Abstract
Non-African humans appear to carry a few per cent archaic DNA due to ancient inter-breeding. This modest legacy and its likely recent timing imply that most introgressed fragments will be rare and hence will occur mainly in the heterozygous state. I tested this prediction by calculating D statistics, a measure of legacy size, for pairs of humans where one of the pair was conditioned always to be either homozygous or heterozygous. Using coalescent simulations, I confirmed that conditioning the non-African to be heterozygous increased D, while conditioning the non-African to be homozygous reduced D to zero. Repeating with real data reveals the exact opposite pattern. In African–non-African comparisons, D is near-zero if the African individual is held homozygous. Conditioning one of two Africans to be either homozygous or heterozygous invariably generates large values of D, even when both individuals are drawn from the same population. Invariably, the African with more heterozygous sites (conditioned heterozygous > unconditioned > conditioned homozygous) appears less related to the archaic. By contrast, the same analysis applied to pairs of non-Africans always yields near-zero D, showing that conditioning does not create large D without an underlying signal to expose. Large D values in humans are therefore driven almost entirely by heterozygous sites in Africans acting to increase divergence from related taxa such as Neanderthals. In comparison with heterozygous Africans, individuals that lack African heterozygous sites, whether non-African or conditioned homozygous African, always appear more similar to archaic outgroups, a signal previously interpreted as evidence for introgression. I hope these analyses will encourage others to consider increased divergence as well as increased similarity to archaics as mechanisms capable of driving asymmetrical base-sharing.
Highlights
The current dogma is that humans inter-bred widely with other archaic hominins such as Neanderthals and Denisovans [1,2,3,4,5,6,7] apparently more or less whenever the species’ ranges overlapped [7,8,9]
With the coalescent simulator MS [22], I simulated a simple scenario in which hominins splits from the chimpanzees 6 million years ago, Neanderthals split from humans 300 000 years ago and the human lineage splits into Africans and non-Africans 70 000 years ago
I calculated six versions of D, always calculated such that positive values indicate introgression of Neanderthals into simulated non-Africans: 1. using all sites; 2. using only sites that are homozygous in the simulated African; 3. using only sites that are heterozygous in the simulated African; 4. using only sites that are homozygous in the simulated non-African; 5. using only sites that are heterozygous in the simulated non-African; and
Summary
The current dogma is that humans inter-bred widely with other archaic hominins such as Neanderthals and Denisovans [1,2,3,4,5,6,7] apparently more or less whenever the species’ ranges overlapped [7,8,9]. There is evidence that archaic DNA has been selected and thereby facilitated adaptation [11,12], with Denisovan haplotypes found in Tibetans living at high altitude [13] and evidence for selection against Neanderthal alleles of meiotic genes [14]. Neanderthal legacies are rather uniformly distributed across Eurasia [17], but increase significantly west to east [18]. Denisovan legacies reach 5% or more in Papua New Guinea and Australia [3,19], but are substantially lower elsewhere
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