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Lin Y, Xiang Y, Wei S, Zhang Q, Liu Y, Zhang Z, Tang S. Genetic diversity and population structure of an insect-pollinated and bird-dispersed dioecious tree Magnolia kwangsiensis in a fragmented karst forest landscape. Ecol Evol 2024; 14:e70094. [PMID: 39091326 PMCID: PMC11291554 DOI: 10.1002/ece3.70094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 06/24/2024] [Accepted: 07/10/2024] [Indexed: 08/04/2024] Open
Abstract
This study combined population genetics and parentage analysis to obtain foundational data for the conservation of Magnolia kwangsiensis. M. kwangsiensis is a Class I tree species that occurs in two disjunct regions in a biodiversity hotspot in southwest China. We assessed the genetic diversity and structure of this species across its distribution range to support its conservation management. Genetic diversity and population structure of 529 individuals sampled from 14 populations were investigated using seven nuclear simple sequence repeat (nSSR) markers and three chloroplast DNA (cpDNA) fragments. Parentage analysis was used to evaluate the pollen and seed dispersal distances. The nSSR marker analysis revealed a high genetic diversity in M. kwangsiensis, with an average observed (Ho) and expected heterozygosities (He) of 0.726 and 0.687, respectively. The mean and maximum pollen and seed dispersal distances were 66.4 and 95.7 m and 535.4 and 553.8 m, respectively. Our data revealed two distinct genetic groups, consistent with the disjunct geographical distribution of the M. kwangsiensis populations. Both pollen and seed dispersal movements help maintain genetic connectivity among M. kwangsiensis populations, contributing to high levels of genetic diversity. Both genetically differentiated groups corresponding to the two disjunct regions should be recognized as separate conservation units.
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Affiliation(s)
- Yanfang Lin
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
- Wuzhou No. 18 Middle SchoolWuzhouChina
| | - Yingying Xiang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Sujian Wei
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Qiwei Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Yanhua Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Zhiyong Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Shaoqing Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
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Gao Y, Dai D, Wang H, Wu W, Xiao P, Wu L, Wei X, Yin S. Genomic insights into differentiation and adaptation of Amorphophallus yunnanensis in the mountainous region of Southwest China. Ecol Evol 2024; 14:e10861. [PMID: 38264337 PMCID: PMC10805605 DOI: 10.1002/ece3.10861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/25/2024] Open
Abstract
The role of geographical isolation and environmental adaptation in driving the differentiation and radiation of species has been a hotspot in evolutionary biology. The extremely complicated and fragmented geography of the mountainous region of Southwest China provides an excellent system for investigating the process of species divergence in heterogeneous habitats. Amorphophallus yunnanensis is a species of extreme habitat preference that resides mainly in the mountainous region of Southwest China. Here, we used restriction site-associated DNA sequencing (RAD-seq) to characterize the geographic pattern of genetic variation among 19 populations of A. yunnanensis as well as the genomic basis of environmental adaptation. A pattern of low population genetic diversity and high level of genetic differentiation was observed. The genomic data revealed a clear east-west genetic differentiation, with two distinct genetic lineages corresponding to the Guizhou plateau and Yunnan plateau, respectively. However, we discovered demographic expansion of the Guizhou Plateau lineage and recent hybridization in populations at the contact region. Significant levels of isolation by distance along with isolation by environment were detected. Outlier tests and genome-environment association analyses identified 89 putatively adaptive loci that might play a role in environmental adaptation. Our results suggest that the genetic divergence of A. yunnanensis is attributed to geographical isolation together with divergent selection in the mountainous region of Southwest China.
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Affiliation(s)
- Yong Gao
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Dongqin Dai
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Haibo Wang
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Weijia Wu
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Penghui Xiao
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Lifang Wu
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Xiaomei Wei
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Si Yin
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
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Zhu X, Tang J, Jiang H, Yang Y, Chen Z, Zou R, Xu A, Luo Y, Deng Z, Wei X, Chai S. Genomic evidence reveals high genetic diversity in a narrowly distributed species and natural hybridization risk with a widespread species in the genus Geodorum. BMC PLANT BIOLOGY 2023; 23:317. [PMID: 37316828 DOI: 10.1186/s12870-023-04285-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND Understanding genetic diversity is a core issue in conservation genetics. However, previous genetic diversity evaluations of narrowly distributed species have rarely used closely related widespread species as a reference. Furthermore, identifying natural hybridization signals between narrowly and widely distributed sympatric species is of great importance for the development of species conservation programs. METHODS In this study, population genotyping by sequencing (GBS) was performed for a narrowly distributed species, Geodorum eulophioides (endemic and endangered in Southwest China), and a widespread species, G. densiflorum. A total of 18,490 high-quality single nucleotide polymorphisms (SNPs) were identified at the whole-genome level. RESULTS The results showed that the nucleotide diversity and heterozygosity of G. eulophioides were significantly higher than those of G. densiflorum, confirming that narrowly distributed species can still preserve high genetic diversity. Consistent with taxonomic boundaries, all sampled individuals from the two species were divided into two genetic clusters and showed high genetic differentiation between species. However, in a sympatric population, a few G. eulophioides individuals were detected with genetic components from G. densiflorum, suggesting potential interspecific natural hybridization. This hypothesis was supported by Treemix analysis and hand-hybridization trials. Invasion of the habitat of G. eulophioides invasion by G. densiflorum under anthropogenic disturbance may be the main factor causing interspecific hybridization. CONCLUSIONS Therefore, reducing or avoiding habitat disturbance is a key measure to protect the G. eulophioides populations. This study provides valuable information for future conservation programs for narrowly distributed species.
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Affiliation(s)
- Xianliang Zhu
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Jianmin Tang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Haidu Jiang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Yishan Yang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Zongyou Chen
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Rong Zou
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Aizhu Xu
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
- College of Tourism and Landscape Architecture, Guilin University of Technology, Guilin, Guangxi, 541006, China
| | - Yajin Luo
- Yachang Orchid National Nature Reserve Management Center, Baise, Guangxi, 533209, China
| | - Zhenhai Deng
- Yachang Orchid National Nature Reserve Management Center, Baise, Guangxi, 533209, China
| | - Xiao Wei
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China.
| | - Shengfeng Chai
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China.
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Wu L, Xu H, Jian S, Gong X, Feng X. Geographic factors and climatic fluctuation drive the genetic structure and demographic history of
Cycas taiwaniana
(Cycadaceae), an endemic endangered species to Hainan Island in China. Ecol Evol 2022; 12:e9508. [DOI: 10.1002/ece3.9508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- Li‐Xin Wu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany Chinese Academy of Sciences Kunming China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany Chinese Academy of Sciences Kunming China
- University of Chinese Academy of Science Beijing China
- Plant Science Institute, School of Life Sciences Yunnan University Kunming China
| | - Hai‐Yan Xu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany Chinese Academy of Sciences Kunming China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany Chinese Academy of Sciences Kunming China
- University of Chinese Academy of Science Beijing China
| | - Shu‐Guang Jian
- CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Xun Gong
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Xiu‐Yan Feng
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany Chinese Academy of Sciences Kunming China
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Zhu X, Liang H, Jiang H, Kang M, Wei X, Deng L, Shi Y. Phylogeographic structure of Heteroplexis (Asteraceae), an endangered endemic genus in the limestone karst regions of southern China. FRONTIERS IN PLANT SCIENCE 2022; 13:999964. [PMID: 36388513 PMCID: PMC9647136 DOI: 10.3389/fpls.2022.999964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Though the karst regions in south and southwest China are plant diversity hotspots, our understanding of the phylogeography and evolutionary history of the plants there remains limited. The genus Heteroplexis (Asteraceae) is one of the typical representative plants isolated by karst habitat islands, and is also an endangered and endemic plant to China. In this study, species-level phylogeographic analysis of the genus Heteroplexis was conducted using restriction site-associated DNA sequencing (RADseq). The genetic structure showed a clear phylogeographic structure consistent with the current species boundaries in the H. microcephala, H. incana, H. vernonioides, H. sericophylla, and H. impressinervia. The significant global (R = 0.37, P < 0.01) and regional (R = 0.650.95, P < 0.05) isolation by distance (IBD) signals among species indicate strong geographic isolation in the karst mountains, which may result in chronically restricted gene flow and increased genetic drift and differentiation. Furthermore, the phylogeographic structure of Heteroplexis suggested a southward migration since the last glacial period. Demographic analysis revealed the karst mountains as a refuge for Heteroplexis species. Finally, both Treemix and ABBA-BABA statistic detected significant historical gene flow between species. Significant historical gene flow and long-term stability of effective population size (Ne) together explain the high genome-wide genetic diversity among species (π = 0.05370.0838). However, the recent collapse of Ne, widespread inbreeding within populations, and restricted contemporary gene flow suggest that Heteroplexis species are probably facing a high risk of genetic diversity loss. Our results help to understand the evolutionary history of karst plants and guide conservation.
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Affiliation(s)
- Xianliang Zhu
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Hui Liang
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
- College of Life Science, Guangxi Normal University, Guilin, China
| | - Haolong Jiang
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Ming Kang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xiao Wei
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Lili Deng
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Yancai Shi
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
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