New mitogenomic lineages in Papio baboons and their phylogeographic implications

Abstract

Objectives: Incomplete and/or biased sampling either on a taxonomic or geographic level can lead to delusive phylogenetic and phylogeographic inferences. However, a complete taxonomic and geographical sampling is often and for various reasons impossible, particularly for widespread taxa such as baboons (Papio spp.). Previous studies on baboon phylogeography identified several sampling gaps, some of which we fill by investigating additional material including samples from museum specimens. Materials and methods: We generated 10 new mitochondrial genomes either via conventional PCR and subsequent Sanger sequencing from two blood samples or via high-throughput shotgun sequencing from degraded DNA extracted from eight museum specimens. Phylogenetic relationships and divergence times among baboon lineages were determined using maximum-likelihood and Bayesian inferences. Results: We identified new mitochondrial lineages in baboons from Central Africa (Chad, the Central African Republic), from the Mahale, and the Udzungwa Mountains (Tanzania), with the latter likely representing a case of mitochondrial capture from sympatric kipunjis (Rungwecebus kipunji). We also found that the mitochondrial clades of olive baboons found in Ivory Coast and Tanzania extend into Niger and the Democratic Republic of Congo, respectively. Moreover, an olive baboon from Sierra Leone carries a mitochondrial haplotype usually found in Guinea baboons, suggesting gene flow between these two species. Discussion: The extension of the geographic sampling by including samples from areas difficult to visit or from populations that are most likely extirpated has improved the geographic and temporal resolution of the mitochondrial phylogeny of baboons considerably. Our study also shows the great value of museum material for genetic analyses even when DNA is highly degraded.

A Pleistocene assemblage of near‐modern Papio hamadryas from the Middle Awash study area, Afar Rift, Ethiopia

“…No static classificatory scheme could reflect the observed reality of ongoing hybridization among the recognized taxa. This issue extends beyond Papio to other cercopithecid taxa, with hybridization documented at the species–and even the genus–levels (e.g., guenons, colobines, and Papio × Rungwecebus and Papio × Theropithecus ; Roos et al, 2020; Walker et al, 2019; and see Cortés‐Ortiz et al, 2019 and references therein). These examples highlight the difficulty of establishing a classification system for these primates, an exercise even more complicated for fossil samples that capture segments of evolving species lineages sampled across geological time by only relatively narrow time windows.…”

“…There is a wide range of anatomical and behavioral variation across the six widely recognized extant forms of Papio . However, despite the notable size, pelage, and behavioral differences, these populations hybridize at multiple points of geographic contact (Ackermann et al, 2019; Fischer et al, 2019; Jolly, 1993; Martinez et al, 2019; Rogers et al, 2019; Roos et al, 2020; and see citations therein). Linnaean classification allows this variation to be divided into either six subspecies within the species P. hamadryas (e.g., Groves, 1989), or six species in the genus Papio with regular admixture events (e.g., Jordan et al, 2018; Rogers et al, 2019), or some combination thereof (e.g., Szalay & Delson, 1979).…”

Adulis and the transshipment of baboons during classical antiquity

“…We extracted DNA with a specific column-based method aimed at the recovery of short DNA fragments following established protocols and necessary precautions for the analysis of aDNA (Dabney, Knapp, et al, 2013;Rohland et al, 2004;Roos et al, 2021). In particular, samples from mummified specimens were extracted separately and in a dedicated aDNA laboratory to prevent cross-contamination.…”

“…We only retained mitogenomes for further analyses for which at least 80% of the sequence were covered at 3X. We augmented our dataset with published mitogenomes of baboons (Roos et al, 2021) and T. gelada as outgroup (Table 1), and aligned sequences with MUSCLE 3.8.81 (Edgar, 2004) as implemented in the package msa 1.28.0 (Bodenhofer et al, 2015) in R 4.2.1 (R Core Team, 2022) using standard settings with a maximum number of 16 iterations.…”

Mitonuclear interactions and introgression genomics of macaque monkeys ( Macaca ) highlight the influence of behaviour on genome evolution

“…[12]). Evolutionary repercussions of extreme female philopatry are evidenced by ancient mitochondrial coalescence times that predate speciation of rhesus macaques [13], pigtail macaques (Macaca nemestrina) [14], olive baboons (Papio anubis) [15] and possibly Sulawesi macaques [14]. By contrast, a deep mitochondrial coalescence time is not observed in hamadryas baboons, Papio hamadryas, but this species has an atypical social system for papionins with more frequent female migration [16].…”