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2016 ; 12
(11
): e1006340
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The Strength of Selection against Neanderthal Introgression
#MMPMID27824859
Juric I
; Aeschbacher S
; Coop G
PLoS Genet
2016[Nov]; 12
(11
): e1006340
PMID27824859
show ga
Hybridization between humans and Neanderthals has resulted in a low level of
Neanderthal ancestry scattered across the genomes of many modern-day humans.
After hybridization, on average, selection appears to have removed Neanderthal
alleles from the human population. Quantifying the strength and causes of this
selection against Neanderthal ancestry is key to understanding our relationship
to Neanderthals and, more broadly, how populations remain distinct after
secondary contact. Here, we develop a novel method for estimating the genome-wide
average strength of selection and the density of selected sites using estimates
of Neanderthal allele frequency along the genomes of modern-day humans. We
confirm that East Asians had somewhat higher initial levels of Neanderthal
ancestry than Europeans even after accounting for selection. We find that the
bulk of purifying selection against Neanderthal ancestry is best understood as
acting on many weakly deleterious alleles. We propose that the majority of these
alleles were effectively neutral-and segregating at high frequency-in
Neanderthals, but became selected against after entering human populations of
much larger effective size. While individually of small effect, these alleles
potentially imposed a heavy genetic load on the early-generation
human-Neanderthal hybrids. This work suggests that differences in effective
population size may play a far more important role in shaping levels of
introgression than previously thought.