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Jiang C, Wu M, He S, Lu Y, Zhao C. Phylogeography of a herbal Pinellia ternata reveals repeated range expansions and inter/postglacial recolonization routes on the fragmented distribution pattern in China. Ecol Evol 2024; 14:e70206. [PMID: 39219572 PMCID: PMC11362505 DOI: 10.1002/ece3.70206] [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: 05/06/2024] [Revised: 08/02/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024] Open
Abstract
Most plant phylogeographic studies in China have focused on the importance of genetic divergence and where should the shelter be located. Little attention has been paid to range expansion and recolonization routes in this region. In this study, two cpDNA fragments (psbK-psbI and trnL-F), two pairs of nuclear gene sequences (ITS and ETS), and nine pairs of SSR molecular markers were used, combined with Bayesian Skyline Plot method, gene barrier analysis, and species distribution models to explore the phylogeographical pattern, potential expansion routes and population dynamic history of Pinellia ternata from 22 population. The results showed that phylogeograhical pattern and genetic structure for P. ternata are effected by environmental heterogeneity and climate fluctuation, and it can be divided into two groups (Southwest group, Central and Eastern group) and thus there are at least two glacial refugia in China. Three expanding routes within groups were explored to contribute to the phylogeogrephic pattern of P. ternata based on the geographical distribution and network analysis of haplotypes. In a word, our study reveals repeated range expansions and inter/postglacial recolonization routes on the fragmented distribution pattern in China and resolves the refugia distributing in China and has also certain reference value for the protection of the medicinal plant P. ternata.
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Affiliation(s)
- Chunxue Jiang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education)College of Life Sciences/Institute of Agro‐Bioengineering, Guizhou UniversityGuiyangGuizhou ProvinceChina
| | - Ming Wu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education)College of Life Sciences/Institute of Agro‐Bioengineering, Guizhou UniversityGuiyangGuizhou ProvinceChina
| | - Shanshan He
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education)College of Life Sciences/Institute of Agro‐Bioengineering, Guizhou UniversityGuiyangGuizhou ProvinceChina
| | - Yuxia Lu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education)College of Life Sciences/Institute of Agro‐Bioengineering, Guizhou UniversityGuiyangGuizhou ProvinceChina
| | - Cai Zhao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education)College of Life Sciences/Institute of Agro‐Bioengineering, Guizhou UniversityGuiyangGuizhou ProvinceChina
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Dong Q, Zhang Y, Zhong S, Zhang Q, Yang H, Yang H, Yi X, Tan F, Chen C, Luo P. Conserved DNA sequence analysis reveals the phylogeography and evolutionary events of Akebia trifoliata in the region across the eastern edge of the Tibetan Plateau and subtropical China. BMC Ecol Evol 2024; 24:52. [PMID: 38654171 DOI: 10.1186/s12862-024-02243-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The eastern edge of the Qinghai‒Tibet Plateau (QTP) and subtropical China have various regions where plant species originate and thrive, but these regions have been the focus of very few integrative studies. Here, we elucidated the phylogeographic structure of a continuous and widespread Akebia trifoliata population across these two regions. RESULTS Sixty-one populations consisting of 391 genotypes were examined to assess population diversity and structure via network distribution analysis, maximum likelihood phylogenetic tree reconstruction, divergence time estimation, demographic history inference, and ancestral area reconstruction of both conserved internal transcribed spacer (ITS) and chloroplast (rps16) DNA sequences. The results showed that the ITS region was more variable than the rps16 region and could be suitable for studying intraspecific phylogeography. The A. trifoliata population displayed high genetic diversity, genetic differentiation and obvious phylogeographical structure, possibly originating on the eastern QTP, expanding during the last glacial-interglacial cycle, diverging in the early Pleistocene and middle Pleistocene, and extensively migrating thereafter. The migration route from west to east along rivers could be largely responsible for the long-distance dispersal of this species, while three main refuges (Qinba Mountains, Nanling Mountains and Yunnan-Guizhou Plateau) with multiple ice shelters facilitated its wide distribution. CONCLUSIONS Our results suggested that the from west to east long migration accompanying with the minor short reciprocal migration in the south-north direction, and the three main refuges (the Qinba Mountains, Nanling Mountains and Yunnan-Guizhou Plateau) contributed to the extant geographical distribution of A. trifoliata. In addition, this finding also strongly reduced the discrepancy between glacial contraction and postglacial expansion and the in situ survival hypothesis by simultaneously considering the existence of many similar climate-related ecological niches and migration influences.
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Affiliation(s)
- Qing Dong
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yongle Zhang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shengfu Zhong
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qiuyi Zhang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hao Yang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Huai Yang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiaoxiao Yi
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Feiquan Tan
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Chen Chen
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Peigao Luo
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
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Fan Z, Gao C, Lin L. Phylogeographical and population genetics of Polyspora sweet in China provides insights into its phylogenetic evolution and subtropical dispersal. BMC PLANT BIOLOGY 2024; 24:89. [PMID: 38317071 PMCID: PMC10845455 DOI: 10.1186/s12870-024-04783-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/29/2024] [Indexed: 02/07/2024]
Abstract
BACKGROUND Geological movements and climatic fluctuations stand as pivotal catalysts driving speciation and phylogenetic evolution. The genus Polyspora Sweet (Theaceae), prominently found across the Malay Archipelagos and Indochina Peninsula in tropical Asia, exhibits its northernmost distribution in China. In this study, we investigated the evolutionary and biogeographical history of the genus Polyspora in China, shedding light on the mechanisms by which these species respond to ancient geological and climatic fluctuations. METHODS Phylogenetic relationships of 32 representative species of Theaceae were reconstructed based on the chloroplast genome and ribosome 18-26 S rRNA datasets. Species divergence time was estimated using molecular clock and five fossil calibration. The phylogeography and population genetics in 379 individuals from 32 populations of eight species were analyzed using chloroplast gene sequences (trnH-psbA, rpoB-trnC and petN-psbM), revealing the glacial refugia of each species, and exploring the causes of the phylogeographic patterns. RESULTS We found that Chinese Polyspora species diverged in the middle Miocene, showing a tropical-subtropical divergence order. A total of 52 haplotypes were identified by the combined chloroplast sequences. Chinese Polyspora exhibited a distinct phylogeographical structure, which could be divided into two clades and eight genealogical subdivisions. The divergence between the two clades occurred approximately 20.67 Ma. Analysis of molecular variance revealed that the genetic variation mainly occurred between species (77.91%). At the species level, Polyspora axillaris consists of three lineages, while P. speciosa had two lineages. The major lineages of Chinese Polyspora diverged between 12 and 15 Ma during the middle to late Miocene. The peak period of haplotype differentiation in each species occurred around the transition from the last interglacial to the last glacial period, approximately 6 Ma ago. CONCLUSION The primary geographical distribution pattern of Chinese Polyspora was established prior to the last glacial maximum, and the population historical dynamics were relatively stable. The geological and climatic turbulence during the Quaternary glacial period had minimal impact on the distribution pattern of the genus. The genus coped with Quaternary climate turbulence by glacial in situ survival in multiple refuges. The Sino-Vietnam border and Nanling corridor might be the genetic mixing center of Polyspora.
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Affiliation(s)
- Zhifeng Fan
- City College, Kunming University of Science and Technology, Kunming, 650093, China.
| | - Can Gao
- College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, China
| | - Lifang Lin
- Hot Spring Sub-district Office, Anning Municipal People's Government, Kunming, 650300, China.
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Hu Q, Qian R, Zhang Y, Ma X, Ye Y, Zhang X, Lin L, Liu H, Zheng J. Complete chloroplast genome molecular structure, comparative and phylogenetic analyses of Sphaeropteris lepifera of Cyatheaceae family: a tree fern from China. Sci Rep 2023; 13:1356. [PMID: 36693990 PMCID: PMC9873718 DOI: 10.1038/s41598-023-28432-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Sphaeropteris lepifera is a tree fern in the Cyatheaceae, a family that has played an important role in the evolution of plant systems. This study aimed to analyze the complete chloroplast genome of S. lepifera and compared it with previously published chloroplast genomes Cyatheaceae family. The chloroplast genome of S. lepifera comprised 162,114 bp, consisting of a large single copy (LSC) region of 86,327 bp, a small single copy (SSC) region of 27,731 bp and a pair of inverted repeats (IRa and IRb) of 24,028 bp each. The chloroplast genome encoded 129 genes, comprising 32 transfer RNAs, 8 ribosomal RNAs, and 89 protein-coding genes. Comparison of the genomes of 7 Cyatheaceae plants showed that the chloroplast genome of S. lepifera was missing the gene trnV-UAC. Expansion of the SSC region led to the difference in the chloroplast genome size of S. lepifera. Eight genes, atpI, ccsA, petA, psaB, rpl16, rpoA, rpoC1, and ycf2 have high nucleic acid diversity and can be regarded as potential molecular markers. The genes trnG-trnR and atpB were suitable for DNA barcodes between different communities of S. lepifera. The S. lepifera groups in Zhejiang Province probably diffused from Pingtan and Ningde, Fujian. The results will provide a basis for species identification, biological studies, and endangerment mechanism of S. lepifera.
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Affiliation(s)
- Qingdi Hu
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Renjuan Qian
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Yanjun Zhang
- China National Bamboo Research Center, Hangzhou, 310012, Zhejiang, China
| | - Xiaohua Ma
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Youju Ye
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Xule Zhang
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Lin Lin
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Hongjian Liu
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Jian Zheng
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China.
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Wang S, Li Y, Zhou J, Jiang K, Chen J, Ye Z, Xue H, Bu W. The anthropogenic effect of land use on population genetics of Malcus inconspicuus. Evol Appl 2022; 16:98-110. [PMID: 36699121 PMCID: PMC9850013 DOI: 10.1111/eva.13512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 11/07/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022] Open
Abstract
Since the beginning of the Holocene era, human activities have seriously impacted animal habitats and vegetative environments. Species that are dependent on natural habitats or with narrow niches might be more severely affected by habitat changes. Malcus inconspicuus is distributed in subtropical China and highly dependent on the mountain environment. Our study investigated the role of the mountainous landscape in the historical evolution of M. inconspicuus and the impact of Holocene human activities on it. A phylogeographical approach was implemented with integrative datasets including double-digest restriction site-associated DNA (ddRAD), mitochondrial data, and distribution data. Three obvious clades and an east-west phylogeographical pattern were found in subtropical China. Mountainous landscape has "multifaceted" effects on the evolutionary history of M. inconspicuus, it has contributed to population differentiation, provided glacial refuges, and provided population expansion corridors during the postglacial period. The effective population size (Ne) of M. inconspicuus showed a sharp decline during the Holocene era, which revealed a significantly negative correlation with the development of cropland in a hilly area at the same time and space. It supported that the species which are highly dependent on natural habitats might undergo greater impact when the habitat was damaged by agricultural activities and we should pay more attention to them, especially in the land development of their distribution areas.
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Affiliation(s)
- Shujing Wang
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Yanfei Li
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Jiayue Zhou
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Kun Jiang
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Juhong Chen
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Zhen Ye
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Huaijun Xue
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Wenjun Bu
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
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Li Y, Wang L, Zhang X, Kang H, Liu C, Mao L, Fang Y. Extensive sharing of chloroplast haplotypes among East Asian Cerris oaks: The imprints of shared ancestral polymorphism and introgression. Ecol Evol 2022; 12:e9142. [PMID: 35923946 PMCID: PMC9339761 DOI: 10.1002/ece3.9142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/27/2022] [Accepted: 07/01/2022] [Indexed: 11/08/2022] Open
Abstract
Shared ancestral polymorphism and introgression are two main causes of chloroplast DNA (cpDNA) haplotype sharing among closely related angiosperms. In this study, we explored the roles of these two processes in shaping the phylogeographic patterns of East Asian Cerris oaks by examining the geographic distributions of randomly and locally distributed shared haplotypes, which coincide with the expectations of shared ancestry and introgression, respectively. We sequenced 1340 bp of non-coding cpDNA from Quercus acutissima (n = 418) and Q. chenii (n = 183) and compiled previously published sequence data of Q. variabilis (n = 439). The phylogenetic relationships among haplotypes were examined using a median-joining network. The geographic patterns of interspecifically shared haplotypes were assessed to test whether nearby populations have a higher degree of interspecific cpDNA sharing than distant ones. We identified a total of 27 haplotypes that were grouped into three non-species-specific lineages with overlapping distributions. Ancestral haplotypes were extensively shared and randomly distributed across populations of the three species. Some young haplotypes were locally shared in mountainous areas that may have been shared refugia. The local exchange of cpDNA resulted in an excess of similar haplotypes between nearby populations. Our study demonstrated that the haplotype sharing pattern among East Asian Cerris oaks reflected the imprints of both shared ancestral polymorphism and introgression. This pattern was also associated with the relatively stable climates and complex landscapes in East Asia, which not only allowed the long-term persistence of ancestral lineages but also connected the survived populations across refugia.
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Affiliation(s)
- Yao Li
- Co‐Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the Environment, Nanjing Forestry UniversityNanjingChina
| | - Lu Wang
- Co‐Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the Environment, Nanjing Forestry UniversityNanjingChina
| | - Xingwang Zhang
- School of Life SciencesHuaibei Normal UniversityHuaibeiChina
| | - Hongzhang Kang
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Chunjiang Liu
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Lingfeng Mao
- Co‐Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the Environment, Nanjing Forestry UniversityNanjingChina
| | - Yanming Fang
- Co‐Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the Environment, Nanjing Forestry UniversityNanjingChina
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Wang L, Li Y, Noshiro S, Suzuki M, Arai T, Kobayashi K, Xie L, Zhang M, He N, Fang Y, Zhang F. Stepped Geomorphology Shaped the Phylogeographic Structure of a Widespread Tree Species ( Toxicodendron vernicifluum, Anacardiaceae) in East Asia. FRONTIERS IN PLANT SCIENCE 2022; 13:920054. [PMID: 35720535 PMCID: PMC9201781 DOI: 10.3389/fpls.2022.920054] [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: 04/14/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Species' phylogeographic patterns reflect the interplay between landscape features, climatic forces, and evolutionary processes. Here, we used two chloroplast DNA (cpDNA) markers (trnL and trnL-F) to explore the role of stepped geomorphology in shaping the phylogeographic structure of Toxicodendron vernicifluum, an economically important tree species widely distributed in East Asia. The range-wide pattern of sequence variation was analyzed based on a dataset including 357 individuals from China, together with published sequences of 92 individuals mainly from Japan and South Korea. We identified five chloroplast haplotypes based on seven substitutions across the 717-bp alignment. A clear east-west phylogeographic break was recovered according to the stepped landforms of mainland China. The wild trees of the western clade were found to be geographically restricted to the "middle step", which is characterized by high mountains and plateaus, while those of the eastern clade were confined to the "low step", which is mainly made up of hills and plains. The two major clades were estimated to have diverged during the Early Pleistocene, suggesting that the cool glacial climate may have caused the ancestral population to retreat to at least two glacial refugia, leading to allopatric divergence in response to long-term geographic isolation. Migration vector analyses based on the outputs of ecological niche models (ENMs) supported a gradual range expansion since the Last Interglacial. Mountain ranges in western China and the East China Sea land bridge were inferred to be dispersal corridors in the western and eastern distributions of T. vernicifluum, respectively. Overall, our study provides solid evidence for the role of stepped geomorphology in shaping the phylogeographic patterns of T. vernicifluum. The resulting east-west genetic discontinuities could persist for a long time, and could occur at a much larger scale than previously reported, extending from subtropical (e.g., the Xuefeng Mountain) to warm-temperate China (e.g., the Taihang Mountain).
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Affiliation(s)
- Lu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Shuichi Noshiro
- Center for Obsidian and Lithic Studies, Meiji University, Tokyo, Japan
| | | | | | | | - Lei Xie
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Mingyue Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Na He
- Xi’an Research Institute of Chinese Lacquer, All China Federation of Supply and Marketing Cooperatives, Xi’an, China
| | - Yanming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Feilong Zhang
- Xi’an Research Institute of Chinese Lacquer, All China Federation of Supply and Marketing Cooperatives, Xi’an, China
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Guo R, Zhang YH, Zhang HJ, Landis JB, Zhang X, Wang HC, Yao XH. Molecular phylogeography and species distribution modelling evidence of 'oceanic' adaptation for Actinidia eriantha with a refugium along the oceanic-continental gradient in a biodiversity hotspot. BMC PLANT BIOLOGY 2022; 22:89. [PMID: 35227218 PMCID: PMC8883688 DOI: 10.1186/s12870-022-03464-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Refugia is considered to be critical for maintaining biodiversity; while discerning the type and pattern of refugia is pivotal for our understanding of evolutionary processes in the context of conservation. Interglacial and glacial refugia have been studied throughout subtropical China. However, studies on refugia along the oceanic-continental gradient have largely been ignored. We used a liana Actinidia eriantha, which occurs across the eastern moist evergreen broad-leaved forests of subtropical China, as a case study to test hypotheses of refugia along the oceanic-continental gradient and 'oceanic' adaptation. RESULTS The phylogeographic pattern of A. eriantha was explored using a combination of three cpDNA markers and 38 nuclear microsatellite loci, Species distribution modelling and dispersal corridors analysis. Our data showed intermediate levels of genetic diversity [haplotype diversity (hT) = 0.498; unbiased expected heterozygosity (UHE) = 0.510] both at the species and population level. Microsatellite loci revealed five clusters largely corresponding to geographic regions. Coalescent time of cpDNA lineages was dated to the middle Pliocene (ca. 4.03 Ma). Both geographic distance and climate difference have important roles for intraspecific divergence of the species. The Zhejiang-Fujian Hilly Region was demonstrated to be a refugium along the oceanic-continental gradient of the species and fit the 'refugia in refugia' pattern. Species distribution modelling analysis indicated that Precipitation of Coldest Quarter (importance of 44%), Temperature Seasonality (29%) and Mean Temperature of Wettest Quarter (25%) contributed the most to model development. By checking the isolines in the three climate layers, we found that A. eriantha prefer higher precipitation during the coldest quarter, lower seasonal temperature difference and lower mean temperature during the wettest quarter, which correspond to 'oceanic' adaptation. Actinidia eriantha expanded to its western distribution range along the dispersal corridor repeatedly during the glacial periods. CONCLUSIONS Overall, our results provide integrated evidence demonstrating that the Zhejiang-Fujian Hilly Region is a refugium along the oceanic-continental gradient of Actinidia eriantha in subtropical China and that speciation is attributed to 'oceanic' adaptation. This study gives a deeper understanding of the refugia in subtropical China and will contribute to the conservation and utilization of kiwifruit wild resources in the context of climate change.
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Affiliation(s)
- Rui Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge, CB2 3EA, UK
| | - Yong-Hua Zhang
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, China
| | - Hua-Jie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14853, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heng-Chang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Xiao-Hong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
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Fan D, Lei S, Liang H, Yao Q, Kou Y, Cheng S, Yang Y, Qiu Y, Zhang Z. More opportunities more species: Pleistocene differentiation and northward expansion of an evergreen broad-leaved tree species Machilus thunbergii (Lauraceae) in Southeast China. BMC PLANT BIOLOGY 2022; 22:35. [PMID: 35038992 PMCID: PMC8762935 DOI: 10.1186/s12870-021-03420-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND The broad continuum between tropical and temperate floras in Eastern Asia (EAS) are thought to be one of the main factors responsible for a prominent species diversity anomaly of temperate plants between EAS and eastern North America (ENS). However, how the broad continuum and niche evolution between tropical and temperate floras in EAS contributes to lineage divergence and species diversity remains largely unknown. RESULTS Population genetic structure, demography, and determinants of genetic structure [i.e., isolation-by-distance (IBD), isolation-by-resistance (IBR), and isolation-by-environment (IBE)] of Machilus thunbergii Sieb. et Zucc. (Lauraceae) were evaluated by examining sequence variation of ten low-copy nuclear genes across 43 populations in southeast China. Climatic niche difference and potential distributions across four periods (Current, mid-Holocene, the last glacial maximum, the last interglacial) of two genetic clusters were determined by niche modelling. North and south clusters of populations in M. thunbergii were revealed and their demarcation line corresponds well with the northern boundary of tropical zone in China of Zhu & Wan. The divergence time between the clusters and demographic expansion of M. thunbergii occurred after the mid-Pleistocene climate transition (MPT, 0.8-1.2 Ma). Migration rates between clusters were asymmetrical, being much greater from north to south than the reverse. Significant effects of IBE, but non-significant effects of IBD and IBR on population genetic divergence were detected. The two clusters have different ecological niches and require different temperature regimes. CONCLUSIONS The north-south genetic differentiation may be common across the temperate-tropical boundary in southeast China. Divergent selection under different temperature regimes (possibly above and below freezing temperature in winter) could account for this divergence pattern. The broad continuum between tropical and temperate floras in EAS may have provided ample opportunities for tropical plant lineages to acquire freezing tolerance and to colonize the temperate regions during the late-Cenozoic global cooling. Our findings shed deeper insights into the high temperate plant species diversity in EAS.
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Affiliation(s)
- Dengmei Fan
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Shuqing Lei
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Hua Liang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Qi Yao
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yixuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China.
| | - Shanmei Cheng
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yi Yang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yingxiong Qiu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhiyong Zhang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China.
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10
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Liu W, Xie J, Zhou H, Kong H, Hao G, Fritsch PW, Gong W. Population dynamics linked to glacial cycles in Cercis chuniana F. P. Metcalf (Fabaceae) endemic to the montane regions of subtropical China. Evol Appl 2021; 14:2647-2663. [PMID: 34815745 PMCID: PMC8591333 DOI: 10.1111/eva.13301] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 08/19/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
The mountains of subtropical China are an excellent system for investigating the processes driving the geographical distribution of biodiversity and radiation of plant populations in response to Pleistocene climate fluctuations. How the major mountain ranges in subtropical China have affected the evolution of plant species in the subtropical evergreen broadleaved forest is an issue with long-term concern. Here, we focused on Cercis chuniana, a woody species endemic to the southern mountain ranges in subtropical China, to elucidate its population dynamics. We used genotyping by sequencing (GBS) to investigate the spatial pattern of genetic variation among 11 populations. Geographical isolation was detected between the populations located in adjacent mountain ranges, thought to function as geographical barriers due to their complex physiography. Bayesian time estimation revealed that population divergence occurred in the middle Pleistocene, when populations in the Nanling Mts. separated from those to the east. The orientation and physiography of the mountain ranges of subtropical China appear to have contributed to the geographical pattern of genetic variation between the eastern and western populations of C. chuniana. Complex physiography plus long-term stable ecological conditions across glacial cycles facilitated the demographic expansion in the Nanling Mts., from which contemporary migration began. The Nanling Mts. are thus considered as a suitable area for preserving population diversity and large population sizes of C. chuniana compared with other regions. As inferred by ecological niche modeling and coalescent simulations, secondary contact occurred during the warm Lushan-Tali Interglacial period, with intensified East Asia summer monsoon and continuous habitat available for occupation. Our data support the strong influence of both climatic history and topographic characteristics on the high regional phytodiversity of the subtropical evergreen broadleaved forest in subtropical China.
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Affiliation(s)
- Wanzhen Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jianguang Xie
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Hui Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- Center of Conservation BiologyCore Botanical GardensChinese Academy of SciencesGuangzhouChina
| | - Gang Hao
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | | | - Wei Gong
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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11
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Sun Z, Orozco-terWengel P, Chen G, Sun R, Sun L, Wang H, Shi W, Zhang B. Spatial dynamics of Chinese Muntjac related to past and future climate fluctuations. Curr Zool 2021; 67:361-370. [PMID: 34616935 PMCID: PMC8489110 DOI: 10.1093/cz/zoaa080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 12/16/2020] [Indexed: 11/23/2022] Open
Abstract
Climate fluctuations in the past and in the future are likely to result in population expansions, shifts, or the contraction of the ecological niche of many species, and potentially leading to the changes in their geographical distributions. Prediction of suitable habitats has been developed as a useful tool for the assessment of habitat suitability and resource conservation to protect wildlife. Here, we model the ancestral demographic history of the extant modern Chinese Muntjac Muntiacus reevesi populations using approximate Bayesian computation (ABC) and used the maximum entropy model to simulate the past and predict the future spatial dynamics of the species under climate oscillations. Our results indicated that the suitable habitats for the M. reevesi shifted to the Southeast and contracted during the Last Glacial Maximum, whereas they covered a broader and more northern position in the Middle Holocene. The ABC analyses revealed that the modern M. reevesi populations diverged in the Middle Holocene coinciding with the significant contraction of the highly suitable habitat areas. Furthermore, our predictions suggest that the potentially suitable environment distribution for the species will expand under all future climate scenarios. These results indicated that the M. reevesi diverged in the recent time after the glacial period and simultaneously as its habitat’s expanded in the Middle Holocene. Furthermore, the past and future climate fluctuation triggered the change of Chinese muntjac spatial distribution, which has great influence on the Chinese muntjac’s population demographic history.
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Affiliation(s)
- Zhonglou Sun
- School of Life Sciences, Anhui University, Hefei, 230601, China
| | | | - Guotao Chen
- School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Ruolei Sun
- School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Lu Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Hui Wang
- School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Wenbo Shi
- School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Baowei Zhang
- School of Life Sciences, Anhui University, Hefei, 230601, China
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12
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Zhang W, Sun C, Zhou S, Zhao W, Wang L, Sheng L, Yi J, Liu T, Yan J, Ma X, Fang B. Recent advances in chemistry and bioactivity of Sargentodoxa cuneata. JOURNAL OF ETHNOPHARMACOLOGY 2021; 270:113840. [PMID: 33460761 DOI: 10.1016/j.jep.2021.113840] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/28/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The genus Sargentodoxa comprises only one species, Sargentodoxa cuneata (Oliv.) Rehd et al., widely distributed in the subtropical zone of China. The plant is extensively used in traditional medicine for treating arthritis, joint pains, amenorrhea, acute appendicitis and inflammatory intestinal obstruction. Pharmacological studies show anti-inflammatory, antioxidant, antitumor, antimicrobial, and anti-sepsis activities. AIM OF THE REVIEW This review aims to summarize the information about distribution, traditional uses, chemical constituents and pharmacological activities of S. cuneata, as an attempt to provide a scientific basis for its traditional uses and to support its application and development for new drug development. METHODOLOGY Scientific information of S. cuneata was retrieved from the online bibliographic databases, including Web of Science, Google Scholar, PubMed, Springer Link, the Wiley online library, SciFinder, Baidu Scholar, China national knowledge infrastructure (CNKI) and WANFANG DATA (up to March 2020). We also search doctoral dissertations, master dissertations conference papers and published books. The keywords were used: "Sargentodoxa", "Da Xue Teng", "Hong Teng", "Xue Teng", "secondary metabolites", "chemical components", "biological activity", "pharmacology", "traditional uses". OBSERVATIONS AND RESULTS S. cuneata is utilized as valuable herbal medicines to treat various diseases in China. Over 110 chemical constituents have been isolated and identified from the stem of S. cuneata, including phenolic acids, phenolic glycosides, lignans, flavones, triterpenoids and other compounds. The extract and compounds of S. cuneata have a wide spectrum of pharmacological activities, including antitumor, anti-inflammatory, antioxidant, antimicrobial, anti-sepsis and anti-arthritis effects, as well as protective activity against cerebrovascular diseases. CONCLUSION S. cuneata has a rich legacy for the treatment of many diseases, especially arthritis and sepsis, which is reinforced by current investigations. However, the present studies about bioactive chemical constituents and detail pharmacological mechanisms of S. cuneata were insufficient. Further studies should focus on these aspects in relation to its clinical applications. This review has systematically summarized the traditional uses, phytochemical constituents and pharmacological effects of S. cuneata, providing references for the therapeutic potential of new drug development.
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Affiliation(s)
- Wen Zhang
- Department of Emergency, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Chengpeng Sun
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, College of Integrative Medicine, Dalian Medical University, Dalian, 116044, China
| | - Shuang Zhou
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Wenyu Zhao
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, College of Integrative Medicine, Dalian Medical University, Dalian, 116044, China
| | - Lin Wang
- Department of Traditional Chinese Medicine Shanghai Pudong New Area People's Hospital Pudong, Shanghai, 201200, China
| | - Lingli Sheng
- Nephrology, Pudong Branch of Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Jing Yi
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, College of Integrative Medicine, Dalian Medical University, Dalian, 116044, China
| | - Tiantian Liu
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, College of Integrative Medicine, Dalian Medical University, Dalian, 116044, China
| | - Juanjuan Yan
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, College of Integrative Medicine, Dalian Medical University, Dalian, 116044, China
| | - Xiaochi Ma
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, College of Integrative Medicine, Dalian Medical University, Dalian, 116044, China.
| | - Bangjiang Fang
- Department of Emergency, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China.
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13
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Chen XD, Yang J, Guo YF, Zhao YM, Zhou T, Zhang X, Ju MM, Li ZH, Zhao GF. Spatial Genetic Structure and Demographic History of the Dominant Forest Oak Quercus fabri Hance in Subtropical China. FRONTIERS IN PLANT SCIENCE 2021; 11:583284. [PMID: 33613578 PMCID: PMC7889815 DOI: 10.3389/fpls.2020.583284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Oak trees (Quercus L.) are important models for estimating abiotic impacts on the population structure and demography of long life span tree species. In this study, we generated genetic data for 17 nuclear microsatellite loci in 29 natural populations of Quercus fabri to estimate the population genetic structure. We also integrated approximate Bayesian computation (ABC) and ecological niche analysis to infer the population differentiation processes and demographic history of this oak species. The genetic analyses indicated two genetic clusters across the 29 populations collected, where most approximately corresponded to the intraspecific differentiation among populations from western and eastern China, whereas admixed populations were mainly found in central mountains of China. The best model obtained from hierarchical ABC simulations suggested that the initial intraspecific divergence of Q. fabri potentially occurred during the late Pliocene (ca. 3.99 Ma) to form the two genetic clusters, and the admixed population group might have been generated by genetic admixture of the two differentiated groups at ca. 53.76 ka. Ecological analyses demonstrated clear differentiation among the Q. fabri population structures, and association estimations also indicated significant correlations between geography and climate with the genetic variation in this oak species. Our results suggest abiotic influences, including past climatic changes and ecological factors, might have affected the genetic differentiation and demographic history of Q. fabri in subtropical China.
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Affiliation(s)
- Xiao-Dan Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Yu-Fan Guo
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Yue-Mei Zhao
- School of Biological Sciences, Guizhou Education University, Guiyang, China
| | - Tao Zhou
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Xiao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Miao-Miao Ju
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Gui-Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
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14
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Zhang W, Sun CP, Peng YL, Zhao WY, Wang ZY, Ning J, Lv X, Yu ZL, Zhou S, Peng W, Fang BJ, Ma XC. Isolation and identification of two new sargentodoxosides from Sargentodoxa cuneata and their agonistic effects against FXR. Nat Prod Res 2021; 36:3665-3672. [PMID: 33538200 DOI: 10.1080/14786419.2021.1880405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Sargentodoxa cuneata (Oliv.) Rehd. et Wils is a traditional Chinese medicine to treat acute appendicitis, rheumarthritis, abdominal pain, and painful menstruation for a long history. The investigation of S. cuneata led to the isolation and identification of twenty-three secondary metabolites, including two new compounds, sargentodoxosides A (1) and B (2), and twenty-one known ones (3-23). Their structural characterization was conducted by HRESIMS, 1 D and 2 D NMR spectra. All the isolated compounds were assayed for their agonistic activities against the farnesoid X receptor (FXR). Nine of the isolated compounds displayed significant agonistic effects against FXR at 0.1 µM, suggesting that they could be served as potential agents for the development of FXR agonists.
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Affiliation(s)
- Wen Zhang
- Department of Emergency, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Cheng-Peng Sun
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, College of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Yu-Lin Peng
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, College of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Wen-Yu Zhao
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, College of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Zheng-Yue Wang
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, College of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Jing Ning
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, College of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Xia Lv
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, College of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Zhen-Long Yu
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, College of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Shuang Zhou
- Department of Emergency, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wei Peng
- Department of Emergency, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Bang-Jiang Fang
- Department of Emergency, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiao-Chi Ma
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, College of Integrative Medicine, Dalian Medical University, Dalian, China
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15
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Kou Y, Zhang L, Fan D, Cheng S, Li D, Hodel RGJ, Zhang Z. Evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae), in south-east China during the late Neogene: old lineage, young populations. ANNALS OF BOTANY 2020; 125:105-117. [PMID: 31765468 PMCID: PMC6948213 DOI: 10.1093/aob/mcz153] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/04/2019] [Accepted: 11/17/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS Many monotypic gymnosperm lineages in south-east China paradoxically remain in relict status despite long evolutionary histories and ample opportunities for allopatric speciation, but this paradox has received little attention and has yet to be resolved. Here, we address this issue by investigating the evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae). METHODS DNA sequences from two chloroplast regions and 14 nuclear loci were obtained for 134 samples. The demographic history was inferred and the contribution of isolation by environment (IBE) in patterning genetic divergence was compared with that of isolation by distance (IBD). KEY RESULTS Three genetic clusters were identified. Approximate Bayesian computation analyses showed that the three clusters diverged in the late Pliocene (~3.68 Ma) and two admixture events were detected. Asymmetric gene flow and similar population divergence times (~ 3.74 Ma) were characterized using the isolation with migration model. Neither IBD nor IBE contributed significantly to genetic divergence, and the contribution of IBE was much smaller than that of IBD. CONCLUSIONS These results suggest that several monotypic relict gymnosperm lineages like P. chienii in south-east China did not remain in situ and undiversified for millions of years. On the contrary, they have been evolving and the extant populations have become established more recently, having insufficient time to speciate. Our findings provide a new perspective for understanding the formation and evolution of the relict gymnosperm flora of China as well as of the Sino-Japanese Flora.
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Affiliation(s)
- Yixuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Li Zhang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Dengmei Fan
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Shanmei Cheng
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Dezhu Li
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Richard G J Hodel
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Zhiyong Zhang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
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16
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Zhu H, Yi XGUI, Li YF, Zhu SX, Li M, Duan YF, Wang XR. Phylogeography and population genetic structure of flowering cherry speciesCerasus dielsianain subtropical China. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1670750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Hong Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Xian-GUI Yi
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Yong-Fu Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Shu-Xia Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Meng Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Yi-Fan Duan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Xian-Rong Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
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17
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Li Y, Zhang X, Fang Y. Landscape Features and Climatic Forces Shape the Genetic Structure and Evolutionary History of an Oak Species ( Quercus chenii) in East China. FRONTIERS IN PLANT SCIENCE 2019; 10:1060. [PMID: 31552065 PMCID: PMC6734190 DOI: 10.3389/fpls.2019.01060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
Major topographic features facilitate intraspecific divergence through geographic isolation. This process may be enhanced by environmental isolation along climatic gradients, but also may be reduced by range shifts under rapid climatic changes. In this study, we examined how topography and climate have interacted over time and space to influence the genetic structure and evolutionary history of Quercus chenii, a deciduous oak species representative of the East China flora. Based on the nuclear microsatellite variation at 14 loci, we identified multiple genetic boundaries that were well associated with persistent landscape barriers of East China. Redundancy analysis indicated that both geography and climate explained similar amounts of intraspecific variation. Ecological differences along altitudinal gradients may have driven the divergence between highlands and lowlands. However, range expansions during the Last Interglacial as inferred from approximate Bayesian computation (ABC) may have increased the genetic diversity and eliminated the differentiation of lowland populations via admixture. Chloroplast (cp) DNA analysis of four intergenic spacers (2,866 bp in length) identified a total of 18 haplotypes, 15 of which were private to a single population, probably a result of long-term isolation among multiple montane habitats. A time-calibrated phylogeny suggested that palaeoclimatic changes of the Miocene underlay the lineage divergence of three major clades. In combination with ecological niche modeling (ENM), we concluded that mountainous areas with higher climatic stability are more likely to be glacial refugia that preserved higher phylogenetic diversity, while plains and basins may have acted as dispersal corridors for the post-glacial south-to-north migration. Our findings provide compelling evidence that both topography and climate have shaped the pattern of genetic variation of Q. chenii. Mountains as barriers facilitated differentiation through both geographic and environmental isolation, whereas lowlands as corridors increased the population connectivity especially when the species experienced range expansions.
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Affiliation(s)
- Yao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, China
| | - Xingwang Zhang
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Yanming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, China
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18
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Integrating Phylogeographic Analysis and Geospatial Methods to Infer Historical Dispersal Routes and Glacial Refugia of Liriodendron chinense. FORESTS 2019. [DOI: 10.3390/f10070565] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liriodendron chinense (Hemsl.), a Tertiary relic tree, is mainly distributed in subtropical China. The causes of the geographical distribution pattern of this species are poorly understood. In this study, we inferred historical dispersal routes and glacial refugia of this species by combining genetic data (chloroplast DNA (cpDNA), nuclear ribosomal DNA (nrDNA), and nuclear DNA (nDNA)) and geospatial data (climate and geology) with the methods of landscape genetics. Additionally, based on sequence variation at multiple loci, we employed GenGIS and Barrier software to analyze L. chinense population genetic structure. Dispersal corridors and historical gene flow between the eastern and western populations were detected, and they were located in mountainous regions. Based on species distribution model (SDMs), the distribution patterns in paleoclimatic periods were consistent with the current pattern, suggesting the presence of multiple refuges in multiple mountainous regions in China. The genetic structure analysis clustered most eastern populations into a clade separated from the western populations. Additionally, a genetic barrier was detected between the eastern and western populations. The dispersal corridors and historical gene flow detected here suggested that the mountains acted as a bridge, facilitating gene flow between the eastern and western populations. Due to Quaternary climatic fluctuations, the habitats and dispersal corridors were frequently inhabited by warm-temperate evergreen forests, which may have fragmented L. chinense habitats and exacerbated the differentiation of eastern and western populations. Ultimately, populations retreated to multiple isolated mountainous refugia, shaping the current geographical distribution pattern. These dispersal corridors and montane refugia suggested that the mountains in subtropical China play a crucial role in the conservation of genetic resources and migration of subspecies or related species in this region.
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Naciri Y, Christe C, Bétrisey S, Song YG, Deng M, Garfì G, Kozlowski G. Species delimitation in the East Asian species of the relict tree genus Zelkova (Ulmaceae): A complex history of diversification and admixture among species. Mol Phylogenet Evol 2019; 134:172-185. [PMID: 30769098 DOI: 10.1016/j.ympev.2019.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 12/04/2018] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
Abstract
Zelkova species, trees of the elm family (Ulmaceae), are part of the Cenozoic relict flora. In western Eurasia, the genus comprises three species that are restricted to disjunct areas (Z. sicula on Sicily, Z. abelicea on Crete and Z. carpinifolia in Transcaucasia). The situation is different in East Asia, where three species (Z. serrata, Z. schneideriana and Z. sinica) have at least partly overlapping distributions. The phylogenetic and phylogeographic status of these East Asian species is still not well understood, mainly since all previous studies used almost exclusively plant material collected in botanical gardens and were based on very small numbers of individuals. Our study is the first based on 33 natural populations covering all important areas with Zelkova species in the Sino-Japanese Floristic Region. Chloroplast and microsatellite markers were used, and Bayesian analyses were run for both types of markers. East Asian Zelkova species cluster into two groups that partially overlap when comparing the two types of markers. For chloroplast markers, the two groups coincide with all Japanese, some Korean and northern Chinese Z. serrata in one group and all other individuals in the other group, regardless of whether they are attributed to Z. serrata, Z. sinica or Z. schneideriana from Korea, mainland China and Taiwan. At the nuclear level, however, the clustering clearly groups all the Z. serrata individuals together, regardless of whether they are from Japan, Korea or China, and the two other species in a second group. This complex genetic pattern in East Asian Zelkova species is most likely due to a combination of ancient diversification and speciation events and more recent hybridization during the last glacial/interglacial retractions and recolonizations. One of the surprising results of our study concerns the populations from Taiwan, which are genetically similar to Z. schneideriana. Thus, their assignation to a separate taxon (Z. tarokoensis) or to a variety of Z. serrata (Z. serrata var. tarokoensis), as currently reported in all local and national floras, might be in need of revision. Furthermore, our results indicate that the East Asian species are more closely related to Z. carpinifolia than to any other Western European species. Haplotypes of Z. sicula and Z. abelicea (Mediterranean region) as well as those of Z. sinica and Z. schneideriana (East Asia) seem to have diversified more recently. The most ancient haplotypes are found among the western Eurasian Z. carpinifolia and the East Asian Z. serrata. This result is in agreement with the carpinifolia and serrata-like morphotypes commonly found in the fossil record.
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Affiliation(s)
- Yamama Naciri
- Conservatoire et Jardin botaniques de la Ville de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Genève, Switzerland; Laboratoire de Systématique végétale et Biodiversité, University of Geneva, Chemin de l'Impératrice 1, 1292 Chambésy, Genève, Switzerland.
| | - Camille Christe
- Conservatoire et Jardin botaniques de la Ville de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Genève, Switzerland
| | - Sébastien Bétrisey
- Natural History Museum Fribourg, Chemin du Musée 6, 1700 Fribourg, Switzerland; Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Yi-Gang Song
- Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland; Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Min Deng
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Giuseppe Garfì
- Institute of Biosciences and BioResources, National Research Council, Corso Calatafimi 414, 90129 Palermo, Italy
| | - Gregor Kozlowski
- Natural History Museum Fribourg, Chemin du Musée 6, 1700 Fribourg, Switzerland; Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
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Yang A, Zhong Y, Liu S, Liu L, Liu T, Li Y, Yu F. New insight into the phylogeographic pattern of Liriodendron chinense (Magnoliaceae) revealed by chloroplast DNA: east-west lineage split and genetic mixture within western subtropical China. PeerJ 2019; 7:e6355. [PMID: 30723627 PMCID: PMC6361005 DOI: 10.7717/peerj.6355] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/26/2018] [Indexed: 11/20/2022] Open
Abstract
Background Subtropical China is a global center of biodiversity and one of the most important refugia worldwide. Mountains play an important role in conserving the genetic resources of species. Liriodendron chinense is a Tertiary relict tree largely endemic to subtropical China. In this study, we aimed to achieve a better understanding of the phylogeographical pattern of L. chinense and to explore the role of mountains in the conservation of L. chinense genetic resources. Methods Three chloroplast regions (psbJ-petA, rpl32-ndhF, and trnK5’-matK) were sequenced in 40 populations of L. chinense for phylogeographical analyses. Relationships among chloroplast DNA (cpDNA) haplotypes were determined using median-joining networks, and genetic structure was examined by spatial analysis of molecular variance (SAMOVA). The ancestral area of the species was reconstructed using the Bayesian binary Markov Chain Monte Carlo (BBM) method according to its geographic distribution and a maximum parsimony (MP) tree based on Bayesian methods. Results Obvious phylogeographic structure was found in L. chinense. SAMOVA revealed seven groups matching the major landscape features of the L. chinense distribution area. The haplotype network showed three clades distributed in the eastern, southwestern, and northwestern regions. Separate northern and southern refugia were found in the Wu Mountains and Yungui Plateau, with genetic admixture in the Dalou Mountains and Wuling Mountains. BBM revealed a more ancient origin of L. chinense in the eastern region, with a west–east split most likely having occurred during the Mindel glacial stage. Discussion The clear geographical distributions of haplotypes suggested multiple mountainous refugia of L. chinense. The east–west lineage split was most likely a process of gradual genetic isolation and allopatric lineage divergence when the Nanling corridor was frequently occupied by evergreen or coniferous forest during Late Quaternary oscillations. Hotspots of haplotype diversity in the Dalou Mountains and Wuling Mountains likely benefited from gene flow from the Wu Mountains and Yungui Plateau. Collectively, these results indicate that mountain regions should be the main units for conserving and collecting genetic resources of L. chinense and other similar species in subtropical China.
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Affiliation(s)
- Aihong Yang
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Yongda Zhong
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Shujuan Liu
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Lipan Liu
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Tengyun Liu
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Yanqiang Li
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Faxin Yu
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
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Song W, Cao LJ, Li BY, Gong YJ, Hoffmann AA, Wei SJ. Multiple refugia from penultimate glaciations in East Asia demonstrated by phylogeography and ecological modelling of an insect pest. BMC Evol Biol 2018; 18:152. [PMID: 30314450 PMCID: PMC6186135 DOI: 10.1186/s12862-018-1269-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 09/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Refugial populations in Quaternary glaciations are critical to understanding the evolutionary history and climatic interactions of many extant species. Compared with the well-studied areas of Europe and Northern America, refugia of species in eastern Asia remain largely unknown. Here, we investigated the phylogeographic history of a globally important insect pest, the oriental fruit moth Grapholita molesta, in its native range of China. RESULTS Genetic structure analyses unveiled three distinct groups and a set of populations with admixture. Approximate Bayesian Computation (ABC) analyses support range expansion of this moth from southwest groups of Yunnan and Sichuan to northern and eastern China. A set of admixed populations was found around these two ancestral groups. This pattern of genetic structure points to two refugia located in the Yunnan region and Sichuan Basin. The split of the two refugia was dated to 329.2 thousand years ago in the penultimate glacial period. One of the lineages was exclusively found around the Sichuan Basin, indicating the formation of endemic populations in this refugium. Ecological niche model analysis suggested a shrinking distribution from the LIG period to the MID period in the Sichuan lineage but a wide and stable distribution in the other lineage. CONCLUSIONS Our results for the first time suggest that Yunnan and Sichuan jointly served as two large-scale refugia in eastern Asia in Quaternary glaciations, helping to maintain genetic diversity overall.
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Affiliation(s)
- Wei Song
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097 China
- College of Forestry, Beijing Forestry University, Beijing, 100083 China
| | - Li-Jun Cao
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097 China
| | - Bing-Yan Li
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097 China
| | - Ya-Jun Gong
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097 China
| | - Ary Anthony Hoffmann
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, VIC 3010 Australia
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097 China
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Fan D, Huang J, Hu H, Sun Z, Cheng S, Kou Y, Zhang Z. Evolutionary Hotspots of Seed Plants in Subtropical China: A Comparison With Species Diversity Hotspots of Woody Seed Plants. Front Genet 2018; 9:333. [PMID: 30177954 PMCID: PMC6109751 DOI: 10.3389/fgene.2018.00333] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/02/2018] [Indexed: 11/13/2022] Open
Abstract
Genetic diversity is a fundamental level of biodiversity. However, it is frequently neglected in conservation prioritization because intraspecific genetic diversity is difficult to measure at large scales. In this study, we synthesized population genetic or phylogeographic datasets of 33 seed plants in subtropical China into multi-species genetic landscapes. The genetic landscapes identified 18 evolutionary hotspots with high within-population genetic diversity (WGD), and among-population genetic diversity (AGD), or both. The western subtropical China is rich in AGD (possessing four major AGD hotspots), deserving a high conservation priority. We found that WGD was positively correlated with longitude, with most WGD hotspots locating in east subtropical China. The results showed that the locations of 12 of 18 evolutionary hotspots corresponded approximately to those of previously identified species diversity (SD) hotspots, however, a positive and significant correlation existed only between AGD and SD, not between WGD and SD. Therefore, spatial patterns of species richness in plants in subtropical China cannot generally be used as surrogate for their intraspecific diversity. This study identified multi-species evolutionary hotspots and correlated multi-species genetic diversity with SD across subtropical China for the first time, providing profound implications for the conservation of biodiversity in this important ecoregion.
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Affiliation(s)
- Dengmei Fan
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Jihong Huang
- Key Laboratory of Forest Ecology and Environment, The State Forestry and Grassland Administration, Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Huili Hu
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Zhixia Sun
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Shanmei Cheng
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Yixuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Zhiyong Zhang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
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Li ZZ, Gichira AW, Wang QF, Chen JM. Genetic diversity and population structure of the endangered basal angiosperm Brasenia schreberi (Cabombaceae) in China. PeerJ 2018; 6:e5296. [PMID: 30013859 PMCID: PMC6047506 DOI: 10.7717/peerj.5296] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/03/2018] [Indexed: 11/20/2022] Open
Abstract
Brasenia schreberi J.F. Gmelin (Cabombaceae), an aquatic herb that occurs in fragmented locations in China, is rare and endangered. Understanding its genetic diversity and structure is crucial for its conservation and management. In this study, 12 microsatellite markers were used to estimate the genetic diversity and variation in 21 populations of B. schreberi in China. A total of 61 alleles were found; assessment of allelic richness (Ar = 1.92) and observed and expected heterozygosity (HO = 0.200, HE = 0.256) suggest lower genetic diversity compared to some endangered species, and higher variation was observed within populations (58.68%) rather than among populations (41.32%). No significant correlation between geographical and genetic distance among populations was detected (Mantel test, r = 0.0694; P = 0.7985), which may have likely resulted from barriers to gene flow (Nm = 0.361) that were produced by habitat fragmentation. However, Bayesian and neighbor-joining cluster analyses suggest a population genetic structure consisting of two clusters (I and II) or four subclusters (I-1, 2 and II-1, 2). The genetic structure and distribution of B. schreberi in China may have involved glacial refugia that underwent range expansions, introgression, and habitat fragmentation. The findings of the present study emphasize the importance for both in situ and ex situ conservation efforts.
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Affiliation(s)
- Zhi-Zhong Li
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Andrew W. Gichira
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Feng Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Jin-Ming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
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Fan L, Zheng H, Milne RI, Zhang L, Mao K. Strong population bottleneck and repeated demographic expansions of Populus adenopoda (Salicaceae) in subtropical China. ANNALS OF BOTANY 2018; 121:665-679. [PMID: 29324975 PMCID: PMC5853028 DOI: 10.1093/aob/mcx198] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/06/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND AND AIMS Glacial refugia and inter-/postglacial recolonization routes during the Quaternary of tree species in Europe and North America are well understood, but far less is known about those of tree species in subtropical eastern Asia. Thus, we have examined the phylogeographic history of Populus adenopoda (Salicaceae), one of the few poplars that naturally occur in this subtropical area. METHODS Genetic variations across the range of the species in subtropical China were surveyed using ten nuclear microsatellite loci and four chloroplast fragments (matK, trnG-psbK, psbK-psbI and ndhC-trnV). Coalescent-based analyses were used to test demographic and migration hypotheses. In addition, species distribution models (SDMs) were constructed to infer past, present and future potential distributions of the species. KEY RESULTS Thirteen chloroplast haplotypes were detected, and haplotype-rich populations were found in central and southern parts of the species' range. STRUCTURE analyses of nuclear microsatellite loci suggest obvious lineage admixture, especially in peripheral and northern populations. DIYABC analysis suggests that the species might have experienced two independent rounds of demographic expansions and a strong bottleneck in the late Quaternary. SDMs indicate that the species' range contracted during the Last Glacial Maximum (LGM), and contracted northward but expanded eastward during the Last Interglacial (LIG). CONCLUSIONS Chloroplast data and SDMs suggest that P. adenopoda might have survived in multiple glacial refugia in central and southern parts of its range during the LGM. Populations of the Yunnan-Guizhou Plateau in the southern part have high chloroplast DNA diversity, but may have contributed little to the postglacial recolonization of northern and eastern parts. The three major demographic events inferred by DIYABC coincide with the initiation of the LIG, start of the LGM and end of the LGM, respectively. The species may have experienced multiple rounds of range contraction during glacial periods and range expansion during interglacial periods. Our study corroborates the importance of combining multiple lines of evidence when reconstructing Quaternary population evolutionary histories.
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Affiliation(s)
- Liqiang Fan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan, P. R. China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Henan, P. R. China
| | - Honglei Zheng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan, P. R. China
| | - Richard I Milne
- Institute of Molecular Plant Sciences, University of Edinburgh, UK
| | - Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan, P. R. China
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan, P. R. China
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Tian S, Kou Y, Zhang Z, Yuan L, Li D, López-Pujol J, Fan D, Zhang Z. Phylogeography of Eomecon chionantha in subtropical China: the dual roles of the Nanling Mountains as a glacial refugium and a dispersal corridor. BMC Evol Biol 2018; 18:20. [PMID: 29426277 PMCID: PMC5807764 DOI: 10.1186/s12862-017-1093-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 11/24/2017] [Indexed: 11/29/2022] Open
Abstract
Background Mountains have not only provided refuge for species, but also offered dispersal corridors during the Neogene and Quaternary global climate changes. Compared with a plethora of studies on the refuge role of China’s mountain ranges, their dispersal corridor role has received little attention in plant phylogeographic studies. Using phylogeographic data of Eomecon chionantha Hance (Papaveraceae), this study explicitly tested whether the Nanling Mountains, which spans from west to east for more than 1000 km in subtropical China, could have functioned as a dispersal corridor during the late Quaternary in addition to a glacial refugium. Results Our analyses revealed a range-wide lack of phylogeographic structure in E. chionantha across three kinds of molecular markers [two chloroplast intergenic spacers, nuclear ribosomal internal transcribed spacer (nrITS), and six nuclear microsatellite loci]. Demographic inferences based on chloroplast and nrITS sequences indicated that E. chionantha could have experienced a strong postglacial range expansion between 6000 and 1000 years ago. Species distribution modelling showed that the Nanling Mountains and the eastern Yungui Plateau were the glacial refugia of E. chionantha. Reconstruction of dispersal corridors indicated that the Nanling Mountains also have acted as a corridor of population connectivity for E. chionantha during the late Quaternary. Conclusions Our results suggest that the Nanling Mountains may acted dual roles as a dispersal corridor in east-west direction and as a glacial refugium in subtropical China during the late Quaternary. The population connectivity mediated by the mountain range and a strong postglacial range expansion are the most likely reasons for the lack of phylogeographic structure in E. chionantha. The hypothesis of dual roles of the mountain range presented here sheds new insights into the phylogeographic patterns of organisms in subtropical China. Electronic supplementary material The online version of this article (10.1186/s12862-017-1093-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuang Tian
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China.,Jingdezhen University, Jingdezhen, Jiangxi, 333000, China
| | - Yixuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China
| | - Zhirong Zhang
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Lin Yuan
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China
| | - Derong Li
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China
| | - Jordi López-Pujol
- Instituto Botánico de Barcelona, IBB, CSIC-ICUB, Passeig del Migdia s/n, 08038, Barcelona, Spain
| | - Dengmei Fan
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China.
| | - Zhiyong Zhang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China.
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Guan BC, Liu X, Gong X, Ge G. Identification of evolutionary hotspots in the Poyang Lake Basin based on genetic data from multiple rare and endangered plant species. ECOL INFORM 2017. [DOI: 10.1016/j.ecoinf.2017.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Fan D, Sun Z, Li B, Kou Y, Hodel RGJ, Jin Z, Zhang Z. Dispersal corridors for plant species in the Poyang Lake Basin of southeast China identified by integration of phylogeographic and geospatial data. Ecol Evol 2017; 7:5140-5148. [PMID: 28770054 PMCID: PMC5528243 DOI: 10.1002/ece3.2999] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 03/15/2017] [Accepted: 03/21/2017] [Indexed: 11/24/2022] Open
Abstract
Measuring the dispersal of wildlife through landscapes is notoriously difficult. Recently, the categorical least cost path algorithm that integrates population genetic data with species distribution models has been applied to reveal population connectivity. In this study, we use this method to identify the possible dispersal corridors of five plant species (Castanopsis tibetana, Schima superba, Cyclocarya paliurus, Sargentodoxa cuneata, Eomecon chionantha) in the Poyang Lake Basin (PLB, largely coinciding with Jiangxi Province), China, in the late Quaternary. The results showed that the strongest population connectivity for the five species occurred in the Wuyi Mountains and the Yu Mountains of the eastern PLB (East Corridor) during the late Quaternary. In the western PLB, populations of the five species were connected by the Luoxiao Mountains and the Jiuling Mountains (West Corridor) but with a lower degree of connectivity. There were some minor connections between the eastern and the western populations across the Gannan Hills. When the corridors of five species were overlaid, the East Corridor and the West Corridor were mostly shared by multiple species. These results indicate that plant species in the PLB could have responded to the Quaternary climate changes by moving along the East Corridor and the West Corridor. Given that dispersal corridors have seldom been considered in the governmental strategies of biodiversity conservation in the PLB, preserving and restoring natural vegetation along these corridors should be prioritized to mitigate the effects of anthropogenic climate change by facilitating migration of plant species and other biota.
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Affiliation(s)
- Dengmei Fan
- Laboratory of Subtropical Biodiversity Jiangxi Agricultural University Nanchang Jiangxi China
| | - Zhixia Sun
- Laboratory of Subtropical Biodiversity Jiangxi Agricultural University Nanchang Jiangxi China
| | - Bo Li
- Laboratory of Subtropical Biodiversity Jiangxi Agricultural University Nanchang Jiangxi China
| | - Yixuan Kou
- Laboratory of Subtropical Biodiversity Jiangxi Agricultural University Nanchang Jiangxi China
| | | | - Zhinong Jin
- Nanchang Institute of Technology Nanchang Jiangxi China
| | - Zhiyong Zhang
- Laboratory of Subtropical Biodiversity Jiangxi Agricultural University Nanchang Jiangxi China
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The demographic response of a deciduous shrub (the Indigofera bungeana complex, Fabaceae) to the Pleistocene climate changes in East Asia. Sci Rep 2017; 7:697. [PMID: 28386059 PMCID: PMC5428846 DOI: 10.1038/s41598-017-00613-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/06/2017] [Indexed: 11/25/2022] Open
Abstract
East Asia harbors the highest level of floristic diversity among the world’s temperate regions. Despite the increase in phylogeographic studies of temperate plants in East Asia, far less attention has been paid to widely distributed deciduous shrubs that widespread across several floral regions. We sequenced two chloroplast DNA (cpDNA) fragments (ndhJ-trnF and trnD-trnT) and one nuclear DNA (Pgk1) of 472 individuals from 51 populations of such a group, the Indigofera bungeana complex. We used population genetic data as well as ecological niche modelling to examine the evolutionary history and glacial refugia during the Last Glacial Maximum (LGM) of this group. We recovered 133 cpDNA and 68 nuclear haplotypes. The star-phylogeny of the recovered cpDNA and nuclear haplotypes and demographic analyses suggested distinct range expansion of I. bungeana complex have occurred during the early and middle Pleistocene. The climate change of the LGM might have affected little on the distribution of this complex based on the niche modelling. However, these climate changes and geographic isolation probably resulted in fixtures of the private haplotypes and genetic differentiations between regions. Our results suggested that this arid-tolerant species complex may have different responses to the Quaternary climate changes with those climate-sensitive species.
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Idiosyncratic responses of evergreen broad-leaved forest constituents in China to the late Quaternary climate changes. Sci Rep 2016; 6:31044. [PMID: 27534981 PMCID: PMC4989166 DOI: 10.1038/srep31044] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/06/2016] [Indexed: 11/24/2022] Open
Abstract
Subtropical evergreen broad-leaved forest (EBLF) is one of the most important vegetation types in China. Inferences from palaeo-biome reconstruction (PBR) and phylogeography regarding range shift history of EBLF during the late Quaternary are controversial and should be reconciled. We compared phylogeographic patterns of three EBLF constituents in China, Castanopsis tibetana, Machilus thunbergii and Schima superba. Contrary to a chorus of previous phylogeographic studies and the results of species distribution modelling (SDM) of this study (in situ survival during the LGM), the three species displayed three different phylogeographic patterns that conform to either an in situ survival model or an expansion-contraction model. These results are partially congruent with the inference of PBR that EBLF was absent to the north of 24° N at the LGM. This study suggests that the constituents of EBLF could have responded idiosyncratically to climate changes during the Late Quaternary. The community assemblages of EBLF could have been changing over time, resulting in no palaeo-analogs to modern-day EBLF, which may be the main reason responsible for the failure of PBR to detect the occurrence of EBLF north of 24° N at the LGM.
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Sun ZX, Ye LJ, Zhang F, Hu W, Fan DM, Zhang ZY. Development of microsatellite markers for Sargentodoxa cuneata (Lardizabalaceae) using next-generation sequencing technology. APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1600003. [PMID: 27213128 PMCID: PMC4873275 DOI: 10.3732/apps.1600003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 02/05/2016] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Microsatellite loci were developed for a woody deciduous liana, Sargentodoxa cuneata (Lardizabalaceae), to help infer the evolutionary histories of ancient monotypic genera in subtropical China. METHODS AND RESULTS Using next-generation sequencing (Illumina MiSeq) technology, 21 polymorphic primer sets were identified in three wild populations. The number of alleles per locus ranged from one to seven. The expected and observed heterozygosities varied from 0 to 0.788 and 0 to 0.917, respectively. Transferability analyses were performed in Stauntonia chinensis, Akebia trifoliata, and A. quinata. Eighteen (85.7%), 18 (85.7%), and 17 (81.0%) markers were successfully amplified, respectively. CONCLUSIONS The newly developed markers will facilitate further studies on genetic diversity and phylogeographic patterns throughout the distributional range of S. cuneata. This set of microsatellite primers represents the second report on molecular markers in Lardizabalaceae.
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Affiliation(s)
- Zhi-Xia Sun
- College of Forestry, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, People’s Republic of China
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, People’s Republic of China
| | - Lin-Jiang Ye
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, People’s Republic of China
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, People’s Republic of China
| | - Fei Zhang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, People’s Republic of China
| | - Wan Hu
- College of Forestry, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, People’s Republic of China
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, People’s Republic of China
| | - Deng-Mei Fan
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, People’s Republic of China
| | - Zhi-Yong Zhang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, People’s Republic of China
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Yuan ZY, Suwannapoom C, Yan F, Poyarkov NA, Nguyen SN, Chen HM, Chomdej S, Murphy RW, Che J. Red River barrier and Pleistocene climatic fluctuations shaped the genetic structure of Microhyla fissipes complex (Anura: Microhylidae) in southern China and Indochina. Curr Zool 2016; 62:531-543. [PMID: 29491943 PMCID: PMC5804247 DOI: 10.1093/cz/zow042] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/14/2016] [Indexed: 11/13/2022] Open
Abstract
South China and Indochina host striking species diversity and endemism. Complex tectonic and climatic evolutions appear to be the main drivers of the biogeographic patterns. In this study, based on the geologic history of this region, we test 2 hypotheses using the evolutionary history of Microhyla fissipes species complex. Using DNA sequence data from both mitochondrial and nuclear genes, we first test the hypothesis that the Red River is a barrier to gene flow and dispersal. Second, we test the hypothesis that Pleistocene climatic cycling affected the genetic structure and population history of these frogs. We detect 2 major genetic splits that associate with the Red River. Time estimation suggests that late Miocene tectonic movement associated with the Red River drove their diversification. Species distribution modeling (SDM) resolves significant ecological differences between sides of the Red River. Thus, ecological divergence also probably promoted and maintained the diversification. Genogeography, historical demography, and SDM associate patterns in southern China with climate changes of the last glacial maximum (LGM), but not Indochina. Differences in geography and climate between the 2 areas best explain the discovery. Responses to the Pleistocene glacial–interglacial cycling vary among species and regions.
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Affiliation(s)
- Zhi-Yong Yuan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Chatmongkon Suwannapoom
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Nikolay A Poyarkov
- Department of Vertebrate Zoology, Biological faculty, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia.,Joint Russian-Vietnamese Tropical Research and Technological Center, A.N. Severtsov Institute of Ecology and Evolution RAS, South Branch, District 10, Ho Chi Minh 700000, Vietnam
| | - Sang Ngoc Nguyen
- Institute of Tropical Biology, Vietnam Academy of Science and Technology, 85 Tran Quoc Toan St., District 3, Ho Chi Minh 700000, Vietnam
| | - Hong-Man Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Siriwadee Chomdej
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand, and
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario M5S2C6, Canada
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
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Cao YN, Comes HP, Sakaguchi S, Chen LY, Qiu YX. Evolution of East Asia's Arcto-Tertiary relict Euptelea (Eupteleaceae) shaped by Late Neogene vicariance and Quaternary climate change. BMC Evol Biol 2016; 16:66. [PMID: 27001058 PMCID: PMC4802896 DOI: 10.1186/s12862-016-0636-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/13/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolutionary origin and historical demography of extant Arcto-Tertiary forest species in East Asia is still poorly understood. Here, we reconstructed the evolutionary and population demographic history of the two extant Euptelea species in China (E. pleiosperma) and Japan (E. polyandra). Chloroplast/nuclear DNA sequences and microsatellite loci were obtained from 36 Euptelea populations to explore molecular structure and diversity in relation to past and present distributions based on ecological niche modelling (ENM). Time-calibrated phylogenetic/phylogeographic inferences and niche-identity tests were used to infer the historical process of lineage formation. RESULTS Euptelea pleiosperma diverged from E. polyandra around the Late Miocene and experienced significant ecological differentiation. A near-simultaneous diversification of six phylogroups occurred during the mid-to-late Pliocene, in response to the abrupt uplift of the eastern Tibetan Plateau and an increasingly cooler and drier climate. Populations of E. pleiosperma seem to have been mostly stationary through the last glacial cycles, while those of E. polyandra reflect more recent climate-induced cycles of range contraction and expansion. CONCLUSIONS Our results illustrate how Late Neogene climatic/tectonic changes promoted speciation and lineage diversification in East Asia's Tertiary relict flora. They also demonstrate for the first time a greater variation in such species' responses to glacial cycles in Japan when compared to congeners in China.
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Affiliation(s)
- Ya-Nan Cao
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hans Peter Comes
- Department of Ecology & Evolution, Salzburg University, A-5020, Salzburg, Austria
| | - Shota Sakaguchi
- Laboratory of Plant Evolution and Biodiversity, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-0041, Japan
| | - Lu-Yao Chen
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ying-Xiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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From glacial refugia to wide distribution range: demographic expansion of Loropetalum chinense (Hamamelidaceae) in Chinese subtropical evergreen broadleaved forest. ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0252-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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