Cryptic divergences and repeated hybridizations within the endangered “living fossil” dove tree (Davidia involucrata) revealed by whole genome resequencing

doi:10.1016/j.pld.2024.02.004

Plant Diversity ›› 2024, Vol. 46 ›› Issue (02): 169-180.DOI: 10.1016/j.pld.2024.02.004

Cryptic divergences and repeated hybridizations within the endangered “living fossil” dove tree (Davidia involucrata) revealed by whole genome resequencing

Yumeng Ren^a, Lushui Zhang^a, Xuchen Yang^a,c, Hao Lin^a, Yupeng Sang^a, Landi Feng^a, Jianquan Liu^a,b, Minghui Kang^a,b

a. Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China;
b. State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China;
c. Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China

收稿日期:2023-11-02 修回日期:2024-02-05 出版日期:2024-03-25 发布日期:2024-04-07
通讯作者: Jianquan Liu,E-mail:liujq@nwipb.ac.cn;Minghui Kang,E-mail:kangminghui0106@gmail.com
基金资助:
This study was supported by the Second Tibetan Plateau Scientific Expedition and Research program (No. 2019QZKK0502), Strategic Priority Research Program of Chinese Academy of Sciences (No. XDB31010300), Fundamental Research Funds for the Central Universities, and International Collaboration 111 Program (BP0719040).

Cryptic divergences and repeated hybridizations within the endangered “living fossil” dove tree (Davidia involucrata) revealed by whole genome resequencing

Yumeng Ren^a, Lushui Zhang^a, Xuchen Yang^a,c, Hao Lin^a, Yupeng Sang^a, Landi Feng^a, Jianquan Liu^a,b, Minghui Kang^a,b

a. Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China;
b. State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China;
c. Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China

Received:2023-11-02 Revised:2024-02-05 Online:2024-03-25 Published:2024-04-07
Contact: Jianquan Liu,E-mail:liujq@nwipb.ac.cn;Minghui Kang,E-mail:kangminghui0106@gmail.com
Supported by:
This study was supported by the Second Tibetan Plateau Scientific Expedition and Research program (No. 2019QZKK0502), Strategic Priority Research Program of Chinese Academy of Sciences (No. XDB31010300), Fundamental Research Funds for the Central Universities, and International Collaboration 111 Program (BP0719040).

摘要/Abstract

摘要： The identification and understanding of cryptic intraspecific evolutionary units (lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species. However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a “living fossil” dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range. Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.

关键词: Davidia involucrata, Cryptic lineage, Hybridization, Population genomics, Positive evolution

Abstract: The identification and understanding of cryptic intraspecific evolutionary units (lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species. However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a “living fossil” dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range. Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.

Key words: Davidia involucrata, Cryptic lineage, Hybridization, Population genomics, Positive evolution

Yumeng Ren, Lushui Zhang, Xuchen Yang, Hao Lin, Yupeng Sang, Landi Feng, Jianquan Liu, Minghui Kang. Cryptic divergences and repeated hybridizations within the endangered “living fossil” dove tree (Davidia involucrata) revealed by whole genome resequencing[J]. Plant Diversity, 2024, 46(02): 169-180.

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Cryptic divergences and repeated hybridizations within the endangered “living fossil” dove tree (Davidia involucrata) revealed by whole genome resequencing

Cryptic divergences and repeated hybridizations within the endangered “living fossil” dove tree (Davidia involucrata) revealed by whole genome resequencing

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