Dipterocarpoidae genomics reveal their demography and adaptations to Asian rainforests

Rong Wang (), Chao-Nan Liu, Simon T. Segar, Yu-Ting Jiang, Kai-Jian Zhang, Kai Jiang, Gang Wang, Jing Cai, Lu-Fan Chen, Shan Chen, Jing Cheng, Stephen G. Compton, Jun-Yin Deng, Yuan-Yuan Ding, Fang K. Du, Xiao-Di Hu, Xing-Hua Hu, Ling Kang, Dong-Hai Li, Ling Lu, Yuan-Yuan Li, Liang Tang, Xin Tong, Zheng-Shi Wang, Wei-Wei Xu, Yang Yang, Run-Guo Zang, Zhuo-Xin Zu, Yuan-Ye Zhang () and Xiao-Yong Chen ()
Additional contact information
Rong Wang: Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University
Chao-Nan Liu: Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University
Simon T. Segar: Harper Adams University
Yu-Ting Jiang: Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University
Kai-Jian Zhang: Novogene Bioinformatics Institute
Kai Jiang: Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University
Gang Wang: Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences
Jing Cai: Northwestern Polytechnical University
Lu-Fan Chen: Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University
Shan Chen: Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University
Jing Cheng: Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University
Stephen G. Compton: University of Leeds
Jun-Yin Deng: Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University
Yuan-Yuan Ding: Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University
Fang K. Du: Beijing Forestry University
Xiao-Di Hu: Novogene Bioinformatics Institute
Xing-Hua Hu: Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences
Ling Kang: Novogene Bioinformatics Institute
Dong-Hai Li: Hainan University
Ling Lu: Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University
Yuan-Yuan Li: Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University
Liang Tang: Hainan University
Xin Tong: Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University
Zheng-Shi Wang: Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University
Wei-Wei Xu: Novogene Bioinformatics Institute
Yang Yang: Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University
Run-Guo Zang: Chinese Academy of Forestry
Zhuo-Xin Zu: Novogene Bioinformatics Institute
Yuan-Ye Zhang: College of the Environment and Ecology, Xiamen University
Xiao-Yong Chen: Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: Abstract Dipterocarpoideae species form the emergent layer of Asian rainforests. They are the indicator species for Asian rainforest distribution, but they are severely threatened. Here, to understand their adaptation and population decline, we assemble high-quality genomes of seven Dipterocarpoideae species including two autotetraploid species. We estimate the divergence time between Dipterocarpoideae and Malvaceae and within Dipterocarpoideae to be 108.2 (97.8‒118.2) and 88.4 (77.7‒102.9) million years ago, and we identify a whole genome duplication event preceding dipterocarp lineage diversification. We find several genes that showed a signature of selection, likely associated with the adaptation to Asian rainforests. By resequencing of two endangered species, we detect an expansion of effective population size after the last glacial period and a recent sharp decline coinciding with the history of local human activities. Our findings contribute to understanding the diversification and adaptation of dipterocarps and highlight anthropogenic disturbances as a major factor in their endangered status.

Date: 2024
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DOI: 10.1038/s41467-024-45836-5

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