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

作者：Jerilyn A. Walker, Vallmer E. Jordan, Jessica M. Storer, Cody J. Steely, Paulina Gonzalez-Quiroga, Thomas O. Beckstrom, Lydia Rewerts, Corey P. St. Romain, Catherine E. Rockwell, Jeffrey Rogers, Clifford J. Jolly, Miriam K. Konkel, Mark A. Batzer · 发表于：Mobile DNA · 年份：2019 · DOI：10.1186/s13100-019-0187-y · 被引用次数：18 · 研究领域：Primate Behavior and Ecology、Chromosomal and Genetic Variations、Bat Biology and Ecology Studies

Abstract 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 O...