X Chromosome Recombination's Impact on DNA Genealogy

by Jared Smith

Please contact me if you have any corrections or clarifications on the following.

Premises and Patterns

First, a few basic premises:

• A man has one X chromosome.
• He gets his single X chromosome from his mother. The X chromosome is NOT passed from father to son.
• A woman has two X chromosomes - one from her father and one from her mother.
• The X chromosome a woman gets from her father is an exact copy of his X chromosome (which, as noted above, he got from his mother).
• The X chromosome men and women get from their mother is typically some combination of their mother's two X chromosomes.

This establishes two patterns that can be helpful in X-DNA genealogical research:

1. Any father-to-son relationship can be excluded from X-DNA research because the X-chromosome is not passed from father to son.
2. Because an X-chromosome is passed exactly from father to daughter, it will remain unchanged for that generation. This means that X chromosomes change less often along father-daughter pedigree lines. Stronger X-DNA matches are more likely to share a common ancestor on father-daughter lines than on mother-daughter lines.

Assuming that how the X chromosome passes from mother to child is always a 50-50 combination of both of her X chromosomes (i.e., a perfect combination of the baby's grandfather's and grandmother's X chromosome), you could expect inheritance patterns and prevalence as in the chart below.

PLEASE keep reading below to learn why the numbers on this chart are NOT ACCURATE!

You'll notice that you're more likely to carry more of the X-chromosome from ancestors along lines with father-daughter occurrences.

Recombination

A typical recombined X chromosome passed from mother to son might look like this (note that in this and all other charts, ONLY the X chromosomes are shown and that color is used only to identify X chromosome segments):

Remember that X isn't passed from father to son, and that sons only have one X chromosome which is a combination of his mother's two X chromosomes.

From parents to daughter, it might look like this:

One chromosome is a copy of the father's and the other is recombined from the mother's X chromosomes.

If you throw in another generation, things get much more complex (only X chromosomes are shown).

Notice that the X-chromosome the daughter got from her father has only one recombination whereas the one she got from her mother has two recombinations. Again, father-to-daughter events are not subject to recombination. An X-DNA test would likely show a stronger relationship to the daughter's paternal grandmother (and her descendants) than to her maternal grandmother or grandfather (and their descendants)... except that things are NOT this straightforward...

Understanding Recombination and Non-recombination

On average, you get around half of your DNA from your mother and half from your father. But this does not mean that each chromosome is inherited 50-50. Recombination (also called crossover) may occur at varying amounts - you may get 80% of the chromosome your mother got from her father and 20% of the chromosome she got from her mother. This means that your X-DNA matches might be found predominantly on one family line over another. This makes the prevalence chart above unreliable in determining actual possible matches.

A few known facts about X chromosome recombination:

• When the two X chromosomes combine within a mother, a segment of one X chromosome starting at one end of the chromosome replaces the corresponding segment on the other chromosome (as illustrated above). Because X chromosome recombination typically occurs only once per child, the number of segments you detect can be a rough indication of how many times it has recombined between the two subjects being compared. However, segments can be entirely overlapped in subsequent recombinations and may not be detectable at all.
• Because recombination happens almost every generation, after several recombinations (i.e., when comparing two people that are not very closely related), the amount of matching X-DNA may be very little... or perhaps none at all.
• Very occasionally double recombination will occur - a segment not at an end of the chromosome will recombine. A middle portion will be from one chromosome and the ends from the other. This can appear to be two recombination events - one at each end of the chromosome.
• There is almost always a bit of recombination on both far ends of the X chromosome - even from father to daughter. Changes in these SNPs can be ignored. The total X chromosome is 196cM in length, but full matches may be slightly less than this.

Additionally, there are instances where a mother's X chromosomes do not recombine at all - she instead passes an exact copy of one of her X chromosomes to her child. This can result in an entire family line where you will not have any X-DNA matches. We're not sure how often non-recombination occurs. Some studies have suggested only 3% of mother-child events don't have X chromosome recombination, though analysis of DNA test results suggests a slightly higher rate. The rate of non-recombination seems to be genetic - it occurs more often in some families than others.

Non-recombination and Family Lines

Consider the following chart where non-recombination has occurred:

You can see that the X-DNA connection from the daughter to her maternal grandmother has been broken. They share none of the same X-chromosome markers. While this means that the daughter will have no X-matches to cousins on her maternal grandmother's line, it also means that she has a 100% match to her maternal grandfather, so any matches she does have are more likely to be on this line. Identifying where non-recombination has occurred or which lines are X-DNA dominant can be valuable to your genetic genealogy research.

Half Matches vs Full Matches

When comparing your X-DNA data with someone else, it's vital to understand half and full matches. These terms are used to describe how your X chromosome SNP markers match another's. The matching tools (such as GEDmatch) will compare the single X chromosome of a man to both X chromosomes of a women. Any of a man's X chromosome SNPs that match EITHER of the woman's X chromosome SNPs will be considered a half match - he only matches one of her X-chromosomes (he can't match both because he only has one X chromosome with which to compare). These display at GEDmatch.com as yellow on the chromosome chart:

This screenshot shows the GEDmatch X-DNA Comparison between myself (a male) and a female cousin. The blue bars indicate matching segments larger than the defined threshold (7cM in this case). The yellow indicates half matches, the green lines indicate full matches, and the red indicates no match. The green lines are full matches only by chance (my cousin's SNPs for both X chromosomes are the same at these locations) - it's the large blocks defined with blue that are of interest.

Full matches for long segments of SNPs (almost) always occur only when comparing men to men. This is because the SNPs of one X chromosome are compared to the SNPs of only one other X chromosome.

This screenshot shows my comparison to an unknown male cousin. Notice the full matches in green and no yellow half matches. This is a match I should look into further. Additionally, because the overlap between both charts above are primarily in the same regions, this means that this unknown cousin is most likely related to me along the same family line as my known female cousin above.

Some matching guidelines to remember:

• A man will always be a 100% (196cM) half match with his mother.
• A daughter will (almost) always be a 100% (196cM) half match with her mother AND her father - one X chromosome is exact to her father and the other will always match SNPs on one of her mother's two X chromosomes.
• Full sisters (or half sisters with the same father) will always be at least 100% (196cM) half matches (they share their father's X chromosome).
• Brothers with the same mother may be full matches, partially full matches, or not matches at all (see below). This depends on how recombination did or did not occur from their mother.
• Notable lengths of fully matching SNPs between women (i.e., both chromosomes match) are quite rare. This typically occurs only when:
  • you're comparing sisters and recombination from their mother results in SNP alignments OR recombination did not occur and both sisters got the same X-chromosome.
  • the parents are related and thus share SNPs on both X chromosomes.

Of note is that the total may be slightly less than 196cM due to testing errors or oddities and recombination that usually occurs at the beginnings and ends of the X chromosome.

A 100% match does not always indicate that X chromosome non-recombination has occurred. And neither does a 0% match.
... but this often causes genetic genealogist to think it happens more frequently than it really does.

Consider two brothers who are not matches. One would assume that non-recombination has occurred and that one brother got his grandmother's X chromosome and the other got his grandfather's X chromosome. This is an unsafe assumption:

The brothers above would not be an X-match, but this does not mean recombination has not occurred - it's possible that recombination happened for both of them, but that it occurred in exactly opposite locations (this is not uncommon).

Because full matches in men indicate portions of the X chromosome that have remained intact over potentially numerous recombination events, you should consider male-male X-matches with much more interest than any other matches.

Piecing Together the X

Consider this chart again...

In this chart, the daughter will be a 100% (196cM) half match to everyone listed EXCEPT her paternal grandfather (no X-chromosome on this path) and her maternal grandmother (the non-recombination results in her not matching any SNPs here). There are no full matches.

What if the daughter had instead been a son and had inherited the non-recombined X chromosome from his mother...

The son would be a 100% (196cM) half match with his mother, but a 100% (196cM) full match with his mother's father. It is possible (though quite rare) that you could be a 100% match to someone many generations back - and as such, you can share notable X-DNA with a very distant cousin.

It's important to note that when comparing any woman, GEDmatch does not indicate which X chromosome you match (the one from her maternal grandmother or the one from her maternal grandfather), only that a match exists. This means that you can only reliably detect non-recombination events by testing grandparents. And even then it can be difficult...

In this example, the son would be a 100% (196cM) half match to both his mother and his grandmother. There would be no way using only these 3 tests to know whether recombination has or has not occurred. You could discover this only by testing the maternal grandfather and discovering that there was no X-match with him.

As you can see, if you're unable to test grandparents (especially maternal grandfathers or paternal grandmothers), X-DNA data will be less useful to you. You can compare X-DNA data for siblings and/or cousins, but piecing together the puzzle is difficult due to the variability of the X chromosome.

Tips and Warnings About Using X-DNA

• Use the amount of autosomal DNA match to determine relatedness, and X-match data to narrow down to particular family lines.
• X-matches that do not share measurable autosomal DNA would generally be distantly related.
• You must consider the type of match (half or full), the gender of those being compared, the number of 'splits' or cross-overs between your matching segments, and the amount of X chromosome overlap (in cM). Like other autosomal comparisons, WHERE the overlaps occur is the most important factor to determining relationships.
• Pay particular attention to male-male X-matches. Even small male-male full matches (perhaps even a few cM) can indicate a relatively close common ancestor.
• X-matches for women can come from either their father's or their mother's lines. However, X-matches for men can only come from their mother's line. If you're a woman, test your brother - any common X-matches will certainly be via your mother's line.
• Notable overlap between women does not always indicate a close common ancestor due to recombination (or the lack thereof). I have a half match on 80.4cM (nearly half of the X chromosome) with a 4th cousin once removed (the first GEDmatch screenshot above)!
• Because X-comparison tools compare both X chromosomes when comparing women, do not set a too low SNP matching threshold. It's possible that it could suggest half matches where it is merely chance that the numerous SNPs match. In other words, comparisons with and between men are typically more reliable.
• Remember the inheritance patterns and ignore father-son lines. If you have a strong X-match you can't identify, look at father-daughter lines where X-DNA can recombine at most once every other generation as opposed to every generation with mother-daughter events (the added complexity of this endeavor is that surnames can change every generation). My 80.4cM cousin and I both have father-daughter alternating lines back to my 4th great grandfather. We would not have found our shared ancestor without deeply examining these lines.
• A strong X-match almost certainly shares a common ancestor with you along the X-inheritance paths. However, lack of an X-match doesn't mean they always fall outside the X-inheritance paths.
• Test your grandparents! Beyond the obvious autosomal matching benefits, knowing how much of your X chromosome you got from each grandparent can be informative.
• If you can't test your grandparents, identify common ancestors you share with cousins. Noting the prevalence of your X-DNA overlap can give insight into how strong or weak that X chromosome line is.
• Non-recombination can make things difficult. It's possible that you will have a 0% match with a grandparent (or even a sibling). But this also means you share a 100% match with that grandparent's mate - this can help you eliminate and favor certain lines with your X matches.

While X-DNA can be a difficult and unpredictable aspect of genetic genealogy, understanding how it works can help you unlock ancestry mysteries.