.

bolton14'

There are many unmarked graves in the Plank cemetery.

Bolton15

A Good Story

Recently, someone commented that these articles make “it sound so easy.”  What sounds easy?  Everything about genealogy – especially finding ancestor’s graves and land.  That’s because it’s only the success stories that I’m sharing.  What you see is what I found, positively, about these ancestors – over a cumulative 35 years of research.

What you don’t see are the complete bombs, near misses and unproductive research trips, and let me tell you, there were many.  But even those misadventures have redeeming qualities.  I want to share one wonderful, but not terribly genealogically successful, trip to Claiborne and Hancock County in the 1990s when I met Mary Parkey, a woman who is very likely a cousin, who graciously agreed to show me around.  How I wish we could test Mary’s DNA to confirm that cousin theory.

Without Mary, I would never have found these locations.  This terrain is beautiful, but confusing and inhospitable and I am constantly lost there, even with a map.  We didn’t have GPS then, but GPS doesn’t work today because in many places the mountains are too steep for the GPS to see their satellites.  Cell phones don’t work either.

Sadly, Mary perished in the fire when her home burned on March 9, 2000.  Along with Mary, all of the genealogical records and holdings of the Claiborne County Historical Society perished as well.

Mary and I found Clarkson burials and land.  They were related, cousins, just not MY ANCESTORS, which is who I wanted to find.  So close, literally, but so far away.  So, come on along with Mary and me on our great adventure in 1992!

Roberta and Mary’s Great Adventure

In 1992, during my last research visit to Claiborne County prior to Mary Parkey’s death, Mary and I had a great adventure, which I am recording here as a fond memory, although at the time, parts of it were really pretty frightening.  Genealogy is always full of adventures of one sort or another but these were, well, unique.

I had recently purchased a small red car, a Chrysler Sundance prior to my visit.  I had decided to drive the smaller Sundance instead of my larger mini-van with higher clearance due to the Sundance’s increased gas mileage.  Mary and I visited many graveyards, and in at least one, we needed both a tractor and Boyd Manning to gain entrance to the Clarkson cemetery behind his house and through his pasture.

Mary indicated that she knew where there was either an old Herrell house or a graveyard, or both.  Much of the area we were traversing was very remote, to the point where if you got lost, it might be days until someone found you.  We started down a long one-track path, and clunk, my car bottomed out on a hidden rock in a large puddle, and we couldn’t go anyplace. We were stuck, like a turtle on a post.  No amount of pushing or pulling would help, so we decided in our infinite wisdom to just walk on down the hill toward the Powell River to wherever it was she thought we should visit.

mary parkey

This is Mary beside the area where we were stuck. Powell River was at the bottom of the hill.

Upon turning the corner at the bottom of the hill, we were stuck by two things.  First, the beauty of the river, still untamed and wild after centuries.  There is simply no place more beautiful than Appalachia in the springtime.

mary parkey spring

Peeking at the Powell River through the leaves budding.

mary parkey powell river

The mountains the beautiful pink flowers.

mary parkey buds

However, turning to look the other way, we were greeted with quite another sight.

mary parkey cabin on powell river

Upon investigating this further, I decided to approach and knock on the door, until I saw the skull.  What you can only see the edge of is a huge pile of beer cans in the lower right spilling into the driveway.  This pile was probably the size of a full sized van.  I don’t think this was quite what Mary, a never-married devoutly religious reverend’s daughter, had in mind.  She looked horrified.  Seeing the look on her face, I knew we were in trouble.

mary parkey cabin closeup

After really taking stock of things, this place seemed rather unfriendly and somewhat inhospitable, to put it mildly, and Mary and I decided to leave very quickly, and hike back up the hill.  However, given that our vehicle was in fact blocking the only exit (or entrance) to this location, and we didn’t really want to meet the residents, we had to figure out how to obtain help quickly.  This was before the days of cell phones, and even today, more than 20 years later, cell coverage in the mountains of Tennessee is spotty at best, and this kind of steep terrain is not a good candidate for any reception.  So we started walking on the “main” road which was at least paved.

No one passed us, and several minutes later we came across an orange truck with someone sleeping in it.  We discussed what to do, so we decided to make noise.  No luck.  So we knocked on the window of the truck.  No luck.  So finally we opened the door and woke the poor guy up.  He was scared half out of his wits.

We told him we were stuck and needed to be pulled off of the rock.  He told us that he wasn’t allowed to do that.  We asked if he was allowed to sleep on the job.  That nice gentleman decided to help us after all and here is the photo of the truck and the car after we were pulled out of the large puddle.  But guess who got to crawl under the car in the mud to attach the tow chain.  Well, it certainly wasn’t him.  However, we were grateful for the help regardless.  We figured it beat the heck out of waiting for the residents of the house to return.

mary parkey adventure

My family hadn’t been interested in coming along on this genealogy adventure.  I told them over and over how much I loved the mountains, and they knew well that I’d love to live there, but didn’t because I couldn’t make a living.

One of the areas that we had to traverse to visit the old Clarkson cemetery behind Boyd Mannings took us through a gully that held an old log cabin.  I don’t know who originally owned this cabin, but it could well have been one of our Clarkson family members who owned the land adjoining the Manning (Mannon) land.  One thing is for sure, certainly our family visited there, as everyone visited all the neighbors in those days.  E. H. Clarkson, who is buried in the cemetery on this land was one of the founding members of the Mt. Zion Church which is also very close by.  This was likely his land.

Mary said the current owners had purchased a mobile home and moved “up the holler”, meaning in this case more near to the road.  However, when they left, it was like the cabin in the hollow was suspended in time.  We went inside as there were no locks and the doors weren’t shut, and mason jars lines the shelves, tattered curtains hung on the windows – time just stopped there many years before.  I could well imagine the voices of generations of children when the cabin wasn’t old – children who had long ago died after living long lives and were in fact buried with their parents and grandparents in the graveyard watching over the house like a silent sentinel from the bluffs above.

As we approached this dwelling, I was struck by the realization of how difficult the lives of those who lived here must have been.

mary parkey clarkson land

Mary and I couldn’t imagine how one could ever get a car into this hollow, let alone back out again.  Maybe they couldn’t which is why there were so many car carcasses abandoned here.

mary parkey clarkson land2

I find old cabins fascinating, and I surely wish this one had been more accessible to a road.  Looking at this building closely, we see the evidence of good years and bad years.  The good years are marked in time by the addition of rooms.  Look at the logs whose ends are protruding half way through the house. This surely looks like the house was built in at least two distinct sections.

mary parkey clarkson land3

Take a look at the elopement door on the second floor in the above photo.  Family history tells us that one of our McNiel ancestors eloped out a door like this with her beau, but not this house or these families.  At least, I don’t think so….

The other end shows evidence of mudding.  This could be a third addition, or the original logs were in such poor condition that they simply tried to mud over the entire end of the structure.  Watch that step though, it’s a doosie.

mary parkey clarkson land4

This family was fortunate.  Their water source, a nice spring, emerged from a small cave and was still running into a little collection pond close by.  This fresh spring would have made this location a prime piece of real estate to original settlers.

If I closed my eyes, I could hear the children running with their buckets to the spring to fetch the water.  I could also see the forlorn folks in the winter when times were cold and when sadness visited with the deaths of children, lovingly washed, then taken up the hill to rest forever.  Trips to the well were not always happy events.

mary parkey clarkson spring

In later years, they would bring water for the many washing machines strewn about the place.  Clearly getting things into the holler was so difficult that there was never a need to remove them. Wash was done outside under a somewhat protected area with 3 or 4 tubs.

There was evidence of outside cooking as well.  A summer kitchen was probably used when possible.

mary parkey clarkson land5

I’m sure when this laundry arrangement was achieved, that some woman that I am probably related to was exceedingly happy and quite the envy of her neighbors with her outside laundry and tubs.  No longer did she have to go to the spring or scrub on a washboard in a tub.  Quite a modern convenience.  Again, closing my eyes, I can hear her husband bringing home a labor saving device, relieving her aching back.  Women then had to do laundry, literally, by hand, for their families which might consist of a dozen or more people plus extended relations.  Yes, he would have been a very popular fellow.

mary parkey clarkson land6

Everywhere we looked were the remnants of the testimony of the hard lives people lived. However, with another glance, was also the beauty in which they lived.  Nothing is free – they sacrificed for this right.  I understood with clarity why my family had always been drawn back to this place of stark beauty, charming, enchanting, captivating.  It had captured my heart.  I would return again and again to these hills to find my ancestors, to find myself, to find my past.

The graveyard was large and may have serviced several families who lived close by.  Many unmarked graves lie under plain field stones, in fact, most weren’t marked by name, but everyone knew who was buried where.  People married their neighbors, so everyone was related in one way or another, just a large extended family.

They feuded like family too, the records of which are in the chancery suits of Hancock County.  After Fairwick Clarkson died, his children fought over his land, some even changing their names.  Some were buried on the old home place with him, others were buried here after moving on, off of the original Clarkson land.  The people buried here are the descendants of Henry Clarkson, Fairwick’s brother, who died in his early 20s.

Regardless, this silent sentinel is not telling the secrets of the decades and now centuries of lives it has watched from these stony bluffs.  The only hints are given by the very worn names on the gravestones, and some of them are now speaking so softly we can no longer hear their voices.

Folks then and some now actively visited the graves of their loved ones and conversed with them.  One of the houses in this cemetery holds the grave of Flossie Akers who died young, probably in child birth or of complications.  Her family built a small gravehouse, enclosed her stone, added her photo which was unheard of in that day and time.  They furnished the house with a table, 2 chairs, curtains, decorations including a vase with flowers on the table, and other homelike accoutrements that make it seems like someone just stepped away and never happened back.

flossie akers grave house

Flossie Akers grave house, above and below.

flossie akers grave house2

Locals tell of the family coming here with picnics to visit with Flossie as long as they lived.  Grave houses were not unusual in this community, especially in the Melungeon familys, but this is the only one in this cemetery.

flossie akers grave house inside

This grave house had a window, curtains, and a door to keep the elements at bay.  Flossie’s stone is inside.

flossie akers stone

I have never seen a photo on a stone this old before, nor in an impoverished area.

flossie akers picture

Flossie was a Minter before her marriage.  Her mother was Martha Clementine Claxton or Clarkson who had married Vig Minter.  Martha was the daughter of Edward Hilton (E.H.) Claxton/Clarkson and Mary Marlene Martin, the daughter of Margaret Herrell and Anson Cook Martin.  Margaret Herrell Martin was the second wife of Joseph Preston Bolton.  Edward Hilton Claxton/Clarkson was the son of Henry Claxton and Martha Walker.  Henry was the son of James Lee Claxton/Clarkson.  After Henry died, Martha married Henry’s brother’s son, William.  Are you confused yet?  So am I.  Welcome to my world of Appalachian endogamy where your family tree looks more like a vine!

So, to figure this all out a little more clearly.  Flossie was related to both Joseph “Dode” Bolton and his wife.  Flossie was Joseph’s half-sister’s granddaughter.  Flossie was also the first cousin twice removed from Margaret Clarkson Bolton, Joseph’s wife.  Intertwined relationships like this are very common among the mountain families.  Both Joseph and Margaret would have stood beside her grave, weeping at her young life gone.

Flossie was 22 when she died in 1915, so the tradition of gravehouses and regularly visiting them was still practiced for some time after her death.  People living in 1992 remembered those cemetery visits.  The furniture in the house was old but not unusable in 1992.  Flossie had lots of Clarkson company in that cemetery.

flora clarkson stone

Flora Clarkson is the granddaughter of Martha Walker through her second Clarkson marriage to William “Billy” Clarkson.

This Clarkson cemetery is full of my family, for as far as I could see, my cousins, although not my direct ancestors who, we would discover years later, are buried in a different cemetery a mile or so up the road.  The earliest marked burials here  E. H. (Edward Hilton) Clarkson and his wife, Mary Martin Clarkson, founders, along with the Bolton family, in 1869, of the Mt. Zion Baptist church nearby.

As always, I have very mixed emotions in old graveyards.  While I’m thrilled to find my relatives, I’m also struck with the sadness of those who have buried loved ones over the years, of deaths too young, of wars and ambushes, of slaves and Indians being forced to leave their land and families, of children leaving their parents, and parents leaving their children.  I am left with a feeling of awe, of reverence, of being allowed to visit a sacred space.  I am always somehow a little amazed that my own flesh and blood is here.  I believe my ancestors accompany me on these adventures, pointing the way sometimes, but others, acting as the trickster.  I can tell my ancestors had quite a sense of humor.  As long as we remember them, our ancestors live.

As I look up after my silent prayers for them, whispered thankfulness for being allowed to find them, I am once again greeted with the spring-kissed beauty, contrasted with barrenness.  It was spring and the land was coming back to life after a well-deserved rest.

I know that I will forever be drawn back here, like a moth to the flame.  I have found what is me.

Upon my return home to Michigan, I shared my experiences with my family whose reactions ranged from complete apathy (teenage son), utter horror (former husband) to mild amusement (grade school daughter).  No one but me thought of it as a great adventure, and certainly, no one wanted to repeat it with me. I tried to convince them of the things that call and pull to me from this land, but they were hearing none of it.  They ignored me.

Finally, in utter exasperation, I pulled out the photos of this long abandoned cabin in the hollow with the wash stations and the elderly cars, spread them out like a big fan on the kitchen table.  I then announced with my best Southern belle drawl, starting with a very slow, “Weellllllll…..”, hands firmly on my hips and a smile on my lips that I had a surprise for everyone…….that I had in fact purchased this ancestral home site and we were moving.

The silence was absolutely deafening, the stares astounded.  Given my love for this land, I truly think they believed me, and had it not been for other circumstances involving my husband’s health, I could have milked this for a good long time.  Suddenly instead of worrying about who was going to get to watch TV, they were worried about who had to do the laundry in the outside tubs, if we’d have electricity and more important yet, a phone, and who had to fetch the water.  These were not the joyful children of my musings I might add.  In fact these children weren’t joyful at all.  Oh, this prank was good, so good, while it lasted.  Sadly, it was just that, a prank.  I didn’t buy the house and there was no cabin in the mountains to call my own that my ancestors had called theirs.

However, in the end, what children are infused with in their youth, they carry with them at some microscopic level, like seeds waiting for the perfect spring moment to sprout.  It would be another 20 years before my daughter would return with me as an adult, herself infected with the love of the mountains and hills, and would ask me, “Mom, where is that cabin and do you think it’s still for sale?

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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.

New Native Mitochondrial DNA Haplogroups Extrapolated from Anzick Match Results

featherI’ve been working with the ancient DNA results these past few days, as discussed in two previous articles, Utilizing Ancient DNA at GedMatch and Analyzing the Native American Clovis Anzick Ancient Results.

As I worked with the Anzick matches at GedMatch at all of the various threshold levels between 1cM and 7cM, each of which produced 1500 matches, except for the 7cM, which produced 1466 matches.  The matches were not always the same, because obviously the sort order was different depending on how matches actually occurred before and after the 1500 cutoff threshold.

Given that, and given the autosomal ethnicity analysis of several individuals, and given that mitochondrial haplogroups A, B, C, and D are not known to be routinely found in the European population, I decided to extract all of the associated mitochondrial DNA haplogroups.  Furthermore, parts of haplogroup X are known to be Native, and haplogroup M, which is quite rare, has long been suspected, but unproven.

In some cases, looking at the Anzick matches, we know that because of the very high level of Native heritage, the individual is either not admixed or only very slightly admixed.  In other words, it makes perfect sense that their mitochondrial DNA is indeed Native as well as their Y haplogroup.  At nearly 100% Native, both of those lines would have to be Native.

We found some surprises.

We found repeated instances of many mitochondrial haplogroups not previously identified as Native.  In fact, with the exception of a couple subgroups of the M and X haplogroups, all of the Native haplogroups were found repeatedly in these samples.

Many of the participants tested at 23andMe, so even if we were to ask them for actual results, they don’t have any to give.  However, even the haplogroup alone is useful, for just this reason – it can be identified as Native.

I maintain an exhaustive list of all Native American mitochondrial haplogroups that have been documented and attributed to Native Americans, along with the source.  To date, there are 62.  I compared the list extracted from the Anzick matches with the known list of proven haplogroups, and found quite a surprise.

There are a total of 85 new haplogroups extracted from this group.  Now granted, there may be a few that will not stand up to scrutiny, in particular, perhaps haplogroup X2b which has long been debated as to whether it is Native as well as European.  Additionally, some of the very basic haplogroups, such as A, B, C, etc. might be broken down further with full sequence testing if that hasn’t already been done. However, the majority of these haplogroups are found repeatedly and in individuals with little or no admixture.  In addition, a paper was released in 2013 that reported that 85-90% of Mexican women’s DNA was indeed Native American.

I view this list of haplogroups as an incredible gift from the analysis of that Anzick child’s remains.  If we can discover this much from the full genomic sequencing of one Native American, imagine what we could do with more.  This new list of 85 provisional Native haplogroups is more, in one fell swoop, than the 62 we have to date from more than 15 years of research.  We’ve increased the list by 138% to a total of 147.

Provisional Native American Haplogroups Extrapolated from Anzick Match Results

  • A
  • A2ab
  • A2c
  • A2c-C64T
  • A2d
  • A2d1a
  • A2e
  • A2f
  • A2f1a
  • A2g
  • A2g1
  • A2h
  • A2h1
  • A2i
  • A2j
  • A2k
  • A2k1
  • A2p
  • A2q
  • A2u
  • A2v
  • A2z
  • B
  • B1
  • B2
  • B2a1a
  • B2a1a1
  • B2b2
  • B2c
  • B2c2b
  • B2d
  • B2f
  • B2g
  • B2g1
  • B4
  • B4’5
  • B4a1a
  • B4a1b1
  • B4f1
  • B5b2a
  • B5b3
  • C1b1
  • C1b11
  • C1b2
  • C1b2a
  • C1b3
  • C1b4
  • C1b7
  • C1ba
  • C1c1
  • C1c1b
  • C1c2
  • C1c5
  • C1c6
  • C2b
  • C4a1
  • C4c1
  • D
  • D1d
  • D4g1
  • D4h1a
  • D4h1a2
  • D4h1a1
  • D4h3a
  • D5a2a
  • D5b1
  • M
  • M1a
  • M1b1
  • M23
  • M3
  • M30c
  • M51
  • M5b3e
  • M7b1’2
  • M9a3a
  • X
  • X2
  • X2a1a
  • X2a1b1a
  • X2b-T225C
  • X2c2
  • X2d
  • X2e1
  • X2e2

I’ll be confirming these as far as possible and  preparing a new comprehensive Native haplogroup list shortly.

 

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.