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A history of hybrids? Genomic patterns of introgression in the True Geese

BACKGROUND: The impacts of hybridization on the process of speciation are manifold, leading to distinct patterns across the genome. Genetic differentiation accumulates in certain genomic regions, while divergence is hampered in other regions by homogenizing gene flow, resulting in a heterogeneous ge...

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Autores principales: Ottenburghs, Jente, Megens, Hendrik-Jan, Kraus, Robert H. S., van Hooft, Pim, van Wieren, Sipke E., Crooijmans, Richard P. M. A., Ydenberg, Ronald C., Groenen, Martien A. M., Prins, Herbert H. T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568201/
https://www.ncbi.nlm.nih.gov/pubmed/28830337
http://dx.doi.org/10.1186/s12862-017-1048-2
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author Ottenburghs, Jente
Megens, Hendrik-Jan
Kraus, Robert H. S.
van Hooft, Pim
van Wieren, Sipke E.
Crooijmans, Richard P. M. A.
Ydenberg, Ronald C.
Groenen, Martien A. M.
Prins, Herbert H. T.
author_facet Ottenburghs, Jente
Megens, Hendrik-Jan
Kraus, Robert H. S.
van Hooft, Pim
van Wieren, Sipke E.
Crooijmans, Richard P. M. A.
Ydenberg, Ronald C.
Groenen, Martien A. M.
Prins, Herbert H. T.
author_sort Ottenburghs, Jente
collection PubMed
description BACKGROUND: The impacts of hybridization on the process of speciation are manifold, leading to distinct patterns across the genome. Genetic differentiation accumulates in certain genomic regions, while divergence is hampered in other regions by homogenizing gene flow, resulting in a heterogeneous genomic landscape. A consequence of this heterogeneity is that genomes are mosaics of different gene histories that can be compared to unravel complex speciation and hybridization events. However, incomplete lineage sorting (often the outcome of rapid speciation) can result in similar patterns. New statistical techniques, such as the D-statistic and hybridization networks, can be applied to disentangle the contributions of hybridization and incomplete lineage sorting. We unravel patterns of hybridization and incomplete lineage sorting during and after the diversification of the True Geese (family Anatidae, tribe Anserini, genera Anser and Branta) using an exon-based hybridization network approach and taking advantage of discordant gene tree histories by re-sequencing all taxa of this clade. In addition, we determine the timing of introgression and reconstruct historical effective population sizes for all goose species to infer which demographic or biogeographic factors might explain the observed patterns of introgression. RESULTS: We find indications for ancient interspecific gene flow during the diversification of the True Geese and were able to pinpoint several putative hybridization events. Specifically, in the genus Branta, both the ancestor of the White-cheeked Geese (Hawaiian Goose, Canada Goose, Cackling Goose and Barnacle Goose) and the ancestor of the Brent Goose hybridized with Red-breasted Goose. One hybridization network suggests a hybrid origin for the Red-breasted Goose, but this scenario seems unlikely and it not supported by the D-statistic analysis. The complex, highly reticulated evolutionary history of the genus Anser hampered the estimation of ancient hybridization events by means of hybridization networks. The reconstruction of historical effective population sizes shows that most species showed a steady increase during the Pliocene and Pleistocene. These large effective population sizes might have facilitated contact between diverging goose species, resulting in the establishment of hybrid zones and consequent gene flow. CONCLUSIONS: Our analyses suggest that the evolutionary history of the True Geese is influenced by introgressive hybridization. The approach that we have used, based on genome-wide phylogenetic incongruence and network analyses, will be a useful procedure to reconstruct the complex evolutionary histories of many naturally hybridizing species groups. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-017-1048-2) contains supplementary material, which is available to authorized users.
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spelling pubmed-55682012017-08-29 A history of hybrids? Genomic patterns of introgression in the True Geese Ottenburghs, Jente Megens, Hendrik-Jan Kraus, Robert H. S. van Hooft, Pim van Wieren, Sipke E. Crooijmans, Richard P. M. A. Ydenberg, Ronald C. Groenen, Martien A. M. Prins, Herbert H. T. BMC Evol Biol Research Article BACKGROUND: The impacts of hybridization on the process of speciation are manifold, leading to distinct patterns across the genome. Genetic differentiation accumulates in certain genomic regions, while divergence is hampered in other regions by homogenizing gene flow, resulting in a heterogeneous genomic landscape. A consequence of this heterogeneity is that genomes are mosaics of different gene histories that can be compared to unravel complex speciation and hybridization events. However, incomplete lineage sorting (often the outcome of rapid speciation) can result in similar patterns. New statistical techniques, such as the D-statistic and hybridization networks, can be applied to disentangle the contributions of hybridization and incomplete lineage sorting. We unravel patterns of hybridization and incomplete lineage sorting during and after the diversification of the True Geese (family Anatidae, tribe Anserini, genera Anser and Branta) using an exon-based hybridization network approach and taking advantage of discordant gene tree histories by re-sequencing all taxa of this clade. In addition, we determine the timing of introgression and reconstruct historical effective population sizes for all goose species to infer which demographic or biogeographic factors might explain the observed patterns of introgression. RESULTS: We find indications for ancient interspecific gene flow during the diversification of the True Geese and were able to pinpoint several putative hybridization events. Specifically, in the genus Branta, both the ancestor of the White-cheeked Geese (Hawaiian Goose, Canada Goose, Cackling Goose and Barnacle Goose) and the ancestor of the Brent Goose hybridized with Red-breasted Goose. One hybridization network suggests a hybrid origin for the Red-breasted Goose, but this scenario seems unlikely and it not supported by the D-statistic analysis. The complex, highly reticulated evolutionary history of the genus Anser hampered the estimation of ancient hybridization events by means of hybridization networks. The reconstruction of historical effective population sizes shows that most species showed a steady increase during the Pliocene and Pleistocene. These large effective population sizes might have facilitated contact between diverging goose species, resulting in the establishment of hybrid zones and consequent gene flow. CONCLUSIONS: Our analyses suggest that the evolutionary history of the True Geese is influenced by introgressive hybridization. The approach that we have used, based on genome-wide phylogenetic incongruence and network analyses, will be a useful procedure to reconstruct the complex evolutionary histories of many naturally hybridizing species groups. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-017-1048-2) contains supplementary material, which is available to authorized users. BioMed Central 2017-08-22 /pmc/articles/PMC5568201/ /pubmed/28830337 http://dx.doi.org/10.1186/s12862-017-1048-2 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Ottenburghs, Jente
Megens, Hendrik-Jan
Kraus, Robert H. S.
van Hooft, Pim
van Wieren, Sipke E.
Crooijmans, Richard P. M. A.
Ydenberg, Ronald C.
Groenen, Martien A. M.
Prins, Herbert H. T.
A history of hybrids? Genomic patterns of introgression in the True Geese
title A history of hybrids? Genomic patterns of introgression in the True Geese
title_full A history of hybrids? Genomic patterns of introgression in the True Geese
title_fullStr A history of hybrids? Genomic patterns of introgression in the True Geese
title_full_unstemmed A history of hybrids? Genomic patterns of introgression in the True Geese
title_short A history of hybrids? Genomic patterns of introgression in the True Geese
title_sort history of hybrids? genomic patterns of introgression in the true geese
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568201/
https://www.ncbi.nlm.nih.gov/pubmed/28830337
http://dx.doi.org/10.1186/s12862-017-1048-2
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