Abstract
BackgroundBaboons (genus Papio) and geladas (Theropithecus gelada) are now generally recognized as close phylogenetic relatives, though morphologically quite distinct and generally classified in separate genera. Primate specific Alu retrotransposons are well-established genomic markers for the study of phylogenetic and population genetic relationships. We previously reported a computational reconstruction of Papio phylogeny using large-scale whole genome sequence (WGS) analysis of Alu insertion polymorphisms. Recently, high coverage WGS was generated for Theropithecus gelada. The objective of this study was to apply the high-throughput “poly-Detect” method to computationally determine the number of Alu insertion polymorphisms shared by T. gelada and Papio, and vice versa, by each individual Papio species and T. gelada. Secondly, we performed locus-specific polymerase chain reaction (PCR) assays on a diverse DNA panel to complement the computational data.ResultsWe identified 27,700 Alu insertions from T. gelada WGS that were also present among six Papio species, with nearly half (12,956) remaining unfixed among 12 Papio individuals. Similarly, each of the six Papio species had species-indicative Alu insertions that were also present in T. gelada. In general, P. kindae shared more insertion polymorphisms with T. gelada than did any of the other five Papio species. PCR-based genotype data provided additional support for the computational findings.ConclusionsOur discovery that several thousand Alu insertion polymorphisms are shared by T. gelada and Papio baboons suggests a much more permeable reproductive barrier between the two genera then previously suspected. Their intertwined evolution likely involves a long history of admixture, gene flow and incomplete lineage sorting.
Highlights
Baboons and geladas (Theropithecus gelada) are generally recognized as close phylogenetic relatives, though morphologically quite distinct and generally classified in separate genera
We recently reported a computational reconstruction of Papio phylogeny using 187,000 Alu insertions identified through a large-scale whole genome sequence analysis [26]
To determine if any particular Papio species or clade was favored or excluded for shared insertion events with T. gelada, we sorted the raw output for the number of shared Alu elements in each bin of 2 to 11 individuals (Table 1)
Summary
Baboons (genus Papio) and geladas (Theropithecus gelada) are generally recognized as close phylogenetic relatives, though morphologically quite distinct and generally classified in separate genera. Primate specific Alu retrotransposons are well-established genomic markers for the study of phylogenetic and population genetic relationships. We previously reported a computational reconstruction of Papio phylogeny using large-scale whole genome sequence (WGS) analysis of Alu insertion polymorphisms. The objective of this study was to apply the high-throughput “poly-Detect” method to computationally determine the number of Alu insertion polymorphisms shared by T. gelada and Papio, and vice versa, by each individual Papio species and T. gelada. Evidence from morphological comparisons and mitochondrial and whole genome sequencing (WGS) all support a primary phylogenetic division into northern (P. anubis, P. papio and P. hamadryas) and southern (P. ursinus, P. cynocephalus and P. kindae) clades [5,6,7]. Theropithecus is estimated to have diverged from a Papio-like ancestor about 4–5 million years ago (mya) based on fossil evidence [2, 4, 21, 22] and analysis of mitochondrial DNA [23], while extant Papio species began to diversify about 2 mya [5, 7, 9, 24]
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