Hey, Peter! The short version is: Other than the fact that the X-chromosome has a unique pattern of inheritance and, for males, it's "naturally phased" (a term Debbie Kennett reminded me of) in that we know positively it came from the mother, in my opinion nothing else about it deserves special treatment for genealogy.
Now, since I never expect anyone to take my opinion as worth anything without explanation, and because we all know I can't say anything in 50 words...
A centiMorgan isn't a physical measurement at all: it's a computation via a linear equation to describe genetic linkage. It's intended to look at something that is a physical measurement--the distance between two base pairs, or loci, along a chromosome--and arrive at an estimation of genetic relationship based on an average of the expected number of per-generation crossovers that will occur in that specific region during formation of a gamete. One centiMorgan is equivalent to a 0.01 (or 1%) chance of a single-generation crossover occurring.
Everybody with me? A centiMorgan isn't a measurement. It's a "mathy" guesstimation of the odds that nucleotides in your chromosomes will swap around with others during meiosis. It's all about genetic diversity. And that's why centiMorgan's are never the same value between different chromosomes, or even between different stretches along the same chromosome. And why we should kinda ignore it when we see centiMorgans evaluated out to two decimal places: the estimation ain't nearly that accurate.
Okay; now. The female and male human genome map is quite different when it comes to the expected number of crossovers. During oogenesis, the production of an egg, the female's DNA goes through crossover significantly more than does a male's during spermatogenesis. In fact, the number of crossover events in males is only about 59% (give or take a little) that of a female. I will refrain from any comments dealing with "underachievement." Ahem.
In rough, whole numbers, the ovum is the result of about 45 crossover events during meiosis, and the sperm the result of about 26. An aside: ya know those autosomal segments we talk about all the time? Ta dah! There they are. For the autosomes, you get 22 segments from your dad and 22 from your mom. Easey peasey. But to get those, your mom produced 45 distinct segments that came from her parents, and your dad produced 26 from his parents. With 71 segments in the mix from each ancestral couple, you can see how things get stirred up and the segments sizes reduced really quickly as the generations proceed.
Part--but by no means all--of that difference between the female and male genomic maps is the X-chromosome. BTW, when the debates begin about using very small segments for genealogy, seemingly often overlooked is that what we see from the testing/reporting companies are sex-averaged centiMorgan values. With small segments, the difference between the two genome maps can be enough to completely wipe-out a supposed segment depending upon segment size and the gender of the test-taker.
In males, the X-chromosome never goes through crossover (except, as noted earlier, in the very small pseudoautosomal regions that the testing companies don't evaluate anyway). In that regard, it behaves like the Y-chromosome. Males always contribute the whole kit and kaboodle to their offspring.
By definition, no crossover events, no centiMorgans. There is no centiMorgan evaluation to be had for the X-chromosome of a male because it will not be recombining during meiosis. Here's a screenshot from Rutgers University showing the centiMorgan evaluation of the X through the first 200,000 base pairs (it can't compute any lower); up to (approximately) the end of the first pseudoautosomal region (PAR2 is minuscule); and then up through 155 million base pairs, close to the whole thing:
In the male genome map, cMs can be calculated for the PAR only. The rest is always zero because the chromosome doesn't go through crossover except in that small initial region which is useless for genealogy (that function, other than the area also containing some protein-producing genes, is really just to allow the X and Y to properly split at fertilization and to pair together in male embryos).
What we see in the results from the testing/reporting companies with X-chromosome matching involving male test-takers is not a direct evaluation of their genome maps, but is the result of a guesstimate of what crossovers occurred in the mother during oogenesis.
As far as our own evaluations for genealogy, there are really only three things that distinguish the X-chromosome from the autosomes:
- It has a unique inheritance chain that can be extremely informative.
- In males it comes packaged as naturally phased: we know exactly which parent donated it. That said, however, male-to-male test-taker comparisons hold no other special properties; the X has gone through crossover just like the autosomes with each and every maternal ancestor.
- The X is a bit...quirky and, while it goes through crossover in oogenesis, the result seems to be somewhat less predictable over generations than with the autosomes. A bunch of people have written about this, from Roberta Estes to Leanne Cooper to Jim Owston to Jared Smith.
All told, though, I agree with Blaine Bettinger's take in this paper. In a crowd-sourced study (not associated with the Shared cM Project) he looked at 250 grandchild/grandparent pairings. What he found was that the X-chromosome could be passed through intact, or go through as many as five crossovers, with an average of 1.655 crossovers per meiosis event. Part of the impetus for the project was a general view that there was something inherently different about crossover and the X-chromosome. There proved not to be. And a general takeaway is that, for genealogy, there's no reason to treat it any differently than the autosomes: i.e., segment sizes--regardless of male or female test-takers--should be evaluated and weighted just like autosomal segment sizes.
