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Gaynor ML, Kortessis N, Soltis DE, Soltis PS, Ponciano JM. Dynamics of Mixed-Ploidy Populations under Demographic and Environmental Stochasticities. Am Nat 2025; 205:413-434. [PMID: 40179426 DOI: 10.1086/734411] [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] [Indexed: 04/05/2025]
Abstract
AbstractThe population dynamics of autopolyploids-organisms with more than two genome copies of a single species-and their diploid progenitors have been extensively studied. The acquisition of multiple genome copies is heavily influenced by stochasticity, which strongly suggests the efficacy of a probabilistic approach to examine the long-term dynamics of a population with multiple cytotypes. Yet our current understanding of the dynamics of autopolyploid populations has not incorporated stochastic population dynamics and coexistence theory. To investigate the factors contributing to the probability and stability of coexisting cytotypes, we designed a new population dynamics model that incorporates demographic and environmental stochasticities to simulate the formation, establishment, and persistence of diploids, triploids, and autotetraploids in the face of gene flow among cytotypes. We found that increased selfing rates and pronounced reproductive isolation promote coexistence of multiple cytotypes. In stressful environments and with strong competitive effects among cytotypes, these dynamics are more complex; our stochastic modeling approach reveals the resulting intricacies that give autotetraploids competitive advantage over their diploid progenitors. Our work is foundational for a better understanding of the dynamics of coexistence of multiple cytotypes.
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Osterman WHA, Hagan JG, Whitton J, Bjorkman AD. The ecology of polyploid establishment and exclusion, with implications for polyploid biogeography. THE NEW PHYTOLOGIST 2025; 246:47-60. [PMID: 39925339 PMCID: PMC11883057 DOI: 10.1111/nph.20451] [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: 07/05/2024] [Accepted: 01/15/2025] [Indexed: 02/11/2025]
Abstract
The relationship between polyploid formation, triploid fitness and plant reproduction has been studied for over a century, and uniparental reproduction has long been recognized to play a crucial role in polyploid establishment. Yet, we lack a synthesized framework of how polyploid establishment is expected to be influenced by different reproductive modes among angiosperms. Here, we provide new perspectives on how uniparental reproduction, pollination ecology, triploid fitness and assortative mating can impact minority cytotype exclusion (MCE) and, thereby, the likelihood of polyploid establishment. We review the current state of knowledge of the reproductive mechanisms that impact polyploid establishment and discuss often overlooked aspects of these processes, such as the influence of pollinator communities on rates of self-pollination. We propose a framework for considering how variation in reproductive strategies and pollinator communities can impact the ability of a polyploid to overcome MCE. Finally, we propose links between patterns of variation in uniparental reproduction across plant communities and observed patterns in the distribution and abundance of polyploids.
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Affiliation(s)
- Wilhelm H. A. Osterman
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburg413 90Sweden
- Gothenburg Global Biodiversity CentreGothenburg413 90Sweden
| | - James G. Hagan
- Gothenburg Global Biodiversity CentreGothenburg413 90Sweden
- Department of Marine SciencesUniversity of GothenburgGothenburg413 90Sweden
| | - Jeannette Whitton
- Department of Botany and Biodiversity Research CentreThe University of British ColumbiaVancouverV6T 1Z4Canada
| | - Anne D. Bjorkman
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburg413 90Sweden
- Gothenburg Global Biodiversity CentreGothenburg413 90Sweden
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3
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Bartolić P, Voltrová A, Macková L, Šrámková G, Šlenker M, Mandáková T, Padilla García N, Marhold K, Kolář F. Overcoming Ploidy Barriers: The Role of Triploid Bridges in the Genetic Introgression of Cardamine amara. Mol Ecol 2025; 34:e17702. [PMID: 39996298 PMCID: PMC11934083 DOI: 10.1111/mec.17702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2024] [Revised: 02/07/2025] [Accepted: 02/11/2025] [Indexed: 02/26/2025]
Abstract
Polyploidisation is a significant reproductive barrier, yet genetic evidence indicates that interploidy admixture is more common than previously thought. Theoretical models and controlled crosses support the 'triploid bridge' hypothesis, proposing that hybrids of intermediate ploidy facilitate gene flow. However, comprehensive evidence combining experimental and genetic data from natural mixed-ploidy species is missing. Here, we investigated the rates and directionality of gene flow within a diploid-autotetraploid contact zone of Cardamine amara, a species with abundant natural triploids. We cytotyped over 400 individuals in the field, conducted reciprocal interploidy crosses, and inferred gene flow based on genome-wide sequencing of 84 individuals. Triploids represent a conspicuous entity in mixed-ploidy populations (5%), yet only part of them arose through interploidy hybridisation. Despite being rarely formed, triploid hybrids can backcross with their parental cytotypes, producing viable offspring that are often euploid (in 42% of cases). In correspondence, D-statistics and coalescent simulations documented a significant genome-wide signal of bidirectional gene flow in sympatric but not allopatric populations. Triploids, though rare, thus seem to play a key role in overcoming polyploidy-related reproductive barriers in C. amara. In sum, we present integrative evidence for interploidy gene flow mediated by a triploid bridge in natural populations.
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Affiliation(s)
- P. Bartolić
- Department of Botany, Faculty of ScienceCharles University in PraguePragueCzechia
| | - A. Voltrová
- Department of Botany, Faculty of ScienceCharles University in PraguePragueCzechia
| | - L. Macková
- Department of Botany, Faculty of ScienceCharles University in PraguePragueCzechia
| | - G. Šrámková
- Department of Botany, Faculty of ScienceCharles University in PraguePragueCzechia
| | - M. Šlenker
- Institute of BotanyPlant Science and Biodiversity Centre, Slovak Academy of SciencesBratislavaSlovakia
| | - T. Mandáková
- Department of Experimental Biology, Faculty of ScienceMasaryk UniversityBrnoCzechia
- Central European Institute of TechnologyMasaryk UniversityBrnoCzechia
| | - N. Padilla García
- Departamento de Botánica y Fisiología VegetalUniversity of SalamancaSalamancaSpain
| | - K. Marhold
- Department of Botany, Faculty of ScienceCharles University in PraguePragueCzechia
- Institute of BotanyPlant Science and Biodiversity Centre, Slovak Academy of SciencesBratislavaSlovakia
| | - F. Kolář
- Department of Botany, Faculty of ScienceCharles University in PraguePragueCzechia
- Institute of Botany of the Czech Academy of SciencesPrůhoniceCzechia
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Zhang XJ, Huang XH, Landis JB, Fu QS, Chen JT, Luo PR, Li LJ, Lu HY, Sun H, Deng T. Shifts in reproductive strategies in the evolutionary trajectory of plant lineages. SCIENCE CHINA. LIFE SCIENCES 2024; 67:2499-2510. [PMID: 39190128 DOI: 10.1007/s11427-024-2597-9] [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: 02/04/2024] [Accepted: 04/16/2024] [Indexed: 08/28/2024]
Abstract
Understanding the maintenance and shift in reproductive strategies is a fundamental question in evolutionary research. Although many efforts have been made to compare different reproductive strategies, the association between reproductive strategies and lineage divergence is largely unknown. To explore the impact of different reproductive strategies on lineage divergence, we investigated the evolution of clonality in Saxifraga sect. Irregulares+Heterisia. By integrating several lines of evidence, we found that the loss of clonality in Irregulares+Heterisia was associated with a progressive increase in diversification rate and intraspecific morphological diversity but with a reduction in species distribution range. Our findings provide insights into the ecological and evolutionary effects of different reproductive strategies, suggesting the necessity of integrating clonality into ecological and evolutional research.
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Affiliation(s)
- Xin-Jian Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xian-Han Huang
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey Hortorium, Cornell University, New York, 14850, USA
- BTI Computational Biology Center, Boyce Thompson Institute, New York, 14853, USA
| | - Quan-Sheng Fu
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-Tong Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Peng-Rui Luo
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Juan Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Heng-Yi Lu
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Hang Sun
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Tao Deng
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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Stiehl-Alves EM, Vieira AT, Trevelin C, Cristante Martins A, Souza-Chies TTD, Kaltchuk-Santos E. Can ploidy levels explain the variation of Herbertia lahue (Iridaceae)? Genet Mol Biol 2024; 46:e20230137. [PMID: 39261305 PMCID: PMC11390242 DOI: 10.1590/1678-4685-gmb-2023-0137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/15/2024] [Indexed: 09/13/2024] Open
Abstract
Polyploidy is often related with phenotypic variation, as observed in Herbertia lahue, a geophyte species. This study examined the H. lahue polyploid series and departure in cytogenetic, morphometric, and pollen data. Diploids (2n=2x=14) present bimodal karyotype with two long and five short chromosome pairs, while hexaploids (2n=6x=42) and octoploids (2n=8x=56) present a gradual decrease in chromosome size. All cytotypes have CMA+/DAPI- bands co-localized with 18S rDNA sites in the satellite region (no DAPI+ bands in any cytotype). Unlike diploids and octoploids, 5S rDNA interstitial sites in hexaploids are not in a syntenic position with 18S rDNA sites. Genome size is effective as an indirect predictor of the cytotypes since 2C-values increased according to ploidy level. The reduction in the number of the rDNA sites in polyploids associated with their lower 1Cx-values compared to diploids may suggest a genome downsizing process. Morphometric analysis revealed significant differences among cytotypes, and discriminant analysis identified three morphometric groupings corresponding to the cytotypes. The phenotypic variation observed in pollen grains, bulbs, and ovary characters suggested the gigas effect. Concluding, remarkable differentiation was observed at both genomic and phenotypic characters in all the cytotypes analyzed, suggesting a possible ongoing speciation process in H. lahue.
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Affiliation(s)
- Eudes Maria Stiehl-Alves
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Botânica, Porto Alegre, RS, Brazil
| | - Ariane Tonetto Vieira
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Caroline Trevelin
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Porto Alegre, RS, Brazil
| | - Alexandre Cristante Martins
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Botânica, Porto Alegre, RS, Brazil
| | - Tatiana Teixeira de Souza-Chies
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Botânica, Porto Alegre, RS, Brazil
| | - Eliane Kaltchuk-Santos
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Botânica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Porto Alegre, RS, Brazil
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Vaz de Sousa D, Greve M, Oberlander KC. Friends without benefits: Extensive cytotype sympatry and polyploid persistence in an African geophyte. AMERICAN JOURNAL OF BOTANY 2024; 111:e16291. [PMID: 38439133 DOI: 10.1002/ajb2.16291] [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: 09/01/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 03/06/2024]
Abstract
PREMISE Polyploidy is a major factor in plant adaptation and speciation. Multiple mechanisms contribute to autopolyploid frequency within populations, but uncertainties remain regarding mechanisms that facilitate polyploid establishment and persistence. Here we aimed to document and predict cytotype distributions of Oxalis obliquifolia Steud. ex A. Rich. across Gauteng, South Africa, and test for evidence of possible mechanisms, including morphological, phenological, and reproductive traits, that may potentially facilitate polyploid persistence. METHODS Over 320 O. obliquifolia plants from 25 sites were cytotyped using flow cytometry, and DNA ploidy was confirmed using meiotic chromosome squashes. Cytotypes were mapped and correlations with abiotic variables assessed using ordinations. To assess morphological and phenological associations with cytotype, we grew multiple cytotypes in a common garden, measured phenotypic traits and compared them using linear models and discriminant analyses. Intercytotype reproductive isolation was assessed using crossing experiments, and AMOVAs based on ITS DNA sequences tested for cytogeographic structure. RESULTS Six cytotypes were identified, and most sites had multiple cytotypes. Abiotic variables were not predictive of cytotype distribution. A clear gigas effect was present. Differences in flower size and phenology suggested pollinator interactions could play a role in polyploid persistence. Intercytotype crosses produced seed at low frequency. DNA data suggested diploids and polyploids were largely reproductively isolated in situ, and polyploidization events were not frequent enough to explain high cytotype sympatry. CONCLUSIONS Diploids and polyploids are behaving as separate species, despite little observable niche differentiation and non-zero potential intercytotype seed set. Tests on biotic interactions and intercytotype F1 fitness may provide insights into diploid and polyploid coexistence.
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Affiliation(s)
- Damian Vaz de Sousa
- Department of Plant and Soil Science, University of Pretoria, Private Bag X20, Hatfield, 0028, Pretoria, South Africa
- H.G.W.J. Schweickerdt Herbarium, Department of Plant and Soil Science, University of Pretoria, Pretoria, South Africa
| | - Michelle Greve
- Department of Plant and Soil Science, University of Pretoria, Private Bag X20, Hatfield, 0028, Pretoria, South Africa
| | - Kenneth C Oberlander
- H.G.W.J. Schweickerdt Herbarium, Department of Plant and Soil Science, University of Pretoria, Pretoria, South Africa
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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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Hagen ER, Vasconcelos T, Boyko JD, Beaulieu JM. Investigating historical drivers of latitudinal gradients in polyploid plant biogeography: A multiclade perspective. AMERICAN JOURNAL OF BOTANY 2024; 111:e16356. [PMID: 38867412 DOI: 10.1002/ajb2.16356] [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: 05/06/2024] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 06/14/2024]
Abstract
PREMISE The proportion of polyploid plants in a community increases with latitude, and different hypotheses have been proposed about which factors drive this pattern. Here, we aimed to understand the historical causes of the latitudinal polyploidy gradient using a combination of ancestral state reconstruction methods. Specifically, we assessed whether (1) polyploidization enables movement to higher latitudes (i.e., polyploidization precedes occurrences in higher latitudes) or (2) higher latitudes facilitate polyploidization (i.e., occurrence in higher latitudes precedes polyploidization). METHODS We reconstructed the ploidy states and ancestral niches of 1032 angiosperm species at four paleoclimatic time slices ranging from 3.3 million years ago to the present, comprising taxa from four well-represented clades: Onagraceae, Primulaceae, Solanum (Solanaceae), and Pooideae (Poaceae). We used ancestral niche reconstruction models alongside a customized discrete character evolution model to allow reconstruction of states at specific time slices. Patterns of latitudinal movement were reconstructed and compared in relation to inferred ploidy shifts. RESULTS No single hypothesis applied equally well across all analyzed clades. While significant differences in median latitudinal occurrence were detected in the largest clade, Poaceae, no significant differences were detected in latitudinal movement in any clade. CONCLUSIONS Our preliminary study is the first to attempt to connect ploidy changes to continuous latitudinal movement, but we cannot favor one hypothesis over another. Given that patterns seem to be clade-specific, more clades must be analyzed in future studies for generalities to be drawn.
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Affiliation(s)
- Eric R Hagen
- Department of Biological Sciences, University of Arkansas, Fayetteville, 72701, AR, USA
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, ON, Canada
| | - Thais Vasconcelos
- Department of Biological Sciences, University of Arkansas, Fayetteville, 72701, AR, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - James D Boyko
- Department of Biological Sciences, University of Arkansas, Fayetteville, 72701, AR, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
- Michigan Institute for Data Science, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Jeremy M Beaulieu
- Department of Biological Sciences, University of Arkansas, Fayetteville, 72701, AR, USA
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Osterman WHA, Hill A, Hagan JG, Whitton J, Bacon CD, Bjorkman AD. Rethinking pathways to the dioecy-polyploidy association: Genera with many dioecious species have fewer polyploids. AMERICAN JOURNAL OF BOTANY 2024; 111:e16318. [PMID: 38654555 DOI: 10.1002/ajb2.16318] [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: 09/18/2023] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 04/26/2024]
Abstract
PREMISE Numerous studies have found a positive association between dioecy and polyploidy; however, this association presents a theoretical conflict: While polyploids are predicted to benefit from self-reproduction for successful establishment, dioecious species cannot self-reproduce. We propose a theoretical framework to resolve this apparent conflict. We hypothesize that the inability of dioecious species to self-reproduce hinders their establishment as polyploids. We therefore expect that genera with many dioecious species have fewer polyploids, leading to a negative association between polyploidy and dioecy across genera. METHODS We used three publicly available databases to determine ploidy and sexual systems for 131 genera and 546 species. We quantified (1) the relationship between the frequency of polyploid species and the frequency of dioecious species across genera, and (2) the proportion of polyploids with hermaphroditism and dioecy across species, adjusting for phylogenetic history. RESULTS Across genera, we found a negative relationship between the proportion of polyploids and the proportion of dioecious species, a consistent trend across clades. Across all species, we found that sexual system (dioecious or not) was not associated with polyploidy. CONCLUSIONS Polyploids are rare in genera in which the majority of species are dioecious, consistent with the theory that self-reproduction favors polyploid establishment. The low frequency of polyploidy among dioecious species indicates the association is not as widespread as previously suggested. Our findings are consistent with previous studies identifying a positive relationship between the two traits, but only if polyploidy promotes a transition to dioecy, and not the reverse.
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Affiliation(s)
- Wilhelm H A Osterman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Adrian Hill
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - James G Hagan
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Jeannette Whitton
- Department of Botany and Biodiversity Research Centre, The University of British Columbia, Vancouver, Canada
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Anne D Bjorkman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
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10
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Vanrell MA, Novaes LR, Afonso A, Arroyo J, Simón-Porcar V. Ecological correlates of population genetics in Linum suffruticosum, an heterostylous polyploid and taxonomic complex endemic to the Western Mediterranean Basin. AOB PLANTS 2024; 16:plae027. [PMID: 39005727 PMCID: PMC11244263 DOI: 10.1093/aobpla/plae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 05/20/2024] [Indexed: 07/16/2024]
Abstract
Linum suffruticosum s.l. is a taxonomic complex widespread in the Western Mediterranean basin. The complex is characterized by a high phenotypic and cytogenetic diversity, and by a unique three-dimensional heterostyly system that makes it an obligate outcrosser. We studied the patterns of genetic diversity and structure of populations throughout the entire distribution of L. suffruticosum s.l. with microsatellite markers. We analysed their relationships with various biological and ecological variables, including the morph ratio and sex organ reciprocity of populations measured with a novel multi-dimensional method. Populations consistently showed an approximate 1:1 morph ratio with high sex organ reciprocity and high genetic diversity. We found high genetic differentiation of populations, showing a pattern of isolation by distance. The Rif mountains in NW Africa were the most important genetic barrier. The taxonomic treatment within the group was not related to the genetic differentiation of populations, but to their environmental differentiation. Genetic diversity was unrelated to latitude, elevation, population size, niche suitability or breeding system. However, there was a clear influence of ploidy level on the genetic diversity of populations, and a seeming centre-periphery pattern in its distribution. Our results suggest that polyploidization events, high outcrossing rates, isolation by distance and important geographical barriers to gene flow have played major roles in the microevolutionary history of this species complex.
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Affiliation(s)
- Maria Antònia Vanrell
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, 41012 Seville, Spain
| | - Letícia R Novaes
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, 41012 Seville, Spain
| | - Ana Afonso
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Juan Arroyo
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, 41012 Seville, Spain
| | - Violeta Simón-Porcar
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, 41012 Seville, Spain
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Usai G, Fambrini M, Pugliesi C, Simoni S. Exploring the patterns of evolution: Core thoughts and focus on the saltational model. Biosystems 2024; 238:105181. [PMID: 38479653 DOI: 10.1016/j.biosystems.2024.105181] [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: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.
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Affiliation(s)
- Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Samuel Simoni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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12
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Huang DQ, Ma XG, Sun H. Phylogenomic analyses and chromosome ploidy identification reveal multiple cryptic species in Allium sikkimense complex (Amaryllidaceae). FRONTIERS IN PLANT SCIENCE 2024; 14:1268546. [PMID: 38239226 PMCID: PMC10794568 DOI: 10.3389/fpls.2023.1268546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/06/2023] [Indexed: 01/22/2024]
Abstract
Polyploidization is a process that typically leads to instantaneous reproductive isolation and has, therefore, been considered as one of the major evolutionary forces in the species-rich Hengduan Mountains (HM), yet this topic remains poorly studied in the region. Allium sikkimense and its relatives (about eight species) compose a natural diploid-polyploid complex with the highest diversity in the HM and adjacent areas. A combination of nuclear ribosomal DNA (nrDNA), plastome, transcriptome, and ploidy identification through chromosome counting and flow cytometry is employed to reconstruct the phylogenetic relationships in this complex and to investigate the frequency and the evolutionary significance of polyploidy in the complex. The plastome failed to resolve the phylogenetic relationships of the different species in the A. sikkimense complex, and the phylogenetic tree based on nrDNA also has limited resolution. However, our study reveals a well-resolved phylogenetic framework for species in the A. sikkimense complex using more than 1,000 orthologous genes from the transcriptome data. Previously recognized morphospecies A. sikkimense are non-monophyletic and comprise at least two independently evolved lineages (i.e., cryptic species), each forming a clade with different diploid species in this complex. The embedded pattern of octoploid A. jichouense and tetraploid A. sp. nov. within different polyploid samples of A. sikkimense supports a possible scenario of budding speciation (via niche divergence). Furthermore, our results reveal that co-occurring species in the A. sikkimense complex usually have different ploidy levels, suggesting that polyploidy is an important process for reproductive isolation of sympatric Allium species. Phylogenetic network analyses suggested that the phylogenetic relationships of the A. sikkimense complex, allowing for reticulation events, always fit the dataset better than a simple bifurcating tree. In addition, the included or exserted filaments, which have long been used to delimit species, are highly unreliable taxonomically due to their extensive parallel and convergent evolution.
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Affiliation(s)
- De-Qing Huang
- College of Pharmacy, Guilin Medical University, Guilin, China
| | - Xiang-Guang Ma
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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13
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Stoeckel S, Becheler R, Bocharova E, Barloy D. GenAPoPop 1.0: A user-friendly software to analyse genetic diversity and structure from partially clonal and selfed autopolyploid organisms. Mol Ecol Resour 2024; 24:e13886. [PMID: 37902131 DOI: 10.1111/1755-0998.13886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 10/05/2023] [Accepted: 10/16/2023] [Indexed: 10/31/2023]
Abstract
Autopolyploidy is quite common in most clades of eukaryotes. The emergence of sequence-based genotyping methods with individual and marker tags now enables confident allele dosage, overcoming the main obstacle to the democratization of the population genetic approaches when studying ecology and evolution of autopolyploid populations and species. Reproductive modes, including clonality, selfing and allogamy, have deep consequences on the ecology and evolution of population and species. Analysing genetic diversity and its dynamics over generations is one efficient way to infer the relative importance of clonality, selfing and allogamy in populations. GenAPoPop is a user-friendly solution to compute the specific corpus of population genetic indices, including indices about genotypic diversity, needed to analyse partially clonal, selfed and allogamous polysomic populations genotyped with confident allele dosage. It also easily provides the posterior probabilities of quantitative reproductive modes in autopolyploid populations genotyped at two-time steps and a graphical representation of the minimum spanning trees of the genetic distances between polyploid individuals, facilitating the interpretation of the genetic coancestry between individuals in hierarchically structured populations. GenAPoPop complements the previously existing solutions, including SPAGEDI and POLYGENE, to use genotypings to study the ecology and evolution of autopolyploid populations. It was specially developed with a simple graphical interface and workflow, and comes with a simulator to facilitate practical courses and teaching of population genetics for autopolyploid populations.
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Affiliation(s)
- Solenn Stoeckel
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, France
- DECOD (Ecosystem Dynamics and Sustainability), Institut Agro, IFREMER, INRAE, Rennes, France
| | - Ronan Becheler
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, France
- DECOD (Ecosystem Dynamics and Sustainability), Institut Agro, IFREMER, INRAE, Rennes, France
| | - Ekaterina Bocharova
- Evolutionary Developmental Biology laboratory, Koltzov Institute of Developmental Biology of Russian Academy of Sciences (IDB RAS), Moscow, Russia
| | - Dominique Barloy
- DECOD (Ecosystem Dynamics and Sustainability), Institut Agro, IFREMER, INRAE, Rennes, France
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14
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Valdés-Florido A, Tan L, Maguilla E, Simón-Porcar VI, Zhou YH, Arroyo J, Escudero M. Drivers of diversification in Linum (Linaceae) by means of chromosome evolution: correlations with biogeography, breeding system and habit. ANNALS OF BOTANY 2023; 132:949-962. [PMID: 37738171 PMCID: PMC10808019 DOI: 10.1093/aob/mcad139] [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: 06/07/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
BACKGROUND AND AIMS Chromosome evolution leads to hybrid dysfunction and recombination patterns and has thus been proposed as a major driver of diversification in all branches of the tree of life, including flowering plants. In this study we used the genus Linum (flax species) to evaluate the effects of chromosomal evolution on diversification rates and on traits that are important for sexual reproduction. Linum is a useful study group because it has considerable reproductive polymorphism (heterostyly) and chromosomal variation (n = 6-36) and a complex pattern of biogeographical distribution. METHODS We tested several traditional hypotheses of chromosomal evolution. We analysed changes in chromosome number across the phylogenetic tree (ChromEvol model) in combination with diversification rates (ChromoSSE model), biogeographical distribution, heterostyly and habit (ChromePlus model). KEY RESULTS Chromosome number evolved across the Linum phylogeny from an estimated ancestral chromosome number of n = 9. While there were few apparent incidences of cladogenesis through chromosome evolution, we inferred up to five chromosomal speciation events. Chromosome evolution was not related to heterostyly but did show significant relationships with habit and geographical range. Polyploidy was negatively correlated with perennial habit, as expected from the relative commonness of perennial woodiness and absence of perennial clonality in the genus. The colonization of new areas was linked to genome rearrangements (polyploidy and dysploidy), which could be associated with speciation events during the colonization process. CONCLUSIONS Chromosome evolution is a key trait in some clades of the Linum phylogeny. Chromosome evolution directly impacts speciation and indirectly influences biogeographical processes and important plant traits.
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Affiliation(s)
- Ana Valdés-Florido
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes no. 6, 41012, Seville, Spain
| | - Lu Tan
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Xichang, Sichuan, 615000, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Enrique Maguilla
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes no. 6, 41012, Seville, Spain
- Área de Botánica, Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Ctra de Utrera km 1 sn, 41013, Seville, Spain
| | - Violeta I Simón-Porcar
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes no. 6, 41012, Seville, Spain
| | - Yong-Hong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Juan Arroyo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes no. 6, 41012, Seville, Spain
| | - Marcial Escudero
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes no. 6, 41012, Seville, Spain
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15
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Šingliarová B, Hojsgaard D, Müller-Schärer H, Mráz P. The novel expression of clonality following whole-genome multiplication compensates for reduced fertility in natural autopolyploids. Proc Biol Sci 2023; 290:20230389. [PMID: 37357859 PMCID: PMC10291721 DOI: 10.1098/rspb.2023.0389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/06/2023] [Indexed: 06/27/2023] Open
Abstract
Exploring the fitness consequences of whole-genome multiplication (WGM) is essential for understanding the establishment of autopolyploids in diploid parental populations, but suitable model systems are rare. We examined the impact of WGM on reproductive traits in three major cytotypes (2x, 3x, 4x) of Pilosella rhodopea, a species with recurrent formation of neo-autopolyploids in mixed-ploidy populations. We found that diploids had normal female sporogenesis and gametogenesis, high fertility, and produced predominantly euploid seed progeny. By contrast, autopolyploids had highly disturbed developmental programs that resulted in significantly lower seed set and a high frequency of aneuploid progeny. All cytotypes, but particularly triploids, produced gametes of varying ploidy, including unreduced ones, that participated in frequent intercytotype mating. Noteworthy, the reduced investment in sexual reproduction in autopolyploids was compensated by increased production of axillary rosettes and the novel expression of two clonal traits: adventitious rosettes on roots (root-sprouting), and aposporous initial cells in ovules which, however, do not result in functional apomixis. The combination of increased vegetative clonal growth in autopolyploids and frequent intercytotype mating are key mechanisms involved in the formation and maintenance of the largest diploid-autopolyploid primary contact zone ever recorded in angiosperms.
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Affiliation(s)
- Barbora Šingliarová
- Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Diego Hojsgaard
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | - Patrik Mráz
- Herbarium Collections and Department of Botany, Charles University, Prague, Czechia
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16
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Anneberg TJ, O'Neill EM, Ashman TL, Turcotte MM. Polyploidy impacts population growth and competition with diploids: multigenerational experiments reveal key life-history trade-offs. THE NEW PHYTOLOGIST 2023; 238:1294-1304. [PMID: 36740596 DOI: 10.1111/nph.18794] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Ecological theory predicts that early generation polyploids ('neopolyploids') should quickly go extinct owing to the disadvantages of rarity and competition with their diploid progenitors. However, polyploids persist in natural habitats globally. This paradox has been addressed theoretically by recognizing that reproductive assurance of neopolyploids and niche differentiation can promote establishment. Despite this, the direct effects of polyploidy at the population level remain largely untested despite establishment being an intrinsically population-level process. We conducted population-level experiments where life-history investment in current and future growth was tracked in four lineage pairs of diploids and synthetic autotetraploids of the aquatic plant Spirodela polyrhiza. Population growth was evaluated with and without competition between diploids and neopolyploids across a range of nutrient treatments. Although neopolyploid populations produce more biomass, they reach lower population sizes and have reduced carrying capacities when growing alone or in competition across all nutrient treatments. Thus, contrary to individual-level studies, our population-level data suggest that neopolyploids are competitively inferior to diploids. Conversely, neopolyploid populations have greater investment in dormant propagule production than diploids. Our results show that neopolyploid populations should not persist based on current growth dynamics, but high potential future growth may allow polyploids to establish in subsequent seasons.
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Affiliation(s)
- Thomas J Anneberg
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Elizabeth M O'Neill
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Martin M Turcotte
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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17
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Mairal M, García-Verdugo C, Le Roux JJ, Chau JH, van Vuuren BJ, Hui C, Münzbergová Z, Chown SL, Shaw JD. Multiple introductions, polyploidy and mixed reproductive strategies are linked to genetic diversity and structure in the most widespread invasive plant across Southern Ocean archipelagos. Mol Ecol 2023; 32:756-771. [PMID: 36478264 DOI: 10.1111/mec.16809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Biological invasions in remote areas that experience low human activity provide unique opportunities to elucidate processes responsible for invasion success. Here we study the most widespread invasive plant species across the isolated islands of the Southern Ocean, the annual bluegrass, Poa annua. To analyse geographical variation in genome size, genetic diversity and reproductive strategies, we sampled all major sub-Antarctic archipelagos in this region and generated microsatellite data for 470 individual plants representing 31 populations. We also estimated genome sizes for a subset of individuals using flow cytometry. Occasional events of island colonization are expected to result in high genetic structure among islands, overall low genetic diversity and increased self-fertilization, but we show that this is not the case for P. annua. Microsatellite data indicated low population genetic structure and lack of isolation by distance among the sub-Antarctic archipelagos we sampled, but high population structure within each archipelago. We identified high levels of genetic diversity, low clonality and low selfing rates in sub-Antarctic P. annua populations (contrary to rates typical of continental populations). In turn, estimates of selfing declined in populations as genetic diversity increased. Additionally, we found that most P. annua individuals are probably tetraploid and that only slight variation exists in genome size across the Southern Ocean. Our findings suggest multiple independent introductions of P. annua into the sub-Antarctic, which promoted the establishment of genetically diverse populations. Despite multiple introductions, the adoption of convergent reproductive strategies (outcrossing) happened independently in each major archipelago. The combination of polyploidy and a mixed reproductive strategy probably benefited P. annua in the Southern Ocean by increasing genetic diversity and its ability to cope with the novel environmental conditions.
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Affiliation(s)
- Mario Mairal
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain.,Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Carlos García-Verdugo
- Departamento de Botánica, Facultad de Ciencias, Universidad de Granada, Granada, Spain.,Departamento de Biología, Universitat de les Illes Balears - Institut Mediterrani d'Estudis Avançats (CSIC-UIB), Mallorca, Spain
| | - Johannes J Le Roux
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain.,School of Natural Sciences, Macquarie University, New South Wales, Sydney, Australia
| | - John H Chau
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, South Africa
| | - Bettine Jansen van Vuuren
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, South Africa
| | - Cang Hui
- Department of Mathematical Sciences, Centre for Invasion Biology, Stellenbosch University, Stellenbosch, South Africa.,Biodiversity Informatics Unit, African Institute for Mathematical Sciences, Cape Town, South Africa
| | - Zuzana Münzbergová
- Faculty of Science, Department of Botany, Charles University, Prague, Czech Republic.,Institute of Botany, Czech Academy of Science, Průhonice, Czech Republic
| | - Steven L Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Justine D Shaw
- Securing Antarctica's Environmental Future, School of Biology and Environmental Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Australian Antarctic Division, Tasmania, Kingston, Australia
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18
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Martínková J, Motyka V, Bitomský M, Adamec L, Dobrev PI, Filartiga A, Filepová R, Gaudinová A, Lacek J, Klimešová J. What determines root-sprouting ability: Injury or phytohormones? AMERICAN JOURNAL OF BOTANY 2023; 110:e16102. [PMID: 36371783 DOI: 10.1002/ajb2.16102] [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: 04/26/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
PREMISE Root-sprouting (RS) is an evolutionarily independent alternative to axillary stem branching for a plant to attain its architecture. Root-sprouting plants are better adapted to disturbance than non-RS plants, and their vigor is frequently boosted by biomass removal. Nevertheless, RS plants are rarer than plants that are not root-sprouters, possibly because they must overcome developmental barriers such as intrinsic phytohormonal balance or because RS ability is conditioned by injury to the plant body. The objective of this study was to identify whether phytohormones or injury enable RS. METHODS In a greenhouse experiment, growth variables, root respiration, and phytohormones were analyzed in two closely related clonal herbs that differ in RS ability (spontaneously RS Inula britannica and rhizomatous non-RS I. salicina) with and without severe biomass removal. RESULTS As previously reported, I. britannica is a root-sprouter, but injury did not boost its RS ability. Root respiration did not differ between the two species and decreased continuously with time irrespectively of injury, but their phytohormone profiles differed significantly. In RS species, the auxins-to-cytokinins ratio was low, and injury further decreased it. CONCLUSIONS This first attempt to test drivers behind different plant growth forms suggests that intrinsic phytohormone regulation, especially the auxins-to-cytokinins ratio, might be behind RS ability. Injury, causing a phytohormonal imbalance, seems to be less important in spontaneously RS species than expected for RS species in general.
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Affiliation(s)
- Jana Martínková
- Department of Experimental and Functional Morphology, Institute of Botany of the Czech Academy of Sciences, Dukelská 135, CZ-379 82, Třeboň, Czech Republic
| | - Václav Motyka
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Martin Bitomský
- Department of Experimental and Functional Morphology, Institute of Botany of the Czech Academy of Sciences, Dukelská 135, CZ-379 82, Třeboň, Czech Republic
- Department of Ecology and Environmental Sciences, Palacký University, Šlechtitelů 241/27, CZ-783 71, Olomouc, Czech Republic
| | - Lubomír Adamec
- Department of Experimental and Functional Morphology, Institute of Botany of the Czech Academy of Sciences, Dukelská 135, CZ-379 82, Třeboň, Czech Republic
| | - Peter I Dobrev
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Arinawa Filartiga
- Department of Experimental and Functional Morphology, Institute of Botany of the Czech Academy of Sciences, Dukelská 135, CZ-379 82, Třeboň, Czech Republic
| | - Roberta Filepová
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Alena Gaudinová
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Jozef Lacek
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Jitka Klimešová
- Department of Experimental and Functional Morphology, Institute of Botany of the Czech Academy of Sciences, Dukelská 135, CZ-379 82, Třeboň, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Praha 2, Czech Republic
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19
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Gao J, Liu R, Luo M, Wang G. The clonal growth in Aconitum carmichaelii Debx. PLANT SIGNALING & BEHAVIOR 2022; 17:2083818. [PMID: 35713121 PMCID: PMC9225526 DOI: 10.1080/15592324.2022.2083818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Aconitum carmichaelii Debx. is used as traditional herbal medicine in China, Japan, and other Asian countries. A. carmichaelii has two modes for reproduction: sexual reproduction with seed and vegetative reproduction with vegetative propagules. The vegetative propagules are belowground and invisible. To date, only a handful of studies for the clonal growth are available. In this study, we investigated the clonal growth by anatomical and morphological changes. Results revealed that the axillary bud appeared on the rhizome. Furthermore, the axillary meristem in the axillary bud differentiated a bud upwards and an adventitious root (AR) downwards. The AR expanded to a tuberous root in order to provide the bud nutrients for the new plant. The AR branched LRs. In addition, some lateral roots (LRs) on the AR also swelled. Both the AR and LR were found to follow a similar pattern of development. However, high lignification in the stele region of LRs inhibited further expansion. AR development was attributed to activities of the cambium and meristem cell, starch accumulation, stele lignification, and a polyarch stele. Our study not only provides a better understanding of clonal growth but also provides clues to explore the regulatory mechanisms underlying AR development in A. carmichaelii.
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Affiliation(s)
- Jing Gao
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Ran Liu
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Min Luo
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Guangzhi Wang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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20
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Becker FW, Oberlander KC, Trávníček P, Dreyer LL. Inconsistent expression of the gigas effect in polyploid Oxalis. AMERICAN JOURNAL OF BOTANY 2022; 109:1607-1621. [PMID: 36193941 DOI: 10.1002/ajb2.16077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
PREMISE It is well-known that whole genome duplication (WGD) has played a significant role in the evolution of plants. The best-known phenotypic effect of WGD is the gigas effect, or the enlargement of polyploid plant traits. WGD is often linked with increased weediness, which could be a result of fitness advantages conferred by the gigas effect. As a result, the gigas effect could potentially explain polyploid persistence and abundance. We test whether a gigas effect is present in the polyploid-rich geophyte Oxalis, at both organ and cellular scales. METHODS We measured traits in conspecific diploid and polyploid accessions of 24 species across the genus. In addition, we measured the same and additional traits in 20 populations of the weedy and highly ploidy-variable species Oxalis purpurea L., including measures of clonality and selfing as a proxy for weediness. Ploidy level was determined using flow cytometry. RESULTS We found substantial variation and no consistent ploidy-related size difference, both between and within species, and across traits. Oxalis purpurea polyploids did, however, produce significantly more underground biomass and more bulbils than diploids, consistent with a potential role of WGD in the weediness of this species. CONCLUSIONS Our results suggest a more nuanced role for the gigas effect, at least in Oxalis. It may be temporary, short-lived, and inconsistently expressed and retained on evolutionary time scales, but in the short term can contribute to lineage success via increased vegetative reproduction.
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Affiliation(s)
- Frederik W Becker
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Kenneth C Oberlander
- H. G. W. J. Schweickerdt Herbarium, Department of Plant and Soil Sciences, Plant Sciences Complex, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Pavel Trávníček
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic, and Department of Botany, Charles University, Praha, Czech Republic
| | - Léanne L Dreyer
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
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21
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Han TS, Hu ZY, Du ZQ, Zheng QJ, Liu J, Mitchell-Olds T, Xing YW. Adaptive responses drive the success of polyploid yellowcresses ( Rorippa, Brassicaceae) in the Hengduan Mountains, a temperate biodiversity hotspot. PLANT DIVERSITY 2022; 44:455-467. [PMID: 36187546 PMCID: PMC9512641 DOI: 10.1016/j.pld.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 06/16/2023]
Abstract
Polyploids contribute substantially to plant evolution and biodiversity; however, the mechanisms by which they succeed are still unclear. According to the polyploid adaptation hypothesis, successful polyploids spread by repeated adaptive responses to new environments. Here, we tested this hypothesis using two tetraploid yellowcresses (Rorippa), the endemic Rorippa elata and the widespread Rorippa palustris, in the temperate biodiversity hotspot of the Hengduan Mountains. Speciation modes were resolved by phylogenetic modeling using 12 low-copy nuclear loci. Phylogeographical patterns were then examined using haplotypes phased from four plastid and ITS markers, coupled with historical niche reconstruction by ecological niche modeling. We inferred the time of hybrid origins for both species as the mid-Pleistocene, with shared glacial refugia within the southern Hengduan Mountains. Phylogeographic and ecological niche reconstruction indicated recurrent northward colonization by both species after speciation, possibly tracking denuded habitats created by glacial retreat during interglacial periods. Common garden experiment involving perennial R. elata conducted over two years revealed significant changes in fitness-related traits across source latitudes or altitudes, including latitudinal increases in survival rate and compactness of plant architecture, suggesting gradual adaptation during range expansion. These findings support the polyploid adaptation hypothesis and suggest that the spread of polyploids was aided by adaptive responses to environmental changes during the Pleistocene. Our results thus provide insight into the evolutionary success of polyploids in high-altitude environments.
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Affiliation(s)
- Ting-Shen Han
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Zheng-Yan Hu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi-Qiang Du
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Quan-Jing Zheng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia Liu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
| | | | - Yao-Wu Xing
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
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22
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Van Drunen WE, Friedman J. Autopolyploid establishment depends on life-history strategy and the mating outcomes of clonal architecture. Evolution 2022; 76:1953-1970. [PMID: 35861365 DOI: 10.1111/evo.14582] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/21/2022] [Accepted: 07/11/2022] [Indexed: 01/22/2023]
Abstract
Polyploidy is a significant component in the evolution of many taxa, particularly plant groups. However, new polyploids face substantial fitness disadvantages due to a lack of same-cytotype mates, and the factors promoting or preventing polyploid establishment in natural populations are often unclear. We develop spatially explicit agent-based simulation models to test the hypothesis that a perennial life history and clonal propagation facilitate the early stages of polyploid establishment and persistence. Our models show that polyploids are more likely to establish when they have longer life spans than diploids, especially when self-fertilization rates are high. Polyploids that combine sexual and clonal reproduction can establish across a wide range of life histories, but their success is moderated by clonal strategy. By tracking individuals and mating events, we reveal that clonal architecture has a substantial impact on the spatial structure of the mixed diploid-polyploid population during polyploid establishment: altering patterns of mating within or between cytotypes via geitonogamous self-fertilization, the mechanisms through which polyploid establishment proceeds, and the final composition of the polyploid population. Overall, our findings provide novel insight into the role of clonal structure in modulating the complex relationship between polyploidy, perenniality, and clonality and offer testable predictions for future empirical work.
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Affiliation(s)
- Wendy E Van Drunen
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada.,Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Jannice Friedman
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
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23
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Clo J. Polyploidization: Consequences of genome doubling on the evolutionary potential of populations. AMERICAN JOURNAL OF BOTANY 2022; 109:1213-1220. [PMID: 35862788 DOI: 10.1002/ajb2.16029] [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: 03/17/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Whole-genome duplication is common in plants and is considered to have a broad range of effects on individuals' phenotypes and genomes and to be an important driver of plant adaptation and speciation. Despite their increased capacity to cope with challenging environments, polyploid lineages are generally as prone to extinction, and sometimes more prone, than their diploid progenitors. Although several explanations have been proposed to explain the short- and long-term disadvantages of polyploidy on the survival probability of populations, the consequences of whole-genome doubling on the heritable variance remain poorly studied. Whole-genome doubling can have major effects not only on the genetics, but also on the ecology and life history of the populations. Modifications of other properties of populations can reverse the effects of polyploidization per se on heritable variance. In this synthesis, I summarize the empirical and theoretical knowledge about the multifarious consequences of genome doubling on the heritable variance of quantitative traits and on the evolutionary potential of polyploid populations compared to their diploid progenitors. I propose several ways to decipher the consequences of whole-genome doubling on survival probability and to study the further consequences of shifting the ecological niche and life-history traits of a population. I also highlight some practical considerations for comparing the heritable variance of a trait among different cytotypes. Such investigations appear to be timely and necessary to understand more about the paradoxical aspects of polyploidization and to understand the evolutionary potential of polyploid lineages in a global warming context.
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Affiliation(s)
- Josselin Clo
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01, Prague, Czech Republic
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24
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Klimešová J, Ottaviani G, Charles-Dominique T, Campetella G, Canullo R, Chelli S, Janovský Z, Lubbe FC, Martínková J, Herben T. Incorporating clonality into the plant ecology research agenda. TRENDS IN PLANT SCIENCE 2021; 26:1236-1247. [PMID: 34419339 DOI: 10.1016/j.tplants.2021.07.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/16/2021] [Accepted: 07/24/2021] [Indexed: 06/13/2023]
Abstract
A longstanding research divide exists in plant ecology: either focusing on plant clonality, with no ambition to address nonclonal plants, or focusing on all plants, ignoring that many ecological processes can be affected by the fact that some plants are clonal while others are not. This gap cascades into a lack of distinction and knowledge about the similarities and differences between clonal and nonclonal plants. Here we aim to bridge this gap by identifying areas that would benefit from the incorporation of clonal growth into one integrated research platform: namely, response to productivity and disturbance, biotic interactions, and population dynamics. We are convinced that this will provide a roadmap to gain valuable insights into the ecoevolutionary dynamics relevant to all plants.
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Affiliation(s)
- Jitka Klimešová
- Institute of Botany, Czech Academy of Sciences, Dukelská 135, 37901 Třeboň, Czech Republic; Department of Botany, Faculty of Sciences, Charles University, Benátská 2, 12800 Praha, Czech Republic.
| | - Gianluigi Ottaviani
- Institute of Botany, Czech Academy of Sciences, Dukelská 135, 37901 Třeboň, Czech Republic
| | - Tristan Charles-Dominique
- CNRS UMR7618, Sorbonne University, Institute of Ecology and Environmental Sciences Paris, 4 Place Jussieu, 75005 Paris, France
| | - Giandiego Campetella
- School of Biosciences and Veterinary Medicine, Plant Diversity and Ecosystems Management Unit, Camerino University, 62032 Camerino, Italy
| | - Roberto Canullo
- School of Biosciences and Veterinary Medicine, Plant Diversity and Ecosystems Management Unit, Camerino University, 62032 Camerino, Italy
| | - Stefano Chelli
- School of Biosciences and Veterinary Medicine, Plant Diversity and Ecosystems Management Unit, Camerino University, 62032 Camerino, Italy
| | - Zdeněk Janovský
- Institute of Botany, Czech Academy of Sciences, Dukelská 135, 37901 Třeboň, Czech Republic; Department of Botany, Faculty of Sciences, Charles University, Benátská 2, 12800 Praha, Czech Republic
| | - F Curtis Lubbe
- Institute of Botany, Czech Academy of Sciences, Dukelská 135, 37901 Třeboň, Czech Republic
| | - Jana Martínková
- Institute of Botany, Czech Academy of Sciences, Dukelská 135, 37901 Třeboň, Czech Republic
| | - Tomáš Herben
- Department of Botany, Faculty of Sciences, Charles University, Benátská 2, 12800 Praha, Czech Republic; Institute of Botany, Czech Academy of Sciences, Zámek 1, 25243 Průhonice, Czech Republic
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25
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Morozov-Leonov SY. Hybrid Form Pelophylax esculentus-ridibundus (Amphibia, Ranidae) from the Tisa River Drainage: Its Origin and Evolutionary Potential. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721060098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Yin L, Zhu Z, Huang L, Luo X, Li Y, Xiao C, Yang J, Wang J, Zou Q, Tao L, Kang Z, Tang R, Wang M, Fu S. DNA repair- and nucleotide metabolism-related genes exhibit differential CHG methylation patterns in natural and synthetic polyploids (Brassica napus L.). HORTICULTURE RESEARCH 2021; 8:142. [PMID: 34193846 PMCID: PMC8245426 DOI: 10.1038/s41438-021-00576-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 03/29/2021] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
Polyploidization plays a crucial role in the evolution of angiosperm species. Almost all newly formed polyploids encounter genetic or epigenetic instabilities. However, the molecular mechanisms contributing to genomic instability in synthetic polyploids have not been clearly elucidated. Here, we performed a comprehensive transcriptomic and methylomic analysis of natural and synthetic polyploid rapeseeds (Brassica napus). Our results showed that the CHG methylation levels of synthetic rapeseed in different genomic contexts (genes, transposon regions, and repeat regions) were significantly lower than those of natural rapeseed. The total number and length of CHG-DMRs between natural and synthetic polyploids were much greater than those of CG-DMRs and CHH-DMRs, and the genes overlapping with these CHG-DMRs were significantly enriched in DNA damage repair and nucleotide metabolism pathways. These results indicated that CHG methylation may be more sensitive than CG and CHH methylation in regulating the stability of the polyploid genome of B. napus. In addition, many genes involved in DNA damage repair, nucleotide metabolism, and cell cycle control were significantly differentially expressed between natural and synthetic rapeseeds. Our results highlight that the genes related to DNA repair and nucleotide metabolism display differential CHG methylation patterns between natural and synthetic polyploids and reveal the potential connection between the genomic instability of polyploid plants with DNA methylation defects and dysregulation of the DNA repair system. In addition, it was found that the maintenance of CHG methylation in B. napus might be partially regulated by MET1. Our study provides novel insights into the establishment and evolution of polyploid plants and offers a potential idea for improving the genomic stability of newly formed Brassica polyploids.
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Affiliation(s)
- Liqin Yin
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China.
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China.
| | - Zhendong Zhu
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Liangjun Huang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
- Agricultural College, Sichuan Agricultural University, 211 Huimin Road, Chengdu, China
| | - Xuan Luo
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
- Agricultural College, Sichuan Agricultural University, 211 Huimin Road, Chengdu, China
| | - Yun Li
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Chaowen Xiao
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China
| | - Jin Yang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Jisheng Wang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Qiong Zou
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Lanrong Tao
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Zeming Kang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Rong Tang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Maolin Wang
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China.
| | - Shaohong Fu
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China.
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27
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Schmickl R, Yant L. Adaptive introgression: how polyploidy reshapes gene flow landscapes. THE NEW PHYTOLOGIST 2021; 230:457-461. [PMID: 33454987 DOI: 10.1111/nph.17204] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Rare yet accumulating evidence in both plants and animals shows that whole genome duplication (WGD, leading to polyploidy) can break down reproductive barriers, facilitating gene flow between otherwise isolated species. Recent population genomic studies in wild, outcrossing Arabidopsis arenosa and Arabidopsis lyrata indicate that this WGD-potentiated gene flow can be adaptive and highly specific in response to particular environmental and intracellular challenges. The mechanistic basis of WGD-mediated easing of species barrier strength seems to primarily lie in the relative dosage of each parental genome in the endosperm. While generalisations about polyploids can be fraught, this evidence indicates that the breakdown of these barriers, combined with diploid to polyploid gene flow and gene flow between polyploids, allows some polyploids to act as adaptable 'allelic sponges', enjoying increased potential to respond to challenging environments.
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Affiliation(s)
- Roswitha Schmickl
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, 128 01, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic
| | - Levi Yant
- Future Food Beacon and School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
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28
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Bohutínská M, Alston M, Monnahan P, Mandáková T, Bray S, Paajanen P, Kolář F, Yant L. Novelty and convergence in adaptation to whole genome duplication. Mol Biol Evol 2021; 38:3910-3924. [PMID: 33783509 PMCID: PMC8382928 DOI: 10.1093/molbev/msab096] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/08/2021] [Accepted: 03/29/2021] [Indexed: 12/26/2022] Open
Abstract
Whole genome duplication (WGD) can promote adaptation but is disruptive to conserved processes, especially meiosis. Studies in Arabidopsis arenosa revealed a coordinated evolutionary response to WGD involving interacting proteins controlling meiotic crossovers, which are minimised in an autotetraploid (within-species polyploid) to avoid mis-segregation. Here we test whether this surprising flexibility of a conserved essential process, meiosis, is recapitulated in an independent WGD system, Cardamine amara, 17 million years diverged from A. arenosa. We assess meiotic stability and perform population-based scans for positive selection, contrasting the genomic response to WGD in C. amara with that of A. arenosa. We found in C. amara the strongest selection signals at genes with predicted functions thought important to adaptation to WGD: meiosis, chromosome remodelling, cell cycle, and ion transport. However, genomic responses to WGD in the two species differ: minimal ortholog-level convergence emerged, with none of the meiosis genes found in A. arenosa exhibiting strong signal in C. amara. This is consistent with our observations of lower meiotic stability and occasional clonal spreading in diploid C. amara, suggesting that nascent C. amara autotetraploid lineages were preadapted by their diploid lifestyle to survive while enduring reduced meiotic fidelity. However, in contrast to a lack of ortholog convergence, we see process-level and network convergence in DNA management, chromosome organisation, stress signalling, and ion homeostasis processes. This gives the first insight into the salient adaptations required to meet the challenges of a WGD state and shows that autopolyploids can utilize multiple evolutionary trajectories to adapt to WGD.
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Affiliation(s)
- Magdalena Bohutínská
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
| | - Mark Alston
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Patrick Monnahan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Terezie Mandáková
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Czech Republic
| | - Sian Bray
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, UK.,School of Biosciences University of Nottingham, Nottingham, UK
| | - Pirita Paajanen
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic.,Natural History Museum, University of Oslo, Oslo, Norway
| | - Levi Yant
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, UK.,School of Life Sciences University of Nottingham, Nottingham, UK
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29
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Levin DA. Propagule pressure and the establishment of emergent polyploid populations. ANNALS OF BOTANY 2021; 127:1-5. [PMID: 33106838 PMCID: PMC7750715 DOI: 10.1093/aob/mcaa187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Whereas the incidence or rate of polyploid speciation in flowering plants is modest, the production of polyploid individuals within local populations is widespread. Explanations for this disparity primarily have focused on properties or interactions of polyploids that limit their persistence. HYPOTHESIS The emergence of local polyploid populations within diploid populations is similar to the arrival of invasive species at new, suitable sites, with the exception that polyploids suffer interference from their progenitor(s). The most consistent predictor of successful colonization by invasive plants is propagule pressure, i.e. the number of seeds introduced. Therefore, insufficient propagule pressure, i.e. the formation of polyploid seeds within diploid populations, ostensibly is a prime factor limiting the establishment of newly emergent polyploids within local populations. Increasing propagule number reduces the effects of genetic, environmental and demographic stochasticity, which thwart population survival. As with invasive species, insufficient seed production within polyploid populations limits seed export, and thus reduces the chance of polyploid expansion. CONCLUSION The extent to which propagule pressure limits the establishment of local polyploid populations remains to be determined, because we know so little. The numbers of auto- or allopolyploid seed in diploid populations rarely have been ascertained, as have the numbers of newly emergent polyploid plants within diploid populations. Moreover, seed production by these polyploids has yet to be assessed.
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Affiliation(s)
- Donald A Levin
- Department of Integrative Biology, University of Texas, Austin, TX, USA
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30
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Wu H, Yu Q, Ran JH, Wang XQ. Unbiased Subgenome Evolution in Allotetraploid Species of Ephedra and Its Implications for the Evolution of Large Genomes in Gymnosperms. Genome Biol Evol 2020; 13:5983329. [PMID: 33196777 PMCID: PMC7900875 DOI: 10.1093/gbe/evaa236] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2020] [Indexed: 12/22/2022] Open
Abstract
The evolutionary dynamics of polyploid genomes and consequences of polyploidy have been studied extensively in angiosperms but very rarely in gymnosperms. The gymnospermous genus Ephedra is characterized by a high frequency of polyploidy, and thus provides an ideal system to investigate the evolutionary mode of allopolyploid genomes and test whether subgenome dominance has occurred in gymnosperms. Here, we sequenced transcriptomes of two allotetraploid species of Ephedra and their putative diploid progenitors, identified expressed homeologs, and analyzed alternative splicing and homeolog expression based on PacBio Iso-Seq and Illumina RNA-seq data. We found that the two subgenomes of the allotetraploids had similar numbers of expressed homeologs, similar percentages of homeologs with dominant expression, and approximately equal numbers of isoforms with alternative splicing, showing an unbiased subgenome evolution as in a few polyploid angiosperms, with a divergence of the two subgenomes at ∼8 Ma. In addition, the nuclear DNA content of the allotetraploid species is almost equal to the sum of two putative progenitors, suggesting limited genome restructuring after allotetraploid speciation. The allopolyploid species of Ephedra might have undergone slow diploidization, and the unbiased subgenome evolution implies that the formation of large genomes in gymnosperms could be attributed to even and slow fractionation following polyploidization.
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Affiliation(s)
- Hui Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Qiong Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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31
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Spoelhof JP, Soltis DE, Soltis PS. Habitat Shape Affects Polyploid Establishment in a Spatial, Stochastic Model. FRONTIERS IN PLANT SCIENCE 2020; 11:592356. [PMID: 33304370 PMCID: PMC7701104 DOI: 10.3389/fpls.2020.592356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/22/2020] [Indexed: 06/12/2023]
Abstract
Polyploidy contributes massively to the taxonomic and genomic diversity of angiosperms, but certain aspects of polyploid evolution are still enigmatic. The establishment of a new polyploid lineage following whole-genome duplication (WGD) is a critical step for all polyploid species, but this process is difficult to identify and observe in nature. Mathematical models offer an opportunity to study this process by varying parameters related to the populations, habitats, and organisms involved in the polyploid establishment process. While several models of polyploid establishment have been published previously, very few incorporate spatial factors, including spatial relationships between organisms, habitat shape, or population density. This study presents a stochastic, spatial model of polyploid establishment that shows how factors such as habitat shape and dispersal type can influence the fixation and persistence of nascent polyploids and modulate the effects of other factors. This model predicts that narrow, constrained habitats such as roadsides and coastlines may enhance polyploid establishment, particularly in combination with frequent clonal reproduction, limited dispersal, and high population density. The similarity between this scenario and the growth of many invasive or colonizing species along disturbed, narrow habitats such as roadsides may offer a partial explanation of the prevalence of polyploidy among invasive species.
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Affiliation(s)
- Jonathan P. Spoelhof
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
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32
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Friedman J. The Evolution of Annual and Perennial Plant Life Histories: Ecological Correlates and Genetic Mechanisms. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-110218-024638] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Flowering plants exhibit two principal life-history strategies: annuality (living and reproducing in one year) and perenniality (living more than one year). The advantages of either strategy depend on the relative benefits of immediate reproduction balanced against survivorship and future reproduction. This trade-off means that life-history strategies are associated with particular environments, with annuals being found more often in unpredictable habitats. Annuality and perenniality are the outcome of developmental genetic programs responding to their environment, with perennials being distinguished by their delayed competence to flower and reversion to growth after flowering. Evolutionary transitions between these strategies are frequent and have consequences for mating systems and genome evolution, with perennials being more likely to outcross with higher inbreeding depression and lower rates of molecular evolution. Integrating expectations from life-history theory with knowledge of the developmental genetics of flowering and seasonality is required to understand the mechanisms involved in the evolution of annual and perennial life histories.
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Affiliation(s)
- Jannice Friedman
- Department of Biology, Queen's University, Kingston, Ontario K7L 3N6, Canada
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33
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Machado RM, de Oliveira FA, de Matos Alves F, de Souza AP, Forni-Martins ER. Population Genetics of Polyploid Complex Psidium cattleyanum Sabine (Myrtaceae): Preliminary Analyses Based on New Species-Specific Microsatellite Loci and Extension to Other Species of the Genus. Biochem Genet 2020; 59:219-234. [PMID: 32980958 DOI: 10.1007/s10528-020-10002-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 09/18/2020] [Indexed: 11/29/2022]
Abstract
Polyploidy is a phenomenon that alters the genetic diversity of populations and has been reported as one of the most important evolutionary forces for plant diversification. The Psidium cattleyanum complex comprises a group of wild populations with several ploidy levels reported in the literature. The multiple cytotypes, associated with its wide distribution area, make this species a potential key model for understanding evolutionary processes related to polyploidization. In this study, we isolated and characterized nuclear microsatellite markers of P. cattleyanum and tested their transferability to other nine species of the genus. We performed a preliminary analysis of genetic diversity and population structure in three populations of P. cattleyanum. The three populations analyzed had different chromosome numbers, being polyploid cytotypes (2n = 6x = 66, 2n = 7x = 77 and 2n = 8x = 88). We designed 46 primer pairs and successfully amplified 37 markers, from which the 10 best were selected for analysis. Considering both the PIC and DP values, most of markers were highly informative. The new SSR markers were used to assess the levels of genetic diversity of the populations and detected one population with predominance of sexual reproduction. DAPC analysis pointed the formation of three groups, which corresponded to the populations analyzed. The markers were successfully amplified in related species, with some species presenting 80% transferability. By producing this panel of polymorphic microsatellites, we contribute to the understanding evolution in groups of natural polyploids for future studies.
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Affiliation(s)
- Raquel Moura Machado
- Instituto de Biologia, Programa de Pós-graduação em Biologia Vegetal, Universidade Estadual de Campinas, Campinas, Rua Monteiro Lobato 255, Campinas, SP, 13083-862, Brazil.
| | - Fernanda Ancelmo de Oliveira
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato 255, Campinas, SP, 13083-862, Brazil
| | - Fábio de Matos Alves
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato 255, Campinas, SP, 13083-862, Brazil
| | - Anete Pereira de Souza
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato 255, Campinas, SP, 13083-862, Brazil
| | - Eliana Regina Forni-Martins
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato 255, Campinas, SP, 13083-862, Brazil
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34
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Spoelhof JP, Keeffe R, McDaniel SF. Does reproductive assurance explain the incidence of polyploidy in plants and animals? THE NEW PHYTOLOGIST 2020; 227:14-21. [PMID: 31883115 DOI: 10.1111/nph.16396] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/17/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Jonathan P Spoelhof
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Rachel Keeffe
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Stuart F McDaniel
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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35
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Herben T, Klimešová J. Evolution of clonal growth forms in angiosperms. THE NEW PHYTOLOGIST 2020; 225:999-1010. [PMID: 31505049 DOI: 10.1111/nph.16188] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/28/2019] [Indexed: 06/10/2023]
Abstract
Clonal growth of plants is attained by a number of morphologically different organs (e.g. stolons, rhizomes, and roots), which are not functionally equivalent. Consequently, these clonal growth organ (CGO) types can determine functional traits that are associated with clonality, although little is known about their evolutionary flexibility or the constraining role they play on clonal traits. We investigated the rates of evolutionary change by which individual CGOs are acquired and lost using a set of 2652 species of Central European flora. Furthermore, we asked how these individual CGOs constrain functionally relevant clonal traits, such as lateral spread, number of offspring, and persistence of connections. We show that plants can easily switch in evolution among individual types of CGO and between clonal and nonclonal habits. However, not all these transitions are equally probable. Namely, stem-based clonal growth and root-based clonal growth constitute evolutionarily separate forms of clonal growth. Clonal traits are strongly constrained by individual CGO types. Specifically, fast lateral spread is attained by stolons or hypogeogenous rhizomes, and persistent connections are attained by all rhizome types. However, the ease with which clonal organs appear and disappear in evolution implies that plants can overcome these constraints by adjusting their morphologies.
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Affiliation(s)
- Tomáš Herben
- Institute of Botany, Czech Academy of Sciences, CZ-252 43, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Praha 2, Czech Republic
| | - Jitka Klimešová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Praha 2, Czech Republic
- Institute of Botany, Czech Academy of Sciences, CZ-379 82, Třeboň, Czech Republic
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36
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Han TS, Zheng QJ, Onstein RE, Rojas-Andrés BM, Hauenschild F, Muellner-Riehl AN, Xing YW. Polyploidy promotes species diversification of Allium through ecological shifts. THE NEW PHYTOLOGIST 2020; 225:571-583. [PMID: 31394010 DOI: 10.1111/nph.16098] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/01/2019] [Indexed: 05/14/2023]
Abstract
Despite the role of polyploidy in multiple evolutionary processes, its impact on plant diversification remains controversial. An increased polyploid frequency may facilitate speciation through shifts in ecology, morphology or both. Here we used Allium to evaluate: (1) the relationship between intraspecific polyploid frequency and species diversification rate; and (2) whether this process is associated with habitat and/or trait shifts. Using eight plastid and nuclear ribosomal markers, we built a phylogeny of 448 Allium species, representing 46% of the total. We quantified intraspecific ploidy diversity, heterogeneity in diversification rates and their relationship along the phylogeny using trait-dependent diversification models. Finally, we evaluated the association between polyploidisation and habitat or trait shifts. We detected high ploidy diversity in Allium and a polyploidy-related diversification rate shift with a probability of 95% in East Asia. Allium lineages with high polyploid frequencies had higher species diversification rates than those of diploids or lineages with lower polyploid frequencies. Shifts in speciation rates were strongly correlated with habitat shifts linked to particular soil conditions; 81.7% of edaphic variation could be explained by polyploidisation. Our study emphasises the role of intraspecific polyploid frequency combined with ecological drivers on Allium diversification, which may explain plant radiations more generally.
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Affiliation(s)
- Ting-Shen Han
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA
| | - Quan-Jing Zheng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Renske E Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, D-04103, Germany
| | - Blanca M Rojas-Andrés
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Leipzig University, Johannisallee 21-23, Leipzig, D-04103, Germany
| | - Frank Hauenschild
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Leipzig University, Johannisallee 21-23, Leipzig, D-04103, Germany
| | - Alexandra N Muellner-Riehl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, D-04103, Germany
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Leipzig University, Johannisallee 21-23, Leipzig, D-04103, Germany
| | - Yao-Wu Xing
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
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37
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Schoen DJ, Johnson MTJ, Wright SI. The ecology, evolution, and genetics of plant reproductive systems. THE NEW PHYTOLOGIST 2019; 224:999-1004. [PMID: 31631365 DOI: 10.1111/nph.16222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Daniel J Schoen
- Department of Biology, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Marc T J Johnson
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
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38
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Wang J, Qin J, Sun P, Ma X, Yu J, Li Y, Sun S, Lei T, Meng F, Wei C, Li X, Guo H, Liu X, Xia R, Wang L, Ge W, Song X, Zhang L, Guo D, Wang J, Bao S, Jiang S, Feng Y, Li X, Paterson AH, Wang X. Polyploidy Index and Its Implications for the Evolution of Polyploids. Front Genet 2019; 10:807. [PMID: 31552101 PMCID: PMC6746930 DOI: 10.3389/fgene.2019.00807] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/02/2019] [Indexed: 11/13/2022] Open
Abstract
Polyploidy has contributed to the divergence and domestication of plants; however, estimation of the relative roles that different types of polyploidy have played during evolution has been difficult. Unbalanced and balanced gene removal was previously related to allopolyploidies and autopolyploidies, respectively. Here, to infer the types of polyploidies and evaluate their evolutionary effects, we devised a statistic, the Polyploidy-index or P-index, to characterize the degree of divergence between subgenomes of a polyploidy, to find whether there has been a balanced or unbalanced gene removal from the homoeologous regions. Based on a P-index threshold of 0.3 that distinguishes between known or previously inferred allo- or autopolyploidies, we found that 87.5% of 24 angiosperm paleo-polyploidies were likely produced by allopolyploidizations, responsible for establishment of major tribes such as Poaceae and Fabaceae, and large groups such as monocots and eudicots. These findings suggest that >99.7% of plant genomes likely derived directly from allopolyploidies, with autopolyploidies responsible for the establishment of only a few small genera, including Glycine, Malus, and Populus, each containing tens of species. Overall, these findings show that polyploids with high divergence between subgenomes (presumably allopolyploids) established the major plant groups, possibly through secondary contact between previously isolated populations and hybrid vigor associated with their re-joining.
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Affiliation(s)
- Jinpeng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun Qin
- Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Pengchuan Sun
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xuelian Ma
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Jigao Yu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Yuxian Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Sangrong Sun
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Tianyu Lei
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Fanbo Meng
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Chendan Wei
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xinyu Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - He Guo
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xiaojian Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Ruiyan Xia
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Li Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Weina Ge
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xiaoming Song
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Lan Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Di Guo
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jinyu Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Shoutong Bao
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Shan Jiang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Yishan Feng
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Xueping Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
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