Human effective sex ratio: different at different time scales

The authors manage to harmonize the seemingly contradictory results of Keinan et al. and Hammer et al.

From the paper:

Recently, two studies estimated Q in order to detect sexbiases in similar human populations16,17 and found seeminglycontradictory conclusions.25 Using SNP data fromthe International HapMap Project,26 Keinan et al. found evidence for a male bias during the dispersal of modern humans out of Africa (Figure 1A).17 Hammer and colleagues, however, found evidence for a female biasthroughout human history in six populations from theHuman Genome Diversity Panel (HGDP) (Figure 1A).16

This figure from the paper shows the model inferred by the authors which resolves the seeming contradiction.

They write:

Long-term sex-biased processes, such as polygyny or higher female dispersal rates in ancestral human populations,likely caused the Qπ estimates found by Hammer et al.

but:

The male bias detected by Keinan et al. can be explained by a recent event associated with the out-of-Africa dispersal, as initially proposed by the authors. The Q ratios detected by Keinan et al. suggest a very strong male bias for the entire portion of the non-African lineage before the split of Asians from Europeans.

I am not entirely convinced of this explanation. The authors' model suggests a higher male/female ratio in Eurasians than in Africans due to male bias in the Eurasian lineage against an ancestral background of high female/male ratio (due to polygyny).

But, an alternative explanation is that the higher female/male ratio in Africans is due to the fact that they are descended from a relatively small number of males who overwhelmed the pre-existing African gene pool.

There are reasons to believe this is the case: Africa has the deepest lineages in the human Y-chromosome phylogeny (A and B), but the balance is made of entirely of haplogroup E chromosomes, the sister clade of Eurasian D. The extremely diverse Eurasian haplogroup F is represented only by some subclades in Africa, due to back-migration.

So, while Eurasian males are descended from the expansion of F and DE males, African males are largely descended from the expansion of E males. These are the Afrasians I've often spoken of, the common ancestors of Eurasians and Africans. In Africa, the Afrasians could take the women of the Paleo-Africans, but Eurasia was largely empty land, and the Eurasians could only take the women they've brought with them.

The American Journal of Human Genetics, 24 November 2010
doi:10.1016/j.ajhg.2010.10.021

Estimators of the Human Effective Sex Ratio Detect Sex Biases on Different Timescales

Leslie S. Emery

Determining historical sex ratios throughout human evolution can provide insight into patterns of genomic variation, the structure and composition of ancient populations, and the cultural factors that influence the sex ratio (e.g., sex-specific migration rates). Although numerous studies have suggested that unequal sex ratios have existed in human evolutionary history, a coherent picture of sex-biased processes has yet to emerge. For example, two recent studies compared human X chromosome to autosomal variation to make inferences about historical sex ratios but reached seemingly contradictory conclusions, with one study finding evidence for a male bias and the other study identifying a female bias. Here, we show that a large part of this discrepancy can be explained by methodological differences. Specifically, through reanalysis of empirical data, derivation of explicit analytical formulae, and extensive simulations we demonstrate that two estimators of the effective sex ratio based on population structure and nucleotide diversity preferentially detect biases that have occurred on different timescales. Our results clarify apparently contradictory evidence on the role of sex-biased processes in human evolutionary history and show that extant patterns of human genomic variation are consistent with both a recent male bias and an earlier, persistent female bias.

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