A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  • Vallmer E. Jordan, Department of Biological Sciences, Louisiana State University, United States
  • Jerilyn A. Walker, Department of Biological Sciences, Louisiana State University, United States
  • Thomas O. Beckstrom, Department of Biological Sciences, Louisiana State University, United States
  • Cody J. Steely, Department of Biological Sciences, Louisiana State University, United States
  • Cullen L. McDaniel, Department of Biological Sciences, Louisiana State University, United States
  • Corey P. St Romain, Department of Biological Sciences, Louisiana State University, United States
  • The Baboon Genome Analysis Consortium
  • ,
  • Kim C. Worley, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA., United States
  • Jane Phillips-Conroy, Washington University, United States
  • Clifford J. Jolly, New York University
  • ,
  • Jeffrey Rogers, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, United States
  • Miriam K. Konkel, Clemson University, Department of Biological Sciences, Louisiana State University
  • ,
  • Mark A. Batzer, Department of Biological Sciences, Louisiana State University, United States

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.

Original languageEnglish
Article number13
JournalMobile DNA
Volume9
Issue1
Number of pages11
ISSN1383-469X
DOIs
Publication statusPublished - 5 Apr 2018

Bibliographical note

Thomas Mailund (Bioinformatics Research Centre, Aahus University) is a member of Baboon Genome Analysis Consortium, hence not mentioned directly by name as author.

    Research areas

  • Alu, Evolutionary genetics, Hybridization, Papio, Phylogeny, Primates, Retrotransposon, Taxonomy, HAMADRYAS BABOONS, HUMAN-EVOLUTION, RETROTRANSPOSITION, HYBRID ZONE, PRIMATES, ANUBIS BABOONS, GENETIC-VARIATION, PRIMED REVERSE TRANSCRIPTION, SINE INSERTIONS, HUMAN GENOMIC DIVERSITY

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