Examining phylogenetic relationships among gibbon genera using whole genome sequence data using an approximate bayesian computation approach

Krishna R. Veeramah, August E. Woerner, Laurel Johnstone, Ivo Gut, Marta Gut, Tomas Marques-Bonet, Lucia Carbone, Jeff D. Wall, Michael F Hammer

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Gibbons are believed to have diverged from the larger great apes ̴16.8 MYA and today reside in the rainforests of Southeast Asia. Based on their diploid chromosome number, the family Hylobatidae is divided into four genera, Nomascus, Symphalangus, Hoolock, and Hylobates. Genetic studies attempting to elucidate the phylogenetic relationships among gibbons using karyotypes, mitochondrial DNA (mtDNA), the Y chromosome, and short autosomal sequences have been inconclusive. To examine the relationships among gibbon genera in more depth, we performed second-generation whole genome sequencing (WGS) to a mean of ̴15x coverage in two individuals from each genus. We developed a coalescent-based approximate Bayesian computation (ABC) method incorporating a model of sequencing error generated by high coverage exome validation to infer the branching order, divergence times, and effective population sizes of gibbon taxa. Although Hoolock and Symphalangus are likely sister taxa, we could not confidently resolve a single bifurcating tree despite the large amount of data analyzed. Instead, our results support the hypothesis that all four gibbon genera diverged at approximately the same time. Assuming an autosomal mutation rate of 1x10<sup>-9</sup>/site/year this speciation process occurred ̴5 MYA during a period in the Early Pliocene characterized by climatic shifts and fragmentation of the Sunda shelf forests. Whole genome sequencing of additional individuals will be vital for inferring the extent of gene flow among species after the separation of the gibbon genera.

Original languageEnglish (US)
Pages (from-to)295-308
Number of pages14
JournalGenetics
Volume200
Issue number1
DOIs
StatePublished - Jan 1 2015

Fingerprint

Hylobates
Bayes Theorem
Genome
Hylobatidae
Exome
Southeastern Asia
Gene Flow
Y Chromosome
Hominidae
Mutation Rate
Population Density
Diploidy
Karyotype
Mitochondrial DNA
Chromosomes

Keywords

  • Approximate bayesian computation
  • Gibbon species
  • Rapid radiation
  • Whole genome sequences

ASJC Scopus subject areas

  • Genetics

Cite this

Examining phylogenetic relationships among gibbon genera using whole genome sequence data using an approximate bayesian computation approach. / Veeramah, Krishna R.; Woerner, August E.; Johnstone, Laurel; Gut, Ivo; Gut, Marta; Marques-Bonet, Tomas; Carbone, Lucia; Wall, Jeff D.; Hammer, Michael F.

In: Genetics, Vol. 200, No. 1, 01.01.2015, p. 295-308.

Research output: Contribution to journalArticle

Veeramah, KR, Woerner, AE, Johnstone, L, Gut, I, Gut, M, Marques-Bonet, T, Carbone, L, Wall, JD & Hammer, MF 2015, 'Examining phylogenetic relationships among gibbon genera using whole genome sequence data using an approximate bayesian computation approach', Genetics, vol. 200, no. 1, pp. 295-308. https://doi.org/10.1534/genetics.115.174425
Veeramah, Krishna R. ; Woerner, August E. ; Johnstone, Laurel ; Gut, Ivo ; Gut, Marta ; Marques-Bonet, Tomas ; Carbone, Lucia ; Wall, Jeff D. ; Hammer, Michael F. / Examining phylogenetic relationships among gibbon genera using whole genome sequence data using an approximate bayesian computation approach. In: Genetics. 2015 ; Vol. 200, No. 1. pp. 295-308.
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