Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii)

Xin Ma; Joanna L Kelley; Kirsten Eilertson; Shaila Musharoff; Jeremiah D Degenhardt; André L Martins; Tomas Vinar; Carolin Kosiol; Adam Siepel; Ryan N Gutenkunst; Carlos D Bustamante

doi:10.1371/journal.pone.0077175

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Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii)

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Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii)

Xin Ma, Joanna L Kelley, Kirsten Eilertson, Shaila Musharoff, Jeremiah D Degenhardt, André L Martins, Tomas Vinar, Carolin Kosiol, Adam Siepel, Ryan N Gutenkunst, …

PloS one, Vol.8(10), pp.e77175-e77175

2013

DOI: https://doi.org/10.1371/journal.pone.0077175

Handle:

https://hdl.handle.net/2376/110385

PMCID: PMC3806739

PMID: 24194868

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Abstract

Genetics, Population

Borneo

Genetic Drift

Species Specificity

Molecular Sequence Annotation

Selection, Genetic

Molecular Sequence Data

Phylogeny

Sequence Analysis, DNA

Pongo - genetics

Genetic Variation

Animals

Base Sequence

Genetic Speciation

Bayes Theorem

Polymorphism, Single Nucleotide - genetics

Animal Migration

Models, Genetic

Evolution, Molecular

Indonesia

To gain insights into evolutionary forces that have shaped the history of Bornean and Sumatran populations of orang-utans, we compare patterns of variation across more than 11 million single nucleotide polymorphisms found by previous mitochondrial and autosomal genome sequencing of 10 wild-caught orang-utans. Our analysis of the mitochondrial data yields a far more ancient split time between the two populations (~3.4 million years ago) than estimates based on autosomal data (0.4 million years ago), suggesting a complex speciation process with moderate levels of primarily male migration. We find that the distribution of selection coefficients consistent with the observed frequency spectrum of autosomal non-synonymous polymorphisms in orang-utans is similar to the distribution in humans. Our analysis indicates that 35% of genes have evolved under detectable negative selection. Overall, our findings suggest that purifying natural selection, genetic drift, and a complex demographic history are the dominant drivers of genome evolution for the two orang-utan populations.

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Title: Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii)
Creators: Xin Ma - Department of Statistics, Stanford University, Stanford, California, United States of America
Joanna L Kelley
Kirsten Eilertson
Shaila Musharoff
Jeremiah D Degenhardt
André L Martins
Tomas Vinar
Carolin Kosiol
Adam Siepel
Ryan N Gutenkunst
Carlos D Bustamante
Publication Details: PloS one, Vol.8(10), pp.e77175-e77175
Academic Unit: Kelley Lab; Biological Sciences, School of
Publisher: Public Library Science; United States
Number of pages: 11
Grant note: P30 GM092391 / NIGMS NIH HHS GM087069 / NIGMS NIH HHS F32 GM087069 / NIGMS NIH HHS P30-GM092391 / NIGMS NIH HHS T32 HG000044 / NHGRI NIH HHS
Identifiers: 99900547025801842
Language: English
Resource Type: Journal article