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Simulating and Summarizing Sources of Gene Tree Incongruence

We introduce a gene tree simulator that is designed for use in conjunction with approximate Bayesian computation approaches. We show that it can be used to determine the relative importance of hybrid speciation and introgression compared with incomplete lineage sorting (ILS) in producing patterns of...

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Autores principales: Woodhams, Michael D., Lockhart, Peter. J., Holland, Barbara R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4898792/
https://www.ncbi.nlm.nih.gov/pubmed/27017528
http://dx.doi.org/10.1093/gbe/evw065
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author Woodhams, Michael D.
Lockhart, Peter. J.
Holland, Barbara R.
author_facet Woodhams, Michael D.
Lockhart, Peter. J.
Holland, Barbara R.
author_sort Woodhams, Michael D.
collection PubMed
description We introduce a gene tree simulator that is designed for use in conjunction with approximate Bayesian computation approaches. We show that it can be used to determine the relative importance of hybrid speciation and introgression compared with incomplete lineage sorting (ILS) in producing patterns of incongruence across gene trees. Important features of the new simulator are (1) a choice of models to capture the decreasing probability of successful hybrid species formation or introgression as a function of genetic distance between potential parent species; (2) the ability for hybrid speciation to result in asymmetrical contributions of genetic material from each parent species; (3) the ability to vary the rates of hybrid speciation, introgression, and divergence speciation in different epochs; and (4) incorporation of the coalescent, so that patterns of incongruence due to ILS can be compared with those due to hybrid evolution. Given a set of gene trees generated by the simulator, we calculate a set of statistics, each measuring in a different way the discordance between the gene trees. We show that these statistics can be used to differentiate whether the gene tree discordance was largely due to hybridization, or only due to lineage sorting.
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spelling pubmed-48987922016-06-10 Simulating and Summarizing Sources of Gene Tree Incongruence Woodhams, Michael D. Lockhart, Peter. J. Holland, Barbara R. Genome Biol Evol Research Article We introduce a gene tree simulator that is designed for use in conjunction with approximate Bayesian computation approaches. We show that it can be used to determine the relative importance of hybrid speciation and introgression compared with incomplete lineage sorting (ILS) in producing patterns of incongruence across gene trees. Important features of the new simulator are (1) a choice of models to capture the decreasing probability of successful hybrid species formation or introgression as a function of genetic distance between potential parent species; (2) the ability for hybrid speciation to result in asymmetrical contributions of genetic material from each parent species; (3) the ability to vary the rates of hybrid speciation, introgression, and divergence speciation in different epochs; and (4) incorporation of the coalescent, so that patterns of incongruence due to ILS can be compared with those due to hybrid evolution. Given a set of gene trees generated by the simulator, we calculate a set of statistics, each measuring in a different way the discordance between the gene trees. We show that these statistics can be used to differentiate whether the gene tree discordance was largely due to hybridization, or only due to lineage sorting. Oxford University Press 2016-03-26 /pmc/articles/PMC4898792/ /pubmed/27017528 http://dx.doi.org/10.1093/gbe/evw065 Text en © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Woodhams, Michael D.
Lockhart, Peter. J.
Holland, Barbara R.
Simulating and Summarizing Sources of Gene Tree Incongruence
title Simulating and Summarizing Sources of Gene Tree Incongruence
title_full Simulating and Summarizing Sources of Gene Tree Incongruence
title_fullStr Simulating and Summarizing Sources of Gene Tree Incongruence
title_full_unstemmed Simulating and Summarizing Sources of Gene Tree Incongruence
title_short Simulating and Summarizing Sources of Gene Tree Incongruence
title_sort simulating and summarizing sources of gene tree incongruence
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4898792/
https://www.ncbi.nlm.nih.gov/pubmed/27017528
http://dx.doi.org/10.1093/gbe/evw065
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