Jerilyn A. Walker, Louisiana State University
Vallmer E. Jordan, Louisiana State University
Jessica M. Storer, Louisiana State University
Cody J. Steely, Louisiana State University
Paulina Gonzalez-Quiroga, Louisiana State University
Thomas O. Beckstrom, Louisiana State University
Lydia C. Rewerts, Louisiana State University
Corey P. St. Romain, Louisiana State University
Catherine E. Rockwell, Louisiana State University
Jeffrey Rogers, Baylor College of Medicine
Clifford J. Jolly, New York University
Miriam K. Konkel, Louisiana State University
Mark A. Batzer, Louisiana State University
R. Alan Harris, Baylor College of Medicine
Muthuswamy Raveendran, Baylor College of Medicine
Yue Liu, Baylor College of Medicine
Shwetha Murali, Baylor College of Medicine
Tauras P. Vilgalys, Duke University
Gregg W.C. Thomas, Indiana University Bloomington
Kymberleigh A. Pagel, Indiana University Bloomington
Vikas Pejaver, Indiana University Bloomington
Claudia R. Catacchio, Università degli Studi di Bari
Nicoletta Archidiacono, Università degli Studi di Bari
Mario Ventura, Università degli Studi di Bari
Alessia Marra-Campanale, Università degli Studi di Bari
Antonio Palazzo, Università degli Studi di Bari
Oronzo Capozzi, Università degli Studi di Bari
Archana Raja, University of Washington, Seattle
John Huddleston, University of Washington, Seattle
Veronica Searles Quick, University of Colorado at Denver Anschutz Medical Campus
Anis Karimpour-Fard, University of Colorado at Denver Anschutz Medical Campus
Dominik Schrempf, Veterinarmedizinische Universitat Wien
Marc de Manuel Montero, Universitat Pompeu Fabra Barcelona
Konstantinos Billis, European Bioinformatics Institute

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© 2019 The Author(s). 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.

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Mobile DNA