Recent demographic histories of temperate deciduous trees inferred from microsatellite markers
Abstract 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 a...
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| Format: | Article |
| Language: | English |
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BMC
2021-05-01
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| Series: | BMC Ecology and Evolution |
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| Online Access: | https://doi.org/10.1186/s12862-021-01805-w |
| _version_ | 1818681776802889728 |
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| author | Yu Cao Da-Yong Zhang Yan-Fei Zeng Wei-Ning Bai |
| author_facet | Yu Cao Da-Yong Zhang Yan-Fei Zeng Wei-Ning Bai |
| author_sort | Yu Cao |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-17T10:08:20Z |
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| id | doaj.art-a09c6243cf044c0bb22d7c39a1330315 |
| institution | Directory Open Access Journal |
| issn | 2730-7182 |
| language | English |
| last_indexed | 2024-12-17T10:08:20Z |
| publishDate | 2021-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Ecology and Evolution |
| spelling | doaj.art-a09c6243cf044c0bb22d7c39a13303152022-12-21T21:53:07ZengBMCBMC Ecology and Evolution2730-71822021-05-012111910.1186/s12862-021-01805-wRecent demographic histories of temperate deciduous trees inferred from microsatellite markersYu Cao0Da-Yong Zhang1Yan-Fei Zeng2Wei-Ning Bai3State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal UniversityState Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal UniversityState Key Laboratory of Tree Genetics and Breeding, Chinese Academy of ForestryState Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal UniversityAbstract 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.https://doi.org/10.1186/s12862-021-01805-wAsian butternutsDemographic inferenceEffective population sizeMIGRAINEOaksVarEff |
| spellingShingle | Yu Cao Da-Yong Zhang Yan-Fei Zeng Wei-Ning Bai Recent demographic histories of temperate deciduous trees inferred from microsatellite markers BMC Ecology and Evolution Asian butternuts Demographic inference Effective population size MIGRAINE Oaks VarEff |
| 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 | Asian butternuts Demographic inference Effective population size MIGRAINE Oaks VarEff |
| url | https://doi.org/10.1186/s12862-021-01805-w |
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