The comparative genomics and complex population history of Papio baboons

Abstract

Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genusPapio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation ofPapiobaboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.

Genomic signatures of extreme body size divergence in baboons

“…Closer inspection of SNPs in RFX4 indicates that, in the most highly differentiated SNP located on chromosome 11 at position 105851669 on the baboon reference genome (Panu2.0, derived from an anubis baboon, Papio anubis) (Rogers et al 2019), the high-frequency allele in chacma baboons is shared with both the anubis baboon reference individual and the rhesus macaque reference individual as an outgroup (Table S3), indicating that the high distinctiveness of RFX4 may be driven by directional selection on Kinda baboons. These interpretations remain speculative, however, in the absence of additional sequence and expression information from RFX4, as well as functional validation.…”

“…Baboons (genus Papio) are well-known and extensively studied cercopithecine primates that exhibit considerable variation in body size, ecology, morphology, and behavior (Jolly 1993;Barrett 2009). The impressive diversity of this genus, combined with a complex evolutionary history following a crown divergence approximately 2.0 -1.5 million years ago (Zinner et al 2013;Rogers et al 2019), have made baboons fruitful models for examining mechanisms of natural selection in wild populations (e.g., Jolly 2001;Henzi & Barrett 2003;Strum 2012). Kinda (Papio kindae) and gray-footed chacma baboons (P. ursinus griseipes) are two parapatrically distributed southern African taxa that in some aspects occupy opposing extremes of phenotypic variation in extant baboons.…”

Genome-wide ancestry and introgression in a Zambian baboon hybrid zone

“…Bioinformatic procedures for sample demultiplexing, sequence alignment to the anubis baboon reference genome (Panu2.0) (Rogers et al 2019), and variant identification followed methods described elsewhere (Chiou & Bergey 2018;Chiou et al 2019). After calling and filtering variants, we identified and removed variants in strong linkage disequilibrium with PLINK (Purcell et al 2007;Chang et al 2015), using a sliding window approach with a window length of 50 SNPs, a step size of 5 SNPs, and an r 2 threshold of 0.5 (--indep-pairwise 50 5 0.5).…”

“…Genome coordinates were based on the baboon reference genome (Panu2.0) gene annotations (Rogers et al 2019).…”

Accurate assembly of the olive baboon (Papio anubis) genome using long-­read and Hi-C data

“…This assembly used a combination of Illumina paired-end and Illumina mate-pair sequence data (with mean library insert sizes ranging from 175 bp to 14 Kbp) to produce a highly fragmented assembly with contig N50 of 29 Kbp and scaffold N50 of 887 Kbp. The public olive baboon assembly, Panu_3.0, suffers from the same problem of having small contigs and scaffolds (contig N50 of 139 Kbp and de novo scaffold N50 of 586 Kbp) [27]. The authors of the public olive baboon assembly chose to distribute a referenceguided assembly with scaffolds mapped onto rhesus (Macaca mulatta) chromosomes.…”