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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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Zhou T, Chen X, López-Pujol J, Bai G, Herrando-Moraira S, Nualart N, Zhang X, Zhao Y, Zhao G. Genetically- and environmentally-dependent processes drive interspecific and intraspecific divergence in the Chinese relict endemic genus Dipteronia. PLANT DIVERSITY 2024; 46:585-599. [PMID: 39290880 PMCID: PMC11403150 DOI: 10.1016/j.pld.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 09/19/2024]
Abstract
China is a hotspot of relict plant species that were once widespread throughout the Northern Hemisphere. Recent research has demonstrated that the occurrence of long-term stable refugia in the mountainous regions of central and south-western China allowed their persistence through the late Neogene climate fluctuations. One of these relict lineages is Dipteronia, an oligotypic tree genus with a fossil record extending to the Paleocene. Here, we investigated the genetic variability, demographic dynamics and diversification patterns of the two currently recognized Dipteronia species (D ipteronia sinensis and D . dyeriana). Molecular data were obtained from 45 populations of Dipteronia by genotyping three cpDNA regions, two single copy nuclear genes and 15 simple sequence repeat loci. The genetic study was combined with niche comparison analyses on the environmental space, ecological niche modeling, and landscape connectivity analysis. We found that the two Dipteronia species have highly diverged both in genetic and ecological terms. Despite the incipient speciation processes that can be observed in D. sinensis, the occurrence of long-term stable refugia and, particularly, a dispersal corridor along Daba Shan-west Qinling, likely ensured its genetic and ecological integrity to date. Our study will not only help us to understand how populations of Dipteronia species responded to the tectonic and climatic changes of the Cenozoic, but also provide insight into how Arcto-Tertiary relict plants in East Asia survived, evolved, and diversified.
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Affiliation(s)
- Tao Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China
| | - Xiaodan Chen
- College of Life Science, Shanxi Normal University, Taiyuan, China
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB), CSIC-CMCNB, Barcelona 08038, Catalonia, Spain
- Escuela de Ciencias Ambientales, Universidad Espíritu Santo (UEES), Samborondón 091650, Ecuador
| | - Guoqing Bai
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Xi'an 710061, China
| | | | - Neus Nualart
- Botanic Institute of Barcelona (IBB), CSIC-CMCNB, Barcelona 08038, Catalonia, Spain
| | - Xiao Zhang
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Xi'an 710061, China
| | - Yuemei Zhao
- School of Biological Sciences, Guizhou Education University, Guiyang, China
| | - Guifang Zhao
- 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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Pokorny L, Pellicer J, Woudstra Y, Christenhusz MJM, Garnatje T, Palazzesi L, Johnson MG, Maurin O, Françoso E, Roy S, Leitch IJ, Forest F, Baker WJ, Hidalgo O. Genomic incongruence accompanies the evolution of flower symmetry in Eudicots: a case study in the poppy family (Papaveraceae, Ranunculales). FRONTIERS IN PLANT SCIENCE 2024; 15:1340056. [PMID: 38947944 PMCID: PMC11212465 DOI: 10.3389/fpls.2024.1340056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/18/2024] [Indexed: 07/02/2024]
Abstract
Reconstructing evolutionary trajectories and transitions that have shaped floral diversity relies heavily on the phylogenetic framework on which traits are modelled. In this study, we focus on the angiosperm order Ranunculales, sister to all other eudicots, to unravel higher-level relationships, especially those tied to evolutionary transitions in flower symmetry within the family Papaveraceae. This family presents an astonishing array of floral diversity, with actinomorphic, disymmetric (two perpendicular symmetry axes), and zygomorphic flowers. We generated nuclear and plastid datasets using the Angiosperms353 universal probe set for target capture sequencing (of 353 single-copy nuclear ortholog genes), together with publicly available transcriptome and plastome data mined from open-access online repositories. We relied on the fossil record of the order Ranunculales to date our phylogenies and to establish a timeline of events. Our phylogenomic workflow shows that nuclear-plastid incongruence accompanies topological uncertainties in Ranunculales. A cocktail of incomplete lineage sorting, post-hybridization introgression, and extinction following rapid speciation most likely explain the observed knots in the topology. These knots coincide with major floral symmetry transitions and thus obscure the order of evolutionary events.
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Affiliation(s)
- Lisa Pokorny
- Real Jardín Botánico (RJB-CSIC), Madrid, Spain
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, Barcelona, Spain
| | - Yannick Woudstra
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Maarten J. M. Christenhusz
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, Barcelona, Spain
- Jardí Botànic Marimurtra, Fundació Carl Faust, Blanes, Spain
| | - Luis Palazzesi
- División Paleobotánica, Museo Argentino de Ciencias Naturales, CONICET, Buenos Aires, Argentina
| | - Matthew G. Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | | | | | - Shyamali Roy
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, Barcelona, Spain
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4
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Wang Z, Wu X, Liu X, Zhang M, Xie C, Chen L. Phylogeographic Structure and Population Dynamics of Baoxing Osmanthus ( Osmanthus serrulatus), an Endemic Species from the Southwest Sichuan Basin, China. PLANTS (BASEL, SWITZERLAND) 2024; 13:1653. [PMID: 38931085 PMCID: PMC11207779 DOI: 10.3390/plants13121653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Abstract
The mountainous regions of southwest China are recognized as pivotal centers for the origin and evolution of Osmanthus species. Baoxing Osmanthus (Osmanthus serrulatus Rehder), a rare and endemic species known for its spring blooms, is sparsely distributed within the high altitude evergreen broad-leaved forests surrounding the southwestern Sichuan Basin. However, persistent anthropogenic disturbances and habitat fragmentation have precipitated a significant decline in its natural population size, leading to the erosion of genetic resources. To assess the genetic status of O. serrulatus and formulate effective conservation strategies, we conducted sampling across ten wild populations, totaling 148 individuals in their natural habitats. We employed two cpDNA fragments (matK and trnS-trnG) to elucidate the phylogeographic structure and historical population dynamics. The results revealed low species-level genetic diversity, alongside pronounced regional differentiation among populations (FST = 0.812, p < 0.05) and a notable phylogeographic structure (NST = 0.698 > GST = 0.396, p < 0.05). Notably, genetic variation was predominantly observed among populations (81.23%), with no evidence of recent demographic expansion across the O. serrulatus distribution range. Furthermore, divergence dating indicated a timeline of approximately 4.85 Mya, corresponding to the late Miocene to early Pleistocene. This temporal correlation coincided with localized uplift events in the southwestern mountains and heightened Asian monsoons, suggesting pivotal roles for these factors in shaping the current phylogeographic pattern of O. serrulatus. These findings support the effective conservation of O. serrulatus germplasm and offer insights into the impact of Quaternary climate oscillations on companion species within evergreen broad-leaved forests. They also enhance our understanding of the origin and evolution of these forests in the southwestern mountains, aiding biodiversity conservation efforts in the region.
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Affiliation(s)
- Zhibei Wang
- Co-Innovation Center for the Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Z.W.); (X.W.); (X.L.); (M.Z.)
- International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing 210037, China
| | - Xi Wu
- Co-Innovation Center for the Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Z.W.); (X.W.); (X.L.); (M.Z.)
- International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing 210037, China
| | - Xin Liu
- Co-Innovation Center for the Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Z.W.); (X.W.); (X.L.); (M.Z.)
- International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing 210037, China
| | - Min Zhang
- Co-Innovation Center for the Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Z.W.); (X.W.); (X.L.); (M.Z.)
- International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing 210037, China
| | - Chunping Xie
- Tropical Biodiversity and Bioresource Utilization Laboratory, Qiongtai Normal University, Haikou 571127, China;
| | - Lin Chen
- Co-Innovation Center for the Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Z.W.); (X.W.); (X.L.); (M.Z.)
- International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing 210037, China
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5
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Zhang Q, Yang Y, Liu B, Lu L, Sauquet H, Li D, Chen Z. Meta-analysis provides insights into the origin and evolution of East Asian evergreen broad-leaved forests. THE NEW PHYTOLOGIST 2024; 242:2369-2379. [PMID: 38186378 DOI: 10.1111/nph.19524] [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: 08/30/2023] [Accepted: 12/18/2023] [Indexed: 01/09/2024]
Abstract
Evergreen broad-leaved forests (EBLFs) are dominated by a monsoon climate and form a distinct biome in East Asia with notably high biodiversity. However, the origin and evolution of East Asian EBLFs (EAEBLFs) remain elusive despite the estimation of divergence times for various representative lineages. Using 72 selected generic-level characteristic lineages, we constructed an integrated lineage accumulation rate (LAR) curve based on their crown ages. According to the crown-based LAR, the EAEBLF origin was identified at least as the early Oligocene (c. 31.8 million years ago (Ma)). The accumulation rate of the characteristic genera peaked at 25.2 and 6.4 Ma, coinciding with the two intensification periods of the Asian monsoon at the Oligocene - Miocene and the Miocene - Pliocene boundaries, respectively. Moreover, the LAR was highly correlated with precipitation in the EAEBLF region and negatively to global temperature, as revealed through time-lag cross-correlation analyses. An early Oligocene origin is suggested for EAEBLFs, bridging the gap between paleobotanical and molecular dating studies and solving conflicts among previous estimates based on individual representative lineages. The strong correlation between the crown-based LAR and the precipitation brought about by the Asian monsoon emphasizes its irreplaceable role in the origin and development of EAEBLFs.
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Affiliation(s)
- Qian Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yuchang Yang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Limin Lu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Hervé Sauquet
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, NSW, 2000, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Dezhu Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhiduan Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
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Xiang KL, Wu SD, Lian L, He WC, Peng D, Peng HW, Zhang XN, Li HL, Xue JY, Shan HY, Xu GX, Liu Y, Wu ZQ, Wang W. Genomic data and ecological niche modeling reveal an unusually slow rate of molecular evolution in the Cretaceous Eupteleaceae. SCIENCE CHINA. LIFE SCIENCES 2024; 67:803-816. [PMID: 38087029 DOI: 10.1007/s11427-023-2448-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 09/11/2023] [Indexed: 04/06/2024]
Abstract
Living fossils are evidence of long-term sustained ecological success. However, whether living fossils have little molecular changes remains poorly known, particularly in plants. Here, we have introduced a novel method that integrates phylogenomic, comparative genomic, and ecological niche modeling analyses to investigate the rate of molecular evolution of Eupteleaceae, a Cretaceous relict angiosperm family endemic to East Asia. We assembled a high-quality chromosome-level nuclear genome, and the chloroplast and mitochondrial genomes of a member of Eupteleaceae (Euptelea pleiosperma). Our results show that Eupteleaceae is most basal in Ranunculales, the earliest-diverging order in eudicots, and shares an ancient whole-genome duplication event with the other Ranunculales. We document that Eupteleaceae has the slowest rate of molecular changes in the observed angiosperms. The unusually low rate of molecular evolution of Eupteleaceae across all three independent inherited genomes and genes within each of the three genomes is in association with its conserved genome architecture, ancestral woody habit, and conserved niche requirements. Our findings reveal the evolution and adaptation of living fossil plants through large-scale environmental change and also provide new insights into early eudicot diversification.
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Affiliation(s)
- Kun-Li Xiang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- China National Botanical Garden, Beijing, 100093, China
| | - Sheng-Dan Wu
- State Key Laboratory of Grassland Agro-Ecosystems and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Lian Lian
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Wen-Chuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Dan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Huan-Wen Peng
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Ni Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong-Yan Shan
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Gui-Xia Xu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yang Liu
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Zhi-Qiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Wei Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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7
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Becker A, Bachelier JB, Carrive L, Conde E Silva N, Damerval C, Del Rio C, Deveaux Y, Di Stilio VS, Gong Y, Jabbour F, Kramer EM, Nadot S, Pabón-Mora N, Wang W. A cornucopia of diversity-Ranunculales as a model lineage. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1800-1822. [PMID: 38109712 DOI: 10.1093/jxb/erad492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
Abstract
The Ranunculales are a hyperdiverse lineage in many aspects of their phenotype, including growth habit, floral and leaf morphology, reproductive mode, and specialized metabolism. Many Ranunculales species, such as opium poppy and goldenseal, have a high medicinal value. In addition, the order includes a large number of commercially important ornamental plants, such as columbines and larkspurs. The phylogenetic position of the order with respect to monocots and core eudicots and the diversity within this lineage make the Ranunculales an excellent group for studying evolutionary processes by comparative studies. Lately, the phylogeny of Ranunculales was revised, and genetic and genomic resources were developed for many species, allowing comparative analyses at the molecular scale. Here, we review the literature on the resources for genetic manipulation and genome sequencing, the recent phylogeny reconstruction of this order, and its fossil record. Further, we explain their habitat range and delve into the diversity in their floral morphology, focusing on perianth organ identity, floral symmetry, occurrences of spurs and nectaries, sexual and pollination systems, and fruit and dehiscence types. The Ranunculales order offers a wealth of opportunities for scientific exploration across various disciplines and scales, to gain novel insights into plant biology for researchers and plant enthusiasts alike.
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Affiliation(s)
- Annette Becker
- Plant Development Group, Institute of Botany, Justus-Liebig-University, Giessen, Germany
| | - Julien B Bachelier
- Institute of Biology/Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Laetitia Carrive
- Université de Rennes, UMR CNRS 6553, Ecosystèmes-Biodiversité-Evolution, Campus de Beaulieu, 35042 Rennes cedex, France
| | - Natalia Conde E Silva
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Catherine Damerval
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Cédric Del Rio
- CR2P - Centre de Recherche en Paléontologie - Paris, MNHN - Sorbonne Université - CNRS, 43 Rue Buffon, 75005 Paris, France
| | - Yves Deveaux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190 Gif-sur-Yvette, France
| | | | - Yan Gong
- Department of Organismic and Evolutionary Biology, Harvard University, MA, 02138, USA
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP39, Paris, 75005, France
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, MA, 02138, USA
| | - Sophie Nadot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie, Systématique et Evolution, Gif-sur-Yvette, France
| | - Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China and University of Chinese Academy of Sciences, Beijing, 100049China
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8
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Wang TR, Meng HH, Wang N, Zheng SS, Jiang Y, Lin DQ, Song YG, Kozlowski G. Adaptive divergence and genetic vulnerability of relict species under climate change: a case study of Pterocarya macroptera. ANNALS OF BOTANY 2023; 132:241-254. [PMID: 37409981 PMCID: PMC10583204 DOI: 10.1093/aob/mcad083] [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: 05/16/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND AND AIMS Understanding adaptive genetic variation and whether it can keep pace with predicted future climate change is critical in assessing the genetic vulnerability of species and developing conservation management strategies. The lack of information on adaptive genetic variation in relict species carrying abundant genetic resources hinders the assessment of genetic vulnerability. Using a landscape genomics approach, this study aimed to determine how adaptive genetic variation shapes population divergence and to predict the adaptive potential of Pterocarya macroptera (a vulnerable relict species in China) under future climate scenarios. METHODS We applied restriction site-associated DNA sequencing (RAD-seq) to obtain 8244 single-nucleotide polymorphisms (SNPs) from 160 individuals across 28 populations. We examined the pattern of genetic diversity and divergence, and then identified outliers by genetic differentiation (FST) and genotype-environment association (GEA) methods. We further dissected the effect of geographical/environmental gradients on genetic variation. Finally, we predicted genetic vulnerability and adaptive risk under future climate scenarios. KEY RESULTS We identified three genetic lineages within P. macroptera: the Qinling-Daba-Tianmu Mountains (QDT), Western Sichuan (WS) and Northwest Yunnan (NWY) lineages, which showed significant signals of isolation by distance (IBD) and isolation by environment (IBE). IBD and IBE explained 3.7-5.7 and 8.6-12.8 % of the genetic structure, respectively. The identified GEA SNP-related genes were involved in chemical defence and gene regulation and may exhibit higher genetic variation to adapt to the environment. Gradient forest analysis revealed that the genetic variation was mainly shaped by temperature-related variables, indicating its adaptation to local thermal environments. A limited adaptive potential was suggested by the high levels of genetic vulnerability in marginal populations. CONCLUSIONS Environmental gradient mainly shaped the population differentiation of P. macroptera. Marginal populations may be at high risk of extinction, and thus proactive management measures, such as assisted gene flow, are required to ensure the survival of these populations.
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Affiliation(s)
- Tian-Rui Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Hong-Hu Meng
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
| | - Nian Wang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai’an, 271018, China
| | - Si-Si Zheng
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yun Jiang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Duo-Qing Lin
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yi-Gang Song
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Department of Biology and Botanic Garden, University of Fribourg, Fribourg, CH-1700, Switzerland
| | - Gregor Kozlowski
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Department of Biology and Botanic Garden, University of Fribourg, Fribourg, CH-1700, Switzerland
- Natural History Museum Fribourg, Fribourg, CH-1700, Switzerland
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Zhang C, Meng R, Meng Y, Guo BL, Liu QR, Nie ZL. Parallel evolution, atavism, and extensive introgression explain the radiation of Epimedium sect. Diphyllon (Berberidaceae) in southern East Asia. FRONTIERS IN PLANT SCIENCE 2023; 14:1234148. [PMID: 37915504 PMCID: PMC10616310 DOI: 10.3389/fpls.2023.1234148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023]
Abstract
East Asia is the richest region of plant biodiversity in the northern temperate zone, and its radiation provides key insights for understanding rapid speciation, including evolutionary patterns and processes. However, it is challenging to investigate the recent evolutionary radiation among plants because of the lack of genetic divergence, phenotypic convergence, and interspecific gene flow. Epimedium sect. Diphyllon is a rarely studied plant lineage endemic to East Asia, especially highly diversified in its southern part. In this study, we report a robust phylogenomic analysis based on genotyping-by-sequencing data of this lineage. The results revealed a clear biogeographic pattern for Epimedium sect. Diphyllon with recognition into two major clades corresponding to the Sino-Himalayan and Sino-Japanese subkingdoms of East Asian Flora and rapid diversification of the extant species dated to the Pleistocene. Evolutionary radiation of Epimedium sect. Diphyllon is characterized by recent and predominant parallel evolution and atavism between the two subkingdom regions, with extensive reticulating hybridization within each region during the course of diversification in southern East Asia. A parallel-atavism-introgression hypothesis is referred to in explaining the radiation of plant diversity in southern East Asia, which represents a potential model for the rapid diversification of plants under global climate cooling in the late Tertiary. Our study advances our understanding of the evolutionary processes of plant radiation in East Asia as well as in other biodiversity hotspot regions.
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Affiliation(s)
- Cheng Zhang
- Key Laboratory of Biodiversity Science and Ecological Engineering of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Ran Meng
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Ying Meng
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Bao-Lin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Quan-Ru Liu
- Key Laboratory of Biodiversity Science and Ecological Engineering of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ze-Long Nie
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
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10
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Ling YY, Xiang KL, Peng HW, Erst AS, Lian L, Zhao L, Jabbour F, Wang W. Biogeographic diversification of Actaea (Ranunculaceae): Insights into the historical assembly of deciduous broad-leaved forests in the Northern Hemisphere. Mol Phylogenet Evol 2023:107870. [PMID: 37406952 DOI: 10.1016/j.ympev.2023.107870] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 03/28/2023] [Accepted: 07/02/2023] [Indexed: 07/07/2023]
Abstract
The deciduous broad-leaved forests (DBLFs) cover large temperate and subtropical high-altitude regions in the Northern Hemisphere. They are home to rich biodiversity, especially to numerous endemic and relict species. However, we know little about how this vegetation in the Northern Hemisphere has developed through time. Here, we used Actaea (Ranunculaceae), an herbaceous genus almost exclusively growing in the understory of the Northern Hemisphere DBLFs, to shed light on the historical assembly of this biome in the Northern Hemisphere. We present a complete species-level phylogenetic analysis of Actaea based on five plastid and nuclear loci. Using the phylogenetic framework, we estimated divergence times, ancestral ranges, and diversification rates. Phylogenetic analyses strongly support Actaea as monophyletic. Sections Podocarpae and Oligocarpae compose a clade, sister to all other Actaea. The sister relationship between sections Chloranthae and Souliea is strongly supported. Section Dichanthera is not monophyletic unless section Cimicifuga is included. Actaea originated in East Asia, likely the Qinghai-Tibet Plateau, in the late Paleocene (c. 57 Ma), and subsequently dispersed into North America in the middle Eocene (c. 43 Ma) via the Thulean bridge. Actaea reached Europe twice, Japan twice, and Taiwan once, and all these five colonization events occurred in the late Miocene-early Pliocene, a period when sea level dropped. Actaea began to diversify at c. 43 Ma. The section-level diversification took place at c. 27-37 Ma and the species-level diversification experienced accelerations twice, which occurred at c. 15 Ma and c. 5 Ma, respectively. Our findings suggest that the Northern Hemisphere DBLFs might have risen in the middle Eocene and further diversified in the late Eocene-Oligocene, middle Miocene and early Pliocene, in association with climatic deterioration during these four periods.
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Affiliation(s)
- Yuan-Yuan Ling
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun-Li Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Huan-Wen Peng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Andrey S Erst
- Central Siberian Botanical Garden, Russian Academy of Sciences, Zolotodolinskaya str. 101, Novosibirsk 630090, Russia
| | - Lian Lian
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris 75005, France
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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11
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Yoichi W, Tamaki I, Oh SH, Nagano AJ, Uehara K, Tomaru N, Abe H. The evolutionary history of rice azaleas (Rhododendron tschonoskii alliance) involved niche evolution to a montane environment. AMERICAN JOURNAL OF BOTANY 2023; 110:e16166. [PMID: 37074769 DOI: 10.1002/ajb2.16166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 05/03/2023]
Abstract
PREMISE The formation of isolated montane geography on islands promotes evolution, speciation, and then radiation if there are ecological changes. Thus, investigating evolutionary histories of montane species and associated ecological changes may help efforts to understand how endemism formed in islands' montane floras. To explore this process, we investigated the evolutionary history of the Rhododendron tschonoskii alliance, which grows in montane environments of the Japanese archipelago and the Korean Peninsula. METHODS We studied the five species in the R. tschonoskii alliance and 30 outgroup species, using genome-wide single-nucleotide polymorphisms and cpDNA sequences, in association with environmental analyses. RESULTS The monophyletic R. tschonoskii alliance diverged since the late Miocene. Species in the alliance currently inhabit a cold climatic niche that is largely different from that of the outgroup species. We observed clear genetic and niche differentiations between the taxa of the alliance. CONCLUSIONS The association of the alliance's evolution with the formation of cooler climates on mountains indicates that it was driven by global cooling since the mid-Miocene and by rapid uplift of mountains since the Pliocene. The combination of geographic and climatic isolation promoted high genetic differentiation between taxa, which has been maintained by climatic oscillations since the Quaternary.
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Affiliation(s)
- Watanabe Yoichi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu, Japan
| | - Sang-Hun Oh
- Department of Biology, Daejeon University, 62 Daehak-ro, Dong-gu, Daejeon, 34520, South Korea
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
| | - Koichi Uehara
- College of Liberal Arts and Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Nobuhiro Tomaru
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Japan
| | - Harue Abe
- Sado Island Center for Ecological Sustainability, Niigata University, 94-2 Koda, Sado, Niigata, 952-2206, Japan
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Li X, Ruhsam M, Wang Y, Zhang HY, Fan XY, Zhang L, Wang J, Mao KS. Wind-dispersed seeds blur phylogeographic breaks: The complex evolutionary history of Populus lasiocarpa around the Sichuan Basin. PLANT DIVERSITY 2023; 45:156-168. [PMID: 37069930 PMCID: PMC10105135 DOI: 10.1016/j.pld.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 06/19/2023]
Abstract
The strength of phylogeographic breaks can vary among species in the same area despite being subject to the same geological and climate history due to differences in biological traits. Several important phylogeographic breaks exist around the Sichuan Basin in Southwest China but few studies have focused on wind-dispersed plants. Here, we investigated the phylogeographic patterns and the evolutionary history of Populus lasiocarpa, a wind-pollinated and wind-dispersed tree species with a circum-Sichuan Basin distribution in southwest China. We sequenced and analyzed three plastid DNA fragments (ptDNA) and eight nuclear microsatellites (nSSRs) of 265 individuals of P. lasiocarpa from 21 populations spanning the entire distribution range. Distribution patterns based on nSSR data revealed that there are three genetic groups in P. lasiocarpa. This is consistent with the three phylogeographic breaks (Sichuan Basin, the Kaiyong Line and the 105°E line), where the Sichuan basin acts as the main barrier to gene flow between western and eastern groups. However, the distribution pattern based on ptDNA haplotypes poorly matched the phylogeographic breaks, and wind-dispersed seeds may be one of the main contributing factors. Species distribution modelling suggested a larger potential distribution in the last glacial maximum with a severe bottleneck during the last interglacial. A DIYABC model also suggested a population contraction and expansion for both western and eastern lineages. These results indicate that biological traits are likely to affect the evolutionary history of plants, and that nuclear molecular markers, which experience higher levels of gene flow, might be better indicators of phylogeographic breaks.
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Affiliation(s)
- Xue 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
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Yi 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
| | - Hong-Ying 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 610065, Sichuan, PR China
| | - Xiao-Yan Fan
- 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
| | - 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 610065, Sichuan, PR China
| | - Jing 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
| | - Kang-Shan 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
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13
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Luo D, Song MS, Xu B, Zhang Y, Zhang JW, Ma XG, Hao XJ, Sun H. A clue to the evolutionary history of modern East Asian flora: insights from phylogeography and diterpenoid alkaloid distribution pattern of the Spiraea japonica complex. Mol Phylogenet Evol 2023; 184:107772. [PMID: 36977458 DOI: 10.1016/j.ympev.2023.107772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/07/2023] [Accepted: 03/21/2023] [Indexed: 03/28/2023]
Abstract
Each subkingdom of East Asian flora (EAF) has a unique evolutionary history, but which has rarely been described based on phylogeographic studies of EAF species. The Spiraea japonica L. complex, which is widespread in East Asia (EA), has received considerable attention because of the presence of diterpenoid alkaloids (DAs). It provides a proxy for understanding the genetic diversity and DA distribution patterns of species under various environmental conditions associated with the geological background in EA. In the present study, the plastome and chloroplast/nuclear DNA of 71 populations belonging to the S. japonica complex and its congeners were sequenced, combined with DA identification, environmental analyses, and ecological niche modelling, to investigate their phylogenetic relationships, genetic and DAs distribution patterns, biogeography, and demographic dynamics. An "ampliative" S. japonica complex was put forward, comprising all species of Sect. Calospira Ser. Japonicae, of which three evolutionary units carrying their respective unique types of DAs were identified and associated with the regionalization of EAF (referring to the Hengduan Mountains, central China, and east China). Moreover, a transition belt in central China with its biogeographic significance was revealed by genetic and DA distribution patterns from the perspective of ecological adaptation. The origin and onset differentiation of the "ampliative" S. japonica complex was estimated in the early Miocene (22.01/19.44 Ma). The formation of Japanese populations (6.75 Ma) was facilitated by the land bridge, which subsequently had a fairly stable demographic history. The populations in east China have undergone a founder effect after the Last Glacial Maximum, which may have been promoted by the expansion potential of polyploidization. Overall, the in-situ origin and diversification of the "ampliative" S. japonica complex since the early Miocene is a vertical section of the formation and development of modern EAF and was shaped by the geological history of each subkingdom.
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Affiliation(s)
- Dong Luo
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Min-Shu Song
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Bo Xu
- College of Forestry, Southwest Forestry University, Kunming 650224, China
| | - Yu Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Jian-Wen Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Xiang-Guang Ma
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Xiao-Jiang Hao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China.
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China.
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Allopatric Lineage Divergence of the East Asian Endemic Herb Conandron ramondioides Inferred from Low-Copy Nuclear and Plastid Markers. Int J Mol Sci 2022; 23:ijms232314932. [PMID: 36499259 PMCID: PMC9740071 DOI: 10.3390/ijms232314932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 12/02/2022] Open
Abstract
The evolutionary histories of ornamental plants have been receiving only limited attention. We examined the origin and divergence processes of an East Asian endemic ornamental plant, Conandron ramondioides. C. ramondioides is an understory herb occurring in primary forests, which has been grouped into two varieties. We reconstructed the evolutionary and population demography history of C. ramondioides to infer its divergence process. Nuclear and chloroplast DNA sequences were obtained from 21 Conandron populations on both sides of the East China Sea (ECS) to explore its genetic diversity, structure, and population differentiation. Interestingly, the reconstructed phylogeny indicated that the populations should be classified into three clades corresponding to geographical regions: the Japan (Honshu+Shikoku) clade, the Taiwan-Iriomote clade, and the Southeast China clade. Lineage divergence between the Japan clade and the Taiwan-Iriomote and Southeast China clades occured 1.14 MYA (95% HPD: 0.82-3.86), followed by divergence between the Taiwan-Iriomote and Southeast China clades approximately 0.75 MYA (95% HPD: 0.45-1.3). Furthermore, corolla traits (floral lobe length to tube length ratios) correlated with geographical distributions. Moreover, restricted gene flow was detected among clades. Lastly, the lack of potential dispersal routes across an exposed ECS seafloor during the last glacial maximum suggests that migration among the Conandron clades was unlikely. In summary, the extant Conandron exhibits a disjunct distribution pattern as a result of vicariance rather than long-distance dispersal. We propose that allopatric divergence has occurred in C. ramondioides since the Pleistocene. Our findings highlight the critical influence of species' biological characteristics on shaping lineage diversification of East Asian relic herb species during climate oscillations since the Quaternary.
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15
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Zhang Y, Yang X, Van de Peer Y, Chen J, Marchal K, Shi T. Evolution of isoform-level gene expression patterns across tissues during lotus species divergence. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:830-846. [PMID: 36123806 PMCID: PMC7613771 DOI: 10.1111/tpj.15984] [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: 05/11/2022] [Accepted: 09/09/2022] [Indexed: 05/03/2023]
Abstract
Both gene duplication and alternative splicing (AS) drive the functional diversity of gene products in plants, yet the relative contributions of the two key mechanisms to the evolution of gene function are largely unclear. Here, we studied AS in two closely related lotus plants, Nelumbo lutea and Nelumbo nucifera, and the outgroup Arabidopsis thaliana, for both single-copy and duplicated genes. We show that most splicing events evolved rapidly between orthologs and that the origin of lineage-specific splice variants or isoforms contributed to gene functional changes during species divergence within Nelumbo. Single-copy genes contain more isoforms, have more AS events conserved across species, and show more complex tissue-dependent expression patterns than their duplicated counterparts. This suggests that expression divergence through isoforms is a mechanism to extend the expression breadth of genes with low copy numbers. As compared to isoforms of local, small-scale duplicates, isoforms of whole-genome duplicates are less conserved and display a less conserved tissue bias, pointing towards their contribution to subfunctionalization. Through comparative analysis of isoform expression networks, we identified orthologous genes of which the expression of at least some of their isoforms displays a conserved tissue bias across species, indicating a strong selection pressure for maintaining a stable expression pattern of these isoforms. Overall, our study shows that both AS and gene duplication contributed to the diversity of gene function during the evolution of lotus.
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Affiliation(s)
- Yue Zhang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan 430081, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, and VIB Center for Plant Systems Biology, Ghent 9052, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinming Chen
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- Corresponding author details: Jinming Chen: ; Kathleen Marchal: ; Tao Shi:
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, and VIB Center for Plant Systems Biology, Ghent 9052, Belgium
- Department of Information Technology, IDLab, IMEC, Ghent University, Ghent 9052, Belgium
- Corresponding author details: Jinming Chen: ; Kathleen Marchal: ; Tao Shi:
| | - Tao Shi
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- Corresponding author details: Jinming Chen: ; Kathleen Marchal: ; Tao Shi:
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16
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Wang L, Li Y, Noshiro S, Suzuki M, Arai T, Kobayashi K, Xie L, Zhang M, He N, Fang Y, Zhang F. Stepped Geomorphology Shaped the Phylogeographic Structure of a Widespread Tree Species ( Toxicodendron vernicifluum, Anacardiaceae) in East Asia. FRONTIERS IN PLANT SCIENCE 2022; 13:920054. [PMID: 35720535 PMCID: PMC9201781 DOI: 10.3389/fpls.2022.920054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Species' phylogeographic patterns reflect the interplay between landscape features, climatic forces, and evolutionary processes. Here, we used two chloroplast DNA (cpDNA) markers (trnL and trnL-F) to explore the role of stepped geomorphology in shaping the phylogeographic structure of Toxicodendron vernicifluum, an economically important tree species widely distributed in East Asia. The range-wide pattern of sequence variation was analyzed based on a dataset including 357 individuals from China, together with published sequences of 92 individuals mainly from Japan and South Korea. We identified five chloroplast haplotypes based on seven substitutions across the 717-bp alignment. A clear east-west phylogeographic break was recovered according to the stepped landforms of mainland China. The wild trees of the western clade were found to be geographically restricted to the "middle step", which is characterized by high mountains and plateaus, while those of the eastern clade were confined to the "low step", which is mainly made up of hills and plains. The two major clades were estimated to have diverged during the Early Pleistocene, suggesting that the cool glacial climate may have caused the ancestral population to retreat to at least two glacial refugia, leading to allopatric divergence in response to long-term geographic isolation. Migration vector analyses based on the outputs of ecological niche models (ENMs) supported a gradual range expansion since the Last Interglacial. Mountain ranges in western China and the East China Sea land bridge were inferred to be dispersal corridors in the western and eastern distributions of T. vernicifluum, respectively. Overall, our study provides solid evidence for the role of stepped geomorphology in shaping the phylogeographic patterns of T. vernicifluum. The resulting east-west genetic discontinuities could persist for a long time, and could occur at a much larger scale than previously reported, extending from subtropical (e.g., the Xuefeng Mountain) to warm-temperate China (e.g., the Taihang Mountain).
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Affiliation(s)
- Lu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Shuichi Noshiro
- Center for Obsidian and Lithic Studies, Meiji University, Tokyo, Japan
| | | | | | | | - Lei Xie
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Mingyue Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Na He
- Xi’an Research Institute of Chinese Lacquer, All China Federation of Supply and Marketing Cooperatives, Xi’an, China
| | - Yanming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Feilong Zhang
- Xi’an Research Institute of Chinese Lacquer, All China Federation of Supply and Marketing Cooperatives, Xi’an, China
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Guo R, Zhang YH, Zhang HJ, Landis JB, Zhang X, Wang HC, Yao XH. Molecular phylogeography and species distribution modelling evidence of 'oceanic' adaptation for Actinidia eriantha with a refugium along the oceanic-continental gradient in a biodiversity hotspot. BMC PLANT BIOLOGY 2022; 22:89. [PMID: 35227218 PMCID: PMC8883688 DOI: 10.1186/s12870-022-03464-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Refugia is considered to be critical for maintaining biodiversity; while discerning the type and pattern of refugia is pivotal for our understanding of evolutionary processes in the context of conservation. Interglacial and glacial refugia have been studied throughout subtropical China. However, studies on refugia along the oceanic-continental gradient have largely been ignored. We used a liana Actinidia eriantha, which occurs across the eastern moist evergreen broad-leaved forests of subtropical China, as a case study to test hypotheses of refugia along the oceanic-continental gradient and 'oceanic' adaptation. RESULTS The phylogeographic pattern of A. eriantha was explored using a combination of three cpDNA markers and 38 nuclear microsatellite loci, Species distribution modelling and dispersal corridors analysis. Our data showed intermediate levels of genetic diversity [haplotype diversity (hT) = 0.498; unbiased expected heterozygosity (UHE) = 0.510] both at the species and population level. Microsatellite loci revealed five clusters largely corresponding to geographic regions. Coalescent time of cpDNA lineages was dated to the middle Pliocene (ca. 4.03 Ma). Both geographic distance and climate difference have important roles for intraspecific divergence of the species. The Zhejiang-Fujian Hilly Region was demonstrated to be a refugium along the oceanic-continental gradient of the species and fit the 'refugia in refugia' pattern. Species distribution modelling analysis indicated that Precipitation of Coldest Quarter (importance of 44%), Temperature Seasonality (29%) and Mean Temperature of Wettest Quarter (25%) contributed the most to model development. By checking the isolines in the three climate layers, we found that A. eriantha prefer higher precipitation during the coldest quarter, lower seasonal temperature difference and lower mean temperature during the wettest quarter, which correspond to 'oceanic' adaptation. Actinidia eriantha expanded to its western distribution range along the dispersal corridor repeatedly during the glacial periods. CONCLUSIONS Overall, our results provide integrated evidence demonstrating that the Zhejiang-Fujian Hilly Region is a refugium along the oceanic-continental gradient of Actinidia eriantha in subtropical China and that speciation is attributed to 'oceanic' adaptation. This study gives a deeper understanding of the refugia in subtropical China and will contribute to the conservation and utilization of kiwifruit wild resources in the context of climate change.
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Affiliation(s)
- Rui Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge, CB2 3EA, UK
| | - Yong-Hua Zhang
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, China
| | - Hua-Jie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14853, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heng-Chang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Xiao-Hong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
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Characterization of Genomic Variation from Lotus (Nelumbo Adans.) Mutants with Wide and Narrow Tepals. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7120593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Compared with rose, chrysanthemum, and water lily, the absence of short-wide and long-narrow tepals of ornamental lotus (Nelumbo Adans.) limits the commercial value of flowers. In this study, the genomes of two groups of lotus mutants with wide-short and narrow-long tepals were resequenced to uncover the genomic variation and candidate genes associated with tepal shape. In group NL (short for N. lutea, containing two mutants and one control of N. lutea), 716,656 single nucleotide polymorphisms (SNPs) and 221,688 insertion-deletion mutations (Indels) were obtained, while 639,953 SNPs and 134,6118 Indels were obtained in group WSH (short for ‘Weishan Hong’, containing one mutant and two controls of N. nucifera ‘Weishan Hong’). Only a small proportion of these SNPs and Indels was mapped to exonic regions of genome: 1.92% and 0.47%, respectively, in the NL group, and 1.66% and 0.48%, respectively, in the WSH group. Gene Ontology (GO) analysis showed that out of 4890 (NL group) and 1272 (WSH group) annotated variant genes, 125 and 62 genes were enriched (Q < 0.05), respectively. Additionally, in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 104 genes (NL group) and 35 genes (WSH group) were selected (p < 0.05). Finally, there were 306 candidate genes that were sieved to determine the development of tepal shape in lotus plants. It will be an essential reference for future identification of tepal-shaped control genes in lotus plants. This is the first comprehensive report of genomic variation controlling tepal shape in lotus, and the mutants in this study are promising materials for breeding novel lotus cultivars with special tepals.
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Wang L, Zhang R, Geng M, Qin Y, Liu H, Li L, Li M. De novo transcriptome assembly and EST-SSR markers development for Zelkova schneideriana Hand.-Mazz. (Ulmaceae). 3 Biotech 2021; 11:420. [PMID: 34603920 DOI: 10.1007/s13205-021-02968-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 08/19/2021] [Indexed: 11/25/2022] Open
Abstract
Zelkova schneideriana Hand.-Mazz. of the Ulmaceae family is a Tertiary relict and economically deciduous tree species endemic to Central and Southern China. In this study, we performed a transcriptome sequencing of Z. schneideriana using high-throughput sequencing approach to detect polymorphic expressed sequence tag-simple sequence repeats (EST-SSR) markers. A total of 3,235 microsatellite loci were detected from 53,517 unigenes. A set of 30 microsatellite markers were randomly selected to validate in 41 individuals from three populations, of which 10 were polymorphic. The number of alleles per locus ranged from 3 to 11. The observed heterozygosity and expected heterozygosity ranged from 0.366 to 0.829 and 0.439 to 0.848, respectively. These polymorphic SSR primers showed good transferability across different Zelkova species, and are valuable for future studies on genetic diversity, conservation, phylogeography, and species delimitation in Z. schneideriana, as well as other Zelkova species. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02968-5.
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Affiliation(s)
- Lingdan Wang
- Central South University of Forestry and Technology, Changsha, 410004 China
| | - Riqing Zhang
- Central South University of Forestry and Technology, Changsha, 410004 China
| | - Maolin Geng
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014 China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014 China
| | - Yufeng Qin
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning, 530002 China
| | - Hailong Liu
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning, 530002 China
| | - Lingli Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014 China
| | - Mimi Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014 China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014 China
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20
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Liu L, Low SL, Sakaguchi S, Feng Y, Ge B, Konowalik K, Li P. Development of nuclear and chloroplast polymorphic microsatellites for Crossostephium chinense (Asteraceae). Mol Biol Rep 2021; 48:6259-6267. [PMID: 34392450 DOI: 10.1007/s11033-021-06590-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 07/23/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Crossostephium chinense is a traditional Chinese medicinal herb and it is often cultivated as an ornamental plant. Previous studies on this species mainly focused on its chemical composition and it was rarely represented in genetic studies, and thus genomic resources remain scarce. METHODS AND RESULTS Both chloroplast and nuclear polymorphic microsatellites of C. chinense were screened from genome skimming data of two individuals. 64 and 63 cpSSR markers were identified from two chloroplast genomes of C. chinense. A total of 133 polymorphic nSSRs were developed. Ten nSSRs were randomly selected to test their transferability across 35 individuals from three populations of C. chinense, and 20 individuals each of Artemisia stolonifera and A. argyi. Cross-amplifications were successfully done for C. chinense and were partially amplified for both Artemisia species. The number of alleles varied from two to nine. The observed heterozygosity and expected heterozygosity per locus ranged from 0.000 to 0.286 and from 0.029 to 0.755, respectively. CONCLUSIONS In this study, we developed polymorphic cpSSRs and nSSRs markers for C. chinense based on genome skimming sequencing. These genomic resources will be valuable for population genetics and conservation studies in C. chinense and Artemisia.
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Affiliation(s)
- Luxian Liu
- Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, 475000, China
| | | | - Shota Sakaguchi
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto, 6068502, Japan
| | - Yu Feng
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Binjie Ge
- Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Kamil Konowalik
- Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, 51-631, Wrocław, Poland.
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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21
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Wang Z, Zhong C, Li D, Yan C, Yao X, Li Z. Cytotype distribution and chloroplast phylogeography of the Actinidia chinensis complex. BMC PLANT BIOLOGY 2021; 21:325. [PMID: 34229602 PMCID: PMC8259359 DOI: 10.1186/s12870-021-03099-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Plant phylogeographic studies of species in subtropical China have mainly focused on rare and endangered species, whereas few studies have been conducted on taxa with relatively wide distribution, especially polyploid species. We investigated the cytotype and haplotype distribution pattern of the Actinidia chinensis complex, a widespread geographically woody liana with variable ploidy in subtropical China comprising two varieties, with three chloroplast fragments DNA (ndhF-rpl132, rps16-trnQ and trnE-trnT). Macroevolutionary, microevolutionary and niche modeling tools were also combined to disentangle the origin and the demographic history of the species or cytotypes. RESULTS The ploidy levels of 3338 individuals from 128 populations sampled throughout the species distribution range were estimated with flow cytometry. The widespread cytotypes were diploids followed by tetraploids and hexaploids, whereas triploids and octoploids occurred in a few populations. Thirty-one chloroplast haplotypes were detected. The genetic diversity and genetic structure were found to be high between varieties (or ploidy races) chinensis and deliciosa. Our results revealed that these two varieties inhabit significantly different climatic niche spaces. Ecological niche models (ENMs) indicate that all varieties' ranges contracted during the Last Inter Glacial (LIG), and expanded eastward or northward during the Last Glacial Maximum (LGM). CONCLUSIONS Pliocene and Plio-Pleistocene climatic fluctuations and vicariance appear to have played key roles in shaping current population structure and historical demography in the A. chinensis complex. The polyploidization process also appears to have played an important role in the historical demography of the complex through improving their adaptability to environmental changes.
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Affiliation(s)
- Zhi Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caihong Zhong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Dawei Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Chunlin Yan
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Xiaohong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
| | - Zuozhou Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
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22
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Magota K, Sakaguchi S, Lee JS, Yamamoto M, Takahashi D, Nagano AJ, Setoguchi H. Phylogeographic analysis of Saxifraga fortunei complex (Saxifragaceae) reveals multiple origins of morphological and ecological variations in the Japanese Archipelago. Mol Phylogenet Evol 2021; 163:107230. [PMID: 34133947 DOI: 10.1016/j.ympev.2021.107230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 11/28/2022]
Abstract
Phenotypic polymorphism within a species is a notable phenomenon in evolutionary biology to understand the process of adaptive speciation and other historical events. The Saxifraga fortunei complex is a widespread herb found in East Asia. It includes several ecotypic taxa corresponding to their habitat environments. The distribution of the various ecotypes in a limited area of the Japanese Archipelago makes the species a suitable model to investigate the impact of population demographic history and natural selection on lineage diversification. Here, Sanger-based sequencing was used to estimate the divergence timeframe between populations of the Eurasian continent and Japan. Genome-wide SNPs obtained by ddRAD sequencing were used to investigate the phylogeographic origins of ecotypic taxa. The phylogenetic analyses revealed the divergence of the Japanese population from the continental population in the late Miocene. Two distinct regional clades of North and South Japan were identified; phenotypic diversification was evident only in the southern clade. The South Japan clades displayed a historical distribution expansion from north to south. The phenotypic variations appeared to have generated during the expansion. The ecotypic boundaries were incongruent with the genetic grouping. We propose that morphological and ecological specialization in Japanese populations was repeatedly generated by local natural selection.
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Affiliation(s)
- Kana Magota
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan.
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
| | - Jung-Sim Lee
- Korean National Arboretum, 415 Gwangneung Sumokwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-Province 11186, Republic of Korea
| | - Masaya Yamamoto
- Hyogo University of Teacher Education, 942-1 Shimokume, Kato, Hyogo 673-1494, Japan
| | - Daiki Takahashi
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga 520-2194, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
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23
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Ye JW, Li DZ. Distinct late Pleistocene subtropical-tropical divergence revealed by fifteen low-copy nuclear genes in a dominant species in South-East China. Sci Rep 2021; 11:4147. [PMID: 33603069 PMCID: PMC7892551 DOI: 10.1038/s41598-021-83473-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 02/01/2021] [Indexed: 01/31/2023] Open
Abstract
In East Asia, genetic divergence is usually considered to be correlated to different floristic regions, however, subtropical-tropical divergence is largely ignored, compared to widely explored temperate-subtropical divergence. Lindera aggregata (Lauraceae), a dominant species in South-East China was selected to address this issue. Fifteen low-copy nuclear genes (LCGs) and four chloroplast DNA (cpDNA) fragments were used to detect its evolutionary history. In LCGs, STRUCTURE and dated Bayesian phylogeny analyses detect distinct subtropical-tropical divergence since late Pleistocene. Approximate Bayesian calculation (ABC) further supports the distinct subtropical-tropical divergence, and close related Taiwan and South China populations are diverged at the last interglacial. Isolation by distance, isolation by environment and isolation by resistance analyses suggest the current climatic difference rather than geographical distance contributes to the genetic differentiation. Principle component analysis shows populations of tropical cluster occur in warmer area with higher precipitation. Ancestral area reconstruction based on Bayesian phylogeny indicates that ancestral L. aggregata populations are distributed in tropical region. In cpDNA, although unique haplotypes are found in tropical region, distinct subtropical-tropical divergence is absent. In conclusion, distinct late Pleistocene subtropical-tropical divergence of L. aggregata is triggered by climate. It is likely that L. aggregata is originated in Southwest-South China and experienced hierarchical dispersal from south to north. The South China Sea land bridge has dual role in connecting or isolating Taiwan and mainland populations since the last glaciation.
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Affiliation(s)
- Jun-Wei Ye
- grid.458460.b0000 0004 1764 155XGermplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China ,grid.464444.20000 0000 8877 107XNatural History Research Centre of Shanghai Natural History Museum, Shanghai Science & Technology Museum, Shanghai, 200041 China
| | - De-Zhu Li
- grid.458460.b0000 0004 1764 155XGermplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
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24
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Kikuchi S, Osone Y. Subspecies divergence and pronounced phylogenetic incongruence in the East-Asia-endemic shrub Magnolia sieboldii. ANNALS OF BOTANY 2021; 127:75-90. [PMID: 32966556 PMCID: PMC7750721 DOI: 10.1093/aob/mcaa174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/22/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND AIMS The biogeographic patterns of the East-Asia-endemic shrub Magnolia sieboldii, in which the range of the subsp. sieboldii is interposed with the disjunct distribution of subsp. japonica, implies a complex evolutionary history, involving rapid speciation and hybridization. Here, we aim to reveal the evolutionary and phylogeographic histories of the species with a particular focus on the time of subspecies divergence, the hypothesis of secondary hybridization and the Pleistocene survival of each subspecies, using a combination of genetic analyses and ecological niche modelling. METHODS Genetic variation, genetic structures and phylogenetic relationships were elucidated based on nuclear low-copy genes, chloroplast DNA, and nuclear simple sequence repeats (SSRs). A scenario selection analysis and divergence time estimation were performed using coalescent simulation in DIYABC and *BEAST. Ecological niche modelling and a test of niche differentiation were performed using Maxent and ENMTools. KEY RESULTS All marker types showed deep, but pronouncedly incongruent, west-east genetic divergences, with the subspecies being delineated only by the nuclear low-copy genes. Phylogenetic tree topologies suggested that ancient hybridization and introgression were likely to have occurred; however, this scenario did not receive significant support in the DIYABC analysis. The subspecies differentiated their niches, but both showed a dependence on high humidity and were predicted to have persisted during the last glacial cycle by maintaining a stable latitudinal distribution via migration to lower altitudes. CONCLUSIONS We found a deep genetic divergence and a pronounced phylogenetic incongruence among the two subspecies of M. sieboldii, which may have been driven by major paleogeographic and paleoclimatic events that have occurred since the Neogene in East Asia, including global cooling, climate oscillations and the formation of land bridges. Both subspecies were, however, considered to persist in situ in stable climatic conditions during the late Pleistocene.
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Affiliation(s)
- Satoshi Kikuchi
- Forestry and Forest Products Research Institute, Forest Research and Management Organization, Matsunosato, Tsukuba City, Ibaraki Prefecture, Japan
- Hokkaido Research Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitsujigaoka, Toyohira, Sapporo City, Hokkaido, Japan
| | - Yoko Osone
- Forestry and Forest Products Research Institute, Forest Research and Management Organization, Matsunosato, Tsukuba City, Ibaraki Prefecture, Japan
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Zhu S, Chen J, Zhao J, Comes HP, Li P, Fu C, Xie X, Lu R, Xu W, Feng Y, Ye W, Sakaguchi S, Isagi Y, Li L, Lascoux M, Qiu Y. Genomic insights on the contribution of balancing selection and local adaptation to the long-term survival of a widespread living fossil tree, Cercidiphyllum japonicum. THE NEW PHYTOLOGIST 2020; 228:1674-1689. [PMID: 32643803 DOI: 10.1111/nph.16798] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 06/27/2020] [Indexed: 05/25/2023]
Abstract
'Living fossils' are testimonies of long-term sustained ecological success, but how demographic history and natural selection contributed to their survival, resilience, and persistence in the face of Quaternary climate fluctuations remains unclear. To better understand the interplay between demographic history and selection in shaping genomic diversity and evolution of such organisms, we assembled the whole genome of Cercidiphyllum japonicum, a widespread East Asian Tertiary relict tree, and resequenced 99 individuals of C. japonicum and its sister species, Cercidiphyllum magnificum (Central Japan). We dated this speciation event to the mid-Miocene, and the intraspecific lineage divergence of C. japonicum (China vs Japan) to the Early Pliocene. Throughout climatic upheavals of the late Tertiary/Quaternary, population bottlenecks greatly reduced the genetic diversity of C. japonicum. However, this polymorphism loss was likely counteracted by, first, long-term balancing selection at multiple chromosomal and heterozygous gene regions, potentially reflecting overdominance, and, second, selective sweeps at stress response and growth-related genes likely involved in local adaptation. Our findings contribute to a better understanding of how living fossils have survived climatic upheaval and maintained an extensive geographic range; that is, both types of selection could be major factors contributing to the species' survival, resilience, and persistence.
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Affiliation(s)
- Shanshan Zhu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jun Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jing Zhao
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Hans Peter Comes
- Department of Biosciences, Salzburg University, Salzburg, A-5020, Austria
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Chengxin Fu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xiao Xie
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Ruisen Lu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wuqin Xu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yu Feng
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wenqing Ye
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics and Science for Life Laboratory, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Yingxiong Qiu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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Hou H, Ye H, Wang Z, Wu J, Gao Y, Han W, Na D, Sun G, Wang Y. Demographic history and genetic differentiation of an endemic and endangered Ulmus lamellosa (Ulmus). BMC PLANT BIOLOGY 2020; 20:526. [PMID: 33203402 PMCID: PMC7672979 DOI: 10.1186/s12870-020-02723-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 10/26/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Ulmus lamellosa (one of the ancient species of Ulmus) is an endemic and endangered plant that has undergone climatic oscillations and geographical changes. The elucidation of its demographic history and genetic differentiation is critical for understanding the evolutionary process and ecological adaption to forests in Northern China. RESULTS Polymorphic haplotypes were detected in most populations of U. lamellosa via DNA sequencing. All haplotypes were divided into three phylogeographic clades fundamentally corresponding to their geographical distribution, namely THM (Taihang Mountains), YM (Yinshan Mountains), and YSM (Yanshan Mountains) groups. The YSM group, which is regarded as ancestral, possessed higher genetic diversity and significant genetic variability in contrast to the YSM and YM groups. Meanwhile, the divergence time of intraspecies haplotypes occurred during the Miocene-Pliocene, which was associated with major Tertiary geological and/or climatic events. Different degrees of gene exchanges were identified between the three groups. During glaciation, the YSM and THM regions might have served as refugia for U. lamellosa. Based on ITS data, range expansion was not expected through evolutionary processes, except for the THM group. A series of mountain uplifts (e.g., Yanshan Mountains and Taihang Mountains) following the Miocene-Pliocene, and subsequently quaternary climatic oscillations in Northern China, further promoted divergence between U. lamellosa populations. CONCLUSIONS Geographical topology and climate change in Northern China played a critical role in establishing the current phylogeographic structural patterns of U. lamellosa. These results provide important data and clues that facilitate the demographic study of tree species in Northern China.
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Affiliation(s)
- Huimin Hou
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Hang Ye
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Zhi Wang
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Jiahui Wu
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Yue Gao
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Wei Han
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Dongchen Na
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Genlou Sun
- Saint Mary’s University, Halifax, Canada
| | - Yiling Wang
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
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Phylogeny, Taxonomy, and Biogeography of Pterocarya (Juglandaceae). PLANTS 2020; 9:plants9111524. [PMID: 33182441 PMCID: PMC7696814 DOI: 10.3390/plants9111524] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/02/2020] [Accepted: 11/06/2020] [Indexed: 12/11/2022]
Abstract
Relict species play an important role in understanding the biogeography of intercontinental disjunctions. Pterocarya (a relict genus) is the valuable model taxon for studying the biogeography of East Asian versus southern European/West Asian disjunct patterns. This disjunction has not been as well studied as others (e.g., between Eastern Asia and North America). Several phylogenetic studies on Pterocarya have been conducted, but none have provided a satisfactory phylogenetic resolution. Here, we report the first well-resolved phylogeny of Pterocarya using restriction site-associated DNA sequencing data based on the sampling of all taxa across the entire distribution area of the genus. Taxonomic treatments were also clarified by combining morphological traits. Furthermore, fossil-calibrated phylogeny was used to explore the biogeography of Pterocarya. Our results support the existence of two sections in Pterocarya, which is in accordance with morphological taxonomy. Section Platyptera comprises three species: P. rhoifolia, P. macroptera, and P. delavayi. Section Pterocarya also comprises three species: P. fraxinifolia, P. hupehensis, and P. stenoptera. The divergence between the two sections took place during the early Miocene (20.5 Ma). The formation of the Gobi Desert and climate cooling of northern Siberia in the Middle Miocene (15.7 Ma) might have caused the split of the continuous distribution of this genus and the formation of the East Asian versus southern European/West Asian disjunct pattern. Lastly, the divergence between P. hupehensis and P. stenoptera as well as between P. rhoifolia and P. macroptera/P. delavayi (10.0 Ma) supports the late Miocene diversification hypothesis in East Asia.
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Zhang Q, Zhang X, Liu J, Mao C, Chen S, Zhang Y, Leng L. Identification of copy number variation and population analysis of the sacred lotus ( Nelumbo nucifera). Biosci Biotechnol Biochem 2020; 84:2037-2044. [PMID: 32594903 DOI: 10.1080/09168451.2020.1786351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The sacred lotus (Nelumbo nucifera) is widely cultured in East Asia for its horticultural, agricultural, and medicinal values. Although many molecular markers had been used to extrapolate population genetics of the sacred lotus, a study of large variations, such as copy number variation (CNV), are absent up to now. In this study, we applied whole-genome re-sequencing to 24 lotus accessions, and use read depth information to genotype and filter original CNV call. Totally 448 duplications and 4,267 deletions were identified in the final CNV set. Further analysis of population structure revealed that the population structure patterns revealed by CNV and SNP are largely consistent with each other. Our result indicated that deep sequencing followed by genotyping is a quick and straightforward way to mine out CNV from the population, and the CNV along with SNP could enable us to better comprehend the biology of the plant.
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Affiliation(s)
- Qing Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing, China
| | - Xueting Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing, China
| | - Jing Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing, China
| | - Chaoyi Mao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing, China
| | - Sha Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing, China
| | - Yujun Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing, China
| | - Liang Leng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing, China
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Cao Y, Zhu S, Chen J, Comes HP, Wang IJ, Chen L, Sakaguchi S, Qiu Y. Genomic insights into historical population dynamics, local adaptation, and climate change vulnerability of the East Asian Tertiary relict Euptelea (Eupteleaceae). Evol Appl 2020; 13:2038-2055. [PMID: 32908603 PMCID: PMC7463308 DOI: 10.1111/eva.12960] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 02/28/2020] [Accepted: 03/17/2020] [Indexed: 12/24/2022] Open
Abstract
The warm-temperate and subtropical climate zones of East Asia are a hotspot of plant species richness and endemism, including a noticeable number of species-poor Tertiary relict tree genera. However, little is understood about when East Asian Tertiary relict plants diversified, how they responded demographically to past environmental change, and to what extent their current genomic composition (and adaptive capacity) might mitigate the effects of global warming. Here, we obtained genomic (RAD-SNP) data for 171 samples from two extant species of Euptelea in China (24 E. pleiosperma populations) and Japan (11 E. polyandra populations) to elucidate their divergence and demographic histories, genome-wide associations with current environmental variables, and genomic vulnerability to future climate change. Our results indicate that Late Miocene changes in climate and/or sea level promoted species divergence, whereas Late Pliocene uplifting in southwest China likely fostered lineage divergence within E. pleiosperma. Its subsequent range expansion into central/east (CE) China bears genomic signatures of climate-driven selection, yet extant CE populations are predicted to be most vulnerable to future climate change. For E. polyandra, geography was the only significant predictor of genomic variation. Our findings indicate a profound impact of Late Neogene geological and climate change on the evolutionary history of Euptelea, with much stronger signals of local adaptation left in China than in Japan. This study deepens our understanding of the complex evolutionary forces that influence the distribution of genetic variation of Tertiary relict trees, and provides insights into their susceptibility to global change and potential for adaptive responses. Our results lay the groundwork for future conservation and restoration programs for Euptelea.
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Affiliation(s)
- Ya‐Nan Cao
- Systematic & Evolutionary Botany and Biodiversity GroupMOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouChina
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouChina
| | - Shan‐Shan Zhu
- Systematic & Evolutionary Botany and Biodiversity GroupMOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouChina
| | - Jun Chen
- Systematic & Evolutionary Botany and Biodiversity GroupMOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouChina
| | - Hans P. Comes
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Ian J. Wang
- Department of Environmental Science, Policy, and ManagementUniversity of California BerkeleyBerkeleyCAUSA
| | - Lu‐Yao Chen
- Systematic & Evolutionary Botany and Biodiversity GroupMOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouChina
| | - Shota Sakaguchi
- Graduate School of Human and Environmental StudiesKyoto UniversityKyotoJapan
| | - Ying‐Xiong Qiu
- Systematic & Evolutionary Botany and Biodiversity GroupMOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouChina
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Zheng Y, Dai Q, Guo X, Zeng X. Dynamics behind disjunct distribution, hotspot-edge refugia, and discordant RADseq/mtDNA variability: insights from the Emei mustache toad. BMC Evol Biol 2020; 20:111. [PMID: 32859147 PMCID: PMC7456009 DOI: 10.1186/s12862-020-01675-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 08/20/2020] [Indexed: 12/01/2022] Open
Abstract
Background The distribution of genetic diversity and the underlying processes are important for conservation planning but are unknown for most species and have not been well studied in many regions. In East Asia, the Sichuan Basin and surrounding mountains constitute an understudied region that exhibits a “ring” of high species richness overlapping the eastern edge of the global biodiversity hotspot Mountains of Southwest China. We examine the distributional history and genetic diversification of the Emei mustache toad Leptobrachium boringii, a typical “ring” element characterized by disjunct ranges in the mountains, by integrating time-calibrated gene tree, genetic variability, individual-level clustering, inference of population splitting and mixing from allele frequencies, and paleoclimatic suitability modeling. Results The results reveal extensive range dynamics, including secondary contact after long-term isolation via westward dispersal accompanied by variability loss. They allow the proposal of a model that combines recurrent contractions caused by Quaternary climatic changes and some failed expansions under suitable conditions for explaining the shared disjunct distribution pattern. Providing exceptional low-elevation habitats in the hotspot area, the eastern edge harbors both long-term refugial and young immigrant populations. This finding and a synthesis of evidence from other taxa demonstrate that a certain contributor to biodiversity, one that preserves and receives low-elevation elements of the east in this case, can be significant for only a particular part of a hotspot. By clarifying the low variability of these refugial populations, we show that discordant mitochondrial estimates of diversity can be obtained for populations that experienced admixture, which would have unlikely left proportional immigrant alleles for each locus. Conclusions Dispersal after long-term isolation can explain much of the spatial distribution of genetic diversity in this species, while secondary contact and long-term persistence do not guarantee a large variation. The model for the formation of disjunct ranges may apply to many other taxa isolated in the mountains surrounding the Sichuan Basin. Furthermore, this study provides insights into the heterogeneous nature of hotspots and discordant variability obtained from genome-wide and mitochondrial data.
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Affiliation(s)
- Yuchi Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, #9 of Section 4, Ren-Min-Nan Road, Wuhou District, Chengdu, 610041, Sichuan Province, China. .,Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, Sichuan Province, China.
| | - Qiang Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, #9 of Section 4, Ren-Min-Nan Road, Wuhou District, Chengdu, 610041, Sichuan Province, China
| | - Xianguang Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, #9 of Section 4, Ren-Min-Nan Road, Wuhou District, Chengdu, 610041, Sichuan Province, China
| | - Xiaomao Zeng
- Chengdu Institute of Biology, Chinese Academy of Sciences, #9 of Section 4, Ren-Min-Nan Road, Wuhou District, Chengdu, 610041, Sichuan Province, China
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Lu RS, Chen Y, Tamaki I, Sakaguchi S, Ding YQ, Takahashi D, Li P, Isaji Y, Chen J, Qiu YX. Pre-quaternary diversification and glacial demographic expansions of Cardiocrinum (Liliaceae) in temperate forest biomes of Sino-Japanese Floristic Region. Mol Phylogenet Evol 2019; 143:106693. [PMID: 31778814 DOI: 10.1016/j.ympev.2019.106693] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/11/2019] [Accepted: 11/22/2019] [Indexed: 11/27/2022]
Abstract
The Sino-Japanese Floristic Region (SJFR) in East Asia is one of the most diverse temperate floras in the world. However, the relative influence of Neogene palaeogeographical changes and Quaternary climatic fluctuations as causal mechanisms on species diversification remains largely controversial, because most divergence time estimates were inferred from single-locus data and have limited geographic or taxonomic sampling. To evaluate these influences, we use SNP markers from restriction site-associated DNA sequencing (RAD-Seq) loci and expressed sequence tags-simple sequence repeat (EST-SSR) markers to investigate the levels of genetic variation, speciation and demographic history of the temperate-deciduous forest (TDF) endemic Cardiocrinum (Endlicher) Lindley (Liliaceae), a genus comprising three species in China (C. giganteum, C. cathayanum) and Japan (C. cordatum). Phylogenomic and population genomic coalescent-based analyses demonstrated that Late Neogene tectonic/climatic events triggered speciation of Cardiocrinum, and Pleistocene climatic fluctuations had limited influence on its divergence history. Population demographic inference using Approximate Bayesian Computation from EST-SSRs and palaeoclimatic niche models both indicated that all three Cardiocrinum species experienced population expansions during the transition from the LIG to the LGM. We also discussed the implications of these results on the conservation of montane TDF species in the SJFR under ongoing environmental change. Our results improve our understanding of how the constituents of montane TDF across the SJFR responded to previous periods of rapid climate and environmental change in terms of speciation and population demographic processes.
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Affiliation(s)
- Rui-Sen Lu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yang Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu 501-3714, Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yan-Qian Ding
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Daiki Takahashi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuji Isaji
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Jun Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ying-Xiong Qiu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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Nogueira FM, Palombini FL, Kuhn SA, Oliveira BF, Mariath JEA. Heat transfer in the tank-inflorescence of Nidularium innocentii (Bromeliaceae): Experimental and finite element analysis based on X-ray microtomography. Micron 2019; 124:102714. [PMID: 31336336 DOI: 10.1016/j.micron.2019.102714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/09/2019] [Accepted: 07/09/2019] [Indexed: 11/27/2022]
Abstract
In Bromeliaceae, various traits have evolved for the uptake and storage of water; however, their roles in bromeliad inflorescences remain unresolved. This study investigates the role of water in the flowers and inflorescences of Nidularium innocentii, and describes water as a protection mechanism. Individuals were divided into groups with and without water provision in inflorescences. Both groups were maintained with water in soil and leaves under the same environmental conditions. During anthesis, individuals were collected, and inflorescences were measured. Another specimen was prepared and scanned using X-ray microtomography (μCT), generating a high-resolution 3D model that was converted into a discretized geometry. Heat transfer finite element analysis (FEA) of the μCT-based geometry was then performed to simulate external temperature dissipation with the presence and absence of water in 3D. Flower size in the control group was significantly larger, and many injuries were observed in the drought group. FEA data indicated that the water environment led to lower temperature variation when compared to the air environment by significantly alleviating thermal amplitude. Water acted as a temperature stabilizer for the inflorescence, while its absence initiated physiological stress responses.
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Affiliation(s)
- Fernanda M Nogueira
- Laboratory of Plant Anatomy (LAVeg), Institute of Biosciences, Department of Botany, Federal University of Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Porto Alegre, RS, Brazil; Graduate Program in Botany, Institute of Biosciences, Department of Botany, Federal University of Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Porto Alegre, RS, Brazil.
| | - Felipe L Palombini
- Graduate Program in Design - PGDesign, Federal University of Rio Grande do Sul - UFRGS, Av. Osvaldo Aranha 99/607, 90035-190, Porto Alegre, RS, Brazil.
| | - Sofia A Kuhn
- Farroupilha Federal Institute of Education, Science and Technology, (IFFar) - RS 527, Julio de Castilhos, RS, Brazil
| | - Branca F Oliveira
- Graduate Program in Design - PGDesign, Federal University of Rio Grande do Sul - UFRGS, Av. Osvaldo Aranha 99/607, 90035-190, Porto Alegre, RS, Brazil; Virtual Design Research Group - ViD, Federal University of Rio Grande do Sul - UFRGS, Av. Osvaldo Aranha 99/408, 90033-190, Porto Alegre, RS, Brazil
| | - Jorge E A Mariath
- Laboratory of Plant Anatomy (LAVeg), Institute of Biosciences, Department of Botany, Federal University of Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Porto Alegre, RS, Brazil
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Integrating Phylogeographic Analysis and Geospatial Methods to Infer Historical Dispersal Routes and Glacial Refugia of Liriodendron chinense. FORESTS 2019. [DOI: 10.3390/f10070565] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liriodendron chinense (Hemsl.), a Tertiary relic tree, is mainly distributed in subtropical China. The causes of the geographical distribution pattern of this species are poorly understood. In this study, we inferred historical dispersal routes and glacial refugia of this species by combining genetic data (chloroplast DNA (cpDNA), nuclear ribosomal DNA (nrDNA), and nuclear DNA (nDNA)) and geospatial data (climate and geology) with the methods of landscape genetics. Additionally, based on sequence variation at multiple loci, we employed GenGIS and Barrier software to analyze L. chinense population genetic structure. Dispersal corridors and historical gene flow between the eastern and western populations were detected, and they were located in mountainous regions. Based on species distribution model (SDMs), the distribution patterns in paleoclimatic periods were consistent with the current pattern, suggesting the presence of multiple refuges in multiple mountainous regions in China. The genetic structure analysis clustered most eastern populations into a clade separated from the western populations. Additionally, a genetic barrier was detected between the eastern and western populations. The dispersal corridors and historical gene flow detected here suggested that the mountains acted as a bridge, facilitating gene flow between the eastern and western populations. Due to Quaternary climatic fluctuations, the habitats and dispersal corridors were frequently inhabited by warm-temperate evergreen forests, which may have fragmented L. chinense habitats and exacerbated the differentiation of eastern and western populations. Ultimately, populations retreated to multiple isolated mountainous refugia, shaping the current geographical distribution pattern. These dispersal corridors and montane refugia suggested that the mountains in subtropical China play a crucial role in the conservation of genetic resources and migration of subspecies or related species in this region.
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Naciri Y, Christe C, Bétrisey S, Song YG, Deng M, Garfì G, Kozlowski G. Species delimitation in the East Asian species of the relict tree genus Zelkova (Ulmaceae): A complex history of diversification and admixture among species. Mol Phylogenet Evol 2019; 134:172-185. [PMID: 30769098 DOI: 10.1016/j.ympev.2019.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 12/04/2018] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
Abstract
Zelkova species, trees of the elm family (Ulmaceae), are part of the Cenozoic relict flora. In western Eurasia, the genus comprises three species that are restricted to disjunct areas (Z. sicula on Sicily, Z. abelicea on Crete and Z. carpinifolia in Transcaucasia). The situation is different in East Asia, where three species (Z. serrata, Z. schneideriana and Z. sinica) have at least partly overlapping distributions. The phylogenetic and phylogeographic status of these East Asian species is still not well understood, mainly since all previous studies used almost exclusively plant material collected in botanical gardens and were based on very small numbers of individuals. Our study is the first based on 33 natural populations covering all important areas with Zelkova species in the Sino-Japanese Floristic Region. Chloroplast and microsatellite markers were used, and Bayesian analyses were run for both types of markers. East Asian Zelkova species cluster into two groups that partially overlap when comparing the two types of markers. For chloroplast markers, the two groups coincide with all Japanese, some Korean and northern Chinese Z. serrata in one group and all other individuals in the other group, regardless of whether they are attributed to Z. serrata, Z. sinica or Z. schneideriana from Korea, mainland China and Taiwan. At the nuclear level, however, the clustering clearly groups all the Z. serrata individuals together, regardless of whether they are from Japan, Korea or China, and the two other species in a second group. This complex genetic pattern in East Asian Zelkova species is most likely due to a combination of ancient diversification and speciation events and more recent hybridization during the last glacial/interglacial retractions and recolonizations. One of the surprising results of our study concerns the populations from Taiwan, which are genetically similar to Z. schneideriana. Thus, their assignation to a separate taxon (Z. tarokoensis) or to a variety of Z. serrata (Z. serrata var. tarokoensis), as currently reported in all local and national floras, might be in need of revision. Furthermore, our results indicate that the East Asian species are more closely related to Z. carpinifolia than to any other Western European species. Haplotypes of Z. sicula and Z. abelicea (Mediterranean region) as well as those of Z. sinica and Z. schneideriana (East Asia) seem to have diversified more recently. The most ancient haplotypes are found among the western Eurasian Z. carpinifolia and the East Asian Z. serrata. This result is in agreement with the carpinifolia and serrata-like morphotypes commonly found in the fossil record.
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Affiliation(s)
- Yamama Naciri
- Conservatoire et Jardin botaniques de la Ville de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Genève, Switzerland; Laboratoire de Systématique végétale et Biodiversité, University of Geneva, Chemin de l'Impératrice 1, 1292 Chambésy, Genève, Switzerland.
| | - Camille Christe
- Conservatoire et Jardin botaniques de la Ville de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Genève, Switzerland
| | - Sébastien Bétrisey
- Natural History Museum Fribourg, Chemin du Musée 6, 1700 Fribourg, Switzerland; Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Yi-Gang Song
- Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland; Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Min Deng
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Giuseppe Garfì
- Institute of Biosciences and BioResources, National Research Council, Corso Calatafimi 414, 90129 Palermo, Italy
| | - Gregor Kozlowski
- Natural History Museum Fribourg, Chemin du Musée 6, 1700 Fribourg, Switzerland; Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
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Yang A, Zhong Y, Liu S, Liu L, Liu T, Li Y, Yu F. New insight into the phylogeographic pattern of Liriodendron chinense (Magnoliaceae) revealed by chloroplast DNA: east-west lineage split and genetic mixture within western subtropical China. PeerJ 2019; 7:e6355. [PMID: 30723627 PMCID: PMC6361005 DOI: 10.7717/peerj.6355] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/26/2018] [Indexed: 11/20/2022] Open
Abstract
Background Subtropical China is a global center of biodiversity and one of the most important refugia worldwide. Mountains play an important role in conserving the genetic resources of species. Liriodendron chinense is a Tertiary relict tree largely endemic to subtropical China. In this study, we aimed to achieve a better understanding of the phylogeographical pattern of L. chinense and to explore the role of mountains in the conservation of L. chinense genetic resources. Methods Three chloroplast regions (psbJ-petA, rpl32-ndhF, and trnK5’-matK) were sequenced in 40 populations of L. chinense for phylogeographical analyses. Relationships among chloroplast DNA (cpDNA) haplotypes were determined using median-joining networks, and genetic structure was examined by spatial analysis of molecular variance (SAMOVA). The ancestral area of the species was reconstructed using the Bayesian binary Markov Chain Monte Carlo (BBM) method according to its geographic distribution and a maximum parsimony (MP) tree based on Bayesian methods. Results Obvious phylogeographic structure was found in L. chinense. SAMOVA revealed seven groups matching the major landscape features of the L. chinense distribution area. The haplotype network showed three clades distributed in the eastern, southwestern, and northwestern regions. Separate northern and southern refugia were found in the Wu Mountains and Yungui Plateau, with genetic admixture in the Dalou Mountains and Wuling Mountains. BBM revealed a more ancient origin of L. chinense in the eastern region, with a west–east split most likely having occurred during the Mindel glacial stage. Discussion The clear geographical distributions of haplotypes suggested multiple mountainous refugia of L. chinense. The east–west lineage split was most likely a process of gradual genetic isolation and allopatric lineage divergence when the Nanling corridor was frequently occupied by evergreen or coniferous forest during Late Quaternary oscillations. Hotspots of haplotype diversity in the Dalou Mountains and Wuling Mountains likely benefited from gene flow from the Wu Mountains and Yungui Plateau. Collectively, these results indicate that mountain regions should be the main units for conserving and collecting genetic resources of L. chinense and other similar species in subtropical China.
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Affiliation(s)
- Aihong Yang
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Yongda Zhong
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Shujuan Liu
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Lipan Liu
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Tengyun Liu
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Yanqiang Li
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Faxin Yu
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
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Phylogenomics recovers monophyly and early Tertiary diversification of Dipteronia (Sapindaceae). Mol Phylogenet Evol 2019; 130:9-17. [DOI: 10.1016/j.ympev.2018.09.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/16/2018] [Accepted: 09/19/2018] [Indexed: 11/23/2022]
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Fan D, Huang J, Hu H, Sun Z, Cheng S, Kou Y, Zhang Z. Evolutionary Hotspots of Seed Plants in Subtropical China: A Comparison With Species Diversity Hotspots of Woody Seed Plants. Front Genet 2018; 9:333. [PMID: 30177954 PMCID: PMC6109751 DOI: 10.3389/fgene.2018.00333] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/02/2018] [Indexed: 11/13/2022] Open
Abstract
Genetic diversity is a fundamental level of biodiversity. However, it is frequently neglected in conservation prioritization because intraspecific genetic diversity is difficult to measure at large scales. In this study, we synthesized population genetic or phylogeographic datasets of 33 seed plants in subtropical China into multi-species genetic landscapes. The genetic landscapes identified 18 evolutionary hotspots with high within-population genetic diversity (WGD), and among-population genetic diversity (AGD), or both. The western subtropical China is rich in AGD (possessing four major AGD hotspots), deserving a high conservation priority. We found that WGD was positively correlated with longitude, with most WGD hotspots locating in east subtropical China. The results showed that the locations of 12 of 18 evolutionary hotspots corresponded approximately to those of previously identified species diversity (SD) hotspots, however, a positive and significant correlation existed only between AGD and SD, not between WGD and SD. Therefore, spatial patterns of species richness in plants in subtropical China cannot generally be used as surrogate for their intraspecific diversity. This study identified multi-species evolutionary hotspots and correlated multi-species genetic diversity with SD across subtropical China for the first time, providing profound implications for the conservation of biodiversity in this important ecoregion.
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Affiliation(s)
- Dengmei Fan
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Jihong Huang
- Key Laboratory of Forest Ecology and Environment, The State Forestry and Grassland Administration, Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Huili Hu
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Zhixia Sun
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Shanmei Cheng
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Yixuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Zhiyong Zhang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
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Wang Y, Liu K, Bi D, Zhou S, Shao J. Molecular phylogeography of East Asian Boea clarkeana (Gesneriaceae) in relation to habitat restriction. PLoS One 2018; 13:e0199780. [PMID: 29969490 PMCID: PMC6029794 DOI: 10.1371/journal.pone.0199780] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 06/13/2018] [Indexed: 11/23/2022] Open
Abstract
Subfamily Cyrtandroideae (Gesneriaceae) comprises a broadly distributed group of rocky-slope herbs, with China being the center of its distributional range. The normal growth of many species within the family is particularly dependent on special habitats. Due to the paucity of molecular studies, very little is known regarding East Asian herb phylogeographic pattern. Here, we investigate the molecular phylogeography of Boea clarkeana Hemsl., a unique resurrection herb endemic to China, focusing on geographically restrictive effects of habitat distribution on evolutionary history. Variation in three chloroplast DNA (cpDNA) intergenic spacers (psbA-trnH, rps12-rpl20, and trnL-trnF), the ribosomal internal transcribed spacer (ITS) and simple sequence repeats in expressed sequence tags (EST-SSRs) was investigated across 18 populations to assess genetic diversity, genetic structure and historical dynamics. Genetic diversity was low within populations (cpDNA, hS = 0.03, πS×10(3) = 0.17; ITS, hS = 0.16, πS×10(3) = 0.43) but high for species (cpDNA, hT = 0.82, πT×10(3) = 3.12; ITS, hT = 0.88, πT×10(3) = 6.39); 76 alleles were detected in this highly inbred species (FIS = 0.22), with a significantly low average of 1.34 alleles per locus. No cpDNA or ITS haplotypes were shared between regions. Based on cpDNA results, the Mt. Huangshan-Tianmu and Mt. Qinling-Daba haplotypes are ancestral; these two regions represent potential refugia. Although no evidence of significant retreat-migration phenomena during glacial cycles was detected, interglacial range expansion from northern Mt. Qinling-Daba was identified (121,457 yr BP). Rapid agricultural growth caused bottlenecks in many populations, especially on Mt. Huang-Tianmu. Habitat restriction and fragmentation, weak seed and pollen dispersal abilities, and long-term isolation caused by human-induced or environmental changes are considered the main causes of extinction of several populations and low genetic diversity within populations and regions. These analyses clarify the effects of habitat restriction on B. clarkeana, representing an evolutionary reference for similar gesneriads, and enrich our understanding of the molecular phylogeography of East Asian rocky-slope herbs.
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Affiliation(s)
- Ying Wang
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu, Anhui, China
| | - Kun Liu
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu, Anhui, China
| | - De Bi
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Shoubiao Zhou
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- College of Environmental Science and Engineering, Anhui Normal University, Wuhu, Anhui, China
| | - Jianwen Shao
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu, Anhui, China
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Xiang KL, Erst AS, Xiang XG, Jabbour F, Wang W. Biogeography of Coptis Salisb. (Ranunculales, Ranunculaceae, Coptidoideae), an Eastern Asian and North American genus. BMC Evol Biol 2018; 18:74. [PMID: 29793422 PMCID: PMC5968522 DOI: 10.1186/s12862-018-1195-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 05/17/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Numerous studies have favored dispersal (colonization) over vicariance (past fragmentation) events to explain eastern Asian-North American distribution patterns. In plants, however the disjunction between eastern Asia and western North America has been rarely examined using the integration of phylogenetic, molecular dating, and biogeographical methods. Meanwhile, the biogeographic patterns within eastern Asia remain poorly understood. The goldthread genus Coptis Salisb. includes 15 species disjunctly distributed in North America, Japan, mainland China, and Taiwan. We present a dated phylogeny for Coptis under the optimal clock model and infer its historical biogeography by comparing different biogeographic models. RESULTS The split of Coptis and Xanthorhiza Marshall occurred in the middle Miocene (ca. 15.47 Ma). Coptis started their diversification in the early late Miocene (ca. 9.55 Ma). A late Miocene vicariance event resulted in the eastern Asian and western North American disjunction in the genus. Within eastern Asia, dispersals from mainland Asia to Japan and from Japan to Taiwan occurred at ca. 4.85 Ma and at ca. 1.34 Ma, respectively. CONCLUSIONS Our analyses provide evidence that both vicariance and dispersal events have played important roles in shaping the current distribution and endemism of Coptis, likely resulting from eustatic sea-level changes, mountain formation processes and an increasing drier and cooler climate from the middle Miocene onwards.
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Affiliation(s)
- Kun-Li Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Andrey S Erst
- Central Siberian Botanical Garden of the Siberian Branch of Russian Academy of Sciences, Zolotodolinskaya str. 101, Novosibirsk, 630090, Russia.,Laboratory of Systematics and Phylogeny of Plants, Tomsk State University, Tomsk, 634050, Russia
| | - Xiao-Guo Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Florian Jabbour
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP39, 75005, Paris, France
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Phylogeny and biogeography of East Asian evergreen oaks (Quercus section Cyclobalanopsis; Fagaceae): Insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia. Mol Phylogenet Evol 2018; 119:170-181. [DOI: 10.1016/j.ympev.2017.11.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 11/14/2017] [Accepted: 11/14/2017] [Indexed: 11/17/2022]
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Wang MN, Duan L, Qiao Q, Wang ZF, Zimmer EA, Li ZC, Chen HF. Phylogeography and conservation genetics of the rare and relict Bretschneidera sinensis (Akaniaceae). PLoS One 2018; 13:e0189034. [PMID: 29329302 PMCID: PMC5766123 DOI: 10.1371/journal.pone.0189034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 11/19/2017] [Indexed: 11/21/2022] Open
Abstract
Bretschneidera sinensis, a class-I protected wild plant in China, is a relic of the ancient Tertiary tropical flora endemic to Asia. However, little is known about its genetics and phylogeography. To elucidate the current phylogeographic patterns and infer the historical population dynamics of B. sinensis, and to make recommendations for its conservation, three non-coding regions of chloroplast DNA (trnQ-rps16, rps8-rps11, and trnT-trnL) were amplified and sequenced across 256 individuals from 23 populations of B. sinensis, spanning 10 provinces of China. We recognized 13 haplotypes, demonstrating relatively high total haplotype diversity (hT = 0.739). Almost all of the variation existed among populations (98.09%, P < 0.001), but that within populations was low (1.91%, P < 0.001). Strong genetic differentiation was detected among populations (GST = 0.855, P < 0.001) with limited estimations of seed flow (Nm = 0.09), indicating that populations were strongly isolated from one another. According to SAMOVA analysis, populations of B. sinensis in China could be divided into five geographic groups: (1) eastern Yunnan to western Guangxi; (2) Guizhou-Hunan-Hubei; (3) central Guangdong; (4) northwestern Guangdong; and (5) the Luoxiao-Nanling-Wuyi -Yangming Mountain. Network analysis showed that the most ancestral haplotypes were located in the first group, i.e., the eastern Yungui Plateau and in eastern Yunnan, which is regarded as a putative glacial refugia for B. sinensis in China. B. sinensis may have expanded its range eastward from these refugia and experienced bottleneck or founder effects in southeastern China. Populations in Liping (Guizhou Province), Longsheng (Guangxi Province), Huizhou (Guangdong Province), Chongyi (Jiangxi Province), Dong-an (Hunan Province), Pingbian (Yunnan Province) and Xinning (Hunan Province) are proposed as the priority protection units.
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Affiliation(s)
- Mei-Na Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Lei Duan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Qi Qiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
| | - Zheng-Feng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Elizabeth A. Zimmer
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, D.C., United States of America
| | - Zhong-Chao Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hong-Feng Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Genetic Differentiation and Population Genetic Structure of the Chinese Endemic Dipteronia Oliv. Revealed by cpDNA and AFLP Data. FORESTS 2017. [DOI: 10.3390/f8110424] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Salas-Leiva DE, Meerow AW, Calonje M, Francisco-Ortega J, Griffith MP, Nakamura K, Sánchez V, Knowles L, Knowles D. Shifting Quaternary migration patterns in the Bahamian archipelago: Evidence from the Zamia pumila complex at the northern limits of the Caribbean island biodiversity hotspot. AMERICAN JOURNAL OF BOTANY 2017; 104:757-771. [PMID: 28515078 DOI: 10.3732/ajb.1700054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/10/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY The Bahamas archipelago is formed by young, tectonically stable carbonate banks that harbor direct geological evidence of global ice-volume changes. We sought to detect signatures of major changes on gene flow patterns and reconstruct the phylogeographic history of the monophyletic Zamia pumila complex across the Bahamas. METHODS Nuclear molecular markers with both high and low mutation rates were used to capture two different time scale signatures and test several gene flow and demographic hypotheses. KEY RESULTS Single-copy nuclear genes unveiled apparent ancestral admixture on Andros, suggesting a significant role of this island as main hub of diversity of the archipelago. We detected demographic and spatial expansion of the Zamia pumila complex on both paleo-provinces around the Piacenzian (Pliocene)/Gelasian (Pleistocene). Populations evidenced signatures of different migration models that have occurred at two different times. Populations on Long Island (Z. lucayana) may either represent a secondary colonization of the Bahamas by Zamia or a rapid and early-divergence event of at least one population on the Bahamas. CONCLUSIONS Despite changes in migration patterns with global climate, expected heterozygosity with both marker systems remains within the range reported for cycads, but with significant levels of increased inbreeding detected by the microsatellites. This finding is likely associated with reduced gene flow between and within paleo-provinces, accompanied by genetic drift, as rising seas enforced isolation. Our study highlights the importance of the maintenance of the predominant direction of genetic exchange and the role of overseas dispersion among the islands during climate oscillations.
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Affiliation(s)
- Dayana E Salas-Leiva
- International Center for Tropical Botany, Department of Biological Sciences, 11200 S.W. 8th Street, Florida International University, Miami, Florida 33199 USA
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
- Montgomery Botanical Center, 11901 Old Cutler Road, Coral Gables, Florida 33156 USA
| | - Alan W Meerow
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
| | - Michael Calonje
- Montgomery Botanical Center, 11901 Old Cutler Road, Coral Gables, Florida 33156 USA
| | - Javier Francisco-Ortega
- International Center for Tropical Botany, Department of Biological Sciences, 11200 S.W. 8th Street, Florida International University, Miami, Florida 33199 USA
- Kushlan Tropical Science Institute, 11935 Old Cutler Road, Fairchild Tropical Botanic Garden, Coral Gables, Florida 33156 USA
| | - M Patrick Griffith
- Montgomery Botanical Center, 11901 Old Cutler Road, Coral Gables, Florida 33156 USA
| | - Kyoko Nakamura
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
| | - Vanessa Sánchez
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
| | - Lindy Knowles
- Bahamas National Trust, P. O. Box N-4105, Bay Street Business Centre, Bay Street, Nassau
| | - David Knowles
- The Bahamas, Bahamas National Trust, Abaco National Park, P.O. Box AB-20953, Marsh Harbour, Abaco, The Bahamas
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Xiang KL, Zhao L, Erst AS, Yu SX, Jabbour F, Wang W. A molecular phylogeny of Dichocarpum (Ranunculaceae): Implications for eastern Asian biogeography. Mol Phylogenet Evol 2017; 107:594-604. [DOI: 10.1016/j.ympev.2016.12.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/08/2016] [Accepted: 12/20/2016] [Indexed: 11/30/2022]
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Quaternary climate change drives allo-peripatric speciation and refugial divergence in the Dysosma versipellis-pleiantha complex from different forest types in China. Sci Rep 2017; 7:40261. [PMID: 28074927 PMCID: PMC5225488 DOI: 10.1038/srep40261] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/05/2016] [Indexed: 01/26/2023] Open
Abstract
Subtropical China harbours the world's most diverse temperate flora, but little is known about the roles of geographical and eco-climatic factors underlying the region's exceptionally high levels of species diversity and endemism. Here we address this key question by investigating the spatio-temporal and ecological processes of divergence within the Dysosma versipellis-pleiantha species complex, endemic to subtropical China. Our cpDNA phylogeny showed that this monophyletic group of understory herbs is derived from a Late Pliocene ancestor of the Qinghai-Tibetan Plateau (QTP)/Southwest China. Genetic and ENM data in conjunction with niche differentiation analyses support that the early divergence of D. versipellis and D. pleiantha proceeded through allo-peripatric speciation, possibly triggered by Early Pleistocene climate change, while subsequent climate-induced cycles of range contractions/expansions enhanced the eco-geographical isolation of both taxa. Furthermore, modelling of population-genetic data indicated that major lineage divergences within D. versipellis likely resulted from long-term allopatric population isolation in multiple localized refugia over the last glacial/interglacial periods, and which in turn fostered endemic species formation (D. difformis, D. majoensis) from within D. versipellis in Southwest China. These findings point to an overriding role of Quaternary climate change in triggering essentially allopatric (incipient) speciation in this group of forest-restricted plant species in subtropical China.
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Lu RS, Li P, Qiu YX. The Complete Chloroplast Genomes of Three Cardiocrinum (Liliaceae) Species: Comparative Genomic and Phylogenetic Analyses. FRONTIERS IN PLANT SCIENCE 2016; 7:2054. [PMID: 28119727 PMCID: PMC5222849 DOI: 10.3389/fpls.2016.02054] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 12/22/2016] [Indexed: 05/22/2023]
Abstract
The genus Cardiocrinum (Endlicher) Lindley (Liliaceae) comprises three herbaceous perennial species that are distributed in East Asian temperate-deciduous forests. Although all three Cardiocrinum species have horticultural and medical uses, studies related to species identification and molecular phylogenetic analysis of this genus have not been reported. Here, we report the complete chloroplast (cp) sequences of each Cardiocrinum species using Illumina paired-end sequencing technology. The cp genomes of C. giganteum, C. cathayanum, and C. cordatum were found to be 152,653, 152,415, and 152,410 bp in length, respectively, including a pair of inverted repeat (IR) regions (26,364-26,500 bp) separated by a large single-copy (LSC) region (82,186-82,368 bp) and a small single-copy (SSC) region (17,309-17,344 bp). Each cp genome contained the same 112 unique genes consisting of 30 transfer RNA genes, 4 ribosomal RNA genes, and 78 protein-coding genes. Gene content, gene order, AT content, and IR/SC boundary structures were almost the same among the three Cardiocrinum cp genomes, yet their lengths varied due to contraction/expansion of the IR/SC borders. Simple sequence repeat (SSR) analysis further indicated the richest SSRs in these cp genomes to be A/T mononucleotides. A total of 45, 57, and 45 repeats were identified in C. giganteum, C. cathayanum, and C. cordatum, respectively. Six cpDNA markers (rps19, rpoC2-rpoC1, trnS-psbZ, trnM-atpE, psaC-ndhE, ycf15-ycf1) with the percentage of variable sites higher than 0.95% were identified. Phylogenomic analyses of the complete cp genomes and 74 protein-coding genes strongly supported the monophyly of Cardiocrinum and a sister relationship between C. cathayanum and C. cordatum. The availability of these cp genomes provides valuable genetic information for further population genetics and phylogeography studies on Cardiocrinum.
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