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An Approximate Bayesian Computation Approach to Examining the Phylogenetic Relationships among the Four Gibbon Genera using Whole Genome Sequence Data

Krishna R. Veeramah, August E. Woerner, Laurel Johnstone, Ivo Gut, Marta Gut, Tomas Marques-Bonet, Lucia Carbone, Jeff D. Wall, Michael F. Hammer
doi: https://doi.org/10.1101/009498
Krishna R. Veeramah
*Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, AZ, USA
§Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
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August E. Woerner
*Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, AZ, USA
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Laurel Johnstone
*Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, AZ, USA
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Ivo Gut
†CNAG (Centro Nacional de Analisis Genomico), Baldiri Reixac 4, 08028 Barcelona, Spain
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Marta Gut
†CNAG (Centro Nacional de Analisis Genomico), Baldiri Reixac 4, 08028 Barcelona, Spain
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Tomas Marques-Bonet
†CNAG (Centro Nacional de Analisis Genomico), Baldiri Reixac 4, 08028 Barcelona, Spain
‡ICREA at Insitit de Biologia Evolutiva (CSIC/UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
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Lucia Carbone
**Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
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Jeff D. Wall
§§Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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Michael F. Hammer
*Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, AZ, USA
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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, mtDNA, the Y chromosome, and short autosomal sequences have been inconclusive. To examine the relationships among gibbon genera in more depth, we performed 2nd generation whole genome sequencing to a mean of ∼15X coverage in two individuals from each genus. We developed a coalescent-based Approximate Bayesian Computation 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. Our combined 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.

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Posted September 22, 2014.
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An Approximate Bayesian Computation Approach to Examining the Phylogenetic Relationships among the Four Gibbon Genera using Whole Genome Sequence Data
Krishna R. Veeramah, August E. Woerner, Laurel Johnstone, Ivo Gut, Marta Gut, Tomas Marques-Bonet, Lucia Carbone, Jeff D. Wall, Michael F. Hammer
bioRxiv 009498; doi: https://doi.org/10.1101/009498
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An Approximate Bayesian Computation Approach to Examining the Phylogenetic Relationships among the Four Gibbon Genera using Whole Genome Sequence Data
Krishna R. Veeramah, August E. Woerner, Laurel Johnstone, Ivo Gut, Marta Gut, Tomas Marques-Bonet, Lucia Carbone, Jeff D. Wall, Michael F. Hammer
bioRxiv 009498; doi: https://doi.org/10.1101/009498

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