There were small but significant differences in measures of genetic diversity between
AJ [Ashkenazi Jewish] and CEU [Utah whites from the HapMap sample]. Analysis of genome-wide LD structure revealed a greater number of haplotype blocks which tended to be smaller in AJ. There was essentially no difference in global LD decay between AJ and CEU, although there was a tendency for faster decay of nearby SNPs and slower decay of intermediate distance SNPs in the AJ. These data are more consistent with the AJ as an older, larger population than CEU, and would suggest that, depending on regional differences in LD structure, AJ populations may not always provide an advantage for whole-genome association mapping.
Re: the population sizes, would a more reasonable non-mathematical rendering be that the smallest AJ bottleneck was larger than the smallest CEU bottleneck, or the average AJ population size was larger than the average CEU population size?
Re Dan’s question: either answer could be right. Instead of thinking about effective size think of the inverse of effective size, (1/Ne), which is the rate of diversity loss. This inverse can be averaged over time, like any speed. A bottleneck has a much larger effect on the average of (1/Ne) than it does on average Ne.
Will this put an end to the talk about a bottleneck in Ashkenazi history and about Ashkenazi disorders being the result of drift?
This is what is so exciting about widespread genetic testing: not only can we actually get answers for some old questions (are there different genepools within the human race? yes) we can ask questions that never would have occured to us before (what was the last year when Jews outnumbered whites?).