TIMBER! Forestry practices at AncestryDNA

How is AncestryDNA's new TIMBER procedure selecting our matches?  This is the story of two matches I had which, before Autosomalgeddon, appeared to be identical.

I became aware of these two matches because they showed up on GEDMATCH, and both matched me 18.9 cM on the far end of Chr. 11, where I have my only SubSaharan African segment.  These new Ancestry matches - R. M. and B. D. - were both estimated as Distant, 5th-8th, Low confidence matches under Ancestry version 1.   At GEDMATCH:

me to R.M. Chr. 11 126390369 to 134436845 18.9 cM 2583 SNPs

me to B.D. Chr. 11 126357648 to 134436845 18.9 cM 2574 SNPs

They matched each other, and matched other matches I have at Gedmatch.

I have been interested in this segment for a few years, and am tracking several other matches to it from 23andme and FTDNA's Family Finder, but B. D. was particularly interesting since she is predominantly subSaharan African.  All the other matches I had previously on this segment were mostly European, although they all shared the SSA segment at the end of Chr. 11.   I have not tracked down a common ancestor, but several (including me) have Collins ancestors, two (including R. M.) have Sexton ancestors, one of the Collins appears to have Lumbee connections, and all  for whom I have any information have Appalachian ancestry.   B. D. had a great grandmother from Roanoke, Virginia, who was believed to have Native American ancestry, which fits the mixed race pattern.

Then came the new, revised match list.  Now R. M. is estimated as a Distant, 5th-8th cousin Good match.  But B. D. is no longer a match at all.

I'm puzzled by this - the segment appears to be the same.  

Since we were all AncestryDNA matches before the rollout of version 2, the lack of phasing at gedmatch isn't the problem, since the version 1 set of AncestryDNA matches were phased.   In addition, I have a sister who is also at gedmatch, and B. D. also has a sister there (both sisters tested at 23andme).  My sister matches B. D. in exactly the same place, B. D.'s sister matches me in exactly the same place, and the two sisters match each other.  If a lack of phasing produced a pseudo-segment, it produced exactly the same segment in all four of us.

So I think TIMBER is the most likely reason for the change, but am still puzzled.  What could make the algorithm treat what is apparently the same segment differently in different people?   

Is this significant? While R. M., B. D. and I all appear to have the same number of matches in our shared segment, over the whole genome R. M. matches 1638 segments and I match 1343 segments, while B. D. matches only 442 (this is at gedmatch).

Could having relatively few matches overall affect the way TIMBER treats a particular match?  After the rollout of version 2 I did note several African-Americans saying they had lost mostly European matches.

The X Chromosome

The previous post described the inheritance of mitochondrial DNA, Y-DNA, and autosomal DNA (Chromosomes 1 through 22), but left out X inheritance, an interesting special case.

You probably know that men carry an X chromosome and a Y chromosome, and women carry two X's.   These are the chromosomes that determine whether you're a man or a woman.    

Women get an X from each parent, recombine them, and pass them on to sons and daughters.   Men get only one, from their mothers, and pass that one chromosome on intact to their daughters.   That causes an interesting pattern of inheritance, shown in charts here from Blaine T. Blettinger's blog, The Genetic Genealogist .

The chart below shows which ancestors can contribute to a male's X chromosome.

This chart shows which ancestors can contribute to a female's X chromosome.

X ancestors include the ancestors who contributed your mitochondrial line, but they also include many more, in the case of females even including some ancestors from the father's side.   One way of thinking of X inheritance is that it can't involve two males in a row in the inheritance line, since X's no man gets an X from his father - he gets a Y.

Because of the special case of fathers passing on the X they inherited from their mothers intact, females have one X that came directly from their paternal grandmothers.    So, in contrast to autosomal DNA, which is divided and recombined every generation, X DNA is divided and recombined only when inherited from a female.   This makes it hard to estimate how many generations back a given size match on the X is.

Haplogroups, Autosomal DNA and DNA Relatives

Autosomal DNA determines your DNA Relatives at 23andMe, and comes from the 22 pairs of autosomal chromosomes that everyone inherits:  22 from your mother, and a matching set of 22 from your father.   Your mother and father sliced and diced the 22 pairs they inherited from their mothers and fathers to come up with the chromosomes they gave you.

Autosomal DNA is divided and recombined in an unpredictable way every generation.  More than 99% of your 2nd cousins (the great grandchildren of your great grandparents) will share enough autosomal DNA with you to detect, but less than 5% of your 6th cousins, the descendants of your GGGGG grandparents, will share enough autosomal DNA with you to detect.   You have thousands of sixth cousins, though, so even 5% of them is quite a few.  Some of your DNA matches may share a common ancestor even further back, since some segments can, through random chance, escape the axe and survive intact for many generations.





I thought my haplogroups would identify my relatives.   What's with all these other haplogroups in my DNA Relatives list?

Although the most important part of our 23andme results are the autosomal results outlined above - those are the results used to identify our DNA Relatives - 23andme also includes our maternal line and paternal line haplogroups, found in our mitochondria, for the maternal line, and Y-DNA, for the paternal line.

Mitochondria are found in every cell, outside the nucleus, and are inherited along the maternal line. Your mitochondrial DNA is inherited with very little change from your mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's mother's (you get the picture) mother.

Only relatives in that direct maternal line share your mitochondrial haplogroup, unless they happened to inherit the same haplogroup by chance.  So most of your relatives don't share your mitochondrial maternal line haplogroup, since they don't have the same female-to-female line.

Y-DNA is found on the Y-Chromosome, which is the chromosome that makes a male a male, so females don't have it.

Men inherit Y-DNA from their father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's father's (etc) father.   Only the men in that direct line share that haplogroup, unless they happened to inherit the same haplogroup by chance.   A female can find her father's Y-DNA haplogroup by testing her father, brother, father's brother, father's brother's son, or other male relative in the direct paternal male-to-male line.  Most of your relatives don't share your paternal Y-DNA haplogroup, because they don't share your direct male-to-male line.

And that is why DNA Relatives is your gateway to finding relatives at 23andMe.   It can include cousins from every part of your family tree, not just the narrow lines that share your haplogroups.