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Jiang C, Wu M, He S, Lu Y, Zhao C. Phylogeography of a herbal Pinellia ternata reveals repeated range expansions and inter/postglacial recolonization routes on the fragmented distribution pattern in China. Ecol Evol 2024; 14:e70206. [PMID: 39219572 PMCID: PMC11362505 DOI: 10.1002/ece3.70206] [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: 05/06/2024] [Revised: 08/02/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024] Open
Abstract
Most plant phylogeographic studies in China have focused on the importance of genetic divergence and where should the shelter be located. Little attention has been paid to range expansion and recolonization routes in this region. In this study, two cpDNA fragments (psbK-psbI and trnL-F), two pairs of nuclear gene sequences (ITS and ETS), and nine pairs of SSR molecular markers were used, combined with Bayesian Skyline Plot method, gene barrier analysis, and species distribution models to explore the phylogeographical pattern, potential expansion routes and population dynamic history of Pinellia ternata from 22 population. The results showed that phylogeograhical pattern and genetic structure for P. ternata are effected by environmental heterogeneity and climate fluctuation, and it can be divided into two groups (Southwest group, Central and Eastern group) and thus there are at least two glacial refugia in China. Three expanding routes within groups were explored to contribute to the phylogeogrephic pattern of P. ternata based on the geographical distribution and network analysis of haplotypes. In a word, our study reveals repeated range expansions and inter/postglacial recolonization routes on the fragmented distribution pattern in China and resolves the refugia distributing in China and has also certain reference value for the protection of the medicinal plant P. ternata.
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Affiliation(s)
- Chunxue Jiang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education)College of Life Sciences/Institute of Agro‐Bioengineering, Guizhou UniversityGuiyangGuizhou ProvinceChina
| | - Ming 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 UniversityGuiyangGuizhou ProvinceChina
| | - Shanshan He
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education)College of Life Sciences/Institute of Agro‐Bioengineering, Guizhou UniversityGuiyangGuizhou ProvinceChina
| | - Yuxia Lu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education)College of Life Sciences/Institute of Agro‐Bioengineering, Guizhou UniversityGuiyangGuizhou ProvinceChina
| | - Cai Zhao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education)College of Life Sciences/Institute of Agro‐Bioengineering, Guizhou UniversityGuiyangGuizhou ProvinceChina
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Cheng XJ, Fritsch PW, Lin YJ, Li GH, Chen YQ, Zhang MY, Lu L. The role of Pleistocene dispersal in shaping species richness of sky island wintergreens from the Himalaya-Hengduan Mountains. Mol Phylogenet Evol 2024; 197:108082. [PMID: 38705251 DOI: 10.1016/j.ympev.2024.108082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 03/19/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024]
Abstract
In addition to topography and climate, biogeographic dispersal has been considered to influence plant diversity in the Himalaya-Hengduan Mountains (HHM), yet, the mode and tempo of sky island dispersal and its influence on species richness has been little explored. Through phylogenetic analysis of Gaultheria ser. Trichophyllae, a sky island alpine clade within the HHM, we test the hypothesis that dispersal has affected current local species richness. We inferred the dynamics of biogeographic dispersal with correlation tests on direction, distance, occurrence time, and regional species richness. We found that G. ser. Trichophyllae originated at the end of the Miocene and mostly dispersed toward higher longitudes (eastward). In particular, shorter intra-regional eastward dispersals and longer inter-regional westward dispersals were most frequently observed. We detected a prevalence of eastward intra-region dispersals in both glacial periods and interglacials. These dispersals may have been facilitated by the reorganization of paleo-drainages and monsoon intensification through time. We suggest that the timing of dispersal corresponding to glacial periods and the prevalence of intra-region dispersal, rather than dispersal frequency, most influenced the pattern of species richness of G. ser. Trichophyllae. This study facilitates a more comprehensive understanding of biodiversity in the sky islands within the HHM.
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Affiliation(s)
- Xiao-Juan Cheng
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Peter W Fritsch
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX 76107, USA
| | - Yan-Jun Lin
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Guo-Hong Li
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Yan-Quan Chen
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China; School of Pharmacy, Sun Yat-sen University, Guangzhou 510000, China
| | - Ming-Ying Zhang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an 712046, China.
| | - Lu Lu
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China.
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Liu H, Liu W, Ahmad I, Xiao Q, Li X, Zhang D, Fang J, Zhang G, Xu B, Gao Q, Chen S. Complete Chloroplast Genome Sequence of Triosteum sinuatum, Insights into Comparative Chloroplast Genomics, Divergence Time Estimation and Phylogenetic Relationships among Dipsacales. Genes (Basel) 2022; 13:genes13050933. [PMID: 35627318 PMCID: PMC9141360 DOI: 10.3390/genes13050933] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/06/2022] [Accepted: 05/17/2022] [Indexed: 12/10/2022] Open
Abstract
Triosteum himalayanum, Triosteum pinnatifidum (Triosteum L., Caprifoliaceae, Dipsacales) are widely distributed in China while Triosteum sinuatum mainly occurrs in northeast China. Few reports have been determined on the genus Triosteum. In the present research, we sequenced 2 chloroplast genomes of Triosteum and analyzed 18 chloroplast genomes, trying to explore the sequence variations and phylogeny of genus Triosteum in the order Dipsacales. The chloroplast genomes of the genus Triosteum ranged from 154,579 bp to 157,178 bp, consisting of 132 genes (86 protein-coding genes, 38 transfer RNA genes, and 8 ribosomal RNA genes). Comparative analyses and phylogenetic analysis supported the division of Dipsacales into two clades, Adoxaceae and six other families. Among the six families, a clade of Valerianaceae+Dipsacaceae was recovered as a sister to a clade of Morinaceae+Linnaeaceae. A closer relationship of T. himalayanum and T. pinnatifidum among three species was revealed. Our research supported that Loniceraferdinandi and Triosteum was closely related. Zabelia had a closer relationship with Linnaea borealis and Dipelta than Morinaceae. The divergence between T. sinuatum and two other species in Triosteum was dated to 13.4 mya.
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Affiliation(s)
- HaiRui Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810008, China; (H.L.); (D.Z.)
- College of Eco-Environmental Engineering, Qinghai University, Xining 810008, China; (Q.X.); (X.L.); (J.F.); (G.Z.); (B.X.)
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China;
| | - WenHui Liu
- Department of Geological Engineering, Qinghai University, Xining 810016, China;
| | - Israr Ahmad
- Department of Botany, Women University of AJK, Bagh 12500, Pakistan;
| | - QingMeng Xiao
- College of Eco-Environmental Engineering, Qinghai University, Xining 810008, China; (Q.X.); (X.L.); (J.F.); (G.Z.); (B.X.)
| | - XuMin Li
- College of Eco-Environmental Engineering, Qinghai University, Xining 810008, China; (Q.X.); (X.L.); (J.F.); (G.Z.); (B.X.)
| | - DeJun Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810008, China; (H.L.); (D.Z.)
- College of Eco-Environmental Engineering, Qinghai University, Xining 810008, China; (Q.X.); (X.L.); (J.F.); (G.Z.); (B.X.)
| | - Jie Fang
- College of Eco-Environmental Engineering, Qinghai University, Xining 810008, China; (Q.X.); (X.L.); (J.F.); (G.Z.); (B.X.)
| | - GuoFan Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining 810008, China; (Q.X.); (X.L.); (J.F.); (G.Z.); (B.X.)
| | - Bin Xu
- College of Eco-Environmental Engineering, Qinghai University, Xining 810008, China; (Q.X.); (X.L.); (J.F.); (G.Z.); (B.X.)
| | - QingBo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China;
- Correspondence:
| | - ShiLong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China;
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Liu HR, Khan G, Gao Q, Zhang F, Liu W, Wang Y, Fang J, Chen S, Afridi SG. Dispersal into the Qinghai-Tibet plateau: evidence from the genetic structure and demography of the alpine plant Triosteum pinnatifidum. PeerJ 2022; 10:e12754. [PMID: 35178292 PMCID: PMC8815373 DOI: 10.7717/peerj.12754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 12/15/2021] [Indexed: 01/07/2023] Open
Abstract
Triosteum pinnatifidum Maxim., an alpine plant, is traditionally used for several medicinal purposes. Here, both chloroplast DNA sequences and nuclear low copy sequence markers were used to investigate the genetic diversity and population structure of T. pinnatifidum. Materials were collected from thirteen localities in the northeast Qinghai-Tibet Plateau (QTP) and adjacent highlands and advanced analytical toolkits were used to access their origin and range shifts. The results revealed a higher level of population differentiation based on chloroplast DNA (cpDNA) concatenated sequences compared with the nuclear DNA sequences (F ST = 0.654 for cpDNA, F ST = 0.398 for AT103), indicating that pollen flow was still extensive in T. pinnatifidum. A decline in haplotype variation was observed from the plateau edge and adjoining highlands toward the platform of the QTP. The hypothesis "dispersal into the QTP," proposing that T. pinnatifidum experienced migration from the plateau edge and adjacent highlands to the platform, was supported. These results were in line with the hypothesis that multiple refugia exist on the plateau edge and adjacent highlands rather than on the plateau platform. Our unimodal mismatch distribution, star-like network supported a recent expansion in T. pinnatifidum.
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Affiliation(s)
- Hai Rui Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai Province, China,College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai Province, China,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province, China
| | - Gulzar Khan
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Lower Saxony, Germany
| | - Qingbo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province, China
| | - Faqi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province, China
| | - Wenhui Liu
- Department of Geological Engineering, Qinghai University, Xining, Qinghai Province, China
| | - Yingfang Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai Province, China
| | - Jie Fang
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai Province, China
| | - Shilong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province, China
| | - Sahib Gul Afridi
- Department of Biochemistry, Abdul Wali Khan University Mardan, Marden, Khyber-Pakhtunkhwa, Pakistan
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Wambulwa MC, Milne R, Wu Z, Spicer RA, Provan J, Luo Y, Zhu G, Wang W, Wang H, Gao L, Li D, Liu J. Spatiotemporal maintenance of flora in the Himalaya biodiversity hotspot: Current knowledge and future perspectives. Ecol Evol 2021; 11:10794-10812. [PMID: 34429882 PMCID: PMC8366862 DOI: 10.1002/ece3.7906] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 01/02/2023] Open
Abstract
Mountain ecosystems support a significant one-third of all terrestrial biodiversity, but our understanding of the spatiotemporal maintenance of this high biodiversity remains poor, or at best controversial. The Himalaya hosts a complex mountain ecosystem with high topographic and climatic heterogeneity and harbors one of the world's richest floras. The high species endemism, together with increasing anthropogenic threats, has qualified the Himalaya as one of the most significant global biodiversity hotspots. The topographic and climatic complexity of the Himalaya makes it an ideal natural laboratory for studying the mechanisms of floral exchange, diversification, and spatiotemporal distributions. Here, we review literature pertaining to the Himalaya in order to generate a concise synthesis of the origin, distribution, and climate change responses of the Himalayan flora. We found that the Himalaya supports a rich biodiversity and that the Hengduan Mountains supplied the majority of the Himalayan floral elements, which subsequently diversified from the late Miocene onward, to create today's relatively high endemicity in the Himalaya. Further, we uncover links between this Miocene diversification and the joint effect of geological and climatic upheavals in the Himalaya. There is marked variance regarding species dispersal, elevational gradients, and impact of climate change among plant species in the Himalaya, and our review highlights some of the general trends and recent advances on these aspects. Finally, we provide some recommendations for conservation planning and future research. Our work could be useful in guiding future research in this important ecosystem and will also provide new insights into the maintenance mechanisms underpinning other mountain systems.
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Affiliation(s)
- Moses C. Wambulwa
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Department of Life SciencesSchool of Pure and Applied SciencesSouth Eastern Kenya UniversityKituiKenya
| | - Richard Milne
- Institute of Molecular Plant SciencesSchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Zeng‐Yuan Wu
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Robert A. Spicer
- CAS Key Laboratory of Tropical Forest EcologyXishuangbanna Tropical Botanical GardenChinese Academy of SciencesXishuangbannaChina
- School of Environment, Earth and Ecosystem SciencesThe Open UniversityMilton KeynesUK
| | - Jim Provan
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Ya‐Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Guang‐Fu Zhu
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- University of the Chinese Academy of SciencesBeijingChina
- Kunming College of Life SciencesUniversity of Chinese Academy of SciencesKunmingChina
| | - Wan‐Ting Wang
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- University of the Chinese Academy of SciencesBeijingChina
- Kunming College of Life SciencesUniversity of Chinese Academy of SciencesKunmingChina
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Lian‐Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - De‐Zhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Kunming College of Life SciencesUniversity of Chinese Academy of SciencesKunmingChina
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
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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: 3] [Impact Index Per Article: 0.8] [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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Zhao F, Li B, Drew BT, Chen YP, Wang Q, Yu WB, Liu ED, Salmaki Y, Peng H, Xiang CL. Leveraging plastomes for comparative analysis and phylogenomic inference within Scutellarioideae (Lamiaceae). PLoS One 2020; 15:e0232602. [PMID: 32379799 PMCID: PMC7205251 DOI: 10.1371/journal.pone.0232602] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/17/2020] [Indexed: 01/02/2023] Open
Abstract
Scutellaria, or skullcaps, are medicinally important herbs in China, India, Japan, and elsewhere. Though Scutellaria is the second largest and one of the more taxonomically challenging genera within Lamiaceae, few molecular systematic studies have been undertaken within the genus; in part due to a paucity of available informative markers. The lack of informative molecular markers for Scutellaria hinders our ability to accurately and robustly reconstruct phylogenetic relationships, which hampers our understanding of the diversity, phylogeny, and evolutionary history of this cosmopolitan genus. Comparative analyses of 15 plastomes, representing 14 species of subfamily Scutellarioideae, indicate that plastomes within Scutellarioideae contain about 151,000 nucleotides, and possess a typical quadripartite structure. In total, 590 simple sequence repeats, 489 longer repeats, and 16 hyper-variable regions were identified from the 15 plastomes. Phylogenetic relationships among the 14 species representing four of the five genera of Scutellarioideae were resolved with high support values, but the current infrageneric classification of Scutellaria was not supported in all analyses. Complete plastome sequences provide better resolution at an interspecific level than using few to several plastid markers in phylogenetic reconstruction. The data presented here will serve as a foundation to facilitate DNA barcoding, species identification, and systematic research within Scutellaria, which is an important medicinal plant resource worldwide.
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Affiliation(s)
- Fei Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Li
- Research Centre of Ecological Sciences, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Bryan T. Drew
- Department of Biology, University of Nebraska at Kearney, Kearney, Nebraska, United States of America
| | - Ya-Ping Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Qiang Wang
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China
| | - Wen-Bin Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - En-De Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yasaman Salmaki
- Center of Excellence in Phylogeny of Living Organisms and Department of Plant Sciences, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Hua Peng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Chun-Lei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Liu HR, Fang J, Xia M, Xiao Q, Zhang D, Xie J, Chen S. The complete chloroplast genome of Triosteum himalayanum (Caprifoliaceae), a perennial alpine herb. Mitochondrial DNA B Resour 2019; 4:4194-4195. [PMID: 33366379 PMCID: PMC7707766 DOI: 10.1080/23802359.2019.1693289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 11/09/2019] [Indexed: 11/26/2022] Open
Abstract
Triosteum himalayanum is a perennial herb which is distributed in the eastern Himalayas, Hengduan Mountains, and central China. The complete chloroplast genome of T. himalayanum is studied for the first time, which is 154,579 bp in length and is divided into four regions: two inverted repeat (IRA and IRB) regions of 23,370 bp, a small single copy (SSC) region of 18,682 bp and a large single copy (LSC) region of 89,157 bp. The plastid genome contains 133 genes, including 86 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. The overall CG content in the chloroplast genome of T. himalayanum is 38.38%. The phylogenetic analysis on the complete plastome sequence of T. himalayanum will help to show the intergeneric diversity of Caprifoliaceae.
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Affiliation(s)
- Hai Rui Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Jie Fang
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Mingze Xia
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Qingmeng Xiao
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Dejun Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Jing Xie
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Shilong 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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9
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Xia M, Tian Z, Zhang F, Khan G, Gao Q, Xing R, Zhang Y, Yu J, Chen S. Deep Intraspecific Divergence in the Endemic Herb Lancea tibetica (Mazaceae) Distributed Over the Qinghai-Tibetan Plateau. Front Genet 2018; 9:492. [PMID: 30429869 PMCID: PMC6220444 DOI: 10.3389/fgene.2018.00492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/03/2018] [Indexed: 11/18/2022] Open
Abstract
Qinghai-Tibetan Plateau (QTP) is an important biodiversity hub, which is very sensitive to climate change. Here in this study, we investigated genetic diversity and past population dynamics of Lancea tibetica (Mazaceae), an endemic herb to QTP and adjacent highlands. We sequenced chloroplast and nuclear ribosomal DNA fragments for 429 individuals, collected from 29 localities, covering their major distribution range at the QTP. A total of 19 chloroplast haplotypes and 13 nuclear genotypes in two well-differentiated lineages, corresponding to populations into two groups isolated by Tanggula and Bayangela Mountains. Meanwhile, significant phylogeographical structure was detected among sampling range of L. tibetica, and 61.50% of genetic variations was partitioned between groups. Gene flow across the whole region appears to be restricted by high mountains, suggesting a significant role of geography in the genetic differences between the two groups. Divergence time between the two lineages dated to 8.63 million years ago, which corresponded to the uplifting of QTP during the late Miocene and Pliocene. Ecological differences were found between both the lineages represent species-specific characteristics, sufficient to keep the lineages separated to a high degree. The simulated distribution from the last interglacial period to the current period showed that the distribution of L. tibetica experienced shrinkage and expansion. Climate changes during the Pleistocene glacial-interglacial cycles had a dramatic effect on L. tibetica distribution ranges. Multiple refugia of L. tibetica might have remained during the species history, to south of the Tanggula and north of Bayangela Mountains, both appeared as topological barrier and contributed to restricting gene flow between the two lineages. Together, geographic isolation and climatic factors have played a fundamental role in promoting diversification and evolution of L. tibetica.
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Affiliation(s)
- Mingze Xia
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zunzhe Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Faqi Zhang
- 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
| | - Gulzar Khan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Qingbo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Rui Xing
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Yu Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Jingya Yu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Shilong Chen
- 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
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