A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms

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 evolut...

Descripción completa

Detalles Bibliográficos
Autores: Jordan, Vallmer E., Walker, Jerilyn A., Beckstrom, Thomas O., Steely, Cody J., McDaniel, Cullen L., St Romain, Corey P., Baboon Genome Analysis Consortium, Worley, Kim C., Phillips-Conroy, Jane, Jolly, Clifford J., Rogers, Jeffrey, Konkel, Miriam K., Batzer, Mark A.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2018
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/37205
Acceso en línea:http://hdl.handle.net/10230/37205
http://dx.doi.org/10.1186/s13100-018-0118-3
Access Level:acceso abierto
Palabra clave:Alu
Retrotransposon
Phylogeny
Primates
Taxonomy
Evolutionary genetics
Papio
Hybridization
id ES_9035dd9ca7fddda8decc5d7c2103cc4c
oai_identifier_str oai:recercat.cat:10230/37205
network_acronym_str ES
network_name_str España
repository_id_str
spelling A computational reconstruction of Papio phylogeny using Alu insertion polymorphismsJordan, Vallmer E.Walker, Jerilyn A.Beckstrom, Thomas O.Steely, Cody J.McDaniel, Cullen L.St Romain, Corey P.Baboon Genome Analysis ConsortiumWorley, Kim C.Phillips-Conroy, JaneJolly, Clifford J.Rogers, JeffreyKonkel, Miriam K.Batzer, Mark A.AluRetrotransposonPhylogenyPrimatesTaxonomyEvolutionary geneticsPapioHybridizationBackground: 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.BioMed Central201920192018info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/37205http://dx.doi.org/10.1186/s13100-018-0118-3reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésMobile DNA. 2018;9:13© 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.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/372052026-05-29T05:05:01Z
dc.title.none.fl_str_mv A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms
title A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms
spellingShingle A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms
Jordan, Vallmer E.
Alu
Retrotransposon
Phylogeny
Primates
Taxonomy
Evolutionary genetics
Papio
Hybridization
title_short A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms
title_full A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms
title_fullStr A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms
title_full_unstemmed A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms
title_sort A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms
dc.creator.none.fl_str_mv Jordan, Vallmer E.
Walker, Jerilyn A.
Beckstrom, Thomas O.
Steely, Cody J.
McDaniel, Cullen L.
St Romain, Corey P.
Baboon Genome Analysis Consortium
Worley, Kim C.
Phillips-Conroy, Jane
Jolly, Clifford J.
Rogers, Jeffrey
Konkel, Miriam K.
Batzer, Mark A.
author Jordan, Vallmer E.
author_facet Jordan, Vallmer E.
Walker, Jerilyn A.
Beckstrom, Thomas O.
Steely, Cody J.
McDaniel, Cullen L.
St Romain, Corey P.
Baboon Genome Analysis Consortium
Worley, Kim C.
Phillips-Conroy, Jane
Jolly, Clifford J.
Rogers, Jeffrey
Konkel, Miriam K.
Batzer, Mark A.
author_role author
author2 Walker, Jerilyn A.
Beckstrom, Thomas O.
Steely, Cody J.
McDaniel, Cullen L.
St Romain, Corey P.
Baboon Genome Analysis Consortium
Worley, Kim C.
Phillips-Conroy, Jane
Jolly, Clifford J.
Rogers, Jeffrey
Konkel, Miriam K.
Batzer, Mark A.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Alu
Retrotransposon
Phylogeny
Primates
Taxonomy
Evolutionary genetics
Papio
Hybridization
topic Alu
Retrotransposon
Phylogeny
Primates
Taxonomy
Evolutionary genetics
Papio
Hybridization
description 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.
publishDate 2018
dc.date.none.fl_str_mv 2018
2019
2019
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/37205
http://dx.doi.org/10.1186/s13100-018-0118-3
url http://hdl.handle.net/10230/37205
http://dx.doi.org/10.1186/s13100-018-0118-3
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Mobile DNA. 2018;9:13
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869413275355054080
score 15,811543

Similares en LA Referencia