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Pamela S. Soltis - One of the best experts on this subject based on the ideXlab platform.
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Habitat Shape Affects Polyploid Establishment in a Spatial, Stochastic Model.
Frontiers in plant science, 2020Co-Authors: Jonathan P. Spoelhof, Douglas E. Soltis, Pamela S. SoltisAbstract: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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The role of genetic and genomic attributes in the success of Polyploids
Proceedings of the National Academy of Sciences of the United States of America, 2000Co-Authors: Pamela S. Soltis, Douglas E. SoltisAbstract:In 1950, G. Ledyard Stebbins devoted two chapters of his book Variation and Evolution in Plants (Columbia Univ. Press, New York) to Polyploidy, one on occurrence and nature and one on distribution and significance. Fifty years later, many of the questions Stebbins posed have not been answered, and many new questions have arisen. In this paper, we review some of the genetic attributes of Polyploids that have been suggested to account for the tremendous success of Polyploid plants. Based on a limited number of studies, we conclude: (i) Polyploids, both individuals and populations, generally maintain higher levels of heterozygosity than do their diploid progenitors. (ii) Polyploids exhibit less inbreeding depression than do their diploid parents and can therefore tolerate higher levels of selfing; Polyploid ferns indeed have higher levels of selfing than do their diploid parents, but Polyploid angiosperms do not differ in outcrossing rates from their diploid parents. (iii) Most Polyploid species are polyphyletic, having formed recurrently from genetically different diploid parents. This mode of formation incorporates genetic diversity from multiple progenitor populations into the Polyploid “species”; thus, genetic diversity in Polyploid species is much higher than expected by models of Polyploid formation involving a single origin. (iv) Genome rearrangement may be a common attribute of Polyploids, based on evidence from genome in situ hybridization (GISH), restriction fragment length polymorphism (RFLP) analysis, and chromosome mapping. (v) Several groups of plants may be ancient Polyploids, with large regions of homologous DNA. These duplicated genes and genomes can undergo divergent evolution and evolve new functions. These genetic and genomic attributes of Polyploids may have both biochemical and ecological benefits that contribute to the success of Polyploids in nature.
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The dynamic nature of Polyploid genomes
Proceedings of the National Academy of Sciences of the United States of America, 1995Co-Authors: Douglas E. Soltis, Pamela S. SoltisAbstract:It is well known that Polyploidy is a major force in evolution, particularly in plants. Perhaps 50% of all angiosperms are of Polyploid origin; estimates for the ferns and fern allies range from 44 to 95% (1, 2). Because of the significant role that it has played in plant evolution, Polyploidy has been the focus of great interest and controversy for >50 years. Diverse aspects of Polyploidy have been reviewed, including types of Polyploids (3-8), ecological and evolutionary attributes of Polyploids (810), genetic consequences of Polyploid evolution (10-17), and mode of Polyploid formation (4, 18, 19). The application of molecular techniques has dramatically increased our understanding of Polyploid evolution and has fundamentally reshaped traditional views. The paper by Song et al. (20) in this journal further elucidates the process of Polyploid evolution and represents a key breakthrough in our understanding of the evolution of Polyploid genomes. To appreciate the great significance of the paper by Song et al. (20), it is important to consider briefly some of the traditional tenets of Polyploid evolution.
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RECURRENT FORMATION AND POLYPHYLY OF NORDIC PolyploidS IN DRABA (BRASSICACEAE)
American Journal of Botany, 1992Co-Authors: Christian Brochmann, Pamela S. Soltis, Douglas E. SoltisAbstract:Draba (Brassicaceae) is well known for its taxonomic complexity in arctic and alpine floras, and the Polyploids in particular present vexing taxonomic problems. It has been suggested that Polyploids in Draba may have formed recurrently from different populations of the parental species (polytopy), and it is also possible that a given taxonomic species may actually comprise several Polyploid races, each originating from different progenitor species (polyphyly). To unravel the taxonomic complexity of Polyploid Draba in the Nordic area, we investigated three of the most morphologically variable species and their possible progenitors using enzyme electrophoresis and restriction site analysis of chloroplast DNA (cpDNA) and nuclear ribosomal RNA genes (rDNA): D. norvegica (6x), D. lactea (6x), and D. corymbosa (1 6x). Electrophoretic analyses of progeny showed high levels of fixed heterozygosity in all three Polyploids, demonstrating that all are genetic alloploids. Electrophoretic and rDNA data indicate that polytopic and/or polyphyletic origins have contributed to the complexity of these Polyploids. However, a lack of cpDNA variation among the species limited the usefulness of this molecule for analysis of Polyploid origins. The considerable electrophoretic variation observed in D. norvegica necessitates a minimum of three and probably 13 independent origins. Electrophoretic and rDNA data suggest that D. lactea and D. corymbosa are polyphyletic Polyploids. Crossing data also support that D. corymbosa is polyphyletic. Given the widespread geographic distributions of these species and their possible progenitors, and that the populations analyzed represent only a small fraction of their geographic distributions, it is likely that these species have formed numerous times in different areas. As more molecular analyses of Polyploids are completed, the data continue to suggest that multiple origins of Polyploids are the rule rather than the exception.
Barbara K Mable - One of the best experts on this subject based on the ideXlab platform.
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recent progress and challenges in population genetics of Polyploid organisms an overview of current state of the art molecular and statistical tools
Molecular Ecology, 2014Co-Authors: Marc Stift, Roland Vergilino, Barbara K MableAbstract:Despite the importance of Polyploidy and the increasing availability of new genomic data, there remain important gaps in our knowledge of Polyploid population genetics. These gaps arise from the complex nature of Polyploid data (e.g. multiple alleles and loci, mixed inheritance patterns, association between ploidy and mating system variation). Furthermore, many of the standard tools for population genetics that have been developed for diploids are often not feasible for Polyploids. This review aims to provide an overview of the state-of-the-art in Polyploid population genetics and to identify the main areas where further development of molecular techniques and statistical theory is required. We review commonly used molecular tools (amplified fragment length polymorphism, microsatellites, Sanger sequencing, next-generation sequencing and derived technologies) and their challenges associated with their use in Polyploid populations: that is, allele dosage determination, null alleles, difficulty of distinguishing orthologues from paralogues and copy number variation. In addition, we review the approaches that have been used for population genetic analysis in Polyploids and their specific problems. These problems are in most cases directly associated with dosage uncertainty and the problem of inferring allele frequencies and assumptions regarding inheritance. This leads us to conclude that for advancing the field of Polyploid population genetics, most priority should be given to development of new molecular approaches that allow efficient dosage determination, and to further development of analytical approaches to circumvent dosage uncertainty and to accommodate ‘flexible’ modes of inheritance. In addition, there is a need for more simulation-based studies that test what kinds of biases could result from both existing and novel approaches.
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Polyploidy and self compatibility is there an association
New Phytologist, 2004Co-Authors: Barbara K MableAbstract:Summary • Researchers have hypothesized that self-compatibility (SC) should be more common in Polyploid taxa than their diploid counterparts because of selection for reproductive assurance and/or the expected decline in inbreeding depression associated with having ‘extra’ gene copies. Support for this view has come from an observed breakdown of self-incompatibility (SI) in some species with a gametophytic system (GSI). The purpose of this research was to assess the strength of this relationship across a wider array of SI systems. • A large database, of diploid chromosome numbers, ploidy levels, and types of SI system, was assembled for angiosperm species and used to test for an association between ploidy and SC. • No strong association was found between SC and Polyploidy at the level of species or families, and there was no evidence that those having a functional SI system also had fewer Polyploid taxa or that most Polyploids experience a breakdown in SI. • These results challenge the assumption that self-fertilization is strongly associated with Polyploidy and suggest directions for further research on the evolution of Polyploidy in relation to SI.
Douglas E. Soltis - One of the best experts on this subject based on the ideXlab platform.
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Habitat Shape Affects Polyploid Establishment in a Spatial, Stochastic Model.
Frontiers in plant science, 2020Co-Authors: Jonathan P. Spoelhof, Douglas E. Soltis, Pamela S. SoltisAbstract: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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The role of genetic and genomic attributes in the success of Polyploids
Proceedings of the National Academy of Sciences of the United States of America, 2000Co-Authors: Pamela S. Soltis, Douglas E. SoltisAbstract:In 1950, G. Ledyard Stebbins devoted two chapters of his book Variation and Evolution in Plants (Columbia Univ. Press, New York) to Polyploidy, one on occurrence and nature and one on distribution and significance. Fifty years later, many of the questions Stebbins posed have not been answered, and many new questions have arisen. In this paper, we review some of the genetic attributes of Polyploids that have been suggested to account for the tremendous success of Polyploid plants. Based on a limited number of studies, we conclude: (i) Polyploids, both individuals and populations, generally maintain higher levels of heterozygosity than do their diploid progenitors. (ii) Polyploids exhibit less inbreeding depression than do their diploid parents and can therefore tolerate higher levels of selfing; Polyploid ferns indeed have higher levels of selfing than do their diploid parents, but Polyploid angiosperms do not differ in outcrossing rates from their diploid parents. (iii) Most Polyploid species are polyphyletic, having formed recurrently from genetically different diploid parents. This mode of formation incorporates genetic diversity from multiple progenitor populations into the Polyploid “species”; thus, genetic diversity in Polyploid species is much higher than expected by models of Polyploid formation involving a single origin. (iv) Genome rearrangement may be a common attribute of Polyploids, based on evidence from genome in situ hybridization (GISH), restriction fragment length polymorphism (RFLP) analysis, and chromosome mapping. (v) Several groups of plants may be ancient Polyploids, with large regions of homologous DNA. These duplicated genes and genomes can undergo divergent evolution and evolve new functions. These genetic and genomic attributes of Polyploids may have both biochemical and ecological benefits that contribute to the success of Polyploids in nature.
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The dynamic nature of Polyploid genomes
Proceedings of the National Academy of Sciences of the United States of America, 1995Co-Authors: Douglas E. Soltis, Pamela S. SoltisAbstract:It is well known that Polyploidy is a major force in evolution, particularly in plants. Perhaps 50% of all angiosperms are of Polyploid origin; estimates for the ferns and fern allies range from 44 to 95% (1, 2). Because of the significant role that it has played in plant evolution, Polyploidy has been the focus of great interest and controversy for >50 years. Diverse aspects of Polyploidy have been reviewed, including types of Polyploids (3-8), ecological and evolutionary attributes of Polyploids (810), genetic consequences of Polyploid evolution (10-17), and mode of Polyploid formation (4, 18, 19). The application of molecular techniques has dramatically increased our understanding of Polyploid evolution and has fundamentally reshaped traditional views. The paper by Song et al. (20) in this journal further elucidates the process of Polyploid evolution and represents a key breakthrough in our understanding of the evolution of Polyploid genomes. To appreciate the great significance of the paper by Song et al. (20), it is important to consider briefly some of the traditional tenets of Polyploid evolution.
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RECURRENT FORMATION AND POLYPHYLY OF NORDIC PolyploidS IN DRABA (BRASSICACEAE)
American Journal of Botany, 1992Co-Authors: Christian Brochmann, Pamela S. Soltis, Douglas E. SoltisAbstract:Draba (Brassicaceae) is well known for its taxonomic complexity in arctic and alpine floras, and the Polyploids in particular present vexing taxonomic problems. It has been suggested that Polyploids in Draba may have formed recurrently from different populations of the parental species (polytopy), and it is also possible that a given taxonomic species may actually comprise several Polyploid races, each originating from different progenitor species (polyphyly). To unravel the taxonomic complexity of Polyploid Draba in the Nordic area, we investigated three of the most morphologically variable species and their possible progenitors using enzyme electrophoresis and restriction site analysis of chloroplast DNA (cpDNA) and nuclear ribosomal RNA genes (rDNA): D. norvegica (6x), D. lactea (6x), and D. corymbosa (1 6x). Electrophoretic analyses of progeny showed high levels of fixed heterozygosity in all three Polyploids, demonstrating that all are genetic alloploids. Electrophoretic and rDNA data indicate that polytopic and/or polyphyletic origins have contributed to the complexity of these Polyploids. However, a lack of cpDNA variation among the species limited the usefulness of this molecule for analysis of Polyploid origins. The considerable electrophoretic variation observed in D. norvegica necessitates a minimum of three and probably 13 independent origins. Electrophoretic and rDNA data suggest that D. lactea and D. corymbosa are polyphyletic Polyploids. Crossing data also support that D. corymbosa is polyphyletic. Given the widespread geographic distributions of these species and their possible progenitors, and that the populations analyzed represent only a small fraction of their geographic distributions, it is likely that these species have formed numerous times in different areas. As more molecular analyses of Polyploids are completed, the data continue to suggest that multiple origins of Polyploids are the rule rather than the exception.
Jonathan F Wendel - One of the best experts on this subject based on the ideXlab platform.
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genetic and epigenetic aspects of Polyploid evolution in plants
Cytogenetic and Genome Research, 2013Co-Authors: Andreas Madlung, Jonathan F WendelAbstract:Polyploidy, the condition of possessing more than 2 complete chromosome sets in the same nucleus, is frequent in nature and has implications for a species' prospects for evolution. Newly formed Polyploids, so-called neoPolyploids, undergo a wide spectrum of genomic changes upon genome merger and duplication. Here, we review recent literature describing genomic and transcriptomic changes along the pathway from neoalloPolyploid formation to the stabilization of species and diversification at the alloPolyploid level. We begin by reviewing pathways of Polyploid formation and discuss the effects of genome doubling and hybridization on chromosome pairing. We then review our knowledge of epigenetic changes in alloPolyploids, followed by a consideration of the effects of these structural genomic and epigenetic changes on the transcriptional activity of genes in alloPolyploids. We discuss the effects of changes in gene expression in Polyploids with respect to current evolutionary theory. Finally, we draw attention to the general question of the relationships between genomic and transcriptomic alteration and incipient diversification among sibling Polyploid lines and populations.
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assessing the monophyly of Polyploid gossypium species
Plant Systematics and Evolution, 2012Co-Authors: Corrinne E Grover, Kara Grupp, R J Wanzek, Jonathan F WendelAbstract:The origin and monophyly of the Polyploid cotton (Gossypium) species has been largely accepted, despite the lack of explicit phylogenetic evidence. Recent studies in other Polyploid systems have demonstrated that multiple origins for Polyploid species are much more common than once thought, raising the possibility that Gossypium Polyploids also had multiple origins, as postulated by some authors. To test the monophyly of Polyploid cotton, we sequenced a 2.8-kb intergenic region from all diploid species belonging to the genome groups from which the Polyploid originates. The resulting phylogenetic analyses strongly support a single origin of Polyploid cotton involving a D-genome ancestor related to Gossypium raimondii and an A-genome ancestor that was sister to both extant A-genome species.
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novel patterns of gene expression in Polyploid plants
Trends in Genetics, 2005Co-Authors: Keith L Adams, Jonathan F WendelAbstract:Genome doubling, or Polyploidy, is a major factor accounting for duplicate genes found in most eukaryotic genomes. Polyploidy has considerable effects on duplicate gene expression, including silencing and up- or downregulation of one of the duplicated genes. These changes can arise with the onset of Polyploidization or within several generations after Polyploid formation and they can have epigenetic causal factors. Many expression alterations are organ-specific. Specific genes can be independently and repeatedly silenced during Polyploidization, whereas patterns for other genes appear to be more stochastic. Three recent reports have provided intriguing new insights into the patterns, timing and mechanisms of gene expression changes that accompany Polyploidy in plants.
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Genome evolution in Polyploids
Plant molecular biology, 2000Co-Authors: Jonathan F WendelAbstract:Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by Polyploidy. Here, processes and mechanisms of gene and genome evolution in Polyploids are reviewed. Genes duplicated by Polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in Polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent Polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of Polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of Polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how Polyploidy facilitates evolution and adaptation.
Eric Jenczewski - One of the best experts on this subject based on the ideXlab platform.
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Evolution: he who grabs too much loses all
Current Biology - CB, 2013Co-Authors: Eric JenczewskiAbstract:Polyploidy can result in both evolutionary dead-ends and successful evolutionary transitions. A pair of recent papers indicates that adapting meiosis is a necessary step on the way to becoming a successful Polyploid.
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Genetic regulation of meiosis in Polyploid species: new insights into an old question
New Phytologist, 2009Co-Authors: Marta Cifuentes, Laurie Grandont, Moore Graham, Anne-marie Chèvre, Eric JenczewskiAbstract:Precise chromosome segregation is vital for Polyploid speciation. Here, we highlight recent findings that revitalize the old question of the genetic control of diploid-like meiosis behaviour in Polyploid species. We first review new nformation on the genetic control of autoPolyploid and alloPolyploid cytological diploidization, notably in wheat and Brassica. These major advances provide new opportunities for speculating about the adaptation of meiosis during Polyploid evolution. Some of these advances are discussed, and it is suggested that research on Polyploidy and on meiosis should no longer be unlinked.
