Genomic insights into population dynamics and adaptive strategies of the endangered dipterocarp, Hopea chinensis
Asian rainforests are a biodiversity hotspot and are dominated by dipterocarps. Thus, protecting endangered dipterocarp species living on the distribution boundary of dipterocarps is a central factor in maintaining the range of Asian rainforests. Despite the perceived conservation priority of these...
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| Language: | English |
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Elsevier
2025-01-01
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| Series: | Global Ecology and Conservation |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2351989424005584 |
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| author | Wei-Min Xiang Yu-Ting Jiang Jie Zou Yan Deng Kai Jiang Kai-Jian Zhang Xin-Yu Zhou Kai-Xi Quan Zi-Wen Han Wei-Chao Liu Liang Tang Yuan-Yuan Li Simon T. Segar Yuan-Ye Zhang Xing-Hua Hu Rong Wang Xiao-Yong Chen |
| author_facet | Wei-Min Xiang Yu-Ting Jiang Jie Zou Yan Deng Kai Jiang Kai-Jian Zhang Xin-Yu Zhou Kai-Xi Quan Zi-Wen Han Wei-Chao Liu Liang Tang Yuan-Yuan Li Simon T. Segar Yuan-Ye Zhang Xing-Hua Hu Rong Wang Xiao-Yong Chen |
| author_sort | Wei-Min Xiang |
| collection | DOAJ |
| description | Asian rainforests are a biodiversity hotspot and are dominated by dipterocarps. Thus, protecting endangered dipterocarp species living on the distribution boundary of dipterocarps is a central factor in maintaining the range of Asian rainforests. Despite the perceived conservation priority of these species, we know little about how they became endangered and how they have adapted to marginal habitats. Here, we focused on the population genomics of Hopea chinensis, an endangered species narrowly distributed at the northern limit of dipterocarps, to (1) reveal its demographic history and infer factors contributing to endangered status; (2) evaluate the genetic consequences of its small remnant population; and (3) identify key genes associated with its adaptation. We found drastic population declines after the Last Glacial Maximum, suggesting the role of human disturbances in the endangered status. Despite high levels of inbreeding, we detected only 441 derived deleterious and 337 derived major-effect mutations, which were not significantly enriched in any KEGG pathway, providing evidence of low genetic loads. Furthermore, selective sweep analysis showed 12 genes associated with cold and drought tolerance and plant defense and immunity. Comparative genomics identified 125 specific and 30 lost gene families in the genome of H. chinensis, many of which were relevant to the responses to biotic and abiotic stresses. Our findings, therefore, reveal the genomic characteristics linked with the endangered status and adaptations for H. chinensis. Together with the population genomic results from two other dipterocarp species, we highlighted the necessity to establish nature reserves to prevent further human disturbances and to comprehensively describe the mutualistic and antagonistic networks associated with endangered dipterocarp species to guide in-situ and ex-situ conservation. |
| format | Article |
| id | doaj-art-e5bdcdd31df64d55893a3ebcdd6c7259 |
| institution | Kabale University |
| issn | 2351-9894 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Global Ecology and Conservation |
| spelling | doaj-art-e5bdcdd31df64d55893a3ebcdd6c72592025-01-23T05:26:52ZengElsevierGlobal Ecology and Conservation2351-98942025-01-0157e03354Genomic insights into population dynamics and adaptive strategies of the endangered dipterocarp, Hopea chinensisWei-Min Xiang0Yu-Ting Jiang1Jie Zou2Yan Deng3Kai Jiang4Kai-Jian Zhang5Xin-Yu Zhou6Kai-Xi Quan7Zi-Wen Han8Wei-Chao Liu9Liang Tang10Yuan-Yuan Li11Simon T. Segar12Yuan-Ye Zhang13Xing-Hua Hu14Rong Wang15Xiao-Yong Chen16Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, ChinaZhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, ChinaZhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, ChinaZhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, ChinaShanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, ChinaNovogene Bioinformatics Institute, Beijing, ChinaZhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, ChinaZhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, ChinaZhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, ChinaZhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, ChinaKey Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Hainan University), Ministry of Education, Haikou 570228, ChinaZhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, ChinaAgriculture & Environment Department, Harper Adams University, Newport, United KingdomKey Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian Province, ChinaGuangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Guilin 541006, China; Correspondence to: No. 85, Yanshan Road, Guilin 541006, China.Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China; Shanghai Engineering Research Center of Sustainable Plant Innovation, Shanghai, China; Institute of Eco-Chongming, Shanghai, China; Correspondence to: No. 500, Dongchuan Road, Minhang District, Shanghai 200241, China.Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, ChinaAsian rainforests are a biodiversity hotspot and are dominated by dipterocarps. Thus, protecting endangered dipterocarp species living on the distribution boundary of dipterocarps is a central factor in maintaining the range of Asian rainforests. Despite the perceived conservation priority of these species, we know little about how they became endangered and how they have adapted to marginal habitats. Here, we focused on the population genomics of Hopea chinensis, an endangered species narrowly distributed at the northern limit of dipterocarps, to (1) reveal its demographic history and infer factors contributing to endangered status; (2) evaluate the genetic consequences of its small remnant population; and (3) identify key genes associated with its adaptation. We found drastic population declines after the Last Glacial Maximum, suggesting the role of human disturbances in the endangered status. Despite high levels of inbreeding, we detected only 441 derived deleterious and 337 derived major-effect mutations, which were not significantly enriched in any KEGG pathway, providing evidence of low genetic loads. Furthermore, selective sweep analysis showed 12 genes associated with cold and drought tolerance and plant defense and immunity. Comparative genomics identified 125 specific and 30 lost gene families in the genome of H. chinensis, many of which were relevant to the responses to biotic and abiotic stresses. Our findings, therefore, reveal the genomic characteristics linked with the endangered status and adaptations for H. chinensis. Together with the population genomic results from two other dipterocarp species, we highlighted the necessity to establish nature reserves to prevent further human disturbances and to comprehensively describe the mutualistic and antagonistic networks associated with endangered dipterocarp species to guide in-situ and ex-situ conservation.http://www.sciencedirect.com/science/article/pii/S2351989424005584Asian rainforestsDipterocarpaceaeEndangered speciesPopulation genomicsDemographyAdaptation |
| spellingShingle | Wei-Min Xiang Yu-Ting Jiang Jie Zou Yan Deng Kai Jiang Kai-Jian Zhang Xin-Yu Zhou Kai-Xi Quan Zi-Wen Han Wei-Chao Liu Liang Tang Yuan-Yuan Li Simon T. Segar Yuan-Ye Zhang Xing-Hua Hu Rong Wang Xiao-Yong Chen Genomic insights into population dynamics and adaptive strategies of the endangered dipterocarp, Hopea chinensis Global Ecology and Conservation Asian rainforests Dipterocarpaceae Endangered species Population genomics Demography Adaptation |
| title | Genomic insights into population dynamics and adaptive strategies of the endangered dipterocarp, Hopea chinensis |
| title_full | Genomic insights into population dynamics and adaptive strategies of the endangered dipterocarp, Hopea chinensis |
| title_fullStr | Genomic insights into population dynamics and adaptive strategies of the endangered dipterocarp, Hopea chinensis |
| title_full_unstemmed | Genomic insights into population dynamics and adaptive strategies of the endangered dipterocarp, Hopea chinensis |
| title_short | Genomic insights into population dynamics and adaptive strategies of the endangered dipterocarp, Hopea chinensis |
| title_sort | genomic insights into population dynamics and adaptive strategies of the endangered dipterocarp hopea chinensis |
| topic | Asian rainforests Dipterocarpaceae Endangered species Population genomics Demography Adaptation |
| url | http://www.sciencedirect.com/science/article/pii/S2351989424005584 |
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