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Impact of long‐term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages

Multispecies coalescent (MSC) theory assumes that gene trees inferred from individual loci are independent trials of the MSC process. As genes might be physically close in syntenic associations spanning along chromosome regions, these assumptions might be flawed in evolutionary lineages with substan...

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Autores principales: Schrago, Carlos G., Mello, Beatriz, Pereira, Anieli G., Furtado, Carolina, Seuánez, Hector N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5773316/
https://www.ncbi.nlm.nih.gov/pubmed/29375791
http://dx.doi.org/10.1002/ece3.3736
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author Schrago, Carlos G.
Mello, Beatriz
Pereira, Anieli G.
Furtado, Carolina
Seuánez, Hector N.
author_facet Schrago, Carlos G.
Mello, Beatriz
Pereira, Anieli G.
Furtado, Carolina
Seuánez, Hector N.
author_sort Schrago, Carlos G.
collection PubMed
description Multispecies coalescent (MSC) theory assumes that gene trees inferred from individual loci are independent trials of the MSC process. As genes might be physically close in syntenic associations spanning along chromosome regions, these assumptions might be flawed in evolutionary lineages with substantial karyotypic shuffling. Neotropical primates (NP) represent an ideal case for assessing the performance of MSC methods in such scenarios because chromosome diploid number varies significantly in this lineage. To this end, we investigated the effect of sequence length on the theoretical expectations of MSC model, as well as the results of coalescent‐based tree inference methods. This was carried out by comparing NP with hominids, a lineage in which chromosome macrostructure has been stable for at least 15 million years. We found that departure from the MSC model in Neotropical primates decreased with smaller sequence fragments, where sites sharing the same evolutionary history were more frequently found than in longer fragments. This scenario probably resulted from extensive karyotypic rearrangement occurring during the radiation of NP, contrary to the comparatively stable chromosome evolution in hominids.
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spelling pubmed-57733162018-01-26 Impact of long‐term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages Schrago, Carlos G. Mello, Beatriz Pereira, Anieli G. Furtado, Carolina Seuánez, Hector N. Ecol Evol Original Research Multispecies coalescent (MSC) theory assumes that gene trees inferred from individual loci are independent trials of the MSC process. As genes might be physically close in syntenic associations spanning along chromosome regions, these assumptions might be flawed in evolutionary lineages with substantial karyotypic shuffling. Neotropical primates (NP) represent an ideal case for assessing the performance of MSC methods in such scenarios because chromosome diploid number varies significantly in this lineage. To this end, we investigated the effect of sequence length on the theoretical expectations of MSC model, as well as the results of coalescent‐based tree inference methods. This was carried out by comparing NP with hominids, a lineage in which chromosome macrostructure has been stable for at least 15 million years. We found that departure from the MSC model in Neotropical primates decreased with smaller sequence fragments, where sites sharing the same evolutionary history were more frequently found than in longer fragments. This scenario probably resulted from extensive karyotypic rearrangement occurring during the radiation of NP, contrary to the comparatively stable chromosome evolution in hominids. John Wiley and Sons Inc. 2017-12-20 /pmc/articles/PMC5773316/ /pubmed/29375791 http://dx.doi.org/10.1002/ece3.3736 Text en © 2017 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution (http://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Research
Schrago, Carlos G.
Mello, Beatriz
Pereira, Anieli G.
Furtado, Carolina
Seuánez, Hector N.
Impact of long‐term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages
title Impact of long‐term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages
title_full Impact of long‐term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages
title_fullStr Impact of long‐term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages
title_full_unstemmed Impact of long‐term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages
title_short Impact of long‐term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages
title_sort impact of long‐term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5773316/
https://www.ncbi.nlm.nih.gov/pubmed/29375791
http://dx.doi.org/10.1002/ece3.3736
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