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Background  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  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.    Results  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.    Conclusions  Our 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.

Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry