May 15, 2014

An excess of X-chromosomal diversity in Africans

A new study provides important new data for African-Eurasian differences in the X-to-autosomal ratio of nucleotide diversity.

In my opinion, an explanation for this phenomenon might be found in the back-migration into Africa of Eurasian males (belonging to Y-haplogroup E). If a Eurasian man has offspring with an African woman, then the autosomal diversity of his offspring will be more than his and less than hers (*). For the pairing's daughters, 1 X chromosome will be contributed by the Eurasian man and 1 from the African woman. But, for its sons, 1 X chromosome will be contributed by the African woman only. Thus, X chromosomal diversity in descendants of such a mixed population will be higher because Africans will contribute 2/3 of the X chromosomes but only 1/2 of the autosomes.

(*) It will probably not be halfway between them, because some increase in diversity will be contributed by mutations (or equivalently archaic introgressions) that occured in the Eurasian and African lineages since their separation.

AJHG doi:10.1016/j.ajhg.2014.04.011

Contrasting X-Linked and Autosomal Diversity across 14 Human Populations

Leonardo Arbiza et al.

Contrasting the genetic diversity of the human X chromosome (X) and autosomes has facilitated understanding historical differences between males and females and the influence of natural selection. Previous studies based on smaller data sets have left questions regarding how empirical patterns extend to additional populations and which forces can explain them. Here, we address these questions by analyzing the ratio of X-to-autosomal (X/A) nucleotide diversity with the complete genomes of 569 females from 14 populations. Results show that X/A diversity is similar within each continental group but notably lower in European (EUR) and East Asian (ASN) populations than in African (AFR) populations. X/A diversity increases in all populations with increasing distance from genes, highlighting the stronger impact of diversity-reducing selection on X than on the autosomes. However, relative X/A diversity (between two populations) is invariant with distance from genes, suggesting that selection does not drive the relative reduction in X/A diversity in non-Africans (0.842 ± 0.012 for EUR-to-AFR and 0.820 ± 0.032 for ASN-to-AFR comparisons). Finally, an array of models with varying population bottlenecks, expansions, and migration from the latest studies of human demographic history account for about half of the observed reduction in relative X/A diversity from the expected value of 1. They predict values between 0.91 and 0.94 for EUR-to-AFR comparisons and between 0.91 and 0.92 for ASN-to-AFR comparisons. Further reductions can be predicted by more extreme demographic events in excess of those captured by the latest studies but, in the absence of these, also by historical sex-biased demographic events or other processes.



mooreisbetter said...

Everything in modern anthropology and genetics was first put forth by the groundbreaking studies by Cavalli-Sforza.

I seem to remember in his book, granted, speaking about autosomal diversity, he stated something like, "there is more genetic diversity in the typical African village than there is in the entire continent of Europe."

LivoniaG said...

Dienekes wrote: "In my opinion, an explanation for this phenomenon might be found in the back-migration into Africa of Eurasian males (belonging to Y-haplogroup E)."

But how does that explain the the lower ratio in Europe? We see as much or more movement of all kinds of Y-haplotypes into Europe. And, when it comes to ancient DNA, that ever-present H X-haplotype shows up along with an alphabet soup of Y types. Why should they have less impact than E into Africa?

I think the problem is in the phrase "the stronger impact of diversity-reducing selection on X." But localized selection actually has the opposite effect, creating pockets of diversity.

I think this unnecessarily sees the African genes are a single population. If they instead represent isolated pockets of people/females, then the diversity can be explained by multiple small selection on X events that had less effect on autosomal genetics. In contrast, European females may have been more wide-ranging and X diversity would have been "diversity-reducing selection."