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Campos M, Kelley E, Gravendeel B, Médail F, Maarten Christenhusz JM, Fay MF, Catalán P, Leitch IJ, Forest F, Wilkin P, Viruel J. Genomic, spatial and morphometric data for discrimination of four species in the Mediterranean Tamus clade of yams (Dioscorea, Dioscoreaceae). ANNALS OF BOTANY 2023; 131:635-654. [PMID: 36681900 PMCID: PMC10147332 DOI: 10.1093/aob/mcad018] [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: 10/22/2022] [Accepted: 01/23/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Among the numerous pantropical species of the yam genus, Dioscorea, only a small group occurs in the Mediterranean basin, including two narrow Pyrenean endemics (Borderea clade) and two Mediterranean-wide species (D. communis and D. orientalis, Tamus clade). However, several currently unrecognized species and infraspecific taxa have been described in the Tamus clade due to significant morphological variation associated with D. communis. Our overarching aim was to investigate taxon delimitation in the Tamus clade using an integrative approach combining phylogenomic, spatial and morphological data. METHODS We analysed 76 herbarium samples using Hyb-Seq genomic capture to sequence 260 low-copy nuclear genes and plastomes, together with morphometric and environmental modelling approaches. KEY RESULTS Phylogenomic reconstructions confirmed that the two previously accepted species of the Tamus clade, D. communis and D. orientalis, are monophyletic and form sister clades. Three subclades showing distinctive geographic patterns were identified within D. communis. These subclades were also identifiable from morphometric and climatic data, and introgression patterns were inferred between subclades in the eastern part of the distribution of D. communis. CONCLUSIONS We propose a taxonomy that maintains D. orientalis, endemic to the eastern Mediterranean region, and splits D. communis sensu lato into three species: D. edulis, endemic to Macaronesia (Canary Islands and Madeira); D. cretica, endemic to the eastern Mediterranean region; and D. communis sensu stricto, widespread across western and central Europe. Introgression inferred between D. communis s.s. and D. cretica is likely to be explained by their relatively recent speciation at the end of the Miocene, disjunct isolation in eastern and western Mediterranean glacial refugia and a subsequent westward recolonization of D. communis s.s. Our study shows that the use of integrated genomic, spatial and morphological approaches allows a more robust definition of species boundaries and the identification of species that previous systematic studies failed to uncover.
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Affiliation(s)
- Miguel Campos
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
- Department of Plant Biology and Ecology, University of Seville, 41012, Spain
- Universidad de Zaragoza-Escuela Politécnica Superior de Huesca, 22071, Huesca, Spain
| | - Emma Kelley
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
| | - Barbara Gravendeel
- Naturalis Biodiversity Center, Leiden 2333 CR, The Netherlands
- Radboud Institute for Biological and Environmental Sciences, RIBES 6500 GL, Nijmegen, The Netherlands
| | - Frédéric Médail
- Institut Méditerranéen de Biodiversité et d’Écologie marine et continentale (IMBE), Aix Marseille University, Avignon University, CNRS, IRD, Campus Aix, Technopôle de l’Environnement Arbois-Méditerranée, F-13545 Aix-en-Provence cedex 4, France
| | | | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Pilar Catalán
- Universidad de Zaragoza-Escuela Politécnica Superior de Huesca, 22071, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza 50018, Spain
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
| | - Juan Viruel
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
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Nagasawa K, Fukumoto S, Setoguchi H, Ishihara M, Hiratsuka KI, Masuda K, Sakaguchi S. Genetic purity of a rear-edge population of Carex podogyna Franch. et Sav. (Cyperaceae) maintained under interspecific hybridization. Gene 2022; 97:93-99. [PMID: 35545526 DOI: 10.1266/ggs.21-00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Interspecific hybridization is a critical issue in conservation biology because it may drive small populations to extinction through direct or indirect processes. In this study, to develop a conservation strategy for an endangered rear-edge population of Carex podogyna in Ashiu, Kyoto, Japan, we performed a molecular genetic analysis of the wild population and an ex-situ population established from wild seeds. Microsatellite genotypic data revealed a complete loss of genetic diversity in the wild population, suggesting that it has long been prone to genetic drift due to isolation as a small population. In contrast, microsatellite analysis of 13 ex-situ individuals detected multiple alleles that are not harbored in the wild C. podogyna population. Sequence analysis revealed that these individuals are likely natural hybrids between C. podogyna and a co-occurring species, C. curvicollis, although established hybrids have never been found in the natural habitat. Based on our observation of variegated leaves in hybrid individuals, we propose that hybrids have been excluded by natural selection and/or interspecific competition caused by insufficient productivity of photosynthesis, although other genetic and ecological factors may also be influential. Overall, this study indicates that natural mechanisms selectively removing the hybrids have maintained the genetic purity of this rear-edge population of C. podogyna, and also emphasizes the importance of genetic assessment in ex-situ conservation programs.
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Affiliation(s)
- Koki Nagasawa
- Graduate School of Human and Environmental Studies, Kyoto University
| | | | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University
| | - Masae Ishihara
- Ashiu Forest Research Station, Field Science Education and Research Center, Kyoto University
| | | | - Kazutoshi Masuda
- Graduate School of Human and Environmental Studies, Kyoto University
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University
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Muniz AC, Pimenta RJG, Cruz MV, Rodrigues JG, Buzatti RSDO, Heuertz M, Lemos‐Filho JP, Lovato MB. Hybrid zone of a tree in a Cerrado/Atlantic Forest ecotone as a hotspot of genetic diversity and conservation. Ecol Evol 2022; 12:e8540. [PMID: 35127043 PMCID: PMC8803295 DOI: 10.1002/ece3.8540] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 12/17/2021] [Indexed: 01/10/2023] Open
Abstract
The Cerrado, the largest Neotropical savanna, and the Brazilian Atlantic Forest form large ecotonal areas where savanna and forest habitats occupy adjacent patches with closely related species occurring side by side, providing opportunities for hybridization. Here, we investigated the evolutionary divergence between the savanna and forest ecotypes of the widely distributed tree Plathymenia reticulata (n = 233 individuals). Genetic structure analysis of P. reticulata was congruent with the recognition of two ecotypes, whose divergence captured the largest proportion of genetic variance in the data (F CT = 0.222 and F ST = 0.307). The ecotonal areas between the Cerrado and the Atlantic Forest constitute a hybrid zone in which a diversity of hybrid classes was observed, most of them corresponding to second-generation hybrids (F2) or backcrosses. Gene flow occurred mainly toward the forest ecotype. The genetic structure was congruent with isolation by environment, and environmental correlates of divergence were identified. The observed pattern of high genetic divergence between ecotypes may reflect an incipient speciation process in P. reticulata. The low genetic diversity of the P. reticulata forest ecotype indicate that it is threatened in areas with high habitat loss on Atlantic Forest. In addition, the high divergence from the savanna ecotype suggests it should be treated as a different unit of management. The high genetic diversity found in the ecotonal hybrid zone supports the view of ecotones as important areas for the origin and conservation of biodiversity in the Neotropics.
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Affiliation(s)
- André Carneiro Muniz
- Departamento de Genética, Ecologia e EvoluçãoUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | - Mariana Vargas Cruz
- Departamento de Genética, Ecologia e EvoluçãoUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | | | | | - José P. Lemos‐Filho
- Departamento de BotânicaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Maria Bernadete Lovato
- Departamento de Genética, Ecologia e EvoluçãoUniversidade Federal de Minas GeraisBelo HorizonteBrazil
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Chan KO, Hutter CR, Wood PL, Grismer LL, Das I, Brown RM. Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex. Mol Ecol 2020; 29:3970-3987. [PMID: 32808335 DOI: 10.1111/mec.15603] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 07/29/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]
Abstract
Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic inference and species delimitation, the influence of these processes is not frequently evaluated. Using large numbers of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional SDMs with more robust genomic analyses that assess population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergence in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7%-10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high levels of cryptic diversity observed in other amphibian groups reflect distinct cryptic species-or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes nonsister) sympatric lineages-a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed "cryptic" groups should not rely solely on conventional SDMs, but should necessarily examine population structure and gene flow to avoid taxonomic inflation.
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Affiliation(s)
- Kin O Chan
- Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, Singapore
| | - Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Perry L Wood
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, AL, USA
| | - L L Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, CA, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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Muniz AC, Lemos-Filho JP, Souza HA, Marinho RC, Buzatti RS, Heuertz M, Lovato MB. The protected tree Dimorphandra wilsonii (Fabaceae) is a population of inter-specific hybrids: recommendations for conservation in the Brazilian Cerrado/Atlantic Forest ecotone. ANNALS OF BOTANY 2020; 126:191-203. [PMID: 32277237 PMCID: PMC7304468 DOI: 10.1093/aob/mcaa066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 04/09/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUNDS AND AIMS Dimorphandra wilsonii Rizzini, a critically endangered and protected tree, has a restricted distribution in the ecotone between the Cerrado and the Atlantic Forest in south-eastern Brazil. In this area, it co-occurs with D. mollis Benth., a common tree from the Cerrado, and D. exaltata Schott., a rare tree from the Atlantic Forest. Previous studies of D. wilsonii indicated heterozygosity excess at the individual level. Field observation of some intermediate phenotypes between D. wilsonii and both congeners suggests hybridization of D. wilsonii with D. mollis and/or D. exaltata. Here, we tested the hypothesis that D. wilsonii may have originated from hybridization between D. exaltata and D. mollis. We also performed cytogenetic analysis to examine if the heterozygosity excess could be explained by polyploidy in D. wilsonii. METHODS We evaluated the genetic diversity and population structure of D. wilsonii using 11 nuclear simple sequence repeats (SSRs) genotyped in 152 individuals sampled across the taxon's range. We performed comparative genetic analyses using overlapping SSR markers between D. wilsonii and previously published SSR data in D. mollis and D. exaltata to subsequently perform a series of allelic comparisons, multivariate and Bayesian analysis. KEY RESULTS Our results suggest that D. wilsonii individuals are most likely to correspond to F1 hybrids between D. exaltata and D. mollis. Cytogenetic analysis indicated that D. wilsonii is diploid with the same chromosome number as D. mollis (2n = 2x = 28). CONCLUSIONS Our study raises questions about the taxonomic status and the evolutionary future of D. wilsonii. We suggest that the conservation and management strategy for D. wilsonii should be revised and that it should take into account both parental Dimorphandra species in the ecotone, with special emphasis on the threatened D. exaltata. Finally, this study highlights the value of genetic information for the design of conservation strategies.
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Affiliation(s)
- André Carneiro Muniz
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP, Belo Horizonte, Brazil
| | - José Pires Lemos-Filho
- Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Helena Augusta Souza
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP, Belo Horizonte, Brazil
| | | | - Renata Santiago Buzatti
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP, Belo Horizonte, Brazil
| | | | - Maria Bernadete Lovato
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP, Belo Horizonte, Brazil
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Centeno‐Cuadros A, Razgour O, García‐Mudarra JL, Mingo‐Casas P, Sandonís V, Redondo A, Ibáñez C, Paz O, Martinez‐Alós S, Pérez Suarez G, Echevarría JE, Juste J. Comparative phylogeography and asymmetric hybridization between cryptic bat species. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12318] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
| | - Orly Razgour
- Biological Sciences University of Southampton Southampton UK
| | | | | | | | - Adrián Redondo
- Departmento de Ecología Evolutiva Estación Biológica de Doñana (CSIC) Sevilla Spain
| | - Carlos Ibáñez
- Departmento de Ecología Evolutiva Estación Biológica de Doñana (CSIC) Sevilla Spain
| | - Oscar Paz
- Departamento de Ciencias de la Vida, Facultad de Ciencias Universidad de Alcalá Alcalá de Henares, Madrid Spain
| | - Susana Martinez‐Alós
- Departamento de Ciencias de la Vida, Facultad de Ciencias Universidad de Alcalá Alcalá de Henares, Madrid Spain
| | - Gonzalo Pérez Suarez
- Departamento de Ciencias de la Vida, Facultad de Ciencias Universidad de Alcalá Alcalá de Henares, Madrid Spain
| | - Juan E. Echevarría
- Instituto de Salud Carlos III Majadahonda, Madrid Spain
- CIBER de Epidemiología y Salud Pública, CIBERESP Madrid Spain
| | - Javier Juste
- Departmento de Ecología Evolutiva Estación Biológica de Doñana (CSIC) Sevilla Spain
- CIBER de Epidemiología y Salud Pública, CIBERESP Madrid Spain
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Maguilla E, Escudero M, Hipp AL, Luceño M. Allopatric speciation despite historical gene flow: Divergence and hybridization in Carex furva and C. lucennoiberica (Cyperaceae) inferred from plastid and nuclear RAD-seq data. Mol Ecol 2017; 26:5646-5662. [PMID: 28742230 DOI: 10.1111/mec.14253] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/29/2017] [Accepted: 06/30/2017] [Indexed: 12/13/2022]
Abstract
Gene flow among incipient species can act as a creative or destructive force in the speciation process, generating variation on which natural selection can act while, potentially, undermining population divergence. The flowering plant genus Carex exhibits a rapid and relatively recent radiation with many species limits still unclear. This is the case with the Iberian Peninsula (Spain and Portugal)-endemic C. lucennoiberica, which lay unrecognized within Carex furva until its recent description as a new species. In this study, we test how these species were impacted by interspecific gene flow during speciation. We sampled the full range of distribution of C. furva (15 individuals sampled) and C. lucennoiberica (88 individuals), sequenced two cpDNA regions (atpI-atpH, psbA-trnH) and performed genomic sequencing of 45,100 SNPs using restriction site-associated DNA sequencing (RAD-seq). We utilized a set of partitioned D-statistic tests and demographic analyses to study the degree and direction of introgression. Additionally, we modelled species distributions to reconstruct changes in range distribution during glacial and interglacial periods. Plastid, nuclear and morphological data strongly support divergence between species with subsequent gene flow. Combined with species distribution modelling, these data support a scenario of allopatry leading to species divergence, followed by secondary contact and gene flow due to long-distance dispersal and/or range expansions and contractions in response to Quaternary glacial cycles. We conclude that this is a case of allopatric speciation despite historical secondary contacts, which could have temporally influenced the speciation process, contributing to the knowledge of forces that are driving or counteracting speciation.
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Affiliation(s)
| | - Marcial Escudero
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Seville, Spain
| | - Andrew L Hipp
- The Morton Arboretum, Lisle, IL, USA.,Botany Department, Field Museum of Natural History, Chicago, IL, USA
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Maguilla E, Escudero M. Correction: Cryptic Species Due to Hybridization: A Combined Approach to Describe a New Species (Carex: Cyperaceae). PLoS One 2017; 12:e0172079. [PMID: 28182788 PMCID: PMC5300142 DOI: 10.1371/journal.pone.0172079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0166949.].
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