Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
268
datasets available to search
ShareScore release 0.7.1
Dataset results
268 results for “polyploid”
High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species
Open the record for dataset details and reuse information.
Unraveling evolutionary pathways: Allopolyploidization and introgression in polyploid Prunus (Rosaceae)
Open the record for dataset details and reuse information.
Variation in reproduction and gene flow between cytotypes in a polyploid complex: one size does not fit all
Open the record for dataset details and reuse information.
Unveiling an asymmetric plant–fungal symbiosis: morphological, cytogenetic, and molecular characterization of a haploid <em>Epichloë festucae</em> strain associated with three polyploid cytotypes of the Iberian endemic grass <em>Festuca rothmaleri</em>
Open the record for dataset details and reuse information.
Data from: Repeated polyploidization shapes divergence in floral morphology in Lithophragma bolanderi (Saxifragaceae)
Open the record for dataset details and reuse information.
Sequencing data for: Chronosequence of invasion reveals minimal losses of population genomic diversity, niche expansion, and trait divergence in the polyploid, leafy spurge
Open the record for dataset details and reuse information.
Comparative transmission genetics of introgressed chromatin in reciprocal advanced backcross populations in Gossypium (cotton) polyploids
Open the record for dataset details and reuse information.
Data from: Substantially adaptive potential in polyploid cyprinid fishes: evidence from biogeographic, phylogenetic and genomic studies
Open the record for dataset details and reuse information.
Drift in small populations predicts mate availability and the breakdown of self-incompatibility in a clonal polyploid
Open the record for dataset details and reuse information.
Polyploidization-enhanced effective clonal reproduction endows the successful invasion of Solidago canadensis
Open the record for dataset details and reuse information.
Polyploids increase overall diversity despite higher turnover than diploids in the Brassicaceae
<p>Although polyploidy is widespread across the plant Tree of Life, its long-term evolutionary significance is still poorly understood. Here we examine the effects of polyploidy in explaining the large-scale evolutionary patterns within angiosperms by focusing on a single family exhibiting extensive inter-specific variation in chromosome numbers. We inferred ploidy from haploid chromosome numbers for 80% of species in the most comprehensive species-level chronogram for the Brassicaceae. After evaluating a total of 94 phylogenetic models of diversification, we found that ploidy influences diversification rates across the Brassicaceae. We also found that despite diversifying at a similar rate to diploids, polyploids have played a significant role in driving present-day differences in species richness among clades. Overall, in addition to highlighting the complexity in the evolutionary consequences of polyploidy, our results suggest that rare successful polyploids persist while significantly contributing to the long-term evolution of clades. Our findings further indicate that polyploidy has played a major role in driving the long-term evolution of the Brassicaceae and highlight the potential of polyploidy in shaping present-day diversity patterns across the plant Tree of Life.</p>
Diversification of a polyploid complex: the biogeography and acoustic communication evolution of North American gray treefrogs throughout the Quaternary
<p>Polyploid speciation and whole genome duplications are major drivers of biological diversity. After polyploid species are formed, the interactions between diploid and polyploid lineages may generate additional diversity in novel cytotypes and phenotypes. In anurans, mate choice by acoustic communication is the primary method by which individuals identify their own species and assess suitable mates. As such, the evolution of acoustic signals is an important mechanism for contributing to reproductive isolation and diversification in this group. The North American gray treefrog complex, consisting of the diploid Hyla chrysoscelis and the tetraploid Hyla versicolor, has long been used to study reproductive isolation and research on this system has consistently driven this field forward. Here, we estimate the biogeographic history of this group, focusing specifically on the geographic origin of whole genome duplication and the expansion of lineages out of refugia following climate oscillations and retreats of the Laurentide ice sheet. We then test for lineage-specific differences in mating signals by applying comparative methods to a large acoustic data set collected over 52 years that includes >1500 individual frogs. Finally, we expand upon our results in light of recent estimates of the complex's genomic evolution to describe the history of diversification in gray treefrogs throughout the Quaternary.</p>
Data from: Evolution and systematics of polyploid Nigritella (Orchidaceae)
Members of the orchid genus Nigritella are widespread in European mountains, but species circumscriptions and evolutionary patterns in the genus are subjects to conflicting opinions. We analyzed a representative material of Nigritella for differentiation at nuclear and plastid marker loci. In agreement with predictions from embryological studies, diploid members of Nigritella are sexual and mostly out-crossing, whereas triploid, tetraploid and pentaploid members are apomicts. The diploid taxa were poorly differentiated in the investigated molecular markers, except for the western N. gabasiana, which was separated in plastid haplotypes. Polyploid Nigritella aggregate into three groups and within each of these groups apomictic polyploids have given rise to new species. Within the N. nigra group, the tetraploid N. nigra ssp. austriaca is somewhat differentiated from the triploid ssp. nigra at nuclear as well as plastid loci. Fusion of an unreduced egg cell from ssp. nigra with a haploid microgamete from Gymnadenia conopsea gave rise to Gymnigritella runei. Within the N. widderi group, N. archiducis-joannis is poorly separated from N. widderi in molecular markers, and the pentaploid N. buschmanniae has evolved by fusion of an unreduced egg cell from N. widderi with a haploid microgamete from a diploid Nigritella. Within the N. miniata group, N. stiriaca is somewhat differentiated from N. miniata at nuclear loci, but no other segregates of N. miniata are supported at species level. Polyploid Nigritella species accumulate genetic diversity by somatic mutations. In the widespread N. nigra ssp. austriaca and N. miniata this diversity is correlated to geography. Although some polyploids may be of recent origins, each polyploid contain genetic markers no longer encountered in diploid members of the genus. According to plastid marker data, Nigritella and Gymnadenia may constitute monophyletic sister genera.
Data from: Genetic diversity and distribution patterns of diploid and polyploid hybrid water frog populations (Pelophylax esculentus complex) across Europe
Polyploidization is a rare yet sometimes successful way for animals to rapidly create geno- and phenotypes that may colonize new habitats and quickly adapt to environmental changes. In this study, we use water frogs of the Pelophylax esculentus complex, comprising two species (Pelophylax lessonae, genotype LL; Pelophylax ridibundus, RR) and various diploid (LR) and triploid (LLR, LRR) hybrid forms, summarized as P. esculentus, as a model for studying recent hybridization and polyploidization in the context of speciation. Specifically, we compared the geographic distribution and genetic diversity of diploid and triploid hybrids across Europe to understand their origin, maintenance and potential role in hybrid speciation. We found that different hybrid and parental genotypes are not evenly distributed across Europe. Rather, their genetic diversity is structured by latitude and longitude and the presence/absence of parental species but not of triploids. Highest genetic diversity was observed in central and eastern Europe, the lowest in the northwestern parts of Europe. This gradient can be explained by the decrease in genetic diversity during postglacial expansion from southeastern glacial refuge areas. Genealogical relationships calculated on the basis of microsatellite data clearly indicate that hybrids are of multiple origin and include a huge variety of parental genomes. Water frogs in mixed-ploidy populations without any parental species (i.e. all-hybrid populations) can be viewed as evolutionary units that may be on their way towards hybrid speciation. Maintenance of such all-hybrid populations requires a continuous exchange of genomes between diploids and triploids, but scenarios for alternative evolutionary trajectories are discussed.
Data from: Genetic diversity and multiple origins of polyploid Atriplex nummularia Lindl. (Chenopodiaceae).
Few studies have described the genetic diversity within and between populations of polyploid plant species despite the general acceptance of the importance of polyploidy in plant diversification and speciation. The genus Atriplex has a complex evolutionary history in Australia that has included polyploidy and hybridization among perennial forms. The octoploid, dioecious species Atriplex nummularia is proposed to have evolved from an octoploid ancestor in the coastal semi-arid fringe of south-western Australia, and to have spread east and diversified into taxa which occupy edaphically different habitats. Despite interest in the diversification of the genus, and the ecological and economic importance of A. nummularia, there are no descriptions of the genetic structure of the species. Nuclear microsatellite markers and principal coordinate analysis, analysis of molecular variance, Bayesian and phenetic analyses were used to investigate the diversity and taxonomic relationships of two common subspecies of A. nummularia. Genetic diversity was high overall (A = 509, A′ = 42.4, Ho = 0.824, H′ = 2.8), but values were significantly lower in the western subspecies, A. nummularia ssp. spathulata. As in other outbreeding, perennial species, most of the genetic diversity was within populations (FST = 0.125). Clear divergence of subspecies was evident in principal coordinate analysis, neighbor-joining and Bayesian clustering analyses and the differentiation of populations was very low within subspecies (FSC = 0.048). These findings support the taxonomic separation of the two subspecies. Clustering patterns based on Bayesian analyses suggested that the polyploid subspecies of A. nummularia have multiple origins.
Data from: Genetic and ecotypic differentiation in a Californian plant polyploid complex (Grindelia, Asteraceae)
Studies of ecotypic differentiation in the California Floristic Province have contributed greatly to plant evolutionary biology since the pioneering work of Clausen, Keck, and Hiesey. The extent of gene flow and genetic differentiation across interfertile ecotypes that span major habitats in the California Floristic Province is understudied, however, and is important for understanding the prospects for local adaptation to evolve or persist in the face of potential gene flow across populations in different ecological settings. We used microsatellite data to examine local differentiation in one of these lineages, the Pacific Coast polyploid complex of the plant genus Grindelia (Asteraceae). We examined 439 individuals in 10 different populations. The plants grouped broadly into a coastal and an inland set of populations. The coastal group contained plants from salt marshes and coastal bluffs, as well as a population growing in a serpentine grassland close to the coast, while the inland group contained grassland plants. No evidence for hybridization was found at the single location where adjacent populations of the two groups were sampled. In addition to differentiation along ecotypic lines, there was also a strong signal of local differentiation, with the plants grouping strongly by population. The strength of local differentiation is consistent with the extensive morphological variation observed across populations and the history of taxonomic confusion in the group. The Pacific Clade of Grindelia and other young Californian plant groups warrant additional analysis of evolutionary divergence along the steep coast-to-inland climatic gradient, which has been associated with local adaptation and ecotype formation since the classic studies of Clausen, Keck, and Hiesey.
Data from: Origin and genome evolution of polyploid green toads in Central Asia: evidence from microsatellite markers
Polyploidization, which is expected to trigger major genomic reorganizations, occurs much less commonly in animals than in plants, possibly because of constraints imposed by sex-determination systems. We investigated the origins and consequences of allopolyploidization in Palearctic green toads (Bufo viridis subgroup) from Central Asia, with three ploidy levels and different modes of genome transmission (sexual versus clonal), to (i) establish a topology for the reticulate phylogeny in a species-rich radiation involving several closely related lineages and (ii) explore processes of genomic reorganization that may follow polyploidization. Sibship analyses based on 30 cross-amplifying microsatellite markers substantiated the maternal origins and revealed the paternal origins and relationships of subgenomes in allopolyploids. Analyses of the synteny of linkage groups identified three markers affected by translocation events, which occurred only within the paternally inherited subgenomes of allopolyploid toads and exclusively affected the linkage group that determines sex in several diploid species of the green toad radiation. Recombination rates did not differ between diploid and polyploid toad species, and were overall much reduced in males, independent of linkage group and ploidy levels. Clonally transmitted subgenomes in allotriploid toads provided support for strong genetic drift, presumably resulting from recombination arrest. The Palearctic green toad radiation seems to offer unique opportunities to investigate the consequences of polyploidization and clonal transmission on the dynamics of genomes in vertebrates.
Data from: Genetic diversity and population structure of Varronia curassavica: a medicinal polyploid species in a threatened ecosystem
Varronia curassavica is an important medicinal species associated with the restinga, one of the most threatened coastal ecosystems of the Atlantic Forest. These circumstances call for studies aimed at estimating effective population size and gene flow to improve conservation efforts. Hence, the present study aimed to characterize the genetic diversity, ploidy level and population structure of this species in different areas of restinga using microsatellites. Varronia curassavica was characterized as an autotetraploid, with high genetic variability, low divergence, and no significant fixation indices, indicating the absence of, or reduced, inbreeding and genetic drift in the study area. About 44 % of the alleles occurred at low frequency in adults of all populations and 41 % in the progenies evaluated. Gene flow was high, consistent with outcrossing species with high dispersal capacity (Nm = 4.87). The results showed no tendency toward isolation by distance. The estimated effective size indicates that the populations studied have the potential to ensure conservation of the species in the long term. The genetic variability and population structure of V. curassavica, as determined in this study, could form the foundation for activities directed toward the sustainable use of this resource and its conservation. Even though the restinga ecosystem has suffered dramatic reductions in area, this study provides evidence that this species is resilient to anthropogenic threats to its genetic integrity, since it is a polyploid with self-incompatibility mechanisms that contribute to maintaining high genetic diversity in an panmictic meta-population along the coast of Santa Catarina.
Data from: An experimental test of local adaptation among cytotypes within a polyploid complex
The geographic distributions of polyploids suggest they can have distinct and sometimes broader niches compared to diploids. However, relatively few field experiments have investigated whether range differences are associated with local adaptation or reflect other processes, such as dispersal limitation. In three years of transplants across the elevational ranges of five cytotypes in the Claytonia perfoliata complex, we found evidence for local adaptation. In at least one study year germination was higher within the natural range for each cytotype, and four of the five cytotypes attained larger biomass within their natural range. Fitness within and beyond range varied across years, with two instances of cytotypes showing higher fitness beyond the range, highlighting a potential role of temporal variability in cytotype differentiation. Polyploids as a group did not outperform diploids, but the cytotype with highest fitness across environments was a hexaploid reported to be invasive. Our results suggest that differences in geographic ranges within the C. perfoliata complex reflect local adaptation of cytotypes. Although we did not find a general polyploid advantage, our findings support the idea that occasional polyploid cytotypes exhibit high fitness relative to other cytotypes, and contribute to growing evidence supporting ecological differentiation of cytotypes within polyploid complexes.
Data from: Parallel polyploid speciation: distinct sympatric gene-pools of recurrently derived allo-octoploid Asplenium ferns
Although polyploidy is widespread, its significance to the generation of biodiversity remains unclear. Many polyploids have been derived recurrently. For a particular polyploid, gene-flow between the products of independent origin is typical where they come into contact. Here, we use AFLP DNA-fingerprinting and chloroplast DNA sequences to demonstrate parallel polyploid speciation within both of the ferns Asplenium cimmeriorum and A. gracillimum. Both of these taxa comprise at least two allopolyploids, recurrently derived from the same progenitor pair. Each of these allopolyploids remain genetically distinguishable even with extensive sympatry, and could therefore be considered distinct species. To our knowledge, parallel speciation on this scale amongst recurrent polyploids has not been previously reported. With their parallel origins, these 'evolutionary replicates' provide an unrivalled opportunity to investigate how the reproductive barriers and ecological differentiation necessary for speciation arise following polyploidy.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.