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Recent demographic histories of temperate deciduous trees inferred from microsatellite markers
BACKGROUND: Accurate inference of demographic histories for temperate tree species can aid our understanding of current climate change as a driver of evolution. Microsatellites are more suitable for inferring recent historical events due to their high mutation rates. However, most programs analyzing...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8130339/ https://www.ncbi.nlm.nih.gov/pubmed/34006219 http://dx.doi.org/10.1186/s12862-021-01805-w |
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author | Cao, Yu Zhang, Da-Yong Zeng, Yan-Fei Bai, Wei-Ning |
author_facet | Cao, Yu Zhang, Da-Yong Zeng, Yan-Fei Bai, Wei-Ning |
author_sort | Cao, Yu |
collection | PubMed |
description | BACKGROUND: Accurate inference of demographic histories for temperate tree species can aid our understanding of current climate change as a driver of evolution. Microsatellites are more suitable for inferring recent historical events due to their high mutation rates. However, most programs analyzing microsatellite data assume a strict stepwise mutation model (SMM), which could cause false detection of population shrinkage when microsatellite mutation does not follow SMM. RESULTS: This study aims to reconstruct the recent demographic histories of five cool-temperate tree species in Eastern Asia, Quercus mongolica, Q. liaotungensis, Juglans cathayensis, J. mandshurica and J. ailantifolia, by using 19 microsatellite markers with two methods considering generalized stepwise mutation model (GSM) (MIGRAINE and VarEff). Both programs revealed that all the five species experienced expansions after the Last Glacial Maximum (LGM). Within butternuts, J. cathayensis experienced a more serious bottleneck than the other species, and within oaks, Q. mongolica showed a moderate increase in population size and remained stable after the expansion. In addition, the point estimates of the multistep mutation proportion in the GSM model (p(GSM)) for all five species were between 0.50 and 0.65, indicating that when inferring population demographic history of the cool-temperate forest species using microsatellite markers, it is better to assume a GSM rather than a SMM. CONCLUSIONS: This study provides the first direct evidence that five cool-temperate tree species in East Asia have experienced expansions after the LGM with microsatellite data. Considering the mutation model of microsatellite has a vital influence on demographic inference, combining multiple programs such as MIGRAINE and VarEff can effectively reduce errors caused by inappropriate model selection and prior setting. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12862-021-01805-w. |
format | Online Article Text |
id | pubmed-8130339 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-81303392021-05-19 Recent demographic histories of temperate deciduous trees inferred from microsatellite markers Cao, Yu Zhang, Da-Yong Zeng, Yan-Fei Bai, Wei-Ning BMC Ecol Evol Research Article BACKGROUND: Accurate inference of demographic histories for temperate tree species can aid our understanding of current climate change as a driver of evolution. Microsatellites are more suitable for inferring recent historical events due to their high mutation rates. However, most programs analyzing microsatellite data assume a strict stepwise mutation model (SMM), which could cause false detection of population shrinkage when microsatellite mutation does not follow SMM. RESULTS: This study aims to reconstruct the recent demographic histories of five cool-temperate tree species in Eastern Asia, Quercus mongolica, Q. liaotungensis, Juglans cathayensis, J. mandshurica and J. ailantifolia, by using 19 microsatellite markers with two methods considering generalized stepwise mutation model (GSM) (MIGRAINE and VarEff). Both programs revealed that all the five species experienced expansions after the Last Glacial Maximum (LGM). Within butternuts, J. cathayensis experienced a more serious bottleneck than the other species, and within oaks, Q. mongolica showed a moderate increase in population size and remained stable after the expansion. In addition, the point estimates of the multistep mutation proportion in the GSM model (p(GSM)) for all five species were between 0.50 and 0.65, indicating that when inferring population demographic history of the cool-temperate forest species using microsatellite markers, it is better to assume a GSM rather than a SMM. CONCLUSIONS: This study provides the first direct evidence that five cool-temperate tree species in East Asia have experienced expansions after the LGM with microsatellite data. Considering the mutation model of microsatellite has a vital influence on demographic inference, combining multiple programs such as MIGRAINE and VarEff can effectively reduce errors caused by inappropriate model selection and prior setting. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12862-021-01805-w. BioMed Central 2021-05-18 /pmc/articles/PMC8130339/ /pubmed/34006219 http://dx.doi.org/10.1186/s12862-021-01805-w Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Article Cao, Yu Zhang, Da-Yong Zeng, Yan-Fei Bai, Wei-Ning Recent demographic histories of temperate deciduous trees inferred from microsatellite markers |
title | Recent demographic histories of temperate deciduous trees inferred from microsatellite markers |
title_full | Recent demographic histories of temperate deciduous trees inferred from microsatellite markers |
title_fullStr | Recent demographic histories of temperate deciduous trees inferred from microsatellite markers |
title_full_unstemmed | Recent demographic histories of temperate deciduous trees inferred from microsatellite markers |
title_short | Recent demographic histories of temperate deciduous trees inferred from microsatellite markers |
title_sort | recent demographic histories of temperate deciduous trees inferred from microsatellite markers |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8130339/ https://www.ncbi.nlm.nih.gov/pubmed/34006219 http://dx.doi.org/10.1186/s12862-021-01805-w |
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