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Xu T, Wang R, La Q, Yonezawa T, Huang X, Sun K, Song Z, Wang Y, Bartish IV, Zhang W, Cheng S. Climate heterogeneity shapes phylogeographic pattern of Hippophae gyantsensis (Elaeagnaceae) in the east Himalaya-Hengduan Mountains. Ecol Evol 2023; 13:e10182. [PMID: 37304372 PMCID: PMC10251425 DOI: 10.1002/ece3.10182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/13/2023] Open
Abstract
The interaction of recent orographic uplift and climate heterogeneity acted as a key role in the East Himalaya-Hengduan Mountains (EHHM) has been reported in many studies. However, how exactly the interaction promotes clade diversification remains poorly understood. In this study, we both used the chloroplast trnT-trnF region and 11 nuclear microsatellite loci to investigate the phylogeographic structure and population dynamics of Hippophae gyantsensis and estimate what role geological barriers or ecological factors play in the spatial genetic structure. The results showed that this species had a strong east-west phylogeographic structure, with several mixed populations identified from microsatellite data in central location. The intraspecies divergence time was estimated to be about 3.59 Ma, corresponding well with the recent uplift of the Tibetan Plateau. Between the two lineages, there was significant climatic differentiation without geographic barriers. High consistency between lineage divergence, climatic heterogeneity, and Qingzang Movement demonstrated that climatic heterogeneity but not geographic isolation drives the divergence of H. gyantsensis, and the recent regional uplift of the QTP, as the Himalayas, creates heterogeneous climates by affecting the flow of the Indian monsoon. The east group of H. gyantsensis experienced population expansion c. 0.12 Ma, closely associated with the last interglacial interval. Subsequently, a genetic admixture event between east and west groups happened at 26.90 ka, a period corresponding to the warm inter-glaciation again. These findings highlight the importance of the Quaternary climatic fluctuations in the recent evolutionary history of H. gyantsensis. Our study will improve the understanding of the history and mechanisms of biodiversity accumulation in the EHHM region.
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Affiliation(s)
- Ting Xu
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Ruixue Wang
- College of Life SciencesNorthwest Normal UniversityLanzhouChina
| | - Qiong La
- Department of BiologyTibet UniversityLhasaChina
| | - Takahiro Yonezawa
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Xinyi Huang
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Kun Sun
- College of Life SciencesNorthwest Normal UniversityLanzhouChina
| | - Zhiping Song
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Yuguo Wang
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Igor V. Bartish
- Institute of Botany of the Czech Academy of SciencesPruhoniceCzech Republic
| | - Wenju Zhang
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Shanmei Cheng
- Laboratory of Subtropical BiodiversityJiangxi Agricultural UniversityNanchangChina
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Liu Y, Wu M, Xu X, Zhu X, Dai Z, Gou G. Genetic diversity and phylogeography of the endemic species Chimonobambusa utilis growing in southwest China: Chloroplast DNA sequence and microsatellite marker analyses. FRONTIERS IN PLANT SCIENCE 2022; 13:943225. [PMID: 36407620 PMCID: PMC9671600 DOI: 10.3389/fpls.2022.943225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Chimonobambusa utilis (Keng) Keng F is an endemic species distributed only in the Daluoshan Mountains, southwest China. Ch. utilis is popular due to its unique flavor and deliciousness and plays an important role in the industrial revolution in many counties in China. A total of 20 natural populations were sampled from the entire distribution range of Ch. utilis. In the present study, we used five EST-SSR molecular markers, three chloroplast DNA (trnH-psbA, atpF-atpH, and psbK-psbI), and one ITS molecular marker to elucidate the genetic diversity and phylogeography analyses of these Ch. utilis populations. The results exhibited that Ch. utilis populations showed lower genetic diversity than other angiosperms (HT = 0.752, HS = 0.364, and FST = 0.05021 for EST-SSR; HT = 0.956, Hs = 0.507, and FST = 0.70121 for cpDNA; HT = 0.868, Hs = 0.495, and FST = 0.70121 for nrDNA). A total of 40 alleles were detected for five polymorphic loci. We detected 20 polymorphic sites and 11 haplotypes within 1,398 bp of cpDNA and 59 polymorphic sites and 32 haplotypes within the 589 bp of the ITS sequence. Based on the haplotype distribution, we infer that there were at least two glacial refuges of Ch. utilis populations during the Quaternary Ice Age. The genetic and geographic distance were correlated (p < 0.05), indicating that narrow distribution might be the primary cause of the low genetic differentiation of Ch. utilis populations. Based on the genetic diversity of Ch. utilis populations, we recommend implementing effective genetic resource management and sustainable utilization.
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Affiliation(s)
- Yanjiang Liu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
- Bamboo Research Institute, Guizhou University, Guiyang, China
| | - Mingli Wu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
- Bamboo Research Institute, Guizhou University, Guiyang, China
| | - Xue Xu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
- Bamboo Research Institute, Guizhou University, Guiyang, China
| | - Xiao Zhu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
- Bamboo Research Institute, Guizhou University, Guiyang, China
| | - Zhaoxia Dai
- Bamboo Research Institute, Guizhou University, Guiyang, China
- College of Forestry, Guizhou University, Guiyang, China
| | - Guangqian Gou
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
- Bamboo Research Institute, Guizhou University, Guiyang, China
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Li M, Zheng Z, Liu J, Yang Y, Ren G, Ru D, Zhang S, Du X, Ma T, Milne R, Liu J. Evolutionary origin of a tetraploid Allium species on the Qinghai-Tibet Plateau. Mol Ecol 2021; 30:5780-5795. [PMID: 34487579 DOI: 10.1111/mec.16168] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/09/2021] [Accepted: 08/31/2021] [Indexed: 12/30/2022]
Abstract
Extinct taxa may be detectable if they were ancestors to extant hybrid species, which retain their genetic signature. In this study, we combined phylogenomics, population genetics and fluorescence in situ hybridization (GISH and FISH) analyses to trace the origin of the alpine tetraploid Allium tetraploideum (2n = 4x = 32), one of the five known members in the subgenus Cyathophora. We found that A. tetraploideum was an obvious allotetrapoploid derived from ancestors including at least two closely related diploid species, A. farreri and A. cyathophorum, from which it differs by multiple ecological and genomic attributes. However, these two species cannot account for the full genome of A. tetraploideum, indicating that at least one extinct diploid is also involved in its ancestry. Furthermore, A. tetraploideum appears to have arisen via homoploid hybrid speciation (HHS) from two extinct allotetraploid parents, which derived in turn from the aforementioned diploids. Other modes of origin were possible, but all were even more complex and involved additional extinct ancestors. Our study together highlights how some polyploid species might have very complex origins, involving both HHS and polyploid speciation and also extinct ancestors.
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Affiliation(s)
- Minjie Li
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zeyu Zheng
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Juncheng Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Guangpeng Ren
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shangzhe Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xin Du
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Richard Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.,Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Li MJ, Yu HX, Guo XL, He XJ. Out of the Qinghai-Tibetan Plateau and rapid radiation across Eurasia for Allium section Daghestanica (Amaryllidaceae). AOB PLANTS 2021; 13:plab017. [PMID: 34055281 PMCID: PMC8152445 DOI: 10.1093/aobpla/plab017] [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: 09/01/2020] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidated the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the Qinghai-Tibetan Plateau (QTP) and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4-3 million years ago (Mya). Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.
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Affiliation(s)
- Min-Jie Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P.R. China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Science, Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Huan-Xi Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P.R. China
- Nanjing Institute of Environmental Science, MEE, Nanjing, Jiangsu 210042, P.R. China
| | - Xian-Lin Guo
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P.R. China
| | - Xing-Jin He
- 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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Hou H, Ye H, Wang Z, Wu J, Gao Y, Han W, Na D, Sun G, Wang Y. Demographic history and genetic differentiation of an endemic and endangered Ulmus lamellosa (Ulmus). BMC PLANT BIOLOGY 2020; 20:526. [PMID: 33203402 PMCID: PMC7672979 DOI: 10.1186/s12870-020-02723-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 10/26/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Ulmus lamellosa (one of the ancient species of Ulmus) is an endemic and endangered plant that has undergone climatic oscillations and geographical changes. The elucidation of its demographic history and genetic differentiation is critical for understanding the evolutionary process and ecological adaption to forests in Northern China. RESULTS Polymorphic haplotypes were detected in most populations of U. lamellosa via DNA sequencing. All haplotypes were divided into three phylogeographic clades fundamentally corresponding to their geographical distribution, namely THM (Taihang Mountains), YM (Yinshan Mountains), and YSM (Yanshan Mountains) groups. The YSM group, which is regarded as ancestral, possessed higher genetic diversity and significant genetic variability in contrast to the YSM and YM groups. Meanwhile, the divergence time of intraspecies haplotypes occurred during the Miocene-Pliocene, which was associated with major Tertiary geological and/or climatic events. Different degrees of gene exchanges were identified between the three groups. During glaciation, the YSM and THM regions might have served as refugia for U. lamellosa. Based on ITS data, range expansion was not expected through evolutionary processes, except for the THM group. A series of mountain uplifts (e.g., Yanshan Mountains and Taihang Mountains) following the Miocene-Pliocene, and subsequently quaternary climatic oscillations in Northern China, further promoted divergence between U. lamellosa populations. CONCLUSIONS Geographical topology and climate change in Northern China played a critical role in establishing the current phylogeographic structural patterns of U. lamellosa. These results provide important data and clues that facilitate the demographic study of tree species in Northern China.
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Affiliation(s)
- Huimin Hou
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Hang Ye
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Zhi Wang
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Jiahui Wu
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Yue Gao
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Wei Han
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Dongchen Na
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Genlou Sun
- Saint Mary’s University, Halifax, Canada
| | - Yiling Wang
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
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