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. 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

Jerilyn A Walker #  1 , Vallmer E Jordan #  1 , Jessica M Storer  1 , Cody J Steely  1 , Paulina Gonzalez-Quiroga  1 , Thomas O Beckstrom  1 , Lydia C Rewerts  1 , Corey P St Romain  1 , Catherine E Rockwell  1 , Jeffrey Rogers  2   3 , Clifford J Jolly  4 , Miriam K Konkel  1   5 ; Baboon Genome Analysis Consortium; Mark A Batzer  1
Collaborators, Affiliations

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

Jerilyn A Walker et al. Mob DNA. .

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.

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Conflict of interest statement

Competing interestsThe authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
The number of times a T. gelada-ascertained Alu insertion polymorphism was predicted to be shared in a Papio species when shared in any of 2 to 11 of the 12 Papio individuals. Vertical bars are the average of the two individuals of a given species +/− the standard deviation (error bars). No Papio individuals are preferentially excluded from having shared insertions with T. gelada in any category. In bin two, P. hamadryas has significantly more shared insertions than P. anubis, P. papio, and P. cynocephalus (+: P ≤ 0.05). In bin six, P. cynocephalus has significantly more shared insertions than the three northern species, P. anubis, P. hamadryas and P. papio (+: P ≤ 0.05). Across bins 2 to 10 shared insertions are predicted in P. kindae significantly more often than all other five Papio species (*) or all except P. ursinus (#) (P ≤ 0.05)
Fig. 2
Fig. 2
Papio species-indicative Alu insertion polymorphisms shared in Theropithecus gelada. Lanes: 1- 100 bp ladder, 2- TLE (negative control), 3- Human (HeLa), 4- P. anubis (27861 Panu_2.0 reference individual), 5- P. anubis (L142), 6- P. anubis (LIV5), 7- P. hamadryas (97124), 8- P. papio (28547), 9- P. papio (30388), 10- P. cynocephalus (16066), 11- P. cynocephalus (16098), 12- P. ursinus (28697), 13- P. ursinus (28755), 14- P. kindae (34474; BZ11050), 15- P. kindae (34472; BZ11047), 16- T. gelada (KB10538), 17- Macaca mulatta. a olive baboon locus AnuGel_12; b hamadryas locus HamGel_76; c Guinea baboon locus PapioGel_38; d Yellow baboon locus YelGel_11; e chacma baboon locus ChacmaGel_43; f kinda baboon locus KindaGel_199. Green bars outline the Papio species with the Alu present (upper band); the blue bar outlines the Alu present band in T. gelada
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References

    1. Geoffroy S-HI. Description des Mammifères Nouveaux ou Imparfaitement Connus de la Collection du Muséum d’Histoire Naturelle, et Remarques sur la Classification et les Caractères des Mammifères. Arch Mus Hist Nat Paris. 1843;2:485–592.
    1. Jablonski NG. Theropithecus: the rise and fall of a primate genus. Cambridge: Cambridge University press, 2005; 2005.
    1. Groves C. Primate taxonomy. Washington, DC: Smithsonian Institution Press; 2001.
    1. Jolly CJ. Species, subspecies and baboon systematics. In: LBM WHK, editor. Species, Species concepts and Primate Evolution. New York: Plenum Press; 1993. pp. 67–107.
    1. Zinner D, Groeneveld LF, Keller C, Roos C. Mitochondrial phylogeography of baboons (Papio spp.): indication for introgressive hybridization? BMC Evol Biol. 2009;9:83. doi: 10.1186/1471-2148-9-83. - DOI - PMC - PubMed

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