A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms

Vallmer E. Jordan; Jerilyn A. Walker; Thomas O. Beckstrom; Cody J. Steely; Cullen L. McDaniel; Corey P. St Romain; The Baboon Genome Analysis Consortium; Kim C. Worley; Jane Phillips-Conroy; Clifford J. Jolly; Jeffrey Rogers; Miriam K. Konkel; Mark A. Batzer

doi:10.1186/s13100-018-0118-3

A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms

Vallmer E. Jordan, Jerilyn A. Walker, Thomas O. Beckstrom, Cody J. Steely, Cullen L. McDaniel, Corey P. St Romain, The Baboon Genome Analysis Consortium, Kim C. Worley, Jane Phillips-Conroy, Clifford J. Jolly, Jeffrey Rogers, Miriam K. Konkel, Mark A. Batzer

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

1 Citation (Scopus)

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.

Original language	English
Article number	13
Journal	Mobile DNA
Volume	9
Issue	1
Number of pages	11
ISSN	1383-469X
DOIs	https://doi.org/10.1186/s13100-018-0118-3
Publication status	Published - 5 Apr 2018

Keywords

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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10.1186/s13100-018-0118-3

http://europepmc.org/articles/pmc5885306?pdf=render; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5885306

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Jordan, V. E., Walker, J. A., Beckstrom, T. O., Steely, C. J., McDaniel, C. L., St Romain, C. P., The Baboon Genome Analysis Consortium, Worley, K. C., Phillips-Conroy, J., Jolly, C. J., Rogers, J., Konkel, M. K., & Batzer, M. A. (2018). A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms. Mobile DNA, 9(1), Article 13. https://doi.org/10.1186/s13100-018-0118-3

@article{87c2e95ed27b4cf4b5a3afdeba690b05,

title = "A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms",

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.",

keywords = "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",

author = "Jordan, {Vallmer E.} and Walker, {Jerilyn A.} and Beckstrom, {Thomas O.} and Steely, {Cody J.} and McDaniel, {Cullen L.} and {St Romain}, {Corey P.} and {The Baboon Genome Analysis Consortium} and Worley, {Kim C.} and Jane Phillips-Conroy and Jolly, {Clifford J.} and Jeffrey Rogers and Konkel, {Miriam K.} and Batzer, {Mark A.} and Dominik Schrempf and Georgios Athanasiadis and Jade Cheng and Kalle Lepp{\"a}l{\"a} and Kasper Munch and Thomas Mailund and Mikkel Schierup",

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

year = "2018",

month = apr,

day = "5",

doi = "10.1186/s13100-018-0118-3",

language = "English",

volume = "9",

journal = "Mobile DNA",

issn = "1383-469X",

publisher = "Springer",

number = "1",

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T1 - A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms

AU - Jordan, Vallmer E.

AU - Walker, Jerilyn A.

AU - Beckstrom, Thomas O.

AU - Steely, Cody J.

AU - McDaniel, Cullen L.

AU - St Romain, Corey P.

AU - The Baboon Genome Analysis Consortium

AU - Worley, Kim C.

AU - Phillips-Conroy, Jane

AU - Jolly, Clifford J.

AU - Rogers, Jeffrey

AU - Konkel, Miriam K.

AU - Batzer, Mark A.

AU - Schrempf, Dominik

AU - Athanasiadis, Georgios

AU - Cheng, Jade

AU - Leppälä, Kalle

AU - Munch, Kasper

AU - Mailund, Thomas

AU - Schierup, Mikkel

N1 - Thomas Mailund (Bioinformatics Research Centre, Aahus University) is a member of Baboon Genome Analysis Consortium, hence not mentioned directly by name as author.

PY - 2018/4/5

Y1 - 2018/4/5

N2 - 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.

AB - 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.

KW - Alu

KW - Evolutionary genetics

KW - Hybridization

KW - Papio

KW - Phylogeny

KW - Primates

KW - Retrotransposon

KW - Taxonomy

KW - HAMADRYAS BABOONS

KW - HUMAN-EVOLUTION

KW - RETROTRANSPOSITION

KW - HYBRID ZONE

KW - PRIMATES

KW - ANUBIS BABOONS

KW - GENETIC-VARIATION

KW - PRIMED REVERSE TRANSCRIPTION

KW - SINE INSERTIONS

KW - HUMAN GENOMIC DIVERSITY

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U2 - 10.1186/s13100-018-0118-3

DO - 10.1186/s13100-018-0118-3

M3 - Journal article

C2 - 29632618

AN - SCOPUS:85044927174

SN - 1383-469X

VL - 9

JO - Mobile DNA

JF - Mobile DNA

IS - 1

M1 - 13

ER -

A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms

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Keywords

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