An Ancient Baboon Genome Demonstrates Long-Term Population Continuity in Southern Africa

Abstract

Baboons are one of the most abundant large nonhuman primates and are widely studied in biomedical, behavioral, and anthropological research. Despite this, our knowledge of their evolutionary and demographic history remains incomplete. Here, we report a 0.9-fold coverage genome sequence from a 5800-year-old baboon from the site of Ha Makotoko in Lesotho. The ancient baboon is closely related to present-day Papio ursinus individuals from southern Africa-indicating a high degree of continuity in the southern African baboon population. This level of population continuity is rare in recent human populations but may provide a good model for the evolution of Homo and other large primates over similar timespans in structured populations throughout Africa.

Keywords: ancient DNA; baboons; demography.

Fig. 1.

—Mitochondrial genome analysis. (A) Image of the ancient baboon phalanx. (B) Location of ancient baboon and geographic distribution of baboon species. Map: modified from Zinner, Groeneveld, et al. (2009) (CC BY). (C) Phylogenetic tree of the ancient baboon and present-day baboons using partial mitochondrial sequences from Zinner, Groeneveld, et al. (2009). The locations of the two most closely related mitochondrial genomes (U13/14) are indicated with labeled arrows in B and C, and those in the other southern ursinus haplogroups U10,11,12 and 15 are indicated with unlabeled arrows.

Fig. 2.

—Autosomal genome analysis. (A) First two principal components of genome-wide data. (B) TreeMix (Pickrell and Pritchard 2012) analysis of southern clade baboons with one northern clade representative (Papio anubis) and the papAnu2 (Pa2) reference genome with two migration edges (worst outlier 3.9 S.E). (C) An admixture graph that is consistent with the data (worst D-statistic Z score 0.4) of southern clade baboons with one northern clade representative (P. anubis) and the papAnu 2 reference genome. Other graphs may be equally consistent. Apparent gene flow (dashed red lines) between the Pa2 lineage and other samples likely reflects the effect of reference mapping bias. Abbreviations: anc, ancient baboon; anu, P. anubis; cyn, Papio cynocephalus; gel, Theropithecus gelada; ham, Papio hamadryas; kin, Papio kindae; pap, Papio papio; Pa2, papAnu2 reference genome.