Comments on: The X chromsome: WTF?

By: p-ter

p-ter — Tue, 23 Dec 2008 17:04:17 +0000

Could it be that Hammer et al. oversampled the descendants of polygamists and vice versa for Keinan?

don't know, i kind of doubt it. I think it's more likely to be something like what hawks suggests--different ways of calibrating mutation rates.

keinan et al have three analyses--one of differentiation, one of the allele frequency spectrum, and one of diversity. hammer et al. present data based on diversity only. looking that those other two aspects of the data in the hammer et al. dataset would probably shed some light on where the discrepancy is coming from.

By: blah

blah — Tue, 23 Dec 2008 10:58:21 +0000

Just thinking out loud, but is it possible that estimators of Ne can exhibit nontrivial sampling variance?

My stats is certainly stronger than my pop gen, but recall the Genghis Y chromosomal incident. Could it be that Hammer et al. oversampled the descendants of polygamists and vice versa for Keinan?

Either that or someone may have a sign error a la poor Geoffrey Chang.

By: bbartlog

bbartlog — Tue, 23 Dec 2008 07:08:34 +0000

There are only two directions of skew possible, so I don’t see what third and fourth conclusions you have in mind. And while it’s easy to (metaphorically) stroke your beard and pontificate about confirmation bias, the methodology used is described in pretty good detail. If there is a shortcoming in either team’s work it should be possible to outline it. Unfortunately I can’t see the full paper of Keinan et. al. to make the point by point comparison.

By: Alan Kellogg

Alan Kellogg — Tue, 23 Dec 2008 01:03:37 +0000

Over at Gene Expression Fils Razid noted that the two different conclusions were drawn from different data. I suspect that an analysis using all available data would produce a third conclusion. And that if one included all relevant data a different conclusion would be reached.

We have a habit of selecting that which supports our thinking, and shying away from observations and evidence that contradicts it. This being as true of those working in genetics as in any other field of inquiry.

By: Jason

Jason — Mon, 22 Dec 2008 10:58:05 +0000

yes, of course. duh. thanks for setting me straight, p-ter.

By: p-ter

p-ter — Sun, 21 Dec 2008 20:18:30 +0000

males account for 1/2 of the chromosomes on the autosomes.

By: Jason

Jason — Sun, 21 Dec 2008 14:22:52 +0000

Unless I’m crazy, polygamy ought to make the Ne inferred from X chromosomes smaller, not greater. Polygamy increases variance in male reproductive success but shouldn’t effect the variance in female RS. High variance in male RS means many X chromosomes in males will be dead ends. This should decrease the Ne of the male fraction of the X (1/3 of the 3/4), thus making the Ne of the X less than 3/4 that of the autosomes. What am I missing?