Vervet monkeys (Chlorocebus sp.) are amongst the most widely distributed non-human primates and are natural hosts of simian immunodeficiency virus (SIV) with a high viral prevalence observed in all sampled African populations. We use whole-genome sequencing data from 163 individuals covering six subspecies across the continent to infer relationships and demonstrate cross-taxon gene flow. A scan for diversifying selection across subtaxa yields strong enrichment for viral response genes and genes whose human orthologs interact with human immunodeficiency virus (HIV). Selection scores are also highly elevated in genes that show a response to experimental SIV infection in vervet monkeys but not in rhesus macaques. Because the latter species is not a natural SIV host, and develops immunodeficiency disease upon SIV infection, this interaction likely reflects adaptation to SIV. We discuss the strongest candidate genes for repeated selection for SIV defence.
I will also discuss more briefly results from whole genome sequencing data from 156 individuals from 71 species of the Lake Malawi cichlid radiation. We find that Lake Malawi cichlid species are much more closely related than previously thought and D-statistics (ABBA-BABA test) reveals massive signatures of ancient genetic exchange both with riverine out-groups and across the major clades within the radiation. Both paleogeological records of low lake level and a striking excess of haplotypes that are approximately 10 times more diverged than the genomic average are consistent with an ancestral hybrid swarm giving rise to the current radiation.