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Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation

The genus Macaca includes 23 species assigned into 4 to 7 groups. It exhibits the largest geographic range and represents the most successful example of adaptive radiation of nonhuman primates. However, intrageneric phylogenetic relationships among species remain controversial and have not been reso...

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Autores principales: Tan, Xinxin, Qi, Jiwei, Liu, Zhijin, Fan, Pengfei, Liu, Gaoming, Zhang, Liye, Shen, Ying, Li, Jing, Roos, Christian, Zhou, Xuming, Li, Ming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10638670/
https://www.ncbi.nlm.nih.gov/pubmed/37823401
http://dx.doi.org/10.1093/molbev/msad229
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author Tan, Xinxin
Qi, Jiwei
Liu, Zhijin
Fan, Pengfei
Liu, Gaoming
Zhang, Liye
Shen, Ying
Li, Jing
Roos, Christian
Zhou, Xuming
Li, Ming
author_facet Tan, Xinxin
Qi, Jiwei
Liu, Zhijin
Fan, Pengfei
Liu, Gaoming
Zhang, Liye
Shen, Ying
Li, Jing
Roos, Christian
Zhou, Xuming
Li, Ming
author_sort Tan, Xinxin
collection PubMed
description The genus Macaca includes 23 species assigned into 4 to 7 groups. It exhibits the largest geographic range and represents the most successful example of adaptive radiation of nonhuman primates. However, intrageneric phylogenetic relationships among species remain controversial and have not been resolved so far. In this study, we conducted a phylogenomic analysis on 16 newly generated and 8 published macaque genomes. We found strong evidence supporting the division of this genus into 7 species groups. Incomplete lineage sorting (ILS) was the primary factor contributing to the discordance observed among gene trees; however, we also found evidence of hybridization events, specifically between the ancestral arctoides/sinica and silenus/nigra lineages that resulted in the hybrid formation of the fascicularis/mulatta group. Combined with fossil data, our phylogenomic data were used to establish a scenario for macaque radiation. These findings provide insights into ILS and potential ancient introgression events that were involved in the radiation of macaques, which will lead to a better understanding of the rapid speciation occurring in nonhuman primates.
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spelling pubmed-106386702023-11-11 Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation Tan, Xinxin Qi, Jiwei Liu, Zhijin Fan, Pengfei Liu, Gaoming Zhang, Liye Shen, Ying Li, Jing Roos, Christian Zhou, Xuming Li, Ming Mol Biol Evol Discoveries The genus Macaca includes 23 species assigned into 4 to 7 groups. It exhibits the largest geographic range and represents the most successful example of adaptive radiation of nonhuman primates. However, intrageneric phylogenetic relationships among species remain controversial and have not been resolved so far. In this study, we conducted a phylogenomic analysis on 16 newly generated and 8 published macaque genomes. We found strong evidence supporting the division of this genus into 7 species groups. Incomplete lineage sorting (ILS) was the primary factor contributing to the discordance observed among gene trees; however, we also found evidence of hybridization events, specifically between the ancestral arctoides/sinica and silenus/nigra lineages that resulted in the hybrid formation of the fascicularis/mulatta group. Combined with fossil data, our phylogenomic data were used to establish a scenario for macaque radiation. These findings provide insights into ILS and potential ancient introgression events that were involved in the radiation of macaques, which will lead to a better understanding of the rapid speciation occurring in nonhuman primates. Oxford University Press 2023-10-12 /pmc/articles/PMC10638670/ /pubmed/37823401 http://dx.doi.org/10.1093/molbev/msad229 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Discoveries
Tan, Xinxin
Qi, Jiwei
Liu, Zhijin
Fan, Pengfei
Liu, Gaoming
Zhang, Liye
Shen, Ying
Li, Jing
Roos, Christian
Zhou, Xuming
Li, Ming
Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation
title Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation
title_full Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation
title_fullStr Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation
title_full_unstemmed Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation
title_short Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation
title_sort phylogenomics reveals high levels of incomplete lineage sorting at the ancestral nodes of the macaque radiation
topic Discoveries
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10638670/
https://www.ncbi.nlm.nih.gov/pubmed/37823401
http://dx.doi.org/10.1093/molbev/msad229
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