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Mob DNA. 2019 Nov 26;10:46. doi: 10.1186/s13100-019-0187-y. eCollection 2019.

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

Author information

1
1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA.
2
2Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA.
3
3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA.
4
4Department of Anthropology, New York University, New York, NY 10003 USA.
5
Department of Genetics & Biochemistry, Clemson Center for Human Genetics, Clemson, SC 29634 USA.
#
Contributed equally

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:

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.

KEYWORDS:

Alu element; Evolutionary biology; Primate phylogeny; Retrotransposon

Conflict of interest statement

Competing interestsThe authors declare that they have no competing interests.

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