Baboons (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 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.
We 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.
Our discovery that several thousand Alu
insertion polymorphisms are shared by T. gelada
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.