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Min Q, Zheng K, Liu T, Wang Z, Xue X, Li W, Liu Y, Zhang Y, Qiao F, Chen J, Su X, Han S. Transcriptomic Profiles of Long Noncoding RNAs and Their Target Protein-Coding Genes Reveals Speciation Adaptation on the Qinghai-Xizang (Tibet) Plateau in Orinus. BIOLOGY 2024; 13:349. [PMID: 38785831 PMCID: PMC11118044 DOI: 10.3390/biology13050349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules longer than 200 nt, which lack the ability to encode proteins and are involved in multifarious growth, development, and regulatory processes in plants and mammals. However, the environmental-regulated expression profiles of lncRNAs in Orinus that may associated with their adaptation on the Qinghai-Xizang (Tibet) Plateau (QTP) have never been characterized. Here, we utilized transcriptomic sequencing data of two Orinus species (O. thoroldii and O. kokonoricus) to identify 1624 lncRNAs, including 1119 intergenic lncRNAs, 200 antisense lncRNAs, five intronic lncRNAs, and 300 sense lncRNAs. In addition, the evolutionary relationships of Orinus lncRNAs showed limited sequence conservation among 39 species, which implied that Orinus-specific lncRNAs contribute to speciation adaptation evolution. Furthermore, considering the cis-regulation mechanism, from 286 differentially expressed lncRNAs (DElncRNAs) and their nearby protein coding genes (PCGs) between O. thoroldii and O. kokonoricus, 128 lncRNA-PCG pairs were obtained in O. thoroldii, whereas 92 lncRNA-PCG pairs were obtained in O. kokonoricus. In addition, a total of 19 lncRNA-PCG pairs in O. thoroldii and 14 lncRNA-PCG pairs in O. kokonoricus were found to participate in different biological processes, indicating that the different expression profiles of DElncRNAs between O. thoroldii and O. kokonoricus were associated with their adaptation at different elevations on the QTP. We also found several pairs of DElncRNA nearby transcription factors (TFs), indicating that these DElncRNAs regulate the expression of TFs to aid O. thoroldii in adapting to the environment. Therefore, this work systematically identified a series of lncRNAs in Orinus, laying the groundwork for further exploration into the biological function of Orinus in environmental adaptation.
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Affiliation(s)
- Qinyue Min
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
| | - Kaifeng Zheng
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (K.Z.); (X.X.); (W.L.)
| | - Tao Liu
- School of Ecology and Environmental Science, Qinghai University of Science and Technology, Xining 810016, China;
| | - Zitao Wang
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
| | - Xiuhua Xue
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (K.Z.); (X.X.); (W.L.)
| | - Wanjie Li
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (K.Z.); (X.X.); (W.L.)
| | - Yuping Liu
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
| | - Yanfen Zhang
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
| | - Feng Qiao
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
| | - Jinyuan Chen
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
| | - Xu Su
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
| | - Shengcheng Han
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (K.Z.); (X.X.); (W.L.)
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
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Morales-Saldaña S, Hipp AL, Valencia-Ávalos S, Hahn M, González-Elizondo MS, Gernandt DS, Pham KK, Oyama K, González-Rodríguez A. Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae). ANNALS OF BOTANY 2024; 133:1007-1024. [PMID: 38428030 PMCID: PMC11089265 DOI: 10.1093/aob/mcae030] [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: 11/07/2023] [Accepted: 02/28/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND AND AIMS Introgressive hybridization poses a challenge to taxonomic and phylogenetic understanding of taxa, particularly when there are high numbers of co-occurring, intercrossable species. The genus Quercus exemplifies this situation. Oaks are highly diverse in sympatry and cross freely, creating syngameons of interfertile species. Although a well-resolved, dated phylogeny is available for the American oak clade, evolutionary relationships within many of the more recently derived clades remain to be defined, particularly for the young and exceptionally diverse Mexican white oak clade. Here, we adopted an approach bridging micro- and macroevolutionary scales to resolve evolutionary relationships in a rapidly diversifying clade endemic to Mexico. METHODS Ecological data and sequences of 155 low-copy nuclear genes were used to identify distinct lineages within the Quercus laeta complex. Concatenated and coalescent approaches were used to assess the phylogenetic placement of these lineages relative to the Mexican white oak clade. Phylogenetic network methods were applied to evaluate the timing and genomic significance of recent or historical introgression among lineages. KEY RESULTS The Q. laeta complex comprises six well-supported lineages, each restricted geographically and with mostly divergent climatic niches. Species trees corroborated that the different lineages are more closely related to other species of Mexican white oaks than to each other, suggesting that this complex is polyphyletic. Phylogenetic networks estimated events of ancient introgression that involved the ancestors of three present-day Q. laeta lineages. CONCLUSIONS The Q. laeta complex is a morphologically and ecologically related group of species rather than a clade. Currently, oak phylogenetics is at a turning point, at which it is necessary to integrate phylogenetics and ecology in broad regional samples to figure out species boundaries. Our study illuminates one of the more complicated of the Mexican white oak groups and lays groundwork for further taxonomic study.
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Affiliation(s)
- Saddan Morales-Saldaña
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
| | - Andrew L Hipp
- The Morton Arboretum, Lisle, IL 60532-1293, USA
- The Field Museum, Chicago, IL 60605, USA
| | - Susana Valencia-Ávalos
- Herbario de la Facultad de Ciencias, Departamento de Biología Comparada, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, México
| | | | | | - David S Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, México
| | - Kasey K Pham
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex‐Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
| | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
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Touchette L, Godbout J, Lamothe M, Porth I, Isabel N. A cryptic syngameon within Betula shrubs revealed: Implications for conservation in changing subarctic environments. Evol Appl 2024; 17:e13689. [PMID: 38633131 PMCID: PMC11022622 DOI: 10.1111/eva.13689] [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: 08/08/2023] [Revised: 02/06/2024] [Accepted: 03/20/2024] [Indexed: 04/19/2024] Open
Abstract
Arctic and subarctic ecosystems are rapidly transforming due to global warming, emphasizing the need to understand the genetic diversity and adaptive strategies of northern plant species for effective conservation. This study focuses on Betula glandulosa, a native North American tundra shrub known as dwarf birch, which demonstrates an apparent capacity to adapt to changing climate conditions. To address the taxonomic challenges associated with shrub birches and logistical complexities of sampling in the northernmost areas where species' ranges overlap, we adopted a multicriteria approach. Incorporating molecular data, ploidy level assessment and leaf morphology, we aimed to distinguish B. glandulosa individuals from other shrub birch species sampled. Our results revealed three distinct species and their hybrids within the 537 collected samples, suggesting the existence of a shrub birch syngameon, a reproductive network of interconnected species. Additionally, we identified two discrete genetic clusters within the core species, B. glandulosa, that likely correspond to two different glacial lineages. A comparison between the nuclear and chloroplast SNP data emphasizes a long history of gene exchange between different birch species and genetic clusters. Furthermore, our results highlight the significance of incorporating interfertile congeneric species in conservation strategies and underscores the need for a holistic approach to conservation in the context of climate change, considering the complex dynamics of species interactions. While further research will be needed to describe this shrub birches syngameon and its constituents, this study is a first step in recognizing its existence and disseminating awareness among ecologists and conservation practitioners. This biological phenomenon, which offers evolutionary flexibility and resilience beyond what its constituent species can achieve individually, may have significant ecological implications.
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Affiliation(s)
- Lyne Touchette
- Department of Wood and Forest SciencesUniversité LavalQuebecQuebecCanada
- Natural Resources Canada, Canadian Forest ServiceLaurentian Forestry CentreQuebecQuebecCanada
- Centre for Forest ResearchUniversité LavalQuebecQuebecCanada
| | - Julie Godbout
- Ministère des Ressources naturelles et des Forêts, Direction de la recherche forestièreQuébecQuébecCanada
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest ServiceLaurentian Forestry CentreQuebecQuebecCanada
| | - Ilga Porth
- Department of Wood and Forest SciencesUniversité LavalQuebecQuebecCanada
- Centre for Forest ResearchUniversité LavalQuebecQuebecCanada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest ServiceLaurentian Forestry CentreQuebecQuebecCanada
- Centre for Forest ResearchUniversité LavalQuebecQuebecCanada
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Qu K, Liu A, Yin M, Mu W, Wu S, Hu H, Chen J, Su X, Dou Q, Ren G. A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera. Commun Biol 2023; 6:1223. [PMID: 38042963 PMCID: PMC10693610 DOI: 10.1038/s42003-023-05620-5] [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: 02/22/2023] [Accepted: 11/21/2023] [Indexed: 12/04/2023] Open
Abstract
Ancient whole-genome duplication (WGD) or polyploidization is prevalent in plants and has played a crucial role in plant adaptation. However, the underlying genomic basis of ecological adaptation and subsequent diversification after WGD are still poorly understood in most plants. Here, we report a chromosome-scale genome assembly for the genus Orinus (Orinus kokonorica as representative) and preform comparative genomics with its closely related genus Cleistogenes (Cleistogenes songorica as representative), both belonging to a newly named subtribe Orininae of the grass subfamily Chloridoideae. The two genera may share one paleo-allotetraploidy event before 10 million years ago, and the two subgenomes of O. kokonorica display neither fractionation bias nor global homoeolog expression dominance. We find substantial genome rearrangements and extensive structural variations (SVs) between the two species. With comparative transcriptomics, we demonstrate that functional innovations of orthologous genes may have played an important role in promoting adaptive evolution and diversification of the two genera after polyploidization. In addition, copy number variations and extensive SVs between orthologs of flower and rhizome related genes may contribute to the morphological differences between the two genera. Our results provide new insights into the adaptive evolution and subsequent diversification of the two genera after polyploidization.
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Affiliation(s)
- Kunjing Qu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ai Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Mou Yin
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Wenjie Mu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Shuang Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Hongyin Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jinyuan Chen
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China
| | - Xu Su
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China
| | - Quanwen Dou
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Guangpeng Ren
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.
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Liu G, Xue G, Zhao T, Li Y, Yue L, Song H, Liu Q. Population structure and phylogeography of three closely related tree peonies. Ecol Evol 2023; 13:e10073. [PMID: 37274151 PMCID: PMC10234759 DOI: 10.1002/ece3.10073] [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: 03/16/2022] [Revised: 04/23/2023] [Accepted: 04/25/2023] [Indexed: 06/06/2023] Open
Abstract
Paeonia decomposita, Paeonia rotundiloba, and Paeonia rockii are three closely related species of Sect. Moutan is distributed in the montane area of the Eastern Hengduan Mountain region. Understanding the population history of these three tree peony species could contribute to unraveling the evolutionary patterns of undergrowth species in this hotspot area. We used one nuclear DNA marker (internal transcribed spacer region, ITS) and two chloroplast DNA markers (matK, ycf1) to reconstruct the phylogeographic pattern of the populations. In total, 228 individuals from 17 populations of the three species were analyzed in this study. Three nuclear clades (Clade I - Clade III) and four maternal clades (Clade A - Clade D) were reconstructed. Molecular dating suggested that young lineages diverged during the late Pliocene and early Pleistocene, younger than the uplift of the Hengduan Mountains but older than the last glacial maximum (LGM). Significant population and phylogeographic structures were detected at both markers. Furthermore, the populations of these tree peonies were overall at equilibrium during the climatic oscillations of the Pleistocene. The simulated palaeoranges of the three species during the LGM period mostly overlapped, which could have led to cross-breeding events. We propose an evolutionary scenario in which mountain orogenesis around the Hengduan Mountain area triggered parapatric isolation between maternal lineages of tree peonies. Subsequent climatic fluctuations drove migration and range recontact of these populations along the valleys. This detailed evolutionary history provides new insights into the phylogeographic pattern of species from mountain-valley systems.
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Affiliation(s)
- Guangli Liu
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Ge Xue
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Tingting Zhao
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Yang Li
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Liangliang Yue
- National Plateau Wetlands Research Center, College of WetlandsSouthwest Forestry UniversityKunmingChina
| | - Huixing Song
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Qinglin Liu
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
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Wu Y, Hipp AL, Fargo G, Stith N, Ricklefs RE. Improving species delimitation for effective conservation: a case study in the endemic maple-leaf oak (Quercus acerifolia). THE NEW PHYTOLOGIST 2023; 238:1278-1293. [PMID: 36707920 DOI: 10.1111/nph.18777] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
Species delimitation is challenging in lineages that exhibit both high plasticity and introgression. This challenge can be compounded by collection biases, which may downweight specimens morphologically intermediate between traditional species. Additionally, mismatch between named species and observable phenotypes can compromise species conservation. We studied the species boundaries of Quercus acerifolia, a tree endemic to Arkansas, U.S. We performed morphometric analyses of leaves and acorns from 527 field and 138 herbarium samples of Q. acerifolia and its close relatives, Q. shumardii and Q. rubra. We employed two novel approaches: sampling ex situ collections to detect phenotypic plasticity caused by environmental variation and comparing random field samples with historical herbarium samples to identify collection biases that might undermine species delimitation. To provide genetic evidence, we also performed molecular analyses on genome-wide SNPs. Quercus acerifolia shows distinctive morphological, ecological, and genomic characteristics, rejecting the hypothesis that Q. acerifolia is a phenotypic variant of Q. shumardii. We found mismatches between traditional taxonomy and phenotypic clusters. We detected underrepresentation of morphological intermediates in herbarium collections, which may bias species discovery and recognition. Rare species conservation requires considering and addressing taxonomic problems related to phenotypic plasticity, mismatch between taxonomy and morphological clusters, and collection biases.
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Affiliation(s)
- Yingtong Wu
- Biology Department, University of Missouri - St Louis, St Louis, MO, 63121, USA
- Whitney R. Harris World Ecology Center, University of Missouri - St Louis, St Louis, MO, 63121, USA
| | - Andrew L Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
- The Field Museum, Integrative Research Center, 1400S Lake Shore Dr., Chicago, IL, 60605, USA
| | - Gregory Fargo
- Biology Department, University of Missouri - St Louis, St Louis, MO, 63121, USA
| | - Nora Stith
- Biology Department, University of Missouri - St Louis, St Louis, MO, 63121, USA
| | - Robert E Ricklefs
- Biology Department, University of Missouri - St Louis, St Louis, MO, 63121, USA
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Su X, Liu T, Liu YP, Harris AJ, Chen JY. Adaptive radiation in Orinus, an endemic alpine grass of the Qinghai-Tibet Plateau, based on comparative transcriptomic analysis. JOURNAL OF PLANT PHYSIOLOGY 2022; 277:153786. [PMID: 35963042 DOI: 10.1016/j.jplph.2022.153786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
The species of Orinus (Poaceae) are important alpine plants with a variety of phenotypic traits and potential usages in molecular breeding toward drought-tolerant forage crops. However, the genetic basis of evolutionary adaption and diversification in the genus is still unclear. In the present study, we obtained transcriptomes for the two most divergent species, O. thoroldii and O. kokonoricus, using the Illumina platform and de novo assembly. In total, we generated 23,029 and 24,086 unigenes with N50 values of 1188 and 1203 for O. thoroldii and O. kokonoricus respectively, and identified 19,005 pairs of putative orthologs between the two species of Orinus. For these orthologs, estimations of non-synonymous/synonymous substitution rate ratios indicated that 568 pairs may be under strongly positive selection (Ka/Ks > 1), and Gene Ontogeny (GO) enrichment analysis revealed that significantly enriched pathways were in DNA repair and resistance to abiotic stress. Meanwhile, the divergence times of species between O. thoroldii and O. kokonoricus occurred 3.2 million years ago (Mya), and the recent evolutionary branch is an allotetraploid species, Cleistogenes songorica. We also detected a Ks peak of ∼0.60 for Orinus. Additionally, we identified 188 pairs of differentially expressed genes (DEGs) between the two species of Orinus, which were significantly enrich in stress resistance and lateral root development. Thus, we considered that the species diversification and evolutionary adaption of this genus was initiated by environmental selection, followed by phenotypic differentiation, finally leading to niche separation in the Qinghai-Tibet Plateau.
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Affiliation(s)
- Xu Su
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Land Surface Processes and Ecological Conservation of the Qinghai-Tibet Plateau, The Ministry of Education, Qinghai Normal University, Xining, 810008, China
| | - Tao Liu
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; School of Geographical Science, Qinghai Normal University, Xining, 810008, China
| | - Yu Ping Liu
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China.
| | - A J Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Jin Yuan Chen
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China
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Qin Y, Hu R, Zhao H, Wei G, Lu Z, Huang Y. Taxonomic delimitation and molecular identification of clusters within the species Zanthoxylumnitidum (Rutaceae) in China. PHYTOKEYS 2022; 196:1-20. [PMID: 36762030 PMCID: PMC9848992 DOI: 10.3897/phytokeys.196.79566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/22/2022] [Indexed: 06/18/2023]
Abstract
Zanthoxylumnitidum, known as Liang-Mian-Zhen in China, is a traditional Chinese medicinal plant used to treat traumatic injury, rheumatism, paralysis, toothache, stomach ache, and venomous snake bites. Two varieties of the species have been described and three morphological types have been reported within the original variety. However, taxonomic delimitation and molecular markers for distinguishing these varieties and types within this species remain unknown. Since different populations exhibit varying chemical compositions, easy identification of intraspecific taxa is crucial. We collected 420 individuals from 38 natural populations, 3 samples of standard medicinal material, and 17 folk-medicine samples to perform classification and identification within Zanthoxylumnitidum. Four distinct genetic clusters (A, B, C, and D) were highly supported by the nuclear barcode. Two distinct chloroplast clusters (A1 and A2) were further detected within A, and three others had one-to-one correspondence with the remaining nuclear clusters. Molecular identification showed that the 17 folk samples comprised A1, A2, B, and D, while the 3 standard samples belonged to A2. The internal transcribed spacer (ITS) region and rbcL gene are proposed as barcodes for rapid and accurate identification of the different Liang-Mian-Zhen lineages in China. This study highlights the importance of accurate taxonomic delimitation in combination with rapid and accurate molecular identification of medicinal plants.
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Affiliation(s)
- Yunrui Qin
- Guangxi Institute of Chinese Medicine and Pharmaceutical Sciences, Nanning 530022, Guangxi, ChinaGuangxi Institute of Chinese Medicine and Pharmaceutical SciencesNanningChina
| | - Renchuan Hu
- Guangxi Institute of Chinese Medicine and Pharmaceutical Sciences, Nanning 530022, Guangxi, ChinaGuangxi Institute of Chinese Medicine and Pharmaceutical SciencesNanningChina
| | - Hui Zhao
- Guangxi Institute of Chinese Medicine and Pharmaceutical Sciences, Nanning 530022, Guangxi, ChinaGuangxi Institute of Chinese Medicine and Pharmaceutical SciencesNanningChina
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, ChinaSouth China Normal UniversityGuangzhouChina
| | - Guiyuan Wei
- Guangxi Institute of Chinese Medicine and Pharmaceutical Sciences, Nanning 530022, Guangxi, ChinaGuangxi Institute of Chinese Medicine and Pharmaceutical SciencesNanningChina
| | - Zhiqiang Lu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, ChinaXishuangbanna Tropical Botanical Garden, Chinese Academy of SciencesMenglaChina
| | - Yunfeng Huang
- Guangxi Institute of Chinese Medicine and Pharmaceutical Sciences, Nanning 530022, Guangxi, ChinaGuangxi Institute of Chinese Medicine and Pharmaceutical SciencesNanningChina
- Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Nanning 530022, Guangxi, ChinaGuangxi Key Laboratory of Traditional Chinese Medicine Quality StandardsNanningChina
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Wu JF, Jia DR, Liu RJ, Zhou ZL, Wang LL, Chen MY, Meng LH, Duan YW. Multiple lines of evidence supports the two varieties of Halenia elliptica (Gentianaceae) as two species. PLANT DIVERSITY 2022; 44:290-299. [PMID: 35769593 PMCID: PMC9209875 DOI: 10.1016/j.pld.2021.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 06/15/2023]
Abstract
Delimiting species requires multiple sources of evidence. Here, we delimited two varieties of Halenia elliptica (Gentianaceae) using several lines of evidence, including morphological traits and mating system in a sympatric population, phylogenetic relationships based on nrITS and cpDNA (rpl16) data, and complete chloroplast genome sequences. Comparative analysis of 21 morphological traits clearly separates the two varieties of H. elliptica. Examination of the flowering process and pollination treatments indicate that H. elliptica var. grandiflora produces seeds via outcrossing, whereas H. elliptica var. elliptica produces seeds via mixed mating. Furthermore, hand-pollinated hybridization of the two varieties produced no seeds. Observations of pollinators showed that when bees began a pollination bout on H. elliptica var. grandiflora they preferred to continue pollinating this variety; however, when they began a pollination bout on H. elliptica var. elliptica, they showed no preference for either variety. Phylogenetic analysis confirmed the monophyly of H. elliptica, which was further divided into two monophyletic clades corresponding to the two varieties. A large number of variants from the chloroplast genomes reflected remarkable genetic dissimilarities between the two varieties of H. elliptica. We recommend that the two varieties of H. elliptica should be revised as two species (H. elliptica and H. grandiflora). Our findings indicate that H. elliptica varieties may have split into two separate species due to a shift in mating system, changes in flowering phenology and/or post-pollination reproductive isolation.
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Affiliation(s)
- Jin-Feng Wu
- School of Life Sciences, Yunnan Normal University, Kunming 650092, PR China
| | - Dong-Rui Jia
- School of Ecology and Environmental Science & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming 650091, PR China
| | - Rui-Juan Liu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, PR China
| | - Zhi-Li Zhou
- The Germplasm Bank of Wild Species, Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
| | - Lin-Lin Wang
- The Germplasm Bank of Wild Species, Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
| | - Min-Yu Chen
- The Germplasm Bank of Wild Species, Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
| | - Li-Hua Meng
- School of Life Sciences, Yunnan Normal University, Kunming 650092, PR China
| | - Yuan-Wen Duan
- The Germplasm Bank of Wild Species, Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
- Yunnan Lijiang Forest Ecosystem National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, Yunnan, PR China
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Franco-Estrada D, Barrios D, Cervantes CR, Granados-Aguilar X, Arias S. Phylogenetic and morphological analyses of Pilosocereus leucocephalus group s.s. (Cactaceae) reveal new taxonomical implications. JOURNAL OF PLANT RESEARCH 2022; 135:423-442. [PMID: 35305187 PMCID: PMC9081079 DOI: 10.1007/s10265-022-01384-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/22/2022] [Indexed: 05/25/2023]
Abstract
Pilosocereus is one of the Cactaceae family's most relevant genera in terms of the number of species and its wide geographical range in the Americas. Within Pilosocereus, five informal taxonomic groups have been recognized, one of which is P. leucocephalus group s.s., whose phylogenetic relationships remain unresolved. Therefore, our objectives are to recognize the circumscriptions of the species in P. leucocephalus group s.s. and to corroborate the monophyly and phylogenetic relationships of this group through a set of morphological and molecular characters. This study is based on representative sampling along the broad distribution of this group in Mexico and Central America using multivariate and phylogenetic analyses. The morphological characters identified to contribute to species recognition and group formation are branch diameter, areole length, the areole length-width ratio, the distance between areoles, the length of the longest radial spine, and branch and spines colors. The chloroplast markers rpl16, trnL-trnF, and petL-psbE and the nuclear marker AT1G18270 support the monophyly of the P. leucocephalus group s.s., and two probable synapomorphies are suggested, including one transversion in rpl16 and another in petL-psbE. Together, our results demonstrate that sampled species of P. leucocephalus group s.s. encompass six species distributed in Mexico and Central America: P. alensis and P. purpusii in the western region, P. chrysacanthus and P. collinsii in the central region, and P. gaumeri and P. leucocephalus in the eastern region. A taxonomic key to recognized species is provided.
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Affiliation(s)
- Daniel Franco-Estrada
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico.
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico.
| | - Duniel Barrios
- Grupo de Ecología y Conservación, Jardín Botánico Nacional, Universidad de La Habana, Carretera El Rocío km 3½, Calabazar, Boyeros, 19 230, Havana, Cuba
| | - Cristian R Cervantes
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
| | - Xochitl Granados-Aguilar
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
| | - Salvador Arias
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico.
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11
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Ji Y, Yang J, Landis JB, Wang S, Jin L, Xie P, Liu H, Yang JB, Yi TS. Genome Skimming Contributes to Clarifying Species Limits in Paris Section Axiparis (Melanthiaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:832034. [PMID: 35444671 PMCID: PMC9014178 DOI: 10.3389/fpls.2022.832034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Paris L. section Axiparis H. Li (Melanthiaceae) is a taxonomically perplexing taxon with considerable confusion regarding species delimitation. Based on the analyses of morphology and geographic distribution of each species currently recognized in the taxon, we propose a revision scheme that reduces the number of species in P. sect. Axiparis from nine to two. To verify this taxonomic proposal, we employed a genome skimming approach to recover the plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) regions of 51 individual plants across the nine described species of P. sect. Axiparis by sampling multiple accessions per species. The species boundaries within P. sect. Axiparis were explored using phylogenetic inference and three different sequence-based species delimitation methods (ABGD, mPTP, and SDP). The mutually reinforcing results indicate that there are two species-level taxonomic units in P. sect. Axiparis (Paris forrestii s.l. and P. vaniotii s.l.) that exhibit morphological uniqueness, non-overlapping distribution, genetic distinctiveness, and potential reproductive isolation, providing strong support to the proposed species delimitation scheme. This study confirms that previous morphology-based taxonomy overemphasized intraspecific and minor morphological differences to delineate species boundaries, therefore resulting in an overestimation of the true species diversity of P. sect. Axiparis. The findings clarify species limits and will facilitate robust taxonomic revision in P. sect. Axiparis.
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Affiliation(s)
- Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jin Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Jacob B. Landis
- Section of Plant Biology and the L. H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, United States
| | - Shuying Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Lei Jin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Pingxuan Xie
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Haiyang Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Wang Z, Jiang Y, Yang X, Bi H, Li J, Mao X, Ma Y, Ru D, Zhang C, Hao G, Wang J, Abbott RJ, Liu J. Molecular signatures of parallel adaptive divergence causing reproductive isolation and speciation across two genera. Innovation (N Y) 2022; 3:100247. [PMID: 35519515 PMCID: PMC9065898 DOI: 10.1016/j.xinn.2022.100247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/16/2022] [Indexed: 11/18/2022] Open
Abstract
Parallel evolution of reproductive isolation (PERI) provides strong evidence for natural selection playing a fundamental role in the origin of species. However, PERI has been rarely demonstrated for well established species drawn from different genera. In particular, parallel molecular signatures for the same genes in response to similar habitat divergence in such different lineages is lacking. Here, based on whole-genome sequencing data, we first explore the speciation process in two sister species of Carpinus (Betulaceae) in response to divergence for temperature and soil-iron concentration in habitats they occupy in northern and southwestern China, respectively. We then determine whether parallel molecular mutations occur during speciation in this pair of species and also in another sister-species pair of the related genus, Ostryopsis, which occupy similarly divergent habitats in China. We show that gene flow occurred during the origin of both pairs of sister species since approximately 9.8 or approximately 2 million years ago, implying strong natural selection during divergence. Also, in both species pairs we detected concurrent positive selection in a gene (LHY) for flowering time and in two paralogous genes (FRO4 and FRO7) of a gene family known to be important for iron tolerance. These changes were in addition to changes in other major genes related to these two traits. The different alleles of these particular candidate genes possessed by the sister species of Carpinus were functionally tested and indicated likely to alter flowering time and iron tolerance as previously demonstrated in the pair of Ostryopsis sister species. Allelic changes in these genes may have effectively resulted in high levels of prezygotic reproductive isolation to evolve between sister species of each pair. Our results show that PERI can occur in different genera at different timescales and involve similar signatures of molecular evolution at genes or paralogues of the same gene family, causing reproductive isolation as a consequence of adaptation to similarly divergent habitats. PERI provides strong evidence for natural selection playing a fundamental role in the origin of species PERI is rarely demonstrated for well-established species drawn from different genera We detected PERI across two genera (Carpinus and Ostryopsis) in the family Betulaceae PERI can occur in different genera at different timescales and involve molecular signatures at similar pathways
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Affiliation(s)
- Zefu Wang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yuanzhong Jiang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xiaoyue Yang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Hao Bi
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jialiang Li
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xingxing Mao
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yazhen Ma
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Cheng Zhang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Guoqian Hao
- Sichuan Tea College, Yibin University, Yibin 644000, China
| | - Jing Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | | | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Corresponding author
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Wang L, Ding J, Borrell JS, Cheek M, McAllister HA, Wang F, Liu L, Zhang H, Zhang Q, Wang Y, Wang N. Molecular and morphological analyses clarify species delimitation in section Costatae and reveal Betula buggsii sp. nov. (sect. Costatae, Betulaceae) in China. ANNALS OF BOTANY 2022; 129:415-428. [PMID: 35018419 PMCID: PMC8944703 DOI: 10.1093/aob/mcac001] [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: 10/22/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS Delineating closely related and morphologically similar species is difficult. Here, we integrate morphology, genetics, ploidy and geography to resolve species and subspecies boundaries in four trees of section Costatae (genus Betula): Betula ashburneri, B. costata, B. ermanii and B. utilis, as well as multiple subspecies and polyploid races. METHODS We genotyped 371 individuals (20-133 per species) from 51 populations at 15 microsatellite markers, as well as a subset of individuals, using restriction-site associated DNA sequencing and nuclear internal transcribed spacers. We determined the ploidy level of eight individuals using flow cytometry and characterized leaf variation for a subset of 109 individuals by morphometric analysis. KEY RESULTS Integration of multiple lines of evidence suggested a series of revisions to the taxonomy of section Costatae. Betula costata and B. ermanii were found to be valid. Molecular and leaf morphology analyses revealed little differentiation between diploid B. albosinensis and some samples of B. utilis ssp. utilis. By contrast, other B. utilis ssp. utilis samples and ssp. albosinensis formed a morphological continuum but differed based on genetics. Specifically, B. utilis ssp. albosinensis was divided into two groups with group I genetically similar to B. utilis ssp. utilis and group II, a distinct cluster, proposed as the new diploid species Betula buggsii sp. nov. Phylogenomic analysis based on 2285 620 single nucleotide polymorphisms identified a well-supported monophyletic clade of B. buggsii. Morphologically, B. buggsii is characterized by elongated lenticels and a distinct pattern of bark peeling and may be geographically restricted to the Qinling-Daba Mountains. CONCLUSIONS Our integrated approach identifies six taxa within section Costatae: B. ashburneri, B. buggsii, B. costata, B. utilis ssp. utilis, B. utilis ssp. albosinensis and B. ermanii. Our research demonstrates the value of an integrative approach using morphological, geographical, genetic and ploidy-level data for species delineation.
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Affiliation(s)
| | | | | | | | - Hugh A McAllister
- School of Life Sciences, Biosciences Building, University of Liverpool, Crown Street, Liverpool, UK
| | - Feifei 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, China
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Lu Liu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai’an, China
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Huayu Zhang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai’an, China
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Qiufeng Zhang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai’an, China
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Yiming 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, China
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, College of Forestry, Shandong Agricultural University, Tai’an, China
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Lu Z, Sun Y, Li Y, Yang Y, Wang G, Liu J. Species delimitation and hybridization history of a hazel species complex. ANNALS OF BOTANY 2021; 127:875-886. [PMID: 33564860 PMCID: PMC8225278 DOI: 10.1093/aob/mcab015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/03/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS Hybridization increases species adaptation and biodiversity but also obscures species boundaries. In this study, species delimitation and hybridization history were examined within one Chinese hazel species complex (Corylus chinensis-Corylus fargesii). Two species including four varieties have already been described for this complex, with overlapping distributions. METHODS A total of 322 trees from 44 populations of these four varieties across their ranges were sampled for morphological and molecular analyses. Climatic datasets based on 108 geographical locations were used to evaluate their niche differentiations. Flowering phenology was also observed for two co-occurring species or varieties. KEY RESULTS Four statistically different phenotypic clusters were revealed, but these clusters were highly inconsistent with the traditional taxonomic groups. All the clusters showed statistically distinct niches, with complete or partial geographical isolation. Only two clusters displayed a distributional overlap, but they had distinct flowering phenologies at the site where they co-occurred. Population-level evidence based on the genotypes of ten simple sequence repeat loci supported four phenotypic clusters. In addition, one cluster was shown to have an admixed genetic composition derived from the other three clusters through repeated historical hybridizations. CONCLUSIONS Based on our new evidence, it is better to treat the four clusters identified here as four independent species. One of them was shown to have an admixed genetic composition derived from the other three through repeated historical hybridizations. This study highlights the importance of applying integrative and statistical methods to infer species delimitations and hybridization history. Such a protocol should be adopted widely for future taxonomic studies.
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Affiliation(s)
- Zhiqiang Lu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Yongshuai Sun
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Gaini Wang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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15
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Cordobés FM, Robbiati FO, Anton AM, Scrivanti LR. Phylogeny, evolution and ecological speciation analyses of Imperata (Poaceae: Andropogoneae) in the Neotropics. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1887959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Fernando Moro Cordobés
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad Nacional de Córdoba, Córdoba, Prov. de Córdoba, Argentina
| | - Federico Omar Robbiati
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad Nacional de Córdoba, Córdoba, Prov. de Córdoba, Argentina
| | - Ana María Anton
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad Nacional de Córdoba, Córdoba, Prov. de Córdoba, Argentina
| | - Lidia Raquel Scrivanti
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad Nacional de Córdoba, Córdoba, Prov. de Córdoba, Argentina
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Mao X, Wang J, Shrestha N, Ma Y, Liu J. Species Identification in the Rhododendron vernicosum- R. decorum Species Complex (Ericaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:608964. [PMID: 33584768 PMCID: PMC7876077 DOI: 10.3389/fpls.2021.608964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Delimitating species boundaries is the primary aim of biological classification and could be critical for evaluating the evolving process of species and conserving biodiversity. Rhododendron is an iconic group with an extraordinary diversity in southwest China. However, it remains unknown whether the recorded species therein comprise independently evolving lineages or artificially delimitated morphological entities. In this study, we carried out species delimitation of four Rhododendron species in the R. vernicosum-R. decorum species complex based on morphological analyses and population genetic data from nuclear simple sequence repeats (SSR) markers. We randomly selected a total of 105 specimens of different individuals identified as four species across their distributional ranges to examine the statistically distinct phenotypic clusters based on 19 morphological traits. Similarly, we genotyped 55 individuals of four species from 21 populations using 15 SSR markers. The morphological analyses sorted R. decorum and the other three species into two different phenotypic clusters. The genetic clusters were consistent with the morphological clusters. However, we also recovered the third genetic cluster, comprising six R. vernicosum populations and containing the admixed genetic compositions of the other two distinct genetic clusters. This hybrid group was morphologically similar to the typical R. vernicosum (including the samples from its type specimen locality and both R. verruciferum and R. gonggashanense) but with more genetic ancestry from R. decorum. Based on our findings, we identify two distinct species and one putative hybrid group due to introgression in the R. vernicosum-R. decorum species complex. We propose to merge R. verruciferum and R. gonggashanense into R. vernicosum based on genetic compositions and our morphological analyses. The hybrid group inferred from our findings, however, needs further investigations.
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Affiliation(s)
- Xingxing Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ji Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Yazhen Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
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Chen J, Wu G, Shrestha N, Wu S, Guo W, Yin M, Li A, Liu J, Ren G. Phylogeny and Species Delimitation of Chinese Medicago (Leguminosae) and Its Relatives Based on Molecular and Morphological Evidence. FRONTIERS IN PLANT SCIENCE 2021; 11:619799. [PMID: 33584760 PMCID: PMC7874099 DOI: 10.3389/fpls.2020.619799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/17/2020] [Indexed: 05/12/2023]
Abstract
Medicago and its relatives, Trigonella and Melilotus comprise the most important forage resources globally. The alfalfa selected from the wild relatives has been cultivated worldwide as the forage queen. In the Flora of China, 15 Medicago, eight Trigonella, and four Melilotus species are recorded, of which six Medicago and two Trigonella species are introduced. Although several studies have been conducted to investigate the phylogenetic relationship within the three genera, many Chinese naturally distributed or endemic species are not included in those studies. Therefore, the taxonomic identity and phylogenetic relationship of these species remains unclear. In this study, we collected samples representing 18 out of 19 Chinese naturally distributed species of these three genera and three introduced Medicago species, and applied an integrative approach by combining evidences from population-based morphological clusters and molecular data to investigate species boundaries. A total of 186 individuals selected from 156 populations and 454 individuals from 124 populations were collected for genetic and morphological analyses, respectively. We sequenced three commonly used DNA barcodes (trnH-psbA, trnK-matK, and ITS) and one nuclear marker (GA3ox1) for phylogenetic analyses. We found that 16 out of 21 species could be well delimited based on phylogenetic analyses and morphological clusters. Two Trigonella species may be merged as one species or treated as two subspecies, and Medicago falcata should be treated as a subspecies of the M. sativa complex. We further found that major incongruences between the chloroplast and nuclear trees mainly occurred among the deep diverging lineages, which may be resulted from hybridization, incomplete lineage sorting and/or sampling errors. Further studies involving a finer sampling of species associated with large scale genomic data should be employed to better understand the species delimitation of these three genera.
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Affiliation(s)
- Jinyuan Chen
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Guili Wu
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Shuang Wu
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Wei Guo
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Mou Yin
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Ao Li
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Guangpeng Ren
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
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Ji Y, Yang J, Landis JB, Wang S, Yang Z, Zhang Y. Deciphering the Taxonomic Delimitation of Ottelia acuminata (Hydrocharitaceae) Using Complete Plastomes as Super-Barcodes. FRONTIERS IN PLANT SCIENCE 2021; 12:681270. [PMID: 34335651 PMCID: PMC8320023 DOI: 10.3389/fpls.2021.681270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/10/2021] [Indexed: 05/08/2023]
Abstract
Accurate species delimitation and identification, which is a challenging task in traditional morphology-based taxonomy, is crucial to species conservation. Ottelia acuminata (Hydrocharitaceae) is a severely threatened submerged macrophyte endemic to southwestern China. The taxonomy of O. acuminata, which has long been in dispute, remains unresolved, impeding effective conservation and management practices. Here, we aim to address the long-standing issues concerning species boundary and intraspecific subdivision of O. acuminata using complete plastome sequences as super-barcodes. The taxonomic delimitation of O. acuminata was explored using phylogenetic inference and two independent sequence-based species delimitation schemes: automatic barcode gap discovery (ABGD) and multi-rate Poisson tree processes (mPTP). The reciprocally reinforcing results support the reduction of the closely related congeneric species, O. balansae and O. guanyangensis, as two conspecific varieties of O. acuminata. Within the newly defined O. acuminata, accurate varietal identification can be achieved using plastome super-barcodes. These findings will help inform future decisions regarding conservation, management and restoration of O. acuminata. This case study suggests that the use of plastome super-barcodes can provide a solution for species delimitation and identification in taxonomically difficult plant taxa, thus providing great potential to lessen the challenges of inventorying biodiversity, as well as biologically monitoring and assessing threatened species.
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Affiliation(s)
- Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- *Correspondence: Yunheng Ji,
| | - Jin Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Jacob B. Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Shuying Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Zhenyan Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yonghong Zhang
- School of Life Sciences, Yunnan Normal University, Kunming, China
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Zhang CY, Ling Low S, Song YG, Nurainas, Kozlowski G, Li L, Zhou SS, Tan YH, Cao GL, Zhou Z, Meng HH, Li J. Shining a light on species delimitation in the tree genus Engelhardia Leschenault ex Blume (Juglandaceae). Mol Phylogenet Evol 2020; 152:106918. [PMID: 32738292 DOI: 10.1016/j.ympev.2020.106918] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 10/23/2022]
Abstract
Enhanced efficacy in species delimitation is critically important in biology given the pending biodiversity crisis under global warming and anthropogenic activity. In particular, delineation of traditional classifications in view of the complexity of species requires an integrative approach to effectively define species boundaries, and this is a major focus of systematic biology. Here, we explored species delimitation of Engelhardia in tropical and subtropical Asia. In total, 716 individuals in 71 populations were genotyped using five chloroplast regions, one nuclear DNA region (nrITS), and 11 nuclear simple sequence repeats (nSSR). Phylogenetic trees were constructed and relationships among species were assessed. Molecular analyses were then combined with 14 morphological characteristics of 720 specimens to further explore the species boundaries of Engelhardia. Integrating phylogenetic and morphological clusters provided well-resolved relationships to delineate seven species. The results suggested that: first, that E. fenzelii, E. roxburghiana, E. hainanensis, E. apoensis, and E. serrata are distinct species; second, E. spicata var. spicata, E. spicata var. aceriflora, E. spicata var. colebrookeana, and E. rigida should be combined under E. spicata and treated as a species complex; third, E. serrata var. cambodica should be raised to species level and named E. villosa. We illuminated that bias thresholds determining the cluster number for delimiting species boundaries were substantially reduced when morphological data were incorporated. Our results urge caution when using the concepts of subspecies and varieties in order to prevent confusion, particularly with respect to species delimitation for tropical and subtropical species. In some cases, re-ranking or combining subspecies and/or varieties may enable more accurate species delimitation.
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Affiliation(s)
- Can-Yu Zhang
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shook Ling Low
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Yi-Gang Song
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602, China; Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Nurainas
- Department of Biology, Faculty of Math. & Nat. Sci. Andalas University, Padang 25163, West Sumatra, Indonesia
| | - Gregor Kozlowski
- Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Lang Li
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, China
| | - Shi-Shun Zhou
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar
| | - Yun-Hong Tan
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, China
| | - Guan-Long Cao
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hong-Hu Meng
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar.
| | - Jie Li
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, China.
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Yuping Liu, Lv T, Liu T, Su X. Characterization and Phylogenetic Analysis of the Complete Chloroplast Genome of Orinus kokonoricus (Poaceae), an Endemic Species from the Qinghai-Tibet Plateau. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452719060045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Su X, Liu Y, Lv T, Ren Z. Characterization of the Complete Chloroplast Genome of an Endemic Perennial Grass Orinus intermedius and Its Phylogenetic Analysis in Poaceae. CYTOL GENET+ 2019. [DOI: 10.3103/s0095452719050128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Yuping Liu, Su X, Lv T, Chen K. Development of Novel Low-Copy Nuclear Gene Primers by Transcriptomes in an Endemic Genus Orinus Hitchc. (Poaceae) from the Qinghai-Tibet Plateau. CYTOL GENET+ 2019. [DOI: 10.3103/s0095452719030113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Liu Y, Harris AJ, Gao Q, Su X, Ren Z. A population genetics perspective on the evolutionary histories of three clonal, endemic, and dominant grass species of the Qinghai-Tibet Plateau: Orinus (Poaceae). Ecol Evol 2019; 9:6014-6037. [PMID: 31161016 PMCID: PMC6540705 DOI: 10.1002/ece3.5186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 11/08/2022] Open
Abstract
We performed analyses of amplified fragment length polymorphism (AFLP) in order to characterize the evolutionary history of Orinus according to its population genetic structure, as well as to investigate putative hybrid origins of O. intermedius and to provide additional insights into relationships among species. The genus Orinus comprises three clonal grasses that are dominant species within xeric alpine grasslands of the Qinghai-Tibet Plateau (QTP). Here, we used eight selectively obtained primer pairs of EcoRI/MseI to perform amplifications in 231 individuals of Orinus representing 48 populations and all three species. We compared our resulting data to genetic models of hybridization using a Bayesian algorithm within NewHybrids software. We determined that genetic variation in Orinus was 56.65% within populations while the among-species component was 30.04% using standard population genetics statistics. Nevertheless, we detected that species of Orinus were clustered into three highly distinct genetic groups corresponding to classic species identities. Our results suggest that there is some introgression among species. Thus, we tested explicit models of hybridization using a Bayesian approach within NewHybrids software. However, O. intermedius likely derives from a common ancestor with O. kokonoricus and is probably not the result of hybrid speciation between O. kokonoricus and O. thoroldii. We suspect that recent isolation of species of Orinus in allopatry via vicariance may explain the patterns in diversity that we observed, and this is corroborated by a Mantel test that showed significant positive correlation between geographic and genetic distance (r = 0.05, p < 0.05). Recent isolation may explain why Orinus differs from many other clonal species by exhibiting the highest diversity within populations rather than among them.
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Affiliation(s)
- Yuping Liu
- Key Laboratory of Medicinal Plant and Animal Resources of the Qinghai‐Tibet Plateau in Qinghai Province, School of Life ScienceQinghai Normal UniversityXiningChina
- Key Laboratory of Physical Geography and Environmental Process in Qinghai Province, School of Life ScienceQinghai Normal UniversityXiningChina
- Key Laboratory of Education Ministry of Environments and Resources in the Qinghai‐Tibet Plateau, School of Life ScienceQinghai Normal UniversityXiningChina
| | - AJ Harris
- Department of BiologyOberlin College and ConservatoryOberlinOhio
| | - Qingbo Gao
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningChina
| | - Xu Su
- Key Laboratory of Medicinal Plant and Animal Resources of the Qinghai‐Tibet Plateau in Qinghai Province, School of Life ScienceQinghai Normal UniversityXiningChina
- Key Laboratory of Physical Geography and Environmental Process in Qinghai Province, School of Life ScienceQinghai Normal UniversityXiningChina
- Key Laboratory of Education Ministry of Environments and Resources in the Qinghai‐Tibet Plateau, School of Life ScienceQinghai Normal UniversityXiningChina
| | - Zhumei Ren
- School of Life ScienceShanxi UniversityTaiyuanChina
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Liang Y, Zhang Y, Wen J, Su X, Ren Z. Evolutionary History of Rhus chinensis (Anacardiaceae) From the Temperate and Subtropical Zones of China Based on cpDNA and Nuclear DNA Sequences and Ecological Niche Model. Front Genet 2019; 10:171. [PMID: 30891066 PMCID: PMC6411847 DOI: 10.3389/fgene.2019.00171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 02/15/2019] [Indexed: 11/28/2022] Open
Abstract
To explore the origin and evolution of local flora and vegetation, we examined the evolutionary history of Rhus chinensis, which is widely distributed in China’s temperate and subtropical zones, by sequencing three maternally inherited chloroplast DNAs (cpDNA: trnL-trnF, psbA-trnH, and rbcL) and the biparentally inherited nuclear DNA (nuDNA: LEAFY) from 19 natural populations of R. chinensis as well as the ecological niche modeling. In all, 23 chloroplast haplotypes (M1–M23) and 15 nuclear alleles (N1–N15) were detected. The estimation of divergence time showed that the most recent common ancestor dated at 4.2 ± 2.5 million years ago (Mya) from cpDNA, and the initial divergence of genotypes occurred at 4.8 ± 3.6 Mya for the nuDNA. Meanwhile, the multimodality mismatch distribution curves and positive Tajima’s D values indicated that R. chinensis did not experience population expansion after the last glacial maximum. Besides, our study was also consistent with the hypothesis that most refugia in the temperate and subtropical zones of China were in situ during the glaciation.
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Affiliation(s)
- Yukang Liang
- School of Life Science, Shanxi University, Taiyuan, China
| | - Yang Zhang
- Natural History Research Center, Shanghai Natural History Museum, Branch of Shanghai Science and Technology Museum, Shanghai, China
| | - Jun Wen
- School of Life Science, Shanxi University, Taiyuan, China.,Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Xu Su
- Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibetan Plateau in Qinghai Province, School of Life Science, Qinghai Normal University, Xining, China
| | - Zhumei Ren
- School of Life Science, Shanxi University, Taiyuan, China
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Heng LM, Zheng YL, Zhao YB, Wang YJ. Radiation of members of the Soroserishookeriana complex (Asteraceae) on the Qinghai-Tibetan Plateau and their proposed taxonomic treatment. PHYTOKEYS 2018; 114:11-25. [PMID: 30613179 PMCID: PMC6308221 DOI: 10.3897/phytokeys.114.29914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
The existence of intermediate types is a major obstacle that can hinder the circumscription of species. Elucidating the mechanism responsible for intermediate types is essential for achieving a reasonable taxonomical treatment. In this study, we explored the evolutionary history and taxonomic treatment of the Soroserishookeriana (C.B.Clarke) Stebbins complex, which comprises six named taxa that may be taxonomically distinct and are all native to the Qingha-Tibetan Plateau (QTP). We made an investigation across the distribution range of Soroseris Stebbins and sampled 27 populations, mostly from the complex. Internal transcribed spacer (ITS) and two chloroplast loci were sequenced and analysed using the neighbour-joining and Bayesian inference methods. The resulting phylogenies show no well supported inconsistence in topologies, in line with the lack of incongruence detected by the length difference test. However, all the trees were largely unresolved within S.hookeriana complex, irrespective of the optimality criterion employed. We interpret these results as an experience of radiation, which is a common process for native genera on the QTP. Thus, we suggest that all of the morphotypes might be different forms, generated by incipient speciation due to recent explosive differentiation, possibly triggered by the drastic environmental changes of the QTP. Given their evolutionary history, we propose a pragmatic method for treating all of these species as subspecies with a total of four new combinations.
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Affiliation(s)
- La-Mei Heng
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR ChinaLanzhou UniversityLanzhouChina
| | - Yu-Lin Zheng
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR ChinaLanzhou UniversityLanzhouChina
| | - Yong-Bao Zhao
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR ChinaLanzhou UniversityLanzhouChina
| | - Yu-Jin Wang
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR ChinaLanzhou UniversityLanzhouChina
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Massó S, López-Pujol J, Vilatersana R. Reinterpretation of an endangered taxon based on integrative taxonomy: The case of Cynara baetica (Compositae). PLoS One 2018; 13:e0207094. [PMID: 30485285 PMCID: PMC6261557 DOI: 10.1371/journal.pone.0207094] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 10/24/2018] [Indexed: 11/18/2022] Open
Abstract
The Strait of Gibraltar, the gateway between the Atlantic Ocean and the Mediterranean Sea, has a convulsive geological history, with recurring closing and opening events since the late Miocene. As a consequence, this region has played a major role in the evolutionary history of many species. Cynara baetica (Compositae) is a diploid perennial herb distributed in both sides of this strait. It is currently subdivided into two subspecies: C. baetica subsp. baetica for the Spanish populations, and C. baetica subsp. maroccana for the Moroccan ones. Following three different approximations of species delimitation, including phylogenetic and population genetic analyses (based on three AFLP primer combinations and two intergenic spacers of cpDNA), ecological niche modeling (ENM) and morphological studies, this taxon is investigated and reinterpreted. The results obtained showed a clear genetic, morphological and ecological differentiation between the two taxa and the important role played by the Strait of Gibraltar as a geographical barrier. Based on this evidence, the current taxonomic treatment is modified (both taxa should recover their specific rank) and specific conservation guidelines are proposed for the newly delimited taxa.
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Affiliation(s)
- Sergi Massó
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Barcelona, Catalonia, Spain
- BioC-GReB, Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- * E-mail:
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Barcelona, Catalonia, Spain
| | - Roser Vilatersana
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Barcelona, Catalonia, Spain
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Tomasello S. How many names for a beloved genus? – Coalescent-based species delimitation in Xanthium L. (Ambrosiinae, Asteraceae). Mol Phylogenet Evol 2018; 127:135-145. [DOI: 10.1016/j.ympev.2018.05.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 11/13/2022]
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Wu W, Ng WL, Yang JX, Li WM, Ge XJ. High cryptic species diversity is revealed by genome-wide polymorphisms in a wild relative of banana, Musa itinerans, and implications for its conservation in subtropical China. BMC PLANT BIOLOGY 2018; 18:194. [PMID: 30217175 PMCID: PMC6137913 DOI: 10.1186/s12870-018-1410-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 08/31/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Species delimitation is a challenging but essential task in conservation biology. Morphologically similar species are sometimes difficult to recognize even after examination by experienced taxonomists. With the advent of molecular approaches in species delimitation, this hidden diversity has received much recent attention. In addition to DNA barcoding approaches, analytical tools based on the multi-species coalescence model (MSC) have been developed for species delimitation. Musa itinerans is widely distributed in subtropical Asia, and at least six varieties have been documented. However, the number of evolutionarily distinct lineages remains unknown. RESULTS Using genome resequencing data of five populations (making up four varieties), we examined genome-wide variation and found four varieties that were evolutionary significant units. A Bayesian Phylogenetics and Phylogeography (BP&P) analysis using 123 single copy nuclear genes support three speciation events of M. itinerans varieties with robust posterior speciation probabilities; However, a Bayes factor delimitation of species with genomic data (BFD*) analysis using 1201 unlinked single nucleotide polymorphisms gave decisive support for a five-lineage model. When reconciling divergence time estimates with a speciation time scale, a modified three-lineage model was consistent with that of BP&P, in which the speciation time of two varieties (M. itinerans var. itinerans and M. itinerans var. lechangensis) were dated to 26.2 kya and 10.7 kya, respectively. In contrast, other two varieties (M. itinerans var. chinensis and M. itinerans var. guangdongensis) diverged only 3.8 kya in the Anthropocene; this may be a consequence of genetic drift rather than a speciation event. CONCLUSION Our results showed that the M. itinerans species complex harbours high cryptic species diversity. We recommend that M. itinerans var. itinerans and M. itinerans var. lechangensis be elevated to subspecies status, and the extremely rare latter subspecies be given priority for conservation. We also recommend that the very recently diverged M. itinerans var. chinensis and M. itinerans var. guangdongensis should be merged under the subspecies M. itinerans var. chinensis. Finally, we speculate that species delimitation of recently diverged lineages may be more effective using genome-wide bi-allelic SNP markers with BFD* than by using unlinked loci and BP&P.
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Affiliation(s)
- Wei Wu
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275 China
| | - Wei-Lun Ng
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275 China
| | - Jun-Xin Yang
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101 China
| | - Wei-Ming Li
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091 China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650 China
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Niu YT, Jabbour F, Barrett RL, Ye JF, Zhang ZZ, Lu KQ, Lu LM, Chen ZD. Combining complete chloroplast genome sequences with target loci data and morphology to resolve species limits in Triplostegia (Caprifoliaceae). Mol Phylogenet Evol 2018; 129:15-26. [PMID: 30026123 DOI: 10.1016/j.ympev.2018.07.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 07/11/2018] [Accepted: 07/14/2018] [Indexed: 02/04/2023]
Abstract
Species represent the most basic unit of taxonomy. As such, species delimitation represents a crucial issue for biodiversity conservation. Taxonomic practices were revolutionized in the last three decades due to the increasing availability of molecular phylogenetic data. The genus Triplostegia (Caprifoliaceae) traditionally consists of two species, T. glandulifera and T. grandiflora, distinguishable mainly based on quantitative morphological features. In this study, we sequenced nine chloroplast loci (i.e., accD, psbK-psbI, rbcL-accD, rpoB-trnC, rps16-trnQ, trnE-trnT, trnF-ndhJ, trnH-psbA, trnS-trnG) and one nuclear locus (ITS) of 16 individuals of Triplostegia representing the entire distribution range of both species recognized. Furthermore, we also obtained whole chloroplast sequences for 11 of the 16 individuals for which silica gel-dried leaves were available. Our phylogenetic analyses integrating chloroplast genome sequences and multiple loci data revealed that Triplostegia includes four main clades that largely match geography. Neither T. grandiflora nor T. glandulifera was recovered as monophyletic and no diagnosable differences in leaf, flower, and pollen traits were detected between the two species, indicating the need for a revised species circumscription within Triplostegia. Our study highlights the importance of combining data from different sources while defining species limits.
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Affiliation(s)
- Yan-Ting Niu
- 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
| | - Florian Jabbour
- Institut de Systématique Evolution Biodiversité (ISYEB), Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP39, Paris 75005, France
| | - Russell L Barrett
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, Mrs Macquaries Road, Sydney 2000, New South Wales, Australia
| | - Jian-Fei Ye
- 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; Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhu-Zhi Zhang
- School of Life Sciences, Shandong University, Jinan 250100, China
| | - Kai-Qing Lu
- 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
| | - Li-Min Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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Lu Z, Li Y, Yang X, Liu J. Carpinus tibetana (Betulaceae), a new species from southeast Tibet, China. PHYTOKEYS 2018; 98:1-13. [PMID: 29750069 PMCID: PMC5943419 DOI: 10.3897/phytokeys.98.23639] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/12/2018] [Indexed: 06/08/2023]
Abstract
A new species Carpinus tibetana Z. Qiang Lu & J. Quan Liu from southeast Tibet is described and illustrated. The specimens of this new species were previously identified and placed under C. monbeigiana Hand.-Mazz. or C. mollicoma Hu. However, the specimens from southeast Tibet differ from those of C. monbeigiana from other regions with more lateral veins (19-24 vs 14-18) on each side of the midvein and dense pubescence on the abaxial leaf surface, while from those of C. mollicoma from other regions differ by nutlet with dense resinous glands and glabrous or sparsely villous at apex. Principal Component Analyses based on morphometric characters recognise the Tibetan populations as a separate group. Nuclear ribosomal ITS sequence variations show stable and distinct genetic divergences between the Tibetan populations and C. monbeigiana or C. mollicoma by two or three fixed nucleotide mutations. Phylogenetic analysis also identified three respective genetic clusters and the C. mollicoma cluster diverged early. In addition, the Tibetan populations show a disjunct geographic isolation from the other two species. Therefore, C. tibetana, based on the Tibetan populations, is here erected as a new species, distinctly different from C. monbeigiana and C. mollicoma.
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Affiliation(s)
- Zhiqiang Lu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Life Science, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan 666303, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystem, College of Life Science, Lanzhou University, Lanzhou 730000, China
| | - Xiaoyue Yang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Life Science, Lanzhou University, Lanzhou 730000, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Life Science, Lanzhou University, Lanzhou 730000, China
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China
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Liu Y, Su X, Lü T, Liu T. Characterization and phylogenetic analysis of the complete chloroplast genome of Orinus thoroldii (Poaceae). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0923-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Liu YP, Su X, Luo WC, Lv T, Chen KL, Harris AJ, Shah SA. Development of SSR markers from transcriptomes for Orinus (Poaceae), an endemic of the Qinghai-Tibetan Plateau. APPLICATIONS IN PLANT SCIENCES 2017; 5:apps1700029. [PMID: 28791207 PMCID: PMC5546167 DOI: 10.3732/apps.1700029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/09/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Transcriptomes were used to develop microsatellite markers for the plant genus Orinus (Poaceae), which comprises three species of grasses (O. thoroldii, O. kokonoricus, and O. intermedius) that are widely distributed in the Qinghai-Tibetan Plateau. METHODS AND RESULTS Primer pairs were developed for 16 high-quality simple sequence repeats (SSRs) using transcriptomes. SSRs were amplified in 248 individuals representing the three species of Orinus; the number of alleles per locus ranged from one to seven, with an average of 2.6. The expected and observed heterozygosity per locus varied from 0.00 to 0.83 and from 0.00 to 1.00, respectively, with respective mean values of 0.32 and 0.34. CONCLUSIONS These newly developed SSR markers will be valuable for evaluating the population genetic structure of Orinus throughout its range.
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Affiliation(s)
- Yu-Ping Liu
- Key Laboratory of Medicinal Plant and Animal Resources in the Qinghai–Tibetan Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, People’s Republic of China
- Key Laboratory of Physical Geography and Environmental Process in Qinghai Province, School of Geography and Life Science, Qinghai Normal University, Xining 810008, People’s Republic of China
| | - Xu Su
- Key Laboratory of Medicinal Plant and Animal Resources in the Qinghai–Tibetan Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, People’s Republic of China
- Key Laboratory of Education, Ministry of Environments and Resources in the Qinghai–Tibetan Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, People’s Republic of China
| | - Wen-Chun Luo
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, People’s Republic of China
| | - Ting Lv
- Key Laboratory of Medicinal Plant and Animal Resources in the Qinghai–Tibetan Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, People’s Republic of China
- Key Laboratory of Physical Geography and Environmental Process in Qinghai Province, School of Geography and Life Science, Qinghai Normal University, Xining 810008, People’s Republic of China
| | - Ke-Long Chen
- Key Laboratory of Physical Geography and Environmental Process in Qinghai Province, School of Geography and Life Science, Qinghai Normal University, Xining 810008, People’s Republic of China
| | - AJ Harris
- Department of Botany, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, D.C. 20013-7012 USA
| | - Sayed Afzal Shah
- Department of Plant Science, Quaid-i-Azam University, Islamabad 44000 Pakistan
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Hao G, Zhang C, AL-Shehbaz IA, Guo X, Bi H, Wang J, Liu J. Eutrema giganteum (Brassicaceae), a new species from Sichuan, southwest China. PHYTOKEYS 2017; 82:15-26. [PMID: 28794679 PMCID: PMC5546392 DOI: 10.3897/phytokeys.82.12329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 06/05/2017] [Indexed: 06/07/2023]
Abstract
Eutrema giganteum (Brassicaceae), a new species from Hengduan Mountains in Sichuan Province, southwest China, is described, and its relationships to the closely related E. yunnanense is discussed based on morphological, cytological, and molecular data. It is similar morphologically to E. yunnanense but is readily distinguished by having robust (vs. slender), erect (vs. decumbent), and branched (vs. mostly simple), and rather tall stems (60-110 cm vs. 20-60 cm); curved (vs. straight), smooth (vs. torulose), and shorter fruit (5-8 mm vs. 8-15 mm); and fewer ovules per ovary (1-4 vs. 6-10). All examined individuals from different populations of E. giganteum clustered into a single clade sister to E. yunnanense in phylogenetic analyses using the combined nuclear ITS and plastid DNA datasets. Our cytological studies revealed that the chromosome number of E. giganteum is 2n = 44, with a genome size of 1160 (±8) Mb, while that of E. yunnanense is 2n = 28, with a genome size of 718 (±15) Mb. Multiple lines of evidence support the recognition of E. giganteum as a distinct species well differentiated from E. yunnanense.
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Affiliation(s)
- Guoqian Hao
- Biodiversity Institute of Mount Emei, Mount Emei Scenic Area Management Committee, Leshan 614000, P. R. China
| | - Changbing Zhang
- Sichuan Academy of Grassland Sciences, Chengdu 610065, P. R. China
| | | | - Xinyi Guo
- MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu 610065, P. R. China
| | - Hao Bi
- MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu 610065, P. R. China
| | - Junyin Wang
- Biodiversity Institute of Mount Emei, Mount Emei Scenic Area Management Committee, Leshan 614000, P. R. China
| | - Jianquan Liu
- MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu 610065, P. R. China
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Shu JP, Shang H, Jin D, Wei HJ, Zhou XL, Liu HM, Gu YF, Wang Y, Wang FG, Shen H, Zhang R, Adjie B, Yan YH. Re-establishment of species from synonymies based on DNA barcoding and phylogenetic analysis using Diplopterygium simulans (Gleicheniaceae) as an example. PLoS One 2017; 12:e0164604. [PMID: 28296890 PMCID: PMC5351838 DOI: 10.1371/journal.pone.0164604] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 07/21/2016] [Indexed: 11/19/2022] Open
Abstract
Because synonymy treatment traditionally relies on morphological judgments, it usually causes many problems in species delimitation and in the biodiversity catalogue. For example, Diplopterygium simulans, which belongs to the Gleicheniaceae family, has been considered to be synonymous with D. glaucum or D. giganteum based mainly on the morphology of its pinna rachis and blade. In the absence of molecular evidence, these revisions remain doubtful. DNA barcoding, which is considered to be a powerful method for species-level identification, was employed to assess the genetic distance among 9 members of the Diplopterygium genus. The results indicate that D. simulans is an independent species rather than a synonymy of D. glaucum or D. giganteum. Moreover, phylogenetic analysis uncovered the sisterhood of D. simulans and D. cantonense, which is supported by their geographical distributions and morphological traits. Incorrect synonymy treatment is prevalent in the characterization of biological diversity, and our study proposes a convenient and effective method for validating synonym treatments and discovering cryptic species.
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Affiliation(s)
- Jiang-Ping Shu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Hui Shang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Dongmei Jin
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Hong-Jin Wei
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Xi-Le Zhou
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Hong-Mei Liu
- Shenzhen Fairylake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China
| | - Yu-Feng Gu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Ying Wang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Fa-Guo Wang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hui Shen
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Rui Zhang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Bayu Adjie
- Bali Botanic Garden, Indonesian Institute of Science, Bali, Indonesia
| | - Yue-Hong Yan
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
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Fernández M, Ezcurra C, Calviño CI. Species limits and morphometric and environmental variation within the South Andean and Patagonian Mulinum spinosum species-group (Apiaceae-Azorelloideae). SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2016.1273975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Martina Fernández
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Universidad Nacional del Comahue-CONICET, Quintral 1250, 8400 Bariloche, Río Negro, Argentina
| | - Cecilia Ezcurra
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Universidad Nacional del Comahue-CONICET, Quintral 1250, 8400 Bariloche, Río Negro, Argentina
| | - Carolina I. Calviño
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Universidad Nacional del Comahue-CONICET, Quintral 1250, 8400 Bariloche, Río Negro, Argentina
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Zheng H, Fan L, Milne RI, Zhang L, Wang Y, Mao K. Species Delimitation and Lineage Separation History of a Species Complex of Aspens in China. FRONTIERS IN PLANT SCIENCE 2017; 8:375. [PMID: 28377782 PMCID: PMC5359289 DOI: 10.3389/fpls.2017.00375] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 03/06/2017] [Indexed: 05/13/2023]
Abstract
Species delimitation in tree species is notoriously challenging due to shared polymorphisms among species. An integrative survey that considers multiple operational criteria is a possible solution, and we aimed to test it in a species complex of aspens in China. Genetic [four chloroplast DNA (cpDNA) fragments and 14 nuclear microsatellite loci (nSSR)] and morphological variations were collected for 76 populations and 53 populations, respectively, covering the major geographic distribution of the Populus davidiana-rotundifolia complex. Bayesian clustering, analysis of molecular variance (AMOVA), Principle Coordinate Analysis (PCoA), ecological niche modeling (ENM), and gene flow (migrants per generation), were employed to detect and test genetic clustering, morphological and habitat differentiation, and gene flow between/among putative species. The nSSR data and ENM suggested that there are two separately evolving meta-population lineages that correspond to P. davidiana (pd) and P. rotundifolia (pr). Furthermore, several lines of evidence supported a subdivision of P. davidiana into Northeastern (NEC) and Central-North (CNC) groups, yet they are still functioning as one species. CpDNA data revealed that five haplotype clades formed a pattern of [pdNEC, ((pdCNC, pr), (pdCNC, pr))], but most haplotypes are species-specific. Meanwhile, PCA based on morphology suggested a closer relationship between the CNC group (P. davidiana) and P. rontundifolia. Discrepancy of nSSR and ENM vs. cpDNA and morphology could have reflected a complex lineage divergence and convergence history. P. davidiana and P. rotundifolia can be regarded as a recently diverged species pair that experienced parapatric speciation due to ecological differentiation in the face of gene flow. Our findings highlight the importance of integrative surveys at population level, as we have undertaken, is an important approach to detect the boundary of a group of species that have experienced complex evolutionary history.
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Affiliation(s)
- Honglei Zheng
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
| | - Liqiang Fan
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
| | - Richard I. Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of EdinburghEdinburgh, UK
| | - Lei Zhang
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
| | - Yaling Wang
- Life Science and Engineering College, Northwest University for NationalitiesLanzhou, China
| | - Kangshan Mao
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
- *Correspondence: Kangshan Mao ;
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Fu PC, Gao QB, Zhang FQ, Xing R, Wang JL, Liu HR, Chen SL. Gene Flow Results in High Genetic Similarity between Sibiraea (Rosaceae) Species in the Qinghai-Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2016; 7:1596. [PMID: 27826314 PMCID: PMC5078775 DOI: 10.3389/fpls.2016.01596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/10/2016] [Indexed: 06/06/2023]
Abstract
Studying closely related species and divergent populations provides insight into the process of speciation. Previous studies showed that the Sibiraea complex's evolutionary history on the Qinghai-Tibetan Plateau (QTP) was confusing and could not be distinguishable on the molecular level. In this study, the genetic structure and gene flow of Sibiraea laevigata and Sibiraea angustata on the QTP was examined across 45 populations using 8 microsatellite loci. Microsatellites revealed high genetic diversity in Sibiraea populations. Most of the variance was detected within populations (87.45%) rather than between species (4.39%). We found no significant correlations between genetic and geographical distances among populations. Bayesian cluster analysis grouped all individuals in the sympatric area of Sibiraea into one cluster and other individuals of S. angustata into another. Divergence history analysis based on the approximate Bayesian computation method indicated that the populations of S. angustata at the sympatric area derived from the admixture of the 2 species. The assignment test assigned all individuals to populations of their own species rather than its congeneric species. Consistently, intraspecies were detected rather than interspecies first-generation migrants. The bidirectional gene flow in long-term patterns between the 2 species was asymmetric, with more from S. angustata to S. laevigata. In conclusion, the Sibiraea complex was distinguishable on the molecular level using microsatellite loci. We found that the high genetic similarity of the complex resulted from huge bidirectional gene flow, especially on the sympatric area where population admixtures occurred. This study sheds light on speciation with gene flow in the QTP.
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Affiliation(s)
- Peng-Cheng Fu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
- College of Life Science, Luoyang Normal UniversityLuoyang, China
| | - Qing-Bo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
| | - Fa-Qi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
| | - Rui Xing
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
| | - Jiu-Li Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
- College of Life Science, University of Chinese Academy of SciencesBeijing, China
| | - Hai-Rui Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
- College of Life Science, University of Chinese Academy of SciencesBeijing, China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
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Lu Z, Zhang D, Liu S, Yang X, Liu X, Liu J. Species delimitation of Chinese hop-hornbeams based on molecular and morphological evidence. Ecol Evol 2016; 6:4731-40. [PMID: 27547308 PMCID: PMC4979702 DOI: 10.1002/ece3.2251] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 05/16/2016] [Accepted: 05/18/2016] [Indexed: 11/08/2022] Open
Abstract
Species delimitation through which infers species boundaries is emerging as a major work in modern systematics. Hop-hornbeam species in Ostrya (Betulaceae) are well known for their hard and heavy woods. Five species were described in China and their interspecific delimitations remain unclear. In this study, we firstly explored their distributions in all recorded field sites distributed in China. We then selected 110 samples from 22 natural populations of five species from this genus and one type specimen of O. yunnanensis, for molecular barcoding analyses. We sequenced four chloroplast (cp) DNA fragments (trnH-psbA, trnL-trnF, rps16, and trnG) and the nuclear internal transcribed spacer (ITS) region for all samples. Sequence variations of Ostrya from four cpDNA fragments identified three groups that showed no correspondence to any morphological delimitation because of the incomplete lineage sorting and/or possible interspecific introgression in the history. However, phylogenetic analyses of ITS sequence variations discerned four species, O. japonica, O. rehderiana, O. trichocarpa, and O. multinervis while O. yunnanensis nested within O. multinervis. Morphological clustering also discerned four species and showed the complete consistency with molecular evidence. Moreover, our phylogenetic analyses-based ITS sequence variations suggested that O. trichocarpa comprised an isolated lineage different from the other Eurasian ones. Based on these results, hop-hornbeams in China should be treated as four separate species. Our results further highlight the importance of ITS sequence variations in delimitating and discerning the closely related species in plants.
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Affiliation(s)
- Zhiqiang Lu
- State Key Laboratory of Grassland Agro‐EcosystemCollege of Life ScienceLanzhou UniversityLanzhouChina
| | - Dan Zhang
- MOE Key Laboratory for Bio‐resources and Eco‐environmentCollege of Life ScienceSichuan UniversityChengduChina
| | - Siyu Liu
- State Key Laboratory of Grassland Agro‐EcosystemCollege of Life ScienceLanzhou UniversityLanzhouChina
| | - Xiaoyue Yang
- State Key Laboratory of Grassland Agro‐EcosystemCollege of Life ScienceLanzhou UniversityLanzhouChina
| | - Xue Liu
- State Key Laboratory of Grassland Agro‐EcosystemCollege of Life ScienceLanzhou UniversityLanzhouChina
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro‐EcosystemCollege of Life ScienceLanzhou UniversityLanzhouChina
- MOE Key Laboratory for Bio‐resources and Eco‐environmentCollege of Life ScienceSichuan UniversityChengduChina
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Ru D, Mao K, Zhang L, Wang X, Lu Z, Sun Y. Genomic evidence for polyphyletic origins and interlineage gene flow within complex taxa: a case study ofPicea brachytylain the Qinghai-Tibet Plateau. Mol Ecol 2016; 25:2373-86. [DOI: 10.1111/mec.13656] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 04/09/2016] [Accepted: 04/14/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Dafu Ru
- Key Laboratory for Bio-resources and Eco-environment; College of Life Sciences; Sichuan University; Chengdu 610065 China
| | - Kangshan Mao
- Key Laboratory for Bio-resources and Eco-environment; College of Life Sciences; Sichuan University; Chengdu 610065 China
| | - Lei Zhang
- Key Laboratory for Bio-resources and Eco-environment; College of Life Sciences; Sichuan University; Chengdu 610065 China
| | - Xiaojuan Wang
- Key Laboratory for Bio-resources and Eco-environment; College of Life Sciences; Sichuan University; Chengdu 610065 China
| | - Zhiqiang Lu
- State Key Laboratory of Grassland Agro-ecosystem; College of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Yongshuai Sun
- Key Laboratory for Bio-resources and Eco-environment; College of Life Sciences; Sichuan University; Chengdu 610065 China
- Key Laboratory of Tropical Forest Ecology; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Mengla 666303 China
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Malavasi V, Škaloud P, Rindi F, Tempesta S, Paoletti M, Pasqualetti M. DNA-Based Taxonomy in Ecologically Versatile Microalgae: A Re-Evaluation of the Species Concept within the Coccoid Green Algal Genus Coccomyxa (Trebouxiophyceae, Chlorophyta). PLoS One 2016; 11:e0151137. [PMID: 27028195 PMCID: PMC4814044 DOI: 10.1371/journal.pone.0151137] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/23/2016] [Indexed: 12/30/2022] Open
Abstract
Coccomyxa is a genus of unicellular green algae of the class Trebouxiophyceae, well known for its cosmopolitan distribution and great ecological amplitude. The taxonomy of this genus has long been problematic, due to reliance on badly-defined and environmentally variable morphological characters. In this study, based on the discovery of a new species from an extreme habitat, we reassess species circumscription in Coccomyxa, a unicellular genus of the class Trebouxiophyceae, using a combination of ecological and DNA sequence data (analyzed with three different methods of algorithmic species delineation). Our results are compared with those of a recent integrative study of Darienko and colleagues that reassessed the taxonomy of Coccomyxa, recognizing 7 species in the genus. Expanding the dataset from 43 to 61 sequences (SSU + ITS rDNA) resulted in a different delimitation, supporting the recognition of a higher number of species (24 to 27 depending on the analysis used, with the 27-species scenario receiving the strongest support). Among these, C. melkonianii sp. nov. is described from material isolated from a river highly polluted by heavy metals (Rio Irvi, Sardinia, Italy). Analyses performed on ecological characters detected a significant phylogenetic signal in six different characters. We conclude that the 27-species scenario is presently the most realistic for Coccomyxa and we suggest that well-supported lineages distinguishable by ecological preferences should be recognized as different species in this genus. We also recommend that for microbial lineages in which the overall diversity is unknown and taxon sampling is sparse, as is often the case for green microalgae, the results of analyses for algorithmic DNA-based species delimitation should be interpreted with extreme caution.
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Affiliation(s)
- Veronica Malavasi
- Interdepartmental Center of Environmental Science and Engineering (CINSA), University of Cagliari, Cagliari, Italy
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University of Prague, Prague, Czech Republic
- * E-mail:
| | - Fabio Rindi
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Sabrina Tempesta
- Department of biological and ecological sciences, Tuscia University, Viterbo, Italy
| | - Michela Paoletti
- Department of biological and ecological sciences, Tuscia University, Viterbo, Italy
| | - Marcella Pasqualetti
- Department of biological and ecological sciences, Tuscia University, Viterbo, Italy
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Feng X, Liu J, Gong X. Species Delimitation of the Cycas segmentifida Complex (Cycadaceae) Resolved by Phylogenetic and Distance Analyses of Molecular Data. FRONTIERS IN PLANT SCIENCE 2016; 7:134. [PMID: 26913044 PMCID: PMC4753401 DOI: 10.3389/fpls.2016.00134] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/25/2016] [Indexed: 06/02/2023]
Abstract
The Cycas segmentifida complex consists of eight species whose distributions overlap in a narrow region in Southwest China. These eight taxa are also morphologically similar and are difficult to be distinguished. Consequently, their taxonomic status has been a matter of discussion in recent years. To study this species complex, we sequenced four plastid intergenic spacers (cpDNA), three nuclear genes and genotyped 12 microsatellites for the eight taxa from 19 different localities. DNA sequences were analyzed using Maximum Likelihood (ML) method and Bayesian Inference (BI), and microsatellites were analyzed using the Neighbor-joining (NJ) and structure inference methods. Results of cpDNA, nuclear gene GTP and microsatellites all rejected the hypotheses that this complex consisted of eight taxa or one distinct lineage (species) but two previously described species were adopted: Cycas guizhouensis K. M. Lan et R. F. Zou and Cycas segmentifida D. Y. Wang et C. Y. Deng. Cycas longlinensis H. T. Chang et Y. C. Zhong was included in C. guizhouensis and the other five taxa were included in C. segmentifida. Our species delimitation inferred from molecular data largely corresponds to morphological differentiation. However, the other two nuclear genes were unable to resolve species boundaries for this complex independently. This study offered evidences from different genomes for dealing with the species boundaries and taxonomical treatment of the C. segmentifida complex in an integrated perspective.
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Affiliation(s)
- Xiuyan Feng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
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