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Wu M, Cheng Y, Jiang C, Zhang M, Shi T, Zhao C. Phylogeography of Morella nana: The Wumeng Mountains as a natural geographical isolation boundary on the Yunnan-Guizhou Plateau. Ecol Evol 2024; 14:e11566. [PMID: 38983704 PMCID: PMC11232048 DOI: 10.1002/ece3.11566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/25/2024] [Accepted: 05/30/2024] [Indexed: 07/11/2024] Open
Abstract
The Yunnan-Guizhou Plateau (YGP) is characterized by the distinctive isolated habitat of the limestone Karst Islands and features the Wumeng Mountains, which divide the YGP into the two Plateaus of Yunnan and Guizhou. This study aimed to assess the effects of geographic isolation and past climate fluctuation on the distribution of flora in the YGP. To achieve this, we carried out the phylogeographical pattern and genetic structure based on chloroplast and nuclear ribosomal DNA sequence in relation to past (Last Glacial Maximum) and present distributions based on ecological niche modeling for Morella nana, an important wild plant resource and endemic to the YGP once considered a vulnerable species. The results suggest that the genetic and chlorotype network structures of M. nana are divided into at least two groups: cpDNA chlorotype H2 (or dominant nrDNA haplotypes h1 and h2), distributed primarily to the east of the Wumeng Mountains, and cpDNA chlorotypes H1 and H3-H10 (or dominant nrDNA haplotype h2 and h3), distributed to the west of the Wumeng Mountains. A deep genetic split was noted within the two groups to reach 25 steps, especially for the cpDNA fragment variation. This east-west divergence reveals the existence of a natural geographical isolation boundary in the form of the Wumeng Mountains, and supports the existence of at least two glacial refuges during the Quaternary glacial period, along with two genetic diversity center, and at least two large geographic protection units for the important species of M. nana. This study indicates that the phylogeographical pattern of M. nana can be attributed to geographic/environmental isolation caused by the Wumeng Mountains and climate fluctuation during the last glacial maximum, and proposes an effective strategy to protecting this important plant resource.
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Affiliation(s)
- Min Wu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro‐Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro‐BioengineeringGuizhou UniversityGuiyangChina
| | - Yu Cheng
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro‐Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro‐BioengineeringGuizhou UniversityGuiyangChina
| | - Chunxue Jiang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro‐Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro‐BioengineeringGuizhou UniversityGuiyangChina
| | - Mingsheng Zhang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro‐Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro‐BioengineeringGuizhou UniversityGuiyangChina
| | - Tian Shi
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro‐Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro‐BioengineeringGuizhou UniversityGuiyangChina
| | - Cai Zhao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro‐Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro‐BioengineeringGuizhou UniversityGuiyangChina
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Li J, Li X, Zhang C, Zhou Q, Chen S. Phylogeographic analysis reveals extensive genetic variation of native grass Elymus nutans (Poaceae) on the Qinghai-Tibetan plateau. FRONTIERS IN PLANT SCIENCE 2024; 15:1349641. [PMID: 38529066 PMCID: PMC10961384 DOI: 10.3389/fpls.2024.1349641] [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: 12/05/2023] [Accepted: 02/26/2024] [Indexed: 03/27/2024]
Abstract
Introduction Elymus nutans holds ecological and pastoral significance due to its adaptability and nutritional value, the Qinghai-Tibet Plateau (QTP) is a key hub for its genetic diversity. To conserve and harness its genetic resources in highland ecosystems, a thorough assessment is vital. However, a comprehensive phylogeographic exploration of E. nutans is lacking. The objective of this study was to unravel the genetic diversity, adaptation, and phylogenetics of E. nutans populations. Methods Encompassing 361 individuals across 35 populations, the species' genetic landscape and dynamic responses to diverse environments were decoded by using four chloroplast DNA (cpDNA) sequences and nine microsatellite markers derived from the transcriptome. Results and discussion This study unveiled a notable degree of genetic diversity in E. nutans populations at nuclear (I = 0.46, He = 0.32) and plastid DNA levels (Hd = 0.805, π = 0.67). Analysis via AMOVA highlighted genetic variation predominantly within populations. Despite limited isolation by distance (IBD), the Mekong-Salween Divide (MSD) emerged as a significant factor influencing genetic differentiation and conserving diversity. Furthermore, correlations were established between external environmental factors and effective alleles of three EST-SSRs (EN5, EN57 and EN80), potentially linked to glutathione S-transferases T1 or hypothetical proteins, affecting adaptation. This study deepens the understanding of the intricate relationship between genetic diversity, adaptation, and environmental factors within E. nutans populations on the QTP. The findings shed light on the species' evolutionary responses to diverse ecological conditions and contribute to a broader comprehension of plant adaptation mechanisms.
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Affiliation(s)
- Jin Li
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu, China
| | - Xinda Li
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Changbing Zhang
- Institute of Grass Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Qingping Zhou
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu, China
| | - Shiyong Chen
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu, China
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
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Yang L, Zhou G. Phylogeography and ecological niche modeling implicate multiple microrefugia of Swertia tetraptera during quaternary glaciations. BMC PLANT BIOLOGY 2023; 23:450. [PMID: 37749488 PMCID: PMC10521563 DOI: 10.1186/s12870-023-04471-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 09/17/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND Climate fluctuations during the Pleistocene and mountain uplift are vital driving forces affecting geographic distribution. Here, we ask how an annual plant responded to the Pleistocene glacial cycles. METHODS In this study, we analyzed the population demographic history of the annual herb Swertia tetraptera Maxim (Gentianaceae) endemic to Qinghai-Tibetan Plateau (QTP). A total of 301 individuals from 35 populations of S. tetraptera were analyzed based on two maternally inherited chloroplast fragments (trnL-trnF and trnS-trnG). Phylogeographic analysis was combined with species distribution modeling to detect the genetic variations in S. tetraptera. RESULTS The genetic diversity of S. tetraptera was high, likely due to its wide natural range, high proportion of endemic haplotypes and evolutionary history. Fifty-four haplotypes were identified in S. tetraptera. Only a few haplotypes were widespread (Hap_4, Hap_1, Hap_3), which were dispersed throughout the present geographical range of S. tetraptera, while many haplotypes were confined to single populations. The cpDNA dataset showed that phylogeographic structuring was lacking across the distribution range of S. tetraptera. Analyses of molecular variance showed that most genetic variation was found within populations (70.51%). In addition, the relationships of the haplotypes were almost completely unresolved by phylogenetic reconstruction. Both mismatch distribution analysis and neutrality tests showed a recent expansion across the distribution range of S. tetraptera. The MaxEnt analysis showed that S. tetraptera had a narrow distribution range during the Last Glacial Maximum (LGM) and a wide distribution range during the current time, with predictions into the future showing the distribution range of S. tetraptera expanding. CONCLUSION Our study implies that the current geographic and genetic distribution of S. tetraptera is likely to have been shaped by Quaternary periods. Multiple microrefugia of S. tetraptera existed during Quaternary glaciations. Rapid intraspecific diversification and hybridization and/or introgression may have played a vital role in shaping the current distribution patterns of S. tetraptera. The distribution range of S. tetraptera appeared to have experienced contraction during the LGM; in the future, when the global climate becomes warmer with rising carbon dioxide levels, the distribution of S. tetraptera will expand.
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Affiliation(s)
- Lucun Yang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
- Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Guoying Zhou
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.
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Jia Y, Liu ML, López-Pujol J, Jia RW, Kou YX, Yue M, Guan TX, Li ZH. The hybridization origin of the Chinese endemic herb genus Notopterygium (Apiaceae): Evidence from population genomics and ecological niche analysis. Mol Phylogenet Evol 2023; 182:107736. [PMID: 36805473 DOI: 10.1016/j.ympev.2023.107736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/03/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
Hybridization is recognized as a major force in species evolution and biodiversity formation, generally leading to the origin and differentiation of new species. Multiple hybridization events cannot easily be reconstructed, yet they offer the potential to study a number of evolutionary processes. Here, we used nuclear expressed sequence tag-simple sequence repeat and large-scale single nucleotide polymorphism variation data, combined with niche analysis, to investigate the putative independent hybridization events in Notopterygium, a group of perennial herb plants endemic to China. Population genomic analysis indicated that the four studied species are genetically well-delimited and that N. forrestii and N. oviforme have originated by hybridization. According to Approximate Bayesian Computation, the best-fit model involved the formation of N. forrestii from the crossing of N. franchetii and N. incisum, with N. forrestii further backcrossing to N. franchetii to form N. oviforme. The niche analyses indicated that niche divergence [likely triggered by the regional climate changes, particularly the intensification of East Asian winter monsoon, and tectonic movements (affecting both Qinghai-Tibetan Plateau and Qinling Mountains)] may have promoted and maintained the reproductive isolation among hybrid species. N. forrestii shows ecological specialization with respect to their parental species, whereas N. oviforme has completely shifted its niche. These results suggested that the climate and environmental factors together triggered the two-step hybridization of the East Asia herb plants. Our study also emphasizes the power of genome-wide SNPs for investigating suspected cases of hybridization, particularly unravelling old hybridization events.
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Affiliation(s)
- Yun Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, Shaanxi, China
| | - Mi-Li Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Barcelona 08038, Catalonia, Spain; Escuela de Ciencias Ambientales, Universidad Espíritu Santo (UEES), Samborondón 091650, Ecuador
| | - Rui-Wen Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Yi-Xuan Kou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, Shaanxi, China
| | - Tian-Xia Guan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Key Laboratory of Hexi Corridor Resources Utilization of Gansu, College of Life Sciences and Engineering, Hexi University, Zhangye 734000, Gansu, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
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Miao J, Farhat P, Wang W, Ruhsam M, Milne R, Yang H, Tso S, Li J, Xu J, Opgenoorth L, Miehe G, Mao K. Evolutionary history of two rare endemic conifer species from the eastern Qinghai-Tibet Plateau. ANNALS OF BOTANY 2021; 128:903-918. [PMID: 34472580 PMCID: PMC8577208 DOI: 10.1093/aob/mcab114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Understanding the population genetics and evolutionary history of endangered species is urgently needed in an era of accelerated biodiversity loss. This knowledge is most important for regions with high endemism that are ecologically vulnerable, such as the Qinghai-Tibet Plateau (QTP). METHODS The genetic variation of 84 juniper trees from six populations of Juniperus microsperma and one population of Juniperus erectopatens, two narrow-endemic junipers from the QTP that are sister to each other, was surveyed using RNA-sequencing data. Coalescent-based analyses were used to test speciation, migration and demographic scenarios. Furthermore, positively selected and climate-associated genes were identified, and the genetic load was assessed for both species. KEY RESULTS Analyses of 149 052 single nucleotide polymorphisms showed that the two species are well differentiated and monophyletic. They diverged around the late Pliocene, but interspecific gene flow continued until the Last Glacial Maximum. Demographic reconstruction by Stairway Plot detected two severe bottlenecks for J. microsperma but only one for J. erectopatens. The identified positively selected genes and climate-associated genes revealed habitat adaptation of the two species. Furthermore, although J. microsperma had a much wider geographical distribution than J. erectopatens, the former possesses lower genetic diversity and a higher genetic load than the latter. CONCLUSIONS This study sheds light on the evolution of two endemic juniper species from the QTP and their responses to Quaternary climate fluctuations. Our findings emphasize the importance of speciation and demographic history reconstructions in understanding the current distribution pattern and genetic diversity of threatened species in mountainous regions.
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Affiliation(s)
- Jibin Miao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
- College of Science, Tibet University, Lhasa 850000, PR China
| | - Perla Farhat
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Wentao Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Richard Milne
- Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh EH9 3JH, UK
| | - Heng Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Sonam Tso
- College of Science, Tibet University, Lhasa 850000, PR China
| | - Jialiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Jingjing Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Lars Opgenoorth
- Faculty of Biology and Geology, University of Marburg, 35032 Marburg, Germany
| | - Georg Miehe
- Faculty of Biology and Geology, University of Marburg, 35032 Marburg, Germany
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
- College of Science, Tibet University, Lhasa 850000, PR China
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Zheng HY, Guo XL, Price M, He XJ, Zhou SD. Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence of Chamaesium (Apiaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:673200. [PMID: 34108984 PMCID: PMC8183463 DOI: 10.3389/fpls.2021.673200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/07/2021] [Indexed: 05/13/2023]
Abstract
Exploring the effects of orographic events and climatic shifts on the geographic distribution of organisms in the Himalayas-Hengduan Mountains (HHM) region and Qinghai-Tibetan Plateau (QTP) is crucial to understand the impact of environmental changes on organism evolution. To gain further insight into these processes, we reconstructed the evolutionary history of nine Chamaesium species distributed across the HHM and QTP regions. In total, 525 individuals from 56 populations of the nine species were analyzed based on three maternally inherited chloroplast fragments (rpl16, trnT-trnL, and trnQ-rps16) and one nuclear DNA region (internal transcribed spacer, ITS). Fifty-two chloroplast DNA (cpDNA) and 47 ITS haplotypes were identified in nine species. All of the cpDNA and ITS haplotypes were species-specific. Phylogenetic analysis suggested that all nine species form a monophyletic clade with high support. Dating analysis and ancestral area reconstruction revealed that the ancestral group of Chamaesium originated in the southern Himalayan region at the beginning of the Paleogene (60.85 Ma). The nine species of Chamaesium then separated well during the last 25 million years started in Miocene. Our maxent modeling indicated the broad-scale distributions of all nine species remained fairly stable from LIG to the present and predicted that it will remain stable into the future. The initial split of Chamaesium was triggered by climate changes following the collision of the Indian plate with the Eurasia plate during the Eocene. Subsequently, divergences within Chamaesium may have been induced by the intense uplift of the QTP, the onset of the monsoon system, and Central Asian aridification. Long evolutionary history, sexual reproduction, and habitat fragmentation could contribute to the high level of genetic diversity of Chamaesium. The higher genetic differentiation among Chamaesium populations may be related to the drastic changes of the external environment in this region and limited seed/pollen dispersal capacity.
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Affiliation(s)
- Hong-Yi Zheng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xian-Lin Guo
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Ghaedi Z, Badri S, Saberi-Pirooz R, Vaissi S, Javidkar M, Ahmadzadeh F. The Zagros Mountains acting as a natural barrier to gene flow in the Middle East: more evidence from the evolutionary history of spiny-tailed lizards (Uromasticinae: Saara). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
We investigated the phylogeographic structure of the genus Saara and studied whether the Zagros Mountain ranges influence the gene flow and dispersal at the landscape scale between the Iranian Saara species, including S. asmussi in the central Iranian plateau and S. loricata in the Mesopotamian lowlands. Phylogenetic analyses clearly show three well-supported species, including S. loricata, S. asmussi and S. hardwickii, that are distinct from Uromastyx species. The S-DIVA and BBM analyses demonstrate that species of Saara originated from an ancestor somewhere in the Iranian Plateau and then dispersed to its current geographical range. Our results indicate that the separation of S. loricata from S. asmussi coincides with the orogenic events of the Zagros Mountains during the Pliocene, and thus it may show a vicariance event. Diversification within populations of S. loricata and S. assmussi are estimated to have occurred during the Pleistocene. The haplotype network indicates one haplogroup for each of the Iranian Saara species. Population genetic analyses shows signals of demographic expansions at the beginning of the Holocene for S. loricata. Our results support the hypothesis that the Zagros Mountains act as a barrier for gene flow and Quaternary climatic oscillations affected intraspecific genetic divergences of S. loricata and S. asmussi.
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Affiliation(s)
- Zeinab Ghaedi
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| | - Sahar Badri
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| | - Reihaneh Saberi-Pirooz
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| | - Somaye Vaissi
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
- Department of Biology, Faculty of Science, Baghabrisham, Razi University, Kermanshah, Iran
| | - Mohammad Javidkar
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
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Yin H, Wang L, Shi Y, Qian C, Zhou H, Wang W, Ma XF, Tran LSP, Zhang B. The East Asian Winter Monsoon Acts as a Major Selective Factor in the Intraspecific Differentiation of Drought-Tolerant Nitraria tangutorum in Northwest China. PLANTS 2020; 9:plants9091100. [PMID: 32867062 PMCID: PMC7570063 DOI: 10.3390/plants9091100] [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: 07/15/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022]
Abstract
The influence of Quaternary climate fluctuation on the geographical structure and genetic diversity of species distributed in the regions of the Qinghai–Tibet Plateau (QTP) has been well established. However, the underlying role of the East Asian monsoon system (EAMS) in shaping the genetic structure of the population and the demography of plants located in the arid northwest of China has not been explored. In the present study, Nitraria tangutorum, a drought-tolerant desert shrub that is distributed in the EAMS zone and has substantial ecological and economic value, was profiled to better understand the influence of EAMS evolution on its biogeographical patterns and demographic history. Thus, the phylogeographical structure and historical dynamics of this plant species were elucidated using its five chloroplast DNA (cpDNA) fragments. Hierarchical structure analysis revealed three distinct, divergent lineages: West, East-A, and East-B. The molecular dating was carried out using a Bayesian approach to estimate the time of intraspecies divergence. Notably, the eastern region, which included East-A and East-B lineages, was revealed to be the original center of distribution and was characterized by a high level of genetic diversity, with the intraspecific divergence time dated to be around 2.53 million years ago (Ma). These findings, combined with the data obtained by ecological niche modeling analysis, indicated that the East lineages have undergone population expansion and differentiation, which were closely correlated with the development of the EAMS, especially the East Asian winter monsoon (EAWM). The West lineage appears to have originated from the migration of N. tangutorum across the Hexi corridor at around 1.85 Ma, and subsequent colonization of the western region. These results suggest that the EAWM accelerated the population expansion of N. tangutorum and subsequent intraspecific differentiation. These findings collectively provide new information on the impact of the evolution of the EAMS on intraspecific diversification and population demography of drought-tolerant plant species in northwest China.
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Affiliation(s)
- Hengxia Yin
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
| | - Lirong Wang
- College of Ecological Environment and Resources, Qinghai Nationalities University, Xining 810007, China;
| | - Yong Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
| | - Chaoju Qian
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, China; (C.Q.); (X.-F.M.)
| | - Huakun Zhou
- The Key Laboratory of Restoration Ecology in Cold Region of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Science, Xining 810008, China;
| | - Wenying Wang
- Department of Life Sciences, Qinghai Normal University, Xining 810008, China;
| | - Xiao-Fei Ma
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, China; (C.Q.); (X.-F.M.)
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang 550000, Vietnam
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-19 22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Correspondence: (L.-S.P.T.); (B.Z.)
| | - Benyin Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China
- Correspondence: (L.-S.P.T.); (B.Z.)
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Chen J, Fan J, Wang D, Yue S, Zhai X, Gong Y, Wang J. Rapid and intelligent discrimination of Notopterygium incisum and Notopterygium franchetii by infrared spectroscopic fingerprints and electronic olfactory fingerprints. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 232:118176. [PMID: 32106026 DOI: 10.1016/j.saa.2020.118176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/10/2020] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
This preliminary research evaluated mid-infrared (MIR) spectroscopy, near-infrared (NIR) spectroscopy and electronic nose (E-nose) for the rapid identification of Notopterygium incisum and Notopterygium franchetii, which were both approved sources of Notopterygii Rhizoma et Radix (Chinese Pharmacopoeia, 2015) but possessed different chemical compositions and pharmacological activities. At the level of single variables, MIR showed quite a few discriminating peaks in the regions of 3000-2800 cm-1 (the stretching bands of CH), 1770-1670 cm-1 (the stretching bands of CO), and 1400-1200 cm-1 (the bending bands of CH and the stretching bands of CO). Meanwhile, NIR only showed an intuitive discriminating peak near 4736 cm-1 (the combination band of OH and CO stretching modes). E-nose response signals of N. incisum and N. franchetii were significant different (p < 0.05) on four sensors, i.e., LY2/LG, LY2/GH, LY2/gCT and LY2/gCTI. Using the infrared spectra or E-nose sensor responses as fingerprints, support vector machine (SVM) models can provide good recognition accuracy (100% for MIR and NIR models, 92.9% for E-nose model). This research indicated the feasibility of MIR, NIR and E-nose for the accurate, rapid, cheap and green identification of N. incisum and N. franchetii, which was desirable to assure the authenticity, efficacy and safety of related herb materials and products.
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Affiliation(s)
- Jianbo Chen
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102488, China.
| | - Jing Fan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Dan Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Shiyan Yue
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Xiaolin Zhai
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yuan Gong
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Jingjuan Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China.
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10
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Li J, Milne RI, Ru D, Miao J, Tao W, Zhang L, Xu J, Liu J, Mao K. Allopatric divergence and hybridization withinCupressus chengiana(Cupressaceae), a threatened conifer in the northern Hengduan Mountains of western China. Mol Ecol 2020; 29:1250-1266. [DOI: 10.1111/mec.15407] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/21/2020] [Accepted: 02/26/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Jialiang Li
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Richard I. Milne
- Institute of Molecular Plant Sciences The University of Edinburgh Edinburgh UK
| | - Dafu Ru
- State Key Laboratory of Grassland Agro‐Ecosystem Institute of Innovation Ecology Lanzhou University Lanzhou China
| | - Jibin Miao
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Wenjing Tao
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Lei Zhang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Jingjing Xu
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Jianquan Liu
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Kangshan Mao
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
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11
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Rana HK, Luo D, Rana SK, Sun H. Geological and Climatic Factors Affect the Population Genetic Connectivity in Mirabilis himalaica (Nyctaginaceae): Insight From Phylogeography and Dispersal Corridors in the Himalaya-Hengduan Biodiversity Hotspot. FRONTIERS IN PLANT SCIENCE 2020; 10:1721. [PMID: 32076425 PMCID: PMC7006540 DOI: 10.3389/fpls.2019.01721] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 12/06/2019] [Indexed: 06/02/2023]
Abstract
The genetic architecture within a species in the Himalaya-Hengduan Mountains (HHM) region was considered as the consolidated consequence of historical orogenesis and climatic oscillations. The visualization of dispersal corridors as the function of population genetic connectivity became crucial to elucidate the spatiotemporal dynamics of organisms. However, geodiversity and physical barriers created by paleo geo-climatic events acted vigorously to impact notable alterations in the phylogeographic pattern and dispersal corridors. Therefore, to achieve detailed phylogeography, locate dispersal corridors and estimate genetic connectivity, we integrated phylogeography with species distribution modelling and least cost path of Mirabilis himalaica (Edgew.) Heimerl in the HHM. We amplified four cpDNA regions (petL-psbE, rps16-trnK, rps16 intron, trnS-trnG), and a low copy nuclear gene (G3pdh) from 241 individuals of 29 populations. SAMOVA, genealogical relationships, and phylogenetic analysis revealed four spatially structured phylogroups for M. himalaica with the onset of diversification in late Pliocene (c. 3.64 Ma). No recent demographic growth was supported by results of neutrality tests, mismatch distribution analysis and Bayesian skyline plot. Paleo-distribution modelling revealed the range dynamics of M. himalaica to be highly sensitive to geo-climatic change with limited long-distance dispersal ability and potential evolutionary adaptation. Furthermore, river drainage systems, valleys and mountain gorges were identified as the corridors for population genetic connectivity among the populations. It is concluded that recent intense mountain uplift and subsequent climatic alterations including monsoonal changes since Pliocene or early Pleistocene formulated fragmented habitats and diverse ecology that governed the habitat connectivity, evolutionary and demographic history of M. himalaica. The integrative genetic and geospatial method would bring new implications for the evolutionary process and conservation priority of HHM endemic species.
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Affiliation(s)
- Hum Kala Rana
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, CAS, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dong Luo
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, CAS, Kunming, China
| | - Santosh Kumar Rana
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, CAS, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, CAS, Kunming, China
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12
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Liu ML, He YL, López-Pujol J, Jia Y, Li ZH. Complex population evolutionary history of four cold-tolerant Notopterygium herb species in the Qinghai-Tibetan Plateau and adjacent areas. Heredity (Edinb) 2019; 123:242-263. [PMID: 30742051 PMCID: PMC6781143 DOI: 10.1038/s41437-019-0186-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 01/20/2019] [Accepted: 01/22/2019] [Indexed: 01/24/2023] Open
Abstract
Historical geological and climatic events are the most important drivers of population expansions/contractions, range shifts, and interspecific divergence in plants. However, the species divergence and spatiotemporal population dynamics of alpine cold-tolerant herbal plants in the high-altitude Qinghai-Tibetan Plateau (QTP) and adjacent areas remain poorly understood. In this study, we investigated population evolutionary history of four endangered Notopterygium herb species in the QTP and adjacent regions. We sequenced 10 nuclear loci, 2 mitochondrial DNA regions, and 4 chloroplast DNA regions in a total of 72 natural populations from the 4 species, and tested the hypothesis that the population history of these alpine herbs was markedly affected by the Miocene-Pliocene QTP uplifts and Quaternary climatic oscillations. We found that the four Notopterygium species had generally low levels of nucleotide variability within populations. Molecular dating and isolation-with-migration analyses suggested that Notopterygium species diverged ~1.74-7.82 million years ago and their differentiation was significantly associated with recent uplifts of the eastern margin of the QTP. In addition, ecological niche modeling and population history analysis showed that N. incisum and N. franchetii underwent considerable demographic expansions during the last glacial period of the Pleistocene, whereas a demographic contraction and a expansion occurred for N. forrestii and N. oviforme during the antepenultimate interglacial period and penultimate glacial period, respectively. These findings highlight the importance of geological and climatic changes during the Miocene-Pliocene and Pleistocene as causes of species divergence and changes in population structure within cold-tolerant herbs in the QTP biodiversity hotspot.
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Affiliation(s)
- Mi-Li Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Yan-Ling He
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Barcelona, 08038, Spain
| | - Yun Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China.
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13
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Jia Y, Bai JQ, Liu ML, Jiang ZF, Wu Y, Fang MF, Li ZH. Transcriptome analysis of the endangered Notopterygium incisum: Cold-tolerance gene discovery and identification of EST-SSR and SNP markers. PLANT DIVERSITY 2019; 41:1-6. [PMID: 30931411 PMCID: PMC6412102 DOI: 10.1016/j.pld.2019.01.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 05/28/2023]
Abstract
Notopterygium incisum C. C. Ting ex H. T. Chang (Apiaceae) is an endangered perennial herb in China. The lack of transcriptomic and genomic resources for N. incisum greatly hinders studies of its population genetics and conservation. In this study, we employed RNA-seq technology to characterize transcriptomes for the flowers, leaves, and stems of this endangered herb. A total of 56 million clean reads were assembled into 120,716 unigenes with an N50 length of 850 bp. Among these unigenes, 70,245 (58.19%) were successfully annotated and 65,965 (54.64%) were identified as coding sequences based on their similarities with sequences in public databases. We identified 21 unigenes that had significant relationships with cold tolerance in N. incisum according to gene ontology (GO) annotation analysis. In addition, 13,149 simple sequence repeats (SSRs) and 85,681 single nucleotide polymorphisms were detected as potential molecular genetic markers. Ninety-six primer pairs of SSRs were randomly selected to validate their amplification efficiency and polymorphism. Nineteen SSR loci exhibited polymorphism in three natural populations of N. incisum. These results provide valuable resources to facilitate future functional genomics and conservation genetics studies of N. incisum.
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Affiliation(s)
- Yun Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ji-Qing Bai
- Shaanxi University of Chinese Medicine, Xianyang 712046, China
| | - Mi-Li Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Zhen-Fang Jiang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yan Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Min-Feng Fang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
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14
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Yang J, Feng L, Yue M, He YL, Zhao GF, Li ZH. Species delimitation and interspecific relationships of the endangered herb genus Notopterygium inferred from multilocus variations. Mol Phylogenet Evol 2019; 133:142-151. [PMID: 30639766 DOI: 10.1016/j.ympev.2019.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 12/28/2018] [Accepted: 01/01/2019] [Indexed: 01/29/2023]
Abstract
Species identification and discrimination is the basis of biodiversity research. In general, it is considered that numerous nucleotide variations (e.g., whole chloroplast genomes) can identify species with higher resolution than a few loci, e.g., partial chloroplast or nuclear gene fragments. In this study, we tested this hypothesis by sampling population genetics samples of the endangered herb genus Notopterygium. We sequenced the complete plastomes, five nuclear gene regions, three chloroplast DNA fragments, and a nuclear internal transcribed spacer (nrITS) region for 18 populations sampled throughout most of the geographic ranges of all six Notopterygium species. Species identification analysis showed that four DNA barcodes (matK, rbcL, trnS-trnG, and nrITS) and/or combinations of these markers achieved Notopterygium species discrimination at higher resolution than the general plastomes and nuclear gene sequences. In particular, nrITS had the highest discriminatory power among all of the individual markers. Molecular data sets and morphological evidence indicated that all six Notopterygium species could be reclassified unambiguously to four putative species clades. N. oviforme and N. franchetii had the closest relationship. Molecular dating showed that the origin and divergence of Notopterygium species was significantly associated with geological and climatic fluctuations during the middle of the Pliocene. In conclusion, our results suggest that a few nucleotide variations can achieve species discrimination with higher resolution than numerous plastomes and general nuclear gene fragments when discerning related Notopterygium species.
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Affiliation(s)
- Jiao Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yan-Ling He
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Gui-Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
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15
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Traditional Tibetan medicinal plants: a highlighted resource for novel therapeutic compounds. Future Med Chem 2018; 10:2537-2555. [PMID: 30499690 DOI: 10.4155/fmc-2018-0235] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Around 70-80% of drugs used in traditional Tibetan medicine (TTM) come from Qinghai Tibet Plateau, the majority of which are plants. The biological and medicinal culture diversity on Qinghai Tibet Plateau are amazing and constitute a less tapped resource for innovative drug research and development. Meanwhile, the problem of the exhausting Tibetan medicine resources is worrying. Here, the latest awareness, as well as the gaps of the traditional Tibetan medicinal plant issues in drug development and clinical usage of TTM compounds, was systematically reviewed and highlighted. The TTM resource studies should be enhanced within the context of deeper and more extensive investigations of molecular biology and genomics of TTM plants, phytometabolites and metabolomics and ethnopharmacology-based bioactivity, thus enabling the sustainable conservation and exploitation of Tibetan medicinal resource.
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16
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Li Y, Gao QB, Gengji ZM, Jia LK, Wang ZH, Chen SL. Rapid Intraspecific Diversification of the Alpine Species Saxifraga sinomontana (Saxifragaceae) in the Qinghai-Tibetan Plateau and Himalayas. Front Genet 2018; 9:381. [PMID: 30279701 PMCID: PMC6153349 DOI: 10.3389/fgene.2018.00381] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 08/27/2018] [Indexed: 11/30/2022] Open
Abstract
An increasing number of phylogeographic studies have been conducted for plant species in the Qinghai-Tibetan Plateau (QTP) and its flanking mountains. However, these studies have mainly focused on the determination of glacial refugia and routes of inter-/post-glacial expansions. Rapid intraspecific diversification of plants in this region have not been thoroughly discussed. Herein, we investigate the effects of the Quaternary climate changes on population genetic structure and diversifications of a herbaceous alpine species, Saxifraga sinomontana, which may have an evolutionary time scale <5 million years in the QTP and Himalayan regions. Using a total of 350 individuals from 29 populations, we studied the evolutionary history of S. sinomontana by analyzing cpDNA trnL-trnF, rpl16 and nrDNA ITS sequences. A total of 89 haplotypes and 158 genotypes were detected for cpDNA and ITS sequences, respectively. Only a few haplotypes/genotypes were widespread, while an extremely large number of haplotypes/genotypes were restricted to single populations, which were scattered throughout the current geographical range of S. sinomontana. This suggests the existence of microrefugia of this species during the Quaternary glaciations. In addition, the relationships of the haplotypes/genotypes were almost completely not resolved by phylogenetic reconstruction. Combining characteristics in terms of high haplotype richness, large proportion of private haplotypes, and shallow haplotype divergence, we speculate that recent intraspecific diversification has occurred in S. sinomontana. Molecular clock analysis estimated that the onset diversification within S. sinomontana to be 1.09 Ma (95% HPD = 0.80–1.45), coinciding with the extensive Quaternary glaciations on the QTP which started ca. 1.17 Ma. The Quaternary climatic oscillations may have triggered rapid intraspecific diversification in this QTP-Himalayan species. However, large niche breadth, as well as introgression/hybridization between the studied species and its closely related sympatric saxifrages, may also played a role to some extent on the current genetic structure of S. sinomontana, which need to be further studied.
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Affiliation(s)
- Yan Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qing-Bo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, China
| | - Zhuo-Ma Gengji
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liu-Kun Jia
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhi-Hua Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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17
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Xie C, Xie DF, Zhong Y, Guo XL, Liu Q, Zhou SD, He XJ. The effect of Hengduan Mountains Region (HMR) uplift to environmental changes in the HMR and its eastern adjacent area: Tracing the evolutionary history of Allium section Sikkimensia (Amaryllidaceae). Mol Phylogenet Evol 2018; 130:380-396. [PMID: 30240912 DOI: 10.1016/j.ympev.2018.09.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 08/29/2018] [Accepted: 09/17/2018] [Indexed: 10/28/2022]
Abstract
Exploring the effects of orographic events and climatic shifts on geographic distribution of organism in the Hengduan Mountains Region (HMR) and its eastern adjacent area is crucial to the understanding of the environmental changes to organismal evolution. To gain further insight into these processes, we reconstruct evolutionary history of ten species in Allium section Sikkimensia, distributed across regions abovementioned. Using chloroplast and nuclear sequence variation of 79 populations of these ten Allium species with known morphological preferences, we elucidate the phylogenetic relationship, divergence time, ancestral area and genetic structures. Climatic variables analysis, Isolation by distance (IBD) and environment (IBE) and Species distribution modeling (SDM) were analyzed along different genetic clades. These analyses indicated that the initial split of Sikkimensia was triggered by climate changes following Qinghai-Tibet Plateau sensu lato (QTPsl) uplift during the late Miocene. Subsequently, divergences within lineage (lineage A)/among lineages (lineage C and D) in Sikkimensia may be induced by the intense uplift of the HMR around 3-4 Ma and abrupt intensifying of the Asian monsoon regimes. Furthermore, Sikkimensia populations exhibited lopsided demographic history in the Last Glacial Maximum (LGM), as was indicated by the expansion of their range in the QDM and contraction in the HMR. Our findings appear to suggest that the HMR uplift could have strengthened the orographic difference between the HMR and its eastern adjacent area and led to a colder climate in the HMR, while geological topography also played an important role for taxa to respond the climate change that had taken place in the HMR and its eastern adjacent area during the Pleistocene.
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Affiliation(s)
- Chuan Xie
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Yan Zhong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Xian-Lin Guo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Qing Liu
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Sichuan, PR China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Xing-Jin He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China.
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18
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Yang J, Zhou S, Huang D, He X. Phylogeography of two closely related species of Allium endemic to East Asia: Population evolution in response to climate oscillations. Ecol Evol 2018; 8:7986-7999. [PMID: 30250678 PMCID: PMC6145274 DOI: 10.1002/ece3.4338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/05/2018] [Accepted: 06/06/2018] [Indexed: 11/30/2022] Open
Abstract
This study investigated the effects of climate oscillations on the evolution of two closely related Allium species, A. neriniflorum and A. tubiflorum. We sequenced three cp DNA (cpDNA) fragments (rps16, rpl32-trnL, and trnD-trnT, together approximately 2,500 bp in length) of two closely related Allium species, with samples from 367 individuals in 47 populations distributed across the total range of these species. The interspecific and intraspecific divergence times of the two species were in the Quaternary glaciation. The population divergence was high for the cpDNA variation, suggesting a significant phylogeographic structure (NST = 0.844, GST = 0.798, p < 0.05). Remarkable ecological differentiation was also revealed by Niche models and statistical analyses. Our results suggest the speciation event of the two species was triggered by violent climatic changes during the Quaternary glaciation.
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Affiliation(s)
- Jingtian Yang
- Key Laboratory of Bio‐Resources and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduChina
| | - Songdong Zhou
- Key Laboratory of Bio‐Resources and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduChina
| | - Deqing Huang
- Key Laboratory of Bio‐Resources and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduChina
| | - Xingjin He
- Key Laboratory of Bio‐Resources and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduChina
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