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A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms

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dc.contributor.author Jordan, Vallmer E.
dc.contributor.author Walker, Jerilyn A.
dc.contributor.author Beckstrom, Thomas O.
dc.contributor.author Steely, Cody J.
dc.contributor.author McDaniel, Cullen L.
dc.contributor.author St Romain, Corey P.
dc.contributor.author Baboon Genome Analysis Consortium
dc.contributor.author Worley, Kim C.
dc.contributor.author Phillips-Conroy, Jane
dc.contributor.author Jolly, Clifford J.
dc.contributor.author Rogers, Jeffrey
dc.contributor.author Konkel, Miriam K.
dc.contributor.author Batzer, Mark A.
dc.date.accessioned 2019-05-10T07:41:10Z
dc.date.available 2019-05-10T07:41:10Z
dc.date.issued 2018
dc.identifier.citation Jordan VE, Walker JA, Beckstrom TO, Steely CJ, McDaniel CL, St Romain CP; Baboon Genome Analysis Consortium (members: de Manuel M, Marques-Bonet T, et al.), Worley KC, Phillips-Conroy J, Jolly CJ, Rogers J, Konkel MK, Batzer MA. A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms. Mob DNA. 2018; 9:13. DOI 10.1186/s13100-018-0118-3
dc.identifier.issn 1759-8753
dc.identifier.uri http://hdl.handle.net/10230/37205
dc.description.abstract Background: Since the completion of the human genome project, the diversity of genome sequencing data produced for non-human primates has increased exponentially. Papio baboons are well-established biological models for studying human biology and evolution. Despite substantial interest in the evolution of Papio, the systematics of these species has been widely debated, and the evolutionary history of Papio diversity is not fully understood. Alu elements are primate-specific transposable elements with a well-documented mutation/insertion mechanism and the capacity for resolving controversial phylogenetic relationships. In this study, we conducted a whole genome analysis of Alu insertion polymorphisms unique to the Papio lineage. To complete these analyses, we created a computational algorithm to identify novel Alu insertions in next-generation sequencing data. Results: We identified 187,379 Alu insertions present in the Papio lineage, yet absent from M. mulatta [Mmul8.0.1]. These elements were characterized using genomic data sequenced from a panel of twelve Papio baboons: two from each of the six extant Papio species. These data were used to construct a whole genome Alu-based phylogeny of Papio baboons. The resulting cladogram fully-resolved relationships within Papio. Conclusions: These data represent the most comprehensive Alu-based phylogenetic reconstruction reported to date. In addition, this study produces the first fully resolved Alu-based phylogeny of Papio baboons.
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartof Mob DNA. 2018; 9:13
dc.rights © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.title A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/s13100-018-0118-3
dc.subject.keyword Alu
dc.subject.keyword Retrotransposon
dc.subject.keyword Phylogeny
dc.subject.keyword Primates
dc.subject.keyword Taxonomy
dc.subject.keyword Evolutionary genetics
dc.subject.keyword Papio
dc.subject.keyword Hybridization
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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