Next-generation museomics disentangles one of the largest primate radiations

Abstract

Guenons (tribe Cercopithecini) are one of the most diverse groups of primates. They occupy all of sub-Saharan Africa and show great variation in ecology, behavior, and morphology. This variation led to the description of over 60 species and subspecies. Here, using next-generation DNA sequencing (NGS) in combination with targeted DNA capture, we sequenced 92 mitochondrial genomes from museum-preserved specimens as old as 117 years. We infer evolutionary relationships and estimate divergence times of almost all guenon taxa based on mitochondrial genome sequences. Using this phylogenetic framework, we infer divergence dates and reconstruct ancestral geographic ranges. We conclude that the extraordinary radiation of guenons has been a complex process driven by, among other factors, localized fluctuations of African forest cover. We find incongruences between phylogenetic trees reconstructed from mitochondrial and nuclear DNA sequences, which can be explained by either incomplete lineage sorting or hybridization. Furthermore, having produced the largest mitochondrial DNA data set from museum specimens, we document how NGS technologies can "unlock" museum collections, thereby helping to unravel the tree-of-life.

Figure 1

Ancestral ranges and the timing of diversification in guenons. Only a single representative for each taxon is shown, for the full tree see Figure 2 and Supplementary Figure S3. Pie charts at the nodes indicate ancestral areas, with color corresponding to the location of these areas on the map of Africa shown in the upper left corner. The relative proportion of each color represents the fraction of the global likelihood for the given geographic area. Gray bars indicate the timing of 4 main speciation events (see “Results” section). Vertical bars next to the species names refer to the species groups with photographs showing one of the species group' members (Mi: C. mitis group, C: C. cephus group, P: C. preussi group, Mo: C. mona group, N: C. neglectus group, Di: C. diana group, A: C. aethiops group, D: C. dryas groups, and H: C. hamlyni group). Tip labels in red highlight the members of the terrestrial clade, also see legend of Figure 2. Myr = million years. Ancestral ranges: A, Congo basin; B, northern DRC; C, northern Rift Valley; D, Upper Guinea; G, Lower Guinea; I, Angola; J, southeastern DRC; K, southeastern Africa; L, northeastern Africa; M, Zambia; N, Ethiopia/Sudan. Photograph of C. m. albogularis by Y.A. de Jong and T.M. Butynski—wildsolutions.nl.

Figure 2

Evolutionary relationships of Cercopithecidae. BI and ML methods produced trees with congruent topology. The BI-inferred phylogenetic tree is shown with first value at the nodes representing BI support and second value representing ML bootstrap support. All nodes with BI/ML support of 1/100 are labeled */*. Tip labels consist of species name, followed by the name of the museum at which the specimen has been collected in brackets (B, MfN; N, NHM London; RB, RBINS; and R, RMCA), followed by the country of origin for the given specimen (AO, Angola; CD, Democratic Republic of the Congo; CF, Central African Republic; CG, Republic of Congo; CI, Cote d'Ivoire; CM, Cameroon; ET, Ethiopia; GA, Gabon; GH, Ghana; GQ, Equatorial Guinea; KE, Kenya; LR, Liberia; MR, Mauritania; MW, Malawi; MZ, Mozambique; NG, Nigeria; SD, Sudan; SL, Sierra Leone; SN, Senegal; ST, São Tomé and Príncipe; TG, Togo; TZ, United Republic of Tanzania; UG, Uganda; ZA, South Africa; ZM, Zambia; gb, GenBank, and DPZ, samples provided by the DPZ Germany). Asterisks at the tip labels indicate cases of likely specimen mix-up (Supplementary Information, Results).

Figure 3

Nuclear (Perelman et al. 2011) versus mitochondrial trees for 17 guenons species belonging to the arboreal and the terrestrial clades. Numbers at the nodes indicate ML bootstrap support, nodes with support of 100 are labeled with asterisks. Taxa from the “terrestrial clade” (Tosi et al. 2004; Tosi 2008) are highlighted in bold.

Figure 4

Geography of speciation based on mtDNA data. Range overlap plotted against divergence time shows the pattern predicted when species splits are driven by geographic isolation (see text for details). The regression line is plotted in black. See Supplementary Figure S8 for the corresponding analyses on nuclear data.