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Valdés-Florido A, González-Toral C, Maguilla E, Cires E, Díaz-Lifante Z, Andrés-Camacho C, Nieto Feliner G, Arroyo J, Escudero M. Polyploidy and hybridization in the Mediterranean: unravelling the evolutionary history of Centaurium (Gentianaceae). Ann Bot 2024:mcae066. [PMID: 38687133 DOI: 10.1093/aob/mcae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND AND AIMS Polyploidy is considered one of the main mechanisms of plant evolution and speciation. In the Mediterranean basin, polyploidy has contributed to making this region a biodiversity hotspot, along with its geological and climatic history and other ecological and biogeographic factors. The Mediterranean genus Centaurium Hill (Gentianaceae) comprises ca. 25 species, of which 60% are polyploids, including tetraploids and hexaploids. To date, the evolutionary history of centauries has been studied using Sanger sequencing phylogenies, which have been insufficient to fully understand the phylogenetic relationships in this lineage. The goal of this study is to gain a better understanding of the evolutionary history of Centaurium by exploring the mechanisms that have driven its diversification, specifically hybridization and polyploidy. We aim at identifying the parentage of hybrid species, at the species or clade level, as well as assessing whether morphological traits are associated with particular ploidy levels. METHODS We sequenced RADseq markers from 42 samples of 28 Centaurium taxa, and performed phylogenomic analyses using maximum likelihood, summary coalescent SVDquartets and NeighborNet approaches. To identify hybrid taxa, we used Phylonetworks and the fastStructure algorithm. To infer the putative parental species of the allopolyploids, we employed genomic analyses (SNIPloid). The association between different traits and particular ploidy levels was explored with NMDS. KEY RESULTS Our phylogenetic analyses confirmed the long-suspected occurrence of recurrent hybridization. The allopolyploid origin of the tetraploid C. serpentinicola and the hexaploids C. mairei, C. malzacianum and C. centaurioides were also confirmed, unlike that of C. discolor. We inferred additional signatures of hybridization events within the genus and identified morphological traits differentially distributed in different ploidy levels. CONCLUSIONS This study highlights the important role that hybridization has played in the evolution of a Mediterranean genus such as Centaurium, leading to a polyploid complex, which facilitated its diversification and may exemplify that of other Mediterranean groups.
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Affiliation(s)
- Ana Valdés-Florido
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, 41012, Seville, Spain
| | | | - Enrique Maguilla
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, 41013, Seville, Spain
| | - Eduardo Cires
- Department of Organisms and Systems Biology, University of Oviedo, 33071, Oviedo, Spain
- Institute of Natural Resources and Territorial Planning (INDUROT), Campus de Mieres, 33600 Mieres, Spain
| | - Zoila Díaz-Lifante
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, 41012, Seville, Spain
| | - Cristina Andrés-Camacho
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, 41012, Seville, Spain
| | | | - Juan Arroyo
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, 41012, Seville, Spain
| | - Marcial Escudero
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, 41012, Seville, Spain
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Nieto Feliner G, Criado Ruiz D, Álvarez I, Villa-Machío I. The puzzle of plant hybridisation: a high propensity to hybridise but few hybrid zones reported. Heredity (Edinb) 2023; 131:307-315. [PMID: 37884616 PMCID: PMC10673867 DOI: 10.1038/s41437-023-00654-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
An interesting conundrum was recently revealed by R. Abbott when he found that the number of hybrid zones reported in the literature for plants is very low, given the propensity of plants to hybridise. In another literature survey on hybrid zones performed over the period 1970-2022, we found that the number of hybrid zones reported for vertebrates was 2.3 times greater than that reported for vascular plants, even though there are about six times more vascular plant species than vertebrates. Looking at the number of papers reporting hybrid zones, there are 4.9 times more on vertebrates than on vascular plants. These figures support the relevance of this conundrum. In this paper we aim to shed light on this question by providing a structured discussion of the causes that may underlie this conundrum. We propose six non-mutually exclusive factors, namely lack or deficit of spatial structure, lack or deficit of genetic structure, effects of hybridisation between non-closely related species, lability of plant hybrid zones over time, botanists' perception of hybridisation, and deficit of population genetic data. There does not appear to be a single factor that explains our puzzle, which applies to all cases of plants where hybridisation is detected but no hybrid zone is reported. It is argued that some plant features suggest that the puzzle is not, at least entirely, due to insufficient knowledge of the specific cases, a hypothesis that should be addressed with a wider range of empirical data across different taxonomic groups.
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Affiliation(s)
| | - David Criado Ruiz
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo 2, 28014, Madrid, Spain
| | - Inés Álvarez
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo 2, 28014, Madrid, Spain
| | - Irene Villa-Machío
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo 2, 28014, Madrid, Spain
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Villa-Machío I, Heuertz M, Álvarez I, Nieto Feliner G. Demography-driven and adaptive introgression in a hybrid zone of the Armeria syngameon. Mol Ecol 2023. [PMID: 37837272 DOI: 10.1111/mec.17167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/30/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023]
Abstract
Syngameons represent networks of otherwise distinct species connected by limited gene exchange. Although most studies have focused on how species maintain their cohesiveness despite gene flow, there are additional relevant questions regarding the evolutionary dynamics of syngameons and their drivers, as well as the success of their members and the network as a whole. Using a ddRADseq approach, we analysed the genetic structure, genomic clines and demographic history of a coastal hybrid zone involving two species of the Armeria (Plumbaginaceae) syngameon in southern Spain. We inferred that a peripheral population of the sand dune-adapted A. pungens diverged from the rest of the conspecific populations and subsequently hybridized with a locally more abundant pinewood congener, A. macrophylla. Both species display extensive plastid DNA haplotype sharing. Genomic cline analysis identified bidirectional introgression, but more outlier loci with excess A. pungens than A. macrophylla ancestry, suggesting the possibility of selection for A. pungens alleles. This is consistent with the finding that the A. pungens phenotype is selected for in open habitats, and with the strong correlation found between ancestry and phenotype. Taken together, our analyses suggest an intriguing scenario in which bidirectional introgression may, on the one hand, help to avoid reduced levels of genetic diversity due to the small size and isolated location of the A. pungens range-edge population, thereby minimizing demographic risks of stochastic extinction. On the other hand, the data also suggest that introgression into A. macrophylla may allow individuals to grow in open, highly irradiated, deep sandy, salt-exposed habitats.
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Affiliation(s)
- Irene Villa-Machío
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| | | | - Inés Álvarez
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| | - Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB), CSIC, Madrid, Spain
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Nieto Feliner G, Cellinese N, Crowl AA, Frajman B. Editorial: Understanding plant diversity and evolution in the Mediterranean Basin. Front Plant Sci 2023; 14:1152340. [PMID: 36866359 PMCID: PMC9972075 DOI: 10.3389/fpls.2023.1152340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| | - Nico Cellinese
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
| | - Andrew A. Crowl
- Department of Biology, Duke University, Durham, NC, United States
| | - Božo Frajman
- Department of Botany, University of Innsbruck, Innsbruck, Austria
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Baumel A, Nieto Feliner G, Médail F, La Malfa S, Di Guardo M, Bou Dagher Kharrat M, Lakhal-Mirleau F, Frelon V, Ouahmane L, Diadema K, Sanguin H, Viruel J. Genome-wide footprints in the carob tree (Ceratonia siliqua) unveil a new domestication pattern of a fruit tree in the Mediterranean. Mol Ecol 2022; 31:4095-4111. [PMID: 35691023 PMCID: PMC9541536 DOI: 10.1111/mec.16563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 05/13/2022] [Accepted: 06/08/2022] [Indexed: 12/22/2022]
Abstract
Intense research efforts over the last two decades have renewed our understanding of plant phylogeography and domestication in the Mediterranean basin. Here we aim to investigate the evolutionary history and the origin of domestication of the carob tree (Ceratonia siliqua), which has been cultivated for millennia for food and fodder. We used >1000 microsatellite genotypes to delimit seven carob evolutionary units (CEUs). We investigated genome‐wide diversity and evolutionary patterns of the CEUs with 3557 single nucleotide polymorphisms generated by restriction‐site associated DNA sequencing (RADseq). To address the complex wild vs. cultivated status of sampled trees, we classified 56 sampled populations across the Mediterranean basin as wild, seminatural or cultivated. Nuclear and cytoplasmic loci were identified from RADseq data and separated for analyses. Phylogenetic analyses of these genomic‐wide data allowed us to resolve west‐to‐east expansions from a single long‐term refugium probably located in the foothills of the High Atlas Mountains near the Atlantic coast. Our findings support multiple origins of domestication with a low impact on the genetic diversity at range‐wide level. The carob was mostly domesticated from locally selected wild genotypes and scattered long‐distance westward dispersals of domesticated varieties by humans, concomitant with major historical migrations by Romans, Greeks and Arabs. Ex situ efforts to preserve carob genetic resources should prioritize accessions from both western and eastern populations, with emphasis on the most differentiated CEUs situated in southwest Morocco, south Spain and eastern Mediterranean. Our study highlights the relevance of wild and seminatural habitats in the conservation of genetic resources for cultivated trees.
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Affiliation(s)
- Alex Baumel
- Aix Marseille University, Avignon University, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Faculté des Sciences et Techniques St-Jérôme, Marseille, France
| | | | - Frédéric Médail
- Aix Marseille University, Avignon University, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Faculté des Sciences et Techniques St-Jérôme, Marseille, France
| | - Stefano La Malfa
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Mario Di Guardo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Magda Bou Dagher Kharrat
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Beirut, Lebanon
| | - Fatma Lakhal-Mirleau
- Aix Marseille University, Avignon University, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Faculté des Sciences et Techniques St-Jérôme, Marseille, France
| | - Valentine Frelon
- Aix Marseille University, Avignon University, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Faculté des Sciences et Techniques St-Jérôme, Marseille, France
| | - Lahcen Ouahmane
- Faculté des Sciences Semlalia, Laboratoire de Biotechnologies Microbiennes Agrosciences et Environnement, Université Cadi Ayyad Marrakech, Marrakech, Morocco
| | - Katia Diadema
- Conservatoire Botanique National Méditerranéen de Porquerolles (CBNMed), Hyères, France
| | - Hervé Sanguin
- CIRAD, UMR PHIM, Montpellier, France.,PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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Maravilla AJ, Rosato M, Álvarez I, Nieto Feliner G, Rosselló JA. Interstitial Arabidopsis-Type Telomeric Repeats in Asteraceae. Plants (Basel) 2021; 10:plants10122794. [PMID: 34961265 PMCID: PMC8705333 DOI: 10.3390/plants10122794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 05/13/2023]
Abstract
Tandem repeats of telomeric-like motifs at intra-chromosomal regions, known as interstitial telomeric repeats (ITR), have drawn attention as potential markers of structural changes, which might convey information about evolutionary relationships if preserved through time. Building on our previous work that reported outstanding ITR polymorphisms in the genus Anacyclus, we undertook a survey across 132 Asteraceae species, focusing on the six most speciose subfamilies and considering all the ITR data published to date. The goal was to assess whether the presence, site number, and chromosomal location of ITRs convey any phylogenetic signal. We conducted fluorescent in situ hybridization (FISH) using an Arabidopsis-type telomeric sequence as a probe on karyotypes obtained from mitotic chromosomes. FISH signals of ITR sites were detected in species of subfamilies Asteroideae, Carduoideae, Cichorioideae, Gymnarhenoideae, and Mutisioideae, but not in Barnadesioideae. Although six small subfamilies have not yet been sampled, altogether, our results suggest that the dynamics of ITR formation in Asteraceae cannot accurately trace the complex karyological evolution that occurred since the early diversification of this family. Thus, ITRs do not convey a reliable signal at deep or shallow phylogenetic levels and cannot help to delimitate taxonomic categories, a conclusion that might also hold for other important families such as Fabaceae.
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Affiliation(s)
- Alexis J. Maravilla
- Jardín Botánico, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, c/Quart 80, E-46008 Valencia, Spain; (A.J.M.); (M.R.)
| | - Marcela Rosato
- Jardín Botánico, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, c/Quart 80, E-46008 Valencia, Spain; (A.J.M.); (M.R.)
| | - Inés Álvarez
- Real Jardín Botánico (RJB), Consejo Superior de Investigaciones Científicas (CSIC), Plaza de Murillo 2, E-28014 Madrid, Spain; (I.Á.); (G.N.F.)
| | - Gonzalo Nieto Feliner
- Real Jardín Botánico (RJB), Consejo Superior de Investigaciones Científicas (CSIC), Plaza de Murillo 2, E-28014 Madrid, Spain; (I.Á.); (G.N.F.)
| | - Josep A. Rosselló
- Jardín Botánico, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, c/Quart 80, E-46008 Valencia, Spain; (A.J.M.); (M.R.)
- Correspondence: ; Tel.: +34-963-156-800
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Criado Ruiz D, Villa Machío I, Herrero Nieto A, Nieto Feliner G. Hybridization and cryptic speciation in the Iberian endemic plant genus Phalacrocarpum (Asteraceae-Anthemideae). Mol Phylogenet Evol 2020; 156:107024. [PMID: 33271372 DOI: 10.1016/j.ympev.2020.107024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 01/28/2023]
Abstract
Understanding the role and impact of reticulation in phylogenetic inquiry has improved with extended use of high throughput sequencing data. Yet, due to the dynamism of genomes over evolutionary time, disentangling old hybridization events remains a serious challenge. Phalacrocarpum (DC.) Willk. is one of the 27 Iberian endemic plant genera, currently considered monotypic but including three subspecies. Its uncertain phylogenetic relationships within tribe Anthemideae (Asteraceae) point to an Early Miocene divergence from its sister group, and its persistent taxonomic instability has been proposed to be due to hybridization. We aim at understanding the evolutionary history of this genus using SNPs called from a genotyping-by-sequencing (GBS) analysis, Sanger sequences-from three plastid DNA regions (psbJ-petA, petB-petD, trnH-psbA) and the nuclear ribosomal ITS regions (cloned)-as well as leaf morphometric multivariate analysis. SNP data and Sanger sequences strongly support the unforeseen existence of a cryptic species in the eastern populations of P. oppositifolium subsp. anomalum. Broad molecular and morphometric patterns of variation found in conflictive populations from the Sanabria Valley region convincingly identify a recent previously undocumented hybrid zone. By contrast, evidence is less conclusive on relationships between subspecies hoffmannseggii, oppositifolium and a second conflictive group distributed along the Galician-Portuguese border (Orense massifs). Although genetic clustering analysis of SNP data suggests that the former subspecies was the maternal progenitor in hybridization events that gave rise to the other two groups, we found considerable uniqueness of ITS ribotypes and plastid haplotypes in them. This result, in the context of Pleistocene climatically-driven range shifts in NW Iberian Peninsula, can be due to periods of isolation, genetic bottlenecks and drift superimposed on old hybridization events. Our study confirms the idea that unravelling old hybridization events may be compromised by the suite of evolutionary processes accumulated subsequently, particularly in areas with a history of climatic instability.
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Affiliation(s)
- David Criado Ruiz
- Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014 Madrid, Spain.
| | - Irene Villa Machío
- Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014 Madrid, Spain
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Abstract
It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically recognized as significant in speciation and adaptation, recognition of the importance of interspecific gene flow has dramatically increased during the genomics era, concomitant with an unending flood of empirical examples, with or without genome doubling. Interspecific gene flow is thus increasingly thought to lead to evolutionary innovation and diversification, via adaptive introgression, homoploid hybrid speciation and allopolyploid speciation. Less well understood, however, are the suite of genetic and genomic mechanisms set in motion by the merger of differentiated genomes, and the temporal scale over which recombinational complexity mediated by gene flow might be expressed and exposed to natural selection. We focus on these issues here, considering the types of molecular genetic and genomic processes that might be set in motion by the saltational event of genome merger between two diverged species, either with or without genome doubling, and how these various processes can contribute to novel phenotypes. Genetic mechanisms include the infusion of new alleles and the genesis of novel structural variation including translocations and inversions, homoeologous exchanges, transposable element mobilization and novel insertional effects, presence-absence variation and copy number variation. Polyploidy generates massive transcriptomic and regulatory alteration, presumably set in motion by disrupted stoichiometries of regulatory factors, small RNAs and other genome interactions that cascade from single-gene expression change up through entire networks of transformed regulatory modules. We highlight both these novel combinatorial possibilities and the range of temporal scales over which such complexity might be generated, and thus exposed to natural selection and drift.
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Affiliation(s)
- Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico, CSIC, Madrid, Spain
| | - Josep Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Barcelona, Spain
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
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Vitales D, Álvarez I, Garcia S, Hidalgo O, Nieto Feliner G, Pellicer J, Vallès J, Garnatje T. Genome size variation at constant chromosome number is not correlated with repetitive DNA dynamism in Anacyclus (Asteraceae). Ann Bot 2020; 125:611-623. [PMID: 31697800 PMCID: PMC7103019 DOI: 10.1093/aob/mcz183] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/06/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Changes in the amount of repetitive DNA (dispersed and tandem repeats) are considered the main contributors to genome size variation across plant species in the absence of polyploidy. However, the study of repeatome dynamism in groups showing contrasting genomic features and complex evolutionary histories is needed to determine whether other processes underlying genome size variation may have been overlooked. The main aim here was to elucidate which mechanism best explains genome size evolution in Anacyclus (Asteraceae). METHODS Using data from Illumina sequencing, we analysed the repetitive DNA in all species of Anacyclus, a genus with a reticulate evolutionary history, which displays significant genome size and karyotype diversity albeit presenting a stable chromosome number. KEY RESULTS By reconstructing ancestral genome size values, we inferred independent episodes of genome size expansions and contractions during the evolution of the genus. However, analysis of the repeatome revealed a similar DNA repeat composition across species, both qualitative and quantitative. Using comparative methods to study repeatome dynamics in the genus, we found no evidence for repeat activity causing genome size variation among species. CONCLUSIONS Our results, combined with previous cytogenetic data, suggest that genome size differences in Anacyclus are probably related to chromosome rearrangements involving losses or gains of chromosome fragments, possibly associated with homoploid hybridization. These could represent balanced rearrangements that do not disrupt gene dosage in merged genomes, for example via chromosome segment exchanges.
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Affiliation(s)
- Daniel Vitales
- Institut Botànic de Barcelona (IBB, CSIC-ICUB), Passeig del Migdia sn, 08038 Barcelona, Catalonia, Spain
- For correspondence. Email
| | - Inés Álvarez
- Department of Biodiversity and Conservation, Real Jardín Botánico (CSIC), Plaza de Murillo 2, 28014 Madrid, Spain
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB, CSIC-ICUB), Passeig del Migdia sn, 08038 Barcelona, Catalonia, Spain
| | - Oriane Hidalgo
- Laboratori de Botànica – Unitat associada CSIC, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27–31, 08028 Barcelona, Catalonia, Spain
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, UK
| | - Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico (CSIC), Plaza de Murillo 2, 28014 Madrid, Spain
| | - Jaume Pellicer
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, UK
| | - Joan Vallès
- Laboratori de Botànica – Unitat associada CSIC, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27–31, 08028 Barcelona, Catalonia, Spain
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB, CSIC-ICUB), Passeig del Migdia sn, 08038 Barcelona, Catalonia, Spain
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Escudero M, Nieto Feliner G, Pokorny L, Spalink D, Viruel J. Editorial: Phylogenomic Approaches to Deal With Particularly Challenging Plant Lineages. Front Plant Sci 2020; 11:591762. [PMID: 33329657 PMCID: PMC7732580 DOI: 10.3389/fpls.2020.591762] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/02/2020] [Indexed: 05/08/2023]
Affiliation(s)
- Marcial Escudero
- Department of Plant Biology and Ecology, University of Seville, Seville, Spain
- *Correspondence: Marcial Escudero
| | - Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico, CSIC, Madrid, Spain
| | - Lisa Pokorny
- Department of Biodiversity and Conservation, Real Jardín Botánico, CSIC, Madrid, Spain
- Centre for Plant Biotechnology and Genomics (CBGP), Technical University of Madrid (UPM)-National Institute of Agriculture and Food Research and Technology (INIA), Madrid, Spain
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Daniel Spalink
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, United States
| | - Juan Viruel
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
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Moharrek F, Sanmartín I, Kazempour-Osaloo S, Nieto Feliner G. Morphological Innovations and Vast Extensions of Mountain Habitats Triggered Rapid Diversification Within the Species-Rich Irano-Turanian Genus Acantholimon (Plumbaginaceae). Front Genet 2019; 9:698. [PMID: 30745908 PMCID: PMC6360523 DOI: 10.3389/fgene.2018.00698] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/12/2018] [Indexed: 01/24/2023] Open
Abstract
The Irano-Turanian floristic region spans a topographically complex and climatically continental territory, which has served as a source of xerophytic taxa for neighboring regions and is represented by a high percent of endemics. Yet, a comprehensive picture of the abiotic and biotic factors that have driven diversification within this biota remains to be established due to the scarcity of phylogenetic studies. Acantholimon is an important component of the subalpine steppe flora of the Irano-Turanian region, containing c. 200 cushion-forming sub-shrubby pungent-leaved species. Our recent molecular phylogenetic study has led to enlarging the circumscription of this genus to include eight mono- or oligospecific genera lacking the characteristic life-form and leaves. Using the same molecular phylogeny, here we investigate the tempo and mode of diversification as well as the biogeographic patterns in this genus, to test the hypothesis that a combination of key morphological innovations and abiotic factors is behind Acantholimon high species diversity. Molecular dating analysis indicates that Acantholimon s.l. started to diversify between the Late Miocene and the Pliocene and the biogeographic analysis points to an Eastern Iran-Afghanistan origin. Macroevolutionary models support the hypothesis that the high diversity of the genus is explained by accelerated diversification rates in two clades associated with the appearance of morphological key innovations such as a cushion life-form and pungent leaves; this would have favored the colonization of water-stressed, substrate-poor mountainous habitats along the newly uplifted IT mountains during the Mio-Pliocene. Given the apparent similarity of mountain habitats for most species of Acantholimon, we hypothesize that its current high species diversity responds to a scenario of non-adaptive radiation fueled by allopatric speciation rather than evolutionary radiation driven by ecological opportunity. Similar scenarios might underlie the high diversity of other speciose genera in the topographically complex Irano-Turanian landscape, though this remains to be tested with fine-grained distribution and climatic data.
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Affiliation(s)
- Farideh Moharrek
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University (TMU), Tehran, Iran
| | - Isabel Sanmartín
- Department of Biodiversity and Conservation, Real Jardín Botánico (CSIC), Madrid, Spain
| | - Shahrokh Kazempour-Osaloo
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University (TMU), Tehran, Iran
| | - Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico (CSIC), Madrid, Spain
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Viruel J, Haguenauer A, Juin M, Mirleau F, Bouteiller D, Boudagher‐Kharrat M, Ouahmane L, La Malfa S, Médail F, Sanguin H, Nieto Feliner G, Baumel A. Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods for Ceratonia siliqua (Leguminosae). Appl Plant Sci 2018; 6:e01201. [PMID: 30598859 PMCID: PMC6303155 DOI: 10.1002/aps3.1201] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/28/2018] [Indexed: 05/25/2023]
Abstract
PREMISE OF THE STUDY Simple sequence repeat (SSR) or microsatellite markers have been used in a broad range of studies mostly scoring alleles on the basis of amplicon size as a proxy for the number of repeat units of an SSR motif. However, additional sources of variation within the SSR or in the flanking regions have largely remained undetected. METHODS In this study, we implemented a next-generation sequencing-based genotyping approach in a newly characterized set of 18 nuclear SSR markers for the carob tree, Ceratonia siliqua. Our aim was to evaluate the effect of three different methods of scoring molecular variation present within microsatellite markers on the genetic diversity and structure results. RESULTS The analysis of the sequences of 77 multilocus genotypes from four populations revealed SSR variation and additional sources of polymorphism in 87% of the loci analyzed (42 single-nucleotide polymorphisms and five insertion/deletion polymorphisms), as well as divergent paralog copies in two loci. Ignoring sequence variation under standard amplicon size genotyping resulted in incorrect identification of 69% of the alleles, with important effects on the genetic diversity and structure estimates. DISCUSSION Next-generation sequencing allows the detection and scoring of SSRs, single-nucleotide polymorphisms, and insertion/deletion polymorphisms to increase the resolution of population genetic studies.
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Affiliation(s)
- Juan Viruel
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Anne Haguenauer
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Marianick Juin
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Fatma Mirleau
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Delphine Bouteiller
- Institut du Cerveau et de la Moelle épinière (ICM)Hôpital Pitié Salpêtrière47 Boulevard de l'Hôpital75013ParisFrance
| | - Magda Boudagher‐Kharrat
- Laboratoire Caractérisation Génétique des PlantesFaculté des sciencesUniversité Saint‐JosephB.P. 11‐514 Riad El SolhBeirut1107 2050Lebanon
| | - Lahcen Ouahmane
- Laboratoire d'Ecologie et EnvironnementFaculté des Sciences SemlaliaUniversité Cadi AyyadMarrakeshMorocco
| | - Stefano La Malfa
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A)Università degli Studi di CataniaVia Valdisavoia 595123CataniaItaly
| | - Frédéric Médail
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Hervé Sanguin
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD)Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM)MontpellierFrance
- LSTM [LSTM is sponsored by University of Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro]TA A‐82/J Campus International de BaillarguetFR‐34398Montpellier CEDEX 5France
| | | | - Alex Baumel
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
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Rosato M, Álvarez I, Feliner GN, Rosselló JA. Inter- and intraspecific hypervariability in interstitial telomeric-like repeats (TTTAGGG)n in Anacyclus (Asteraceae). Ann Bot 2018; 122:387-395. [PMID: 29800070 PMCID: PMC6110349 DOI: 10.1093/aob/mcy079] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 04/24/2018] [Indexed: 05/18/2023]
Abstract
Background and Aims Interstitial telomeric repeat (ITR) sites, consisting of tandem repeats of telomeric motifs localized at intrachromosomal sites, have been reported in a few unrelated organisms including plants. However, the causes for the occurrence of ITRs outside of the chromosomal termini are not fully understood. One possible explanation are the chromosomal rearrangements involving telomeric sites, which could also affect the location of other structural genome elements, such as the 45S rDNA. Taking advantage of the high dynamism in 45S rDNA loci previously found in Anacyclus (Asteraceae, Anthemideae), the occurrence and patterns of variation of ITRs were explored in this genus with the aim of finding common underlying causes. Methods In total, 132 individuals from 44 populations of nine species were analysed by fluorescence in situ hybridization using an Arabidopsis-type telomeric sequence as a probe. Key results Variable presence of ITR sites was detected in six out of nine species of Anacyclus, ranging from two to 45 sites and showing contrasting chromosomal locations and a differential presence of the ITR site on homologous chromosome pairs. At the intraspecific level, the ranges were as large as 0-12 ITR sites. Although only 26 % of the total observed ITR sites were localized in chromosomes bearing 45S rDNA loci, all cases of interstitial 45S rDNA reported in a previous work co-occurred with ITRs in close proximity in the same chromosome arms. Conclusions High levels of ITR polymorphism within a single species have not been previously reported in plants and suggest that this pattern might have been overlooked due to insufficient sampling. Although ancient Robertsonian translocations or the amplification of terminal 45S rDNA sites cannot, on their own, explain all of the levels of variability in ITRs reported here, there are suggestions that they may have been involved in the evolutionary history of this genus or its ancestors in Anthemideae.
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Affiliation(s)
- Marcela Rosato
- Jardín Botánico, ICBIBE-Unidad Asociada CSIC, Universidad de Valencia, Spain
| | - Inés Álvarez
- Real Jardín Botánico (CSIC), Plaza de Murillo, Spain
| | | | - Josep A Rosselló
- Jardín Botánico, ICBIBE-Unidad Asociada CSIC, Universidad de Valencia, Spain
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Marques I, Jürgens A, Aguilar JF, Feliner GN. Convergent recruitment of new pollinators is triggered by independent hybridization events in Narcissus. New Phytol 2016; 210:731-742. [PMID: 26738752 DOI: 10.1111/nph.13805] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 11/11/2015] [Indexed: 06/05/2023]
Abstract
Hybridization can generate new species if some degree of isolation prevents gene flow between the hybrids and their progenitors. The recruitment of novel pollinators by hybrids has been hypothesized to be one way in which such reproductive isolation can be achieved. We tested whether pollinators contributed to isolation between two natural Narcissus hybrids and their progenitors using pollination experiments, observations, plus morphological and floral-volatile measurements. These hybrids share the same maternal but different paternal progenitors. We found that only the hybrids were visited by and pollinated by ants. The two hybrids exceeded their progenitors in floral-tube aperture size and nectar production. The emission of floral volatiles by hybrid plants was not only equal to or higher than the progenitor species, but also contained some new compounds not produced by the progenitors. The recruitment of ants as novel pollinators in the hybrids involved the combination of increased nectar secretion and the production of novel floral scent compounds. A breakdown of chemical defence against ants may also be involved. This study provides support for the hypothesis that the recruitment of novel pollinators can contribute to reproductive isolation between hybrids and their progenitors.
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Affiliation(s)
- Isabel Marques
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, C/Carretera de Cuarte Km 1, Huesca, E22071, Spain
- UBC Botanical Garden & Centre for Plant Research and Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Andreas Jürgens
- School of Life Sciences, University of KwaZulu-Natal, Post Bag X01 Scottsville, Pietermaritzburg, 3209, South Africa
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García-Fernández A, Iriondo JM, Escudero A, Aguilar JF, Feliner GN. Genetic patterns of habitat fragmentation and past climate-change effects in the Mediterranean high-mountain plant Armeria caespitosa (Plumbaginaceae). Am J Bot 2013; 100:1641-1650. [PMID: 23857736 DOI: 10.3732/ajb.1200653] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY Mountain plants are among the species most vulnerable to global warming, because of their isolation, narrow geographic distribution, and limited geographic range shifts. Stochastic and selective processes can act on the genome, modulating genetic structure and diversity. Fragmentation and historical processes also have a great influence on current genetic patterns, but the spatial and temporal contexts of these processes are poorly known. We aimed to evaluate the microevolutionary processes that may have taken place in Mediterranean high-mountain plants in response to changing historical environmental conditions. METHODS Genetic structure, diversity, and loci under selection were analyzed using AFLP markers in 17 populations distributed over the whole geographic range of Armeria caespitosa, an endemic plant that inhabits isolated mountains (Sierra de Guadarrama, Spain). Differences in altitude, geographic location, and climate conditions were considered in the analyses, because they may play an important role in selective and stochastic processes. KEY RESULTS Bayesian clustering approaches identified nine genetic groups, although some discrepancies in assignment were found between alternative analyses. Spatially explicit analyses showed a weak relationship between genetic parameters and spatial or environmental distances. However, a large proportion of outlier loci were detected, and some outliers were related to environmental variables. CONCLUSIONS A. caespitosa populations exhibit spatial patterns of genetic structure that cannot be explained by the isolation-by-distance model. Shifts along the altitude gradient in response to Pleistocene climatic oscillations and environmentally mediated selective forces might explain the resulting structure and genetic diversity values found.
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Marques I, Aguilar JF, Martins-Loução MA, Feliner GN. Spatial–temporal patterns of flowering asynchrony and pollinator fidelity in hybridizing species of Narcissus. Evol Ecol 2012. [DOI: 10.1007/s10682-012-9554-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Marques I, Nieto Feliner G, Martins-Loução MA, Fuertes Aguilar J. Genome size and base composition variation in natural and experimental Narcissus (Amaryllidaceae) hybrids. Ann Bot 2012; 109:257-64. [PMID: 22080093 PMCID: PMC3241596 DOI: 10.1093/aob/mcr282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Although there is evidence that both allopolyploid and homoploid hybridization lead to rapid genomic changes, much less is known about hybrids from parents with different basic numbers without further chromosome doubling. Two natural hybrids, Narcissus × alentejanus (2n = 19) and N. × perezlarae (2n = 29), originated by one progenitor (N. cavanillesii, 2n = 28) and two others (N. serotinus, 2n = 10 and N. miniatus, 2n = 30, respectively) allow us to study how DNA content and composition varies in such hybrids. METHODS Flow cytometry measurements with two staining techniques, PI and DAPI, were used to estimate 2C values and base composition (AT/GC ratio) in 390 samples from 54 wild populations of the two natural hybrids and their parental species. In addition, 20 synthetic F(1) hybrid individuals were also studied for comparison. KEY RESULTS Natural hybrids presented 2C values intermediate between those found in their parental species, although intra-population variance was very high in both hybrids, particularly for PI. Genome size estimated from DAPI was higher in synthetic hybrids than in hybrids from natural populations. In addition, differences for PI 2C values were detected between synthetic reciprocal crosses, attributable to maternal effects, as well as between natural hybrids and those synthetic F(1) hybrids in which N. cavanillesii acted as a mother. CONCLUSIONS Our results suggest that natural hybrid populations are composed of a mixture of markedly different hybrid genotypes produced either by structural chromosome changes, consistent with classic cytogenetic studies in Narcissus, or by transposon-mediated events.
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Affiliation(s)
- Isabel Marques
- Universidade de Lisboa, Museu Nacional de História Natural, Jardim Botânico, Lisbon, Portugal.
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Marques I, Feliner GN, Draper Munt D, Martins-Loução MA, Aguilar JF. Unraveling cryptic reticulate relationships and the origin of orphan hybrid disjunct populations in Narcissus. Evolution 2010; 64:2353-68. [PMID: 20199565 DOI: 10.1111/j.1558-5646.2010.00983.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Evolutionary consequences of natural hybridization between species may vary so drastically depending on spatial, genetic, and ecological factors that multiple approaches are required to uncover them. To unravel the evolutionary history of a controversial hybrid (Narcissus x perezlarae), here we use four approaches: DNA sequences from five regions (four organellar, one nuclear), cytological studies (chromosome counts and genome size), crossing experiments, and niche modeling. We conclude that (1) it actually consists of two different hybrid taxa, N.xperezlarae s.s. (N. cavanillesii x N. miniatus) and N.xalentejanus (N. cavanillesii x N. serotinus); (2) both have been formed several times independently, that is, polytopically; (3) N. cavanillesii was the mother progenitor in most hybridization events. We also address the origin of orphan hybrid populations of N.xperezlarae in eastern Spain, hundreds of kilometers away from N. cavanillesii. Although long-distance dispersal of already formed hybrids cannot be completely rejected, extirpation of N. cavanillesii via demographic competition is a more likely explanation. Low-reproductive barriers to fertilization by foreign pollen in N. cavanillesii, molecular footprints of the former presence of this species in the area, active asexual propagation by bulbs in N.xperezlarae, and overlapping ecological niches are consistent with the extirpation scenario.
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Affiliation(s)
- Isabel Marques
- Universidade de Lisboa. Museu Nacional de História Natural, Jardim Botânico, Rua da Escola Politécnica 58. 1280-102 Lisboa, Portugal.
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Escobar García P, Schönswetter P, Fuertes Aguilar J, Nieto Feliner G, Schneeweiss GM. Five molecular markers reveal extensive morphological homoplasy and reticulate evolution in the Malva alliance (Malvaceae). Mol Phylogenet Evol 2009; 50:226-39. [DOI: 10.1016/j.ympev.2008.10.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 09/26/2008] [Accepted: 10/20/2008] [Indexed: 11/25/2022]
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Piñeiro R, Fuertes Aguilar J, Munt DD, Nieto Feliner G. Ecology matters: Atlantic-Mediterranean disjunction in the sand-dune shrub Armeria pungens (Plumbaginaceae). Mol Ecol 2008; 16:2155-71. [PMID: 17498238 DOI: 10.1111/j.1365-294x.2007.03280.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Inferring the evolutionary history of Mediterranean plant lineages from current genetic, distributional and taxonomic patterns is complex because of a number of palaeoclimatic and geological interconnected factors together with landscape heterogeneity and human influence. Therefore, choosing spatially simplified systems as study groups is a suitable approach. An amplified fragment length polymorphism (AFLP) study using two restriction enzyme combinations (EcoRI/MseI and KpnI/MseI) was carried out to estimate the structure of genetic variation throughout the range of Armeria pungens. This species has a West Iberian-Corso/Sardinian disjunct distribution on coastal sand-dune ecosystems. Bayesian, amova and genetic distance analyses of the AFLP data revealed the same distinguishable genetic groups, which do not match the main geographical disjunction. Corso-Sardinian populations were found to be genetically closer to southwest Portuguese than to those from the Gulf of Cadiz (the closest geographically). Eastwards long-distance dispersal is therefore invoked to explain this geographical disjunction. A GIS analysis based on bioclimatic envelope modelling aiming to characterize the current locations of A. pungens found strong similarities between the Portugal and Corsica-Sardinia sites and less so between these areas and the Gulf of Cadiz. This coincident pattern between AFLP and climatic data suggests that the geographical disjunction is better explained by climatic factors than by the likeliness of a stochastic dispersal event. Such a combined phylogeographical-GIS modelling approach proves to be enlightening in reconstructing the evolutionary history of plant species.
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Affiliation(s)
- Rosalía Piñeiro
- Real Jardín Botánico de Madrid, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain.
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Nieto Feliner G, Rosselló JA. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol Phylogenet Evol 2007; 44:911-9. [PMID: 17383902 DOI: 10.1016/j.ympev.2007.01.013] [Citation(s) in RCA: 254] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Revised: 12/03/2006] [Accepted: 01/10/2007] [Indexed: 11/20/2022]
Abstract
The internal transcribed spacers (ITS) of the nuclear ribosomal 18S-5.8S-26S cistron continue to be the most popular non-plastid region for species-level phylogenetic studies of plant groups despite the early warnings about their potential flaws, which may ultimately result in incorrect assumptions of orthology. It has been gradually realized that the alternative target regions in the nuclear genome (low-copy nuclear genes, LCNG) are burdened with similar problems. The consequence is that, to date, developing useful LCNG for non-model organisms requires an investment in time and effort that hinders its use as a real practical alternative for many labs. It is here argued that ITS sequences, despite drawbacks, can still produce insightful results in species-level phylogenetic studies or when non-anonymous nuclear markers are required, provided that a thoughtful use of them is made. To facilitate this, two series of guidelines are proposed. One helps to circumvent problems of ITS amplification from the target organism, including spurious results from contaminants, paralogs and pseudogenes, as well as detection of sequencing artifacts. The other series helps to find out causes for unresolved clades in phylogenetic reconstruction, to integrate gene phylogenies, to distinguish horizontal transfer from lineage sorting, and to reveal if ITS phylogeny is not a good estimate of organism phylogeny.
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Lihová J, Fuertes Aguilar J, Marhold K, Nieto Feliner G. Origin of the disjunct tetraploid Cardamine amporitana (Brassicaceae) assessed with nuclear and chloroplast DNA sequence data. Am J Bot 2004; 91:1231-1242. [PMID: 21653480 DOI: 10.3732/ajb.91.8.1231] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Seventy-four nucleotide sequences from the ITS regions of nuclear ribosomal DNA and 76 from the trnL-trnF spacer of chloroplast DNA were used to address the origin of tetraploid Cardamine amporitana, the conspecifity of central Italian and northeastern Spanish populations, and the possible cause for such geographic disjunction. Because of the complex lineage relationships in Cardamine, the sampling included 22 taxa. In the results, both data sets are highly congruent in supporting a close relationship of C. amporitana to the widespread Eurasian C. amara. Low genetic variability in northeastern Spanish populations of C. amporitana suggests long-distance dispersal from central Italy. The interior position of the single northeastern Spanish haplotype in a statistical parsimony network of trnL-trnF haplotypes however does not support this scenario and invokes other plausible phylogeographic explanations. The disappearance of geographically intermediate populations and genetic impoverishment by migration and isolation, both probably associated with Quaternary climatic oscillations, appears as an alternative hypothesis to explain the phylogeographic pattern. A recent hybridization event is reported between C. amporitana and a diploid from the C. pratensis group in central Italy on the basis of additive polymorphisms in ITS for all the 22 distinguishing nucleotides.
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Affiliation(s)
- Judita Lihová
- Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 14, SK-845 23 Bratislava, Slovak Republic
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Nieto Feliner G, Gutiérrez Larena B, Fuertes Aguilar J. Fine-scale geographical structure, intra-individual polymorphism and recombination in nuclear ribosomal internal transcribed spacers in Armeria (Plumbaginaceae). Ann Bot 2004; 93:189-200. [PMID: 14707002 PMCID: PMC4241081 DOI: 10.1093/aob/mch027] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS Isolation and drift are the main causes for geographic structure of molecular variation. In contrast, the one found in a previous survey in Armeria (Plumbaginaceae) for nuclear ribosomal ITS multicopy regions was species-independent and has been hypothesized to be due to extensive gene-flow and biased concerted evolution. Since this was inferred from a genus-level phylogenetic analysis, the aim of this study was to check for the occurrence of such structure and the validity of the proposed model at a local scale, in a southern Spanish massif (Sierra Nevada), as well as to examine the evolutionary implications at the organism level. METHODS In addition to 117 sequences of direct PCR products from genomic DNA, 50 sequences of PCR products from cloned DNA were obtained to analyse cases of intragenomic polymorphisms for the ITS regions. KEY RESULTS Sequence data confirm the occurrence of a species-independent structure at a local scale and reveal insights through the analysis of contact areas between different ITS copies (ribotypes). A comparison between cloned and direct sequences (a) confirms that, within these contact areas, ITS copies co-occur both in different individuals and within single genomes; and (b) reveals recombination between different copies. CONCLUSIONS This study supports the utility of direct sequences for detecting intra-individual polymorphism and for partially inferring the ITS copies involved, given previous knowledge of the variability. The main evolutionary implication at the organism level is that gene-flow and concerted evolution shape the geographic structure of ITS variation.
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Abstract
A parsimony analysis of 133 sequences of the nuclear ribosomal DNA ITS1+5.8S+ITS2 region from 71 taxa in Armeria was carried out. The presence of additive polymorphic sites (APS; occurring in 14 accessions) fits the reticulate scenario proposed in previous work for explaining the ITS pattern of variation on a much smaller scale and is based mainly on the geographical structure of the data, irrespective of taxonomic boundaries. Despite the relatively low bootstrap values and large polytomies, part of which are likely due to disruptive effects of reticulation and concerted evolution in these multicopy sequences, the ITS analysis has phylogenetic and biogeographic implications. APS detected in this study are consistent with hypothesized hybridization events, although biased concerted evolution, previously documented in the genus, needs to be invoked for specific cases and may be responsible for a possible "sink" effect in terminals from a large clade. The causes for sequences of the same species appearing in different clades (here termed transclade) are discussed.
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Feliner GN, Aguilar JF, Rossello JA. Can Extensive Reticulation and Concerted Evolution Result in a Cladistically Structured Molecular Data Set? Cladistics 2001. [DOI: 10.1111/j.1096-0031.2001.tb00128.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Aguilar JF, Panero JL, Feliner GN. A phylogenetic analysis of Doronicum (Asteraceae, Senecioneae) based on morphological, nuclear ribosomal (ITS), and chloroplast (trnL-F) evidence. Mol Phylogenet Evol 2001; 20:41-64. [PMID: 11421647 DOI: 10.1006/mpev.2001.0954] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A phylogenetic analysis of the Old World genus Doronicum (26 species, 4 subspecies) based on sequence data of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA, the chloroplast spacer trnL-F, and morphology is presented. Congruence among the three data sets was explored by the computing of several indices, all of which suggest homogeneity between only the two molecular matrices. We argue that the morphological data set contains poor phylogenetic signal and advocate simultaneous analysis of the three data sets (total evidence approach) so that morphological characters are tested for homology by congruence with molecular data. The resulting phylogenetic hypothesis allows several well-supported conclusions including the placement of a Corsican endemic (D. corsicum), sister to the remainder of the genus, and the inference that an early southern European or Mediterranean diversification took place in the genus. Shifts in morphological characters (e.g., homocarpy to heterocarpy) are confirmed to have evolved several times. Results from comparative studies of sequence data of the chloroplast gene ndhF support inclusion of Doronicum in tribe Senecioneae.
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Abstract
The breeding system of 13 populations belonging to eight species of Erysimum (Cruciferae) was studied and its relation with the life-span of the plants is discussed. To assess the breeding system of each population, greenhouse tests for apomixis, self-compatibility, and self-pollination were carried out, morphological characters like petal size and anther length were measured and pollen to ovule ratios were computed. The evidence gathered supports the selfing behavior of the three annuals, E. cheiranthoides L., E. incanum G. Kunze, and E. repandum L., and the outcrossing behavior of the perennials E. linifolium (Pers.) Gay, E. asperum (Nutt.) DC, and E. menziesii (Hook.) Wettst. Among those two groups, E. inconspicuum (S. Wats.) MacMillan and E. suffruticosum Sprengel apparently occupy an intermediate position, although the former tends more towards autogamy, whereas the latter tends towards allogamy. The importance of the breeding system data in the systematics of this genus, particularly, in studying the apparent links between the Mediterranean annuals and the temperate E. hieracifolium L. group is briefly discussed. Key words: Erysimum, breeding systems, pollen to ovule ratio, life-span.
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