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9-27-2014 – Please note that kit F999912 has been replaced by kit F999913.

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!

Identifying Possible Common Ancestors Utilizing Multiple Tests

There is a significant amount of confusion about DNA matching and which ancestors and ancestral lines can match in which way.

To review, there are 4 different kinds of DNA that we can utilize for genealogy, the Y DNA for males, mitochondrial, X chromosome and autosomal DNA for both males and females.  You can read an intro article about how these different types of DNA are utilized here.

Clearly, the mitochondrial DNA addresses only one line – your mother’s matrilineal line, shown in red below – and the mitochondrial DNA is never divided or mixed with that of the father.  So you share the mitochondrial DNA with thousands of generations of your matrilineal ancestors.  You’ve accumulated a few mutations over those generations, which serve to show us who you are most closely related to.

Y and mito

The Y chromosome is passed only from father to son, shown in blue above.

If you haven’t read this article I wrote about X matching, please do.  Males and females have a different inheritance path for the X chromosome because males don’t inherit an X from their father’s, but females do.

Even better, if you utilize software that can interface with Progeny Software’s Charting Companion, by all means, purchase this add-on program because it shows you on your own tree which of your ancestors X chromosome you have the potential of carrying.  I wrote about how to utilize this great tool here.

x fan

The X chromosome acts like autosomal DNA, the DNA we receive from all of our ancestral lines, including red and blue lines above, and all of the blank ones in-between, meaning that the X chromosome is a candidate to be recombined and divided in each generation.  I say a candidate, because sometimes the X is passed in very large pieces. Not quite what or how we might expect.  I wrote about that here.

But we can’t and don’t know whose X we carry, or which pieces of which ancestors’ Xs we carry – but we do know, based on how DNA is passed generation to generation, whose X DNA we MIGHT carry – and whose we cannot carry.

Because women inherit an X from both parents, and men only inherit the X from their mother, the inheritance pattern through the generations is different for males and females, so each person needs to plot out their potential X ancestors.

A female could carry some part of the X chromosome of any of the ancestors whose names would fall into the pink or blue boxes of this fan chart.  You can NOT inherit any X from someone whose box is blank (no color).

female x chart

These blank charts are courtesy of Blaine Bettinger.  He originally published them on his blog, The Genetic Genealogist, in December 2008 and January 2009 in his articles about how to use the X chromosome for genealogy.

A male’s fan chart for the X chromosome looks a bit different because the male doesn’t inherit an X from his father.  Instead, he inherits the Y chromosome which makes him a male.

x chart male

So let’s see if we can approach this combination of information and DNA test types in a bit of a different way.  A female can inherit the following kinds of DNA from the ancestors listed at the left in the chart below.  This chart compiles information from all of the 4 different types of DNA that we can use for genealogical purposes. Generation number is in parenthesis.

Female’s Ancestor Inheritance Chart

Here’s how to read this chart.

Does a female inherit Y DNA from her mother?  No

Does a female inherit mtDNA from her mother?  Yes

Does a female inherit the X chromosome from her mother?  Yes

Does a female inherit autosomal DNA from her mother?  Yes

­Ancestor Y DNA mtDNA X Chr Autosomal
Mother (1) No – she doesn’t have one Yes Yes Yes
Father (1) No – you’re a female No – only passed from mother Yes Yes
Mother’s mother (2) No Yes Yes Yes
Mother’s father (2) No No Yes Yes
Father’s father (2) No No No – your father didn’t get an X from his father Yes
Father’s mother (2) No No – father’s don’t contribute mtDNA to children Yes Yes
Mother’s mother’s mother (3) No Yes Yes Yes
Mother’s mother’s father (3) No No Yes Yes
Mother’ father’s mother (3) No No Yes Yes
Mother’s father’sFather (3) No No No Yes
Father’s father’s father (3) No No No Yes
Father’s father’s mother (3) No No No Yes
Father’s mother’s mother (3) No No Yes Yes
Father’s mother’s father (3) No No Yes Yes

You can personalize this chart by inserting your own ancestor’s names and complete additional generations by:

  • First following the Y chromosome, which women don’t have to be concerned with, but men certainly do
  • Second, following the mitochondrial DNA inheritance path through the matrilineal line
  • Third, charting your X chromosome potential ancestor into the X Chr column
  • Fourth, simply put yes in the column for everyone for autosomal

This same chart for a male would look somewhat different, but only in the X and Y columns.

Males’ Ancestor Inheritance Chart

Ancestor Y DNA mtDNA X Chr Autosomal
Mother (1) No – she doesn’t have one Yes Yes Yes
Father (1) Yes, you received your father’s No – only passed from mother No – You received the Y instead Yes
Mother’s mother (2) No Yes Yes Yes
Mother’s father (2) No No Yes Yes
Father’s father (2) Yes, your father received his Y No No – your father didn’t get an X from his father Yes
Father’s mother (2) No No – father’s don’t contribute mtDNA to children No – you received no X from your father Yes
Mother’s mother’s mother (3) No Yes Yes Yes
Mother’s mother’s father (3) No No Yes Yes
Mother’ father’s mother (3) No No Yes Yes
Mother’s father’sFather (3) No No No Yes
Father’s father’s father (3) Yes No No Yes
Father’s father’s mother (3) No No No Yes
Father’s mother’s mother (3) No No No Yes
Father’s mother’s father (3) No No No Yes

So, how could this help you with your genealogy?  Let’s say that you match someone on the X chromosome, but you know that you are not a mitochondrial match.  You can look on this chart and eliminate any line that includes a mtDNA match.  You know your X match is not from that line.  You can also eliminate any ancestral line that does not include a potential X match.  The ancestors you are left with are your possible match ancestors.

Let’s use the female chart below as an example.  The greyed out ancestors are those removed by virtue of no mitochondrial DNA match, so anyone with a Yes in that box.  It also eliminates anyone who could not contribute an X chromosome, so with a No in that box.  Any greyed out box eliminated that specific ancestor from consideration.

Please note that by eliminating your mother, it does not eliminate her entire line.  It only means, in this case, that if your mitochondrial DNA doesn’t match, then you and your match don’t share a common mother.  Your mother’s father is still a possibility.  And you can still match on just the X but not through the dual mito line.

Female Example of X Match Ancestor Elimination

female X match ancestor elimination crop

Therefore, only the ancestors left unshaded are candidates for matches.

Male Example of Ancestor Elimination

Of course, on a male’s chart, the X becomes much more restricted due to the fact that men inherit the Y chromosome and not the X from their fathers.  You’ll notice that if a specific ancestor carries a matching Y chromosome, they cannot carry the matching X – they are mutually exclusive.

male x match ancestor elimination2

As you can see, by the time we’re done eliminating possibilities, there are only three possible ancestral lines to pursue for the X match who doesn’t match on the Y or the mitochondrial DNA.

Conversely, if you have someone who matches on the X AND on a mitochondrial line, that is a huge hint and that line would be the first one I would pursue.

You can expand this chart to any number of generations.  I stopped at 3 for illustration purposes.

While this methodology doesn’t exactly tell you who your common X matching ancestor is, it certainly narrows the playing field substantially.  Finding an X chromosome match can be a real bonus, especially when combined with other types of DNA testing.

Ollie Bolton Estes Robbins (1874-1955) and the Wrath of a Woman Scorned – 52 Ancestors #9

Ollie Bolton 1950s

Ollie Bolton was born on May 5, 1874 in a neighborhood called Hoop Creek in Hancock County, Tennessee near the Claiborne/Hancock County line in 1874 to Joseph B. “Dode” Bolton and Margaret N. Claxton/Clarkson.  We don’t know the middle names of either of her parents.

Hoop Creek Map cropped

Ollie was my grandmother, my father’s mother, but I never knew her.  She died in April, 1955, before my birth.

She is the least known of my grandparents.  My Estes family told me stories of her first husband, my grandfather, William George Estes, who she married in Claiborne County, Tennessee on September 26, 1892, but there was no one to tell me stories about Ollie.

We don’t even know Ollie’s middle name for sure.  In some places it’s recorded as Florence, but on my father’s Social Security application, he gives it as Ollie Elsie Bolton.

Ollie applied for a social security number on July 31, 1939.  She is living at 117 S. Hamilton in Chicago.  She is not employed and is age 65 at her last birthday.  She gives her birthdate as May 5, 1874 and her parents as Joseph Bolton and Margreat Clarkson.  No, that is not a typo.

Life Was Hard

Ollie’s life was hard.  She lost her first baby at six weeks of age, the year after she was married, a month and 6 days before her first wedding anniversary.  Her second child followed in 1894.  Not long thereafter, Ollie and William George Estes moved to Springdale in Washington County, Arkansas where Ollie ran a boarding house and tended to her children, with little help from William George.

They moved back to Claiborne County and were living there in 1900, but William George was out of work more than he wasn’t, and he drank.

The 1907 photo of Ollie doesn’t portray her as a happy woman.  Of course, photos can be poor or deceiving, but as of the time this photo was taken, 3 of the 7 children she had born were dead, and one had died tragically.

Estes family 1907

This photo was labeled “1907 Cumberland Gap.”

According to the 1910 census, three of Ollie’s children had died.  We know who two of them are, Samuel who died at 6 weeks of age, and Robert who died when their cabin burned, but there appears to be a third child who died as well – probably born in the spot between 1894 and 1898 – and probably buried in Arkansas.  It’s sad, that child is lost to us and we only knew of their existence from the census records.

Margaret says the family Bible was destroyed in the fire.  It would have told us more.

The death of the child in the cabin fire must have been torturous for Ollie.  The family in Estes Holler says that Ollie had left the children to go to a party.  They don’t say where William George was.  Odd that her absence is mentioned, somewhat scornfully, but his was simply accepted without mention.

It looks like Robert died before 1907.  He was born in 1898 and the photo of the children in 1907 is without Robert.  We know he died after they returned to Claiborne County, which was before the 1900 census.  Cousin George showed me where the cabin that burned had stood, and the willow he planted in honor of the child who died.

I have often wondered if I was named after this child.  It was my father that selected my name of Roberta.

Moving to Indiana

Shortly after the 1910 census, the family moved to Fowler, Indiana and were tenant farmers.

Estes Fowler Indiana

There appear to be some happy times there.  Well, Ollie looks happy even if William George doesn’t. Ollie and William George are on the left and their friends, the Friar’s possibly, on the right.

Estes 1913 Fowler cropped

This family photo is labeled “1913, Fowler, Indiana.”  The adults, other than Ollie and George to the right in the back row, are Ollie’s cousins, with the exception of a family friend.  One of their sons, Joseph was missing in this photo, reportedly at scouts.  My father, William Sterling Estes is the youngest male in the front row on the left beside his brother, their oldest son, Estle.  Beside Estle at the right of the front row are cousins Lee and George Smith.

The Crazy Aunts, adversaries for life, Margaret, brunette on the left and Minnie, blonde on the right, are standing in the second row.

In the rear, left to right, cousins Clara and Mont Bolton, friend Ted Barneo and cousin Elizabeth Baker.

Estes family 1914

This is the only existing photo of the entire family.  Margaret said that it was taken by setting a timer on William George’s camera.  This photo was also taken about 1913.

Shortly thereafter, the family scuttlebutt is that Ollie’s young cousin came to visit.  By young, the young lady was born about the time that Ollie and William George were married.  Ollie came home and discovered her cousin and William George in “the act.”  Ollie grabbed either a bullwhip or a horsewhip, stories vary, but it really doesn’t matter, and proceeded to use it on him/them.  The only thing that saved them was that there were others nearby.  The Crazy Aunts tell us that it took “5 grown men” to restrain her.  Never underestimate the wrath of a woman scorned.

All the Children

Ollie Bolton and William George Estes had the following children, for sure, in Claiborne County, Tennessee, unless noted otherwise.

  • Samuel T. Estes born July 8, 1893, died August 20, 1893
  • Charles Estel Sebastian Estes born November 1, 1894, died August 26, 1972
  • Unknown child per the 1910 census, probably born and died in Arkansas
  • Robert Estes born June 1898, Arkansas, died before 1907, Claiborne County, TN
  • William Sterling Estes born October 1, 1901, 1902 or 1903, died August 27, 1963, Jay County, Indiana
  • Joseph “Dode” Harry Estes born September 13, 1904 died December 9, 1994, Wayne Co., IL
  • Margaret LeJean Estes born November 16, 1906, died August 6, 2005, California
  • Minnie May Estes born October 1, 1908, died February 3, 2008, Steinhatchee, Florida

Moving on to Chicago

There are other family stories surrounding this time as well.  One story says that Ollie was pregnant with twins, that she lost after the scandalous “cheating husband” event.  Another story says that another child, Elsie, was born and eventually died, and that Elsie was “retarded.”  From what was said, Elsie likely had Downs Syndrome.  One Crazy Aunt said Elsie died in Chicago, but there is no death record to support this, or any photos, nor any other indication that this child existed.  Another rumor said there was also a second set of twins that died.  By 1914, Ollie was 40 years old.  She could well have had a Downs Syndrome baby.  However, neither Benton County, Indiana, nor Cook County, Illinois records show the birth or death of any Elsia Estes or infant twins.

Ollie and Margaret 1918

The photos above and below were labeled by Aunt Margaret as “Ollie Bolton Estes and Margaret 1918 Franklin Park, Illinois.”  I have always questioned whether this was Ollie or Ollie’s mother.  Another cousin has this same photo labeled differently which might imply that the women is Ollie’s mother, Margaret Claxton/Clarkson.  The identifier “grandmother” is a matter of perspective.  However, Crazy Aunt or not, Margaret was there in the photo and she should have known if it was her mother or grandmother.

Ollie and Margaret 1918 2

I have a note in my file that Ollie moved to Chicago in 1919, and Margaret sent a photo of Minnie in Chicago in 1922, if she is correct about where it was taken.  I cannot find Ollie in the census in 1920.

In the 1930 census, Ollie had remarried and she and John Robbins lived on Flournoy St. in Chicago.  They had been married for 6 years which tells us that they married in 1924.  She was 55 and he was 47.   He was a clerk with the railroad.  Minnie said she married John Robbins in Chicago, but Chicago marriage records don’t include their marriage.

Ollie was noted in her sister’s obituary in 1935 as Ollie Robbins.  However, in 1953, she is called Ollie Estes in her sister, Ida’s obituary.

In the 1940 census, John and Ollie Robbins are living at 117 Hamilton.  He is 56 and she is 66.  They indicate they lived in the same location in 1935.  Ollie says that she completed the 8th grade.  The 1940 census included several employment questions.  It looks like neither of them were working and neither are seeking work. Ollie indicates she is unable to work.  They rent for $12 a month, which is about half of what other rents seem to be.  There were a few at $10 but mostly they ranged from about $16-$25 with $25 being very common.

By the time my mother met Ollie, about 1950, Ollie was already ill.  Mother didn’t know if John Robbins had died or they were divorced, but he was not in the picture.  Ollie lived with my mother and father during her last illness during my mother’s pregnancy.

Ollie’s death certificate lists her death date as April 9, 1955 and her address as 639 N. Kedzie in Chicago.  Ollie Bolton Robbins, widowed, born May 5, 1872, age 82, was a housewife at home, born in Tennessee and lists her parents as Joseph Bolton and Margaret Claxton.  She was never in the armed forces and the informant was William S. Estes,  listed at the same address, and he signed as her son.  Note that her birth year is off by two years on her death certificate.  I’ve seen this situation many, many times.

Ollie is buried in the Elmwood Cemetery in Chicago.  John Robbins is not buried there.  I visited several years ago and let me say that this grave was not easy to find and the Chicago traffic was abysmal.  I’d rather climb over fences and brave brambles any day.

Cemetery records show that my father bought the lot and the stone, although one of the Crazy Aunts claims that she did, along with two extra plots, asserting that “someone” had then sold the extra plots and pocketed the money.  That’s not what the cemetery records showed, however.  It’s beyond me why anyone would purchase extra plots there.  There was no one else to bury.  But then again, that’s why we call them the Crazy Aunts!  They did make life very interesting with their various wild goose chases!  Every now and then, one produced a goose, or at least a few feathers.

Ollie’s X Chromosome

My father carried all of Ollie’s X chromosome.  Men only inherit an X from their mother, because they inherit the Y chromosome, which makes them male, from their father.  Therefore, I too carry Ollie’s X chromosome, intact, because my father only had one X chromosome to give me.  Therefore, one of my 2 X chromosome is actually Ollie Bolton’s X and theoretically half of what I gave to my children is Ollie’s.  In reality, my children could have inherited anyplace between all and nothing of Ollie’s X, but I definitely carry it intact.

Ollie X fan cropped

My father’s autosomal DNA has never been tested, as he died in 1963, but by phasing my mother’s DNA against mine, I can, in this case, determine my father’s X chromosome and therefore, Ollie’s too.

Phasing is a process where, by process of elimination, when you don’t have both parents DNA, you can determine which DNA belongs to which parent.  For every DNA location, every person carries two nucleotides, either T, A, C or G.  So let’s say that I carry a T and a C for one particular address.  If my Mom carries two Cs, or a C and an A, then we can say for sure that the T came from Dad.  This method isn’t foolproof, because if Mom carried both a T and a C, we have no way of knowing which she gave me and which came from Dad, but it’s better than nothing.

X phased

Therefore, when dealing with X matches, if an X match doesn’t also match my mother, then I know it came from my father, and therefore, also from Ollie.  It’s interesting, the innovative ways we are discovering to identify, “obtain” and utilize the DNA of those long gone.

Ollie stone

Charting Companion from Progeny Software

I’ve got to tell you, I love Charting Companion.  I’ve used it for many years now with my PAF software, although it is compatible with virtually every genealogy software program on the market, as well as Family Search.

Recently, the owners updated the software to include a wonderful new feature where appropriate on reports.  They map and color the X chromosome inheritance path.  I did have to upgrade my Charting Companion software, but at $29.95, it certainly won’t break the bank….and it’s worth every penny.

If you’re jumping up and down, doing the happy dance and hollering “WooHoooo,” I certainly understand.  I did the same thing.

This option is available for all charts that have ancestors: Ancestor, Fan, Hourglass and Bowtie.

There are several ways to select charts in this software, but the most comprehensive selection in one place is on the menu bar.

chart companion

Select the type of chart you want to produce.  Click through the various options and select the information you want to include on your chart.

To select the X-chromosome option, the user simply selects “X-chromosome” in the Color option tab:

Ancestor chart options

When finished, click preview to be sure it’s what you want.  Here are a couple examples of my reports with the X chromosome selected.

X with Fan

x fan

This fan chart can’t reasonably be made much larger than this, in terms of generations.  If you need more, shift to the Ancestor chart which can span pages.  I would suggest providing at least 10 generations when sending information to people you match on autosomal DNA tests.  I include 12 generations to at least get every ancestor off of US soil and back into the old country – or as many as I can get off of US soil:)

Ancestor – X Pedigree

x pedigree 1

x pedigree 2

I love these X reports.  When you match someone on the X, you can send them one of these and they can visually see which of your lines are available for X matching.  These, utilized in conjunction with the regular Charting Companion Pedigree Chart report are a powerful combinational tool.

My Favorite Report

I generate a pedigree chart for each “side” of my tree, Moms and my Dad’s.  Often, based on my matches, I immediately know which side the new match is from, so I only send them the relevant information.  If need be, I just send both files.

I’ve been a long time user of this software.  I do have a tree at Ancestry but I hate to refer anyone there.  Conversely, I hate receiving links to Ancestry trees.  I much prefer Rootsweb/WorldConnect.

All trees have some inherent problems.  First, how would a match even begin to know what surname to search for or where to find it on my tree.  Secondly, every time I view someone’s tree, Ancestry does me the favor of forever mailing me after that with their updates and such by attaching their tree to my account.  I hate that.  And yes, I know I can go in and one-by-one, undo Ancestry’s favor, but why should I have to do that?  And I certainly don’t want to make anyone else do that either.  Sending a pedigree chart provides them with only the relevant information without being invasive, problematic or being a “forever” thing with an attached tree.  We’re only looking here, not getting married:)

So, I send a pedigree chart of 12 generations in a pdf file with an index at the end.

If you select 4 generations per page, each item will have the associated location information.  5 generations per page makes the 5th generation default to only date information, meaning they won’t be able to see locations, so don’t do that.

Select the index option to add the index at the end.  This makes it easy for people to skim quickly for surnames that look familiar.

Lastly, when you have your selection in order, you can preview, and then the “publish” button saves this to a file on your system.

Please note that if you include submitter information, it includes everything including your address and phone number in the lower left hand corner.  I do not include that information in the pdf file I send to matches.  I wish the software had a submitter name/e-mail only option.  That’s it though, my only suggestion for this software.  I love it!

pedigree chart

Chart above, index below.

pedigree index

Neanderthal Genome Further Defined in Contemporary Eurasians

DNA X

A new study released by Howard Hughes Medical Institute at Harvard Medical School on January 29th titled “When Populations Collide” provides some interesting insights about Neanderthal DNA in modern humans.  This study compared the full Neanderthal genome to that of 1004 living individuals.

In general, people in East Asia carry more Neanderthal than Europeans who carry 1-3%, and Africans carry none or very little.  It appears, according to David Reich, that Neanderthal DNA is not proportionately represented in contemporary humans, meaning that some areas of Neanderthal DNA are commonly found and others not at all.  Some Neanderthal genes are carried by more than 60% of Europeans or Asians, most often associated with skin and hair color, or keratin.  Reich’s thought is that people exiting Africa assimilated with Neanderthals and selected for these genes that gave them an adaptive and survival advantage in the cooler non-African climate.

One particularly big Neanderthal genetic desert is the X chromosome, a phenomenon called hybrid sterility.  Reich suggests that this means that when Neanderthals and humans exiting from Africa interbred, they were on the cusp of being unable to reproduce successfully.  Reich explains that “when two populations are distantly related, genes related to fertility inherited on the X chromosome can interact poorly with genes elsewhere in the genome and that interference can render males, who carry only one X, sterile.”

Given the recent discussions about the X chromosome and the possibility that it may be inherited in an all-or-nothing manner more often than the other chromosomes, I had to wonder how they determined that this was hybrid sterility and not an case of absence of recombination.

Reich’s team apparently had the same question, so they evaluated the genes related to the function of the testes, confirming they too had a particularly low inheritance frequency of Neanderthal DNA.  These, combined, would eventually cause the X to be present in very small quantities in the genome of descendants since the Neanderthal X could only be inherited from women and then would cause the resulting males to be sterile.  So in essence, only females could pass the X on and only their daughters would pass it further.  Males carrying that X not only wouldn’t pass the X, they wouldn’t pass anything at all due to sterility.

If, in addition to this, the X has unusual recombination features, that could exacerbate the situation.  Conversely, if the X is inherited intact more often than not at all, it could increase the likelihood of the X being brought forward in the population.

Reich says his team is now focused on looking at Neanderthal DNA and human disease genes.  He says that his new study revealed that lupus, diabetes and Crohn’s Disease likely originate from Neanderthals.

Another study, published the same day in Science titled “Resurrecting Surviving Neandertal Lineages from Modern Human Genomes,” reaches the same conclusions about the Neanderthal inherited traits related to skin color.  This study compared the full genomes of 379 East Asians and 286 Europeans to Neanderthal genomes and discovered that they could map about 20% of the Neanderthal DNA in those individuals today.  This, conversely, means that 80% of the Neanderthal genome is missing, so either truly missing or simply missing in the people whose DNA they sequenced.  It will be interesting to see what is found as more contemporary genetic sequences are compared against Neanderthal, and as more Neanderthal DNA is found and sequenced.

Fortunately, recent advances in dealing with contaminated ancient DNA hold a great deal of promise in terms of increasing our ability to sequence DNA that was previously thought to be useless.  This report is described in the article “Separating endogenous ancient DNA from modern day contamination in a Siberian Neanderthal” and was used in the sequencing and analysis of the Neanderthal toe bone found in Siberia.

To better understand the legacy of Neanderthals, Dr. Reich and his colleagues are collaborating with the UK Biobank, which collects genetic information from hundreds of thousands of volunteers. The scientists will search for Neanderthal genetic markers, and investigate whether Neanderthal genes cause any noticeable differences in anything from weight to blood pressure to scores on memory tests.

“This experiment of nature has been done,” says Dr. Reich, “and we can study it.”

That Unruly X….Chromosome That Is

Iceberg

Something is wrong with the X chromosome.  More specifically, something is amiss with trying to use it, the way we normally use recombinant chromosomes for genealogy.  In short, there’s a problem.

If you don’t understand how the X chromosome recombines and is passed from generation to generation, now would be a good time to read my article, “X Marks the Spot” about how this works.  You’ll need this basic information to understand what I’m about to discuss.

The first hint of this “problem” is apparent in Jim Owston’s “Phasing the X Chromosome” article.  Jim’s interest in phasing his X, or figuring out where it came from genealogically, was spurred by his lack of X matches with his brothers.  This is noteworthy, because men don’t inherit any X from their father, so Jim’s failure to share much of his X with his brothers meant that he had inherited most of his X from just one of his mother’s parents, and his brothers inherited theirs from the other parent.  Utilizing cousins, Jim was able to further phase his X, meaning to attribute portions to the various grandparents from whence it came.  After doing this work, Jim said the following”

“Since I can only confirm the originating grandparent of 51% my X-DNA, I tend to believe (but cannot confirm at the present) that my X-chromosome may be an exact copy of my mother’s inherited X from her mother. If this is the case, I would not have inherited any X-DNA from my grandfather. This would also indicate that my brother Chuck’s X-DNA is 97% from our grandfather and only 3% from our grandmother. My brother John would then have 77% of his X-DNA from our grandfather and 23% from our grandmother.”

As a genetic genealogist, at the time Jim wrote this piece, I was most interested in the fact that he had phased or attributed the pieces of the X to specific ancestors and the process he used to do that.  I found the very skewed inheritance “interesting” but basically attributed it to an anomaly.  It now appears that this is not an anomaly.  It was, instead the tip of the iceberg and we didn’t recognize it as such.  Let’s look at what we would normally expect.

Recombination

The X chromosome does recombine when it can, or at least has the capacity to do so.  This means that a female who receives an X from both her father and mother receives a recombined X from her mother, but receives an X that is not recombined from her father.  That is because her father only receives one X, from his mother, so he has nothing to recombine with.  In the mother, the X recombines “in the normal way” meaning that parts of both her mother’s and her father’s X are given to her children, or at least that opportunity exists.  If you’re beginning to see some “weasel words” here or “hedge betting,” that’s because we’ve discovered that things aren’t always what they seem or could be.

The 50% Rule

In the statistical world of DNA, on the average, we believe that each generation receives roughly half of the DNA of the generations before them.  We know that each child absolutely receives 50% of the DNA of both parents, but how the grandparents DNA is divided up into that 50% that goes to each offspring differs.  It may not be 50%.  I am in the process of doing a generational inheritance study, which I will publish soon, which discusses this as a whole.

However, let’s use the 50% rule here, because it’s all we have and it’s what we’ve been working with forever.

In a normal autosomal, meaning non-X, situation, every generation provides to the current generation the following approximate % of DNA:

Autosomal % chart

Please note Blaine Bettinger’s X maternal inheritance chart percentages from his “More X-Chromosome Charts” article, and used with his kind permission in the X Marks the Spot article.

Blaine's maternal X %

I’m enlarging the inheritance percentage portion so you can see it better.

Blaine's maternal X % cropped

Taking a look at these percentages, it becomes evident that we cannot utilize the normal predictive methods of saying that if we share a certain percentage of DNA with an individual, then we are most likely a specific relationship.  This is because the percentage of X chromosome inherited varies based on the inheritance path, since men don’t receive an X from their fathers.  Not only does this mean that you receive no X from many ancestors, you receive a different percentage of the X from your maternal grandmother, 25%, because your mother inherited an X from both of her parents, versus from your paternal grandmother, 50%, because your father inherited an X from only his mother.

The Genetic Kinship chart, below, from the ISOGG wiki, is the “Bible” that we use in terms of estimating relationships.  It doesn’t work for the X.

Mapping cousin chart

Let’s look at the normal autosomal inheritance model as compared to the maternal X chart fan chart percentages, above, and similar calculations for the paternal side.  Remember, the Maternal Only column applies only to men, because in the very first generation, men’s and women’s inheritance percentages diverge.  Men receive 100% of their X from their mothers, while women receive 50% from each parent.

Generational X %s

Recombination – The Next Problem

The genetic genealogy community has been hounding Family Tree DNA incessantly to add the X chromosome matching into their Family Finder matching calculations.

On January 2, 2014, they did exactly that.  What’s that old saying, “Be careful what you ask for….”  Well, we got it, but “it” doesn’t seem to be providing us with exactly what we expected.

First, there were many reports of women having many more matches than men.  That’s to be expected at some level because women have so many more ancestors in the “mix,” especially when matching other women.

23andMe takes this unique mixture into consideration, or at least attempts to compensate for it at some level.  I’m not sure if this is a good or bad thing or if it’s useful, truthfully.  While their normal autosomal SNP matching threshold is 7cM and 700 matching SNPs within that segment, for X, their thresholds are:

  • Male matched to male – 1cM/200 SNPs
  • Male matched to female – 6cM/600 SNPs
  • Female matched to female – 6cM/1200 SNPs

Family Tree DNA does not use the X exclusively for matching.  This means that if you match someone utilizing their normal autosomal matching criteria of approximately 7.7cM and 500 SNPs, and you match them on the X chromosome, they will report your X as matching.  If you don’t match someone on any chromosome except the X, you will not be reported as a match.

The X matching criteria at Family Tree DNA is:

  • 1cM/500 SNPs

However, matching isn’t all of the story.

The X appears to not recombine normally.  By normally, I don’t mean something is medically wrong, I mean that it’s not what we are expecting to see in terms of the 50% rule.  In essence, we would expect to see approximately half of the X of each parent, grandfather and grandmother, passed on to the child from the mother in the maternal line where recombination is a possibility.  That appears to not be happening reliably.  Not only is this not happening in the nice neat 50% number, the X chromosome seems to be often not recombining at all.  If you think the percentages in the chart above threw a monkey wrench into genetic genealogy predictions, this information, if it holds up in a much larger test, in essence throws our predictive capability, at least as we know it today, out the window.

The X Doesn’t Recombine as Expected

In my generational study, I noticed that the X seemed not to be recombining.  Then I remembered something that Matt Dexter said at the Family Tree DNA Conference in November 2013 in Houston.  Matt has the benefit of having a full 3 generation pedigree chart where everyone has been tested, and he has 5 children, so he can clearly see who got the DNA from which of their grandparents.

I contacted Matt, and he provided me with his X chromosomal information about his family, giving me permission to share it with you.  I have taken the liberty of reformatting it in a spreadsheet so that we can view various aspects of this data.

Dexter table

First, note that I have sorted these by grandchild.  There are two females, who have the opportunity to inherit from 3 grandparents.  The females inherited one copy of the X from their mother, who had two copies herself, and one copy of the X from her father who only had his mother’s copy.  Therefore, the paternal grandfather is listed above, but with the note “cannot inherit.”  This distinguishes this event from the circumstance with Grandson 1 where he could inherit some part of his maternal grandfather’s X, but did not.

For the three grandsons, I have listed all 4 grandparents and noted the paternal grandmother and grandfather as “cannot inherit.”  This is of course because the grandsons don’t inherit an X from their father.  Instead they inherit the Y, which is what makes them male.

According to the Rule of 50%, each child should receive approximately half of the DNA of each maternal grandparent that they can inherit from.  I added the columns, % Inherited cM and % Inherited SNP to illustrate whether or not this number comes close to the 50% we would expect.  The child MUST have a complete X chromosome which is comprised of 18092 SNPs and is 195.93cM in length, barring anomalies like read errors and such, which do periodically occur.  In these columns, 1=100%, so in the Granddaughter 1 column of % Inherited cM, we see 85% for the maternal grandfather and about 15% for the maternal grandmother.  That is hardly 50-50, and worse yet, it’s no place close to 50%.

Granddaughter 1 and 2 must inherit their paternal grandmother’s X intact, because there is nothing to recombine with.

Granddaughter 2 inherited even more unevenly, with about 90% and 10%, but in favor of the other grandparent.  So, statistically speaking, it’s about 50% for each grandparent between the two grandchildren, but it is widely variant when looking at them individually.

Grandson 1, as mentioned, inherited his entire X from his maternal grandmother with absolutely no recombination.

Grandsons 2 and 3 fall much closer to the expected 50%.

The problem for most of us is that you need 3 or 4 consecutive generations to really see this happening, and most of us simply don’t have data that deep or robust.

A recent discussion on the DNA Genealogy Rootsweb mailing list revealed several more of these documented occurrences, among them, two separate examples where the X chromosome was unrecombined for 4 generations.

Robert Paine, a long-time genetic genealogy contributor and project administrator reported that in his family medical/history project, at 23andMe, 25% of his participants show no recombination on the X chromosome.  That’s a staggering percentage.  His project consists of  21 people in with 2 blood lines tested 5 generations deep and 2 bloodlines tested at 4 generations

One woman’s X matches her great-great-grandmother’s X exactly.  That’s 4 separate inheritance events in a row where the X was not recombined at all.

The graphic below, provided by Robert,  shows the chromosome browser at 23andMe where you can see the X matches exactly for all three participants being compared.

The screen shot is of the gg-granddaughter Evelyn being compared to her gg-grandmother, Shevy, Evelyn’s g-grandfather Rich and Evelyn’s grandmother Cyndi. 23andme only lets you compare 3 individuals at a time so Robert did not include Evelyn’s mother Shay, who is an exact match with Evelyn.

Paine X

Where Are We?

So what does this mean to genetic genealogy?  It certainly does not mean we should throw the baby out with the bath water.  What it is, is an iceberg warning that there is more lurking beneath the surface.  What and how big?  I can’t tell you.  I simply don’t know.

Here’s what I can tell you.

  • The X chromosome matching can tell you that you do share a common ancestor someplace back in time.
  • The amount of DNA shared is not a reliable predictor of how long ago you shared that ancestor.
  • The amount of DNA shared cannot predict your relationship with your match.  In fact, even a very large match can be many generations removed.
  • The absence of an X match, even with someone closely related whom you should match does not disprove a descendant relationship/common ancestor.
  • The X appears to not recombine at a higher rate than previously thought, the previous expectation being that this would almost never happen.
  • The X, when it does recombine appears to do so in a manner not governed by the 50% rule.  In fact, the 50% rule may not apply at all except as an average in large population studies, but may well be entirely irrelevant or even misleading to the understanding of X chromosome inheritance in genetic genealogy.

The X is still useful to genetic genealogists, just not in the same way that other autosomal data is utilized.  The X is more of an auxiliary chromosome that can provide information in addition to your other matches because of its unique inheritance pattern.

Unfortunately, this discovery leaves us with more questions than answers.  I found it incomprehensible that this phenomenon has never been studied in humans, or in animals, for that matter, at least not that I could find.  What few references I did find indicated that the X seems to recombine with the same frequency as the other autosomes, which we are finding to be untrue.

What is needed is a comprehensive study of hundreds of X transmission events at least 3 generations deep.

As it turns out, we’re not the only ones confused by the behavior of the X chromosome.  Just yesterday, the New York Times had an article about Seeing the X Chromosome in a New Light.  It seems that either one copy of the X, or the other, is disabled cell by cell in the human body.  If you are interested in this aspect of science, it’s a very interesting read.  Indeed, our DNA continues to both amaze and amuse us.

A special thank you to Jim Owston, Matt Dexter, Blaine Bettinger and Robert Paine for sharing their information.

Additional sources:

Polymorphic Variation in Human Meiotic
Recombination (2007)
Vivian G. Cheung
University of Pennsylvania
http://repository.upenn.edu/cgi/viewcontent.cgi?article=1102&context=be_papers

A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome, Science October 2005, Myers et al
http://www.sciencemag.org/content/310/5746/321.full.pdf
Supplemental Material
http://www.sciencemag.org/content/suppl/2005/10/11/310.5746.321.DC1

X-Chromosome Matching at Family Tree DNA

Just as they promised, and right on schedule, Family Tree DNA today announced X chromosome matching.  They have fully integrated X matching into their autosomal Family Finder product matching.  This will be rolling live today.  Happy New Year from Family Tree DNA!!!

In the article, X Marks the Spot, I showed the unique inheritance properties of the X chromosome.  In a nutshell, men only inherit one copy from their mother, because they inherit a Y from their father, but women get a copy from both parents.  Still, you don’t inherit parts of your X from all of your ancestors, so knowing your own X inheritance pattern can help immensely to rule out common genealogy lines when you match someone on the X.

In their informational rollout, Family Tree DNA provided the following information about their new features.

Here is the menu link to the Family Finder Matches menu.

x match 1

On the Family Finder Matches page, there is a filter to show only X-Matches.

x match 2

When you use the X-Match filter on a male Family Finder kit, you should get only matches from the maternal X-Chromosome.

x match 3

Next, like other Family Finder Matches you can expand the advanced bar for a match and click to add the match to the Compare in Chromosome Browser list.

x match 4

Matches are added to the Compare in Chromosome Browser list. You could go right to the Chromosome Browser by clicking on the compare arrow at this point.

x match 5

Next we can also go right to the Chromosome Browser.

x match 6

The Chromosome Browser also lets you filter the match list by X-Matches.

x match 7

Here are three immediate relatives. The first two share X-Chromosome DNA. The third (green) one does not.

x match 8

When we scroll down to the X at the bottom, we see that X-Matching is displayed for the first two but not the third.

x match 9

Moving to the Advance Matching page, X-Chromosome matches have also been integrated.

x match 10

X-Match is an option that can be checked alongside other types of testing.

x match 11