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Yisilam G, Wang CX, Xia MQ, Comes HP, Li P, Li J, Tian XM. Phylogeography and Population Genetics Analyses Reveal Evolutionary History of the Desert Resource Plant Lycium ruthenicum (Solanaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:915526. [PMID: 35845630 PMCID: PMC9280156 DOI: 10.3389/fpls.2022.915526] [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: 04/08/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Climactic oscillations during the Quaternary played a significant role in the formation of genetic diversity and historical demography of numerous plant species in northwestern China. In this study, we used 11 simple sequence repeats derived from expressed sequence tag (EST-SSR), two chloroplast DNA (cpDNA) fragments, and ecological niche modeling (ENM) to investigate the population structure and the phylogeographic history of Lycium ruthenicum, a plant species adapted to the climate in northwestern China. We identified 20 chloroplast haplotypes of which two were dominant and widely distributed in almost all populations. The species has high haplotype diversity and low nucleotide diversity based on the cpDNA data. The EST-SSR results showed a high percentage of total genetic variation within populations. Both the cpDNA and EST-SSR results indicated no significant differentiation among populations. By combining the evidence from ENM and demographic analysis, we confirmed that both the last interglacial (LIG) and late-glacial maximum (LGM) climatic fluctuations, aridification might have substantially narrowed the distribution range of this desert species, the southern parts of the Junggar Basin, the Tarim Basin, and the eastern Pamir Plateau were the potential glacial refugia for L. ruthenicum during the late middle Pleistocene to late Pleistocene Period. During the early Holocene, the warm, and humid climate promoted its demographic expansion in northwestern China. This work may provide new insights into the mechanism of formation of plant diversity in this arid region.
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Affiliation(s)
- Gulbar Yisilam
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, College of Life Science, Xinjiang Normal University, Urumqi, China
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chen-Xi Wang
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Mao-Qin Xia
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hans Peter Comes
- Department of Environment and Biodiversity, University of Salzburg, Salzburg, Austria
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jin Li
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Xin-Min Tian
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
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Sun J, Wang S, Wang Y, Wang R, Liu K, Li E, Qiao P, Shi L, Dong W, Huang L, Guo L. Phylogenomics and Genetic Diversity of Arnebiae Radix and Its Allies ( Arnebia, Boraginaceae) in China. FRONTIERS IN PLANT SCIENCE 2022; 13:920826. [PMID: 35755641 PMCID: PMC9218939 DOI: 10.3389/fpls.2022.920826] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/11/2022] [Indexed: 05/03/2023]
Abstract
Arnebiae Radix is a traditional medicine with pleiotropic properties that has been used for several 100 years. There are five species of Arnebia in China, and the two species Arnebia euchroma and Arnebia guttata are the source plants of Arnebiae Radix according to the Chinese Pharmacopoeia. Molecular markers that permit species identification and facilitate studies of the genetic diversity and divergence of the wild populations of these two source plants have not yet been developed. Here, we sequenced the chloroplast genomes of 56 samples of five Arnebia species using genome skimming methods. The Arnebia chloroplast genomes exhibited quadripartite structures with lengths from 149,539 and 152,040 bp. Three variable markers (rps16-trnQ, ndhF-rpl32, and ycf1b) were identified, and these markers exhibited more variable sites than universal chloroplast markers. The phylogenetic relationships among the five Arnebia species were completely resolved using the whole chloroplast genome sequences. Arnebia arose during the Oligocene and diversified in the middle Miocene; this coincided with two geological events during the late Oligocene and early Miocene: warming and the progressive uplift of Tianshan and the Himalayas. Our analyses revealed that A. euchroma and A. guttata have high levels of genetic diversity and comprise two and three subclades, respectively. The two clades of A. euchroma exhibited significant genetic differences and diverged at 10.18 Ma in the middle Miocene. Three clades of A. guttata diverged in the Pleistocene. The results provided new insight into evolutionary history of Arnebia species and promoted the conservation and exploitation of A. euchroma and A. guttata.
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Affiliation(s)
- Jiahui Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Sheng Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yiheng Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ruishan Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Kangjia Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Enze Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Ping Qiao
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Linyuan Shi
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Zhang L, Sun F, Ma S, Wang C, Wei B, Zhang Y. Phylogeography of Amygdalus mongolica in relation to Quaternary climatic aridification and oscillations in northwestern China. PeerJ 2022; 10:e13345. [PMID: 35509965 PMCID: PMC9059755 DOI: 10.7717/peerj.13345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 04/06/2022] [Indexed: 01/14/2023] Open
Abstract
Quaternary period geological events and climatic oscillations significantly affect the geographic structure and genetic diversity of species distribution in arid northwestern China. Amygdalus mongolica is a relict and endangered shrub that occurs primarily in arid areas of northwestern China. Based on variation patterns present at three cpDNA regions (psbK-psbI, trnL-trnF and trnV) and in one nDNA sequence (ITS1-ITS4) in 174 individuals representing 15 populations, the spatial genetic structure and demographic history of A. mongolica was examined across its entire geographic range. The 17 different haplotypes and 10 ribotypes showed two lineages, distributed across the Western (Mazong Mountains, Hexi Corridor, and Alxa Left Banner) and Eastern regions (Urad Houqi, Yinshan Mountains, Urad Zhongqi, and Daqing Mountains) according to the median-joining network and the BI (Bayesian inference) and ML (Maximum likelihood) trees. AMOVA analysis demonstrated that over 65% of the observed genetic variation was related to this lineage split. The expansions of the Ulanbuhe and Tengger deserts and the eastward extension of the Yinshan Mountains since the Quaternary period likely interrupted gene flow and triggered the observed divergence in the two allopatric regions; arid landscape fragmentation accompanied by local environmental heterogeneity further increased local adaptive differentiation between the Western and Eastern groups. Based on the evidence from phylogeographical patterns and the distribution of genetic variation, A. mongolica distributed in the eastern and western regions are speculated to have experienced eastward migration along the southern slopes of the Lang Mountains and westward migration along the margins of the Ulanbuhe and Tengger deserts to the Hexi Corridor, respectively. For setting a conservation management plan, it is recommended that the south slopes of the Lang Mountains and northern Helan Mountains be identified as the two primary conservation areas, as they have high genetic variation and habitats that are more suitable.
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Affiliation(s)
- Lin Zhang
- Shihezi University, Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Science, Shihezi, Xinjiang, China
| | - Fangfang Sun
- Shihezi University, Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Science, Shihezi, Xinjiang, China
| | - Songmei Ma
- Shihezi University, Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Science, Shihezi, Xinjiang, China
| | - Chuncheng Wang
- Shihezi University, Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Life Sciences, Shihezi, Xinjiang, China
| | - Bo Wei
- Institute of Geographic Sciences and Natural Resources Research, Beijing, China
| | - Yunling Zhang
- General grassland station of Xinjiang, Urumqi, Xingjiang, China
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Fu MJ, Wu HY, Jia DR, Tian B. Evolutionary history of a desert perennial Arnebia szechenyi (Boraginaceae): Intraspecific divergence, regional expansion and asymmetric gene flow. PLANT DIVERSITY 2021; 43:462-471. [PMID: 35024515 PMCID: PMC8720688 DOI: 10.1016/j.pld.2021.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 05/20/2023]
Abstract
The complex interactions of historical, geological and climatic events on plant evolution have been an important research focus for many years. However, the role of desert formation and expansion in shaping the genetic structures and demographic histories of plants occurring in arid areas has not been well explored. In the present study, we investigated the phylogeography of Arnebia szechenyi, a desert herb showing a near-circular distribution surrounding the Tengger Desert in Northwest China. We measured genetic diversity of populations using three maternally inherited chloroplast DNA (cpDNA) fragments and seven bi-paternally inherited nuclear DNA (nDNA) loci that were sequenced from individuals collected from 16 natural populations across its range and modelled current and historical potential habitats of the species. Our data indicated a considerably high level of genetic variation within A. szechenyi and noteworthy asymmetry in historical migration from the east to the west. Moreover, two nuclear genetic groups of populations were revealed, corresponding to the two geographic regions separated by the Tengger Desert. However, analysis of cpDNA data did not show significant geographic structure. The most plausible explanation for the discrepancy between our findings based on cpDNA and nDNA data is that A. szechenyi populations experienced long periods of geographic isolation followed by range expansion, which would have promoted generalized recombination of the nuclear genome. Our findings further highlight the important role that the Tengger Desert, together with the Helan Mountains, has played in the evolution of desert plants and the preservation of biodiversity in arid Northwest China.
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Affiliation(s)
- Meng-Jiao Fu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
| | - Hai-Yang Wu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
| | - Dong-Rui Jia
- School of Ecology and Environmental Science & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming 650091, China
- Corresponding author.
| | - Bin Tian
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
- CAS Key Laboratory for Plant Diversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
- Corresponding author. Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.
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Lv T, Harris AJ, Liu Y, Liu T, Liang R, Ma Z, Su X. Population genetic structure and evolutionary history of Psammochloa villosa (Trin.) Bor (Poaceae) revealed by AFLP marker. Ecol Evol 2021; 11:10258-10276. [PMID: 34367573 PMCID: PMC8328423 DOI: 10.1002/ece3.7831] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/17/2021] [Accepted: 06/09/2021] [Indexed: 01/26/2023] Open
Abstract
Psammochloa villosa is an ecologically important desert grass that occurs in the Inner Mongolian Plateau where it is frequently the dominant species and is involved in sand stabilization and wind breaking. We sought to generate a preliminary demographic framework for P. villosa to support the future studies of this species, its conservation, and sustainable utilization. To accomplish this, we characterized the genetic diversity and structure of 210 individuals from 43 natural populations of P. villosa using amplified fragment length polymorphism (AFLP) markers. We obtained 1,728 well-defined amplified bands from eight pairs of primers, of which 1,654 bands (95.7%) were polymorphic. Results obtained from the AFLPs suggested effective alleles among populations of 1.32, a Nei's standard genetic distance value of 0.206, a Shannon index of 0.332, a coefficient of gene differentiation (G ST) of 0.469, and a gene flow parameter (Nm) of 0.576. All these values indicate that there is abundant genetic diversity in P. villosa, but limited gene flow. An analysis of molecular variance (AMOVA) showed that genetic variation mainly exists within populations (64.2%), and we found that the most genetically similar populations were often not geographically adjacent. Thus, this suggests that the mechanisms of gene flow are surprisingly complex in this species and may occur over long distances. In addition, we predicted the distribution dynamics of P. villosa based on the spatial distribution modeling and found that its range has contracted continuously since the last interglacial period. We speculate that dry, cold climates have been critical in determining the geographic distribution of P. villosa during the Quaternary period. Our study provides new insights into the population genetics and evolutionary history of P. villosa in the Inner Mongolian Plateau and provides a resource that can be used to design in situ conservation actions and prioritize sustainable utilization.
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Affiliation(s)
- Ting Lv
- School of GeosciencesQinghai Normal UniversityXiningChina
- Academy of Plateau Science and SustainabilityXiningChina
| | - AJ Harris
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Yuping Liu
- Academy of Plateau Science and SustainabilityXiningChina
- Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai‐Tibet Plateau in Qinghai ProvinceSchool of Life ScienceQinghai Normal UniversityXiningChina
| | - Tao Liu
- School of GeosciencesQinghai Normal UniversityXiningChina
| | - Ruifang Liang
- Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai‐Tibet Plateau in Qinghai ProvinceSchool of Life ScienceQinghai Normal UniversityXiningChina
| | - Zilan Ma
- Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai‐Tibet Plateau in Qinghai ProvinceSchool of Life ScienceQinghai Normal UniversityXiningChina
| | - Xu Su
- School of GeosciencesQinghai Normal UniversityXiningChina
- Academy of Plateau Science and SustainabilityXiningChina
- Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai‐Tibet Plateau in Qinghai ProvinceSchool of Life ScienceQinghai Normal UniversityXiningChina
- Key Laboratory of Education Ministry of Earth Surface Processes and Ecological Conservation of the Qinghai‐Tibet PlateauQinghai Normal UniversityXiningChina
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Ye JW, Wu HY, Fu MJ, Zhang P, Tian B. Insights Into the Significance of the Chinense Loess Plateau for Preserving Biodiversity From the Phylogeography of Speranskia tuberculata (Euphorbiaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:604251. [PMID: 33613598 PMCID: PMC7889603 DOI: 10.3389/fpls.2021.604251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
The significance of the Chinese Loess Plateau (CLP) in maintaining biodiversity for northern China has rarely been shown, as previous phylogeographic studies are mostly woody species and they have revealed that Quaternary refugia are mainly located in mountain regions. We selected a drought-enduring endemic herb, Speranskia tuberculata (Euphorbiaceae), to determine its glacial refugia and postglacial demographic history. To this end, we sampled 423 individuals from 38 populations covering its entire geographic distribution. Three chloroplast DNA (cpDNA) fragments, two low-copy nuclear genes, and six nuclear microsatellites (nSSRs) were used and supplemented with ecological niche modeling (ENM) to infer the phylogeographic history of this species. Populations with private haplotypes and high haplotype diversity of cpDNA are mainly located in the CLP or scattered around northeastern China and the coastal region. Spatial expansion, detected using a neutrality test and mismatch distribution, may have resulted in a widely distributed ancestral cpDNA haplotype, especially outside of the CLP. For nuclear DNA, private haplotypes are also distributed mainly in the CLP. In nSSRs, STRUCTURE clustering identified two genetic clusters, which are distributed in the west (western cluster) and east (eastern cluster), respectively. Many populations belonged, with little to no admixture, to the western cluster while (hardly) pure populations of the eastern cluster were barely found. Genetic differentiation is significantly correlated with geographic distance, although genetic diversity is uniformly distributed. ENM suggests that the distribution of S. tuberculata has recently expanded northwards from the southern CLP, whereas it has experienced habitat loss in the south. Thus, S. tuberculata populations probably survived the last glacial maximum (LGM) in the southern CLP and experienced post-glacial expansion. Wind-dispersed pollen could bring the majority of genotypes to the front during spatial expansion, resulting in uniformly distributed genetic diversity. Based on evidence from molecular data and vegetation and climate changes since the LGM, we conclude that drought-enduring species, especially herbaceous species, are likely to have persisted in the CLP during the LGM and to have experienced expansion to other regions in northern China.
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Affiliation(s)
- Jun-Wei Ye
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hai-Yang Wu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Meng-Jiao Fu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Pei Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Bin Tian
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
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Li Y, Song F, Zhang XN, Lv GH. Phylogeography suggest the Yili Valley being the glacial refuge of the genus Ixiolirion (Amaryllidaceae) in China. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1612966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yan Li
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, 830046, China
- Key Laboratory of Oasis Ecology, Xinjiang University, Urumqi, 830046, China
| | - Feng Song
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Xue-Ni Zhang
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, 830046, China
- Key Laboratory of Oasis Ecology, Xinjiang University, Urumqi, 830046, China
| | - Guang-Hui Lv
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, 830046, China
- Key Laboratory of Oasis Ecology, Xinjiang University, Urumqi, 830046, China
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Kumar B, Cheng J, Ge D, Xia L, Yang Q. Phylogeography and ecological niche modeling unravel the evolutionary history of the Yarkand hare, Lepus yarkandensis (Mammalia: Leporidae), through the Quaternary. BMC Evol Biol 2019; 19:113. [PMID: 31153378 PMCID: PMC6545225 DOI: 10.1186/s12862-019-1426-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 04/22/2019] [Indexed: 01/29/2023] Open
Abstract
Background The Taklimakan Desert in China is characterized by unique geological and historical dynamics and endemic flora and fauna, but the influence of historical climate oscillations on the evolutionary history of endemic animals is poorly understood. Lepus yarkandensis is an oases-dependent Near Threatened species that lives in fragmented oasis habitats in the Taklimakan Desert, China. We investigated the geological and climatic impacts on its geographical differentiation, demographic history and influence of Pleistocene glacial-interglacial cycles on the evolutionary history of L. yarkandensis. Further, studied the impact of climatic oscillation based modification on phylogeography, distribution and diversification pattern of Yarkand hare by using Cytb (1140 bp), MGF (592 bp) and SPTBN1 (619 bp) markers. Ecological niche modeling (ENM) revealed the evolutionary history of this species in response to climate change during the Quaternary. Paleodistribution modeling was used to identify putative refugia and estimate their historical distributions. Results Both historical demographic analyses and climatic niche modeling revealed strong effects of glacial climate changes, suggesting recurrent range contractions and expansions. The EBSP results indicated clear population expansion of L. yarkandensis since the Pleistocene. In the “early Pleistocene”, the demographic expansion continued from 0.83 MYA to the last glacial period. The ENM analysis supported a wide distribution of Lepus yarkandensis at high altitudes during the last interglacial (LIG) period. During the last glacial maximum (LGM), the suitable climate was reduced and restricted to the western part of the Taklimakan Desert. Conclusions Inland aridification, oasis evolution and river flow played major roles in the population differentiation and demographic history of Yarkand hares. Historically, the large, continuous oases in the Taklimakan Desert contained a viable and unique population of L. yarkandensis. The fragmented desert environment might have caused low gene flow between individuals or groups, thus leading to predominant genetic differentiation. The Pleistocene climatic cycles triggered the diversification and expansion of this species during cold and warm periods, respectively, leading to multiple colonization events within the Taklimakan Desert. These events might be due to the expansion of the Taklimakan Desert during the Middle Pleistocene. Yarkand hare previously occupied vast areas at low and intermediate altitudes in Xinjiang, Gansu, Shanxi, Henan and Shaanxi Provinces in China. The past aridification, climate change-induced oasis modifications, changes in river volumes and flow directions, and human activities all affected the population demography and phylogeography of the Yarkand hare. Electronic supplementary material The online version of this article (10.1186/s12862-019-1426-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Brawin Kumar
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China.,International College, University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China.
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Jia S, Zhang M. Pleistocene climate change and phylogeographic structure of the Gymnocarpos przewalskii (Caryophyllaceae) in the northwest China: Evidence from plastid DNA, ITS sequences, and Microsatellite. Ecol Evol 2019; 9:5219-5235. [PMID: 31110674 PMCID: PMC6509395 DOI: 10.1002/ece3.5113] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 04/11/2018] [Accepted: 09/05/2018] [Indexed: 11/17/2022] Open
Abstract
Northwestern China has a wealth of endemic species, which has been hypothesized to be affected by the complex paleoclimatic and paleogeographic history during Quaternary. In this paper, we used Gymnocarpos przewalskii as a model to address the evolutionary history and current population genetic structure of species in northwestern China. We employed two chloroplast DNA fragments (rps16 and psbB-psbI), one nuclear DNA fragment (ITS), and simple sequence repeat (SSRs) to investigate the spatial genetic pattern of G. przewalskii. High genetic diversity (cpDNA: h S = 0.330, h T = 0.866; ITS: h S = 0.458, h T = 0.872) was identified in almost all populations, and most of the population have private haplotypes. Moreover, multimodal mismatch distributions were observed and estimates of Tajima's D and Fu's FS tests did not identify significantly departures from neutrality, indicating that recent expansion of G. przewalskii was rejected. Thus, we inferred that G. przewalskii survived generally in northwestern China during the Pleistocene. All data together support the genotypes of G. przewalskii into three groups, consistent with their respective geographical distributions in the western regions-Tarim Basin, the central regions-Hami Basin and Hexi Corridor, and the eastern regions-Alxa Desert and Wulate Prairie. Divergence among most lineages of G. przewalskii occurred in the Pleistocene, and the range of potential distributions is associated with glacial cycles. We concluded that climate oscillation during Pleistocene significantly affected the distribution of the species.
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Affiliation(s)
- Shu‐wen Jia
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ming‐li Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiChina
- Institute of BotanyChinese Academy of SciencesBeijingChina
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Zhao Y, Pan B, Zhang M. Phylogeography and conservation genetics of the endangered Tugarinovia mongolica (Asteraceae) from Inner Mongolia, Northwest China. PLoS One 2019; 14:e0211696. [PMID: 30730930 PMCID: PMC6366884 DOI: 10.1371/journal.pone.0211696] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 01/20/2019] [Indexed: 11/23/2022] Open
Abstract
Tugarinovia (Family Asteraceae) is a monotypic genus. It’s sole species, Tugarinovia mongolica Iljin, is distributed in the northern part of Inner Mongolia, with one additional variety, Tugarinovia mongolica var ovatifolia, which is distributed in the southern part of Inner Mongolia. The species has a limited geographical range and declining populations. To understand the phylogeographic structure of T. mongolica, we sequenced two chloroplast DNA regions (psbA-trnH and psbK-psbI) from 219 individuals of 16 populations, and investigated the genetic variation and phylogeographic patterns of T. mongolica. The results identified a total of 17 (H1-H17) chloroplast haplotypes. There were no haplotypes shared between the northern (T. mongolica) and southern groups (T. mongolica var. ovatifolia), and they formed two distinct lineages. The regional split was also supported by AMOVA and BEAST analyses. AMOVA showed the main variation that occurred between the two geographic groups. The time of divergence of the two groups can be dated to the early Pleistocene epoch, when climate fluctuations most likely resulted in the allopatric divergence of T. mongolica. The formation of the desert blocked genetic flow and enhanced the divergence of the northern and southern groups. Our results indicate that the genetic differences between T. mongolica and T. mongolica var. ovatifolia are consistent with previously proposed morphological differences. We speculate that the dry, cold climate and the expansion of the desert during the Quaternary resulted in the currently observed distribution of extant populations of T. mongolica. In the northern group, the populations Chuanjinsumu, Wuliji and Yingen displayed the highest genetic diversity and should be given priority protection. The southern group showed a higher genetic drift (FST = 1, GST = 1), and the inbreeding load (HS = 0) required protection for each population. Our results propose that the protection of T. mongolica should be implemented through in situ and ex situ conservation practices to increase the effective population size and genetic diversity.
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Affiliation(s)
- Yanfen Zhao
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Borong Pan
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- * E-mail:
| | - Mingli Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Zhao Y, Zhang H, Pan B, Zhang M. Intraspecific divergences and phylogeography of Panzerina lanata (Lamiaceae) in northwest China. PeerJ 2019; 7:e6264. [PMID: 30697480 PMCID: PMC6348092 DOI: 10.7717/peerj.6264] [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: 04/04/2018] [Accepted: 12/11/2018] [Indexed: 11/20/2022] Open
Abstract
Climatic fluctuations during the Quaternary significantly affect many species in their intraspecific divergence and population structure across northwest China. In order to investigate the impact of climate change on herbaceous plants, we studied Panzerina lanata (Lamiaceae), a widely distributed species. Sequences of two chloroplast DNA (cpDNA) intergenic spacers (trnH-psbA and rpoB-trnC) and a nuclear ribosomal region (nrDNA, ITS) were generated from 27 populations of Panzerina lanata and resulted in the identification of seven chloroplast haplotypes and thirty-two nuclear haplotypes. We applied AMOVA, neutrality test and mismatch distribution analysis to estimate genetic differentiation and demographic characteristics. The divergence times of the seven cpDNA haplotypes were estimated using BEAST. Our results revealed high levels of genetic diversity (cpDNA: Hcp = 0.6691, H T = 0.673; nrDNA: Hnr = 0.5668, H T = 0.577). High level of genetic differentiation (G ST = 0.950) among populations was observed in the cpDNA sequences, while the genetic differentiation values (G ST = 0.348) were low in nuclear sequences. AMOVA results revealed major genetic variation among the three groups: northern, central, and eastern group. However, the genetic differentiation in ITS data was not found. The species distribution modeling and demographic analysis indicated that P. lanata had not experienced recent range expansion. The occurrence of divergence between seven cpDNA haplotypes, probably during Pleistocene, coincides with aridification and expansion of the desert across northwest China that resulted in species diversification and habitat fragmentation. In addition, we discovered that the deserts and the Helan Mountains acted as effective geographic barriers that promoting the intraspecific diversity of P. lanata.
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Affiliation(s)
- Yanfen Zhao
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hongxiang Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China
| | - Borong Pan
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China
| | - Mingli Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China
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Liu Y, Dietrich CH, Wei C. Genetic divergence, population differentiation and phylogeography of the cicada Subpsaltria yangi based on molecular and acoustic data: an example of the early stage of speciation? BMC Evol Biol 2019; 19:5. [PMID: 30621591 PMCID: PMC6323834 DOI: 10.1186/s12862-018-1317-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 12/04/2018] [Indexed: 11/17/2022] Open
Abstract
Background Geographical isolation combined with historical climatic fluctuations have been identified as two major factors that contribute to the formation of new species. On the other hand, biotic factors such as competition and predation are also able to drive the evolution and diversification of organisms. To determine whether geographical barriers contributed to population divergence or speciation in the rare endemic cicada Subpsaltria yangi the population differentiation, genetic structure and phylogeography of the species were investigated in the Loess Plateau and adjacent areas of northwestern China by analysing mitochondrial and nuclear DNA and comparing the calling song structure of 161 male individuals. Results The results reveal a low level of genetic differentiation and relatively simple phylogeographic structure for this species, but two independent clades corresponding to geographically isolated populations were recognised. Genetic and geographical distances were significantly correlated among lineages. Results of divergence-time estimation are consistent with a scenario of isolation due to glacial refugia and interglacial climate oscillation in northwestern China. Significant genetic divergence was found between the population occurring in the Helan Mountains and other populations, and recent population expansion has occurred in the Helan Mountains and/or adjacent areas. This population is also significantly different in calling song structure from other populations. Conclusions Geographical barriers (i.e., the deserts and semi-deserts surrounding the Helan Mountains), possibly coupled with related ecological differences, may have driven population divergence and allopatric speciation. This provides a possible example of incipient speciation in Cicadidae, improves understanding of population differentiation, acoustic signal diversification and phylogeographic relationships of this rare cicada species of conservation concern, and informs future studies on population differentiation, speciation and phylogeography of other insects with a high degree of endemism in the Helan Mountains and adjacent areas. Electronic supplementary material The online version of this article (10.1186/s12862-018-1317-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunxiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, 61820, USA
| | - Cong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Meng HH, Su T, Gao XY, Li J, Jiang XL, Sun H, Zhou ZK. Warm-cold colonization: response of oaks to uplift of the Himalaya-Hengduan Mountains. Mol Ecol 2017; 26:3276-3294. [DOI: 10.1111/mec.14092] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 02/14/2017] [Accepted: 02/24/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Hong-Hu Meng
- Key Laboratory of Tropical Forest Ecology; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Mengla 666303 China
- Center for Integrative Conservation; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Kunming 650223 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Tao Su
- Key Laboratory of Tropical Forest Ecology; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Mengla 666303 China
| | - Xiao-Yang Gao
- Key Laboratory of Tropical Plant Resources and Sustainable Use; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Mengla 666303 China
| | - Jie Li
- Center for Integrative Conservation; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Kunming 650223 China
| | - Xiao-Long Jiang
- Shanghai Chenshan Plant Science Research Center; Chinese Academy of Sciences; Shanghai 201602 China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650204 China
| | - Zhe-Kun Zhou
- Key Laboratory of Tropical Forest Ecology; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Mengla 666303 China
- 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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Wen Z, Xu Z, Shi X, Zhang J, Zhang M. Genetic structure of Salsola junatovii (Chenopodiaceae) in the northern edge of the Taklimakan desert and conservational implications. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.05.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Wang P, Zhang X, Tang N, Liu J, Xu L, Wang K. Phylogeography of Libanotis buchtormensis (Umbelliferae) in Disjunct Populations along the Deserts in Northwest China. PLoS One 2016; 11:e0159790. [PMID: 27442136 PMCID: PMC4956107 DOI: 10.1371/journal.pone.0159790] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 07/10/2016] [Indexed: 11/18/2022] Open
Abstract
In Northwest China, aridification and desert expansion play significant roles in promoting desert plant diversification and speciation. However, to date, little is known about the effects of the desert barrier on the population structure of montane, non-desert species in the area. In this study, we sequenced chloroplast DNA regions (trnL–trnF and trnS–trnG) and a nuclear gene (rpb2) to investigate the population differentiation and phylogeographical history of Libanotis buchtormensis, a perennial montane species possessing a disjunct distribution at the periphery of the central desert. In total, 23 chloroplast haplotypes and 24 nuclear haplotypes were recovered from the 21 natural populations and six hebarium specimens. Phylogenetic analysis based on the combined plastid and nuclear dataset revealed two distinct lineages of L. buchtormensis, which inhabit the disjunct areas on both sides of the desert zone. The molecular dating analysis indicated that the divergence between the southeastern and the northwestern populations occurred in the middle Pleistocene, concomitantly with the desert expansion. The geographical vicariance likely contributed to the present disjunct distribution of L. buchtormensis across the deserts in Northwest China. Populations in the southeastern region may have migrated from the northwestern region, and seem to be a peripheral distribution of L. buchtormensis.
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Affiliation(s)
- Ping Wang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Xianzhi Zhang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Nan Tang
- Plateau Flower Research Centre, Qinghai University, Xining, Qinghai, China
| | - Jianjun Liu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail: (JJL); (KW)
| | - Langran Xu
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Kai Wang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail: (JJL); (KW)
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Cytoplasmic DNA disclose high nucleotide diversity and different phylogenetic pattern in Taihangia rupestris Yu et Li. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Liu S, Jiang N, Xue D, Cheng R, Qu Y, Li X, Lei F, Han H. Evolutionary history ofApocheima cinerarius(Lepidoptera: Geometridae), a female flightless moth in northern China. ZOOL SCR 2015. [DOI: 10.1111/zsc.12147] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shuxian Liu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- University of the Chinese Academy of Sciences; Beijing 100049 China
| | - Nan Jiang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Dayong Xue
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Rui Cheng
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- University of the Chinese Academy of Sciences; Beijing 100049 China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Xinxin Li
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- University of the Chinese Academy of Sciences; Beijing 100049 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Hongxiang Han
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
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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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Xu Z, Zhang ML. The effect of past climatic oscillations on spatial genetic structure of Atraphaxis manshurica (Polygonoideae) in the Horqin sandlands, northern China. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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Shi XJ, Zhang ML. Phylogeographical structure inferred from cpDNA sequence variation of Zygophyllum xanthoxylon across north-west China. JOURNAL OF PLANT RESEARCH 2015; 128:269-82. [PMID: 25626403 DOI: 10.1007/s10265-014-0699-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 09/06/2014] [Indexed: 05/27/2023]
Abstract
Zygophyllum xanthoxylon, a desert species, displaying a broad east-west continuous distribution pattern in arid Northwestern China, can be considered as a model species to investigate the biogeographical history of this region. We sequenced two chloroplast DNA spacers (psbK-psbI and rpl32-trnL) in 226 individuals from 31 populations to explore the phylogeographical structure. Median-joining network was constructed and analysis of AMOVA, SMOVA, neutrality tests and distribution analysis were used to examine genetic structure and potential range expansion. Using species distribution modeling, the geographical distribution of Z. xanthoxylon was modeled during the present and at the Last Glacial Maximum (LGM). Among 26 haplotypes, one was widely distributed, but most was restricted to either the eastern or western region. The populations with the highest levels of haplotype diversity were found in the Tianshan Mountains and its surroundings in the west, and the Helan Mountains and Alxa Plateau in the east. AMOVA and SAMOVA showed that over all populations, the species lacks phylogeographical structure, which is speculated to be the result of its specific biology. Neutrality tests and mismatch distribution analysis support past range expansions of the species. Comparing the current distribution to those cold and dry conditions in LGM, Z. xanthoxylon had a shrunken and more fragmented range during LGM. Based on the evidences from phylogeographical patterns, distribution of genetic variability, and paleodistribution modeling, Z. xanthoxylon is speculated most likely to have originated from the east and migrated westward via the Hexi Corridor.
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Affiliation(s)
- Xiao-Jun Shi
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 818 South Beijing Road, Urumqi, 830011, Xinjiang, China,
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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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Xu Z, Zhang ML. Phylogeography of the arid shrub Atraphaxis frutescens (Polygonaceae) in northwestern China: evidence from cpDNA sequences. J Hered 2014; 106:184-95. [PMID: 25516612 DOI: 10.1093/jhered/esu078] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Climatic fluctuations during the Pleistocene are usually considered as a significant factor in shaping intraspecific genetic variation and influencing demographic histories. To well-understand these processes in desert northwest China, we selected arid adapted Atraphaxis frutescens as the study species. Two cpDNA regions (psbK-psbI, psbB-psbH) were sequenced in 272 individuals from 33 natural populations across the range of this shrub, and 10 haplotypes were identified. It was found to contain high levels of total gene diversity (H T = 0.858), and low levels of within-population diversity (H S = 0.092). Analysis of molecular variance (AMOVA) indicates that genetic differentiation primarily occurs among groups of populations. Based on BEAST (Bayesian Evolutionary Analysis Sampling Trees) analysis, we suggest that intraspecific differentiation of the species, resulting from isolated populations, accompanied enhanced desertification during the middle and late Pleistocene. The expansion of the Gurbantunggut and Kumtag deserts in this area appears to have triggered divergence among populations of the western, central, and eastern portions of the region and shaped genetic differentiation among them. Two possible independent glacial refugia were predicted, the Ili Valley and the northern Junggar Basin. Extensive development of arid habitats (desert margin and arid piedmont grassland) coupled with a more equable climate because the early Holocene are factors likely to have generated recent expansion of A. frutescens.
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Affiliation(s)
- Zhe Xu
- From the Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China (Xu and Zhang); The University of Chinese Academy of Sciences, Beijing, China (Xu); and Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (Zhang)
| | - Ming-Li Zhang
- From the Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China (Xu and Zhang); The University of Chinese Academy of Sciences, Beijing, China (Xu); and Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (Zhang).
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Gao XY, Meng HH, Zhang ML. Diversification and vicariance of desert plants: Evidence inferred from chloroplast DNA sequence variation of Lagochilus ilicifolius (Lamiaceae). BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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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Su Z, Zhang M. Evolutionary response to Quaternary climate aridification and oscillations in north-western China revealed by chloroplast phylogeography of the desert shrubNitraria sphaerocarpa(Nitrariaceae). Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12088] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Zhihao Su
- Key Laboratory of Biogeography and Bioresource in Arid Land; Xinjiang Institute of Ecology and Geography; Chinese Academy of Sciences; Urumqi; 830011; China
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Zhao C, Wang CB, Ma XG, Liang QL, He XJ. Phylogeographic analysis of a temperate-deciduous forest restricted plant (Bupleurum longiradiatum Turcz.) reveals two refuge areas in China with subsequent refugial isolation promoting speciation. Mol Phylogenet Evol 2013; 68:628-43. [PMID: 23624194 DOI: 10.1016/j.ympev.2013.04.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 01/30/2013] [Accepted: 04/11/2013] [Indexed: 11/25/2022]
Abstract
This study investigates the influence of climate-induced oscillations and complicated geological conditions on the evolutionary processes responsible for species formation in presently fragmented temperate forest habitats, located in continental East Asia. In addition to this, we also investigate the heavily debated issue of whether temperate forests migrated southwards during such glacial periods or, alternatively, whether there existed refugia within north China, enabling localized survival of temperate forests within this region. In order to achieve these, we surveyed the phylogeography of Bupleurum longiradiatum Turcz. (a herbaceous plant solely confined to temperate forests) constructed from sequence variation in three chloroplast (cp) DNA fragments: trnL-trnF, psbA-trnH and rps16. Our analyses show high genetic diversity within species (h(T)=0.948) and pronounced genetic differentiation among groups (yellow and purple flowers) with a significant phylogeographical pattern (N(ST)>G(ST), P<0.05). Forty-three haplotypes were identified and clustered into two lineages (the purple-flowered lineage and the yellow-flowered lineage). Two corresponding refuge areas, one in Qinling and its adjacent regions and one in the Changbai Mountains/eastern China, were revealed across the entire distribution ranges of Bupleurum longiradiatum. These results provide evidence for the hypothesis that independent refugia were maintained across the range of temperate forests in northern China during the last glacial maximum or earlier cold periods. Bupleurum longiradiatum var. porphyranthum formed a single taxon based on molecular data. This specific formation process suggests that the historical vicariance factors, i.e. climate-induced eco-geographic isolation through the biotic displacement of temperate-deciduous forest habitats, enhanced the divergence of the yellow and purple flower lineages at different spatial-temporal scales and over glacial and interglacial periods. Additionally, geological conditions that restricted gene flow might also be responsible for the observed high genetic and geographic differentiation. A nested clade analysis (NCA) revealed that allopatric fragmentation was a major factor responsible for the phylogeographic pattern observed, and also supported a role for historical vicariance factors. Our results therefore support the inference that Quaternary refugial isolation promoted allopatric speciation of temperate plants in East Asia. This may help to explain the existence of high diversity and endemism of plant species in East Asia.
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Affiliation(s)
- Cai Zhao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
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