Neutral nuclear variation inBaboons (genusPapio) provides insights into their evolutionary and demographic histories

Abstract

Baboons (genus Papio) are distributed over most of sub-Saharan Africa and in the southern portion of the Arabian Peninsula. Six distinct morphotypes, with clearly defined geographic distributions, are recognized (the olive, chacma, yellow, Guinea, Kinda and hamadryas baboons). The evolutionary relationships among baboon forms have long been a controversial issue. Phylogenetic analyses based on mitochondrial DNA sequences revealed that the modern baboon morphotypes are mitochondrially paraphyletic or polyphyletic. The discordance between mitochondrial lineages and morphology is indicative of extensive introgressive hybridization between ancestral baboon populations. To gain insights into the evolutionary relationships among morphotypes and their demographic history, we performed an analysis of nuclear variation in baboons. We sequenced 13 non-coding, putatively neutral, nuclear regions and scored the presence/absence of 18 polymorphic transposable elements in a sample of 45 baboons belonging to five of the six recognized baboon forms. We found that the chacma baboon is the sister-taxon to all other baboons and the yellow baboon is the sister-taxon to an unresolved northern clade containing the olive, Guinea and hamadryas baboons. We estimated that the diversification of baboons occurred entirely in the Pleistocene, the earliest split dating ~1.5 million years ago, and that baboons have experienced relatively large and constant population sizes for most of their evolutionary history (~30,000 to 95,000 individuals).

Genomewide ancestry and divergence patterns from low‐coverage sequencing data reveal a complex history of admixture in wild baboons

“…; Boissinot et al . ), with π equal to 0.206% in the anubis individual (SWA), 0.210% in the SNPRC yellow individual (SWY) and 0.251% in the Amboseli animal (HAP). We also found substantial genomewide differentiation between yellow and anubis baboons in this set, with F ST equal to 0.23 in the HAP vs. SWA comparison and 0.33 in the SWY vs. SWA comparison.…”

“…Finally, we present several new tools and resources of more general interest to the research community. Indeed, recent phylogenies for Papio indicate that yellow baboons and anubis baboons are among the most distantly related of the currently recognized baboon species, with an estimated divergence time~1-2 million years ago (Zinner et al 2013;Boissinot et al 2014). Thus, the draft yellow baboon assembly we produced here should complement the fully assembled and annotated anubis baboon genome that is soon to be released.…”

“…; Boissinot et al . ). Thus, the draft yellow baboon assembly we produced here should complement the fully assembled and annotated anubis baboon genome that is soon to be released.…”

“…Thus, the draft yellow baboon assembly we produced here should complement the fully assembled and annotated anubis baboon genome that is soon to be released. If existing estimates hold, yellow baboons may be among the most genetically diverse of the baboon species as well (Boissinot et al 2014), meaning that the data sets we generated will help capture a substantial fraction of the genetic diversity within the genus. Notably, we identified a large set of putative high and low divergence regions separating anubis and Amboseli yellow baboons that could be indicative of a past history of selection (Table S6, Supporting information).…”

Genetic diversity in humans and non-human primates and its evolutionary consequences

“…Among the other groups of Old World monkeys, the sequencing of 12 autosomal loci in baboons (Papio) revealed a range of π from 4.2 × 10 −4 to 1.9 × 10 −3 and the existence of rampant gene flow between species (Boissinot et al, 2014). A recent study employing whole-genome sequencing in snub-nosed monkeys (genus Rhinopithecus) revealed extremely low genetic diversity in this group: 2.1 × 10 −4 in Rhinopithecus strykeri, 3.9 × 10 −4 in R. bieti, 4.1 × 10 −4 in R. roxellana and 6.9 × 10 −4 in R. brelichi (Zhou et al, 2014).…”