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Jin J, Zhao W, Chen S, Gu C, Chen Z, Liu Z, Liao W, Fan Q. Which contributes more to the relict flora distribution pattern in East Asia, geographical processes or climate change? New evidence from the phylogeography of Rehderodendron kwangtungense. BMC PLANT BIOLOGY 2024; 24:459. [PMID: 38797839 PMCID: PMC11129394 DOI: 10.1186/s12870-024-05181-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/21/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Relict species are important for enhancing the understanding of modern biogeographic distribution patterns. Although both geological and climatic changes since the Cenozoic have affected the relict flora in East Asia, the contributions of geographical processes remain unclear. In this study, we employed restriction-site associated DNA sequencing (RAD-seq) and shallow genome sequencing data, in conjunction with ecological niche modeling (ENM), to investigate the spatial genetic patterns and population differentiation history of the relict species Rehderodendron kwangtungense Chun. RESULTS A total of 138 individuals from 16 populations were collected, largely covering the natural distribution of R. kwangtungense. The genetic diversity within the R. kwangtungense populations was extremely low (HO = 0.048 ± 0.019; HE = 0.033 ± 0.011). Mantel tests revealed isolation-by-distance pattern (R2 = 0.38, P < 0.001), and AMOVA analysis showed that the genetic variation of R. kwangtungense occurs mainly between populations (86.88%, K = 7). Between 23 and 21 Ma, R. kwangtungense underwent a period of rapid differentiation that coincided with the rise of the Himalayas and the establishment of the East Asian monsoon. According to ENM and population demographic history, the suitable area and effective population size of R. kwangtungense decreased sharply during the glacial period and expanded after the last glacial maximum (LGM). CONCLUSION Our study shows that the distribution pattern of southern China mountain relict flora may have developed during the panplain stage between the middle Oligocene and the early Miocene. Then, the flora later fragmented under the force of orogenesis, including intermittent uplift during the Cenozoic Himalayan orogeny and the formation of abundant rainfall associated with the East Asian monsoon. The findings emphasized the predominant role of geographical processes in shaping relict plant distribution patterns.
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Affiliation(s)
- Jiehao Jin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wanyi Zhao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Sufang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chao Gu
- Shenzhen Dapeng Peninsula National Geopark, Shenzhen, 518121, China
| | - Zhihui Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhongcheng Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wenbo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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Ye H, Wang Y, Liu H, Lei D, Li H, Gao Z, Feng X, Han M, Qie Q, Zhou H. The Phylogeography of Deciduous Tree Ulmus macrocarpa (Ulmaceae) in Northern China. PLANTS (BASEL, SWITZERLAND) 2024; 13:1334. [PMID: 38794406 PMCID: PMC11125379 DOI: 10.3390/plants13101334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
Disentangling how climate oscillations and geographical events significantly influence plants' genetic architecture and demographic history is a central topic in phytogeography. The deciduous ancient tree species Ulmus macrocarpa is primarily distributed throughout Northern China and has timber and horticultural value. In the current study, we studied the phylogenic architecture and demographical history of U. macrocarpa using chloroplast DNA with ecological niche modeling. The results indicated that the populations' genetic differentiation coefficient (NST) value was significantly greater than the haplotype frequency (GST) (p < 0.05), suggesting that U. macrocarpa had a clear phylogeographical structure. Phylogenetic inference showed that the putative chloroplast haplotypes could be divided into three groups, in which the group Ⅰ was considered to be ancestral. Despite significant genetic differentiation among these groups, gene flow was detected. The common ancestor of all haplotypes was inferred to originate in the middle-late Miocene, followed by the haplotype overwhelming diversification that occurred in the Quaternary. Combined with demography pattern and ecological niche modeling, we speculated that the surrounding areas of Shanxi and Inner Mongolia were potential refugia for U. macrocarpa during the glacial period in Northern China. Our results illuminated the demography pattern of U. macrocarpa and provided clues and references for further population genetics investigations of precious tree species distributed in Northern China.
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Affiliation(s)
- Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yiling Wang
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Dingfan Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Haochen Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Zhimei Gao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xiaolong Feng
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Mian Han
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Qiyang Qie
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Huijuan Zhou
- Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, China
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Dai X, Xiang S, Zhang Y, Yang S, Hu Q, Wu Z, Zhou T, Xiang J, Chen G, Tan X, Wang J, Ding J. Genomic evidence for evolutionary history and local adaptation of two endemic apricots: Prunus hongpingensis and P. zhengheensis. HORTICULTURE RESEARCH 2024; 11:uhad215. [PMID: 38689695 PMCID: PMC11059793 DOI: 10.1093/hr/uhad215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 10/16/2023] [Indexed: 05/02/2024]
Abstract
Apricot, belonging to the Armeniaca section of Rosaceae, is one of the economically important crop fruits that has been extensively cultivated. The natural wild apricots offer valuable genetic resources for crop improvement. However, some of them are endemic, with small populations, and are even at risk of extinction. In this study we unveil chromosome-level genome assemblies for two southern China endemic apricots, Prunus hongpingensis (PHP) and P. zhengheensis (PZH). We also characterize their evolutionary history and the genomic basis of their local adaptation using whole-genome resequencing data. Our findings reveal that PHP and PZH are closely related to Prunus armeniaca and form a distinct lineage. Both species experienced a decline in effective population size following the Last Glacial Maximum (LGM), which likely contributed to their current small population sizes. Despite the observed decrease in genetic diversity and heterozygosity, we do not observe an increased accumulation of deleterious mutations in these two endemic apricots. This is likely due to the combined effects of a low inbreeding coefficient and strong purifying selection. Furthermore, we identify a set of genes that have undergone positive selection and are associated with local environmental adaptation in PHP and PZH, respectively. These candidate genes can serve as valuable genetic resources for targeted breeding and improvement of cultivated apricots. Overall, our study not only enriches our comprehension of the evolutionary history of apricot species but also offers crucial insights for the conservation and future breeding of other endemic species amidst rapid climate changes.
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Affiliation(s)
- Xiaokang Dai
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Hubei Hongshan Laboratory, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Songzhu Xiang
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Yulin Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, China
| | - Siting Yang
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Qianqian Hu
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Zhihao Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Hubei Hongshan Laboratory, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Tingting Zhou
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Hubei Hongshan Laboratory, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Jingsong Xiang
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Gongyou Chen
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Xiaohua Tan
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Jing Wang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, China
| | - Jihua Ding
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Hubei Hongshan Laboratory, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
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Ren Y, Zhang L, Yang X, Lin H, Sang Y, Feng L, Liu J, Kang M. Cryptic divergences and repeated hybridizations within the endangered "living fossil" dove tree ( Davidia involucrata) revealed by whole genome resequencing. PLANT DIVERSITY 2024; 46:169-180. [PMID: 38807904 PMCID: PMC11128880 DOI: 10.1016/j.pld.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/05/2024] [Accepted: 02/08/2024] [Indexed: 05/30/2024]
Abstract
The identification and understanding of cryptic intraspecific evolutionary units (lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species. However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a "living fossil" dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range. Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.
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Affiliation(s)
- Yumeng Ren
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Lushui Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xuchen Yang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Hao Lin
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yupeng Sang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Landi Feng
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jianquan Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Minghui Kang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
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Zhang Q, Yang Y, Liu B, Lu L, Sauquet H, Li D, Chen Z. Meta-analysis provides insights into the origin and evolution of East Asian evergreen broad-leaved forests. THE NEW PHYTOLOGIST 2024. [PMID: 38186378 DOI: 10.1111/nph.19524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/18/2023] [Indexed: 01/09/2024]
Abstract
Evergreen broad-leaved forests (EBLFs) are dominated by a monsoon climate and form a distinct biome in East Asia with notably high biodiversity. However, the origin and evolution of East Asian EBLFs (EAEBLFs) remain elusive despite the estimation of divergence times for various representative lineages. Using 72 selected generic-level characteristic lineages, we constructed an integrated lineage accumulation rate (LAR) curve based on their crown ages. According to the crown-based LAR, the EAEBLF origin was identified at least as the early Oligocene (c. 31.8 million years ago (Ma)). The accumulation rate of the characteristic genera peaked at 25.2 and 6.4 Ma, coinciding with the two intensification periods of the Asian monsoon at the Oligocene - Miocene and the Miocene - Pliocene boundaries, respectively. Moreover, the LAR was highly correlated with precipitation in the EAEBLF region and negatively to global temperature, as revealed through time-lag cross-correlation analyses. An early Oligocene origin is suggested for EAEBLFs, bridging the gap between paleobotanical and molecular dating studies and solving conflicts among previous estimates based on individual representative lineages. The strong correlation between the crown-based LAR and the precipitation brought about by the Asian monsoon emphasizes its irreplaceable role in the origin and development of EAEBLFs.
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Affiliation(s)
- Qian Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yuchang Yang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Limin Lu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Hervé Sauquet
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, NSW, 2000, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Dezhu Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhiduan Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
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Ong HG, Kim Y, Lee J, Kim B, Kang D, Jung E, Shin J, Kim Y. Approximate Bayesian computation and ecological niche models elucidate the demographic history and current fragmented population distribution of a Korean endemic shrub. Ecol Evol 2023; 13:e10792. [PMID: 38077507 PMCID: PMC10700048 DOI: 10.1002/ece3.10792] [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: 04/06/2023] [Revised: 09/15/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Climatic fluctuations and geological events since the LGM are believed to have significantly impacted the population size, distribution, and mobility of many species that we observe today. In this paper, we determined the processes driving the phylogeographic structure of the Korean endemic white forsythia by combining the use of genome-wide SNPs and predicting paleoclimatic habitats during the LGM (21 kya), Early Holocene (10 kya), Mid-Holocene (6 kya), and Late Holocene (3 kya). Using a maximum of 1897 SNPs retrieved from 124 samples across nine wild populations, five environmental predictors, and the species' natural occurrence records, we aimed to infer the species' demographic history and reconstruct its possible paleodistributions with the use of approximate Bayesian computation and ecological niche models, respectively. Under this integrated framework, we found strong evidence for patterns of range shift and expansion, and population divergence events from the onset of the Holocene, resulting in the formation of its five distinct genetic units. The most highly supported model inferred that after the split of an ancestral population into the southern group and a larger central metapopulation lineage, the latter gave rise to the eastern and northern clusters, before finally dividing into two sub-central groups. While the use of molecular data allowed us to identify and refine the (phylo)genetic relationships of the species' lineages and populations, the use of ecological data helped us infer a past LGM refugium and the directions of post-glacial range dynamics. The time frames of these demographic events were shown to be congruent with climatic and geological events that affected the central Korean Peninsula during these periods. These findings gave us a better understanding of the consequences of past spatiotemporal factors that may have resulted in the current fragmented population distribution of this endangered plant.
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Affiliation(s)
| | - Yong‐In Kim
- On Biological Resource Research Institute (OBRRI)ChuncheonSouth Korea
| | - Jung‐Hoon Lee
- On Biological Resource Research Institute (OBRRI)ChuncheonSouth Korea
| | - Bo‐Yun Kim
- National Institute of Biological Resources (NIBR)IncheonSouth Korea
| | - Dae‐Hyun Kang
- Korea National Park Research InstituteWonjuSouth Korea
| | - Eui‐Kwon Jung
- Department of Life ScienceHallym UniversityChuncheonSouth Korea
| | - Jae‐Seo Shin
- Department of Life ScienceHallym UniversityChuncheonSouth Korea
| | - Young‐Dong Kim
- Multidisciplinary Genome InstituteHallym UniversityChuncheonSouth Korea
- Department of Life ScienceHallym UniversityChuncheonSouth Korea
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Han Q, Liu Y, Jiang H, Chen X, Feng H. Evaluation of Climate Change Impacts on the Potential Distribution of Wild Radish in East Asia. PLANTS (BASEL, SWITZERLAND) 2023; 12:3187. [PMID: 37765351 PMCID: PMC10534784 DOI: 10.3390/plants12183187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023]
Abstract
Climate change can exert a considerable influence on the geographic distribution of many taxa, including coastal plants and populations of some plant species closely related to those used as agricultural crops. East Asian wild radish, Raphanus raphanistrum subsp. sativus, is an annual coastal plant that is a wild relative of the cultivated radish (R. sativus). It has served as source of genetic material that has been helpful to develop and improve the quality and yield of radish crops. To assess the impact of climate change on wild radish in East Asia, we analyzed its distribution at different periods using the maximum entropy model (MaxEnt). The results indicated that the precipitation of the driest month (bio14) and precipitation seasonality (bio15) were the two most dominant environmental factors that affected the geographical distribution of wild radish in East Asia. The total potential area suitable for wild radish is 102.5574 × 104 km2, mainly located along the seacoasts of southern China, Korea, and the Japanese archipelago. Compared with its current distribution regions, the potentially suitable areas for wild radish in the 2070s will further increase and expand northwards in Japan, especially on the sand beach habitats of Hokkaido. This research reveals the spatiotemporal changes for the coastal plant wild radish under global warming and simultaneously provides a vital scientific basis for effective utilization and germplasm innovation for radish cultivars to achieve sustainable agriculture development.
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Affiliation(s)
- Qingxiang Han
- College of Life Sciences, Zaozhuang University, Zaozhuang 277160, China;
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China;
| | - Ye Liu
- School of Environmental Studies, University of Geosciences (Wuhan), Wuhan 430078, China;
| | - Hongsheng Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China;
| | - Xietian Chen
- Wuhan Britain-China School, Wuhan 430030, China;
| | - Huizhe Feng
- College of Life Sciences, Zaozhuang University, Zaozhuang 277160, China;
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Liu G, Xue G, Zhao T, Li Y, Yue L, Song H, Liu Q. Population structure and phylogeography of three closely related tree peonies. Ecol Evol 2023; 13:e10073. [PMID: 37274151 PMCID: PMC10234759 DOI: 10.1002/ece3.10073] [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: 03/16/2022] [Revised: 04/23/2023] [Accepted: 04/25/2023] [Indexed: 06/06/2023] Open
Abstract
Paeonia decomposita, Paeonia rotundiloba, and Paeonia rockii are three closely related species of Sect. Moutan is distributed in the montane area of the Eastern Hengduan Mountain region. Understanding the population history of these three tree peony species could contribute to unraveling the evolutionary patterns of undergrowth species in this hotspot area. We used one nuclear DNA marker (internal transcribed spacer region, ITS) and two chloroplast DNA markers (matK, ycf1) to reconstruct the phylogeographic pattern of the populations. In total, 228 individuals from 17 populations of the three species were analyzed in this study. Three nuclear clades (Clade I - Clade III) and four maternal clades (Clade A - Clade D) were reconstructed. Molecular dating suggested that young lineages diverged during the late Pliocene and early Pleistocene, younger than the uplift of the Hengduan Mountains but older than the last glacial maximum (LGM). Significant population and phylogeographic structures were detected at both markers. Furthermore, the populations of these tree peonies were overall at equilibrium during the climatic oscillations of the Pleistocene. The simulated palaeoranges of the three species during the LGM period mostly overlapped, which could have led to cross-breeding events. We propose an evolutionary scenario in which mountain orogenesis around the Hengduan Mountain area triggered parapatric isolation between maternal lineages of tree peonies. Subsequent climatic fluctuations drove migration and range recontact of these populations along the valleys. This detailed evolutionary history provides new insights into the phylogeographic pattern of species from mountain-valley systems.
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Affiliation(s)
- Guangli Liu
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Ge Xue
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Tingting Zhao
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Yang Li
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Liangliang Yue
- National Plateau Wetlands Research Center, College of WetlandsSouthwest Forestry UniversityKunmingChina
| | - Huixing Song
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Qinglin Liu
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
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Phylogenomics of Aralia sect. Aralia (Araliaceae): Signals of hybridization and insights into its species delimitations and intercontinental biogeography. Mol Phylogenet Evol 2023; 181:107727. [PMID: 36754338 DOI: 10.1016/j.ympev.2023.107727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023]
Abstract
Genome-scale data have significantly increased the number of informative characters for phylogenetic analyses and recent studies have also revealed widespread phylogenomic discordance in many plant lineages. Aralia sect. Aralia is a small plant lineage (14 spp.) of the ginseng family Araliaceae with a disjunct distribution between eastern Asia (11 spp.) and North America (3 spp.). We herein employ sequences of hundreds of nuclear loci and the complete plastomes using targeted sequence capture and genome skimming to reconstruct the phylogenetic and biogeographic history of this section. We detected substantial conflicts among nuclear genes, yet different analytical strategies generated largely congruent topologies from the nuclear data. Significant cytonuclear discordance was detected, especially concerning the positions of the three North American species. The phylogenomic results support two intercontinental disjunctions: (1) Aralia californica of western North America is sister to the eastern Asian clade consisting of A. cordata and A. continentalis in the nuclear tree, and (2) the eastern North American A. racemosa forms a clade with A. bicrenata from southwestern North America, and the North American A. racemosa - A. bicrenata clade is then sister to the eastern Asian clade consisting of A. glabra (Japan), A. fargesii (C China), and A. apioides and A. atropurpurea (the Hengduan Mountains). Aralia cordata is supported to be disjunctly distributed in Japan, Taiwan, the Ulleung island of Korea, and in Central, Southwest and South China, and Aralia continentalis is redefined with a narrower distribution in Northeast China, eastern Russia and peninsular Korea.
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Li X, Ruhsam M, Wang Y, Zhang HY, Fan XY, Zhang L, Wang J, Mao KS. Wind-dispersed seeds blur phylogeographic breaks: The complex evolutionary history of Populus lasiocarpa around the Sichuan Basin. PLANT DIVERSITY 2023; 45:156-168. [PMID: 37069930 PMCID: PMC10105135 DOI: 10.1016/j.pld.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 06/19/2023]
Abstract
The strength of phylogeographic breaks can vary among species in the same area despite being subject to the same geological and climate history due to differences in biological traits. Several important phylogeographic breaks exist around the Sichuan Basin in Southwest China but few studies have focused on wind-dispersed plants. Here, we investigated the phylogeographic patterns and the evolutionary history of Populus lasiocarpa, a wind-pollinated and wind-dispersed tree species with a circum-Sichuan Basin distribution in southwest China. We sequenced and analyzed three plastid DNA fragments (ptDNA) and eight nuclear microsatellites (nSSRs) of 265 individuals of P. lasiocarpa from 21 populations spanning the entire distribution range. Distribution patterns based on nSSR data revealed that there are three genetic groups in P. lasiocarpa. This is consistent with the three phylogeographic breaks (Sichuan Basin, the Kaiyong Line and the 105°E line), where the Sichuan basin acts as the main barrier to gene flow between western and eastern groups. However, the distribution pattern based on ptDNA haplotypes poorly matched the phylogeographic breaks, and wind-dispersed seeds may be one of the main contributing factors. Species distribution modelling suggested a larger potential distribution in the last glacial maximum with a severe bottleneck during the last interglacial. A DIYABC model also suggested a population contraction and expansion for both western and eastern lineages. These results indicate that biological traits are likely to affect the evolutionary history of plants, and that nuclear molecular markers, which experience higher levels of gene flow, might be better indicators of phylogeographic breaks.
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Affiliation(s)
- Xue Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Yi Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Hong-Ying Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Xiao-Yan Fan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Jing Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Kang-Shan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
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11
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Luo D, Song MS, Xu B, Zhang Y, Zhang JW, Ma XG, Hao XJ, Sun H. A clue to the evolutionary history of modern East Asian flora: insights from phylogeography and diterpenoid alkaloid distribution pattern of the Spiraea japonica complex. Mol Phylogenet Evol 2023; 184:107772. [PMID: 36977458 DOI: 10.1016/j.ympev.2023.107772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/07/2023] [Accepted: 03/21/2023] [Indexed: 03/28/2023]
Abstract
Each subkingdom of East Asian flora (EAF) has a unique evolutionary history, but which has rarely been described based on phylogeographic studies of EAF species. The Spiraea japonica L. complex, which is widespread in East Asia (EA), has received considerable attention because of the presence of diterpenoid alkaloids (DAs). It provides a proxy for understanding the genetic diversity and DA distribution patterns of species under various environmental conditions associated with the geological background in EA. In the present study, the plastome and chloroplast/nuclear DNA of 71 populations belonging to the S. japonica complex and its congeners were sequenced, combined with DA identification, environmental analyses, and ecological niche modelling, to investigate their phylogenetic relationships, genetic and DAs distribution patterns, biogeography, and demographic dynamics. An "ampliative" S. japonica complex was put forward, comprising all species of Sect. Calospira Ser. Japonicae, of which three evolutionary units carrying their respective unique types of DAs were identified and associated with the regionalization of EAF (referring to the Hengduan Mountains, central China, and east China). Moreover, a transition belt in central China with its biogeographic significance was revealed by genetic and DA distribution patterns from the perspective of ecological adaptation. The origin and onset differentiation of the "ampliative" S. japonica complex was estimated in the early Miocene (22.01/19.44 Ma). The formation of Japanese populations (6.75 Ma) was facilitated by the land bridge, which subsequently had a fairly stable demographic history. The populations in east China have undergone a founder effect after the Last Glacial Maximum, which may have been promoted by the expansion potential of polyploidization. Overall, the in-situ origin and diversification of the "ampliative" S. japonica complex since the early Miocene is a vertical section of the formation and development of modern EAF and was shaped by the geological history of each subkingdom.
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Affiliation(s)
- Dong Luo
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Min-Shu Song
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Bo Xu
- College of Forestry, Southwest Forestry University, Kunming 650224, China
| | - Yu Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Jian-Wen Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Xiang-Guang Ma
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Xiao-Jiang Hao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China.
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China.
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12
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Allopatric Lineage Divergence of the East Asian Endemic Herb Conandron ramondioides Inferred from Low-Copy Nuclear and Plastid Markers. Int J Mol Sci 2022; 23:ijms232314932. [PMID: 36499259 PMCID: PMC9740071 DOI: 10.3390/ijms232314932] [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: 10/21/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 12/02/2022] Open
Abstract
The evolutionary histories of ornamental plants have been receiving only limited attention. We examined the origin and divergence processes of an East Asian endemic ornamental plant, Conandron ramondioides. C. ramondioides is an understory herb occurring in primary forests, which has been grouped into two varieties. We reconstructed the evolutionary and population demography history of C. ramondioides to infer its divergence process. Nuclear and chloroplast DNA sequences were obtained from 21 Conandron populations on both sides of the East China Sea (ECS) to explore its genetic diversity, structure, and population differentiation. Interestingly, the reconstructed phylogeny indicated that the populations should be classified into three clades corresponding to geographical regions: the Japan (Honshu+Shikoku) clade, the Taiwan-Iriomote clade, and the Southeast China clade. Lineage divergence between the Japan clade and the Taiwan-Iriomote and Southeast China clades occured 1.14 MYA (95% HPD: 0.82-3.86), followed by divergence between the Taiwan-Iriomote and Southeast China clades approximately 0.75 MYA (95% HPD: 0.45-1.3). Furthermore, corolla traits (floral lobe length to tube length ratios) correlated with geographical distributions. Moreover, restricted gene flow was detected among clades. Lastly, the lack of potential dispersal routes across an exposed ECS seafloor during the last glacial maximum suggests that migration among the Conandron clades was unlikely. In summary, the extant Conandron exhibits a disjunct distribution pattern as a result of vicariance rather than long-distance dispersal. We propose that allopatric divergence has occurred in C. ramondioides since the Pleistocene. Our findings highlight the critical influence of species' biological characteristics on shaping lineage diversification of East Asian relic herb species during climate oscillations since the Quaternary.
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Jamal A, Wen J, Ma ZY, Ahmed I, Abdullah, Chen LQ, Nie ZL, Liu XQ. Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic Genus Chimonanthus (Calycanthaceae) With Implications For Its Phylogeny and Diversification. Front Genet 2021; 12:709996. [PMID: 34917123 PMCID: PMC8670589 DOI: 10.3389/fgene.2021.709996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Chimonanthus of Calycanthaceae is a small endemic genus in China, with unusual winter-blooming sweet flowers widely cultivated for ornamentals and medicinal uses. The evolution of Chimonanthus plastomes and its phylogenetic relationships remain unresolved due to limited availability of genetic resources. Here, we report fully assembled and annotated chloroplast genomes of five Chimonanthus species. The chloroplast genomes of the genus (size range 153,010 – 153,299 bp) reveal high similarities in gene content, gene order, GC content, codon usage, amino acid frequency, simple sequence repeats, oligonucleotide repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions. Signatures of positive selection are detected in atpF and rpoB genes in C. campanulatus. The correlations among substitutions, InDels, and oligonucleotide repeats reveal weak to strong correlations in distantly related species at the intergeneric levels, and very weak to weak correlations among closely related Chimonanthus species. Chloroplast genomes are used to reconstruct a well-resolved phylogenetic tree, which supports the monophyly of Chimonanthus. Within Chimonanthus, C. praecox and C. campanulatus form one clade, while C. grammatus, C. salicifolius, C. zhejiangensis, and C. nitens constitute another clade. Chimonanthus nitens appears paraphyletic and is closely related to C. salicifolius and C. zhejiangensis, suggesting the need to reevaluate the species delimitation of C. nitens. Chimonanthus and Calycanthus diverged in mid-Oligocene; the radiation of extant Chimonanthus species was dated to the mid-Miocene, while C. grammatus diverged from other Chimonanthus species in the late Miocene. C. salicifolius, C. nitens(a), and C. zhejiangensis are inferred to have diverged in the Pleistocene of the Quaternary period, suggesting recent speciation of a relict lineage in the subtropical forest regions in eastern China. This study provides important insights into the chloroplast genome features and evolutionary history of Chimonanthus and family Calycanthaceae.
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Affiliation(s)
- Abbas Jamal
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC, United States
| | - Zhi-Yao Ma
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC, United States
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
| | - Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Long-Qing Chen
- Southwest Engineering Technology and Research Center of Landscape Architecture, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Xiu-Qun Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
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14
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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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15
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Wang Z, Zhong C, Li D, Yan C, Yao X, Li Z. Cytotype distribution and chloroplast phylogeography of the Actinidia chinensis complex. BMC PLANT BIOLOGY 2021; 21:325. [PMID: 34229602 PMCID: PMC8259359 DOI: 10.1186/s12870-021-03099-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Plant phylogeographic studies of species in subtropical China have mainly focused on rare and endangered species, whereas few studies have been conducted on taxa with relatively wide distribution, especially polyploid species. We investigated the cytotype and haplotype distribution pattern of the Actinidia chinensis complex, a widespread geographically woody liana with variable ploidy in subtropical China comprising two varieties, with three chloroplast fragments DNA (ndhF-rpl132, rps16-trnQ and trnE-trnT). Macroevolutionary, microevolutionary and niche modeling tools were also combined to disentangle the origin and the demographic history of the species or cytotypes. RESULTS The ploidy levels of 3338 individuals from 128 populations sampled throughout the species distribution range were estimated with flow cytometry. The widespread cytotypes were diploids followed by tetraploids and hexaploids, whereas triploids and octoploids occurred in a few populations. Thirty-one chloroplast haplotypes were detected. The genetic diversity and genetic structure were found to be high between varieties (or ploidy races) chinensis and deliciosa. Our results revealed that these two varieties inhabit significantly different climatic niche spaces. Ecological niche models (ENMs) indicate that all varieties' ranges contracted during the Last Inter Glacial (LIG), and expanded eastward or northward during the Last Glacial Maximum (LGM). CONCLUSIONS Pliocene and Plio-Pleistocene climatic fluctuations and vicariance appear to have played key roles in shaping current population structure and historical demography in the A. chinensis complex. The polyploidization process also appears to have played an important role in the historical demography of the complex through improving their adaptability to environmental changes.
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Affiliation(s)
- Zhi Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caihong Zhong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Dawei Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Chunlin Yan
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Xiaohong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
| | - Zuozhou Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
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16
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Sakaguchi S, Asaoka Y, Takahashi D, Isagi Y, Imai R, Nagano AJ, Qiu YX, Li P, Lu R, Setoguchi H. Inferring historical survivals of climate relicts: the effects of climate changes, geography, and population-specific factors on herbaceous hydrangeas. Heredity (Edinb) 2021; 126:615-629. [PMID: 33510468 PMCID: PMC8115046 DOI: 10.1038/s41437-020-00396-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 11/25/2020] [Accepted: 12/08/2020] [Indexed: 01/29/2023] Open
Abstract
Climate relicts hold considerable importance because they have resulted from numerous historical changes. However, there are major interspecific variations among the ways by which they survived climate changes. Therefore, investigating the factors and timing that affected population demographics can expand our understanding of how climate relicts responded to historical environmental changes. Here, we examined herbaceous hydrangeas of genus Deinanthe in East Asia, which show limited distributions and a remarkable disjunction between Japan and central China. Chloroplast genome and restriction site-associated DNA sequencing revealed that speciation event occurred in the late Miocene (ca. 7-9 Mya) in response to global climate change. Two lineages apparently remained not branched until the middle Quaternary, and afterwards started to diverge to regional population groups. The narrow endemic species in central China showed lower genetic diversity (He = 0.082), as its population size rapidly decreased during the Holocene due to isolation in montane refugia. Insular populations in the three Japanese islands (He = 0.137-0.160) showed a genetic structure that was inconsistent with sea barriers, indicating that it was shaped in the glacial period when its range retreated to coastal refugia on the exposed sea floor. Demographic modelling by stairway-plot analysis reconstructed variable responses of Japanese populations: some experienced glacial bottlenecks in refugial isolation, while post-glacial range expansion seemingly exerted founder effects on other populations. Overall, this study demonstrated the involvement of not just one, but multiple factors, such as the interplay between climate changes, geography, and other population-specific factors, that determine the demographics of climate relicts.
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Affiliation(s)
- Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, 606-8501, Japan.
| | - Yui Asaoka
- Faculty of Integrated Human Studies, Kyoto University, Kyoto, 606-8501, Japan
- Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan
| | - Daiki Takahashi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, 606-8501, Japan
| | - Yuji Isagi
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Ryosuke Imai
- Iriomote Station, Tropical Biosphere Research Centre, University of the Ryukyus, Okinawa, 907-1541, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Shiga, 520-2194, Japan
| | - Ying-Xiong Qiu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Pan Li
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ruisen Lu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, 606-8501, Japan
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17
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Zhao YJ, Yin GS, Pan YZ, Tian B, Gong X. Climatic Refugia and Geographical Isolation Contribute to the Speciation and Genetic Divergence in Himalayan-Hengduan Tree Peonies ( Paeonia delavayi and Paeonia ludlowii). Front Genet 2021; 11:595334. [PMID: 33584794 PMCID: PMC7874331 DOI: 10.3389/fgene.2020.595334] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 12/21/2020] [Indexed: 11/13/2022] Open
Abstract
Himalaya and Hengduan Mountains (HHM) is a biodiversity hotspot, and very rich in endemic species. Previous phylogeographical studies proposed different hypotheses (vicariance and climate-driven speciation) in explaining diversification and the observed pattern of extant biodiversity, but it is likely that taxa are forming in this area in species-specific ways. Here, we reexplored the phylogenetic relationship and tested the corresponding hypotheses within Paeonia subsect. Delavayanae composed of one widespread species (Paeonia delavayi) and the other geographically confined species (Paeonia ludlowii). We gathered genetic variation data at three chloroplast DNA fragments and one nuclear gene from 335 individuals of 34 populations sampled from HHM. We performed a combination of population genetic summary statistics, isolation-with-migration divergence models, isolation by environment, and demographic history analyses. We found evidence for the current taxonomic treatment that P. ludlowii and P. delavayi are two different species with significant genetic differentiation. The significant isolation by environment was revealed within all sampled populations but genetic distances only explained by geographical distances within P. delavayi populations. The results of population divergence models and demographic history analyses indicated a progenitor–derivative relationship and the Late Quaternary divergence without gene flow between them. The coalescence of all sampled cpDNA haplotypes could date to the Late Miocene, and P. delavayi populations probably underwent a severe bottleneck in population size during the last glacial period. Genetic variation in Paeonia subsect. Delavayanae is associated with geographical and environmental distances. These findings point to the importance of geological and climatic changes as causes of the speciation event and lineage diversification within Paeonia subsect. Delavayanae.
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Affiliation(s)
- Yu-Juan Zhao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, China.,Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, China
| | - Gen-Shen Yin
- College of Agriculture and Life Sciences, Kunming University, Chinese Academy of Sciences (CAS), Kunming, China
| | - Yue-Zhi Pan
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, China
| | - Bo Tian
- Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, China.,Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, China
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18
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Meng H, Wu H, Wei X, Jiang M. Adaptive strategies and driving factors of a montane riparian tree: Trait-specific mechanisms across latitude. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:141578. [PMID: 33370904 DOI: 10.1016/j.scitotenv.2020.141578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 06/12/2023]
Abstract
Investigating the drivers of phenotypic and genetic divergence can reveal the underlying processes and strategies that species adopt in rapidly changing environments. However, knowledge of adaptive strategies and the underlying mechanisms is lacking for the majority of taxa, especially those living in habitats sensitive to climate change. Here, we investigated 20 populations of a Tertiary-relict tree species, Euptelea pleiospermum (Eupteleaceae), scattered in a mountain riparian habitat in China. We integrated genetic, growth, and reproductive traits, and evaluated the relative contributions of climatic and soil factors on genetic and functional trait divergence. The E. pleiospermum populations were divided into south and north genetic clusters, and there were significant differences in leaf density and seed mass of adult trees between the two. The spatial pattern of genetic divergence resulted from effects of both isolation by distance (IBD) and isolation by environment (IBE), whereas the divergence of growth and reproductive traits resulted solely from IBE effects. Spatial distance and selection by temperature and soils played dominant roles in genetic divergence. Precipitation drove the spatial divergence of sprouting. Both divergence of leaf density and seed mass were prominently induced by genetic divergence, and the influences might be enhanced by temperature and soil nutrients. We infer that E. pleiospermum populations adopt a resource-conservative strategy with low growth rates and higher sprouting under flooding disturbance, with larger seeds for improved seedling recruitment at lower latitudes. In contrast, high growth rate and sexual reproduction with small seeds are strategies adopted by populations at higher latitudes. We conclude that sprouting reflects a plastic response to precipitation, and leaf density and seed mass reflect local adaption under selection by temperature and soil factors. The underlying mechanisms of species adaptation strategies were trait-specific. Temperature and soil conditions are likely the main ecological factors shaping plant divergence in montane riparian regions.
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Affiliation(s)
- Hongjie Meng
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Hao Wu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xinzeng Wei
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Mingxi Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China.
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19
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The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements. Genome Biol 2020; 21:291. [PMID: 33267872 PMCID: PMC7709256 DOI: 10.1186/s13059-020-02198-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 11/06/2020] [Indexed: 12/25/2022] Open
Abstract
Background Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species. Results Here, we report a chromosome-scale assembly of the T. sinense genome. We assemble the 1.07 Gb genome sequence into 24 chromosomes and annotate 32,690 protein-coding genes. Phylogenomic analyses verify that the Trochodendrales and core eudicots are sister lineages and showed that two whole-genome duplications occurred in the Trochodendrales approximately 82 and 59 million years ago. Synteny analyses suggest that the γ event, resulting in paleohexaploidy, may have only happened in core eudicots. Interestingly, we find that vessel elements are present in T. sinense, which has two orthologs of AtVND7, the master regulator of vessel formation. T. sinense also has several key genes regulated by or regulating TsVND7.2 and their regulatory relationship resembles that in Arabidopsis thaliana. Resequencing and population genomics reveals high levels of genetic diversity of T. sinense and identifies four refugia in China. Conclusions The T. sinense genome provides a unique reference for inferring the early evolution of eudicots and the mechanisms underlying vessel element formation. Population genomics analysis of T. sinense reveals its genetic diversity and geographic structure with implications for conservation. Supplementary information The online version contains supplementary material available at 10.1186/s13059-020-02198-7.
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Zhu S, Chen J, Zhao J, Comes HP, Li P, Fu C, Xie X, Lu R, Xu W, Feng Y, Ye W, Sakaguchi S, Isagi Y, Li L, Lascoux M, Qiu Y. Genomic insights on the contribution of balancing selection and local adaptation to the long-term survival of a widespread living fossil tree, Cercidiphyllum japonicum. THE NEW PHYTOLOGIST 2020; 228:1674-1689. [PMID: 32643803 DOI: 10.1111/nph.16798] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 06/27/2020] [Indexed: 05/25/2023]
Abstract
'Living fossils' are testimonies of long-term sustained ecological success, but how demographic history and natural selection contributed to their survival, resilience, and persistence in the face of Quaternary climate fluctuations remains unclear. To better understand the interplay between demographic history and selection in shaping genomic diversity and evolution of such organisms, we assembled the whole genome of Cercidiphyllum japonicum, a widespread East Asian Tertiary relict tree, and resequenced 99 individuals of C. japonicum and its sister species, Cercidiphyllum magnificum (Central Japan). We dated this speciation event to the mid-Miocene, and the intraspecific lineage divergence of C. japonicum (China vs Japan) to the Early Pliocene. Throughout climatic upheavals of the late Tertiary/Quaternary, population bottlenecks greatly reduced the genetic diversity of C. japonicum. However, this polymorphism loss was likely counteracted by, first, long-term balancing selection at multiple chromosomal and heterozygous gene regions, potentially reflecting overdominance, and, second, selective sweeps at stress response and growth-related genes likely involved in local adaptation. Our findings contribute to a better understanding of how living fossils have survived climatic upheaval and maintained an extensive geographic range; that is, both types of selection could be major factors contributing to the species' survival, resilience, and persistence.
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Affiliation(s)
- Shanshan Zhu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jun Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jing Zhao
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Hans Peter Comes
- Department of Biosciences, Salzburg University, Salzburg, A-5020, Austria
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Chengxin Fu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xiao Xie
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Ruisen Lu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wuqin Xu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yu Feng
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wenqing Ye
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics and Science for Life Laboratory, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Yingxiong Qiu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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Phylogeny, Taxonomy, and Biogeography of Pterocarya (Juglandaceae). PLANTS 2020; 9:plants9111524. [PMID: 33182441 PMCID: PMC7696814 DOI: 10.3390/plants9111524] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/02/2020] [Accepted: 11/06/2020] [Indexed: 12/11/2022]
Abstract
Relict species play an important role in understanding the biogeography of intercontinental disjunctions. Pterocarya (a relict genus) is the valuable model taxon for studying the biogeography of East Asian versus southern European/West Asian disjunct patterns. This disjunction has not been as well studied as others (e.g., between Eastern Asia and North America). Several phylogenetic studies on Pterocarya have been conducted, but none have provided a satisfactory phylogenetic resolution. Here, we report the first well-resolved phylogeny of Pterocarya using restriction site-associated DNA sequencing data based on the sampling of all taxa across the entire distribution area of the genus. Taxonomic treatments were also clarified by combining morphological traits. Furthermore, fossil-calibrated phylogeny was used to explore the biogeography of Pterocarya. Our results support the existence of two sections in Pterocarya, which is in accordance with morphological taxonomy. Section Platyptera comprises three species: P. rhoifolia, P. macroptera, and P. delavayi. Section Pterocarya also comprises three species: P. fraxinifolia, P. hupehensis, and P. stenoptera. The divergence between the two sections took place during the early Miocene (20.5 Ma). The formation of the Gobi Desert and climate cooling of northern Siberia in the Middle Miocene (15.7 Ma) might have caused the split of the continuous distribution of this genus and the formation of the East Asian versus southern European/West Asian disjunct pattern. Lastly, the divergence between P. hupehensis and P. stenoptera as well as between P. rhoifolia and P. macroptera/P. delavayi (10.0 Ma) supports the late Miocene diversification hypothesis in East Asia.
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Feng S, Liu Z, Hu Y, Tian J, Yang T, Wei A. Genomic analysis reveals the genetic diversity, population structure, evolutionary history and relationships of Chinese pepper. HORTICULTURE RESEARCH 2020; 7:158. [PMID: 33082965 PMCID: PMC7527552 DOI: 10.1038/s41438-020-00376-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 07/07/2020] [Accepted: 07/13/2020] [Indexed: 05/26/2023]
Abstract
Chinese pepper, mainly including Zanthoxylum bungeanum and Zanthoxylum armatum, is an economically important crop popular in Asian countries due to its unique taste characteristics and potential medical uses. Numerous cultivars of Chinese pepper have been developed in China through long-term domestication. To better understand the population structure, demographic history, and speciation of Chinese pepper, we performed a comprehensive analysis at a genome-wide level by analyzing 38,395 genomic SNPs that were identified in 112 cultivated and wild accessions using a high-throughput genome-wide genotyping-by-sequencing (GBS) approach. Our analysis provides genetic evidence of multiple splitting events occurring between and within species, resulting in at least four clades in Z. bungeanum and two clades in Z. armatum. Despite no evidence of recent admixture between species, we detected substantial gene flow within species. Estimates of demographic dynamics and species distribution modeling suggest that climatic oscillations during the Pleistocene (including the Penultimate Glaciation and the Last Glacial Maximum) and recent domestication events together shaped the demography and evolution of Chinese pepper. Our analyses also suggest that southeastern Gansu province is the most likely origin of Z. bungeanum in China. These findings provide comprehensive insights into genetic diversity, population structure, demography, and adaptation in Zanthoxylum.
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Affiliation(s)
- Shijing Feng
- College of Forestry, Northwest A&F University, Yangling, 712100 Shaanxi China
- College of Life Science, Northwest A&F University, Yangling, 712100 Shaanxi China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, 712100 Shaanxi China
| | - Zhenshan Liu
- College of Life Science, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yang Hu
- College of Forestry, Northwest A&F University, Yangling, 712100 Shaanxi China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, 712100 Shaanxi China
| | - Jieyun Tian
- College of Forestry, Northwest A&F University, Yangling, 712100 Shaanxi China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, 712100 Shaanxi China
| | - Tuxi Yang
- College of Forestry, Northwest A&F University, Yangling, 712100 Shaanxi China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, 712100 Shaanxi China
| | - Anzhi Wei
- College of Forestry, Northwest A&F University, Yangling, 712100 Shaanxi China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, 712100 Shaanxi China
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Cao Y, Zhu S, Chen J, Comes HP, Wang IJ, Chen L, Sakaguchi S, Qiu Y. Genomic insights into historical population dynamics, local adaptation, and climate change vulnerability of the East Asian Tertiary relict Euptelea (Eupteleaceae). Evol Appl 2020; 13:2038-2055. [PMID: 32908603 PMCID: PMC7463308 DOI: 10.1111/eva.12960] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 02/28/2020] [Accepted: 03/17/2020] [Indexed: 12/24/2022] Open
Abstract
The warm-temperate and subtropical climate zones of East Asia are a hotspot of plant species richness and endemism, including a noticeable number of species-poor Tertiary relict tree genera. However, little is understood about when East Asian Tertiary relict plants diversified, how they responded demographically to past environmental change, and to what extent their current genomic composition (and adaptive capacity) might mitigate the effects of global warming. Here, we obtained genomic (RAD-SNP) data for 171 samples from two extant species of Euptelea in China (24 E. pleiosperma populations) and Japan (11 E. polyandra populations) to elucidate their divergence and demographic histories, genome-wide associations with current environmental variables, and genomic vulnerability to future climate change. Our results indicate that Late Miocene changes in climate and/or sea level promoted species divergence, whereas Late Pliocene uplifting in southwest China likely fostered lineage divergence within E. pleiosperma. Its subsequent range expansion into central/east (CE) China bears genomic signatures of climate-driven selection, yet extant CE populations are predicted to be most vulnerable to future climate change. For E. polyandra, geography was the only significant predictor of genomic variation. Our findings indicate a profound impact of Late Neogene geological and climate change on the evolutionary history of Euptelea, with much stronger signals of local adaptation left in China than in Japan. This study deepens our understanding of the complex evolutionary forces that influence the distribution of genetic variation of Tertiary relict trees, and provides insights into their susceptibility to global change and potential for adaptive responses. Our results lay the groundwork for future conservation and restoration programs for Euptelea.
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Affiliation(s)
- Ya‐Nan Cao
- Systematic & Evolutionary Botany and Biodiversity GroupMOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouChina
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouChina
| | - Shan‐Shan Zhu
- Systematic & Evolutionary Botany and Biodiversity GroupMOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouChina
| | - Jun Chen
- Systematic & Evolutionary Botany and Biodiversity GroupMOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouChina
| | - Hans P. Comes
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Ian J. Wang
- Department of Environmental Science, Policy, and ManagementUniversity of California BerkeleyBerkeleyCAUSA
| | - Lu‐Yao Chen
- Systematic & Evolutionary Botany and Biodiversity GroupMOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouChina
| | - Shota Sakaguchi
- Graduate School of Human and Environmental StudiesKyoto UniversityKyotoJapan
| | - Ying‐Xiong Qiu
- Systematic & Evolutionary Botany and Biodiversity GroupMOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouChina
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24
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Zheng Y, Dai Q, Guo X, Zeng X. Dynamics behind disjunct distribution, hotspot-edge refugia, and discordant RADseq/mtDNA variability: insights from the Emei mustache toad. BMC Evol Biol 2020; 20:111. [PMID: 32859147 PMCID: PMC7456009 DOI: 10.1186/s12862-020-01675-8] [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: 12/04/2019] [Accepted: 08/20/2020] [Indexed: 12/01/2022] Open
Abstract
Background The distribution of genetic diversity and the underlying processes are important for conservation planning but are unknown for most species and have not been well studied in many regions. In East Asia, the Sichuan Basin and surrounding mountains constitute an understudied region that exhibits a “ring” of high species richness overlapping the eastern edge of the global biodiversity hotspot Mountains of Southwest China. We examine the distributional history and genetic diversification of the Emei mustache toad Leptobrachium boringii, a typical “ring” element characterized by disjunct ranges in the mountains, by integrating time-calibrated gene tree, genetic variability, individual-level clustering, inference of population splitting and mixing from allele frequencies, and paleoclimatic suitability modeling. Results The results reveal extensive range dynamics, including secondary contact after long-term isolation via westward dispersal accompanied by variability loss. They allow the proposal of a model that combines recurrent contractions caused by Quaternary climatic changes and some failed expansions under suitable conditions for explaining the shared disjunct distribution pattern. Providing exceptional low-elevation habitats in the hotspot area, the eastern edge harbors both long-term refugial and young immigrant populations. This finding and a synthesis of evidence from other taxa demonstrate that a certain contributor to biodiversity, one that preserves and receives low-elevation elements of the east in this case, can be significant for only a particular part of a hotspot. By clarifying the low variability of these refugial populations, we show that discordant mitochondrial estimates of diversity can be obtained for populations that experienced admixture, which would have unlikely left proportional immigrant alleles for each locus. Conclusions Dispersal after long-term isolation can explain much of the spatial distribution of genetic diversity in this species, while secondary contact and long-term persistence do not guarantee a large variation. The model for the formation of disjunct ranges may apply to many other taxa isolated in the mountains surrounding the Sichuan Basin. Furthermore, this study provides insights into the heterogeneous nature of hotspots and discordant variability obtained from genome-wide and mitochondrial data.
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Affiliation(s)
- Yuchi Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, #9 of Section 4, Ren-Min-Nan Road, Wuhou District, Chengdu, 610041, Sichuan Province, China. .,Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, Sichuan Province, China.
| | - Qiang Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, #9 of Section 4, Ren-Min-Nan Road, Wuhou District, Chengdu, 610041, Sichuan Province, China
| | - Xianguang Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, #9 of Section 4, Ren-Min-Nan Road, Wuhou District, Chengdu, 610041, Sichuan Province, China
| | - Xiaomao Zeng
- Chengdu Institute of Biology, Chinese Academy of Sciences, #9 of Section 4, Ren-Min-Nan Road, Wuhou District, Chengdu, 610041, Sichuan Province, China
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25
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Xiao JH, Ding X, Li L, Ma H, Ci XQ, van der Merwe M, Conran JG, Li J. Miocene diversification of a golden-thread nanmu tree species ( Phoebe zhennan, Lauraceae) around the Sichuan Basin shaped by the East Asian monsoon. Ecol Evol 2020; 10:10543-10557. [PMID: 33072279 PMCID: PMC7548194 DOI: 10.1002/ece3.6710] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 01/04/2023] Open
Abstract
Understanding the role of climate changes and geography as drivers of population divergence and speciation is a long‐standing goal of evolutionary biology and can inform conservation. In this study, we used restriction site‐associated DNA sequencing (RAD‐seq) to evaluate genetic diversity, population structure, and infer demographic history of the endangered tree, Phoebe zhennan which is distributed around the Sichuan Basin. Genomic patterns revealed two distinct clusters, each largely confined to the West and East. Despite sympatry of the two genomic clusters at some sites, individuals show little or no evidence of genomic introgression. Demographic modeling supported an initial divergence time between the West and East lineages at ~15.08 Ma with further diversification within the West lineage at ~7.12 Ma. These times largely coincide with the two independent intensifications of the East Asian monsoon that were initiated during the middle (Langhian) and late Miocene (Messinian), respectively. These results suggest that the Miocene intensification phases of the East Asian monsoon played a pivotal role in shaping the current landscape‐level patterns of genetic diversity within P. zhennan, as has been found for the interspecific divergence of other subtropical Chinese plants. Based on isolation‐by‐distance and species distribution modeling, we hypothesize that P. zhennan followed a ring diversification which was facilitated by the Sichuan Basin acting as barrier to gene flow. In situ and ex situ conservation management plans should consider the results obtained in this study to help secure the future of this beautiful and culturally significant endangered tree.
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Affiliation(s)
- Jian-Hua Xiao
- Plant Phylogenetics and Conservation Group Centre for Integrative Conservation Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Kunming China.,University of Chinese Academy of Sciences Beijing China
| | - Xin Ding
- Department of Landscape Architecture Guangdong Eco-engineering Polytechnic Guangzhou China
| | - Lang Li
- Plant Phylogenetics and Conservation Group Centre for Integrative Conservation Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Kunming China.,Center of Conservation Biology Core Botanical Gardens Chinese Academy of Sciences Mengla China
| | - Hui Ma
- Plant Phylogenetics and Conservation Group Centre for Integrative Conservation Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Kunming China
| | - Xiu-Qin Ci
- Plant Phylogenetics and Conservation Group Centre for Integrative Conservation Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Kunming China.,Center of Conservation Biology Core Botanical Gardens Chinese Academy of Sciences Mengla China
| | - Marlien van der Merwe
- Research Centre for Ecological Resilience Australian Institute of Botanical Science The Royal Botanic Garden Sydney Sydney NSW Australia
| | - John G Conran
- Australian Centre for Evolutionary Biology and Biodiversity (ACEBB) Sprigg Geobiology Centre (SGC) School of Biological Sciences The University of Adelaide Adelaide SA Australia
| | - Jie Li
- Plant Phylogenetics and Conservation Group Centre for Integrative Conservation Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Kunming China.,Center of Conservation Biology Core Botanical Gardens Chinese Academy of Sciences Mengla China
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Fujiwara T, Watano Y. Independent allopatric polyploidizations shaped the geographical structure and initial stage of reproductive isolation in an allotetraploid fern, Lepisorus nigripes (Polypodiaceae). PLoS One 2020; 15:e0233095. [PMID: 32433707 PMCID: PMC7239481 DOI: 10.1371/journal.pone.0233095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/28/2020] [Indexed: 11/29/2022] Open
Abstract
Although polyploidy is pervasive and its evolutionary significance has been recognized, it remains unclear how newly formed polyploid species become established. In particular, the impact of multiple origins on genetic differentiation among populations of a polyploid species and whether lineages of independent origins have different evolutionary potentials remain open questions. We used population genetic and phylogenetic approaches to identify genetic differentiation between lineages with independent origins within an allotetraploid fern, Lepisorus nigripes. A total of 352 individuals from 51 populations were collected throughout the distribution range. To examine the genetic structure, multilocus genotyping, Bayesian population structure analysis, and neighbor-net analysis were carried out using single-copy nuclear genes. Phylogenetic trees were constructed to detect recurrent polyploid origins. Proportions of abortive spores were analysed as the measure of postzygotic reproductive isolation. Two genetically distinct lineages, the East-type and the West-type, were distributed mainly in the eastern and western parts, respectively, of the Japanese archipelago. Phylogenetic analyses indicated independent origins of these types and detected additional independent origins within each type. We also revealed limited genetic recombination between both types, even in their sympatric regions. F1 hybrids between the East- and West-types showed a reduction in fertility. It is likely that the East- and West-types formed independently in the eastern and western parts of Japan, respectively. The limited genetic recombination and reduced fertility of hybrids suggest that the two types are at an incipient stage of speciation. Two polyploid lineages with independent geographic origins could develop reproductive isolation barrier(s).
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Affiliation(s)
- Tao Fujiwara
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
- * E-mail:
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
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27
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Deng JY, Fu RH, Compton SG, Liu M, Wang Q, Yuan C, Zhang LS, Chen Y. Sky islands as foci for divergence of fig trees and their pollinators in southwest China. Mol Ecol 2020; 29:762-782. [PMID: 31943487 DOI: 10.1111/mec.15353] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 11/26/2019] [Accepted: 01/03/2020] [Indexed: 12/11/2022]
Abstract
The dynamics of populations and their divergence over time have shaped current levels of biodiversity and in the case of the "sky islands" of mountainous southwest (SW) China have resulted in an area of exceptional botanical diversity. Ficus tikoua is a prostrate fig tree subendemic to the area that displays unique intraspecific diversity, producing figs typical of different pollination modes in different parts of its range. By combining climate models, genetic variation in populations of the tree's obligate fig wasp pollinators and distributions of the different plant phenotypes, we examined how this unusual situation may have developed. We identified three genetically distinct groups of a single Ceratosolen pollinator species that have largely parapatric distributions. The complex topography of the region contributed to genetic divergence among the pollinators by facilitating geographical isolation and providing refugia. Migration along elevations in response to climate oscillations further enhanced genetic differentiation of the three pollinator groups. Their distributions loosely correspond to the distributions of the functionally significant morphological differences in the male figs of their host plants, but postglacial expansion of one group has not been matched by spread of its associated plant phenotype, possibly due to a major river barrier. The results highlight how interplay between the complex topography of the "sky island" complex and climate change has shaped intraspecies differentiation and relationships between the plant and its pollinator. Similar processes may explain the exceptional botanical diversity of SW China.
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Affiliation(s)
- Jun-Yin Deng
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China.,Division of Genetics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Rong-Hua Fu
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | | | - Mei Liu
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Qin Wang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Chuan Yuan
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Lu-Shui Zhang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Yan Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
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28
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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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29
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Boo GH, Qiu YX, Kim JY, Ang PO, Bosch S, De Clerck O, He P, Higa A, Huang B, Kogame K, Liu SL, van Nguyen T, Suda S, Terada R, Miller KA, Boo SM. Contrasting patterns of genetic structure and phylogeography in the marine agarophytes Gelidiophycus divaricatus and G. freshwateri (Gelidiales, Rhodophyta) from East Asia. JOURNAL OF PHYCOLOGY 2019; 55:1319-1334. [PMID: 31390066 DOI: 10.1111/jpy.12910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
The evolutionary and population demographic history of marine red algae in East Asia is poorly understood. Here, we reconstructed the phylogeographies of two upper intertidal species endemic to East Asia, Gelidiophycus divaricatus and G. freshwateri. Phylogenetic and phylogeographic inferences of 393 mitochondrial cox1, 128 plastid rbcL, and 342 nuclear ITS2 sequences were complemented with ecological niche models. Gelidiophycus divaricatus, a southern species adapted to warm water, is characterized by a high genetic diversity and a strong geographical population structure, characteristic of stable population sizes and sudden reduction to recent expansion. In contrast, G. freshwateri, a northern species adapted to cold temperate conditions, is genetically relatively homogeneous with a shallow population structure resulting from steady population growth and recent equilibrium. The overlap zone of the two species roughly matches summer and winter isotherms, indicating that surface seawater temperature is a key feature influencing species range. Unidirectional genetic introgression was detected at two sites on Jeju Island where G. divaricatus was rare while G. freshwateri was common, suggesting the occurrence of asymmetric natural hybrids, a rarely reported event for rhodophytes. Our results illustrate that Quaternary climate oscillations have left strong imprints on the current day genetic structure and highlight the importance of seawater temperature and sea level change in driving speciation in upper intertidal seaweed species.
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Affiliation(s)
- Ga Hun Boo
- University Herbarium, University of California, 1001 Valley Life Sciences Building #2465, Berkeley, California, 94720, USA
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
| | - 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
| | - Jung Yeon Kim
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Put O Ang
- Marine Science Laboratory, The Chinese University of Hong Kong, Shatin N.T, Hong Kong SAR, China
| | - Samuel Bosch
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), 9000, Gent, Belgium
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), 9000, Gent, Belgium
| | - Peimin He
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Atsushi Higa
- Okinawa Environmental Analysis Center Co. Ltd, 3-7-24 Maehara, Ginowan, Okinawa, 901-2215, Japan
| | - Bangqin Huang
- Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Fujian, China
| | - Kazuhiro Kogame
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Shao-Lun Liu
- Department of Life Science, Tunghai University, Taichung, 40704, Taiwan
| | - Tu van Nguyen
- Department of Ecology, Institute of Tropical Biology, Vietnam Academy of Science and Technology, 85 Tran Quoc Toan, District 3, Ho Chi Minh City, Vietnam
| | - Shoichiro Suda
- Department of Chemistry, Biology & Marine Science, Faculty of Science, University of the Ryukyus, Okinawa, 903-0213, Japan
| | - Ryuta Terada
- United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto 1-21-24, Kagoshima, 890-0065, Japan
| | - Kathy Ann Miller
- University Herbarium, University of California, 1001 Valley Life Sciences Building #2465, Berkeley, California, 94720, USA
| | - Sung Min Boo
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
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30
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Lu RS, Chen Y, Tamaki I, Sakaguchi S, Ding YQ, Takahashi D, Li P, Isaji Y, Chen J, Qiu YX. Pre-quaternary diversification and glacial demographic expansions of Cardiocrinum (Liliaceae) in temperate forest biomes of Sino-Japanese Floristic Region. Mol Phylogenet Evol 2019; 143:106693. [PMID: 31778814 DOI: 10.1016/j.ympev.2019.106693] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/11/2019] [Accepted: 11/22/2019] [Indexed: 11/27/2022]
Abstract
The Sino-Japanese Floristic Region (SJFR) in East Asia is one of the most diverse temperate floras in the world. However, the relative influence of Neogene palaeogeographical changes and Quaternary climatic fluctuations as causal mechanisms on species diversification remains largely controversial, because most divergence time estimates were inferred from single-locus data and have limited geographic or taxonomic sampling. To evaluate these influences, we use SNP markers from restriction site-associated DNA sequencing (RAD-Seq) loci and expressed sequence tags-simple sequence repeat (EST-SSR) markers to investigate the levels of genetic variation, speciation and demographic history of the temperate-deciduous forest (TDF) endemic Cardiocrinum (Endlicher) Lindley (Liliaceae), a genus comprising three species in China (C. giganteum, C. cathayanum) and Japan (C. cordatum). Phylogenomic and population genomic coalescent-based analyses demonstrated that Late Neogene tectonic/climatic events triggered speciation of Cardiocrinum, and Pleistocene climatic fluctuations had limited influence on its divergence history. Population demographic inference using Approximate Bayesian Computation from EST-SSRs and palaeoclimatic niche models both indicated that all three Cardiocrinum species experienced population expansions during the transition from the LIG to the LGM. We also discussed the implications of these results on the conservation of montane TDF species in the SJFR under ongoing environmental change. Our results improve our understanding of how the constituents of montane TDF across the SJFR responded to previous periods of rapid climate and environmental change in terms of speciation and population demographic processes.
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Affiliation(s)
- Rui-Sen Lu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yang Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu 501-3714, Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yan-Qian Ding
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Daiki Takahashi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuji Isaji
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Jun Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ying-Xiong Qiu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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31
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Ohashi H, Hasegawa T, Hirata A, Fujimori S, Takahashi K, Tsuyama I, Nakao K, Kominami Y, Tanaka N, Hijioka Y, Matsui T. Biodiversity can benefit from climate stabilization despite adverse side effects of land-based mitigation. Nat Commun 2019; 10:5240. [PMID: 31748549 PMCID: PMC6868141 DOI: 10.1038/s41467-019-13241-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 10/30/2019] [Indexed: 11/09/2022] Open
Abstract
Limiting the magnitude of climate change via stringent greenhouse gas (GHG) mitigation is necessary to prevent further biodiversity loss. However, some strategies to mitigate GHG emission involve greater land-based mitigation efforts, which may cause biodiversity loss from land-use changes. Here we estimate how climate and land-based mitigation efforts interact with global biodiversity by using an integrated assessment model framework to project potential habitat for five major taxonomic groups. We find that stringent GHG mitigation can generally bring a net benefit to global biodiversity even if land-based mitigation is adopted. This trend is strengthened in the latter half of this century. In contrast, some regions projected to experience much growth in land-based mitigation efforts (i.e., Europe and Oceania) are expected to suffer biodiversity loss. Our results support the enactment of stringent GHG mitigation policies in terms of biodiversity. To conserve local biodiversity, however, these policies must be carefully designed in conjunction with land-use regulations and societal transformation in order to minimize the conversion of natural habitats. Greenhouse gas mitigation can involve land-use changes that alter the habitat available for wildlife. Here, Ohashi et al. perform an integrated assessment showing that climate mitigation can be beneficial for global biodiversity but may entail local biodiversity losses where land-based mitigation is implemented.
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Affiliation(s)
- Haruka Ohashi
- Center for International Partnerships and Research on Climate Change, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Matsunosato 1, Tsukuba, Ibaraki, 305-8687, Japan.
| | - Tomoko Hasegawa
- Department of Civil and Environmental Engineering, College of Science and Engineering, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.,Center for Social and Environmental Systems Research, National Institute for Environmental Studies, Japan, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Akiko Hirata
- Center for International Partnerships and Research on Climate Change, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Matsunosato 1, Tsukuba, Ibaraki, 305-8687, Japan.,Center for Climate Change Adaptation, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Shinichiro Fujimori
- Center for Social and Environmental Systems Research, National Institute for Environmental Studies, Japan, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan.,Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, 361, C1-3, Nishikyo, Kyoto, Kyoto, 615-8540, Japan.,Energy Program, International Institute for Applied System Analysis, Schlossplatz 1, A-2361, Laxenburg, Austria
| | - Kiyoshi Takahashi
- Center for Social and Environmental Systems Research, National Institute for Environmental Studies, Japan, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Ikutaro Tsuyama
- Hokkaido Research Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitsujigaoka 7, Toyohira, Sapporo, Hokkaido, 062-8516, Japan
| | - Katsuhiro Nakao
- Kansai Research Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Nagai-kyutaro 68, Momoyama, Fushimi, Kyoto, Kyoto, 612-0855, Japan
| | - Yuji Kominami
- Department of Disaster Prevention, Meteorology and Hydrology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Matsunosato 1, Tsukuba, Ibaraki, 305-8687, Japan
| | - Nobuyuki Tanaka
- Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan
| | - Yasuaki Hijioka
- Center for Climate Change Adaptation, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Tetsuya Matsui
- Center for International Partnerships and Research on Climate Change, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Matsunosato 1, Tsukuba, Ibaraki, 305-8687, Japan
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32
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Wang H, Yin X, Yin D, Li L, Xiao H. Population genetic structures of two ecologically distinct species Betula platyphylla and B. ermanii inferred based on nuclear and chloroplast DNA markers. Ecol Evol 2019; 9:11406-11419. [PMID: 31641482 PMCID: PMC6802015 DOI: 10.1002/ece3.5643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 01/26/2023] Open
Abstract
Climatic oscillations during the last glacial maximum (LGM) significantly affected the distribution patterns and genetic structure of extant plants. Northeast China (NEC) is a major biodiversity center in East Asia, and the influence of historical climate change on NEC populations is critical for understanding species responses to future climate change. However, only a few phylogeographic studies of cool temperate deciduous tree species have been conducted in the area, and results are inconsistent for species with different niches or distribution areas. We employed multiple chloroplast and nuclear markers to investigate the genetic structure of two ecologically contrasting species, Betula platyphylla and B. ermanii, in NEC. Rare haplotypes were identified in the chloroplast genome of these species, and both exhibited high levels of nucleotide diversity based on a fragment of the nuclear gene G3PDH and microsatellites. Moreover, significant phylogeographic structure was detected for B. platyphylla, suggesting that these populations had recolonized from independent glacial refuges, whereas no genetic structure was found for B. ermanii. OPEN RESEARCH BADGES The nSSR datasets used in the current study and the table of pairwise FST (below diagonal) and its standardized F'ST (above diagonal) among 25 populations based on seven SSRs are available from the Dryad (DOI: https://doi.org/10.5061/dryad.230d176). Sequences generated from this study were deposited in GenBank under Accession nos. KY199568-KY200162 and MK819541-MK819970.
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Affiliation(s)
- Hua‐Ying Wang
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchunChina
| | - Xiao Yin
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchunChina
| | - Dong‐Xu Yin
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchunChina
| | - Lin Li
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchunChina
| | - Hong‐Xing Xiao
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchunChina
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33
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Yang J, Pak JH, Maki M, Kim SC. Multiple origins and the population genetic structure of Rubus takesimensis (Rosaceae) on Ulleung Island: Implications for the genetic consequences of anagenetic speciation. PLoS One 2019; 14:e0222707. [PMID: 31536553 PMCID: PMC6752786 DOI: 10.1371/journal.pone.0222707] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/05/2019] [Indexed: 11/19/2022] Open
Abstract
To determine the origin and genetic consequences of anagenesis in Rubus takesimensis on Ulleung Island, Korea, we compared the genetic diversity and population structure of R. takesimensis with those of its continental progenitor R. crataegifolius. We broadly sampled a total of 315 accessions in 35 populations and sequenced five noncoding regions of chloroplast DNA. Rubus takesimensis emerged as nonmonophyletic and several geographically diverse continental populations were likely responsible for the origin of R. takesimensis; the majority of R. takesimensis accessions were sisters to the clade containing accessions of R. crataegifolius, primarily from the Korean peninsula, while rare accessions from three populations shared common ancestors with the ones from the southern part of the Korean peninsula, Jeju Island, and Japan. A few accessions from the Chusan population originated independently from the Korean peninsula. Of 129 haplotypes, 81 and 48 were found exclusively in R. crataegifolius and R. takesimensis, respectively. We found unusually high genetic diversity in two regions on Ulleung Island and no geographic population structure. For R. crataegifolius, two major haplotype groups were found; one for the northern mainland Korean peninsula, and the other for the southern Korean peninsula and the Japanese archipelago. Compared with populations of R. crataegifolius sampled from Japan, much higher haplotype diversity was found in populations from the Korean peninsula. The patterns of genetic consequences in R. takesimensis need to be verified for other endemic species based on chloroplast DNA and independent nuclear markers to synthesize emerging patterns of anagenetic speciation on Ulleung Island.
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Affiliation(s)
- JiYoung Yang
- Department of Biology, Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, Gyeongsangbuk-do, Korea
| | - Jae-Hong Pak
- Department of Biology, Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, Gyeongsangbuk-do, Korea
- * E-mail: (SCK); (JHP)
| | - Masayuki Maki
- Botanical Gardens, Tohoku University, Sendai, Miyagi, Japan
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
- * E-mail: (SCK); (JHP)
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Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil. Nat Commun 2019; 10:4201. [PMID: 31519986 PMCID: PMC6744486 DOI: 10.1038/s41467-019-12133-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 08/23/2019] [Indexed: 12/30/2022] Open
Abstract
As Charles Darwin anticipated, living fossils provide excellent opportunities to study evolutionary questions related to extinction, competition, and adaptation. Ginkgo (Ginkgo biloba L.) is one of the oldest living plants and a fascinating example of how people have saved a species from extinction and assisted its resurgence. By resequencing 545 genomes of ginkgo trees sampled from 51 populations across the world, we identify three refugia in China and detect multiple cycles of population expansion and reduction along with glacial admixture between relict populations in the southwestern and southern refugia. We demonstrate multiple anthropogenic introductions of ginkgo from eastern China into different continents. Further analyses reveal bioclimatic variables that have affected the geographic distribution of ginkgo and the role of natural selection in ginkgo’s adaptation and resilience. These investigations provide insights into the evolutionary history of ginkgo trees and valuable genomic resources for further addressing various questions involving living fossil species. Ginkgo is one of the living fossils from the plant kingdom. Here, authors conduct population genomics analyses to reveal its refugia and demographic history, and provide evidence of multiple anthropogenic introductions of ginkgo from eastern China into different continents.
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Zhao KK, Landrein S, Barrett RL, Sakaguchi S, Maki M, Mu WX, Yang T, Zhu ZX, Liu H, Wang HF. Phylogeographic Analysis and Genetic Structure of an Endemic Sino-Japanese Disjunctive Genus Diabelia (Caprifoliaceae). FRONTIERS IN PLANT SCIENCE 2019; 10:913. [PMID: 31379899 PMCID: PMC6646888 DOI: 10.3389/fpls.2019.00913] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/27/2019] [Indexed: 05/30/2023]
Abstract
The Sino-Japanese Floristic Region (SJFR) is a key area for plant phylogeographical research, due to its very high species diversity and disjunct distributions of a large number of species and genera. At present, the root cause and temporal origin of the discontinuous distribution of many plants in the Sino-Japanese flora are still unclear. Diabelia (Caprifoliaceae; Linnaeoideae) is a genus endemic to Asia, mostly in Japan, but two recent discoveries in China raised questions over the role of the East China Sea (ECS) in these species' disjunctions. Chloroplast DNA sequence data were generated from 402 population samples for two regions (rpl32-trnL, and trnH-psbA) and 11 nuclear microsatellite loci were screened for 549 individuals. Haplotype, population-level structure, combined analyses of ecological niche modeling, and reconstruction of ancestral state in phylogenies were also performed. During the Last Glacial Maximum (LGM) period after the Tertiary, Diabelia was potentially widely distributed in southeastern China, the continental shelf of the East China Sea and Japan (excluding Hokkaido). After LGM, all populations in China have disappeared except those in Zhejiang which may represent a Glacial refuge. Populations of Diabelia in Japan have not experienced significant bottleneck effects, and populations have maintained a relatively stable state. The observed discontinuous distribution of Diabelia species between China and Japan are interpreted as the result of relatively ancient divergence. The phylogenetic tree of chloroplast fragments shows the characteristics of multi-origin evolution (except for D. sanguinea). STRUCTURE analysis of nuclear Simple Sequence Repeat (nSSR) showed that the plants of the Diabelia were divided into five gene pools: D. serrata, D. spathulata, D. sanguinea, D. ionostachya (D. spathulata var. spathulata-Korea), and populations of D. ionostachya var. ionostachya in Yamagata prefecture, northern Japan. Molecular evidence provides new insights of Diabelia into biogeography, a potential glacial refuge, and population-level genetic structure within species. In the process of species differentiation, ECS acts as a corridor for two-way migration of animals and plants between China and Japan during glacial maxima, providing the possibility of secondary contact for discontinuously distributed species between China and Japan, or as a filter (creating isolation) during glacial minima. The influence of the ECS in speciation and biogeography of Diabelia in the Tertiary remains unresolved in this study. Understanding origins, evolutionary histories, and speciation will provide a framework for the conservation and cultivation of Diabelia.
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Affiliation(s)
- Kun-Kun Zhao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Sven Landrein
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Russell L. Barrett
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | | | - Wei-Xue Mu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ting Yang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Zhi-Xin Zhu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Huan Liu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Hua-Feng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
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36
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Liang Y, Zhang Y, Wen J, Su X, Ren Z. Evolutionary History of Rhus chinensis (Anacardiaceae) From the Temperate and Subtropical Zones of China Based on cpDNA and Nuclear DNA Sequences and Ecological Niche Model. Front Genet 2019; 10:171. [PMID: 30891066 PMCID: PMC6411847 DOI: 10.3389/fgene.2019.00171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 02/15/2019] [Indexed: 11/28/2022] Open
Abstract
To explore the origin and evolution of local flora and vegetation, we examined the evolutionary history of Rhus chinensis, which is widely distributed in China’s temperate and subtropical zones, by sequencing three maternally inherited chloroplast DNAs (cpDNA: trnL-trnF, psbA-trnH, and rbcL) and the biparentally inherited nuclear DNA (nuDNA: LEAFY) from 19 natural populations of R. chinensis as well as the ecological niche modeling. In all, 23 chloroplast haplotypes (M1–M23) and 15 nuclear alleles (N1–N15) were detected. The estimation of divergence time showed that the most recent common ancestor dated at 4.2 ± 2.5 million years ago (Mya) from cpDNA, and the initial divergence of genotypes occurred at 4.8 ± 3.6 Mya for the nuDNA. Meanwhile, the multimodality mismatch distribution curves and positive Tajima’s D values indicated that R. chinensis did not experience population expansion after the last glacial maximum. Besides, our study was also consistent with the hypothesis that most refugia in the temperate and subtropical zones of China were in situ during the glaciation.
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Affiliation(s)
- Yukang Liang
- School of Life Science, Shanxi University, Taiyuan, China
| | - Yang Zhang
- Natural History Research Center, Shanghai Natural History Museum, Branch of Shanghai Science and Technology Museum, Shanghai, China
| | - Jun Wen
- School of Life Science, Shanxi University, Taiyuan, China.,Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Xu Su
- Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibetan Plateau in Qinghai Province, School of Life Science, Qinghai Normal University, Xining, China
| | - Zhumei Ren
- School of Life Science, Shanxi University, Taiyuan, China
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37
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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: 9] [Impact Index Per Article: 1.8] [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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Phylogenomics recovers monophyly and early Tertiary diversification of Dipteronia (Sapindaceae). Mol Phylogenet Evol 2019; 130:9-17. [DOI: 10.1016/j.ympev.2018.09.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/16/2018] [Accepted: 09/19/2018] [Indexed: 11/23/2022]
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Feng L, Xu ZY, Wang L. Genetic diversity and demographic analysis of an endangered tree species Diplopanax stachyanthus in subtropical China: implications for conservation and management. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1133-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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: 5] [Impact Index Per Article: 0.8] [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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Wang Y, Liu K, Bi D, Zhou S, Shao J. Molecular phylogeography of East Asian Boea clarkeana (Gesneriaceae) in relation to habitat restriction. PLoS One 2018; 13:e0199780. [PMID: 29969490 PMCID: PMC6029794 DOI: 10.1371/journal.pone.0199780] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 06/13/2018] [Indexed: 11/23/2022] Open
Abstract
Subfamily Cyrtandroideae (Gesneriaceae) comprises a broadly distributed group of rocky-slope herbs, with China being the center of its distributional range. The normal growth of many species within the family is particularly dependent on special habitats. Due to the paucity of molecular studies, very little is known regarding East Asian herb phylogeographic pattern. Here, we investigate the molecular phylogeography of Boea clarkeana Hemsl., a unique resurrection herb endemic to China, focusing on geographically restrictive effects of habitat distribution on evolutionary history. Variation in three chloroplast DNA (cpDNA) intergenic spacers (psbA-trnH, rps12-rpl20, and trnL-trnF), the ribosomal internal transcribed spacer (ITS) and simple sequence repeats in expressed sequence tags (EST-SSRs) was investigated across 18 populations to assess genetic diversity, genetic structure and historical dynamics. Genetic diversity was low within populations (cpDNA, hS = 0.03, πS×10(3) = 0.17; ITS, hS = 0.16, πS×10(3) = 0.43) but high for species (cpDNA, hT = 0.82, πT×10(3) = 3.12; ITS, hT = 0.88, πT×10(3) = 6.39); 76 alleles were detected in this highly inbred species (FIS = 0.22), with a significantly low average of 1.34 alleles per locus. No cpDNA or ITS haplotypes were shared between regions. Based on cpDNA results, the Mt. Huangshan-Tianmu and Mt. Qinling-Daba haplotypes are ancestral; these two regions represent potential refugia. Although no evidence of significant retreat-migration phenomena during glacial cycles was detected, interglacial range expansion from northern Mt. Qinling-Daba was identified (121,457 yr BP). Rapid agricultural growth caused bottlenecks in many populations, especially on Mt. Huang-Tianmu. Habitat restriction and fragmentation, weak seed and pollen dispersal abilities, and long-term isolation caused by human-induced or environmental changes are considered the main causes of extinction of several populations and low genetic diversity within populations and regions. These analyses clarify the effects of habitat restriction on B. clarkeana, representing an evolutionary reference for similar gesneriads, and enrich our understanding of the molecular phylogeography of East Asian rocky-slope herbs.
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Affiliation(s)
- Ying Wang
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu, Anhui, China
| | - Kun Liu
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu, Anhui, China
| | - De Bi
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Shoubiao Zhou
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- College of Environmental Science and Engineering, Anhui Normal University, Wuhu, Anhui, China
| | - Jianwen Shao
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu, Anhui, China
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Yan M, Xiong Y, Liu R, Deng M, Song J. The Application and Limitation of Universal Chloroplast Markers in Discriminating East Asian Evergreen Oaks. FRONTIERS IN PLANT SCIENCE 2018; 9:569. [PMID: 29868047 PMCID: PMC5952231 DOI: 10.3389/fpls.2018.00569] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/11/2018] [Indexed: 05/10/2023]
Abstract
The East Asian subtropics mostly occupied by evergreen broad-leaved forests (EBLFs), is one of the global diversity centers for evergreen oaks. Evergreen oaks are keystone canopy trees in EBLFs with important ecosystem function and crucial significance for regional biodiversity conservation. However, the species composition and diversity of Asian evergreen oaks are poorly understood. Here, we test whether the four chloroplast markers atpI-atpH, matK, psbA-trnH, and ycf1, can discriminate the two evergreen oak sections in Asia - Cyclobalanopsis and Ilex. Two hundred and seventy-two individuals representing 57 species were scanned and 17 species from other oaks sections were included for phylogenetic reconstruction. The genetic diversity of the Quercus sections was also compared. Overall, we found that universal chloroplast DNA (cpDNA) barcoding markers could resolve two clades in Quercus, i.e., subgenus Cerris (Old World Clade) and subgenus Quercus (New World Clade). The chloroplast markers distinguished the main sections, with few exceptions. Each cpDNA region showed no barcoding gap and none of them provided good resolution at the species level. The best species resolution (27.78%) was obtained when three or four markers were combined and analyzed using BLAST. The high conservation of the cpDNA and complicated evolutionary patterns, due to incomplete lineage sorting, interspecific hybridization and introgressions may hinder the ability of cpDNA markers to discriminate different species. When comparing diversification pattern across Quercus sections (Cyclobalanopsis, Ilex, Cerris, Quercus, and Protobalanus), we found that section Ilex was the most genetically diverse, and section Cyclobalanopsis was lower genetically diverse. This diversification pattern may have resulted from the interplay of the Eurasia Cenozoic tectonic movements, climate changes and different niches of their ancestral lineages.
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Affiliation(s)
- Mengxiao Yan
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Yanshi Xiong
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Ruibin Liu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Min Deng
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jiaojiao Song
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life Sciences, Shangrao Normal University, Shangrao, China
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Hohmann N, Wolf EM, Rigault P, Zhou W, Kiefer M, Zhao Y, Fu CX, Koch MA. Ginkgo biloba's footprint of dynamic Pleistocene history dates back only 390,000 years ago. BMC Genomics 2018; 19:299. [PMID: 29703145 PMCID: PMC5921299 DOI: 10.1186/s12864-018-4673-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/13/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND At the end of the Pliocene and the beginning of Pleistocene glaciation and deglaciation cycles Ginkgo biloba went extinct all over the world, and only few populations remained in China in relict areas serving as sanctuary for Tertiary relict trees. Yet the status of these regions as refuge areas with naturally existing populations has been proven not earlier than one decade ago. Herein we elaborated the hypothesis that during the Pleistocene cooling periods G. biloba expanded its distribution range in China repeatedly. Whole plastid genomes were sequenced, assembled and annotated, and sequence data was analyzed in a phylogenetic framework of the entire gymnosperms to establish a robust spatio-temporal framework for gymnosperms and in particular for G. biloba Pleistocene evolutionary history. RESULTS Using a phylogenetic approach, we identified that Ginkgoatae stem group age is about 325 million years, whereas crown group radiation of extant Ginkgo started not earlier than 390,000 years ago. During repeated warming phases, Gingko populations were separated and isolated by contraction of distribution range and retreated into mountainous regions serving as refuge for warm-temperate deciduous forests. Diversification and phylogenetic splits correlate with the onset of cooling phases when Ginkgo expanded its distribution range and gene pools merged. CONCLUSIONS Analysis of whole plastid genome sequence data representing the entire spatio-temporal genetic variation of wild extant Ginkgo populations revealed the deepest temporal footprint dating back to approximately 390,000 years ago. Present-day directional West-East admixture of genetic diversity is shown to be the result of pronounced effects of the last cooling period. Our evolutionary framework will serve as a conceptual roadmap for forthcoming genomic sequence data, which can then provide deep insights into the demographic history of Ginkgo.
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Affiliation(s)
- Nora Hohmann
- Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany.,Present address: Department of Environmental Sciences, Botany, University of Basel, Schönbeinstrasse 6, CH-4056, Basel, Switzerland
| | - Eva M Wolf
- Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany
| | - Philippe Rigault
- Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany.,GYDLE Inc., 1135 Grande Allée Ouest, Suite 220, QC, Québec, G1S 1E7, Canada
| | - Wenbin Zhou
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Markus Kiefer
- Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany
| | - Yunpeng Zhao
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Cheng-Xin Fu
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Marcus A Koch
- Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany.
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Zhou W, Ji X, Obata S, Pais A, Dong Y, Peet R, Xiang QYJ. Resolving relationships and phylogeographic history of the Nyssa sylvatica complex using data from RAD-seq and species distribution modeling. Mol Phylogenet Evol 2018; 126:1-16. [PMID: 29631052 DOI: 10.1016/j.ympev.2018.04.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 03/30/2018] [Accepted: 04/01/2018] [Indexed: 01/08/2023]
Abstract
Nyssa sylvatica complex consists of several woody taxa occurring in eastern North America. These taxa were recognized as two or three species including three or four varieties by different authors. Due to high morphological similarities and complexity of morphological variation, classification and delineation of taxa in the group have been difficult and controversial. Here we employ data from RAD-seq to elucidate the genetic structure and phylogenetic relationships within the group. Using the genetic evidence, we evaluate previous classifications and delineate species. We also employ Species Distribution Modeling (SDM) to evaluate impacts of climatic changes on the ranges of the taxa and to gain insights into the relevant refugia in eastern North America. Results from Molecular Variance Analysis (AMOVA), STRUCTURE, phylogenetic analyses using Maximum likelihood, Bayesian Inference, and Splittree methods of RAD-seq data strongly support a two-clade pattern, largely separating samples of N. sylvatica from those of N. biflora-N. ursina mix. Divergence time analysis with BEAST suggests the two clades diverged in the mid Miocene. The ancestor of the present trees of N. sylvatica was suggested to be in the Pliocene and that of N. biflora-N. ursina mix in the end of the Miocene. Results from SDM predicted a smaller range in the southern part of the species present range of each clade during the Last Glacial Maximum (LGM). A northward expansion of the ranges during interglacial period and a northward shift of the ranges in the future under a model of global warming were also predicted. Our results support the recognition of two species in the complex, N. sylvatica and N. biflora, following the phylogenetic species concept. We found no genetic evidence supporting recognitions of intraspecific taxa. However, we propose subsp. ursina and subsp. biflora within N. biflora due to their distinction in habits, distributions, and habitats. Our results further support movements of trees in eastern North America in response to climatic changes. Finally, our study demonstrates that RAD-seq data and a combination of population genomics and SDM are valuable in resolving relationship and biogeographic history of closely related species that are taxonomically difficult.
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Affiliation(s)
- Wenbin Zhou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7612, USA
| | - Xiang Ji
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695-7566, USA; Department of Statistics, North Carolina State University, Raleigh, NC 27695-8203, USA
| | - Shihori Obata
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7612, USA
| | - Andrew Pais
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7612, USA
| | - Yibo Dong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7612, USA
| | - Robert Peet
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA.
| | - Qiu-Yun Jenny Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7612, USA.
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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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Sakaguchi S, Kimura T, Kyan R, Maki M, Nishino T, Ishikawa N, Nagano AJ, Honjo MN, Yasugi M, Kudoh H, Li P, Choi HJ, Chernyagina OA, Ito M. Phylogeographic analysis of the East Asian goldenrod (Solidago virgaurea complex, Asteraceae) reveals hidden ecological diversification with recurrent formation of ecotypes. ANNALS OF BOTANY 2018; 121:489-500. [PMID: 29300816 PMCID: PMC5838820 DOI: 10.1093/aob/mcx182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/13/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS The processes and mechanisms underlying lineage diversification are major topics in evolutionary biology. Eurasian goldenrod species of the Solidago virgaurea complex show remarkable morphological and ecological diversity in the Japanese Archipelago, with ecotypic taxa well adapted to specific environments (climate, edaphic conditions and disturbance regimes). The species complex is a suitable model to investigate the evolutionary processes of actively speciating plant groups, due to its ability to evolve in relation to environmental adaptation and its historical population dynamics. METHODS Two chloroplast markers, 18 nuclear microsatellite markers and ddRAD-sequencing were used to infer population genetic demography of S. virgaurea complex with its related species/genera. KEY RESULTS Our analysis showed that populations in Japan form an evolutionary unit, which was genetically diverged from adjacent continental populations. The phylogenetic structure within the archipelago strongly corresponds to the geography, but interestingly there is no concordance between genetic structure and ecotypic boundaries; neighbouring populations of distinct ecotypes share a genetic background. CONCLUSIONS We propose that the traits specific to the ecotypic entities are maintained by natural selection or are very recently generated and have little effect on the genomes, making genome-wide genetic markers unsuitable for detecting ecotypic differentiation. Furthermore, some sporadically distributed taxa (found as rheophytes and alpine plants) were repeatedly generated from a more widespread taxon in geographically distant areas by means of selection. Overall, this study showed that the goldenrod complex has a high ability to evolve, enabling rapid ecological diversification over a recent timeframe.
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Affiliation(s)
- Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, Japan
- For correspondence. E-mail
| | - Takuma Kimura
- Botanical Gardens, Tohoku University, Kawauchi, Sendai, Japan
| | - Ryuta Kyan
- Botanical Gardens, Tohoku University, Kawauchi, Sendai, Japan
| | - Masayuki Maki
- Botanical Gardens, Tohoku University, Kawauchi, Sendai, Japan
| | - Takako Nishino
- Graduate School of Science, Osaka Prefecture University, Osaka, Japan
| | - Naoko Ishikawa
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- JST CREST, Honcho, Kawaguchi, Saitama, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Masaki Yasugi
- National Institute for Basic Biology, Higashiyama, Myodaiji, Okazaki, Aichi, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Pan Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hyeok Jae Choi
- Department of Biology & Chemistry, Changwon National University, Changwon, Gyeongnam, Korea
| | - Olga A Chernyagina
- Kamchatka Branch of Pacific Geographical Institute, Petropavlovsk-Kamchatskyi, Russia
| | - Motomi Ito
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
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48
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Phylogeny and biogeography of East Asian evergreen oaks (Quercus section Cyclobalanopsis; Fagaceae): Insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia. Mol Phylogenet Evol 2018; 119:170-181. [DOI: 10.1016/j.ympev.2017.11.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 11/14/2017] [Accepted: 11/14/2017] [Indexed: 11/17/2022]
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49
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Zhao Y, Yin G, Pan Y, Gong X. Ecological and Genetic Divergences with Gene Flow of Two Sister Species ( Leucomeris decora and Nouelia insignis) Driving by Climatic Transition in Southwest China. FRONTIERS IN PLANT SCIENCE 2018; 9:31. [PMID: 29422911 PMCID: PMC5789531 DOI: 10.3389/fpls.2018.00031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/09/2018] [Indexed: 06/08/2023]
Abstract
Understanding of the processes of divergence and speciation is a major task for biodiversity researches and may offer clearer insight into mechanisms generating biological diversity. Here, we employ an integrative approach to explore genetic and ecological differentiation of Leucomeris decora and Nouelia insignis distributed allopatrically along the two sides of the biogeographic boundary 'Tanaka Line' in Southwest China. We addressed these questions using ten low-copy nuclear genes and nine plastid DNA regions sequenced among individuals sampled from 28 populations across their geographic ranges in China. Phylogenetic, coalescent-based population genetic analyses, approximate Bayesian computation (ABC) framework and ecological niche models (ENMs) were conducted. We identified a closer phylogenetic relationship in maternal lineage of L. decora with N. insignis than that between L. decora and congeneric Leucomeris spectabilis. A deep divergence between the two species was observed and occurred at the boundary between later Pliocene and early Pleistocene. However, the evidence of significant chloroplast DNA gene flow was also detected between the marginal populations of L. decora and N. insignis. Niche models and statistical analyses showed significant ecological differentiation, and two nuclear loci among the ten nuclear genes may be under divergent selection. These integrative results imply that the role of climatic shift from Pliocene to Pleistocene may be the prominent factor for the divergence of L. decora and N. insignis, and population expansion after divergence may have given rise to chloroplast DNA introgression. The divergence was maintained by differential selection despite in the face of gene flow.
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Affiliation(s)
- Yujuan Zhao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Genshen Yin
- Department of Biological Science and Technology, Kunming University, Kunming, China
| | - Yuezhi Pan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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50
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Wang MN, Duan L, Qiao Q, Wang ZF, Zimmer EA, Li ZC, Chen HF. Phylogeography and conservation genetics of the rare and relict Bretschneidera sinensis (Akaniaceae). PLoS One 2018; 13:e0189034. [PMID: 29329302 PMCID: PMC5766123 DOI: 10.1371/journal.pone.0189034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 11/19/2017] [Indexed: 11/21/2022] Open
Abstract
Bretschneidera sinensis, a class-I protected wild plant in China, is a relic of the ancient Tertiary tropical flora endemic to Asia. However, little is known about its genetics and phylogeography. To elucidate the current phylogeographic patterns and infer the historical population dynamics of B. sinensis, and to make recommendations for its conservation, three non-coding regions of chloroplast DNA (trnQ-rps16, rps8-rps11, and trnT-trnL) were amplified and sequenced across 256 individuals from 23 populations of B. sinensis, spanning 10 provinces of China. We recognized 13 haplotypes, demonstrating relatively high total haplotype diversity (hT = 0.739). Almost all of the variation existed among populations (98.09%, P < 0.001), but that within populations was low (1.91%, P < 0.001). Strong genetic differentiation was detected among populations (GST = 0.855, P < 0.001) with limited estimations of seed flow (Nm = 0.09), indicating that populations were strongly isolated from one another. According to SAMOVA analysis, populations of B. sinensis in China could be divided into five geographic groups: (1) eastern Yunnan to western Guangxi; (2) Guizhou-Hunan-Hubei; (3) central Guangdong; (4) northwestern Guangdong; and (5) the Luoxiao-Nanling-Wuyi -Yangming Mountain. Network analysis showed that the most ancestral haplotypes were located in the first group, i.e., the eastern Yungui Plateau and in eastern Yunnan, which is regarded as a putative glacial refugia for B. sinensis in China. B. sinensis may have expanded its range eastward from these refugia and experienced bottleneck or founder effects in southeastern China. Populations in Liping (Guizhou Province), Longsheng (Guangxi Province), Huizhou (Guangdong Province), Chongyi (Jiangxi Province), Dong-an (Hunan Province), Pingbian (Yunnan Province) and Xinning (Hunan Province) are proposed as the priority protection units.
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Affiliation(s)
- Mei-Na Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Lei Duan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Qi Qiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
| | - Zheng-Feng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Elizabeth A. Zimmer
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, D.C., United States of America
| | - Zhong-Chao Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hong-Feng Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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