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107 results for “ploidy”
Spatial, climate and ploidy factors drive genomic diversity and resilience in the widespread grass Themeda triandra
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Data from: Population genomic variation reveals roles of history, adaptation, and ploidy in switchgrass
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Data from: Wide variation in ploidy level and genome size in a New Zealand freshwater snail with coexisting sexual and asexual lineages
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Data from: Interspecific variation in ploidy as a key plant trait outlining local extinction risks and community patterns in fragmented landscapes
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Valenzuela phylogenomic dataset from: Illumina whole genome sequencing indicates ploidy level differences within the Valenzuela flavidus (Psocodea: Psocomorpha: Caeciliusidae) species complex
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Figure 3 from: Shiotani Y, Fukuda T, Marchuk EA, Petrunenko EA, Krestov PV, Bondarchuk SN, Nishikawa Y, Shimamura T, Fujimura Y, Nakamura K (2020) Merger of Betula tatewakiana (Betulaceae) from northern Japan with northeast Asian B. ovalifolia based on ploidy level. PhytoKeys 170: 83-91. https://doi.org/10.3897/phytokeys.170.58585
Figure 3 Leaf traits of B. tatewakiana and B. ovalifolia. White hairs on adaxial leaf surface (A, C, E) and densely resinous glands on abaxial leaf surface (B, D, F) are shown for the holotype of B. tatewakiana (H. Suzuki and M. Ohki, s.n., A, B), B. tatewakiana of our collection (Yuki Shiotani 38, C, D), and B. ovalifolia in Russia (Koh Nakamura 14188, E, F). Scale bar: 1 mm.
Figure 2 from: Shiotani Y, Fukuda T, Marchuk EA, Petrunenko EA, Krestov PV, Bondarchuk SN, Nishikawa Y, Shimamura T, Fujimura Y, Nakamura K (2020) Merger of Betula tatewakiana (Betulaceae) from northern Japan with northeast Asian B. ovalifolia based on ploidy level. PhytoKeys 170: 83-91. https://doi.org/10.3897/phytokeys.170.58585
Figure 2 Somatic chromosomes at metaphase of B. tatewakiana and B. ovalifolia. Photomicrographs of B. tatewakiana from Sarabetsu mire (A, 2n = 56: HUBG 14746 A) and Nishibetsu mire (C, 2n = 56: Yuki Shiotani 29), and B. ovalifolia from Primorsky Krai (E, 2n = 56: Koh Nakamura 14198) are shown. B, D, F are drawings of A, C, E, respectively. Scale bar: 5 µm.
Figure 1 from: Shiotani Y, Fukuda T, Marchuk EA, Petrunenko EA, Krestov PV, Bondarchuk SN, Nishikawa Y, Shimamura T, Fujimura Y, Nakamura K (2020) Merger of Betula tatewakiana (Betulaceae) from northern Japan with northeast Asian B. ovalifolia based on ploidy level. PhytoKeys 170: 83-91. https://doi.org/10.3897/phytokeys.170.58585
Figure 1 Species distribution ranges of Betula ovalifolia (A) and B. tatewakiana (B). Map data 2020 (C) Google.
Data from: Ploidy tug-of-war: evolutionary and genetic environments influence the rate of ploidy drive in a human fungal pathogen
Variation in baseline ploidy is seen throughout the tree of life, yet the factors that determine why one ploidy level is maintained over another remain poorly understood. Experimental evolution studies using asexual fungal microbes with manipulated ploidy levels intriguingly reveals a propensity to return to the historical baseline ploidy, a phenomenon that we term 'ploidy drive'. We evolved haploid, diploid, and polyploid strains of the human fungal pathogen Candida albicans under three different nutrient limitation environments to test whether these conditions, hypothesized to select for low ploidy levels, could counteract ploidy drive. Strains generally maintained or acquired smaller genome sizes size (measured as total nuclear DNA through flow cytometry) in minimal medium and under phosphorus depletion compared to in a complete medium, while mostly maintained or acquired increased genome sizes under nitrogen depletion. Improvements in fitness often ran counter to changes in genome size; in a number of scenarios lines that maintained their original genome size often increased in fitness more than lines that converged towards diploidy. Combined, this work demonstrates a role for both the environment and genotype in determination of the rate of ploidy drive, and highlights questions that remain about the force(s) that cause genome size variation.
Data from: Hybridization between two cryptic filamentous brown seaweeds along the shore: analysing pre- and post-zygotic barriers in populations of individuals with varying ploidy levels
We aimed to study the importance of hybridization between two cryptic species of the genus Ectocarpus, a group of filamentous algae with haploid-diploid life cycles that include the principal genetic model organism for the brown algae. In haploid-diploid species, the genetic structure of the two phases of the life cycle can be analysed separately in natural populations. Such life cycles provide a unique opportunity to estimate the frequency of hybrid genotypes in diploid sporophytes and meiotic recombinant genotypes in haploid gametophytes allowing the effects of reproductive barriers preventing fertilization or preventing meiosis to be untangle. The level of hybridization between E. siliculosus and E. crouaniorum was quantified along the European coast. Clonal cultures (568 diploid, 336 haploid) isolated from field samples were genotyped using cytoplasmic and nuclear markers to estimate the frequency of hybrid genotypes in diploids and recombinant haploids. We identified admixed individuals using microsatellite loci, classical assignment methods and a newly developed Bayesian method (XPloidAssignment), which allows the analysis of populations that exhibit variations in ploidy level. Over all populations, the level of hybridization was estimated at 8.7%. Hybrids were exclusively observed in sympatric populations. More than 98% of hybrids were diploids (40% of which showed signs of aneuploidy) with a high frequency of rare alleles. The near absence of haploid recombinant hybrids demonstrates that the reproductive barriers are mostly post-zygotic and suggests that abnormal chromosome segregation during meiosis following hybridisation of species with different genome sizes could be a major cause of interspecific incompatibility in this system.
Data from: STRUCTURE is more robust than other clustering methods in simulated mixed-ploidy populations
Analyses of population genetic structure has become a standard approach in population genetics. In polyploid complexes, clustering analyses can elucidate the origin of polyploid populations and patterns of admixture between different cytotypes. However, combining diploid and polyploid data can theoretically lead to biased inference with (artefactual) clustering by ploidy. We used simulated mixed-ploidy (diploid-autotetraploid) data to systematically compare the performance of k-means clustering and the model-based clustering methods implemented in STRUCTURE, ADMIXTURE, FASTSTRUCTURE and INSTRUCT under different scenarios of differentiation and with different marker types. Under scenarios of strong population differentiation, the tested applications performed equally well. However, when population differentiation was weak, STRUCTURE was the only method that allowed unbiased inference with markers with limited genotypic information (co-dominant markers with unknown do sage or dominant markers). Still, since STRUCTURE was comparably slow the much faster but less powerful FASTSTRUCTURE provides a reasonable alternative for large datasets. Finally, although bias makes k-means clustering unsuitable for markers with incomplete genotype information, given large numbers of loci (>1000) with known dosage k-means clustering was superior to FASTSTRUCTURE in terms of power and speed. We conclude that STRUCTURE is the most robust method for the analysis of genetic structure in mixed-ploidy populations, although alternative methods should be considered under some specific conditions.
Interactions between breeding system and ploidy affect niche breadth in Solanum
<p>As climate changes understanding what drives the way plants evolve to exist in new ecological niches becomes increasingly important. Here we find that in Solanum section Petota that specific breeding system and ploidy combinations increase niche divergence through the decoupling of geographical range and niche diversity. This allows for more targeted use for plant breeding and plant conservation. This is the data and code associated with the manuscript that describes these results. </p>
Data from: Plasticity in ploidy underlies plant fitness compensation to herbivore damage
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Data from: Ploidy elicits a whole-genome dosage effect: growth of triploid Atlantic salmon is linked to the genetic origin of the second maternal chromosome set
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Data from: Hybridization between two cryptic filamentous brown seaweeds along the shore: analysing pre- and post-zygotic barriers in populations of individuals with varying ploidy levels
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Data from: STRUCTURE is more robust than other clustering methods in simulated mixed-ploidy populations
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Data from: Reciprocal transplantations reveal strong niche differentiation among ploidy-differentiated species of the Senecio carniolicus aggregate (Asteraceae) in the easternmost Alps
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Data from: Genotyping SNPs and inferring ploidy by amplicon sequencing for polyploid, ploidy-variable organisms
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Data from: Sensitivity to phosphorus limitation increases with ploidy level in a New Zealand snail
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Data from: Mutational effects depend on ploidy level: all else is not equal
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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.