I know I excoriate readers of this weblog for being stupid, ignorant, or lazy. But this constant badgering does result in genuinely insightful and important comments precisely and carefully stated on occasion. I put up my previous post in haste, and when I published it I wasn’t totally happy with the evidence from which the authors adduced that Ashkenazi Jews were not inbred. Here’s why, from the comments: Doesn’t identity-by-state permutations test reflect a counterbalance of admixture vs. inbredness + drift? Rather than just the degree of inbreeding? Since the population has strong admixture effects, a low IBS doesn’t exclude strong inbreeding, does it?
From my little personal experience IBS is not the best statistic from which to generalize widely, and can be highly misleading in admixed individuals, as implied by the commenter. First, since I’ve stated above that the Ashkenazi Jews are admixed, let me go into a tangent as to why Ashkenazi are admixed between a Middle Eastern and Western European population, as opposed to being a relatively unadmixed ancient Eastern Mediterranean group with affinities to both regions. The previous previous paper found evidence of linkage disequilibrium decay. This means that LD was high in admixed individuals in the past, and declined over time. Why?
Jews, and Ashkenazi Jews in particular, are very genetically distinctive. A short and sweet way to think about this population is that they’re a moderately recent admixture between a Middle Eastern population, and Western Europeans, which has been relatively isolated due to sociocultural forces. As far as their inbreeding, well, here’s one recent paper, Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population: To explore the amount of genetic variation within the AJ and European populations, we first measured the mean heterozygosity. Surprisingly, we found a higher level of heterozygosity among AJ individuals compared with Europeans…confirming speculation made in one recent report and a trend seen in another…Although this difference may appear small, it is highly statistically significant because of the large number of individuals and markers analyzed, even after pruning SNPs that are in high LD. The higher diversity in the AJ population was paralleled by a lower inbreeding coefficient, F, indicating the AJ population is more outbred than Europeans, not inbred, as has long been assumed…The greater genetic variation among the AJ population was further confirmed using a pairwise identity-by-state (IBS) permutation test, which showed that average pairs of AJ individuals have significantly less genome-wide IBS sharing than pairs of EA or Euro individuals…Thus, our results show that the AJ population is more genetically diverse than Europeans. How could Ashkenazi Jews be more diverse? Look at what I wrote above, and what most people intuitively assume: Ashkenazi Jews are an admixed population, so they likely carry the alleles unique to both Western Europeans and Middle Eastern peoples! On the other hand, Ashkenazi Jews do have a lot of the genome identical by descent, as befits a population which has long been endogamous, and entered into a recent population expansion from a more modest base.
Image credit: Georges Beard.