Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach
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.
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Format: | artículo biblioteca |
Language: | English |
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Genetics Society of America
2015-05-01
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Subjects: | Approximate Bayesian computation, Gibbon species, Rapid radiation, Whole genome sequences, |
Online Access: | http://hdl.handle.net/10261/151541 http://dx.doi.org/10.13039/100000002 http://dx.doi.org/10.13039/501100000781 http://dx.doi.org/10.13039/501100004837 |
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dig-ibe-es-10261-1515412021-11-22T12:56:18Z 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 Marqués-Bonet, Tomàs Carbone, Lucia Wall, Jeff D. Hammer, Michael F. National Institutes of Health (US) European Research Council Ministerio de Ciencia e Innovación (España) Approximate Bayesian computation Gibbon species Rapid radiation Whole genome sequences 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. Support for this work was provided by the National Institutes of Health to J.D.W. and M.F.H. (R01_HG005226) and an European Research Council Starting Grant (260372) and Ministerio de Ciencia e Innovación (Spain) BFU2011-28549 to T.M.-B. Peer reviewed 2017-06-16T09:16:49Z 2017-06-16T09:16:49Z 2015-05-01 artículo http://purl.org/coar/resource_type/c_6501 Genetics 200(1): 295-308 (2015) 0016-6731 http://hdl.handle.net/10261/151541 10.1534/genetics.115.174425 1943-2631 http://dx.doi.org/10.13039/100000002 http://dx.doi.org/10.13039/501100000781 http://dx.doi.org/10.13039/501100004837 25769979 en #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/EC/FP7/260372 https://doi.org/10.1534/genetics.115.174425 Sí none Genetics Society of America |
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Approximate Bayesian computation Gibbon species Rapid radiation Whole genome sequences Approximate Bayesian computation Gibbon species Rapid radiation Whole genome sequences |
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Approximate Bayesian computation Gibbon species Rapid radiation Whole genome sequences Approximate Bayesian computation Gibbon species Rapid radiation Whole genome sequences Veeramah, Krishna R. Woerner, August E. Johnstone, Laurel Gut, Ivo Gut, Marta Marqués-Bonet, Tomàs 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 |
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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. |
author2 |
National Institutes of Health (US) |
author_facet |
National Institutes of Health (US) Veeramah, Krishna R. Woerner, August E. Johnstone, Laurel Gut, Ivo Gut, Marta Marqués-Bonet, Tomàs Carbone, Lucia Wall, Jeff D. Hammer, Michael F. |
format |
artículo |
topic_facet |
Approximate Bayesian computation Gibbon species Rapid radiation Whole genome sequences |
author |
Veeramah, Krishna R. Woerner, August E. Johnstone, Laurel Gut, Ivo Gut, Marta Marqués-Bonet, Tomàs Carbone, Lucia Wall, Jeff D. Hammer, Michael F. |
author_sort |
Veeramah, Krishna R. |
title |
Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach |
title_short |
Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach |
title_full |
Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach |
title_fullStr |
Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach |
title_full_unstemmed |
Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach |
title_sort |
examining phylogenetic relationships among gibbon genera using whole genome sequence data using an approximate bayesian computation approach |
publisher |
Genetics Society of America |
publishDate |
2015-05-01 |
url |
http://hdl.handle.net/10261/151541 http://dx.doi.org/10.13039/100000002 http://dx.doi.org/10.13039/501100000781 http://dx.doi.org/10.13039/501100004837 |
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