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

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

Posted 22 Sep 2014
bioRxiv DOI: 10.1101/009498 (published DOI: 10.1534/genetics.115.174425)

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 1x10-9/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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