title: Examining phylogenetic relationships among gibbon genera using whole genome sequence data using an approximate bayesian computation approach.
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 ∼15× 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 1 × 10(-9)/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.
authors.affiliation: Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721 Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794.
authors.forename: Krishna R
authors.initials: KR
authors.lastname: Veeramah
authors.affiliation: Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721.
authors.forename: August E
authors.initials: AE
authors.lastname: Woerner
authors.affiliation: Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721.
authors.forename: Laurel
authors.initials: L
authors.lastname: Johnstone
authors.affiliation: Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794.
authors.forename: Ivo
authors.initials: I
authors.lastname: Gut
authors.affiliation: Centro Nacional de Analisis Genomico, 08028 Barcelona, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Gut
authors.affiliation: Centro Nacional de Analisis Genomico, 08028 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats at Insitit de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas/Universitat Pompeu Fabra), 08003 Barcelona, Spain.
authors.forename: Tomas
authors.initials: T
authors.lastname: Marques-Bonet
authors.affiliation: Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon 97239.
authors.forename: Lucia
authors.initials: L
authors.lastname: Carbone
authors.affiliation: Institute for Human Genetics, University of California, San Francisco, California 94143.
authors.forename: Jeff D
authors.initials: JD
authors.lastname: Wall
authors.affiliation: Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721 mfh@email.arizona.edu.
authors.forename: Michael F
authors.initials: MF
authors.lastname: Hammer
mesh_terms: D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D019143:Evolution, Molecular; D016678:Genome; D006922:Hylobates / Q000145:classification / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA
keywords: approximate Bayesian computation; gibbon species; rapid radiation; whole genome sequences