Genomic insights into local adaptation and vulnerability of Quercus longinux to climate change
Abstract Background Climate change is expected to alter the factors that drive changes in adaptive variation. This is especially true for species with long life spans and limited dispersal capabilities. Rapid climate changes may disrupt the migration of beneficial genetic variations, making it chall...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2024-04-01
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| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-024-04942-8 |
| _version_ | 1797209400145870848 |
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| author | Pei-Wei Sun Jui-Tse Chang Min-Xin Luo Pei-Chun Liao |
| author_facet | Pei-Wei Sun Jui-Tse Chang Min-Xin Luo Pei-Chun Liao |
| author_sort | Pei-Wei Sun |
| collection | DOAJ |
| description | Abstract Background Climate change is expected to alter the factors that drive changes in adaptive variation. This is especially true for species with long life spans and limited dispersal capabilities. Rapid climate changes may disrupt the migration of beneficial genetic variations, making it challenging for them to keep up with changing environments. Understanding adaptive genetic variations in tree species is crucial for conservation and effective forest management. Our study used landscape genomic analyses and phenotypic traits from a thorough sampling across the entire range of Quercus longinux, an oak species native to Taiwan, to investigate the signals of adaptation within this species. Results Using ecological data, phenotypic traits, and 1,933 single-nucleotide polymorphisms (SNPs) from 205 individuals, we classified three genetic groups, which were also phenotypically and ecologically divergent. Thirty-five genes related to drought and freeze resistance displayed signatures of natural selection. The adaptive variation was driven by diverse environmental pressures such as low spring precipitation, low annual temperature, and soil grid sizes. Using linear-regression-based methods, we identified isolation by environment (IBE) as the optimal model for adaptive SNPs. Redundancy analysis (RDA) further revealed a substantial joint influence of demography, geology, and environments, suggesting a covariation between environmental gradients and colonization history. Lastly, we utilized adaptive signals to estimate the genetic offset for each individual under diverse climate change scenarios. The required genetic changes and migration distance are larger in severe climates. Our prediction also reveals potential threats to edge populations in northern and southeastern Taiwan due to escalating temperatures and precipitation reallocation. Conclusions We demonstrate the intricate influence of ecological heterogeneity on genetic and phenotypic adaptation of an oak species. The adaptation is also driven by some rarely studied environmental factors, including wind speed and soil features. Furthermore, the genetic offset analysis predicted that the edge populations of Q. longinux in lower elevations might face higher risks of local extinctions under climate change. |
| first_indexed | 2024-04-24T09:54:06Z |
| format | Article |
| id | doaj.art-3c23aecb4896484aabf1833488c6095b |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-24T09:54:06Z |
| publishDate | 2024-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-3c23aecb4896484aabf1833488c6095b2024-04-14T11:11:57ZengBMCBMC Plant Biology1471-22292024-04-0124111810.1186/s12870-024-04942-8Genomic insights into local adaptation and vulnerability of Quercus longinux to climate changePei-Wei Sun0Jui-Tse Chang1Min-Xin Luo2Pei-Chun Liao3School of Life Science, National Taiwan Normal UniversitySchool of Life Science, National Taiwan Normal UniversitySchool of Life Science, National Taiwan Normal UniversitySchool of Life Science, National Taiwan Normal UniversityAbstract Background Climate change is expected to alter the factors that drive changes in adaptive variation. This is especially true for species with long life spans and limited dispersal capabilities. Rapid climate changes may disrupt the migration of beneficial genetic variations, making it challenging for them to keep up with changing environments. Understanding adaptive genetic variations in tree species is crucial for conservation and effective forest management. Our study used landscape genomic analyses and phenotypic traits from a thorough sampling across the entire range of Quercus longinux, an oak species native to Taiwan, to investigate the signals of adaptation within this species. Results Using ecological data, phenotypic traits, and 1,933 single-nucleotide polymorphisms (SNPs) from 205 individuals, we classified three genetic groups, which were also phenotypically and ecologically divergent. Thirty-five genes related to drought and freeze resistance displayed signatures of natural selection. The adaptive variation was driven by diverse environmental pressures such as low spring precipitation, low annual temperature, and soil grid sizes. Using linear-regression-based methods, we identified isolation by environment (IBE) as the optimal model for adaptive SNPs. Redundancy analysis (RDA) further revealed a substantial joint influence of demography, geology, and environments, suggesting a covariation between environmental gradients and colonization history. Lastly, we utilized adaptive signals to estimate the genetic offset for each individual under diverse climate change scenarios. The required genetic changes and migration distance are larger in severe climates. Our prediction also reveals potential threats to edge populations in northern and southeastern Taiwan due to escalating temperatures and precipitation reallocation. Conclusions We demonstrate the intricate influence of ecological heterogeneity on genetic and phenotypic adaptation of an oak species. The adaptation is also driven by some rarely studied environmental factors, including wind speed and soil features. Furthermore, the genetic offset analysis predicted that the edge populations of Q. longinux in lower elevations might face higher risks of local extinctions under climate change.https://doi.org/10.1186/s12870-024-04942-8Climate changeGenetic offsetLandscape genomicsLocal adaptationNatural selectionQuercus |
| spellingShingle | Pei-Wei Sun Jui-Tse Chang Min-Xin Luo Pei-Chun Liao Genomic insights into local adaptation and vulnerability of Quercus longinux to climate change BMC Plant Biology Climate change Genetic offset Landscape genomics Local adaptation Natural selection Quercus |
| title | Genomic insights into local adaptation and vulnerability of Quercus longinux to climate change |
| title_full | Genomic insights into local adaptation and vulnerability of Quercus longinux to climate change |
| title_fullStr | Genomic insights into local adaptation and vulnerability of Quercus longinux to climate change |
| title_full_unstemmed | Genomic insights into local adaptation and vulnerability of Quercus longinux to climate change |
| title_short | Genomic insights into local adaptation and vulnerability of Quercus longinux to climate change |
| title_sort | genomic insights into local adaptation and vulnerability of quercus longinux to climate change |
| topic | Climate change Genetic offset Landscape genomics Local adaptation Natural selection Quercus |
| url | https://doi.org/10.1186/s12870-024-04942-8 |
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