Negative selection on baboon admixture is strongest on chromosome X

Background The six admixing baboon species offer a natural experiment to study negative selection on admixture and the nature of genetic incompatibility. In Tanzania, a secondary contact between olive and yellow baboons allows admixture despite 1.3 million years of divergence. An independent secondary contact occurred in Ethiopia, upon which olive baboons invaded and displaced an ancient Hamadryas-like population separated by 0.6 million years, mirroring the displacement of Neanderthals by modern humans. Results We analyze 156 high-coverage genomes sampled from seven olive and four yellow baboon populations in East Africa. Analyzing local ancestry across the whole genome, we find evidence of negative selection on minor parent ancestry in both Tanzanian yellow and olive baboon populations that reaches far beyond the hybrid zone. Across populations, we find that selection on minor parent ancestry is stronger on the X chromosome than on autosomes, most extremely in one yellow baboon population, which shows a seven-fold difference. The proportion of minor parent ancestry (MPA) is substantially higher on the X chromosome in Ethiopian olive and yellow baboon populations, which both displaced the populations now representing their minor parent ancestry, owing mainly to a few genomic regions with MPA at very high frequencies. We hypothesize that strong negative selection on MPA allowed these X chromosome regions to retain the original ancestry, as this was slowly displaced across the remaining genome. Conclusions Our findings provide deeper insights into admixture dynamics in primates, highlighting the persistence of selection against admixture across various levels of admixture, and underscoring the need to include chromosome X in admixture analyses.