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Blankers T, Shaw KL. The biogeographic and evolutionary processes shaping population divergence in Laupala. Mol Ecol 2024; 33:e17444. [PMID: 38984705 DOI: 10.1111/mec.17444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 05/21/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024]
Abstract
Speciation generates biodiversity and the mechanisms involved are thought to vary across the tree of life and across environments. For example, well-studied adaptive radiations are thought to be fuelled by divergent ecological selection, but additionally are influenced heavily by biogeographic, genomic and demographic factors. Mechanisms of non-adaptive radiations, producing ecologically cryptic taxa, have been less well-studied but should likewise be influenced by these latter factors. Comparing among contexts can help pinpoint universal mechanisms and outcomes, especially if we integrate biogeographic, ecological and evolutionary processes. We investigate population divergence in the swordtail cricket Laupala cerasina, a wide-spread endemic on Hawai'i Island and one of 38 ecologically cryptic Laupala species. The nine sampled populations show striking population genetic structure at small spatio-temporal scales. The rapid differentiation among populations and species of Laupala shows that neither a specific geographical context nor ecological opportunity are pre-requisites for rapid divergence. Spatio-temporal patterns in population divergence, population size change, and gene flow are aligned with the chronosequence of the four volcanoes on which L. cerasina occurs and reveal the composite effects of geological dynamics and Quaternary climate change on population dynamics. Spatio-temporal patterns in genetic variation along the genome reveal the interplay of genetic and genomic architecture in shaping population divergence. In early phases of divergence, we find elevated differentiation in genomic regions harbouring mating song loci. In later stages of divergence, we find a signature of linked selection that interacts with recombination rate variation. Comparing our findings with recent work on complementary systems supports the conclusion that mostly universal factors influence the speciation process.
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Affiliation(s)
- Thomas Blankers
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Kerry L Shaw
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA
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2
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Liao X, Shih Y, Jia C, Gao T. Complete Mitochondrial Genome of Four Peristediidae Fish Species: Genome Characterization and Phylogenetic Analysis. Genes (Basel) 2024; 15:557. [PMID: 38790187 PMCID: PMC11121196 DOI: 10.3390/genes15050557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
The systematic revision of the family Peristediidae remains an unresolved issue due to their diverse and unique morphology. Despite the popularity of using mitochondrial genome research to comprehensively understand phylogenetic relationships in fish, genetic data for peristediid fish need to be included. Therefore, this study aims to investigate the mitochondrial genomic characteristics and intra-family phylogenetic relationships of Peristediidae by utilizing mitochondrial genome analysis. Therefore, this study aims to investigate the phylogenetic relationship of Peristediidae by utilizing mitochondrial genome analysis. The mitochondrial genome of four species of Peristediidae (Peristedion liorhynchus, Satyrichthys welchi, Satyrichthys rieffeli, and Scalicus amiscus) collected in the East China Sea was studied. The mitochondrial gene sequence lengths of four fish species were 16,533 bp, 16,526 bp, 16,527 bp, and 16,526 bp, respectively. They had the same mitochondrial structure and were all composed of 37 genes and one control region. Most PCGs used ATG as the start codon, and a few used GTG as the start codon. An incomplete stop codon (TA/T) occurred. The AT-skew and GC-skew values of 13 PCGs from four species were negative, and the GC-skew amplitude was greater than that of AT-skew. All cases of D-arm were found in tRNA-Ser (GCT). The Ka/Ks ratio analysis indicated that 13 PCGs were suffering purifying selection. Based on 12 PCGs (excluding ND6) sequences, a phylogenetic tree was constructed using Bayesian inference (BI) and maximum likelihood (ML) methods, providing a further supplement to the scientific classification of Peristediidae fish. According to the results of divergence time, the four species of fish had apparent divergence in the Early Cenozoic, which indicates that the geological events at that time caused the climax of species divergence and evolution.
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Affiliation(s)
- Xianhui Liao
- Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Yijia Shih
- Fisheries College, Jimei University, Xiamen 361021, China;
| | - Chenghao Jia
- School of Ecology and Environment, Hainan University, Haikou 570228, China;
| | - Tianxiang Gao
- Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China;
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Xiao Y, Li XJ, Jiang XL, Li C, Li XP, Li WP, Tian DK. Spatial genetic patterns and distribution dynamics of Begonia grandis (Begoniaceae), a widespread herbaceous species in China. FRONTIERS IN PLANT SCIENCE 2023; 14:1178245. [PMID: 37235032 PMCID: PMC10206317 DOI: 10.3389/fpls.2023.1178245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023]
Abstract
Introduction Begonia L., one of the 10 largest plant genera, contains over 2,100 species, most of which have a very limited distribution range. Understanding the spatial genetic structure and distribution dynamics of a widespread species in this genus will contribute to clarifying the mechanism responsible for Begonia speciation. Methods In this study, we used three chloroplast DNA markers (ndhF-rpl32, atpI-atpH, and ndhA intron), coupled with species distribution modeling (SDM), to investigate the population genetic structure and distribution dynamics of Begonia grandis Dryand., the species of Begonia with the widest distribution in China. Results Thirty-five haplotypes from 44 populations clustered into two groups, and haplotype divergence began in the Pleistocene (1.75 Mya). High genetic diversity (H d = 0.894, H T = 0.910), strong genetic differentiation (F ST = 0.835), and significant phylogeographical structure (G ST/N ST = 0.848/0.917, P < 0.05) were observed. The distribution range of B. grandis migrated northwards after the last glacial maximum, but its core distribution area remained stable. Discussion Combined, the observed spatial genetic patterns and SDM results identified the Yunnan-Guizhou Plateau, the Three Gorges region, and the Daba Mountains as potential refugia of B. grandis. BEAST-derived chronogram and haplotype network analysis do not support the Flora Reipublicae Popularis Sinicae and Flora of China for subspecies classification based on morphological characteristics. Our results support the hypothesis that population-level allopatric differentiation may be an important speciation process for the Begonia genus and a key contributor to its rich diversity.
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Affiliation(s)
- Yan Xiao
- College of Life Sciences, Hunan Normal University, Changsha, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Xing-Juan Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Xiao-Long Jiang
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Chun Li
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Horticulture Institute of Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xiang-Peng Li
- Institute of Plant Conservation, Hunan Botanic Garden, Changsha, China
| | - Wei-Ping Li
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Dai-Ke Tian
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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Hu L, Yang R, Wang YH, Gong X. The natural hybridization between species Ligularia nelumbifolia and Cremanthodium stenoglossum (Senecioneae, Asteraceae) suggests underdeveloped reproductive isolation and ambiguous intergeneric boundary. AOB PLANTS 2021; 13:plab012. [PMID: 33796247 PMCID: PMC7994929 DOI: 10.1093/aobpla/plab012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Natural hybridization is frequent in plants and is considered an important factor facilitating speciation. The natural intergeneric hybridization between Ligularia and Cremanthodium was previously confirmed using a couple of DNA markers. However, the mechanism of this intergeneric hybridization and the role of reproductive isolation in the process of hybridization remain unclear. Here we used double-digest restriction site-associated DNA sequencing (ddRAD-seq) to further quantify the occurrence of hybridization, the genetic structure of the hybrid population and the role of reproductive isolation between Ligularia nelumbifolia and Cremanthodium stenoglossum. The results based on the ddRAD-seq SNP data sets indicated that hybridization between L. nelumbifolia and C. stenoglossum was restricted to F1s, and no gene introgression was identified between these two species. STRUCTURE analysis and maximum likelihood (ML) tree results showed a slightly larger genetic contribution of L. nelumbifolia to putative hybrid F1s. We deduced that the reproductive isolation between these two parent species is not well-developed but still strong enough to maintain the genetic integrity of the species, and that their F1s are sterile or with low fertility. Given the poorly resolved phylogenetic relationship between Ligularia and Cremanthodium, the occurrence of natural hybridization between L. nelumbifolia and C. stenoglossum may provide new insights into the re-circumscription and re-delimitation of these two genera.
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Affiliation(s)
- Li Hu
- Plant Science Institute, School of Life Sciences, Yunnan University, Kunming 650201, Yunnan, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue-Hua Wang
- Plant Science Institute, School of Life Sciences, Yunnan University, Kunming 650201, Yunnan, China
| | - Xun Gong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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5
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Fu PC, Twyford AD, Sun SS, Wang HY, Xia MZ, Tan CX, Zhou XJ, Chen SL. Recurrent hybridization underlies the evolution of novelty in Gentiana (Gentianaceae) in the Qinghai-Tibetan Plateau. AOB PLANTS 2021; 13:plaa068. [PMID: 33510891 PMCID: PMC7821390 DOI: 10.1093/aobpla/plaa068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 11/30/2020] [Indexed: 05/31/2023]
Abstract
The Qinghai-Tibetan Plateau (QTP) and adjacent areas are centres of diversity for several alpine groups. Although it is known that the QTP acted as a source area for diversification of the alpine genus Gentiana, the evolutionary processes underlying diversity in this genus, especially the formation of narrow endemics, are still poorly understood. Hybridization has been proposed as a driver of plant endemism in the QTP but few cases have been documented with genetic data. Here, we describe a new endemic species in Gentiana section Cruciata as G. hoae sp. nov., and explore its evolutionary history with complete plastid genomes and nuclear ribosomal internal transcribed spacer sequence data. Genetic divergence within G. hoae ~3 million years ago was followed by postglacial expansion on the QTP, suggesting Pleistocene glaciations as a key factor shaping the population history of G. hoae. Furthermore, a mismatch between plastid and nuclear data suggest that G. hoae participated in historical hybridization, while population sequencing show this species continues to hybridize with the co-occurring congener G. straminea in three locations. Our results indicate that hybridization may be a common process in the evolution of Gentiana and may be widespread among recently diverged taxa of the QTP.
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Affiliation(s)
- Peng-Cheng Fu
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Alex D Twyford
- Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, UK
| | - Shan-Shan Sun
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Hong-Yu Wang
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Ming-Ze Xia
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Cheng-Xi Tan
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Xiao-Jun Zhou
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, P.R. China
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Becher H, Brown MR, Powell G, Metherell C, Riddiford NJ, Twyford AD. Maintenance of Species Differences in Closely Related Tetraploid Parasitic Euphrasia (Orobanchaceae) on an Isolated Island. PLANT COMMUNICATIONS 2020; 1:100105. [PMID: 33367265 PMCID: PMC7748025 DOI: 10.1016/j.xplc.2020.100105] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/24/2020] [Accepted: 08/27/2020] [Indexed: 05/02/2023]
Abstract
Polyploidy is pervasive in angiosperm evolution and plays important roles in adaptation and speciation. However, polyploid groups are understudied due to complex sequence homology, challenging genome assembly, and taxonomic complexity. Here, we study adaptive divergence in taxonomically complex eyebrights (Euphrasia), where recent divergence, phenotypic plasticity, and hybridization blur species boundaries. We focus on three closely related tetraploid species with contrasting ecological preferences that are sympatric on Fair Isle, a small isolated island in the British Isles. Using a common garden experiment, we show a genetic component to the morphological differences present between these species. Using whole-genome sequencing and a novel k-mer approach we call "Tetmer", we demonstrate that the species are of allopolyploid origin, with a sub-genome divergence of approximately 5%. Using ∼2 million SNPs, we show sub-genome homology across species, with a very low sequence divergence characteristic of recent speciation. This genetic variation is broadly structured by species, with clear divergence of Fair Isle heathland Euphrasia micrantha, while grassland Euphrasia arctica and coastal Euphrasia foulaensis are more closely related. Overall, we show that tetraploid Euphrasia is a system of allopolyploids of postglacial species divergence, where adaptation to novel environments may be conferred by old variants rearranged into new genetic lineages.
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Affiliation(s)
- Hannes Becher
- University of Edinburgh, School of Biological Sciences, Institute of Evolutionary Biology, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
- Corresponding author
| | - Max R. Brown
- University of Edinburgh, School of Biological Sciences, Institute of Evolutionary Biology, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Gavin Powell
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Chris Metherell
- Botanical Society of Britain and Ireland, 4 High Firs Crescent, Harpenden, Hertfordshire AL5 1NA, UK
| | | | - Alex D. Twyford
- University of Edinburgh, School of Biological Sciences, Institute of Evolutionary Biology, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
- Corresponding author
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7
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Ren G, Mateo RG, Conti E, Salamin N. Population Genetic Structure and Demographic History of Primula fasciculata in Southwest China. FRONTIERS IN PLANT SCIENCE 2020; 11:986. [PMID: 32714358 PMCID: PMC7351516 DOI: 10.3389/fpls.2020.00986] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Understanding the factors that drive the genetic structure of a species and its responses to past climatic changes is an important first step in modern population management. The response to the last glacial maximum (LGM) has been well studied, however, the effect of previous glaciation periods on plant demographic history is still not well studied. Here we investigated the population structure and demographic history of Primula fasciculata that widely occurs in the Hengduan Mountains and Qinghai-Tibetan Plateau. We obtained genomic data for 234 samples of the species using restriction site-associated DNA (RAD) sequencing and combined approximate Bayesian computation (ABC) and species distribution modeling (SDM) to evaluate the effects of multiple glaciation periods by testing several population divergence models and demographic scenarios. The analyses of population structure showed that P. fasciculata displays a striking population structure with six groups that could be identified genetically. Our ABC modeling suggested that the current groups diverged from ancestral populations located in the eastern Hengduan Mountains after the largest glaciation occurred in the region (~ 0.8-0.5 million years ago), which is consistent with the result of SDMs. Each current group has survived in different glacial refugia during the LGM and experienced expansions and/or bottlenecks since their divergence during or across the following Quaternary glacial cycles. Our study demonstrates the usefulness of population genomics for evaluating the effects of past climatic changes in alpine plant species with shallow population structure.
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Affiliation(s)
- Guangpeng Ren
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Science, Lanzhou University, Lanzhou, China
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland
| | - Rubén G. Mateo
- Departamento de Biología (Botánica), Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Elena Conti
- Department of Systematic and Evolutionary Botany and Botanic Garden, University of Zurich, Zurich, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland
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8
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Niu Z, Hou Z, Wang M, Ye M, Zhang B, Xue Q, Liu W, Ding X. A comparative plastomics approach reveals available molecular markers for the phylogeographic study of Dendrobium huoshanense, an endangered orchid with extremely small populations. Ecol Evol 2020; 10:5332-5342. [PMID: 32607156 PMCID: PMC7319108 DOI: 10.1002/ece3.6277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 03/13/2020] [Accepted: 03/25/2020] [Indexed: 11/08/2022] Open
Abstract
Comparative plastomics approaches have been used to identify available molecular markers for different taxonomic level studies of orchid species. However, the adoption of such methods has been largely limited in phylogeographic studies. Therefore, in this study, Dendrobium huoshanense, an endangered species with extremely small populations, was used as a model system to test whether the comparative plastomic approaches could screen available molecular markers for the phylogeographic study. We sequenced two more plastomes of D. huoshanense and compared them with our previously published one. A total of 27 mutational hotspot regions and six polymorphic cpSSRs have been screened for the phylogeographic studies of D. huoshanense. The cpDNA haplotype data revealed that the existence of haplotype distribution center was located in Dabieshan Mts. (Huoshan). The genetic diversity and phylogenetic analyses showed that the populations of D. huoshanense have been isolated and evolved independently for long period. On the contrary, based on cpSSR data, the genetic structure analysis revealed a mixed structure among the populations in Anhui and Jiangxi province, which suggested that the hybridization or introgression events have occurred among the populations of D. huoshanense. These results indicated that human activities have played key roles in shaping the genetic diversity and distributional patterns of D. huoshanense. According to our results, both two markers showed a high resolution for the phylogeographic studies of D. huoshanense. Therefore, we put forth that comparative plastomic approaches could revealed available molecular markers for phylogeographic study, especially for the species with extremely small populations.
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Affiliation(s)
- Zhitao Niu
- College of Life SciencesNanjing Normal UniversityNanjingChina
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for DendrobiumNanjingChina
| | - Zhenyu Hou
- College of Life SciencesNanjing Normal UniversityNanjingChina
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for DendrobiumNanjingChina
| | - Mengting Wang
- College of Life SciencesNanjing Normal UniversityNanjingChina
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for DendrobiumNanjingChina
| | - Meirong Ye
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for DendrobiumNanjingChina
| | - Benhou Zhang
- College of Life SciencesNanjing Normal UniversityNanjingChina
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for DendrobiumNanjingChina
| | - Qingyun Xue
- College of Life SciencesNanjing Normal UniversityNanjingChina
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for DendrobiumNanjingChina
| | - Wei Liu
- College of Life SciencesNanjing Normal UniversityNanjingChina
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for DendrobiumNanjingChina
| | - Xiaoyu Ding
- College of Life SciencesNanjing Normal UniversityNanjingChina
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for DendrobiumNanjingChina
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9
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Yang R, Folk R, Zhang N, Gong X. Homoploid hybridization of plants in the Hengduan mountains region. Ecol Evol 2019; 9:8399-8410. [PMID: 31380098 PMCID: PMC6662326 DOI: 10.1002/ece3.5393] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 04/24/2019] [Accepted: 05/30/2019] [Indexed: 12/24/2022] Open
Abstract
The Hengduan Mountains Region (HMR) is a major global biodiversity hotspot. Complex tectonic and historical climatic conditions created opportunities for natural interspecific hybridization. Likewise, anthropogenic disturbance potentially raises the frequency of hybridization. Among species studies to date, the frequency of homoploid hybridization appears in the HMR. Of nine taxa in which natural hybridization has been detected, three groups are involved in homoploid hybrid speciation, and species pairs from the remaining six genera suggest that continuous gene flow occurs in hybrid zones. Reproductive isolation may greatly affect the dynamic and architecture of hybrid zones in the HMR. Asymmetrical hybridization and introgression can primarily be attributed to both prezygotic and postzygotic barriers. The frequent observation of such asymmetry may imply that reproductive barrier contributes to maintaining species boundaries in the alpine region. Ecological isolations with environmental disturbance may promote breeding barriers between parental species and hybrids. Hybrid zones may be an important phase for homoploid hybrid speciation. Hybrid zones potentially provided abundant genetic resources for the diversification of the HMR flora. The ecological and molecular mechanisms of control and mediation for natural hybridization will help biologists to understand the formation of biodiversity in the HMR. More researches from ecological and molecular aspects were required in future studies.
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Affiliation(s)
- Rui Yang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- Key Laboratory of Economic Plants and BiotechnologyKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ryan Folk
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
| | - Ningning Zhang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- Key Laboratory of Economic Plants and BiotechnologyKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- Key Laboratory of Economic Plants and BiotechnologyKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- Yunnan Key Laboratory for Wild Plant ResourcesKunmingChina
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10
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Mota MR, Pinheiro F, Leal BSS, Wendt T, Palma-Silva C. The role of hybridization and introgression in maintaining species integrity and cohesion in naturally isolated inselberg bromeliad populations. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:122-132. [PMID: 30195257 DOI: 10.1111/plb.12909] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 09/06/2018] [Indexed: 05/02/2023]
Abstract
Hybridization is a widespread phenomenon present in numerous lineages across the tree of life. Its evolutionary consequences range from effects on the origin and maintenance, to the loss of biodiversity. We studied genetic diversity and intra- and interspecific gene flow between two sympatric populations of closely-related species, Pitcairnia flammea and P. corcovadensis (Bromeliaceae), which are adapted to naturally fragmented Neotropical inselbergs, based on nuclear and plastidial DNA. Our main results indicate a strong reproductive isolation barrier, although low levels of interspecific gene flow were observed in both sympatric populations. The low rates of intraspecific gene flow observed for both P. corcovadensis and P. flammea populations corroborate the increasing body of evidence that inselberg bromeliad species are maintained as discrete evolutionary units despite the presence of low genetic connectivity. Nuclear patterns of genetic diversity and gene flow revealed that hybridization and introgression might not cause species extinction via genetic assimilation of the rare P. corcovadensis. In the face of reduced intraspecific gene exchange, hybridization and introgression may be important aspects of the Pitcairnia diversification process, with a positive evolutionary impact at the bromeliad community level, and thus contribute to increasing and maintaining genetic diversity in local isolated inselberg populations.
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Affiliation(s)
- M R Mota
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, Brazil
| | - F Pinheiro
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - B S S Leal
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, Brazil
| | - T Wendt
- Departamento de Botânica, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - C Palma-Silva
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
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11
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Zhang N, Ma Y, Folk RA, Yu J, Pan Y, Gong X. Maintenance of species boundaries in three sympatric Ligularia (Senecioneae, Asteraceae) species. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:986-999. [PMID: 29877612 DOI: 10.1111/jipb.12674] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
The key process in speciation concerns the formation and maintenance of reproductive isolating barriers between diverging lineages. Although species boundaries are frequently investigated between two species across many taxa, reproductive isolating barriers among multiple species (>2) that would represent the most common phenomenon in nature, remain to be clarified. Here, we use double digest restriction-site associated DNA (ddRAD) sequencing to examine patterns of hybridization at a sympatric site where three Ligularia species grow together and verify whether those patterns contribute to the maintenance of boundaries among species. The results based on the RAD SNP datasets indicated hybridization Ligularia cyathiceps × L. duciformis and L. duciformis × L. yunnanensis were both restricted to F1 s plus a few first-generation backcrosses and no gene introgression were identified, giving rise to strong reproductive isolation among hybridizing species. Moreover, hybrid swarm simulation, using HYBRIDLAB, indicated the RAD SNP datasets had sufficient discriminatory power for accurate hybrid detection. We conclude that parental species show strong reproductive isolation and they still maintain species boundaries, which may be the key mechanism to maintain species diversity of Ligularia in the eastern Qinghai-Tibetan Plateau and adjacent areas. Moreover, this study highlights the effectiveness of RAD sequencing in hybridization studies.
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Affiliation(s)
- Ningning Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yongpeng Ma
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China
| | - Ryan A Folk
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Jiaojun Yu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China
| | - Yuezhi Pan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China
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12
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Grabenstein KC, Taylor SA. Breaking Barriers: Causes, Consequences, and Experimental Utility of Human-Mediated Hybridization. Trends Ecol Evol 2018; 33:198-212. [DOI: 10.1016/j.tree.2017.12.008] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 11/08/2017] [Accepted: 12/12/2017] [Indexed: 12/21/2022]
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13
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Jordan CY, Lohse K, Turner F, Thomson M, Gharbi K, Ennos RA. Maintaining their genetic distance: Little evidence for introgression between widely hybridizing species of Geum with contrasting mating systems. Mol Ecol 2018; 27:1214-1228. [PMID: 29134729 PMCID: PMC5900869 DOI: 10.1111/mec.14426] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 11/02/2017] [Accepted: 11/02/2017] [Indexed: 01/02/2023]
Abstract
Within the plant kingdom, many genera contain sister lineages with contrasting outcrossing and inbreeding mating systems that are known to hybridize. The evolutionary fate of these sister lineages is likely to be influenced by the extent to which they exchange genes. We measured gene flow between outcrossing Geum rivale and selfing Geum urbanum, sister species that hybridize in contemporary populations. We generated and used a draft genome of G. urbanum to develop dd-RAD data scorable in both species. Coalescent analysis of RAD data from allopatric populations indicated that the species diverged 2-3 Mya, and that historical gene flow between them was extremely low (1 migrant every 25 generations). Comparison of genetic divergence between species in sympatry and allopatry, together with an analysis of allele frequencies in potential parental and hybrid populations, provided no evidence of contemporary introgression in sympatric populations. Cluster- and species-specific marker analyses revealed that, apart from four early-generation hybrids, individuals in sympatric populations fell into two genetically distinct groups that corresponded exactly to their morphological species classification with maximum individual admixture estimates of only 1-3%. However, we did observe joint segregation of four putatively introgressed SNPs across two scaffolds in the G. urbanum population that was associated with significant morphological variation, interpreted as tentative evidence for rare, recent interspecific gene flow. Overall, our results indicate that despite the presence of hybrids in contemporary populations, genetic exchange between G. rivale and G. urbanum has been extremely limited throughout their evolutionary history.
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Affiliation(s)
- Crispin Y. Jordan
- Ashworth LaboratoriesInstitute of Evolutionary BiologyUniversity of EdinburghEdinburghUK
| | - Konrad Lohse
- Ashworth LaboratoriesInstitute of Evolutionary BiologyUniversity of EdinburghEdinburghUK
| | | | | | - Karim Gharbi
- Ashworth LaboratoriesEdinburgh GenomicsEdinburghUK
| | - Richard A. Ennos
- Ashworth LaboratoriesInstitute of Evolutionary BiologyUniversity of EdinburghEdinburghUK
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14
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Valderrama E, Richardson JE, Kidner CA, Madriñán S, Stone GN. Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae). Mol Phylogenet Evol 2018; 119:13-24. [DOI: 10.1016/j.ympev.2017.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/17/2017] [Accepted: 10/03/2017] [Indexed: 11/25/2022]
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15
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Zhang NN, Yu JJ, Wang YH, Gong X. Molecular evidence for asymmetric hybridization in three closely related sympatric species. AOB PLANTS 2018; 10:ply011. [PMID: 29492242 PMCID: PMC5824843 DOI: 10.1093/aobpla/ply011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 02/07/2018] [Indexed: 05/14/2023]
Abstract
Natural hybridization is common in plants and results in different evolutionary consequences to hybridizing species. Pre- and post-zygotic reproductive isolating barriers can impede hybridization between closely related species to maintain their species integrity. In Northwest Yunnan, three Ligularia species (Ligularia cyathiceps, L. duciformis and L. yunnanensis) and four types of morphologically intermediate individuals were discovered growing together in an area subject to human disturbance. In this study, we used three low-copy nuclear loci to test the natural hybridization hypothesis and the hybridization direction was ascertained by three chloroplast DNA fragments. The results indicated there were two hybridization groups at the study site, L. cyathiceps × L. duciformis and L. duciformis × L. yunnanensis, and two types of morphologically intermediate individuals were produced by L. cyathiceps and L. duciformis, and another two types were produced by L. duciformis and L. yunnanensis, while no hybrids between L. cyathiceps and L. yunnanensis were observed. Both hybridizing groups showed bidirectional but asymmetric hybridization and the factors influencing the symmetry are discussed. Most hybrids produced by the two hybridization groups seemed to be F1 generation. Hybrids with different morphologies within the same hybridization group showed similar genetic components. The results suggest that although human disturbance may promote natural hybridization among the three Ligularia species bringing them together, hybrids are limited to F1s and therefore species boundaries might be maintained.
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Affiliation(s)
- Ning-Ning Zhang
- Plant Science Institute, School of Life Sciences, Yunnan University, 650201 Kunming, Yunnan, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201 Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Jiao-Jun Yu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201 Kunming, Yunnan, China
| | - Yue-Hua Wang
- Plant Science Institute, School of Life Sciences, Yunnan University, 650201 Kunming, Yunnan, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201 Kunming, Yunnan, China
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16
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Neri J, Wendt T, Palma-Silva C. Natural hybridization and genetic and morphological variation between two epiphytic bromeliads. AOB PLANTS 2018; 10:plx061. [PMID: 29308124 PMCID: PMC5751037 DOI: 10.1093/aobpla/plx061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 11/22/2017] [Indexed: 05/18/2023]
Abstract
Reproductive isolation is of fundamental importance for maintaining species boundaries in sympatry. Here, we examine the genetic and morphological differences between two closely related bromeliad species: Vriesea simplex and Vriesea scalaris. Furthermore, we examined the occurrence of natural hybridization and discuss the action of reproductive isolation barriers. Nuclear genomic admixture suggests hybridization in sympatric populations, although interspecific gene flow is low among species in all sympatric zones (Nem < 0.5). Thus, morphological and genetic divergence (10.99 %) between species can be maintained despite ongoing natural hybridization. Cross-evaluation of our genetic and morphological data suggests that species integrity is maintained by the simultaneous action of multiple barriers, such as divergent reproductive systems among species, differences in floral traits and low hybrid seed viability.
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Affiliation(s)
- Jordana Neri
- Programa de Pós Graduação em Botânica, Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, São Cristóvão, Rio de Janeiro, RJ, Brazil
| | - Tânia Wendt
- Departamento de Botânica, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Clarisse Palma-Silva
- Programa de Pós Graduação em Ecologia, Departamento de Ecologia – Universidade Estadual Paulista Julio Mesquita Filho, Rio Claro, SP, Brazil
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17
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Hou B, Luo J, Zhang Y, Niu Z, Xue Q, Ding X. Iteration expansion and regional evolution: phylogeography of Dendrobium officinale and four related taxa in southern China. Sci Rep 2017; 7:43525. [PMID: 28262789 PMCID: PMC5337965 DOI: 10.1038/srep43525] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/27/2017] [Indexed: 11/24/2022] Open
Abstract
The genus Dendrobium was used as a case study to elucidate the evolutionary history of Orchidaceae in the Sino-Japanese Floristic Region (SJFR) and Southeast Asia region. These evolutionary histories remain largely unknown, including the temporal and spatial distribution of the evolutionary events. The present study used nuclear and plastid DNA to determine the phylogeography of Dendrobium officinale and four closely related taxa. Plastid DNA haplotype and nuclear data were shown to be discordant, suggesting reticulate evolution drove the species' diversification. Rapid radiation and genetic drift appeared to drive the evolution of D. tosaense and D. flexicaule, whereas introgression or hybridization might have been involved in the evolution of D. scoriarum and D. shixingense. The phylogeographical structure of D. officinale revealed that core natural distribution regions might have served as its glacial refuges. In recent years, human disturbances caused its artificial migration and population extinction. The five taxa may have originated from the Nanling Mountains and the Yungui Plateau and then migrated northward or eastward. After the initial iteration expansion, D. officinale populations appeared to experience the regional evolutionary patterns in different regions and follow the sequential or rapid decline in gene exchange.
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Affiliation(s)
- Beiwei Hou
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Nanjing Institute for Comprehensive Utilization of Wild Plants, Nanjing 210042, China
| | - Jing Luo
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yusi Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Jiangsu Industrial Technology Research Institute, Nanjing 210042, China
| | - Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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18
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Pinheiro F, Zanfra de Melo E Gouveia TM, Cozzolino S, Cafasso D, Cardoso-Gustavson P, Suzuki RM, Palma-Silva C. Strong but permeable barriers to gene exchange between sister species of Epidendrum. AMERICAN JOURNAL OF BOTANY 2016; 103:1472-1482. [PMID: 27519428 DOI: 10.3732/ajb.1600064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY The investigation of reproductive barriers between sister species can provide insights into how new lineages arise, and how species integrity is maintained in the face of interspecific gene flow. Different pre- and postzygotic barriers can limit interspecific gene exchange in sympatric populations, and different sources of evidence are often required to investigate the role of multiple reproductive isolation (RI) mechanisms. METHODS We tested the hypothesis of hybridization and potential introgression between Epidendrum secundum and Epidendrum xanthinum, two Neotropical food-deceptive orchid species, using nuclear and plastid microsatellites, experimental crosses, pollen tube growth observations, and genome size estimates. KEY RESULTS A large number of hybrids between E. secundum and E. xanthinum were detected, suggesting weak premating barriers. The low fertility of hybrid plants and the absence of haplotype sharing between parental species indicated strong postmating barriers, reducing interspecific gene exchange and the development of advanced generation hybrids. Despite the strength of reproductive barriers, fertile seeds were produced in some backcrossing experiments, and the existence of interspecific gene exchange could not be excluded. CONCLUSIONS Strong but permeable barriers were found between E. secundum and E. xanthinum. Indeed, haplotype sharing was not detected between parental species, suggesting that introgression is limited by a combination of genic incompatibilities, including negative cytonuclear interactions. Most taxonomic uncertainties in this group were potentially influenced by incomplete RI barriers between species, which mainly occurred sympatrically.
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Affiliation(s)
- Fábio Pinheiro
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas 13083-862, Campinas, SP, Brazil Instituto de Botânica, Núcleo de Pesquisa do Orquidário do Estado04301-902, São Paulo, SP, Brazil
| | | | - Salvatore Cozzolino
- Dipartimento di Biologia, Complesso Universitario di Monte S. Ângelo, Università degli Studidi Napoli Federico II 80100 Napoli, Italy Institute for Sustenible Plant Protection, Consiglio Nazionale delle Ricerche, Via Madonna del Piano 10, I-50019 Sesto Fiorentino (FI), Italy
| | - Donata Cafasso
- Dipartimento di Biologia, Complesso Universitario di Monte S. Ângelo, Università degli Studidi Napoli Federico II 80100 Napoli, Italy
| | | | - Rogério Mamoru Suzuki
- Instituto de Botânica, Núcleo de Pesquisa do Orquidário do Estado04301-902, São Paulo, SP, Brazil
| | - Clarisse Palma-Silva
- Departamento de Ecologia, Universidade Estadual Paulista 13506-900, Rio Claro, SP, Brazil
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