The chacma baboon (Papio ursinus) through time: a model of potential core habitat regions during a glacial–interglacial cycle

A Comprehensive Overview of Baboon Phylogenetic History

Baboons (genus Papio) are an intriguing study system to investigate complex evolutionary processes and the evolution of social systems. An increasing number of studies over the last 20 years has shown that considerable incongruences exist between phylogenies based on morphology, mitochondrial, and nuclear sequence data of modern baboons, and hybridization and introgression have been suggested as the main drivers of these patterns. Baboons, therefore, present an excellent opportunity to study these phenomena and their impact on speciation. Advances both in geographic and genomic coverage provide increasing details on the complexity of the phylogeography of baboons. Here, we compile the georeferenced genetic data of baboons and review the current knowledge on baboon phylogeny, discuss the evolutionary processes that may have shaped the patterns that we observe today, and propose future avenues for research.

Genomic variation in baboons from central Mozambique unveils complex evolutionary relationships with other Papio species

Background

Gorongosa National Park in Mozambique hosts a large population of baboons, numbering over 200 troops. Gorongosa baboons have been tentatively identified as part of Papio ursinus on the basis of previous limited morphological analysis and a handful of mitochondrial DNA sequences. However, a recent morphological and morphometric analysis of Gorongosa baboons pinpointed the occurrence of several traits intermediate between P. ursinus and P. cynocephalus, leaving open the possibility of past and/or ongoing gene flow in the baboon population of Gorongosa National Park. In order to investigate the evolutionary history of baboons in Gorongosa, we generated high and low coverage whole genome sequence data of Gorongosa baboons and compared it to available Papio genomes.

Results

We confirmed that P. ursinus is the species closest to Gorongosa baboons. However, the Gorongosa baboon genomes share more derived alleles with P. cynocephalus than P. ursinus does, but no recent gene flow between P. ursinus and P. cynocephalus was detected when available Papio genomes were analyzed. Our results, based on the analysis of autosomal, mitochondrial and Y chromosome data, suggest complex, possibly male-biased, gene flow between Gorongosa baboons and P. cynocephalus, hinting to direct or indirect contributions from baboons belonging to the “northern” Papio clade, and signal the presence of population structure within P. ursinus.

Conclusions

The analysis of genome data generated from baboon samples collected in central Mozambique highlighted a complex set of evolutionary relationships with other baboons. Our results provided new insights in the population dynamics that have shaped baboon diversity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01999-7.

Species-specific effects of climate change on the distribution of suitable baboon habitats - Ecological niche modeling of current and Last Glacial Maximum conditions

Baboons (genus Papio) have been proposed as a possible analogous phylogeographic model for intra-African dispersal of hominins during the Pleistocene. Previous studies of the genus reveal complex evolutionary dynamics including introgressive hybridization and, as for hominins, it has been hypothesized that past climate change has been a major driver in their evolutionary history. However, how historical climate changes affected the distribution and extent of baboon habitats is not clear. We therefore employed three ecological niche modeling algorithms (maximum entropy model: MaxEnt; general additive model: GAM; gradient boosting model: GBM) to map suitable habitat of baboons at both genus and species levels under two extreme late-Quaternary climates: current (warm period) and Last Glacial Maximum (LGM, cold period). The three model algorithms predicted habitat suitabilities for the baboon species with high accuracy, as indicated by AUC values of 0.83-0.85 at genus level and ≥0.90 for species. The results suggest that climate change from LGM to current affected the distribution and extent of suitable habitats for the genus Papio only slightly (>80% of the habitat remained suitable). However, and in contrast to our expectation for ecological generalists, individual species have been differentially affected. While P. ursinus and P. anubis lost some of their suitable habitats (net loss 25.5% and 13.3% respectively), P. kindae and P. papio gained large portions (net gain >62%), and P. cynocephalus and P. hamadryas smaller portions (net gain >20%). Overlap among the specific realized climate niches remained small, suggesting only slight overlap of suitable habitat among species. Results of our study further suggest that shifts of suitable habitats could have led to isolation and reconnection of populations which most likely affected gene flow among them. The impact of historic climate changes on baboon habitats might have been similar for other savanna living species, such as hominins.