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Wang RF, Ning Y, Li XJ, Tan K, Nguyen KS. Hiptage yangshuoensis (Malpighiaceae), a new species on karst hills close to Lijiang River, Guangxi, China, based on molecular and morphological data. Ecol Evol 2024; 14:e70099. [PMID: 39091333 PMCID: PMC11290907 DOI: 10.1002/ece3.70099] [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: 04/19/2024] [Revised: 07/10/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024] Open
Abstract
Hiptage yangshuoensis K.Tan & K.S.Nguyen, a new species of Hiptage collected from a karst cliff close to the Lijiang River, Northeast of Guangxi Zhuang Autonomous Region, China, is described and illustrated based on molecular and morphological data. Hiptage yangshuoensis shares some morphological similarities with the H. multiflora F.N.Wei, but easily distinguished by its long pedicels with articulate at top, one large calyx gland, oblanceolate middle wing and lanceolate lateral wings of samara, and young branch covered rusty sericeous. The new species status is also supported by molecular phylogenetic analyses based on nuclear ribosome internal transcribed spacer (nrITS), which showed distinct systematic distinctiveness from the most morphologically similar species, H. multiflora.
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Affiliation(s)
- Ren-Fen Wang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences Guilin Guangxi China
| | - Yao Ning
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences Guilin Guangxi China
| | - Xiao-Juan Li
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences Guilin Guangxi China
| | - Ke Tan
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences Guilin Guangxi China
| | - Khang Sinh Nguyen
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Ha Noi Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi Vietnam
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Huang J, Lu Z, Lin C, Xu W, Liu Y. Comprehensive Comparative Analyses of Aspidistra Chloroplast Genomes: Insights into Interspecific Plastid Diversity and Phylogeny. Genes (Basel) 2023; 14:1894. [PMID: 37895243 PMCID: PMC10606303 DOI: 10.3390/genes14101894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
Limestone karsts are renowned for extremely high species richness and endemism. Aspidistra (Asparagaceae) is among the highly diversified genera distributed in karst areas, making it an ideal group for studying the evolutionary mechanisms of karst plants. The taxonomy and identification of Aspidistra species are mainly based on their specialized and diverse floral structures. Aspidistra plants have inconspicuous flowers, and the similarity in vegetative morphology often leads to difficulties in species discrimination. Chloroplast genomes possess variable genetic information and offer the potential for interspecies identification. However, as yet there is little information about the interspecific diversity and evolution of the plastid genomes of Aspidistra. In this study, we reported chloroplast (cp) genomes of seven Aspidistra species (A. crassifila, A. dolichanthera, A. erecta, A. longgangensis, A. minutiflora, A. nankunshanensis, and A. retusa). These seven highly-conserved plastid genomes all have a typical quartile structure and include a total of 113 unique genes, comprising 79 protein-coding genes, 4 rRNA genes and 30 tRNA genes. Additionally, we conducted a comprehensive comparative analysis of Aspidistra cp genomes. We identified eight divergent hotspot regions (trnC-GCA-petN, trnE-UUC-psbD, accD-psaI, petA-psbJ, rpl20-rps12, rpl36-rps8, ccsA-ndhD and rps15-ycf1) that serve as potential molecular markers. Our newly generated Aspidistra plastomes enrich the resources of plastid genomes of karst plants, and an investigation into the plastome diversity offers novel perspectives on the taxonomy, phylogeny and evolution of Aspidistra species.
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Affiliation(s)
- Jie Huang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China; (J.H.); (Z.L.); (Y.L.)
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China
| | - Zhaocen Lu
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China; (J.H.); (Z.L.); (Y.L.)
| | - Chunrui Lin
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China; (J.H.); (Z.L.); (Y.L.)
| | - Weibin Xu
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China
| | - Yan Liu
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China; (J.H.); (Z.L.); (Y.L.)
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Zhang Y, Zhang J, Zou S, Liu Z, Huang H, Feng C. Genome-wide analysis of the cellulose toolbox of Primulina eburnea, a calcium-rich vegetable. BMC PLANT BIOLOGY 2023; 23:259. [PMID: 37189063 DOI: 10.1186/s12870-023-04266-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/05/2023] [Indexed: 05/17/2023]
Abstract
BACKGROUND Human-guided crop domestication has lasted for more than 10,000 years. In terms of the domestication and breeding of vegetables, cellulose content in edible tissues is one of the most important traits. Primulina eburnea is a recently developed calcium-rich vegetable with a high soluble and bioavailable calcium content in its leaves. However, the high cellulose content in the leaves hampers the taste, and no research has been reported on the genetic basis of cellulose biosynthesis in this calcium-rich vegetable. RESULTS We identified 36 cellulose biosynthesis-involved genes belonging to eight gene families in the P. eburnea genome. The cellulose accumulated decreasingly throughout leaf development. Nineteen genes were considered core genes in cellulose biosynthesis, which were highly expressed in buds but lowly expressed in mature leaves. In the nitrogen fertilization experiment, exogenous nitrogen decreased the cellulose content in the buds. The expressing pattern of 14 genes were consistent with phenotypic variation in the nitrogen fertilization experiment, and thus they were proposed as cellulose toolbox genes. CONCLUSIONS The present study provides a strong basis for the subsequent functional research of cellulose biosynthesis-involved genes in P. eburnea, and provides a reference for breeding and/or engineering this calcium-rich vegetable with decreased leaf cellulose content to improve the taste.
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Affiliation(s)
- Yi Zhang
- College of Life Science, Nanchang University, Nanchang, China
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, No. 9, Zhiqing Rd, Jiujiang, 332900, Jiangxi, China
| | - Jie Zhang
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, No. 9, Zhiqing Rd, Jiujiang, 332900, Jiangxi, China
| | - Shuaiyu Zou
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, No. 9, Zhiqing Rd, Jiujiang, 332900, Jiangxi, China
| | - Ziwei Liu
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, No. 9, Zhiqing Rd, Jiujiang, 332900, Jiangxi, China
| | - Hongwen Huang
- College of Life Science, Nanchang University, Nanchang, China.
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, No. 9, Zhiqing Rd, Jiujiang, 332900, Jiangxi, China.
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Chen Feng
- College of Life Science, Nanchang University, Nanchang, China.
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, No. 9, Zhiqing Rd, Jiujiang, 332900, Jiangxi, China.
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Wei S, Zhang Q, Tang S, Liao W. Genetic and ecophysiological evidence that hybridization facilitated lineage diversification in yellow Camellia (Theaceae) species: a case study of natural hybridization between C. micrantha and C. flavida. BMC PLANT BIOLOGY 2023; 23:154. [PMID: 36944951 PMCID: PMC10031943 DOI: 10.1186/s12870-023-04164-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/11/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Hybridization is generally considered an important creative evolutionary force, yet this evolutionary process is still poorly characterized in karst plants. In this study, we focus on natural hybridization in yellow Camellia species, a group of habitat specialists confined to karst/non-karst habitats in southwestern China. RESULTS Based on population genome data obtain from double digest restriction-site associated DNA (ddRAD) sequencing, we found evidence for natural hybridization and introgression between C. micrantha and C. flavida, and specifically confirmed their hybrid population, C. "ptilosperma". Ecophysiological results suggested that extreme hydraulic traits were fixed in C. "ptilosperma", these being consistent with its distinct ecological niche, which lies outside its parental ranges. CONCLUSION The identified hybridization event is expected to have played a role in generating novel variation during, in which the hybrid population displays different phenological characteristics and novel ecophysiological traits associated with the colonization of a new niche in limestone karst.
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Affiliation(s)
- Sujuan Wei
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, 541004, China
| | - Qiwei Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, 541004, China
| | - Shaoqing Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, 541004, China.
| | - Wenbo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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Comparative transcriptome analyses of three Gentiana species provides signals for the molecular footprints of selection effects and the phylogenetic relationships. Mol Genet Genomics 2023; 298:399-411. [PMID: 36592219 DOI: 10.1007/s00438-022-01991-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/27/2022] [Indexed: 01/03/2023]
Abstract
Species in Gentiana section Cruciata are important alpine plants with a center of diversity and speciation in Qinghai-Tibet Plateau (QTP), and some of these species are sympatrically distributed in northeastern QTP. Studies on genome features and natural selection signatures of sympatric species in section Crucata have been impeded by a lack of genomic resources. Here, we showed transcript characterizations and molecular footprints of selection effects on G. straminea, G. dahurica and G. officinalis based on the comparative transcriptome. A total of 62.97 Gb clean reads were obtained with unigene numbers per species ranging from 141,819 to 236,408 after assembly. We found that these three species had similar distribution of functional categories in different databases, and key enzyme-encoding genes involved in the iridoids biosynthesis were also obtained. The selective pressure analyses indicated that most paired orthologs between these three species were subject to negative selection, and only a low proportion of the orthologs that underwent positive selection were detected. We found that some positive selected genes were involved in "catalytic activity", "metabolic process", "response to stimulus" and "response to stress". Besides, large numbers of SSR primer pairs with transferabilities were successfully designed based on the available transcriptome datasets of three Gentiana species. The phylogenetic relationships reconstructed based on 352 single-copy nuclear genes provided a rough phylogenetic framework for this genus and confirmed the monophyly of section Cruciata. Our study not only provides insights for the natural selection effects on sympatric Gentiana species, but also enhances future genetic breeding or evolutionary studies on Qinjiao species.
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Zhu X, Liang H, Jiang H, Kang M, Wei X, Deng L, Shi Y. Phylogeographic structure of Heteroplexis (Asteraceae), an endangered endemic genus in the limestone karst regions of southern China. FRONTIERS IN PLANT SCIENCE 2022; 13:999964. [PMID: 36388513 PMCID: PMC9647136 DOI: 10.3389/fpls.2022.999964] [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: 07/26/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Though the karst regions in south and southwest China are plant diversity hotspots, our understanding of the phylogeography and evolutionary history of the plants there remains limited. The genus Heteroplexis (Asteraceae) is one of the typical representative plants isolated by karst habitat islands, and is also an endangered and endemic plant to China. In this study, species-level phylogeographic analysis of the genus Heteroplexis was conducted using restriction site-associated DNA sequencing (RADseq). The genetic structure showed a clear phylogeographic structure consistent with the current species boundaries in the H. microcephala, H. incana, H. vernonioides, H. sericophylla, and H. impressinervia. The significant global (R = 0.37, P < 0.01) and regional (R = 0.650.95, P < 0.05) isolation by distance (IBD) signals among species indicate strong geographic isolation in the karst mountains, which may result in chronically restricted gene flow and increased genetic drift and differentiation. Furthermore, the phylogeographic structure of Heteroplexis suggested a southward migration since the last glacial period. Demographic analysis revealed the karst mountains as a refuge for Heteroplexis species. Finally, both Treemix and ABBA-BABA statistic detected significant historical gene flow between species. Significant historical gene flow and long-term stability of effective population size (Ne) together explain the high genome-wide genetic diversity among species (π = 0.05370.0838). However, the recent collapse of Ne, widespread inbreeding within populations, and restricted contemporary gene flow suggest that Heteroplexis species are probably facing a high risk of genetic diversity loss. Our results help to understand the evolutionary history of karst plants and guide conservation.
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Affiliation(s)
- Xianliang Zhu
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Hui Liang
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
- College of Life Science, Guangxi Normal University, Guilin, China
| | - Haolong Jiang
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Ming Kang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xiao Wei
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Lili Deng
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Yancai Shi
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
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Plastomes of limestone karst gesneriad genera Petrocodon and Primulina, and the comparative plastid phylogenomics of Gesneriaceae. Sci Rep 2022; 12:15800. [PMID: 36138079 PMCID: PMC9500069 DOI: 10.1038/s41598-022-19812-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
Petrocodon and Primulina are two characteristic genera of Gesneriaceae that exhibit remarkable species and floral diversity, and high endemism across the Sino-Vietnamese Limestone Karsts. To better understand the evolution of limestone gesneriad plastomes, we report nine complete plastomes of seven Primulina and two Petrocodon which have never been assembled before. The newly generated plastomes range from 152,323 to 153,786 bp in size and display a typical quadripartite structure. To further explore the plastome evolution across Gesneriaceae, we assembled five additional plastomes from public reads data and incorporated 38 complete Gesneriaceae plastomes available online into comparative and phylogenomic analyses. The comparison of 52 Gesneriaceae plastomes reveals that not only Primulina and Petrocodon but all gesneriad genera analyzed are highly conserved in genome size, genome structure, gene contents, IR boundary configurations, and codon usage bias. Additionally, sliding window analyses were implemented across alignments of Primulina and Petrocodon for identifying highly variable regions, providing informative markers for future studies. Meanwhile, the SSRs and long repeats of Gesneriaceae plastomes were characterized, serving as useful data in studying population and repetitive sequence evolutions. The results of plastome phylogenetics represent a preliminary but highly resolved maternal backbone genealogy of Primulina and the Old World subtribes of Gesneriaceae.
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Chao YS, Ebihara A, Chiou WL, Tsai JM, Huang YW, Ranker TA. Reticulate evolution in the Pteris fauriei group (Pteridaceae). Sci Rep 2022; 12:9145. [PMID: 35650209 PMCID: PMC9159987 DOI: 10.1038/s41598-022-11390-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 04/14/2022] [Indexed: 11/10/2022] Open
Abstract
The Pteris fauriei group (Pteridaceae) has a wide distribution in Eastern Asia and includes 18 species with similar but varied morphology. We collected more than 300 specimens of the P. fauriei group and determined ploidy by flow cytometry and inferred phylogenies by molecular analyses of chloroplast and nuclear DNA markers. Our results reveal a complicated reticulate evolution, consisting of seven parental taxa and 58 hybrids. The large number of hybrid taxa have added significant morphological complexity to the group leading to difficult taxonomic issues. The hybrids generally had broader ranges and more populations than their parental taxa. Genetic combination of different pairs of parental species created divergent phenotypes of hybrids, exhibited by both morphological characteristics and ecological fidelities. Niche novelty could facilitate hybrid speciation. Apogamy is common in this group and potentially contributes to the sustainability of the whole group. We propose that frequent hybridizations among members of the P. fauriei group generate and maintain genetic diversity, via novel genetic combinations, niche differentiation, and apogamy.
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Affiliation(s)
- Yi-Shan Chao
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, 100, Shih-Chuan 1st Rd., Kaohsiung, 80708, Taiwan.
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, 4-1-1, Amakubo, Tsukuba-shi, Ibaraki, 305-0005, Japan
| | - Wen-Liang Chiou
- Taiwan Forestry Research Institute, 53 Nan-Hai Rd., Taipei, 100051, Taiwan
| | - Jer-Min Tsai
- Department of Information and Communication, Kun Shan University, 195, Kunda Rd., Tainan, 710303, Taiwan
| | - Yu-Wen Huang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, 100, Shih-Chuan 1st Rd., Kaohsiung, 80708, Taiwan
| | - Tom A Ranker
- University of Hawai'i at Mānoa, School of Life Sciences, Honolulu, HI, 96822, USA
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Ke F, Vasseur L, Yi H, Yang L, Wei X, Wang B, Kang M. Gene flow, linked selection, and divergent sorting of ancient polymorphism shape genomic divergence landscape in a group of edaphic specialists. Mol Ecol 2021; 31:104-118. [PMID: 34664755 DOI: 10.1111/mec.16226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 12/24/2022]
Abstract
Interpreting the formation of genomic variation landscape, especially genomic regions with elevated differentiation (i.e. islands), is fundamental to a better understanding of the genomic consequences of adaptation and speciation. Edaphic islands provide excellent systems for understanding the interplay of gene flow and selection in driving population divergence and speciation. However, discerning the relative contribution of these factors that modify patterns of genomic variation remains difficult. We analysed 132 genomes from five recently divergent species in Primulina genus, with four species distributed in Karst limestone habitats and the fifth one growing in Danxia habitats. We demonstrated that both gene flow and linked selection have contributed to genome-wide variation landscape, where genomic regions with elevated differentiation (i.e., islands) were largely derived by divergent sorting of ancient polymorphism. Specifically, we identified several lineage-specific genomic islands that might have facilitated adaptation of P. suichuanensis to Danxia habitats. Our study is amongst the first cases disentangling evolutionary processes that shape genomic variation of plant specialists, and demonstrates the important role of ancient polymorphism in the formation of genomic islands that potentially mediate adaptation and speciation of endemic plants in special soil habitats.
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Affiliation(s)
- Fushi Ke
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Liette Vasseur
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
| | - Huiqin Yi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xiao Wei
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Guilin, China
| | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
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10
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Linscott TM, Weaver K, Morales V, Parent CE. Assessing species number and genetic diversity of the Mountainsnails (Oreohelicidae). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01302-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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11
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Feng C, Ding D, Feng C, Kang M. The identification of an R2R3-MYB transcription factor involved in regulating anthocyanin biosynthesis in Primulina swinglei flowers. Gene 2020; 752:144788. [PMID: 32439375 DOI: 10.1016/j.gene.2020.144788] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/24/2020] [Accepted: 05/15/2020] [Indexed: 12/26/2022]
Abstract
Primulina genus is an ideal wild ornamental flower and emerging model for studying biosynthesis, diversity, and evolution of flower pigment. However, the molecular mechanism underlying anthocyanin biosynthesis and regulation in Primulina remains unknown. Here, changes in anthocyanin content and the expression profiles of anthocyanin biosynthetic structural genes were examined in developing Primulina swinglei flowers and three other organs. Seventy-three R2R3-MYB transcription factor genes were identified from transcriptome of P. swinglei flowers, two of which, PsMYB1 and PsMYB2, are candidate regulators of anthocyanin biosynthesis according to clustering analysis. Furthermore, transient over-expression studies using tobacco leaves showed distinct pigment accumulation following co-infection with PsMYB1 and MrbHLH1 (a previously confirmed anthocyanin regulator from Morella rubra). Additionally, dual luciferase assays showed that PsMYB1 trans-activated the PsANS promoter, with the addition of MrbHLH1 resulting in a 5-fold increase in the intensity of this interaction. PsMYB1 did not, however, have any effect on the PsF3H promoter. The expression profile and dual luciferase assays showed that PsMYB2 plays no roles in anthocyanin regulation. Therefore, PsMYB1 is proposed to be the transcription factor gene regulating anthocyanin biosynthesis in P. swinglei.
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Affiliation(s)
- Chen Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Dehui Ding
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Chao Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China.
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12
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Feng C, Wang J, Wu L, Kong H, Yang L, Feng C, Wang K, Rausher M, Kang M. The genome of a cave plant, Primulina huaijiensis, provides insights into adaptation to limestone karst habitats. THE NEW PHYTOLOGIST 2020; 227:1249-1263. [PMID: 32274804 DOI: 10.1111/nph.16588] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/29/2020] [Indexed: 05/22/2023]
Abstract
Although whole genome duplication (WGD) has been suggested to facilitate adaptive evolution and diversification, the role of specific WGD events in promoting diversification and adaptation in angiosperms remains poorly understood. Primulina, a species-rich genus with > 180 species associated with limestone karst habitat, constitutes an ideal system for studying the impact of WGD events on speciation and evolutionary adaptation. We sequenced and assembled a chromosome-level genome of the cave-dwelling species P. huaijiensis to study gene family expansion and gene retention following WGDs. We provide evidence that P. huaijiensis has undergone two WGDs since the γ triplication event shared by all eudicots. In addition to a WGD shared by almost all Lamiales (L event), we identified a lineage-specific WGD (D event) that occurred in the early Miocene around 20.6-24.2 Myr ago and that is shared by almost the entire subtribe Didymocarpinae. We found that gene retentions following the D event led to gene family proliferation (e.g. WRKYs) that probably facilitated adaptation to the high salinity and drought stress in limestone karst. Our study highlights the role of lineage-specific WGD in species diversification and adaptation of plants from special habitats.
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Affiliation(s)
- Chao Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Lingqing Wu
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Chen Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Kai Wang
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Mark Rausher
- Department of Biology, Duke University, 125 Science Drive, Durham, NC, 27705, USA
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
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13
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Wang XH, Li J, Zhang LM, He ZW, Mei QM, Gong X, Jian SG. Population Differentiation and Demographic History of the Cycas taiwaniana Complex (Cycadaceae) Endemic to South China as Indicated by DNA Sequences and Microsatellite Markers. Front Genet 2019; 10:1238. [PMID: 31921292 PMCID: PMC6935862 DOI: 10.3389/fgene.2019.01238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/08/2019] [Indexed: 11/13/2022] Open
Abstract
Historical geology, climatic oscillations, and seed dispersal capabilities are thought to influence the population dynamics and genetics of plants, especially for distribution-restricted and threatened species. Investigating the genetic resources within and among taxa is a prerequisite for conservation management. The Cycas taiwaniana complex consists of six endangered species that are endemic to South China. In this study, we investigated the relationship between phylogeographic history and the genetic structure of the C. taiwaniana complex. To estimate the phylogeographic history of the complex, we assessed the genetic structure and divergence time, and performed phylogenetic and demographic historical analyses. Two chloroplast DNA intergenic regions (cpDNA), two single-copy nuclear genes (SCNGs), and six microsatellite loci (SSR) were sequenced for 18 populations. The SCNG data indicated a high genetic diversity within populations, a low genetic diversity among populations, and significant genetic differentiation among populations. Significant phylogeographical structure was detected. Structure and phylogenetic analyses both revealed that the 18 populations of the C. taiwaniana complex have two main lineages, which were estimated to diverge in the Middle Pleistocene. We propose that Cycas fairylakea was incorporated into Cycas szechuanensis and that the other populations, which are mainly located on Hainan Island, merged into one lineage. Bayesian skyline plot analyses revealed that the C. taiwaniana complex experienced a recent decline, suggesting that the complex probably experienced a bottleneck event. We infer that the genetic structure of the C. taiwaniana complex has been affected by Pleistocene climate shifts, sea-level oscillations, and human activities. In addition to providing new insights into the evolutionary legacy of the genus, the genetic characterizations will be useful for the conservation of Cycas species.
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Affiliation(s)
- Xin-Hui Wang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Jie Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Li-Min Zhang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Zi-Wen He
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qi-Ming Mei
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Shu-Guang Jian
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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14
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Jiang H, Deng T, Lv XY, Zhang RB, Wen F. Primulina serrulata (Gesneriaceae), a new species from southeastern Guizhou, China. PHYTOKEYS 2019; 132:11-18. [PMID: 31579145 PMCID: PMC6763502 DOI: 10.3897/phytokeys.132.36717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/30/2019] [Indexed: 06/02/2023]
Abstract
Primulina serrulata R.B.Zhang & F. Wen, a new species from a limestone area in southeastern Guizhou, China, is described and illustrated here. The new species is morphologically related to P. fimbrisepala (Hand.-Mazz.) Y.Z.Wang. We examined the morphological differences between these congeners and provide illustrations and photographs of this new species in this paper.
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Affiliation(s)
- Hong Jiang
- Department of Biology, Zunyi Normal College, Zunyi, Guizhou 563002, ChinaZunyi Normal CollegeZunyiChina
| | - Tan Deng
- Department of Biology, Zunyi Normal College, Zunyi, Guizhou 563002, ChinaZunyi Normal CollegeZunyiChina
| | - Xin-Yun Lv
- Department of Biology, Zunyi Normal College, Zunyi, Guizhou 563002, ChinaZunyi Normal CollegeZunyiChina
| | - Ren-Bo Zhang
- Department of Biology, Zunyi Normal College, Zunyi, Guizhou 563002, ChinaZunyi Normal CollegeZunyiChina
| | - Fang Wen
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guilin Botanical Garden, Guangxi Institute of Botany, Guangxi Zhuangzu Autonomous Region and Chinese Academy of Sciences, Guilin 541006, ChinaGuangxi Institute of Botany, Guangxi Zhuangzu Autonomous Region and Chinese Academy of SciencesGuilinChina
- Gesneriad Conservation Center of China, Guilin Botanical Garden, Chinese Academy of Sciences, Guilin 541006, ChinaGuilin Botanical Garden, Chinese Academy of SciencesGuilinChina
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaSouth China Botanical Garden, Chinese Academy of SciencesGuangzhouChina
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15
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Xu WB, Chang H, Huang J, Chung KF. Molecular systematics of Chiritopsis-like Primulina (Gesneriaceae): one new species, one new name, two new combinations, and new synonyms. BOTANICAL STUDIES 2019; 60:18. [PMID: 31468230 PMCID: PMC6715764 DOI: 10.1186/s40529-019-0266-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 08/08/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND The Gesneriaceae genus Chiritopsis, confined almost exclusively to cave or cave-like microhabitats of limestone karsts of southern China, was described to distinguish it from Chirita by much smaller flowers and generally miniature plant sizes in the former genus. However, molecular phylogenetic analyses showed that Chiritopsis is polyphyletic and its species delimitation has been problematic. To understand how many times Chiritopsis-like species have evolved from within the recircumscribed Primulina and to further clarify their species identification, we sampled all but two recently described species of Chiritopsis-like Primulina and reconstructed their phylogenetic relationship based on DNA sequences of nuclear ITS and chloroplast trnL-F and trnH-psbA. RESULTS With 182 accessions of 165 taxa of Primulina sampled, our analyses placed the 40 accessions of 25 taxa of Chiritopsis-like Primulina in 17 unrelated positions, indicating at least 17 independent origins of the traits associated with caves or cave-like microhabitats. Of the 17 clades containing Chiritopsis-like Primulina, Clade 1 is composed of P. bipinnatifida, P. cangwuensis, P. jianghuaensis, P. lingchuanensis, and P. zhoui, as well as additional samples that show variable and overlapping morphology in leaf shapes. Clade 10 includes P. cordifolia, P. huangii, and P. repanda, while Primulina repanda var. guilinensis is not placed within Clade 10. Primulina glandulosa var. yangshuoensis is not placed in the same clade of P. glandulosa. CONCLUSIONS Based on our data, P. cangwuensis, P. jianghuaensis, and P. lingchuanensis are proposed to synonymize under P. bipinnatifida, with P. zhoui treated as a variety of P. bipinnatifida. Primulina repanda var. guilinensis is transferred as P. subulata var. guilinensis comb. nov. and Primulina pseudoglandulosa nom. nov. is proposed for P. glandulosa var. yangshuoensis. One new species is named P. chingipengii to honor the late Dr. Ching-I Peng (1950-2018).
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Affiliation(s)
- Wei-Bin Xu
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuangzu Autonomous Region and Chinese Academy of Sciences, Guilin, 541006 China
| | - Hsuan Chang
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Jie Huang
- School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Kuo-Fang Chung
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
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16
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Different species or genetically divergent populations? Integrative species delimitation of the Primulina hochiensis complex from isolated karst habitats. Mol Phylogenet Evol 2019; 132:219-231. [DOI: 10.1016/j.ympev.2018.12.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 12/09/2018] [Accepted: 12/09/2018] [Indexed: 12/15/2022]
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17
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Yang LH, Chen JL, Wen F, Kang M. Primulina malipoensis (Gesneriaceae), a new species from Sino-Vietnamese border area. PHYTOKEYS 2018; 94:107-116. [PMID: 29416425 PMCID: PMC5799778 DOI: 10.3897/phytokeys.94.20861] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 01/20/2018] [Indexed: 06/01/2023]
Abstract
Primulina malipoensis, a new species from limestone areas around the Sino-Vietnamese border, is described and illustrated. This new species is morphologically similar to P. maguanensis and P. lungzhouensis, but obviously differs from the latter two species by its pale greenish-yellow flowers (vs. purple, with different colour patterns). The phylogenetic affinity, illustration and photographs of this new species are provided in this paper.
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Affiliation(s)
- Li-Hua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilisation, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun-Lin Chen
- College of Humanities Sichuan Agricultural University, Ya’an, Sichuan 625014, China
| | | | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilisation, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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18
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Wang J, Feng C, Jiao T, Von Wettberg EB, Kang M. Genomic Signature of Adaptive Divergence despite Strong Nonadaptive Forces on Edaphic Islands: A Case Study of Primulina juliae. Genome Biol Evol 2017; 9:3495-3508. [PMID: 29272422 PMCID: PMC5751081 DOI: 10.1093/gbe/evx263] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2017] [Indexed: 12/28/2022] Open
Abstract
Both genetic drift and divergent selection are expected to be strong evolutionary forces driving population differentiation on edaphic habitat islands. However, the relative contribution of genetic drift and divergent selection to population divergence has rarely been tested simultaneously. In this study, restriction-site associated DNA-based population genomic analyses were applied to assess the relative importance of drift and divergent selection on population divergence of Primulina juliae, an edaphic specialist from southern China. All populations were found with low standing genetic variation, small effective population size (NE), and signatures of bottlenecks. Populations with the lowest genetic variation were most genetically differentiated from other populations and the extent of genetic drift increased with geographic distance from other populations. Together with evidence of isolation by distance, these results support neutral drift as a critical evolutionary driver. Nonetheless, redundancy analysis revealed that genomic variation is significantly associated with both edaphic habitats and climatic factors independently of spatial effects. Moreover, more genomic variation was explained by environmental factors than by geographic variables, suggesting that local adaptation might have played an important role in driving population divergence. Finally, outlier tests and environment association analyses identified 31 single-nucleotide polymorphisms as candidates for adaptive divergence. Among these candidates, 26 single-nucleotide polymorphisms occur in/near genes that potentially play a role in adaptation to edaphic specialization. This study has important implications that improve our understanding of the joint roles of genetic drift and adaptation in generating population divergence and diversity of edaphic specialists.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Chao Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Tenglong Jiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Myanmar
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19
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Wang J, Ai B, Kong H, Kang M. Speciation history of a species complex of Primulina eburnea (Gesneriaceae) from limestone karsts of southern China, a biodiversity hot spot. Evol Appl 2017; 10:919-934. [PMID: 29151883 PMCID: PMC5680421 DOI: 10.1111/eva.12495] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/22/2017] [Indexed: 11/30/2022] Open
Abstract
Limestone karsts in southern China are characterized by high edaphic and topographic heterogeneity and host high levels of species richness and endemism. However, the evolutionary mechanisms for generating such biodiversity remain poorly understood. Here, we performed species delimitation, population genetic analyses, simulations of gene flow and analyses of floral morphological traits to infer the geographic history of speciation in a species complex of Primulina eburnea from limestone karsts of southern China. Using Bayesian species delimitation, we determined that there are seven distinct species that correspond well to the putative morphological species. Species tree reconstruction, Structure and Neighbor‐Net analyses all recovered four lineages in agreement with currently species geographic boundaries. High levels of genetic differentiation were observed both within and among species. Isolation–migration coalescent analysis provides evidence for significant but low gene flow among species. Approximate Bayesian computation (ABC) analysis supports a scenario of historical gene flow rather than recent contemporary gene flow for most species divergences. Finally, we found no evidence of divergent selection contributing to population differentiation of a suite of flower traits. These results support the prevalence of allopatric speciation and highlight the role of geographic isolation in the diversification process. At small geographic scales, limited hybridization occurred in the past between proximate populations but did not eliminate species boundaries. We conclude that limited gene flow might have been the predominant evolutionary force in promoting population differentiation and speciation.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Bin Ai
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China.,Southeast Asia Biodiversity Research Institute Chinese Academy of Sciences Nay Pyi Taw Myanmar
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