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Cheng XJ, Fritsch PW, Lin YJ, Li GH, Chen YQ, Zhang MY, Lu L. The role of Pleistocene dispersal in shaping species richness of sky island wintergreens from the Himalaya-Hengduan Mountains. Mol Phylogenet Evol 2024; 197:108082. [PMID: 38705251 DOI: 10.1016/j.ympev.2024.108082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 03/19/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024]
Abstract
In addition to topography and climate, biogeographic dispersal has been considered to influence plant diversity in the Himalaya-Hengduan Mountains (HHM), yet, the mode and tempo of sky island dispersal and its influence on species richness has been little explored. Through phylogenetic analysis of Gaultheria ser. Trichophyllae, a sky island alpine clade within the HHM, we test the hypothesis that dispersal has affected current local species richness. We inferred the dynamics of biogeographic dispersal with correlation tests on direction, distance, occurrence time, and regional species richness. We found that G. ser. Trichophyllae originated at the end of the Miocene and mostly dispersed toward higher longitudes (eastward). In particular, shorter intra-regional eastward dispersals and longer inter-regional westward dispersals were most frequently observed. We detected a prevalence of eastward intra-region dispersals in both glacial periods and interglacials. These dispersals may have been facilitated by the reorganization of paleo-drainages and monsoon intensification through time. We suggest that the timing of dispersal corresponding to glacial periods and the prevalence of intra-region dispersal, rather than dispersal frequency, most influenced the pattern of species richness of G. ser. Trichophyllae. This study facilitates a more comprehensive understanding of biodiversity in the sky islands within the HHM.
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Affiliation(s)
- Xiao-Juan Cheng
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Peter W Fritsch
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX 76107, USA
| | - Yan-Jun Lin
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Guo-Hong Li
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Yan-Quan Chen
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China; School of Pharmacy, Sun Yat-sen University, Guangzhou 510000, China
| | - Ming-Ying Zhang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an 712046, China.
| | - Lu Lu
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China.
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Li YR, Fritsch PW, Zhao GG, Cheng XJ, Ding ZL, Lu L. Population differentiation and dynamics of five pioneer species of Gaultheria from the secondary forests in subtropical China. BMC PLANT BIOLOGY 2024; 24:516. [PMID: 38851686 PMCID: PMC11161945 DOI: 10.1186/s12870-024-05189-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 05/23/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND The influence of native secondary succession associated with anthropogenic disturbance on the biodiversity of the forests in subtropical China remains uncertain. In particular, the evolutionary response of small understory shrubs, particularly pioneer species inhabiting continuously disturbed habitats, to topographic heterogeneity and climate change is poorly understood. This study aimed to address this knowledge gap by focusing on the Gaultheria crenulata group, a clade of small pioneer shrubs in subtropical China. RESULTS We examined the genetic structure and demographic history of all five species of the G. crenulata group with two maternally inherited chloroplast DNA (cpDNA) fragments and two biparentally inherited low-copy nuclear genes (LCG) over 89 natural populations. We found that the genetic differentiation of this group was influenced by the geomorphological boundary between different regions of China in association with Quaternary climatic events. Despite low overall genetic diversity, we observed an isolation-by-distance (IBD) pattern at a regional scale, rather than isolation-by-environment (IBE), which was attributed to ongoing human disturbance in the region. CONCLUSION Our findings suggest that the genetic structure of the G. crenulata group reflects the interplay of geological topography, historical climates, and anthropogenic disturbance during the Pliocene-Pleistocene-Holocene periods in subtropical China. The observed IBD pattern, particularly prominent in western China, highlights the role of limited dispersal and gene flow, possibly influenced by physical barriers or decreased connectivity over geographic distance. Furthermore, the east-to-west trend of gene flow, potentially facilitated by the East Asian monsoon system, underscores the complex interplay of biotic and abiotic factors shaping the genetic dynamics of pioneer species in subtropical China's secondary forests. These findings can be used to assess the impact of environmental changes on the adaptation and persistence of biodiversity in subtropical forest ecosystems.
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Affiliation(s)
- Yi-Rong Li
- School of Pharmaceutical Sciences, Yunnan Key Laboratory of Pharmacology for Natural Products, Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming, 650500, Yunnan, China
| | - Peter W Fritsch
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX, 76017, USA
| | - Gui-Gang Zhao
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, 650223, China
| | - Xiao-Juan Cheng
- School of Pharmaceutical Sciences, Yunnan Key Laboratory of Pharmacology for Natural Products, Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming, 650500, Yunnan, China
| | - Zhao-Li Ding
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, 650223, China.
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, 650223, China.
| | - Lu Lu
- School of Pharmaceutical Sciences, Yunnan Key Laboratory of Pharmacology for Natural Products, Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming, 650500, Yunnan, China.
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Sun X, Pan Q, Hubley B, Ye Z, Zhang P, Xie Q. Geomorphic impacts within Red River Fault and island shifting as witnessed by the phylogeography of the largest water strider. Mol Phylogenet Evol 2024; 195:108062. [PMID: 38485104 DOI: 10.1016/j.ympev.2024.108062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/16/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Palaeogeological events and climate oscillations profoundly impact the demographics and distributions of small-range species, increasing the extinction risk. The largest water strider worldwide, Gigantometra gigas (Hemiptera: Gerridae), exhibits restricted distributions in Vietnam and southern China. Herein, we generated three genomic datasets (mitogenomes, 146 nuclear protein-coding genes and single nucleotide polymorphisms) with ecological niche modelling (ENM) to explicitly test whether the present-day distribution of G. gigas actually resulted from geographical and climatic effects. We found that the origin of this largest water strider reached the divergence time of the genus within Gerridae, providing a greater opportunity to explore its response to geographic movements. The right-lateral motion of the Red River Fault facilitated the divergence of two phylogeographic lineages, resulting in the "north-south component" genetic pattern in G. gigas. The Hainan and southeast Vietnam populations of the southern linage were completely separated by the Beibu Gulf but exhibited similar genetic compositions, confirming that Hainan had a continental origin and that Hainan Island joined with the Indo-China Peninsula to promote gene exchange among populations. Additionally, we noticed the low genetic diversity but long demographic history of the northern lineage, which displayed population dynamics opposite to those of other organisms. Integrating the demographic changes and ENM findings revealed that suitable habitat contraction and rapid demographic decline during the Last Glacial Maximum (LGM) triggered the low genetic diversity of the northern lineage. Overall, the demographic history of the largest water strider was mainly shaped by geographical features, and first provided evidence from the phylogeographic perspective of aquatic insects to support the hypothesis of Hainan Island shifting.
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Affiliation(s)
- Xiaoya Sun
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity & Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China.
| | - Qiqi Pan
- School of Life Sciences, State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Brad Hubley
- Natural History - Entomology Royal Ontario Museum, 100 Queen's Park, Toronto, Canada
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China.
| | - Peng Zhang
- School of Life Sciences, State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Qiang Xie
- School of Life Sciences, State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, China
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Zhou D, Gong J, Duan C, He J, Zhang Y, Xu J. Genetic structure and triazole resistance among Aspergillus fumigatus populations from remote and undeveloped regions in Eastern Himalaya. mSphere 2023; 8:e0007123. [PMID: 37341484 PMCID: PMC10449526 DOI: 10.1128/msphere.00071-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/03/2023] [Indexed: 06/22/2023] Open
Abstract
Aspergillus fumigatus is a ubiquitous mold and a common human fungal pathogen. Recent molecular population genetic and epidemiological analyses have revealed evidence for long-distance gene flow and high genetic diversity within most local populations of A. fumigatus. However, little is known about the impact of regional landscape factors in shaping the population diversity patterns of this species. Here we sampled extensively and investigated the population structure of A. fumigatus from soils in the Three Parallel Rivers (TPR) region in Eastern Himalaya. This region is remote, undeveloped and sparsely populated, bordered by glaciated peaks more than 6,000 m above sea level, and contained three rivers separated by tall mountains over very short horizontal distances. A total of 358 A. fumigatus strains from 19 sites along the three rivers were isolated and analyzed at nine loci containing short tandem repeats. Our analyses revealed that mountain barriers, elevation differences, and drainage systems all contributed low but statistically significant genetic variations to the total A. fumigatus population in this region. We found abundant novel alleles and genotypes in the TPR population of A. fumigatus and significant genetic differentiation between this population and those from other parts of Yunnan and the globe. Surprisingly, despite limited human presence in this region, about 7% of the A. fumigatus isolates were resistant to at least one of the two medical triazoles commonly used for treating aspergillosis. Our results call for greater surveillance of this and other human fungal pathogens in the environment. IMPORTANCE The extreme habitat fragmentation and substantial environmental heterogeneity in the TPR region have long known to contribute to geographically shaped genetic structure and local adaptation in several plant and animal species. However, there have been limited studies of fungi in this region. Aspergillus fumigatus is a ubiquitous pathogen capable of long-distance dispersal and growth in diverse environments. In this study, using A. fumigatus as a model, we investigated how localized landscape features contribute to genetic variations in fungal populations. Our results revealed that elevation and drainage isolation rather than direct physical distances significantly impacted genetic exchange and diversity among the local A. fumigatus populations. Interestingly, within each local population, we found high allelic and genotypic diversities, and with evidence ~7% of all isolates being resistant to two medical triazoles, itraconazole and voriconazole. Given the high frequency of ARAF found in mostly natural soils of sparsely populated sites in the TPR region, close monitoring of their dynamics in nature and their effects on human health is needed.
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Affiliation(s)
- Duanyong Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Life Science, Yunnan University, Kunming, China
- Key Laboratory of Biological Genetic Resources Mining and Molecular Breeding of Qianxinan Prefecture, Minzu Normal University of Xingyi, Xingyi, China
| | - Jianchuan Gong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Life Science, Yunnan University, Kunming, China
| | - Chengyan Duan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Life Science, Yunnan University, Kunming, China
| | - Jingrui He
- School of Life Science, Yunnan University, Kunming, China
| | - Ying Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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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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Liu H, Wang Z, Zhang Y, Li M, Wang T, Su Y. Geographic isolation and environmental heterogeneity contribute to genetic differentiation in Cephalotaxus oliveri. Ecol Evol 2023; 13:e9869. [PMID: 36919017 PMCID: PMC10008294 DOI: 10.1002/ece3.9869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/30/2023] [Accepted: 02/14/2023] [Indexed: 03/14/2023] Open
Abstract
Evaluating the contributions of geographic distance and environmental heterogeneity to the genetic divergence can inform the demographic history and responses to environmental change of natural populations. The isolation-by-distance (IBD) reveals that genetic differentiation among populations increases with geographic distance, while the isolation-by-environment (IBE) assumes a linear relationship between genetic variation and environmental differences among populations. Here, we sampled and genotyped 330 individuals from 18 natural populations of Cephalotaxus oliveri throughout the species' distribution. Twenty-eight EST-SSR markers were applied to analyze population genetics, for the investigation of the driving factors that shaped spatial structure. In addition, we identified the outlier loci under positive selection and tested their association with environmental factors. The results showed a moderate genetic diversity in C. oliveri and high genetic differentiation among populations. Population structure analyses indicated that 18 populations were clustered into two major groups. We observed that the genetic diversity of central populations decreased and the genetic differentiation increased towards the marginal populations. Additionally, the signatures of IBD and IBE were detected in C. oliveri, and IBE provided a better contribution to genetic differentiation. Six outlier loci under positive selection were demonstrated to be closely correlated with environmental variables, among which bio8 was associated with the greatest number of loci. Genetic evidence suggests the consistency of the central-marginal hypothesis (CMH) for C. oliveri. Furthermore, our results suggest that temperature-related variables played an important role in shaping genetic differentiation.
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Affiliation(s)
- Hanjing Liu
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Zhen Wang
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Yuli Zhang
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Minghui Li
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Ting Wang
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
| | - Yingjuan Su
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
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Qiao Y, Liu J, Gong X. Phylogeography of Himalrandia lichiangensis from the dry-hot valleys in Southwest China. FRONTIERS IN PLANT SCIENCE 2022; 13:1002519. [PMID: 36325543 PMCID: PMC9618719 DOI: 10.3389/fpls.2022.1002519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Both changing tectonics and climate may shape the phylogeographic patterns of plant species. The dry-hot valleys in southwestern China harbor a high number of endemic plants. In this study, we investigated the evolutionary history and potential distribution of an endemic shrub Himalrandia lichiangensis (Rubiaceae), to evaluate the effects of tectonic and climatic processes on this thermophilic plant species from the dry-hot valleys. By sequencing DNA from four plastid non-coding regions (psbM-trnD, trnD-trnT, atpB-rbcL and accD-psaI) and the CAMX1F-CAMX2R region and ITS for 423 individuals from 23 populations, we investigated the genetic diversity, phylogeographical pattern and population dynamics of H. lichiangensis. We found a high degree of differentiation in H. lichiangensis during the middle Miocene (15-13 Myr), possibly triggered by the rapid tectonic uplift event in this period area. accompanied by frequent orogeneses in this period. This hypothesis is also supported by the association between genetic differentiation and altitudinal gradients among populations. The middle reach of the Jinsha River, which harbors the greatest genetic diversity, is most likely to have been a refugia for H. lichiangensis during Quaternary. We also detected a strong barrier effect between the Nanpan River and Jinsha River, suggesting the river system may play a role in geographical isolation between clades on both sides of the barrier. The Maximum Entropy Model (MaxEnt) results showed that future climate warming will lead to the niche expansion in some areas for H. lichiangensis but will also cause a scattered and fragmented distribution. Given the high among-population differentiation and no recent expansion detected in H. lichiangensis, its current phylogeographical pattern is possibly due to a long-term geographical barrier caused by uplifting mountains since the Miocene, as well as Quaternary climate refugia isolated also by high mountains. This study illustrated tectonic and climatic processes may have a continuous effect on plant phylogeography and offers insights into the origin of biodiversity and endemism in the dry-hot valleys of southwestern China.
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Affiliation(s)
- Yaomei Qiao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Yang X, Qin F, Xue T, Xia C, Gadagkar SR, Yu S. Insights into plant biodiversity conservation in large river valleys in China: A spatial analysis of species and phylogenetic diversity. Ecol Evol 2022; 12:e8940. [PMID: 35600693 PMCID: PMC9120211 DOI: 10.1002/ece3.8940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 04/21/2022] [Accepted: 05/03/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Xudong Yang
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Fei Qin
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Tiantian Xue
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Changying Xia
- School of Life Sciences Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation Southwest University Chongqing China
| | - Sudhindra R. Gadagkar
- Biomedical Sciences Program College of Graduate Studies Midwestern University Glendale Arizona USA
- College of Veterinary Medicine Midwestern University Glendale Arizona USA
| | - Shengxiang Yu
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
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Wu S, Wang Y, Wang Z, Shrestha N, Liu J. Species divergence with gene flow and hybrid speciation on the Qinghai-Tibet Plateau. THE NEW PHYTOLOGIST 2022; 234:392-404. [PMID: 35020198 DOI: 10.1111/nph.17956] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
The Qinghai-Tibet Plateau (QTP) sensu lato (sl), comprising the platform, the Himalaya and the Hengduan Mountains, is characterized by a large number of endemic plant species. This evolutionary cradle may have arisen from explosive species diversification because of geographic isolation. However, gene flow has been widely detected during the speciation processes of all groups examined, suggesting that natural selection may have also played an important role during species divergence in this region. In addition, natural hybrids have been recovered in almost all species-rich genera. This suggests that numerous species in this region are still 'on the speciation pathway to complete reproductive isolation (RI)'. Such hybrids could directly develop into new species through hybrid polyploidization and homoploid hybrid speciation (HHS). HHS may take place more easily than previously thought through alternate inheritance of alleles of parents at multiple RI loci. Therefore, isolation, selection and hybridization could together have promoted species diversification of numerous plant genera on the QTP sl. We emphasize the need for identification and functional analysis of alleles of major genes for speciation, and especially encourage investigations of parallel adaptive divergence causing RI across different lineages within similar but specific habitats in this region.
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Affiliation(s)
- Shengdan Wu
- State Key Laboratory of Grassland Agro-Ecosystems and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Yi Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zefu Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystems and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystems and College of Ecology, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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Wang X, Tong L, Deng J, Li L, Xiang P, Xu L, Luo Z, Yang K, Song Z. Insights into historical drainage evolution based on the phylogeography of Schizopygopsis malacanthus Herzenstein (Cypriniformes, Cyprinidae) across the upper and middle Yalong River drainage in the Hengduan Mountains region, southwest China. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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11
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Zheng SS, Jiang XL, Huang QJ, Deng M. Historical Dynamics of Semi-Humid Evergreen Forests in the Southeast Himalaya Biodiversity Hotspot: A Case Study of the Quercus franchetii Complex (Fagaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:774232. [PMID: 35035389 PMCID: PMC8753985 DOI: 10.3389/fpls.2021.774232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 10/28/2021] [Indexed: 06/14/2023]
Abstract
The Oligocene and Miocene are key periods in the formation of the modern topography and flora of East Asian and Indo-China. However, it is unclear how geological and climatic factors contributed to the high endemism and species richness of this region. The Quercus franchetii complex is widespread in the southeast Himalaya fringe and northern Indo-China with a long evolutionary history. It provides a unique proxy for studying the diversity pattern of evergreen woody lineages in this region since the Oligocene. In this study, we combined chloroplast (cpDNA) sequences, nuclear microsatellite loci (nSSRs), and species distribution modeling (SDM) to investigate the impacts of geological events on genetic diversity of the Q. franchetii complex. The results showed that the initial cpDNA haplotype divergence was estimated to occur during the middle Oligocene (30.7 Ma), which might have been raised by the tectonic activity at this episode to the Miocene. The nSSR results revealed two major groups of populations, the central Yunnan-Guizhou plateau (YGP) group and the peripheral distribution group when K = 2, in responding to the rapid YGP uplift during the late Miocene, which restricted gene flow between the populations in core and marginal areas. SDM analysis indicated that the distribution ranges of the Q. franchetii complex expanded northwards after the last glacial maximum, but the core distribution range in YGP was stable. Our results showed that the divergence of Q. franchetii complex is rooted in the mid-Oligocene. The early geological events during the Oligocene, and the late Miocene may play key roles to restrict seed-mediated gene flow among regions, but the pollen-mediated gene flow was less impacted. The uplifts of the YGP and the climate since LGM subsequently boosted the divergence of the populations in core and marginal areas.
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Affiliation(s)
- Si-Si Zheng
- Shanghai Chenshan Botanical Garden, Shanghai, China
- School of Ecological Technique and Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Xiao-Long Jiang
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, China
| | - Qing-Jun Huang
- School of Ecological Technique and Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Min Deng
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
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Phylogeography of two widespread C4 grass species suggest that tableland and valley grassy biome in southwestern China pre-date human modification. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01835] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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13
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Leal BSS, Chaves CJN, Graciano VA, Boury C, Huacre LAP, Heuertz M, Palma-Silva C. Evidence of local adaptation despite strong drift in a Neotropical patchily distributed bromeliad. Heredity (Edinb) 2021; 127:203-218. [PMID: 33953353 PMCID: PMC8322333 DOI: 10.1038/s41437-021-00442-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 02/03/2023] Open
Abstract
Both genetic drift and divergent selection are predicted to be drivers of population differentiation across patchy habitats, but the extent to which these forces act on natural populations to shape traits is strongly affected by species' ecological features. In this study, we infer the genomic structure of Pitcairnia lanuginosa, a widespread herbaceous perennial plant with a patchy distribution. We sampled populations in the Brazilian Cerrado and the Central Andean Yungas and discovered and genotyped SNP markers using double-digest restriction-site associated DNA sequencing. In addition, we analyzed ecophysiological traits obtained from a common garden experiment and compared patterns of phenotypic and genetic divergence (PST-FST comparisons) in a subset of populations from the Cerrado. Our results from molecular analyses pointed to extremely low genetic diversity and a remarkable population differentiation, supporting a major role of genetic drift. Approximately 0.3% of genotyped SNPs were flagged as differentiation outliers by at least two distinct methods, and Bayesian generalized linear mixed models revealed a signature of isolation by environment in addition to isolation by distance for high-differentiation outlier SNPs among the Cerrado populations. PST-FST comparisons suggested divergent selection on two ecophysiological traits linked to drought tolerance. We showed that these traits vary among populations, although without any particular macro-spatial pattern, suggesting local adaptation to differences in micro-habitats. Our study shows that selection might be a relevant force, particularly for traits involved in drought stress, even for populations experiencing strong drift, which improves our knowledge on eco-evolutionary processes acting on non-continuously distributed species.
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Affiliation(s)
- Bárbara Simões Santos Leal
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil
| | - Cleber Juliano Neves Chaves
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil
| | - Vanessa Araujo Graciano
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil
| | - Christophe Boury
- grid.412041.20000 0001 2106 639XINRAE, Univ. Bordeaux, Biogeco, Cestas France
| | - Luis Alberto Pillaca Huacre
- grid.10800.390000 0001 2107 4576Departamento de Ecología, Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Myriam Heuertz
- grid.412041.20000 0001 2106 639XINRAE, Univ. Bordeaux, Biogeco, Cestas France
| | - Clarisse Palma-Silva
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil ,grid.411087.b0000 0001 0723 2494Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
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14
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Wan T, Oaks JR, Jiang XL, Huang H, Knowles LL. Differences in Quaternary co-divergence reveals community-wide diversification in the mountains of southwest China varied among species. Proc Biol Sci 2021; 288:20202567. [PMID: 33402075 DOI: 10.1098/rspb.2020.2567] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The mountains of southwest China (MSWC) is a biodiversity hotspot with highly complex and unusual terrain. However, with the majority of studies focusing on the biogeographic consequences of massive mountain building, the Quaternary legacy of biodiversity for the MSWC has long been overlooked. Here, we took a statistical comparative phylogeography approach to examine factors that shaped community-wide diversification. With data from 30 vertebrate species, the results reveal spatially concordant genetic structure, and temporally clustered co-divergence events associated with river barriers during severe glacial cycles. This indicates the importance of riverine barriers in the phylogeographic history of the MSWC vertebrate community. We conclude that the repeated glacial cycles are associated with co-divergences that are themselves structured by the heterogeneity of the montane landscape of the MSWC. This orderly process of diversification has profound implications for conservation by highlighting the relative independence of different geographical areas in which some, but not all species in communities have responded similarly to climate change and calls for further comparative phylogeographic investigations to reveal the connection between biological traits and divergence pulses in this biodiversity hotspot.
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Affiliation(s)
- Tao Wan
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, People's Republic of China.,Mammal Ecology and Evolution, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.,College of Life Sciences, Sichuan Normal University, Chengdu 610066, People's Republic of China
| | - Jamie R Oaks
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - Xue-Long Jiang
- Mammal Ecology and Evolution, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China
| | - Huateng Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, People's Republic of China
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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15
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Ye H, Wu J, Wang Z, Hou H, Gao Y, Han W, Ru W, Sun G, Wang Y. Population genetic variation characterization of the boreal tree Acer ginnala in Northern China. Sci Rep 2020; 10:13515. [PMID: 32782277 PMCID: PMC7419535 DOI: 10.1038/s41598-020-70444-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/24/2020] [Indexed: 11/09/2022] Open
Abstract
Genetic diversity and differentiation are revealed particularly through spatio-temporal environmental heterogeneity. Acer ginnala, as a deciduous shrub/small tree, is a foundation species in many terrestrial ecosystems of Northern China. Owing to its increased use as an economic resource, this species has been in the vulnerability. Therefore, the elucidations of the genetic differentiation and influence of environmental factors on A. ginnala are very critical for its management and future utilization strategies. In this study, high genetic diversity and differentiation occurred in A. ginnala, which might be resulted from its pollination mechanism and species characteristics. Compared with the species level, relatively low genetic diversity was detected at the population level that might be the cause for its vulnerability. There was no significant relationship between genetic and geographical distances, while a significant correlation existed between genetic and environmental distances. Among nineteen climate variables, Annual Mean Temperature (bio1), Mean Diurnal Range (bio2), Isothermality (bio3), Temperature Seasonality (bio4), Precipitation of Wettest Month (bio13), Precipitation Seasonality (bio15), and Precipitation of Warmest Quarter (bio18) could explain the substantial levels of genetic variation (> 40%) in this species. The A. ginnala populations were isolated into multi-subpopulations by the heterogeneous climate conditions, which subsequently promoted the genetic divergence. Climatic heterogeneity played an important role in the pattern of genetic differentiation and population distribution of A. ginnala across a relatively wide range in Northern China. These would provide some clues for the conservation and management of this vulnerable species.
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Affiliation(s)
- Hang Ye
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Jiahui Wu
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China.,Changzhi University, Changzhi, 046011, Shanxi, China
| | - Zhi Wang
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Huimin Hou
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Yue Gao
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Wei Han
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Wenming Ru
- Changzhi University, Changzhi, 046011, Shanxi, China.
| | - Genlou Sun
- Department of Biology, Saint Mary's University, Halifax, NS, B3H3C3, Canada.
| | - Yiling Wang
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China.
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16
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Feng L, Ruhsam M, Wang YH, Li ZH, Wang XM. Using demographic model selection to untangle allopatric divergence and diversification mechanisms in the Rheum palmatum complex in the Eastern Asiatic Region. Mol Ecol 2020; 29:1791-1805. [PMID: 32306487 DOI: 10.1111/mec.15448] [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: 12/03/2019] [Revised: 03/30/2020] [Accepted: 04/08/2020] [Indexed: 12/22/2022]
Abstract
Allopatric divergence is often initiated by geological uplift and restriction to sky-islands, climate oscillations, or river capture. However, it can be difficult to establish which mechanism was the most likely to generate the current phylogeographical structure of a species. Recently, genomic data in conjunction with a model testing framework have been applied to address this issue in animals. To test whether such an approach is also likely to be successful in plants, we used population genomic data of the Rheum palmatum complex from the Eastern Asiatic Region, in conjunction with biogeographical reconstruction and demographic model selection, to identify the potential mechanism(s) which have led to the current level of divergence. Our results indicate that the R. palmatum complex originated in the central Hengduan Mts and possibly in regions further east, and then dispersed westward and eastward resulting in genetically distinct lineages. Populations are likely to have diverged in refugia during climate oscillations followed by subsequent expansion and secondary contact. However, model simulations within the western lineage of the R. palmatum complex cannot reject a restriction to sky-islands as a possible mechanism of diversification due to the genetically ambiguous position of one population. This highlights that genetically mixed populations might introduce ambiguity regarding the best diversification model in some cases. Although it might be possible to resolve this ambiguity using other data, sometimes this could prove to be difficult in complex biogeographical areas.
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Affiliation(s)
- Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory of Qiyao Resources and Anti-tumor Activities, Shaanxi Administration of Traditional Chinese Medicine, School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | | | - Yi-Han Wang
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Zhong-Hu Li
- College of Life Sciences, Northwest University, Xi'an, China
| | - Xu-Mei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory of Qiyao Resources and Anti-tumor Activities, Shaanxi Administration of Traditional Chinese Medicine, School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
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17
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Zhang D, Hui H, Yu G, Song X, Liu S, Yuan S, Xiao H, Rao D. Shared response to changes in drainage basin: Phylogeography of the Yunnan small narrow-mouthed frog, Glyphoglossus yunnanensis (Anura: Microhylidae). Ecol Evol 2020; 10:1567-1580. [PMID: 32076534 PMCID: PMC7029061 DOI: 10.1002/ece3.6011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 12/13/2019] [Accepted: 12/17/2019] [Indexed: 11/23/2022] Open
Abstract
AIM With the late Cenozoic uplift of the Qinghai-Tibetan Plateau (QTP), drainage of the southeastern edge of the QTP changed significantly. However, the impact of this dramatic change on the geographical distribution and genetic diversity of endemic organisms is still poorly understood. Here, we examined the geographical patterns of genetic variation in the Yunnan small narrow-mouthed frog, Glyphoglossus yunnanensis (Microhylidae), and two alternative hypotheses were tested: That is, the geographical distribution of genetic variation was determined by either the contemporary drainage basin or historical drainage basins. LOCATION The Mountains of southwest China. MATERIALS AND METHODS Analyses were based on 417 specimens collected from across the distribution of the species. We reconstructed the genealogy (Bayesian and maximum parsimony methods) and assessed demographic history based on DNA sequencing data from mitochondrial and nuclear markers. We also mapped the genetic diversity and estimated the divergence times by a relaxed clock model. RESULTS The species has maintained a relatively stable population size without recent population expansion. Four major maternal lineages were identified with good support, one representing a possible cryptic species and the other three showing further subdivision. The distribution of these deeply differentiated lineages/sublineages corresponded well to geographical regions. The secondary contact zones and phylogeographic breaks in distinct lineages of G. yunnanensis were almost concordant with those of Nanorana yunnanensis. MAIN CONCLUSIONS Lineage division conformed to the hypothesis of drainage system evolution, that is, the phylogeographic pattern of G. yunnanensis was shaped by historical drainage patterns. Concordance in phylogeographic patterns may suggest a shared response to common hydrogeological history and also might indicate that there was more contribution of the drainage history than ecological or life-history traits in structuring genetic variation between these two disparate codistributed taxa G. yunnanensis and N. yunnanensis.
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Affiliation(s)
- Dong‐Ru Zhang
- College of Life SciencesYunnan UniversityKunmingChina
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Hong Hui
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Guo‐Hua Yu
- College of Life SciencesGuangxi Normal UniversityGuilinChina
| | - Xin‐Qiang Song
- Yingjing Administration of Daxiangling Nature ReserveYaanChina
| | - Shuo Liu
- Kunming Natural History Museum of ZoologyKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Si‐Qi Yuan
- Bioengineering CollegeSichuan University of Science and EngineeringYibinChina
| | - Heng Xiao
- College of Life SciencesYunnan UniversityKunmingChina
| | - Ding‐Qi Rao
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
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18
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Xiao S, Ji Y, Liu J, Gong X. Genetic characterization of the entire range of Cycas panzhihuaensis (Cycadaceae). PLANT DIVERSITY 2020; 42:7-18. [PMID: 32140633 PMCID: PMC7046506 DOI: 10.1016/j.pld.2019.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 06/10/2023]
Abstract
Cycas panzhihuaensis L. Zhou & S. Y. Yang (Cycadaceae) is an endangered gymnosperm species endemic to the dry-hot valley of the Jinsha River basin in southwest China. Although the wild C. panzhihuaensis population from Panzhihua Cycad Natural Reserve is well protected and its genetic diversity has been well assessed, the genetic characteristics of populations outside the nature reserve, which face larger risks of extinction, remain unknown. Furthermore, the population genetics and historical dynamics of this endemic and endangered species have not been examined across its entire range. In this study, to analyze the genetic diversity, phylogeographical structure and demographic history of C. panzhihuaensis from all its seven known locations, we sequenced and compared molecular data from chloroplastic DNA (psbA-trnH, psbM-trnD, and trnS-trnG), single-copy nuclear genes (PHYP, AC5, HSP70, and AAT) from 61 individuals, as well as 11 nuclear microsatellite loci (SSR) from 102 individuals. We found relatively high genetic diversity within populations and high genetic differentiation among populations of C. panzhihuaensis, which is consistent with the patterns of other Asian inland cycads. Although no significant phylogeographical structure was detected, we found that small and unprotected populations possess higher genetic diversity and more unique haplotypes, which revises our understanding of diversity within this species and deserves due attention. Analysis of demographic dynamics suggest that human activity might be the key threat to C. panzhihuaensis. Based on the genetic characterization of C. panzhihuaensis, we propose several practical guidelines for the conservation of this species, especially for the populations with small sizes.
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Affiliation(s)
- Siyue Xiao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei RD, Panlong District, Kunming, Yunnan province, 650201, China
- University of Chinese Academy of Sciences, No. 19A, Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Yunheng Ji
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei RD, Panlong District, Kunming, Yunnan province, 650201, China
| | - Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei RD, Panlong District, Kunming, Yunnan province, 650201, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei RD, Panlong District, Kunming, Yunnan province, 650201, China
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19
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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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20
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Qian ZH, Li Y, Li MW, He YX, Li JX, Ye XF. Molecular Phylogeography Analysis Reveals Population Dynamics and Genetic Divergence of a Widespread Tree Pterocarya stenoptera in China. Front Genet 2019; 10:1089. [PMID: 31737056 PMCID: PMC6838215 DOI: 10.3389/fgene.2019.01089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 10/09/2019] [Indexed: 01/19/2023] Open
Abstract
The geological events, past climatic fluctuations, and river systems played key roles in the spatial distribution, population dynamics, and genetic differentiation of species. In this work, we selected Pterocarya stenoptera, a widespread tree species in China, to test the roles of these factors. Four noncoding spacers, eight microsatellite (simple sequence repeat) markers, and species distribution modeling were used to examine the phylogeographical pattern of P. stenoptera. Based on chloroplast DNA data, populations of P. stenoptera were clearly clustered into three groups. The divergence time of these groups fell into the stage of the Qinghai–Tibet Movement, 1.7–2.6 Ma. For simple sequence repeat data, only one western marginal population YNYB could be separated from other populations, whereas other populations were mixed together. Our results indicated that the environmental heterogeneity resulting from the Qinghai–Tibet movement might be response for this genetic divergence. The climatic fluctuations in the Pleistocene did not cause the substantial range shift of P. stenoptera, while the fluctuations affected its population size. Moreover, we also confirmed the river systems did not act as channels or barrier of dispersal for P. stenoptera.
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Affiliation(s)
- Zhi-Hao Qian
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Yong Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Ming-Wan Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Yan-Xia He
- School of Life Sciences, Henan University, Kaifeng, China
| | - Jia-Xin Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Xiao-Fan Ye
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
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21
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Zhang X, Zhang L, Schinnerl J, Sun WB, Chen G. Genetic diversity and population structure of Hibiscus aridicola, an endangered ornamental species in dry-hot valleys of Jinsha River. PLANT DIVERSITY 2019; 41:300-306. [PMID: 31934674 PMCID: PMC6951272 DOI: 10.1016/j.pld.2019.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 06/30/2019] [Accepted: 07/02/2019] [Indexed: 06/10/2023]
Abstract
Hibiscus aridicola is an endangered ornamental shrub of the family Malvaceae that is endemic to the dry-hot valleys of Jinsha River in southwestern China. This species is a typical plant species with extremely small populations (PSESP). To support and monitor future conservation, develop management measures, and genotype this species, we performed extensive field studies together with genetic analyses. Specifically, we screened eleven microsatellite loci of 69 individuals of H. aridicola from four accessions. The population genetics analyses indicated that H. aridicola possesses high genetic diversity at both the population (0.6962-0.7293) and species level (0.7837) compared to other endemic/endangered species in China. The low differentiation of populations (Fst = 0.0971) and the high gene flow between populations of H. aridicola (Nm = 2.3236) could be due to its distribution along rivers in the hot-valleys of the Jinsha River and the wind-mediated dispersal of its seeds. Furthermore, the genetic diversity of H. aridicola is slightly positively correlated with geographic distance. Two populations are undergoing a genetic bottleneck, and require more specific attention from conservationists. Additionally, our analyses of the population genetics of H. aridicola demonstrate that the declines in populations are not the result of the internal genetics of these populations but due to external human activities over the past decades.
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Affiliation(s)
- Xin Zhang
- Yunnan Forestry Technological College, Kunming, 650224, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming, 650204, China
| | - Le Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming, 650204, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Johann Schinnerl
- Chemodiversity Research Group, Division of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030, Vienna, Austria
| | - Wei-Bang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming, 650204, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Gao Chen
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming, 650204, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
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22
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Dong W, Wang D, Tian H, Pu Y, Yu L, Duan X, Liu S, Chen D. Genetic structure of two sympatric gudgeon fishes ( Xenophysogobio boulengeri and X. nudicorpa) in the upper reaches of Yangtze River Basin. PeerJ 2019; 7:e7393. [PMID: 31404431 PMCID: PMC6688597 DOI: 10.7717/peerj.7393] [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: 10/31/2018] [Accepted: 07/02/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Xenophysogobio boulengeri and X. nudicorpa are the only two species within the genus Xenophysogobio (Cyprinidae, Cypriniformes), and both are endemic to the upper reaches of the Yangtze River. In recent years, due to human activities, the natural resources available to both species have declined sharply. Sympatric species with overlapping niches inevitably compete for their habitats, and genetic structure and diversity can reflect population history and their potential for adaptation to changing environments, which is useful for management decisions. METHODS In the present study, microsatellite DNA and mitochondrial DNA (mtDNA) markers were used to investigate the patterns of population genetic structure for X. boulengeri and X. nudicorpa. Microsatellite DNA data, jointly with traditional summary statistics including F ST and F is, were used to assess the population genetic structure by structure analysis. The mtDNA sequences were then used to examine these patterns through time to detect demographic history. RESULTS Xenophysogobio boulengeri and X. nudicorpa exhibited high levels of genetic diversity in Yangtze River populations, except for two populations of X. nudicorpa in the Jinsha River, which were low in mtDNA diversity. X. boulengeri showed genetic homogeneity among populations, whereas X. nudicorpa appeared to have significant geographic genetic divergence. Both species experienced a late-Pleistocene sudden population expansion in Yangtze River populations, but not in the Jinsha River populations of X. nudicorpa. DISCUSSION The genetic homogeneity of X. boulengeri populations might result from similar population expansion events and environment features. The geographic genetic subdivision for X. nudicorpa between the Jinsha and Yangtze Rivers might be caused by the geographic isolation in the middle Pliocene, as well as climate and environmental heterogeneity.
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Affiliation(s)
- Weiwei Dong
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, China
| | - Dengqiang Wang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, China
| | - Huiwu Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, China
| | - Yan Pu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, China
| | - Lixiong Yu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, China
| | - Xinbin Duan
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, China
| | - Shaoping Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, China
| | - Daqing Chen
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, China
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Wang Z, Meng S, Rao G. Quaternary climate change and habitat preference shaped the genetic differentiation and phylogeography of Rhodiola sect. Prainia in the southern Qinghai-Tibetan Plateau. Ecol Evol 2019; 9:8305-8319. [PMID: 31380091 PMCID: PMC6662313 DOI: 10.1002/ece3.5406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 11/19/2022] Open
Abstract
There are two long-standing biogeographic hypotheses regarding the glacial survival of plant species in the Qinghai-Tibetan Plateau (QTP): the in situ survival hypothesis and the tabula rasa hypothesis. We tested these two hypotheses in a phylogeographic study of Rhodiola sect. Prainia, a monophyletic section with ecologically divergent lineages. Molecular data from the nuclear internal transcribed spacer, six plastid markers and 13 nuclear microsatellite loci were analyzed for 240 individuals from 19 populations of this section. Environmental data were used to analyze the niches of major phylogenetic lineages within this section and to model changes in their distributions since the Last Glacial Maximum (LGM). We found that Rhodiola sect. Prainia consists of three evolutionary lineages: all populations of R. stapfii, R. prainii populations at the southern edge of the QTP, and R. prainii populations in the interior part of the QTP. During the LGM, the survival of R. prainii in the interior part of the QTP corresponded with the in situ survival hypothesis, while R. stapfii most probably survived the LGM in a manner corresponding with the tabula rasa hypothesis. The evolutionary history of different lineages of this section was shaped by topography, climate change, and lineage-specific habitat preferences.
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Affiliation(s)
- Zi‐Meng Wang
- School of Life SciencesPeking UniversityBeijingChina
| | - Shi‐Yong Meng
- School of Life SciencesPeking UniversityBeijingChina
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Muellner-Riehl AN. Mountains as Evolutionary Arenas: Patterns, Emerging Approaches, Paradigm Shifts, and Their Implications for Plant Phylogeographic Research in the Tibeto-Himalayan Region. FRONTIERS IN PLANT SCIENCE 2019; 10:195. [PMID: 30936883 PMCID: PMC6431670 DOI: 10.3389/fpls.2019.00195] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 02/05/2019] [Indexed: 05/05/2023]
Abstract
Recently, the "mountain-geobiodiversity hypothesis" (MGH) was proposed as a key concept for explaining the high levels of biodiversity found in mountain systems of the Tibeto-Himalayan region (THR), which comprises the Qinghai-Tibetan Plateau, the Himalayas, and the biodiversity hotspot known as the "Mountains of Southwest China" (Hengduan Mountains region). In addition to the MGH, which covers the entire life span of a mountain system, a complementary concept, the so-called "flickering connectivity system" (FCS), was recently proposed for the period of the Quaternary. The FCS focuses on connectivity dynamics in alpine ecosystems caused by the drastic climatic changes during the past ca. 2.6 million years, emphasizing that range fragmentation and allopatric speciation are not the sole factors for accelerated evolution of species richness and endemism in mountains. I here provide a review of the current state of knowledge concerning geological uplift, Quaternary glaciation, and the main phylogeographic patterns ("contraction/recolonization," "platform refugia/local expansion," and "microrefugia") of seed plant species in the THR. In addition, I make specific suggestions as to which factors future avenues of phylogeographic research should take into account based on the fundamentals presented by the MGH and FCS, and associated complementary paradigm shifts.
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Affiliation(s)
- Alexandra N. Muellner-Riehl
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Leipzig University, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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Ma X, Wang Z, Tian B, Sun H. Phylogeographic Analyses of the East Asian Endemic Genus Prinsepia and the Role of the East Asian Monsoon System in Shaping a North-South Divergence Pattern in China. Front Genet 2019; 10:128. [PMID: 30863425 PMCID: PMC6399409 DOI: 10.3389/fgene.2019.00128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/05/2019] [Indexed: 11/13/2022] Open
Abstract
Prinsepia Royle (Rosaceae) is a genus native to China and the Himalayan region. In order to explain its current fragmented distribution pattern and to compare the impact of relatively recent climate changes on the genetic structure of Prinsepia species in different regions of China, a total of 66 populations and 617 individuals of four species of Prinsepia were genotyped, using three cpDNA markers. Meanwhile, phylogenetic reconstructions and divergence dating were conducted using the cpDNA haplotypes dataset and the nuclear ribosomal internal transcribed spacer (ITS) dataset, respectively. Ecological niche modeling (ENM) was performed to predict the potential distribution of each species of Prinsepia at present and during the Last Glacial Maximum. Both ITS and cpDNA gene trees support a north-south divergence of Prinsepia species in China. The divergence time of the northern and southern Clades occurred around the late Oligocene epoch. Combining the present distribution of Prinsepia species and their habitats, we inferred that the transition to a monsoon climate system in East Asia during the late Oligocene epoch, created a humid forest vegetation zone from central to East China, which potentially gave rise to the north-south divergence of Prinsepia species. Both regional climates and allopatric divergence may have played an important role in the speciation of P. sinensis and P. uniflora. P. sinensis had the lowest genetic diversity and a putative northward post-glacial colonization. The distribution range of P. uniflora was also extremely sensitive to interglacial-glacial cycles. P. utilis from southwestern China preserved more haplotypes than P. sinensis and P. uniflora due to its multiple and isolated refugia.
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Affiliation(s)
- Xiangguang Ma
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhiwei Wang
- Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Bin Tian
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Low population genetic differentiation in two Tamarix species (Tamarix austromongolica and Tamarix chinensis) along the Yellow River. Genetica 2018; 147:13-22. [DOI: 10.1007/s10709-018-0047-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 11/16/2018] [Indexed: 10/27/2022]
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Yu H, Favre A, Sui X, Chen Z, Qi W, Xie G. Mapping the genetic patterns of plants in the region of the Qinghai-Tibet Plateau: Implications for conservation strategies. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12847] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Haibin Yu
- School of Life Sciences; Guangzhou University; Guangzhou China
| | - Adrien Favre
- Senckenberg Research Institute and Natural History Museum; Frankfurt am Main Germany
| | - Xinghua Sui
- State Key Laboratory of Biocontrol; School of Life Sciences; Sun Yat-sen University; Guangzhou China
| | - Zhao Chen
- Guangdong Institute of Eco-environmental Science & Technology; Guangzhou China
| | - Wei Qi
- Institute of Polar Meteorology; Chinese Academy of Meteorological Sciences; Beijing China
| | - Guowen Xie
- School of Life Sciences; Guangzhou University; Guangzhou China
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28
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Feng B, Yang Z. Studies on diversity of higher fungi in Yunnan, southwestern China: A review. PLANT DIVERSITY 2018; 40:165-171. [PMID: 30740561 PMCID: PMC6137262 DOI: 10.1016/j.pld.2018.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 06/02/2023]
Abstract
Yunnan is exceedingly rich in higher fungi (Ascomycota and Basidiomycota). Given that the number of fungi (including lichens) occurring in a given area is, as Hawksworth suggested, roughly six times that of local vascular plants, a total of approximately 104,000 fungal species would be expected in Yunnan. However, to date only about 6000 fungal species, including roughly 3000 species of higher fungi, have been reported from the province. Although studies on Yunnan's fungi started in the late nineteenth century, significant progress has been made only in the last forty-five years. Over the first twenty-five years of this period, studies on fungal diversity in this area have largely been about taxonomy based on morphological characters and partially on geographical distribution. Over the past twenty years, the combination of both morphological and molecular phylogenetic approaches has become the preferred method to help understand the diversity and evolution of higher fungi. This review focuses on our current knowledge of how geological, geographical, and ecological factors may have contributed to the diversity patterns of higher fungi in Yunnan. Based on this knowledge, three aspects for future studies are suggested.
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Affiliation(s)
| | - Zhuliang Yang
- Corresponding author. Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road #132, Kunming 650201, Yunnan, China.
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29
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Yu WB, Randle CP, Lu L, Wang H, Yang JB, dePamphilis CW, Corlett RT, Li DZ. The Hemiparasitic Plant Phtheirospermum (Orobanchaceae) Is Polyphyletic and Contains Cryptic Species in the Hengduan Mountains of Southwest China. FRONTIERS IN PLANT SCIENCE 2018; 9:142. [PMID: 29479366 PMCID: PMC5812252 DOI: 10.3389/fpls.2018.00142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/25/2018] [Indexed: 05/04/2023]
Abstract
Phtheirospermum (Orobanchaceae), a hemiparasitic genus of Eastern Asia, is characterized by having long and viscous glandular hairs on stems and leaves. Despite this unifying character, previous phylogenetic analyses indicate that Phtheirospermum is polyphyletic, with Phtheirospermum japonicum allied with tribe Pedicularideae and members of the Ph. tenuisectum complex allied with members of tribe Rhinantheae. However, no analyses to date have included broad phylogenetic sampling necessary to test the monophyly of Phtheirospermum species, and to place these species into the existing subfamiliar taxonomic organization of Orobanchaceae. Two other genera of uncertain phylogenetic placement are Brandisia and Pterygiella, also both of Eastern Asia. In this study, broadly sampled phylogenetic analyses of nrITS and plastid DNA revealed hard incongruence between these datasets in the placement of Brandisia. However, both nrITS and the plastid datasets supported the placement of Ph. japonicum within tribe Pedicularideae, and a separate clade consisting of the Ph. tenuisectum complex and a monophyletic Pterygiella. Analyses were largely in agreement that Pterygiella, the Ptheirospermum complex, and Xizangia form a clade not nested within any of the monophyletic tribes of Orobanchaceae recognized to date. Ph. japonicum, a model species for parasitic plant research, is widely distributed in Eastern Asia. Despite this broad distribution, both nrITS and plastid DNA regions from a wide sampling of this species showed high genetic identity, suggesting that the wide species range is likely due to a recent population expansion. The Ph. tenuisectum complex is mainly distributed in the Hengduan Mountains region. Two cryptic species were identified by both phylogenetic analyses and morphological characters. Relationships among species of the Ph. tenuisectum complex and Pterygiella remain uncertain. Estimated divergence ages of the Ph. tenuisectum complex corresponding to the last two uplifts of the Qinghai-Tibet Plateau at around 8.0-7.0 Mya and 3.6-1.5 Mya indicated that the development of a hot-dry valley climate during these uplifts may have driven species diversification in the Ph. tenuisectum complex.
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Affiliation(s)
- Wen-Bin Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden (CAS), Mengla, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Myanmar
| | - Christopher P. Randle
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, United States
| | - Lu Lu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hong Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jun-Bo Yang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Claude W. dePamphilis
- Department of Biology, Graduate Program in Plant Biology, The Pennsylvania State University, State College, PA, United States
| | - Richard T. Corlett
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden (CAS), Mengla, China
| | - De-Zhu Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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30
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Liang HY, Feng ZP, Pei B, Li Y, Yang XT. Demographic expansion of two Tamarix species along the Yellow River caused by geological events and climate change in the Pleistocene. Sci Rep 2018; 8:60. [PMID: 29311687 PMCID: PMC5758526 DOI: 10.1038/s41598-017-19034-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 12/20/2017] [Indexed: 11/13/2022] Open
Abstract
The geological events and climatic fluctuations during the Pleistocene played important roles in shaping patterns of species distribution. However, few studies have evaluated the patterns of species distribution that were influenced by the Yellow River. The present work analyzed the demography of two endemic tree species that are widely distributed along the Yellow River, Tamarix austromongolica and Tamarix chinensis, to understand the role of the Yellow River and Pleistocene climate in shaping their distribution patterns. The most common chlorotype, chlorotype 1, was found in all populations, and its divergence time could be dated back to 0.19 million years ago (Ma). This dating coincides well with the formation of the modern Yellow River and the timing of Marine Isotope Stages 5e-6 (MIS 5e-6). Bayesian reconstructions along with models of paleodistribution revealed that these two species experienced a demographic expansion in population size during the Quaternary period. Approximate Bayesian computation analyses supported a scenario of expansion approximately from the upper to lower reaches of the Yellow River. Our results provide support for the roles of the Yellow River and the Pleistocene climate in driving demographic expansion of the populations of T. austromongolica and T. chinensis. These findings are useful for understanding the effects of geological events and past climatic fluctuations on species distribution patterns.
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Affiliation(s)
- Hong-Yan Liang
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China.,Sanmenxia Polytechnic, Sanmenxia, 472000, China
| | - Zhi-Pei Feng
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Bing Pei
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yong Li
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xi-Tian Yang
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China.
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31
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Ratnam J, Tomlinson KW, Rasquinha DN, Sankaran M. Savannahs of Asia: antiquity, biogeography, and an uncertain future. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0305. [PMID: 27502371 DOI: 10.1098/rstb.2015.0305] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2016] [Indexed: 11/12/2022] Open
Abstract
The savannahs of Asia remain locally unrecognized as distinctive ecosystems, and continue to be viewed as degraded forests or seasonally dry tropical forests. These colonial-era legacies are problematic, because they fail to recognize the unique diversity of Asian savannahs and the critical roles of fire and herbivory in maintaining ecosystem health and diversity. In this review, we show that: the palaeo-historical evidence suggests that the savannahs of Asia have existed for at least 1 million years, long before widespread landscape modification by humans; savannah regions across Asia have levels of C4 grass endemism and diversity that are consistent with area-based expectations for non-Asian savannahs; there are at least three distinct Asian savannah communities, namely deciduous broadleaf savannahs, deciduous fine-leafed and spiny savannahs and evergreen pine savannahs, with distinct functional ecologies consistent with fire- and herbivory-driven community assembly. Via an analysis of savannah climate domains on other continents, we map the potential extent of savannahs across Asia. We find that the climates of African savannahs provide the closest analogues for those of Asian deciduous savannahs, but that Asian pine savannahs occur in climates different to any of the savannahs in the southern continents. Finally, we review major threats to the persistence of savannahs in Asia, including the mismanagement of fire and herbivory, alien woody encroachment, afforestation policies and future climate uncertainty associated with the changing Asian monsoon. Research agendas that target these issues are urgently needed to manage and conserve these ecosystems.This article is part of the themed issue 'Tropical grassy biomes: linking ecology, human use and conservation'.
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Affiliation(s)
- Jayashree Ratnam
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Kyle W Tomlinson
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, Yunnan, People's Republic of China
| | - Dina N Rasquinha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Mahesh Sankaran
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560065, India Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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Sun H, Zhang J, Deng T. Origins and evolution of plant diversity in the Hengduan Mountains, China. PLANT DIVERSITY 2017; 39:161-166. [PMID: 30159507 PMCID: PMC6112316 DOI: 10.1016/j.pld.2017.09.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 05/07/2023]
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Chen W, Shen Y, Gan X, Wang X, He S. Genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River (upper Mekong). Ecol Evol 2016; 6:6023-36. [PMID: 27648223 PMCID: PMC5016629 DOI: 10.1002/ece3.2319] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 11/28/2022] Open
Abstract
The genus Schizothorax (Cyprinidae), one of the most diverse genera of ichthyofauna of the Qinghai‐Tibetan Plateau (QTP), is a good candidate for investigating patterns of genetic variation and evolutionary mechanisms. In this study, sequences from the mitochondrial control region, the cytochrome b gene, and two nuclear genes were used to re‐examine the genetic diversity and investigate the evolutionary history of the Schizothorax species complex inhabiting the Lancang River. Three maternal clades were detected in the Schizothorax species complex, but frequent nuclear allele sharing also occurred among the three maternal clades. A discrepancy between topologies of mitochondrial and nuclear loci might result from introgression or/and incomplete lineage sorting. The divergence of the clades of the Schizothorax species complex was closely related to the Late Pliocene and Early Pleistocene orogenesis of the QTP and Southwest Mountains of China. Demographic analyses indicated that the species complex subsequently persisted in situ with stable populations during Pleistocene glacial cycling, which suggested that Pleistocene climate changes did not exert a remarkable influence on the species complex. Our study provides a comprehensive analysis of the genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River.
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Affiliation(s)
- Weitao Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei 430072 China; Graduate School of Chinese Academy of Sciences Beijing 10001 China
| | - Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei 430072 China; Graduate School of Chinese Academy of Sciences Beijing 10001 China
| | - Xiaoni Gan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei 430072 China
| | - Xuzhen Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei 430072 China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei 430072 China
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Feng B, Zhao Q, Xu J, Qin J, Yang ZL. Drainage isolation and climate change-driven population expansion shape the genetic structures of Tuber indicum complex in the Hengduan Mountains region. Sci Rep 2016; 6:21811. [PMID: 26906144 PMCID: PMC4764814 DOI: 10.1038/srep21811] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 02/01/2016] [Indexed: 11/29/2022] Open
Abstract
The orogenesis of the Qinghai-Tibetan Plateau and the Quaternary climate changes have played key roles in driving the evolution of flora and fauna in Southwest China, but their effects on higher fungi are poorly addressed. In this study, we investigated the phylogeographic pattern of the Tuber indicum species complex, an economically important fungal group distributed in the Hengduan Mountains region. Our data confirmed the existence of two distinct lineages, T. indicum and T. himalayense, within this species complex. Three geographic groups (Groups W, N and C) were revealed within T. indicum, with Group W found in the paleo-Lancang River region, while Groups N and C corresponded to the two banks along the contemporary Jinsha River, suggesting that rivers have acted as barriers for gene flow among populations from different drainages. Historical range expansion resulted from climate changes was inferred in Group C, contributing to the observed gene flow among geographic populations within this group. Although no significant geographic structure was identified in T. himalayense, evidence of drainage isolation for this species was also detected. Our findings demonstrate that both topographic changes and Quaternary climate oscillations have played important roles in driving the genetic structures of the T. indicum species complex.
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Affiliation(s)
- Bang Feng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Qi Zhao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Jiao Qin
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming, Yunnan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhu L Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming, Yunnan, China
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Climatic Factors Drive Population Divergence and Demography: Insights Based on the Phylogeography of a Riparian Plant Species Endemic to the Hengduan Mountains and Adjacent Regions. PLoS One 2015; 10:e0145014. [PMID: 26689776 PMCID: PMC4687034 DOI: 10.1371/journal.pone.0145014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/26/2015] [Indexed: 11/19/2022] Open
Abstract
Quaternary climatic factors have played a significant role in population divergence and demography. Here we investigated the phylogeography of Osteomeles schwerinae, a dominant riparian plant species of the hot/warm-dry river valleys of the Hengduan Mountains (HDM), Qinling Mountains (QLM) and Yunnan-Guizhou Plateau (YGP). Three chloroplast DNA (cpDNA) regions (trnD-trnT, psbD-trnT, petL-psbE), one single copy nuclear gene (glyceraldehyde 3-phosphate dehydrogenase; G3pdh), and climatic data during the Last Interglacial (LIG; c. 120–140 ka), Last Glacial Maximum (LGM; c. 21 ka), and Current (c. 1950–2000) periods were used in this study. Six cpDNA haplotypes and 15 nuclear DNA (nDNA) haplotypes were identified in the 40 populations of O. schwerinae. Spatial Analysis of Molecular Variance, median-joining networks, and Bayesian phylogenetic trees based on the cpDNA and nDNA datasets, all suggested population divergence between the QLM and HDM-YGP regions. Our climatic analysis identified significant heterogeneity of the climatic factors in the QLM and HDM-YGP regions during the aforementioned three periods. The divergence times based on cpDNA and nDNA haplotypes were estimated to be 466.4–159.4 ka and 315.8–160.3 ka, respectively, which coincide with the time of the weakening of the Asian monsoons in these regions. In addition, unimodal pairwise mismatch distribution curves, expansion times, and Ecological Niche Modeling suggested a history of population expansion (rather than contraction) during the last glaciation. Interestingly, the expansion times were found being well consistent with the intensification of the Asian monsoons during this period. We inferred that the divergence between the two main lineages is probably caused by disruption of more continuous distribution because of weakening of monsoons/less precipitation, whilst subsequent intensification of the Asian monsoons during the last glaciation facilitated the expansion of O. schwerinae populations.
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Wen Z, Xu Z, Zhang H, Feng Y. Chloroplast phylogeography of a desert shrub, Calligonum calliphysa (Calligonum, Polygonaceae), in arid Northwest China. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Tian B, Zhou Z, Du FK, He C, Xin P, Ma H. The Tanaka Line shaped the phylogeographic pattern of the cotton tree (Bombax ceiba) in southwest China. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.04.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Meng L, Chen G, Li Z, Yang Y, Wang Z, Wang L. Refugial isolation and range expansions drive the genetic structure of Oxyria sinensis (Polygonaceae) in the Himalaya-Hengduan Mountains. Sci Rep 2015; 5:10396. [PMID: 26013161 PMCID: PMC4445061 DOI: 10.1038/srep10396] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 04/10/2015] [Indexed: 11/11/2022] Open
Abstract
The formation of the Mekong-Salween Divide and climatic oscillations in Pleistocene were the main drivers for the contemporary diversity and genetic structure of plants in the Himalaya-Hengduan Mountains (HHM). To identify the relative roles of the two historical events in shaping population history of plants in HHM, we investigated the phylogeographic pattern of Oxyria sinensis, a perennial plant endemic to the HHM. Sixteen chloroplast haplotypes were identified and were clustered into three phylogenetic clades. The age of the major clades was estimated to be in the Pleistocene, falling into several Pleistocene glacial stages and postdating the formation of the Mekong-Salween Divide. Range expansions occurred at least twice in the early and middle Pleistocene, but the spatial genetic distribution rarely changed since the Last Glacial Maximum. Our results suggest that temporary mountain glaciers may act as barriers in promoting the lineage divergence in O. sinensis and that subsequential range expansions and secondary contacts might reshape the genetic distribution in geography and blur the boundary of population differentiation created in the earlier glacial stages. This study demonstrates that Pleistocene climatic change and mountain glaciers, rather than the Mekong-Salween Divide, play the primary role in shaping the spatial genetic structure of O. sinensis.
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Affiliation(s)
- Lihua Meng
- School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy Ministry of Education, Yunnan Normal University, Kunming 650092, Yunnan, P. R. China
| | - Gang Chen
- Graduate School of Oceanography, University of Rhode Island, 02881, RI USA
| | - Zhonghu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, Shanxi, P. R.China
| | - Yongping Yang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, Yunnan, P. R. China
| | - Zhengkun Wang
- School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy Ministry of Education, Yunnan Normal University, Kunming 650092, Yunnan, P. R. China
| | - Liuyang Wang
- Department of Biology, Duke University, Durham, 27708, NC USA
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Zhao Y, Zhang L. The phylogeographic history of the self-pollinated herb Tacca chantrieri (Dioscoreaceae) in the tropics of mainland Southeast Asia. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2014.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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40
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Zhang JQ, Meng SY, Rao GY. Phylogeography of Rhodiola kirilowii (Crassulaceae): a story of Miocene divergence and quaternary expansion. PLoS One 2014; 9:e112923. [PMID: 25389750 PMCID: PMC4229298 DOI: 10.1371/journal.pone.0112923] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/16/2014] [Indexed: 02/07/2023] Open
Abstract
The evolution and current distribution of the Sino-Tibetan flora have been greatly affected by historical geological events, such as the uplift of the Qinghai-Tibetan Plateau (QTP), and Quaternary climatic oscillations. Rhodiola kirilowii, a perennial herb with its distribution ranging from the southeastern QTP and the Hengduan Mountains (HM) to adjacent northern China and central Asia, provides an excellent model to examine and disentangle the effect of both geological orogeny and climatic oscillation on the evolutionary history of species with such distribution patterns. We here conducted a phylogeographic study using sequences of two chloroplast fragments (trnL-F and trnS-G) and internal transcribed spacers in 29 populations of R. kirilowii. A total of 25 plastid haplotypes and 12 ITS ribotypes were found. Molecular clock estimation revealed deep divergence between the central Asian populations and other populations from the HM and northern China; this split occurred ca. 2.84 million year ago. The majority of populations from the mountains of northern China were dominated by a single haplotype or ribotype, while populations of the HM harbored both high genetic diversity and high haplotype diversity. This distribution pattern indicates that HM was either a diversification center or a refugium for R. kirilowii during the Quaternary climatic oscillations. The present distribution of this species on mountains in northern China may have resulted from a rapid glacial population expansion from the HM. This expansion was confirmed by the mismatch distribution analysis and negative Tajima's D and Fu's FS values, and was dated to ca. 168 thousand years ago. High genetic diversity and population differentiation in both plastid and ITS sequences were revealed; these imply restricted gene flow between populations. A distinct isolation-by-distance pattern was suggested by the Mantel test. Our results show that in old lineages, populations may harbour divergent genetic forms that are sufficient to maintain or even increase overall genetic diversity despite fragmentation and low within-population variation.
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Affiliation(s)
| | - Shi-Yong Meng
- College of Life Sciences, Peking University, Beijing, China
| | - Guang-Yuan Rao
- College of Life Sciences, Peking University, Beijing, China
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Guo XD, Wang HF, Bao L, Wang TM, Bai WN, Ye JW, Ge JP. Evolutionary history of a widespread tree species Acer mono in East Asia. Ecol Evol 2014; 4:4332-45. [PMID: 25540694 PMCID: PMC4267871 DOI: 10.1002/ece3.1278] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 09/12/2014] [Accepted: 09/16/2014] [Indexed: 11/13/2022] Open
Abstract
East Asia has the most diverse temperate flora in the world primarily due to the lack of Pleistocene glaciation and the geographic heterogeneity. Although increasing phylogeography studies in this region provided more proofs in this issue, discrepancies and uncertainty still exist, especially in northern temperate deciduous broad-leaved and coniferous mixed forest region (II). And a widespread plant species could reduce the complexity to infer the relationship between diversity and physiographical pattern. Hence, we studied the evolution history of a widespread temperate tree, Acer mono, populations in region II and the influence of physiographic patterns on intraspecific genetic diversity. Analyses of chloroplast sequences and nuclear microsatellites indicated high levels of genetic diversity. The diversity distribution was spatially heterogeneous and a latitudinal cline existed in both markers. The spatial distribution pattern between genetic diversity within A. mono and the diversity at species level was generally consistent. Western subtropical evergreen broad-leaved forest subregion (IVb) had a unique ancient chloroplast clade (CP3) and a nuclear gene pool (GP5) with dominance indicating the critical role of this area in species diversification. Genetic data and ecological niche model results both suggested that populations in region II disappeared during the last glacial maximum (LGM) and recovered from south of Changbai Mt. and the Korean Peninsula. Two distribution centers were likely during the LGM, one in the north edge of warm temperate deciduous broad-leaved forest region (III) and another in the south edge of region III. This was reflected by the genetic pattern with two spatially independent genetic groups. This study highlights the key role of region III in sustaining genetic diversity in the northern range and connecting diversity between southern and northern range. We elucidated the diversity relationship between vegetation regions which could facilitate the understanding of biodiversity origin and maintenance in East Asia.
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Affiliation(s)
- Xi-Di Guo
- State Key Laboratory of Earth Surface Processes and Resource Ecology & College of Life Sciences, Beijing Normal University Beijing, 100875, China
| | - Hong-Fang Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology & College of Life Sciences, Beijing Normal University Beijing, 100875, China
| | - Lei Bao
- State Key Laboratory of Earth Surface Processes and Resource Ecology & College of Life Sciences, Beijing Normal University Beijing, 100875, China
| | - Tian-Ming Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology & College of Life Sciences, Beijing Normal University Beijing, 100875, China
| | - Wei-Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology & College of Life Sciences, Beijing Normal University Beijing, 100875, China
| | - Jun-Wei Ye
- State Key Laboratory of Earth Surface Processes and Resource Ecology & College of Life Sciences, Beijing Normal University Beijing, 100875, China
| | - Jian-Ping Ge
- State Key Laboratory of Earth Surface Processes and Resource Ecology & College of Life Sciences, Beijing Normal University Beijing, 100875, China
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Wang CB, Wang T, Su YJ. Phylogeography of Cephalotaxus oliveri (Cephalotaxaceae) in relation to habitat heterogeneity, physical barriers and the uplift of the Yungui Plateau. Mol Phylogenet Evol 2014; 80:205-16. [PMID: 25160902 DOI: 10.1016/j.ympev.2014.08.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 08/11/2014] [Accepted: 08/13/2014] [Indexed: 11/28/2022]
Abstract
Habitat heterogeneity, physical barriers, and the uplift of the Yungui Plateau were found to deeply affect the phylogeographic pattern and evolutionary history of Cephalotaxus oliveri, a perennial conifer endemic to China. In this study, we explored the phylogeography using three chloroplast sequences (trnL-trnF, trnT-trnD and atpB-rbcL) in 22 natural populations of C. oliveri distributed throughout its range. The Yungui Plateau populations of C. oliveri were revealed to origin ca. 9.15Ma by molecular clock estimation, which is consistent with rapid uplift of the Qinghai-Tibetan Plateau (QTP) ca. 8-10Ma. Additionally, geological effects of the Yungui Plateau were suggested to promote the rapid intra-specific differentiation of C. oliveri in the Pliocene and Early Pleistocene. The relatively low level of genetic diversity (h=0.719, θ=1.17×10(-3)) and high population differentiation (NST=0.771 and GST=0.642) implied restricted gene flow among populations, which was confirmed by the Nested Clade Analysis (NCA). Mismatch distribution and haplotypes network provided evidences of recent demographic population expansion. Furthermore, the statistical dispersal-vicariance analysis indicated that the center of origin was in Central China. The comparison of haplotype distribution patterns indicated that the regions of HNHPS and HBLD were the potential refugia during the Pleistocene ice ages. Our results highlighted that habitat heterogeneity and physical barriers presenting in a species range can predict genetic patterns.
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Affiliation(s)
- C B Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - T Wang
- College of Life Science, South China Agricultural University, Guangzhou 510642, China.
| | - Y J Su
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen 518057, China; State Key Laboratory of Biocontrol Shenzhen R&D Center, Shenzhen 518057, China; Institute for Technology Research and Innovation of Sun Yat-sen University, Zhuhai 519000, China.
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Quan QM, Chen LL, Wang X, Li S, Yang XL, Zhu YG, Wang M, Cheng Z. Genetic diversity and distribution patterns of host insects of Caterpillar Fungus Ophiocordyceps sinensis in the Qinghai-Tibet Plateau. PLoS One 2014; 9:e92293. [PMID: 24667533 PMCID: PMC3965410 DOI: 10.1371/journal.pone.0092293] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 02/20/2014] [Indexed: 11/25/2022] Open
Abstract
The caterpillar fungus Ophiocordyceps sinensis is one of the most valuable medicinal fungi in the world, and it requires host insects in family Hepialidae (Lepidoptera) to complete its life cycle. However, the genetic diversity and phylogeographic structures of the host insects remain to be explored. We analyzed the genetic diversity and temporal and spatial distribution patterns of genetic variation of the host insects throughout the O. sinensis distribution. Abundant haplotype and nucleotide diversity mainly existed in the areas of Nyingchi, ShangriLa, and around the edge of the Qinghai-Tibet Plateau, where are considered as the diversity center or micro-refuges of the host insects of O. sinensis. However, there was little genetic variation among host insects from 72.1% of all populations, indicating that the host species composition might be relatively simple in large-scale O. sinensis populations. All host insects are monophyletic except for those from four O. sinensis populations around Qinghai Lake. Significant phylogeographic structure (NST>GST, P<0.05) was revealed for the monophyletic host insects, and the three major phylogenetic groups corresponded with specific geographical areas. The divergence of most host insects was estimated to have occurred at ca. 3.7 Ma, shortly before the rapid uplift of the QTP. The geographical distribution and star-like network of the haplotypes implied that most host insects were derived from the relicts of a once-widespread host that subsequently became fragmented. Neutrality tests, mismatch distribution analysis, and expansion time estimation confirmed that most host insects presented recent demographic expansions that began ca. 0.118 Ma in the late Pleistocene. Therefore, the genetic diversity and distribution of the present-day insects should be attributed to effects of the Qinghai-Tibet Plateau uplift and glacial advance/retreat cycles during the Quaternary ice age. These results provide valuable information to guide the protection and sustainable use of these host insects as well as O. sinensis.
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Affiliation(s)
- Qing-Mei Quan
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Ling-Ling Chen
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Xi Wang
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Shan Li
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Xiao-Ling Yang
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Yun-Guo Zhu
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Mu Wang
- School of Plant Sciences and Technology, Agriculture and Animal Husbandry College of Tibet, Nyingchi, Tibet, China
| | - Zhou Cheng
- School of Life Science and Technology, Tongji University, Shanghai, China
- * E-mail:
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Fan DM, Yue JP, Nie ZL, Li ZM, Comes HP, Sun H. Phylogeography ofSophora davidii(Leguminosae) across the ‘Tanaka-Kaiyong Line’, an important phytogeographic boundary in Southwest China. Mol Ecol 2013; 22:4270-4288. [DOI: 10.1111/mec.12388] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 05/13/2013] [Accepted: 05/13/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Deng Mei Fan
- Key Laboratory of Biodiversity and Biogeography; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650204 China
- Laboratory of Subtropical Biodiversity; Jiangxi Agricultural University; Nanchang Jiangxi 330045 China
| | - Ji Pei Yue
- Key Laboratory of Biodiversity and Biogeography; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650204 China
| | - Ze Long Nie
- Key Laboratory of Biodiversity and Biogeography; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650204 China
| | - Zhi Min Li
- School of Life Science; Yunnan Normal University; Kunming 650092 Yunnan China
| | - Hans Peter Comes
- Department of Organismic Biology; University of Salzburg; Hellbrunnerstrasse 34 A-5020 Salzburg Austria
| | - Hang Sun
- Key Laboratory of Biodiversity and Biogeography; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650204 China
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Potts AJ, Hedderson TA, Cowling RM. Testing large-scale conservation corridors designed for patterns and processes: comparative phylogeography of three tree species. DIVERS DISTRIB 2013. [DOI: 10.1111/ddi.12113] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Alastair J. Potts
- Department of Biological Sciences; Bolus Herbarium; University of Cape Town; Cape Town Western Cape 7700 South Africa
| | - Terry A. Hedderson
- Department of Biological Sciences; Bolus Herbarium; University of Cape Town; Cape Town Western Cape 7700 South Africa
| | - Richard M. Cowling
- Department of Botany; Nelson Mandela Metropolitan University; Port Elizabeth Eastern Cape 6031 South Africa
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Wang B, Mao JF, Zhao W, Wang XR. Impact of Geography and Climate on the Genetic Differentiation of the Subtropical Pine Pinus yunnanensis. PLoS One 2013; 8:e67345. [PMID: 23840668 PMCID: PMC3693954 DOI: 10.1371/journal.pone.0067345] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 05/16/2013] [Indexed: 12/22/2022] Open
Abstract
Southwest China is a biodiversity hotspot characterized by complex topography, heterogeneous regional climates and rich flora. The processes and driving factors underlying this hotspot remain to be explicitly tested across taxa to gain a general understanding of the evolution of biodiversity and speciation in the region. In this study, we examined the role played by historically neutral processes, geography and environment in producing the current genetic diversity of the subtropical pine Pinus yunnanensis. We used genetic and ecological methods to investigate the patterns of genetic differentiation and ecological niche divergence across the distribution range of this species. We found both continuous genetic differentiation over the majority of its range, and discrete isolated local clusters. The discrete differentiation between two genetic groups in the west and east peripheries is consistent with niche divergence and geographical isolation of these groups. In the central area of the species' range, population structure was shaped mainly by neutral processes and geography rather than by ecological selection. These results show that geographical and environmental factors together created stronger and more discrete genetic differentiation than isolation by distance alone, and illustrate the importance of ecological factors in forming or maintaining genetic divergence across a complex landscape. Our findings differ from other phylogenetic studies that identified the historical drainage system in the region as the primary factor shaping population structure, and highlight the heterogeneous contributions that geography and environment have made to genetic diversity among taxa in southwest China.
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Affiliation(s)
- Baosheng Wang
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Jian-Feng Mao
- National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
| | - Wei Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- * E-mail:
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Wang M, Yang JX, Chen XY. Molecular phylogeny and biogeography of percocypris (Cyprinidae, Teleostei). PLoS One 2013; 8:e61827. [PMID: 23750199 PMCID: PMC3672144 DOI: 10.1371/journal.pone.0061827] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 03/18/2013] [Indexed: 12/05/2022] Open
Abstract
Fierce predatory freshwater fishes, the species of Percocypris (Cyprinidae, Teleostei) inhabit large rivers or lakes, and have a specific distribution pattern. Only a single species or subspecies occurs in each large-scale drainage basin of the Southeastern Tibetan Plateau. In this study, the molecular phylogenetic relationships for all but one of the described subspecies/species of Percocypris were investigated based on three mitochondrial genes (16S; COI; Cyt b) and one nuclear marker (Rag2). The results of Maximum Likelihood and Bayesian Inference analyses show that Percocypris is a strongly supported monophyletic group and that it is the sister group of Schizothorax. Combined with analyses of morphological characters, our results suggest that Percocypris needs to be reclassified, and we propose that six species be recognized, with corresponding distributions in five main drainages (including one lake). In addition, based on the results of the estimation of divergence times and ancestral drainages, we hypothesize that Percocypris likely originated in the early Miocene from a paleo-connected drainage system containing the contemporary main drainages of the Southeastern Tibetan Plateau. This study suggests that vicariance (due to the uplift of the Tibetan Plateau modifying the large-scale morphologies of drainage basins in the Southeastern Tibetan Plateau) has played an important role in the speciation of the genus. Furthermore, external morphological characters (such as the length of the fins) and an internal trait (the position of pterygiophore) appear to be correlated with different habitats in rivers and the lake.
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Affiliation(s)
- Mo Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Xing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- * E-mail: (XYC); (JXY)
| | - Xiao-Yong Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- * E-mail: (XYC); (JXY)
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Diversification of plant species in arid Northwest China: species-level phylogeographical history of Lagochilus Bunge ex Bentham (Lamiaceae). Mol Phylogenet Evol 2013; 68:398-409. [PMID: 23629053 DOI: 10.1016/j.ympev.2013.04.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 04/16/2013] [Accepted: 04/16/2013] [Indexed: 11/24/2022]
Abstract
Lagochilus occurs in the arid zones across temperate steppe and desert regions of Northwest China. Cooling with strong dessication in the Pleistocene, along with rapid uplift of mountain ranges peripheral to the Qinghai-Tibet Plateau, appear to have had major impacts on the genetic structure of the flora. To understand the evolutionary history of Lagochilus and the divergence related to these past shifts of habitats among these regions, we sequenced the plastid intergenic spacers, psbA-trnH and trnS-trnG from populations throughout the known distributions of ten species of the genus. We investigated species-level phylogeographical patterns within Lagochilus. Phylogenetic trees were constructed using Neighbor-joining and Bayesian inference. The divergence times of major lineages were estimated with BEAST and IMa. Genetic structure and demographic history were inferred by AMOVA, neutrality tests, mismatch distribution, and Bayesian skyline plot analyses. The results showed that most chloroplast haplotypes were species-specific, and that the phylogeny of Lagochilus is geographically structured. The estimated Bayesian chronology and IMa suggested that the main divergence events for species between major eastern and western portions of the Chinese desert occurred at the Plio-/Pleistocene boundary (ca. 2.1-2.8 Ma ago), and likely coinciding with the formation of these deserts in Northwest China. The regional demographic expansions, in the western region at ca. 0.39 Ma, and in the eastern at ca. 0.06 Ma, or across all regions at ca. 0.26 Ma, showed the response to aridification accompanied by cooling of the Pleistocene sharply increased aridity in the Chinese deserts, which reflects a major influence of geologic and climatic events on the evolution of species of Lagochilus. We suggest that diversification is most likely the result of the past fragmentation due to aridification; the expansion of the range of species along with the deserts was an adaptation to dry and cold environments during the Quaternary.
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Chen JM, Du ZY, Sun SS, Gituru RW, Wang QF. Chloroplast DNA phylogeography reveals repeated range expansion in a widespread aquatic herb Hippuris vulgaris in the Qinghai-Tibetan Plateau and adjacent areas. PLoS One 2013; 8:e60948. [PMID: 23565290 PMCID: PMC3614902 DOI: 10.1371/journal.pone.0060948] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 03/06/2013] [Indexed: 11/18/2022] Open
Abstract
Background The Qinghai-Tibetan Plateau (QTP) is one of the most extensive habitats for alpine plants in the world. Climatic oscillations during the Quaternary ice age had a dramatic effect on species ranges on the QTP and the adjacent areas. However, how the distribution ranges of aquatic plant species shifted on the QTP in response to Quaternary climatic changes remains almost unknown. Methodology and Principal Findings We studied the phylogeography and demographic history of the widespread aquatic herb Hippuris vulgaris from the QTP and adjacent areas. Our sampling included 385 individuals from 47 natural populations of H. vulgaris. Using sequences from four chloroplast DNA (cpDNA) non-coding regions, we distinguished eight different cpDNA haplotypes. From the cpDNA variation in H. vulgaris, we found a very high level of population differentiation (GST = 0.819) but the phylogeographical structure remained obscure (NST = 0.853>GST = 0.819, P>0.05). Phylogenetic analyses revealed two main cpDNA haplotype lineages. The split between these two haplotype groups can be dated back to the mid-to-late Pleistocene (ca. 0.480 Myr). Mismatch distribution analyses showed that each of these had experienced a recent range expansion. These two expansions (ca. 0.12 and 0.17 Myr) might have begun from the different refugees before the Last Glacial Maximum (LGM). Conclusions/Significance This study initiates a research on the phylogeography of aquatic herbs in the QTP and for the first time sheds light on the response of an alpine aquatic seed plant species in the QTP to Quaternary climate oscillations.
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Affiliation(s)
- Jin-Ming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, China
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