Jerilyn A. Walker, Vallmer E. Jordan, Jessica M. Storer, Cody J. Steely, Paulina Gonzalez-Quiroga, Thomas O. Beckstrom, Lydia C. Rewerts, Corey P. {St Romain}, Catherine E. Rockwell, Jeffrey Rogers, Clifford J. Jolly, Miriam K. Konkel, {Baboon Genome Analysis Consortium}, Mark A. Batzer. Alu insertion polymorphisms shared by Papio baboons and Theropithecus geladareveal an intertwined common ancestry. Mobile DNA, 10:46. 2019. Tomas Vinar is a member of the Baboon Genome Analysis Consortium.

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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