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Milosavljevic S, Kauai F, Mortier F, Van de Peer Y, Bonte D. A metabolic perspective on polyploid invasion and the emergence of life histories: Insights from a mechanistic model. AMERICAN JOURNAL OF BOTANY 2024; 111:e16387. [PMID: 39113228 PMCID: PMC7616395 DOI: 10.1002/ajb2.16387] [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: 10/13/2023] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 08/24/2024]
Abstract
PREMISE Whole-genome duplication (WGD, polyploidization) has been identified as a driver of genetic and phenotypic novelty, having pervasive consequences for the evolution of lineages. While polyploids are widespread, especially among plants, the long-term establishment of polyploids is exceedingly rare. Genome doubling commonly results in increased cell sizes and metabolic expenses, which may be sufficient to modulate polyploid establishment in environments where their diploid ancestors thrive. METHODS We developed a mechanistic simulation model of photosynthetic individuals to test whether changes in size and metabolic efficiency allow autopolyploids to coexist with, or even invade, ancestral diploid populations. Central to the model is metabolic efficiency, which determines how energy obtained from size-dependent photosynthetic production is allocated to basal metabolism as opposed to somatic and reproductive growth. We expected neopolyploids to establish successfully if they have equal or higher metabolic efficiency as diploids or to adapt their life history to offset metabolic inefficiency. RESULTS Polyploid invasion was observed across a wide range of metabolic efficiency differences between polyploids and diploids. Polyploids became established in diploid populations even when they had a lower metabolic efficiency, which was facilitated by recurrent formation. Competition for nutrients is a major driver of population dynamics in this model. Perenniality did not qualitatively affect the relative metabolic efficiency from which tetraploids tended to establish. CONCLUSIONS Feedback between size-dependent metabolism and energy allocation generated size and age differences between plants with different ploidies. We demonstrated that even small changes in metabolic efficiency are sufficient for the establishment of polyploids.
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Affiliation(s)
- Silvija Milosavljevic
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB - UGent Center for Plant Systems Biology, B-9052Ghent, Belgium
- Department of Biology, Terrestrial Ecology Unit, Ghent University, Karel Lodewijk Ledeganckstraat 35, BE-9000Ghent, Belgium
| | - Felipe Kauai
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB - UGent Center for Plant Systems Biology, B-9052Ghent, Belgium
- Department of Biology, Terrestrial Ecology Unit, Ghent University, Karel Lodewijk Ledeganckstraat 35, BE-9000Ghent, Belgium
| | - Frederik Mortier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB - UGent Center for Plant Systems Biology, B-9052Ghent, Belgium
- Department of Biology, Terrestrial Ecology Unit, Ghent University, Karel Lodewijk Ledeganckstraat 35, BE-9000Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB - UGent Center for Plant Systems Biology, B-9052Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Dries Bonte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB - UGent Center for Plant Systems Biology, B-9052Ghent, Belgium
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Lipánová V, Kabátová KN, Zeisek V, Kolář F, Chrtek J. Evolution of the Sabulina verna group (Caryophyllaceae) in Europe: A deep split, followed by secondary contacts, multiple allopolyploidization and colonization of challenging substrates. Mol Phylogenet Evol 2023; 189:107940. [PMID: 37820762 DOI: 10.1016/j.ympev.2023.107940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 08/10/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023]
Abstract
One of the major goals of contemporary evolutionary biology is to elucidate the relative roles of allopatric and ecological differentiation and polyploidy in speciation. In this study, we address the taxonomically intricate Sabulina verna group, which has a disjunct Arctic-alpine postglacial range in Europe and occupies a broad range of ecological niches, including substrates toxic to plants. Using genome-wide ddRAD sequencing combined with morphometric analyses based on extensive sampling of 111 natural populations, we aimed to disentangle internal evolutionary relationships and examine their correspondence with the pronounced edaphic and ploidy diversity within the group. We identified two spatially distinct groups of diploids: a widespread Arctic-alpine group and a spatially restricted yet diverse Balkan group. Most tetraploids exhibited a considerably admixed ancestry derived from both these groups, suggesting their allopolyploid origin. Four genetic clusters in congruence with geography and mostly supported by morphological traits were recognized in the diploid Arctic-alpine group. Tetraploids are split into two distinct and geographically vicariant groups, indicating their repeated polytopic origin. Furthermore, our results also revealed at least five-fold parallel colonization of toxic substrates (serpentine and metalliferous), altogether demonstrating a complex interaction between geography, challenging substrates and polyploidy in the evolution of the group. Finally, we propose a new taxonomic treatment of this complex.
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Affiliation(s)
- Veronika Lipánová
- Department of Botany, Faculty of Science, Charles University, 128 00 Prague, Czech Republic; Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic; Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | | | - Vojtěch Zeisek
- Department of Botany, Faculty of Science, Charles University, 128 00 Prague, Czech Republic; Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, 128 00 Prague, Czech Republic; Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic
| | - Jindřich Chrtek
- Department of Botany, Faculty of Science, Charles University, 128 00 Prague, Czech Republic; Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic.
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Šemberová K, Svitok M, Marhold K, Suda J, Schmickl RE. Morphological and environmental differentiation as prezygotic reproductive barriers between parapatric and allopatric Campanula rotundifolia agg. cytotypes. ANNALS OF BOTANY 2023; 131:71-86. [PMID: 34559179 PMCID: PMC9904352 DOI: 10.1093/aob/mcab123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 09/21/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Reproductive isolation and local establishment are necessary for plant speciation. Polyploidy, the possession of more than two complete chromosome sets, creates a strong postzygotic reproductive barrier between diploid and tetraploid cytotypes. However, this barrier weakens between polyploids (e.g. tetraploids and hexaploids). Reproductive isolation may be enhanced by cytotype morphological and environmental differentiation. Moreover, morphological adaptations to local conditions contribute to plant establishment. However, the relative contributions of ploidy level and the environment to morphology have generally been neglected. Thus, the extent of morphological variation driven by ploidy level and the environment was modelled for diploid, tetraploid and hexaploid cytotypes of Campanula rotundifolia agg. Cytotype distribution was updated, and morphological and environmental differentiation was tested in the presence and absence of natural contact zones. METHODS Cytotype distribution was assessed from 231 localities in Central Europe, including 48 localities with known chromosome counts, using flow cytometry. Differentiation in environmental niche and morphology was tested for cytotype pairs using discriminant analyses. A structural equation model was used to explore the synergies between cytotype, environment and morphology. KEY RESULTS Tremendous discrepancies were revealed between the reported and detected cytotype distribution. Neither mixed-ploidy populations nor interploidy hybrids were detected in the contact zones. Diploids had the broadest environmental niche, while hexaploids had the smallest and specialized niche. Hexaploids and spatially isolated cytotype pairs differed morphologically, including allopatric tetraploids. While leaf and shoot morphology were influenced by environmental conditions and polyploidy, flower morphology depended exclusively on the cytotype. CONCLUSIONS Reproductive isolation mechanisms vary between cytotypes. While diploids and polyploids are isolated postzygotically, the environmental niche shift is essential between higher polyploids. The impact of polyploidy and the environment on plant morphology implies the adaptive potential of polyploids, while the exclusive relationship between flower morphology and cytotype highlights the role of polyploidy in reproductive isolation.
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Affiliation(s)
| | - Marek Svitok
- Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, T. G. Masaryka, Zvolen, Slovakia
- Faculty of Science, Department of Ecosystem Biology, University of South Bohemia, Branišovská, České Budějovice, Czech Republic
| | - Karol Marhold
- Faculty of Science, Department of Botany, Charles University, Benátská, Prague, Czech Republic
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta, Bratislava, Slovakia
| | | | - Roswitha E Schmickl
- Faculty of Science, Department of Botany, Charles University, Benátská, Prague, Czech Republic
- Czech Academy of Sciences, Institute of Botany, Department of Evolutionary Plant Biology, Zámek, Průhonice, Czech Republic
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Linscott TM, González-González A, Hirano T, Parent CE. De novo genome assembly and genome skims reveal LTRs dominate the genome of a limestone endemic Mountainsnail (Oreohelix idahoensis). BMC Genomics 2022; 23:796. [PMID: 36460988 PMCID: PMC9719178 DOI: 10.1186/s12864-022-09000-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/10/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Calcareous outcrops, rocky areas composed of calcium carbonate (CaCO3), often host a diverse, specialized, and threatened biomineralizing fauna. Despite the repeated evolution of physiological and morphological adaptations to colonize these mineral rich substrates, there is a lack of genomic resources for calcareous rock endemic species. This has hampered our ability to understand the genomic mechanisms underlying calcareous rock specialization and manage these threatened species. RESULTS Here, we present a new draft genome assembly of the threatened limestone endemic land snail Oreohelix idahoensis and genome skim data for two other Oreohelix species. The O. idahoensis genome assembly (scaffold N50: 404.19 kb; 86.6% BUSCO genes) is the largest (~ 5.4 Gb) and most repetitive mollusc genome assembled to date (85.74% assembly size). The repetitive landscape was unusually dominated by an expansion of long terminal repeat (LTR) transposable elements (57.73% assembly size) which have shaped the evolution genome size, gene composition through retrotransposition of host genes, and ectopic recombination. Genome skims revealed repeat content is more than 2-3 fold higher in limestone endemic O. idahoensis compared to non-calcareous Oreohelix species. Gene family size analysis revealed stress and biomineralization genes have expanded significantly in the O. idahoensis genome. CONCLUSIONS Hundreds of threatened land snail species are endemic to calcareous rock regions but there are very few genomic resources available to guide their conservation or determine the genomic architecture underlying CaCO3 resource specialization. Our study provides one of the first high quality draft genomes of a calcareous rock endemic land snail which will serve as a foundation for the conservation genomics of this threatened species and for other groups. The high proportion and activity of LTRs in the O. idahoensis genome is unprecedented in molluscan genomics and sheds new light how transposable element content can vary across molluscs. The genomic resources reported here will enable further studies of the genomic mechanisms underlying calcareous rock specialization and the evolution of transposable element content across molluscs.
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Affiliation(s)
- T. Mason Linscott
- grid.266456.50000 0001 2284 9900Department of Biological Sciences, University of Idaho, Moscow, ID USA ,grid.266456.50000 0001 2284 9900Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID USA
| | - Andrea González-González
- grid.15276.370000 0004 1936 8091Department of Biology, University of Florida, Gainesville, Florida USA
| | - Takahiro Hirano
- grid.69566.3a0000 0001 2248 6943Center for Northeast Asian Studies, Tohoku University, Sendai, Miyagi Japan
| | - Christine E. Parent
- grid.266456.50000 0001 2284 9900Department of Biological Sciences, University of Idaho, Moscow, ID USA ,grid.266456.50000 0001 2284 9900Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID USA
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Rupprecht D, Hölzel N, Bucharova A. Is there local adaptation in plant species to soil reaction? A lesson from a multispecies experiment. Restor Ecol 2021. [DOI: 10.1111/rec.13393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Denise Rupprecht
- Biodiversity and Ecosystem Research Group University of Münster, Institute of Landscape Ecology Münster Germany
| | - Norbert Hölzel
- Biodiversity and Ecosystem Research Group University of Münster, Institute of Landscape Ecology Münster Germany
| | - Anna Bucharova
- Biodiversity and Ecosystem Research Group University of Münster, Institute of Landscape Ecology Münster Germany
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Konečná V, Yant L, Kolář F. The Evolutionary Genomics of Serpentine Adaptation. FRONTIERS IN PLANT SCIENCE 2020; 11:574616. [PMID: 33391295 PMCID: PMC7772150 DOI: 10.3389/fpls.2020.574616] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Serpentine barrens are among the most challenging settings for plant life. Representing a perfect storm of hazards, serpentines consist of broadly skewed elemental profiles, including abundant toxic metals and low nutrient contents on drought-prone, patchily distributed substrates. Accordingly, plants that can tolerate the challenges of serpentine have fascinated biologists for decades, yielding important insights into adaptation to novel ecologies through physiological change. Here we highlight recent progress from studies which demonstrate the power of serpentine as a model for the genomics of adaptation. Given the moderate - but still tractable - complexity presented by the mix of hazards on serpentine, these venues are well-suited for the experimental inquiry of adaptation both in natural and manipulated conditions. Moreover, the island-like distribution of serpentines across landscapes provides abundant natural replicates, offering power to evolutionary genomic inference. Exciting recent insights into the genomic basis of serpentine adaptation point to a partly shared basis that involves sampling from common allele pools available from retained ancestral polymorphism or via gene flow. However, a lack of integrated studies deconstructing complex adaptations and linking candidate alleles with fitness consequences leaves room for much deeper exploration. Thus, we still seek the crucial direct link between the phenotypic effect of candidate alleles and their measured adaptive value - a prize that is exceedingly rare to achieve in any study of adaptation. We expect that closing this gap is not far off using the promising model systems described here.
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Affiliation(s)
- Veronika Konečná
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Pru˚honice, Czechia
| | - Levi Yant
- Future Food Beacon and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Pru˚honice, Czechia
- Natural History Museum, University of Oslo, Oslo, Norway
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Burge D. Conservation genomics and pollination biology of an endangered, edaphic-endemic, octoploid herb: El Dorado bedstraw ( Galium californicum subsp. sierrae; Rubiaceae). PeerJ 2020; 8:e10042. [PMID: 33173616 PMCID: PMC7594638 DOI: 10.7717/peerj.10042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 09/04/2020] [Indexed: 01/25/2023] Open
Abstract
El Dorado bedstraw (Galium californicum subsp. sierrae) is a federally endangered dioecious, octoploid, perennial herb found only in the Pine Hill region of El Dorado County, CA, USA. Like many species of Galium, El Dorado bedstraw is capable of both sexual and asexual reproduction, spreading via stem-layering as well as seeds. El Dorado bedstraw is also dioecious, and thus dependent on pollinators to transfer pollen from male to female stems. The capacity for asexual reproduction has conservation implications for this plant, due to the potential for populations to become dominated by a small number of clones in the absence of recruitment from seeds. No previous work has examined either the population genetics or pollination biology of this plant. Here, double-digest restriction site-associated DNA sequencing was used to develop a genetic dataset for a sample of El Dorado bedstraw (12 individuals from each of seven locations). Genomic data was used to calculate population genetic statistics and quantify the degree to which clonality affects the sampled populations. Visual observation of insect visitors at every sampling location was used to assess the potential for pollen transfer within and among locations. A total of 23 clonal colonies were detected across 82 successfully sequenced stems, consisting of an average of 2.4 individuals (range: 2–6). Significant isolation by distance among locations was detected using a Mantel test. Insect pollinators were from eleven families, consisting mainly of small species with weak flight. It is recommended that clonality and small-scale population differentiation be taken into account in conservation measures.
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Affiliation(s)
- Dylan Burge
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
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Stift M, Kolář F, Meirmans PG. STRUCTURE is more robust than other clustering methods in simulated mixed-ploidy populations. Heredity (Edinb) 2019; 123:429-441. [PMID: 31285566 PMCID: PMC6781132 DOI: 10.1038/s41437-019-0247-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/19/2019] [Accepted: 05/20/2019] [Indexed: 01/19/2023] Open
Abstract
Analysis of population genetic structure has become a standard approach in population genetics. In polyploid complexes, clustering analyses can elucidate the origin of polyploid populations and patterns of admixture between different cytotypes. However, combining diploid and polyploid data can theoretically lead to biased inference with (artefactual) clustering by ploidy. We used simulated mixed-ploidy (diploid-autotetraploid) data to systematically compare the performance of k-means clustering and the model-based clustering methods implemented in STRUCTURE, ADMIXTURE, FASTSTRUCTURE and INSTRUCT under different scenarios of differentiation and with different marker types. Under scenarios of strong population differentiation, the tested applications performed equally well. However, when population differentiation was weak, STRUCTURE was the only method that allowed unbiased inference with markers with limited genotypic information (co-dominant markers with unknown dosage or dominant markers). Still, since STRUCTURE was comparatively slow, the much faster but less powerful FASTSTRUCTURE provides a reasonable alternative for large datasets. Finally, although bias makes k-means clustering unsuitable for markers with incomplete genotype information, for large numbers of loci (>1000) with known dosage k-means clustering was superior to FASTSTRUCTURE in terms of power and speed. We conclude that STRUCTURE is the most robust method for the analysis of genetic structure in mixed-ploidy populations, although alternative methods should be considered under some specific conditions.
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Affiliation(s)
- Marc Stift
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czechia.,Department of Botany, University of Innsbruck, Innsbruck, Austria
| | - Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.
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Čertner M, Sudová R, Weiser M, Suda J, Kolář F. Ploidy-altered phenotype interacts with local environment and may enhance polyploid establishment in Knautia serpentinicola (Caprifoliaceae). THE NEW PHYTOLOGIST 2019; 221:1117-1127. [PMID: 30221362 DOI: 10.1111/nph.15426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/24/2018] [Indexed: 06/08/2023]
Abstract
Whole genome duplication is a key process in plant evolution and has direct phenotypic consequences. However, it remains unclear whether ploidy-related phenotypic changes can significantly alter the fitness of polyploids in nature and thus contribute to establishment of new polyploid mutants in diploid populations. We addressed this question using a unique natural system encompassing a diploid and its sympatric locally established autotetraploid derivative. By setting a common garden experiment with two manipulated environmental factors (presence/absence of serpentine substrate and competition), we tested whether these two locally important factors differently shape the phenotypic response of the two ploidy levels. Tetraploids attained significantly higher values of both above- and below-ground biomass, and root : shoot ratio compared to their diploid progenitors. Tetraploid superiority in vegetative fitness indicators was most prominent when they were cultivated together with a competitor in nutrient-rich nonserpentine substrate. We show that even genetically very closely related diploids and tetraploids can respond differently to key environmental factors. Provided there are sufficient nutrients, tetraploids can be more successful in tolerating interspecific competition than their diploid progenitors. Such superior performance might have provided an adaptive advantage for the newly established tetraploid promoting colonisation of new (micro-)habitats, which was indeed observed at the natural site.
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Affiliation(s)
- Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 00, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
| | - Radka Sudová
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
| | - Martin Weiser
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 00, Prague, Czech Republic
| | - Jan Suda
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 00, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 00, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
- Institute of Botany, University of Innsbruck, AT-6020, Innsbruck, Austria
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Knotek A, Kolář F. Different low-competition island habitats in Central Europe harbour similar levels of genetic diversity in relict populations of Galium pusillum agg. (Rubiaceae). Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Adam Knotek
- Department of Botany, Charles University, Benátská, CZ Prague, Czech Republic
| | - Filip Kolář
- Department of Botany, Charles University, Benátská, CZ Prague, Czech Republic
- Department of Botany, University of Innsbruck, Sternwartestrasse, AT Innsbruck, Austria
- Institute of Botany, The Czech Academy of Sciences, Zámek, CZ Průhonice, Czech Republic
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Kolář F, Čertner M, Suda J, Schönswetter P, Husband BC. Mixed-Ploidy Species: Progress and Opportunities in Polyploid Research. TRENDS IN PLANT SCIENCE 2017; 22:1041-1055. [PMID: 29054346 DOI: 10.1016/j.tplants.2017.09.011] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 09/12/2017] [Accepted: 09/18/2017] [Indexed: 05/07/2023]
Abstract
Mixed-ploidy species harbor a unique form of genomic and phenotypic variation that influences ecological interactions, facilitates genetic divergence, and offers insights into the mechanisms of polyploid evolution. However, there have been few attempts to synthesize this literature. We review here research on the cytotype distribution, diversity, and dynamics of intensively studied mixed-ploidy species and consider the implications for understanding mechanisms of polyploidization such as cytotype formation, establishment, coexistence, and post-polyploid divergence. In general, mixed-ploidy species are unevenly represented among families: they exhibit high cytotype diversity, often within populations, and frequently comprise rare and odd-numbered ploidies. Odd-ploidies often occur in association with asexuality. We highlight research hypotheses and opportunities that take advantage of the unique properties of ploidy variation.
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Affiliation(s)
- Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Praha, CZ-128 00, Czech Republic; Institute of Botany, The Czech Academy of Sciences, Zámek 1, Průhonice, CZ-252 43, Czech Republic
| | - Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Praha, CZ-128 00, Czech Republic; Institute of Botany, The Czech Academy of Sciences, Zámek 1, Průhonice, CZ-252 43, Czech Republic
| | - Jan Suda
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Praha, CZ-128 00, Czech Republic; Institute of Botany, The Czech Academy of Sciences, Zámek 1, Průhonice, CZ-252 43, Czech Republic
| | - Peter Schönswetter
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, A-6020 Innsbruck, Austria
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, ON, N0B 2K0 Canada.
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Galey ML, van der Ent A, Iqbal MCM, Rajakaruna N. Ultramafic geoecology of South and Southeast Asia. BOTANICAL STUDIES 2017; 58:18. [PMID: 28510201 PMCID: PMC5432931 DOI: 10.1186/s40529-017-0167-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/01/2017] [Indexed: 05/30/2023]
Abstract
Globally, ultramafic outcrops are renowned for hosting floras with high levels of endemism, including plants with specialised adaptations such as nickel or manganese hyperaccumulation. Soils derived from ultramafic regoliths are generally nutrient-deficient, have major cation imbalances, and have concomitant high concentrations of potentially phytotoxic trace elements, especially nickel. The South and Southeast Asian region has the largest surface occurrences of ultramafic regoliths in the world, but the geoecology of these outcrops is still poorly studied despite severe conservation threats. Due to the paucity of systematic plant collections in many areas and the lack of georeferenced herbarium records and databased information, it is not possible to determine the distribution of species, levels of endemism, and the species most threatened. However, site-specific studies provide insights to the ultramafic geoecology of several locations in South and Southeast Asia. The geoecology of tropical ultramafic regions differs substantially from those in temperate regions in that the vegetation at lower elevations is generally tall forest with relatively low levels of endemism. On ultramafic mountaintops, where the combined forces of edaphic and climatic factors intersect, obligate ultramafic species and hyperendemics often occur. Forest clearing, agricultural development, mining, and climate change-related stressors have contributed to rapid and unprecedented loss of ultramafic-associated habitats in the region. The geoecology of the large ultramafic outcrops of Indonesia's Sulawesi, Obi and Halmahera, and many other smaller outcrops in South and Southeast Asia, remains largely unexplored, and should be prioritised for study and conservation.
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Affiliation(s)
- M. L. Galey
- Center for Water and Environment, Natural Resources Research Institute, University of Minnesota, Duluth, MN 55811 USA
| | - A. van der Ent
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD Australia
- Laboratoire Sols et Environnement, Université de Lorraine-INRA, UMR 1120, Nancy, France
| | - M. C. M. Iqbal
- Plant Biology Laboratory, National Institute of Fundamental Studies, Kandy, 20000 Sri Lanka
| | - N. Rajakaruna
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407 USA
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2520 South Africa
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He J, Wang S, Li J, Fan Z, Liu X, Wang Y. Genetic differentiation and spatiotemporal history of diploidy and tetraploidy of Clintonia udensis. Ecol Evol 2017; 7:10243-10251. [PMID: 29238551 PMCID: PMC5723609 DOI: 10.1002/ece3.3510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 08/16/2017] [Accepted: 09/20/2017] [Indexed: 11/21/2022] Open
Abstract
Polyploidy is an important factor shaping the geographic range of a species. Clintonia udensis (Clintonia) is a primary perennial herb widely distributed in China with two karyotypic characteristics—diploid and tetraploid and thereby used to understand the ploidy and distribution. This study unraveled the patterns of genetic variation and spatiotemporal history among the cytotypes of C. udensis using simple sequence repeat or microsatellites. The results showed that the diploids and tetraploids showed the medium level of genetic differentiation; tetraploid was slightly lower than diploid in genetic diversity; recurrent polyploidization seems to have opened new possibilities for the local genotype; the spatiotemporal history of C. udensis allows tracing the interplay of polyploidy evolution; isolated and different ecological surroundings could act as evolutionary capacitors, preserve distinct karyological, and genetic diversity. The approaches of integrating genetic differentiation and spatiotemporal history of diploidy and tetraploidy of Clintonia udens would possibly provide a powerful way to understand the ploidy and plant distribution and undertaken in similar studies in other plant species simultaneously contained the diploid and tetraploid.
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Affiliation(s)
- Juan He
- College of Life Science Shanxi Normal University Linfen China
| | - Shengnan Wang
- College of Animal Science and Technology Nanjing Agricultural University Nanjing China
| | - Jia Li
- College of Life Science Shanxi Normal University Linfen China
| | - Zelu Fan
- College of Life Science Shanxi Normal University Linfen China
| | - Xin Liu
- College of Life Science Shanxi Normal University Linfen China
| | - Yiling Wang
- College of Life Science Shanxi Normal University Linfen China
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15
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Winkler M, Escobar García P, Gattringer A, Sonnleitner M, Hülber K, Schönswetter P, Schneeweiss GM. A novel method to infer the origin of polyploids from Amplified Fragment Length Polymorphism data reveals that the alpine polyploid complex of Senecio carniolicus (Asteraceae) evolved mainly via autopolyploidy. Mol Ecol Resour 2017; 17:877-892. [PMID: 27978605 DOI: 10.1111/1755-0998.12641] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 11/24/2016] [Accepted: 12/06/2016] [Indexed: 11/30/2022]
Abstract
Despite its evolutionary and ecological relevance, the mode of polyploid origin has been notoriously difficult to be reconstructed from molecular data. Here, we present a method to identify the putative parents of polyploids and thus to infer the mode of their origin (auto- vs. allopolyploidy) from Amplified Fragment Length Polymorphism (AFLP) data. To this end, we use Cohen's d of distances between in silico polyploids, generated within a priori defined scenarios of origin from a priori delimited putative parental entities (e.g. taxa, genetic lineages), and natural polyploids. Simulations show that the discriminatory power of the proposed method increases mainly with increasing divergence between the lower-ploid putative ancestors and less so with increasing delay of polyploidization relative to the time of divergence. We apply the new method to the Senecio carniolicus aggregate, distributed in the European Alps and comprising two diploid, one tetraploid and one hexaploid species. In the eastern part of its distribution, the S. carniolicus aggregate was inferred to comprise an autopolyploid series, whereas for western populations of the tetraploid species, an allopolyploid origin involving the two diploid species was the most likely scenario. Although this suggests that the tetraploid species has two independent origins, other evidence (ribotype distribution, morphology) is consistent with the hypothesis of an autopolyploid origin with subsequent introgression by the second diploid species. Altogether, identifying the best among alternative scenarios using Cohen's d can be straightforward, but particular scenarios, such as allopolyploid origin vs. autopolyploid origin with subsequent introgression, remain difficult to be distinguished.
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Affiliation(s)
- Manuela Winkler
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria.,GLORIA Co-ordination, Center for Global Change and Sustainability, University of Natural Resources and Life Sciences Vienna (BOKU) & Institute for Interdisciplinary Mountain Research, Austrian Academy of Sciences, Silbergasse 30/3, Vienna, A-1190, Austria
| | - Pedro Escobar García
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Andreas Gattringer
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Michaela Sonnleitner
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Karl Hülber
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria.,Vienna Institute for Nature Conservation & Analyses, Giessergasse 6/7, Vienna, A-1090, Austria
| | - Peter Schönswetter
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, Innsbruck, A-6020, Austria
| | - Gerald M Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
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16
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Sobczyk MK, Smith JAC, Pollard AJ, Filatov DA. Evolution of nickel hyperaccumulation and serpentine adaptation in the Alyssum serpyllifolium species complex. Heredity (Edinb) 2017; 118:31-41. [PMID: 27782119 PMCID: PMC5176119 DOI: 10.1038/hdy.2016.93] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 08/07/2016] [Accepted: 08/12/2016] [Indexed: 02/06/2023] Open
Abstract
Metal hyperaccumulation is an uncommon but highly distinctive adaptation found in certain plants that can grow on metalliferous soils. Here we review what is known about evolution of metal hyperaccumulation in plants and describe a population-genetic analysis of the Alyssum serpyllifolium (Brassicaceae) species complex that includes populations of nickel-hyperaccumulating as well as non-accumulating plants growing on serpentine (S) and non-serpentine (NS) soils, respectively. To test whether the S and NS populations belong to the same or separate closely related species, we analysed genetic variation within and between four S and four NS populations from across the Iberian peninsula. Based on microsatellites, genetic variation was similar in S and NS populations (average Ho=0.48). The populations were significantly differentiated from each other (overall FST=0.23), and the degree of differentiation between S and NS populations was similar to that within these two groups. However, high S versus NS differentiation was observed in DNA polymorphism of two genes putatively involved in adaptation to serpentine environments, IREG1 and NRAMP4, whereas no such differentiation was found in a gene (ASIL1) not expected to play a specific role in ecological adaptation in A. serpyllifolium. These results indicate that S and NS populations belong to the same species and that nickel hyperaccumulation in A. serpyllifolium appears to represent a case of adaptation to growth on serpentine soils. Further functional and evolutionary genetic work in this system has the potential to significantly advance our understanding of the evolution of metal hyperaccumulation in plants.
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Affiliation(s)
- M K Sobczyk
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - J A C Smith
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - A J Pollard
- Department of Biology, Furman University, Greenville, SC, USA
| | - D A Filatov
- Department of Plant Sciences, University of Oxford, Oxford, UK
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17
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Frajman B, Rešetnik I, Niketić M, Ehrendorfer F, Schönswetter P. Patterns of rapid diversification in heteroploid Knautia sect. Trichera (Caprifoliaceae, Dipsacoideae), one of the most intricate taxa of the European flora. BMC Evol Biol 2016; 16:204. [PMID: 27724874 PMCID: PMC5057222 DOI: 10.1186/s12862-016-0773-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 09/28/2016] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Polyploidy is one of the most important evolutionary pathways in flowering plants and has significantly contributed to their diversification and radiation. Due to the prevalence of reticulate evolution spanning three ploidy levels, Knautia is considered one of the taxonomically most intricate groups in the European flora. On the basis of ITS and plastid DNA sequences as well as AFLP fingerprints obtained from 381 populations of almost all species of the genus we asked the following questions. (1) Where and when did the initial diversification in Knautia take place, and how did it proceed further? (2) Did Knautia undergo a similarly recent (Pliocene/Pleistocene) rapid radiation as other genera with similar ecology and overlapping distribution? (3) Did polyploids evolve within the previously recognised diploid groups or rather from hybridisation between groups? RESULTS The diversification of Knautia was centred in the Eastern Mediterranean. According to our genetic data, the genus originated in the Early Miocene and started to diversify in the Middle Miocene, whereas the onset of radiation of sect. Trichera was in central parts of the Balkan Peninsula, roughly 4 Ma. Extensive spread out of the Balkans started in the Pleistocene about 1.5 Ma. Diversification of sect. Trichera was strongly fostered by polyploidisation, which occurred independently many times. Tetraploids are observed in almost all evolutionary lineages whereas hexaploids are rarer and restricted to a few phylogenetic groups. Whether polyploids originated via autopolyploidy or allopolyploidy is unclear due to the weak genetic separation among species. In spite of the complexity of sect. Trichera, we present nine AFLP-characterised informal species groups, which coincide only partly with former traditional groups. CONCLUSIONS Knautia sect. Trichera is a prime example for rapid diversification, mostly taking place during Pliocene and Pleistocene. Numerous cycles of habitat fragmentation and subsequent reconnections likely promoted hybridisation and polyploidisation. Extensive haplotype sharing and unresolved phylogenetic relationships suggest that these processes occurred rapidly and extensively. Thus, the dynamic polyploid evolution, the lack of crossing barriers within ploidy levels supported by conserved floral morphology, the highly variable leaf morphology and unstable indumentum composition prevent establishing a well-founded taxonomic framework.
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Affiliation(s)
- Božo Frajman
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, A-6020 Innsbruck, Austria
| | - Ivana Rešetnik
- Faculty of Science, University of Zagreb, Marulićev trg 20, HR-10000 Zagreb, Croatia
| | - Marjan Niketić
- Natural History Museum, Njegoševa 51, 11000 Belgrade, Serbia
| | - Friedrich Ehrendorfer
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Peter Schönswetter
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, A-6020 Innsbruck, Austria
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Mandák B, Vít P, Krak K, Trávníček P, Havrdová A, Hadincová V, Zákravský P, Jarolímová V, Bacles CFE, Douda J. Flow cytometry, microsatellites and niche models reveal the origins and geographical structure of Alnus glutinosa populations in Europe. ANNALS OF BOTANY 2016; 117:107-20. [PMID: 26467247 PMCID: PMC4701152 DOI: 10.1093/aob/mcv158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 09/01/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND AIMS Polyploidy in plants has been studied extensively. In many groups, two or more cytotypes represent separate biological entities with distinct distributions, histories and ecology. This study examines the distribution and origins of cytotypes of Alnus glutinosa in Europe, North Africa and western Asia. METHODS A combined approach was used involving flow cytometry and microsatellite analysis of 12 loci in 2200 plants from 209 populations combined with species distribution modelling using MIROC and CCSM climatic models, in order to analyse (1) ploidy and genetic variation, (2) the origin of tetraploid A. glutinosa, considering A. incana as a putative parent, and (3) past distributions of the species. KEY RESULTS The occurrence of tetraploid populations of A. glutinosa in Europe is determined for the first time. The distribution of tetraploids is far from random, forming two geographically well-delimited clusters located in the Iberian Peninsula and the Dinaric Alps. Based on microsatellite analysis, both tetraploid clusters are probably of autopolyploid origin, with no indication that A. incana was involved in their evolutionary history. A projection of the MIROC distribution model into the Last Glacial Maximum (LGM) showed that (1) populations occurring in the Iberian Peninsula and North Africa were probably interconnected during the LGM and (2) populations occurring in the Dinaric Alps did not exist throughout the last glacial periods, having retreated southwards into lowland areas of the Balkan Peninsula. CONCLUSIONS Newly discovered tetraploid populations are situated in the putative main glacial refugia, and neither of them was likely to have been involved in the colonization of central and northern Europe after glacial withdrawal. This could mean that neither the Iberian Peninsula nor the western part of the Balkan Peninsula served as effective refugial areas for northward post-glacial expansion of A. glutinosa.
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Affiliation(s)
- Bohumil Mandák
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic; Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6-Suchdol, CZ-165 21, Czech Republic;
| | - Petr Vít
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic; Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6-Suchdol, CZ-165 21, Czech Republic
| | - Karol Krak
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic; Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6-Suchdol, CZ-165 21, Czech Republic
| | - Pavel Trávníček
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic; Faculty of Agriculture, University of South Bohemia, Studentská 13, CZ-370 05, České Budějovice, Czech Republic and
| | - Alena Havrdová
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic; Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6-Suchdol, CZ-165 21, Czech Republic
| | - Věroslava Hadincová
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
| | - Petr Zákravský
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
| | - Vlasta Jarolímová
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
| | - Cecile Fanny Emilie Bacles
- University of Pau and Pays Adour, UFR Sciences et Techniques, Departement de Biologie, F-64100 Pau, France
| | - Jan Douda
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic; Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6-Suchdol, CZ-165 21, Czech Republic
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19
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Čertner M, Kolář F, Schönswetter P, Frajman B. Does hybridization with a widespread congener threaten the long-term persistence of the Eastern Alpine rare local endemic Knautia carinthiaca? Ecol Evol 2015; 5:4263-76. [PMID: 26664677 PMCID: PMC4667829 DOI: 10.1002/ece3.1686] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 07/31/2015] [Accepted: 08/05/2015] [Indexed: 12/22/2022] Open
Abstract
Interspecific hybridization, especially when regularly followed by backcrossing (i.e., introgressive hybridization), conveys a substantial risk for many endangered organisms. This is particularly true for narrow endemics occurring within distributional ranges of widespread congeners. An excellent example is provided by the plant genus Knautia (Caprifoliaceae): Locally endemic K. carinthiaca is reported from two isolated populations in southern Austria situated within an area predominantly occupied by widespread K. arvensis. While K. carinthiaca usually inhabits low-competition communities on rocky outcrops, K. arvensis occurs mainly in dry to mesic managed grasslands, yet both species can coexist in marginal environments and were suspected to hybridize. Flow cytometry revealed that diploid K. carinthiaca only occurs at its locus classicus, whereas the second locality is inhabited by the morphologically similar but tetraploid K. norica. In the, therefore, single population of K. carinthiaca, flow cytometry and AFLP fingerprinting showed signs of introgressive hybridization with diploid K. arvensis. Hybridization patterns were also reflected in intermediate habitat preferences and morphology of the hybrids. Environmental barriers to gene flow seem to prevent genetic erosion of K. carinthiaca individuals from the core ecological niches, restricting most introgressed individuals to peripheral habitats. Efficient conservation of K. carinthiaca will require strict protection of its habitat and ban on forest clear cuts in a buffer zone to prevent invasion of K. arvensis. We demonstrate the large potential of multidisciplinary approaches combining molecular, cytometric, and ecological tools for a reliable inventory and threat assessment of rare species.
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Affiliation(s)
- Martin Čertner
- Department of BotanyFaculty of ScienceCharles University in PragueBenátská 2CZ‐128 00PragueCzech Republic
- Institute of BotanyThe Czech Academy of SciencesZámek 1CZ‐252 43PrůhoniceCzech Republic
| | - Filip Kolář
- Department of BotanyFaculty of ScienceCharles University in PragueBenátská 2CZ‐128 00PragueCzech Republic
- Institute of BotanyThe Czech Academy of SciencesZámek 1CZ‐252 43PrůhoniceCzech Republic
- National Centre for BiosystematicsNatural History MuseumUniversity of OsloNO‐0318OsloNorway
| | - Peter Schönswetter
- Institute of BotanyUniversity of InnsbruckSternwartestraße 156020InnsbruckAustria
| | - Božo Frajman
- Institute of BotanyUniversity of InnsbruckSternwartestraße 156020InnsbruckAustria
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20
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Frajman B, Rešetnik I, Weiss-Schneeweiss H, Ehrendorfer F, Schönswetter P. Cytotype diversity and genome size variation in Knautia (Caprifoliaceae, Dipsacoideae). BMC Evol Biol 2015; 15:140. [PMID: 26182989 PMCID: PMC4504173 DOI: 10.1186/s12862-015-0425-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/26/2015] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Polyploidisation is one of the most important mechanisms in the evolution of angiosperms. As in many other genera, formation of polyploids has significantly contributed to diversification and radiation of Knautia (Caprifoliaceae, Dipsacoideae). Comprehensive studies of fine- and broad-scale patterns of ploidy and genome size (GS) variation are, however, still limited to relatively few genera and little is known about the geographic distribution of ploidy levels within these genera. Here, we explore ploidy and GS variation in Knautia based on a near-complete taxonomic and comprehensive geographic sampling. RESULTS Genome size is a reliable indicator of ploidy level in Knautia, even if monoploid genome downsizing is observed in the polyploid cytotypes. Twenty-four species studied are diploid, 16 tetraploid and two hexaploid, whereas ten species possess two, and two species possess three ploidy levels. Di- and tetraploids are distributed across most of the distribution area of Knautia, while hexaploids were sampled in the Balkan and Iberian Peninsulas and the Alps. CONCLUSIONS We show that the frequency of polyploidisation is unevenly distributed in Knautia both in a geographic and phylogenetic context. Monoploid GS varies considerably among three evolutionary lineages (sections) of Knautia, but also within sections Trichera and Tricheroides, as well as within some of the species. Although the exact causes of this variation remain elusive, we demonstrate that monoploid GS increases significantly towards the limits of the genus' distribution.
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Affiliation(s)
- Božo Frajman
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, A-6020, Innsbruck, Austria
| | - Ivana Rešetnik
- Faculty of Science, University of Zagreb, Marulićev trg 20/II, HR-10000, Zagreb, Croatia
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030, Vienna, Austria.
| | - Friedrich Ehrendorfer
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030, Vienna, Austria
| | - Peter Schönswetter
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, A-6020, Innsbruck, Austria
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Kolář F, Píšová S, Záveská E, Fér T, Weiser M, Ehrendorfer F, Suda J. The origin of unique diversity in deglaciated areas: traces of Pleistocene processes in north-European endemics from theGalium pusillumpolyploid complex (Rubiaceae). Mol Ecol 2015; 24:1311-34. [DOI: 10.1111/mec.13110] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Filip Kolář
- National Centre for Biosystematics, Natural History Museum; University of Oslo; Oslo NO-0318 Norway
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 Prague CZ-128 01 Czech Republic
- Institute of Botany; The Czech Academy of Sciences; Průhonice 1 CZ-252 43 Czech Republic
| | - Soňa Píšová
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 Prague CZ-128 01 Czech Republic
- Institute of Botany; The Czech Academy of Sciences; Průhonice 1 CZ-252 43 Czech Republic
| | - Eliška Záveská
- Institute of Botany; University of Innsbruck; Sternwartestraße 15 Innsbruck A-6020 Austria
| | - Tomáš Fér
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 Prague CZ-128 01 Czech Republic
| | - Martin Weiser
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 Prague CZ-128 01 Czech Republic
| | - Friedrich Ehrendorfer
- Department of Systematic and Evolutionary Botany; Faculty Centre for Biodiversity; University of Vienna; Rennweg 14 Vienna A-1030 Austria
| | - Jan Suda
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 Prague CZ-128 01 Czech Republic
- Institute of Botany; The Czech Academy of Sciences; Průhonice 1 CZ-252 43 Czech Republic
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Prančl J, Kaplan Z, Trávníček P, Jarolímová V. Genome size as a key to evolutionary complex aquatic plants: polyploidy and hybridization in Callitriche (Plantaginaceae). PLoS One 2014; 9:e105997. [PMID: 25211149 PMCID: PMC4161354 DOI: 10.1371/journal.pone.0105997] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 07/26/2014] [Indexed: 01/31/2023] Open
Abstract
Despite their complex evolutionary histories, aquatic plants are highly underrepresented in contemporary biosystematic studies. Of them, the genus Callitriche is particularly interesting because of such evolutionary features as wide variation in chromosome numbers and pollination systems. However, taxonomic difficulties have prevented broader investigation of this genus. In this study we applied flow cytometry to Callitriche for the first time in order to gain an insight into evolutionary processes and genome size differentiation in the genus. Flow cytometry complemented by confirmation of chromosome counts was applied to an extensive dataset of 1077 Callitriche individuals from 495 localities in 11 European countries and the USA. Genome size was determined for 12 taxa. The results suggest that many important processes have interacted in the evolution of the genus, including polyploidization and hybridization. Incongruence between genome size and ploidy level, intraspecific variation in genome size, formation of autotriploid and hybridization between species with different pollination systems were also detected. Hybridization takes place particularly in the diploid-tetraploid complex C. cophocarpa-C. platycarpa, for which the triploid hybrids were frequently recorded in the area of co-occurrence of its parents. A hitherto unknown hybrid (probably C. hamulata × C. cophocarpa) with a unique chromosome number was discovered in the Czech Republic. However, hybridization occurs very rarely among most of the studied species. The main ecological preferences were also compared among the taxa collected. Although Callitriche taxa often grow in mixed populations, the ecological preferences of individual species are distinctly different in some cases. Anyway, flow cytometry is a very efficient method for taxonomic delimitation, determination and investigation of Callitriche species, and is even able to distinguish homoploid taxa and identify introduced species.
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Affiliation(s)
- Jan Prančl
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
- Department of Botany, Charles University, Praha, Czech Republic
| | - Zdeněk Kaplan
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
| | - Pavel Trávníček
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
- Department of Botany, Charles University, Praha, Czech Republic
| | - Vlasta Jarolímová
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
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23
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Soltis PS, Liu X, Marchant DB, Visger CJ, Soltis DE. Polyploidy and novelty: Gottlieb's legacy. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130351. [PMID: 24958924 PMCID: PMC4071524 DOI: 10.1098/rstb.2013.0351] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nearly four decades ago, Roose & Gottlieb (Roose & Gottlieb 1976 Evolution 30, 818-830. (doi:10.2307/2407821)) showed that the recently derived allotetraploids Tragopogon mirus and T. miscellus combined the allozyme profiles of their diploid parents (T. dubius and T. porrifolius, and T. dubius and T. pratensis, respectively). This classic paper addressed the link between genotype and biochemical phenotype and documented enzyme additivity in allopolyploids. Perhaps more important than their model of additivity, however, was their demonstration of novelty at the biochemical level. Enzyme multiplicity-the production of novel enzyme forms in the allopolyploids-can provide an extensive array of polymorphism for a polyploid individual and may explain, for example, the expanded ranges of polyploids relative to their diploid progenitors. In this paper, we extend the concept of evolutionary novelty in allopolyploids to a range of genetic and ecological features. We observe that the dynamic nature of polyploid genomes-with alterations in gene content, gene number, gene arrangement, gene expression and transposon activity-may generate sufficient novelty that every individual in a polyploid population or species may be unique. Whereas certain combinations of these features will undoubtedly be maladaptive, some unique combinations of newly generated variation may provide tremendous evolutionary potential and adaptive capabilities.
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Affiliation(s)
- Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Xiaoxian Liu
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - D Blaine Marchant
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Clayton J Visger
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA Department of Biology, University of Florida, Gainesville, FL 32611, USA
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Hanzl M, Kolář F, Nováková D, Suda J. Nonadaptive processes governing early stages of polyploid evolution: Insights from a primary contact zone of relict serpentine Knautia arvensis (Caprifoliaceae). AMERICAN JOURNAL OF BOTANY 2014; 101:935-945. [PMID: 24920762 DOI: 10.3732/ajb.1400005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
• Premise of the study: Contact zones between polyploids and their diploid progenitors may provide important insights into the mechanisms of sympatric speciation and local adaptation. However, most published studies investigated secondary contact zones where the effects of genome duplication can be confounded by previous independent evolution of currently sympatric cytotypes. We compared genetically close diploid and autotetraploid serpentine cytotypes of Knautia arvensis (Caprifoliaceae) in a primary contact zone and evaluated the role of adaptive and nonadaptive processes for cytotype coexistence.• Methods: DNA flow cytometry was used to determine ploidy distribution at various spatial scales (from across the entire contact zone to microgeographic). Habitat preferences of diploids and polyploids were assessed by comparing vegetation composition of nearby ploidy-uniform sites and by recording plant species immediately surrounding both cytotypes in mixed-ploidy plots.• Key results: Tetraploids considerably outnumbered their diploid progenitors in the contact zone. Both cytotypes were segregated at all investigated spatial scales. This pattern was not driven by ecological shifts, because both diploids and tetraploids inhabited sites with nearly identical vegetation cover. Certain interploidy niche differentiation was indicated only at the smallest spatial scale; ecologically nonadaptive processes were most likely responsible for this difference.• Conclusions: We conclude that a shift in ecological preferences (i.e., the adaptive scenario) is not necessary for the establishment and evolutionary success of autopolyploid derivatives in primary contact zones. Spatial segregation that would support ploidy coexistence can also be achieved by ecologically nonadaptive processes, including the founder effect, limited dispersal ability, intense clonal growth, and triploid block.
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Affiliation(s)
- Martin Hanzl
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01 Prague, Czech Republic Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01 Prague, Czech Republic Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Dora Nováková
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01 Prague, Czech Republic
| | - Jan Suda
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01 Prague, Czech Republic Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43 Průhonice, Czech Republic
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25
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Rešetnik I, Frajman B, Bogdanović S, Ehrendorfer F, Schönswetter P. Disentangling relationships among the diploid members of the intricate genus Knautia (Caprifoliaceae, Dipsacoideae). Mol Phylogenet Evol 2014; 74:97-110. [PMID: 24508604 DOI: 10.1016/j.ympev.2014.01.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 01/19/2014] [Accepted: 01/27/2014] [Indexed: 01/05/2023]
Abstract
The genus Knautia (Caprifoliaceae, Dipsacoideae) encompasses 40-60 species mainly distributed in western Eurasia, with highest species diversity in the Alps and the Balkan Peninsula. It is traditionally regarded as one of the taxonomically most challenging European genera due to the widespread occurrence of polyploidy, the high incidence of hybridisation and the maintenance of morphologically intermediate forms. A prerequisite for assessing the complex spatiotemporal diversification of a polyploid group is a comprehensive hypothesis of the phylogenetic relationships among its diploid members. To this end, DNA sequence data (nrDNA ITS and plastid petN(ycf6)-psbM) combined with AFLP fingerprinting were performed on 148 diploid populations belonging to 35 taxa. Phylogenies obtained by maximum parsimony and Bayesian analyses were used to test the monophyly of the genus and its three sections Trichera, Tricheroides and Knautia, to provide insights into its evolutionary history and to test previous hypotheses of inter- and intrasectional classification. Both nuclear and chloroplast datasets support the monophyly of Knautia and its three sections, with ambiguous placement of K. cf. degenii. The majority of species belong to the nearly exclusively perennial section Trichera (x=10). Within section Trichera all markers revealed largely unresolved phylogenetic relationships suggesting rapid radiation and recent range expansion. In addition, extensive sharing of plastid haplotypes across taxa and wide geographic ranges of plastid haplotypes and ribotype groups were observed. The molecular data are partly at odds with the traditional informal grouping of taxa within section Trichera. Whereas the traditional groups of K. dinarica, K. drymeia and K. montana can be maintained, the new, smaller and well supported Midzorensis and Pancicii Groups as well as the SW European Group are separated from the heterogeneous traditional K. longifolia group. The former groups of K. arvensis, K. dalmatica, K. fleischmannii and K. velutina are clearly polyphyletic. Their diploid members have to be rearranged into the Xerophytic Group, the Carinthiaca Group, and the Northern and Southern Arvensis Groups. The annual sections Tricheroides (x=10) and Knautia (x=8) with only a few taxa are resolved in the ITS and plastid trees on long branches as early diverging lineages within the genus.
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Affiliation(s)
- Ivana Rešetnik
- Faculty of Science, University of Zagreb, Marulićev trg 9a, HR-10000 Zagreb, Croatia.
| | - Božo Frajman
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, A-6020 Innsbruck, Austria.
| | - Sandro Bogdanović
- Faculty of Agriculture, University of Zagreb, Svetošimunska 25, HR-10000 Zagreb, Croatia.
| | - Friedrich Ehrendorfer
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
| | - Peter Schönswetter
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, A-6020 Innsbruck, Austria.
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Poulíčková A, Poulíèková A, Mazalová P, Vašut RJ, Šarhanová P, Neustupa J, Neustupa J, Škaloud P. DNA content variation and its significance in the evolution of the genus Micrasterias (Desmidiales, Streptophyta). PLoS One 2014; 9:e86247. [PMID: 24465986 PMCID: PMC3897674 DOI: 10.1371/journal.pone.0086247] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 12/12/2013] [Indexed: 01/06/2023] Open
Abstract
It is now clear that whole genome duplications have occurred in all eukaryotic evolutionary lineages, and that the vast majority of flowering plants have experienced polyploidisation in their evolutionary history. However, study of genome size variation in microalgae lags behind that of higher plants and seaweeds. In this study, we have addressed the question whether microalgal phylogeny is associated with DNA content variation in order to evaluate the evolutionary significance of polyploidy in the model genus Micrasterias. We applied flow-cytometric techniques of DNA quantification to microalgae and mapped the estimated DNA content along the phylogenetic tree. Correlations between DNA content and cell morphometric parameters were also tested using geometric morphometrics. In total, DNA content was successfully determined for 34 strains of the genus Micrasterias. The estimated absolute 2C nuclear DNA amount ranged from 2.1 to 64.7 pg; intraspecific variation being 17.4–30.7 pg in M. truncata and 32.0–64.7 pg in M. rotata. There were significant differences between DNA contents of related species. We found strong correlation between the absolute nuclear DNA content and chromosome numbers and significant positive correlation between the DNA content and both cell size and number of terminal lobes. Moreover, the results showed the importance of cell/life cycle studies for interpretation of DNA content measurements in microalgae.
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Affiliation(s)
| | - Aloisie Poulíèková
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Petra Mazalová
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Olomouc, Czech Republic ; Department of Biology, Faculty of Science, University of Hradec Králové, Hradec Králové, Czech Republic
| | - Radim J Vašut
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Petra Šarhanová
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Olomouc, Czech Republic
| | | | - Jiøí Neustupa
- Department of Botany, Charles University in Prague, Prague, Czech Republic
| | - Pavel Škaloud
- Department of Botany, Charles University in Prague, Prague, Czech Republic
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27
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Bourne EC, Mina D, Gonçalves SC, Loureiro J, Freitas H, Muller LAH. Large and variable genome size unrelated to serpentine adaptation but supportive of cryptic sexuality in Cenococcum geophilum. MYCORRHIZA 2014; 24:13-20. [PMID: 23754539 DOI: 10.1007/s00572-013-0501-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 04/17/2013] [Indexed: 05/14/2023]
Abstract
Estimations of genome size and its variation can provide valuable information regarding the genetic diversity of organisms and their adaptation potential to heterogeneous environments. We used flow cytometry to characterize the variation in genome size among 40 isolates of Cenococcum geophilum, an ectomycorrhizal fungus with a wide ecological and geographical distribution, obtained from two serpentine and two non-serpentine sites in Portugal. Besides determining the genome size and its intraspecies variation, we wanted to assess whether a relationship exists between genome size and the edaphic background of the C. geophilum isolates. Our results reveal C. geophilum to have one of the largest genome sizes so far measured in the Ascomycota, with a mean haploid genome size estimate of 0.208 pg (203 Mbp). However, no relationship was found between genome size and the edaphic background of the sampled isolates, indicating genetic and demographic processes to be more important for shaping the genome size variation in this species than environmental selection. The detection of variation in ploidy level among our isolates, including a single individual with both presumed haploid and diploid nuclei, provides supportive evidence for a possible cryptic sexual or parasexual cycle in C. geophilum (although other mechanisms may have caused this variation). The existence of such a cycle would have wide significance, explaining the high levels of genetic diversity and likelihood of recombination previously reported in this species, and adds to the increasing number of studies suggesting sexual cycles in previously assumed asexual fungi.
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Affiliation(s)
- Elizabeth C Bourne
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3001-401, Coimbra, Portugal
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28
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Róis AS, Rodríguez López CM, Cortinhas A, Erben M, Espírito-Santo D, Wilkinson MJ, Caperta AD. Epigenetic rather than genetic factors may explain phenotypic divergence between coastal populations of diploid and tetraploid Limonium spp. (Plumbaginaceae) in Portugal. BMC PLANT BIOLOGY 2013; 13:205. [PMID: 24314092 PMCID: PMC3884021 DOI: 10.1186/1471-2229-13-205] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 11/26/2013] [Indexed: 05/09/2023]
Abstract
BACKGROUND The genus Limonium Miller comprises annual and perennial halophytes that can produce sexual and/or asexual seeds (apomixis). Genetic and epigenetic (DNA methylation) variation patterns were investigated in populations of three phenotypically similar putative sexual diploid species (L. nydeggeri, L. ovalifolium, L. lanceolatum), one sexual tetraploid species (L. vulgare) and two apomict tetraploid species thought to be related (L. dodartii, L. multiflorum). The extent of morphological differentiation between these species was assessed using ten diagnostic morphometric characters. RESULTS A discriminant analysis using the morphometric variables reliably assigns individuals into their respective species groups. We found that only modest genetic and epigenetic differentiation was revealed between species by Methylation Sensitive Amplification Polymorphism (MSAP). However, whilst there was little separation possible between ploidy levels on the basis of genetic profiles, there was clear and pronounced interploidy discrimination on the basis of epigenetic profiles. Here we investigate the relative contribution of genetic and epigenetic factors in explaining the complex phenotypic variability seen in problematic taxonomic groups such as Limonium that operate both apomixis and sexual modes of reproduction. CONCLUSIONS Our results suggest that epigenetic variation might be one of the drivers of the phenotypic divergence between diploid and tetraploid taxa and discuss that intergenome silencing offers a plausible mechanistic explanation for the observed phenotypic divergence between these microspecies. These results also suggest that epigenetic profiling offer an additional tool to infer ploidy level in stored specimens and that stable epigenetic change may play an important role in apomict evolution and species recognition.
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Affiliation(s)
- Ana Sofia Róis
- Plant Diversity and Conservation Group, Centro de Botânica Aplicada à Agricultura (CBAA), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Carlos M Rodríguez López
- Plant Genomics Centre, School of Agriculture, Food and Wine, Faculty of Sciences, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA 5064 Australia
| | - Ana Cortinhas
- Plant Diversity and Conservation Group, Centro de Botânica Aplicada à Agricultura (CBAA), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Matthias Erben
- Section Biodiversity Research & Systematic Botany, Maximilian University of Munich, Munich, Germany
| | - Dalila Espírito-Santo
- Plant Diversity and Conservation Group, Centro de Botânica Aplicada à Agricultura (CBAA), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
- Research Network in Biodiversity and Evolutionary Biology (InBIO), ISA, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Michael J Wilkinson
- Plant Genomics Centre, School of Agriculture, Food and Wine, Faculty of Sciences, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA 5064 Australia
| | - Ana D Caperta
- Plant Diversity and Conservation Group, Centro de Botânica Aplicada à Agricultura (CBAA), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
- Research Network in Biodiversity and Evolutionary Biology (InBIO), ISA, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
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29
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Dufresne F, Stift M, Vergilino R, Mable BK. Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools. Mol Ecol 2013; 23:40-69. [DOI: 10.1111/mec.12581] [Citation(s) in RCA: 248] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 12/19/2022]
Affiliation(s)
- France Dufresne
- Département de Biologie; Université du Québec à Rimouski; Québec QC Canada G5L 3A1
| | - Marc Stift
- Department of Biology; University of Konstanz; Konstanz D 78457 Germany
| | - Roland Vergilino
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | - Barbara K. Mable
- Institute of Biodiversity; Animal Health and Comparative Medicine; College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow UK
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30
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Sonnleitner M, Weis B, Flatscher R, García PE, Suda J, Krejčíková J, Schneeweiss GM, Winkler M, Schönswetter P, Hülber K. Parental ploidy strongly affects offspring fitness in heteroploid crosses among three cytotypes of autopolyploid Jacobaea carniolica (Asteraceae). PLoS One 2013; 8:e78959. [PMID: 24265735 PMCID: PMC3827125 DOI: 10.1371/journal.pone.0078959] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 09/17/2013] [Indexed: 11/25/2022] Open
Abstract
Reproductive interactions among cytotypes in their contact zones determine whether these cytotypes can co-exist and form stable contact zones or not. In autopolyploids, heteroploid cross-compatibilities might depend on parental ploidy, but tests of this hypothesis in autopolyploid systems with more than two ploidies are lacking. Here, we study Jacobaea carniolica, which comprises diploid, tetraploid, and hexaploid individuals regularly forming contact zones. Seeds obtained from in situ cross-pollinations within and among cytotypes were subjected to DNA flow cytometry and greenhouse germination experiments. Hybrid fitness and parental effects on hybrid fitness were tested with regression models comparing fitness parameters of early life stages. Irrespective of the direction of crosses, seed viability and seedling survival in diploid-polyploid crosses were substantially lower than in tetraploid-hexaploid crosses. In contrast, seedling growth traits indicated neither transgressive character expression nor any selection against hybrid offspring. Congruent with a model of genome dosage effects, these traits differed between reciprocal crosses, especially of diploids and tetraploids, where trait values resembled those of the maternal parent. The strong effect of parental ploidy on offspring fitness in heteroploid crosses may cause contact zones involving exclusively polyploid cytotypes to be less stable over longer terms than those involving diploids and polyploids.
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Affiliation(s)
- Michaela Sonnleitner
- Department of Systematic and Evolutionary Botany, University of Vienna, Vienna, Austria
- Department of Conservation Biology, Vegetation Ecology and Landscape Ecology, University of Vienna, Vienna, Austria
| | - Birgit Weis
- Department of Systematic and Evolutionary Botany, University of Vienna, Vienna, Austria
| | - Ruth Flatscher
- Department of Systematic and Evolutionary Botany, University of Vienna, Vienna, Austria
- Institute of Botany, University of Innsbruck, Innsbruck, Austria
| | - Pedro Escobar García
- Department of Systematic and Evolutionary Botany, University of Vienna, Vienna, Austria
| | - Jan Suda
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
| | - Jana Krejčíková
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
| | - Gerald M. Schneeweiss
- Department of Systematic and Evolutionary Botany, University of Vienna, Vienna, Austria
| | - Manuela Winkler
- Department of Systematic and Evolutionary Botany, University of Vienna, Vienna, Austria
| | | | - Karl Hülber
- Department of Conservation Biology, Vegetation Ecology and Landscape Ecology, University of Vienna, Vienna, Austria
- Vienna Institute for Nature Conservation & Analyses, Vienna, Austria
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31
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Weiss-Schneeweiss H, Emadzade K, Jang TS, Schneeweiss G. Evolutionary consequences, constraints and potential of polyploidy in plants. Cytogenet Genome Res 2013; 140:137-50. [PMID: 23796571 PMCID: PMC3859924 DOI: 10.1159/000351727] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Polyploidy, the possession of more than 2 complete genomes, is a major force in plant evolution known to affect the genetic and genomic constitution and the phenotype of an organism, which will have consequences for its ecology and geography as well as for lineage diversification and speciation. In this review, we discuss phylogenetic patterns in the incidence of polyploidy including possible underlying causes, the role of polyploidy for diversification, the effects of polyploidy on geographical and ecological patterns, and putative underlying mechanisms as well as chromosome evolution and evolution of repetitive DNA following polyploidization. Spurred by technological advances, a lot has been learned about these aspects both in model and increasingly also in nonmodel species. Despite this enormous progress, long-standing questions about polyploidy still cannot be unambiguously answered, due to frequently idiosyncratic outcomes and insufficient integration of different organizational levels (from genes to ecology), but likely this will change in the near future. See also the sister article focusing on animals by Choleva and Janko in this themed issue.
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Affiliation(s)
- H. Weiss-Schneeweiss
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - K. Emadzade
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - T.-S. Jang
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - G.M. Schneeweiss
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
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32
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Kolář F, Lučanová M, Vít P, Urfus T, Chrtek J, Fér T, Ehrendorfer F, Suda J. Diversity and endemism in deglaciated areas: ploidy, relative genome size and niche differentiation in the Galium pusillum complex (Rubiaceae) in Northern and Central Europe. ANNALS OF BOTANY 2013; 111:1095-1108. [PMID: 23589633 PMCID: PMC3662515 DOI: 10.1093/aob/mct074] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Accepted: 02/11/2013] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Plants endemic to areas covered by ice sheets during the last glaciation represent paradigmatic examples of rapid speciation in changing environments, yet very few systems outside the harsh arctic zone have been comprehensively investigated so far. The Galium pusillum aggregate (Rubiaceae) is a challenging species complex that exhibits a marked differentiation in boreal parts of Northern Europe. As a first step towards understanding its evolutionary history in deglaciated regions, this study assesses cytological variation and ecological preferences of the northern endemics and compares the results with corresponding data for species occurring in neighbouring unglaciated parts of Central and Western Europe. METHODS DNA flow cytometry was used together with confirmatory chromosome counts to determine ploidy levels and relative genome sizes in 1158 individuals from 181 populations. A formalized analysis of habitat preferences was applied to explore niche differentiation among species and ploidy levels. KEY RESULTS The G. pusillum complex evolved at diploid and tetraploid levels in Northern Europe, in contrast to the high-polyploid evolution of most other northern endemics. A high level of eco-geographic segregation was observed between different species (particularly along gradients of soil pH and competition) which is unusual for plants in deglaciated areas and most probably contributes to maintaining species integrity. Relative monoploid DNA contents of the species from previously glaciated regions were significantly lower than those of their counterparts from mostly unglaciated Central Europe, suggesting independent evolutionary histories. CONCLUSIONS The aggregate of G. pusillum in Northern Europe represents an exceptional case with a geographically vicariant and ecologically distinct diploid/tetraploid species endemic to formerly glaciated areas. The high level of interspecific differentiation substantially widens our perception of the evolutionary dynamics and speciation rates in the dramatically changing environments of Northern Europe.
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Affiliation(s)
- Filip Kolář
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01 Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice 1, CZ-252 43 Czech Republic
| | - Magdalena Lučanová
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01 Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice 1, CZ-252 43 Czech Republic
| | - Petr Vít
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01 Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice 1, CZ-252 43 Czech Republic
| | - Tomáš Urfus
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01 Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice 1, CZ-252 43 Czech Republic
| | - Jindřich Chrtek
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01 Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice 1, CZ-252 43 Czech Republic
| | - Tomáš Fér
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01 Czech Republic
| | - Friedrich Ehrendorfer
- Department of Systematic and Evolutionary Botany, Faculty Centre for Biodiversity, University of Vienna, Rennweg 14, Vienna, A-1030 Austria
| | - Jan Suda
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01 Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice 1, CZ-252 43 Czech Republic
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