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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms
Mobile DNA, Volume 9, No. 1, Article 13, Year 2018
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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. © 2018 The Author(s).
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC5885306/bin/13100_2018_118_MOESM1_ESM.xlsx
https://efashare.b-cdn.net/share/pmc/articles/PMC5885306/bin/13100_2018_118_MOESM2_ESM.docx
https://efashare.b-cdn.net/share/pmc/articles/PMC5885306/bin/13100_2018_118_MOESM3_ESM.docx
https://efashare.b-cdn.net/share/pmc/articles/PMC5885306/bin/13100_2018_118_MOESM4_ESM.xlsx
https://efashare.b-cdn.net/share/pmc/articles/PMC5885306/bin/13100_2018_118_MOESM5_ESM.docx
Authors & Co-Authors
Jordan, Vallmer E.
United States, Baton Rouge
Louisiana State University
Walker, Jerilyn A.
United States, Baton Rouge
Louisiana State University
Beckstrom, Thomas O.
United States, Baton Rouge
Louisiana State University
Steely, Cody J.
United States, Baton Rouge
Louisiana State University
Worley, Kim Carlyle
United States, Houston
Baylor College of Medicine
Phillips-Conroy, Jane Elizabeth
United States, St. Louis
Washington University School of Medicine in St. Louis
Jolly, Clifford J.
United States, New York
New York University
Rogers, Jeffrey A.
United States, Houston
Baylor College of Medicine
Konkel, Miriam K.
United States, Baton Rouge
Louisiana State University
United States, Clemson
Clemson University
Batzer, Mark A.
United States, Baton Rouge
Louisiana State University
Harris, Ronald Alan
Unknown Affiliation
Raveendran, Muthuswamy
Unknown Affiliation
Liu, Yue
Unknown Affiliation
Murali, Shwetha Canchi
Unknown Affiliation
Vilgalys, Tauras P.
Unknown Affiliation
Thomas, Gregg W.C.
Unknown Affiliation
Pagel, Kymberleigh A.
Unknown Affiliation
Pejaver, Vikas Rao
Unknown Affiliation
Catacchio, Claudia Rita
Unknown Affiliation
Archidiacono, Nicoletta
Unknown Affiliation
Ventura, Mario
Unknown Affiliation
Marra-Campanale, Alessia
Unknown Affiliation
Palazzo, Antonio
Unknown Affiliation
Capozzi, Oronzo
Unknown Affiliation
Raja, Archana N.
Unknown Affiliation
Huddleston, John
Unknown Affiliation
Quick, Veronica Searles
Unknown Affiliation
Karimpour-Fard, Anis
Unknown Affiliation
Schrempf, Dominik
Unknown Affiliation
Billis, Konstantinos
Unknown Affiliation
Martin, Fergal J.
Unknown Affiliation
Muffato, Matthieu
Unknown Affiliation
Athanasiadis, Georgios
Unknown Affiliation
Bergey, Christina M.
Unknown Affiliation
Burrell, Andrew S.
Unknown Affiliation
Cheng, Jadeyu
Unknown Affiliation
Cox, Laura A.
Unknown Affiliation
Else, James G.
Unknown Affiliation
Han, Yi
Unknown Affiliation
Kopp, Gisela H.
Unknown Affiliation
Kothe, Maximilian
Unknown Affiliation
Leppälä, Kalle
Unknown Affiliation
Noll, Angela
Unknown Affiliation
Pecotte, Jera
Unknown Affiliation
Pipes, Lenore
Unknown Affiliation
Rice, Karen S.
Unknown Affiliation
Mason, Christopher E.
Unknown Affiliation
Disotell, Todd R.
Unknown Affiliation
Walter, Lutz
Unknown Affiliation
Munch, Kasper
Unknown Affiliation
Mailund, Thomas
Unknown Affiliation
Schierup, Mikkel Heide
Unknown Affiliation
Kosiol, Carolin
Unknown Affiliation
Vinař, Tomáš
Unknown Affiliation
Sikela, James M.
Unknown Affiliation
Zinner, Dietmar P.
Unknown Affiliation
Roos, Christian
Unknown Affiliation
Radivojac, Predrag
Unknown Affiliation
Stanyon, R. R.
Unknown Affiliation
Rocchi, Mariano
Unknown Affiliation
Eichler, Evan E.
Unknown Affiliation
Aken, Bronwen L.
Unknown Affiliation
Hahn, Matthew W.
Unknown Affiliation
Batzer, Mark A.
Unknown Affiliation
Marques-Bonet, Tomas
Unknown Affiliation
Tung, Jenny
Unknown Affiliation
Muzny, Donna Marie
Unknown Affiliation
Gibbs, Richard A.L.
Unknown Affiliation
Statistics
Citations: 14
Authors: 68
Affiliations: 5
Identifiers
Doi:
10.1186/s13100-018-0118-3
ISSN:
17598753
Research Areas
Cancer