TY - JOUR T1 - Strong selection in the human-chimpanzee ancestor links the X chromosome to speciation JF - bioRxiv DO - 10.1101/011601 SP - 011601 AU - Julien Y. Dutheil AU - Kasper Munch AU - Kiwoong Nam AU - Thomas Mailund AU - Mikkel H. Schierup Y1 - 2014/01/01 UR - http://biorxiv.org/content/early/2014/11/19/011601.abstract N2 - The human and chimpanzee X chromosomes are less divergent than expected based on autosomal divergence. This has led to a controversial hypothesis proposing a unique role of the X chromosome in complex human-chimpanzee speciation. Here, we study incomplete lineage sorting patterns between humans, chimpanzees and gorillas to show that this low divergence is entirely due to megabase-sized regions comprising one-third of the X chromosome, where polymorphism in the human-chimpanzee ancestral species was severely reduced. Background selection can explain 10% of this reduction at most. Instead, we show that several strong selective sweeps in the ancestral species can explain these patterns. We also report evidence of population specific sweeps of a similar magnitude in extant humans that overlap the regions of low diversity in the ancestral species. These regions further correspond to chromosomal sections shown to be devoid of Neanderthal introgression into modern humans. This suggests that these X-linked regions are directly involved in forming reproductive barriers.Authors' Summary Because the speciation events leading to human, chimpanzee and gorilla were close in time, their genetic relationships varies along the genome. While human and chimpanzee are the most closely related species, 15% of the human genome is more closely related to the gorilla genome than the chimpanzee genome, a phenomenon called incomplete lineage sorting (ILS). The amount and distribution of ILS can be predicted using population genetics theory, and is affected by the demographic and selective history of the underlying populations. In contrast to autosomes, it was previously reported that the X chromosome was deprived of ILS, leading to controversial theories on the speciation event that splits humans and chimpanzees. Using a full genome alignment of the X chromosome, we show that only one third of the chromosome displays such strong reduction of ILS. The identified regions also show reduced diversity in extant population of human and great apes, and coincide with regions devoid of Neanderthal introgression. We propose that these regions are the target of selection and played a role in the formation of reproductive barriers. ER -