Sunday, December 21, 2008

The X chromsome: WTF?   posted by p-ter @ 12/21/2008 12:06:00 PM

The X chromosome in humans is something of an exception with regards to the rest of the genome--as it's diploid only in females, the population genetic forces on it are slightly different. In particular, the effective population size of loci on the X, in a standard neutral model, is 3/4 that of the autosomes. In different demographic models, this fraction can change, so comparing the X to the autosomes is potentially an important tool for understanding human demography.

In a paper published earlier this year, Hammer et al. analysed a data set they had collected of sequences at 40 loci (20 autosomal and 20 on the X) in a number of populations. They saw a striking pattern (the relevant figure from their paper is on the right): in every population they looked at, their estimate of the ratio of effective population sizes on the X and autosomes was greater than 0.75. After additional analyses, they interpreted this as the signature of polygamy in human history.

At the same time, another group (Keinan et al.) was independently looking at this issue in other datasets. Their analysis, published today is markedly different. In particular, they see the exact opposite of the pattern in Hammer et al.--a decrease in the X/autosome ratio in effective population size compared to 0.75 (a figure from their paper is on the right. Note that the y-axis is the same in both this and the Hammer et al. figure--the x/autosome ratio in Ne. In both, the solid horizontal line is at 0.75). . And this is not due to extremely different methodologies--one of the analyses presented by Keinan et al. is very similar to that in Hammer et al., only using different data.

So this is all a bit odd, to say the least.