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370 results for “diploid”

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dryad40/100

Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation (Part 2/2)

Open the record for dataset details and reuse information.

publicAug 2023View details →
dryad40/100

The genetic consequences of range expansion and its influence on diploidization in polyploids

Open the record for dataset details and reuse information.

publicOct 2024View details →
zenodo36/100

Whole genome assembly and gene annotation of a diploid genotype of Brachiaria ruziziensis (syn. Urochloa ruziziensis)

<p>In this work, we have presented a comprehensive analysis of the molecular mechanism linked to aluminium tolerance in <em>Brachiaria</em> species. By assembling and annotating a diploid genotype of <em>B. ruziziensis</em> we have developed the capability for genomic-based studies of desirable phenotypic traits. Using this resource, we have identified three QTLs associated to root architecture and vigour during Al<sup>3+</sup> stress in a hybrid population from a high and low tolerant accession. We have also identified a number of genes and molecular responses that impact on different aspects of signalling, cell-wall composition and active transports as a response to aluminium stress. <em>Brachiaria </em>tolerance appears to build in the same genes than in rice. However, we found that external mechanisms such as sequestration of Al<sup>3+</sup> common in other grasses might be not that important in <em>Brachiaria. </em>Also, contrasting regulation in the same genotype after 8 or 72 hours of Al<sup>3+</sup> stress of numerous genes involved in RNA translation can explain the different levels of tolerance among different Brachiaria species. The newly annotated draft genome represents an important base upon which study other aspects of <em>Brachiaria</em> biology.</p>

opencc-by-4.0Mar 2020View details →
dryad36/100

Phase resolution of heterozygous sites in diploid genomes is important to phylogenomic analysis under the multispecies coalescent model

<p>Genome sequencing projects routinely generate haploid consensus sequences from diploid genomes, which are effectively chimeric sequences with the phase at heterozygous sites resolved at random. The impact of phasing errors on phylogenomic analyses under the multispecies coalescent (MSC) model is largely unknown. Here we conduct a computer simulation to evaluate the performance of four phase-resolution strategies (the true phase resolution, the diploid analytical integration algorithm which averages over all phase resolutions, computational phase resolution using the program PHASE, and random resolution) on estimation of the species tree and evolutionary parameters in analysis of multi-locus genomic data under the MSC model. We found that species tree estimation is robust to phasing errors when species divergences were much older than average coalescent times but may be affected by phasing errors when the species tree is shallow. Estimation of parameters under the MSC model with and without introgression is affected by phasing errors. In particular, random phase resolution causes serious overestimation of population sizes for modern species and biased estimation of cross-species introgression probability. In general the impact of phasing errors is greater when the mutation rate is higher, the data include more samples per species, and the species tree is shallower with recent divergences. Use of phased sequences inferred by the PHASE program produced small biases in parameter estimates. We analyze two real datasets, one of East Asian brown frogs and another of Rocky Mountains chipmunks, to demonstrate that heterozygote phase-resolution strategies have similar impacts on practical data analyses. We suggest that genome sequencing projects should produce unphased diploid genotype sequences if fully phased data are too challenging to generate, and avoid haploid consensus sequences, which have heterozygous sites phased at random. In case the analytical integration algorithm is computationally unfeasible, computational phasing prior to population genomic analyses is an acceptable alternative. </p>

opencc-zeroOct 2020View details →
dryad36/100

Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species

<ul> <li>Polyploidization is pervasive in plants, but little is known about the niche divergence of wild allopolyploids (species that harbor polyploid genomes originating from different diploid species) relative to their diploid progenitor species and the gene expression patterns that may underlie such ecological divergence. We conducted a fine-scale empirical study on habitat and gene expression of an allopolyploid and its diploid progenitors.</li> <li> We quantified soil properties and light availability of habitats of an allotetraploid <i>Cardamine flexuosa</i> and its diploid progenitors <i>C. amara</i> and <i>C. hirsuta</i> in two seasons. We analyzed expression patterns of genes and homeologs (homeologous gene copies in allopolyploids) using RNA-seq.</li> <li>We detected niche divergence between the allopolyploid and its diploid progenitors along water availability gradient at a fine scale: the diploids in opposite extremes and the allopolyploid in a broader range between diploids, with limited overlap with diploids at both ends. Most of the genes whose homeolog expression ratio changed among habitats in <i>C. flexuosa</i> varied spatially and temporally. </li> <li>These findings provide empirical evidence for niche divergence between an allopolyploid and its diploid progenitor species at a fine scale and suggest that divergent expression patterns of homeologs in an allopolyploid may underlie its persistence in diverse habitats.</li> </ul>

opencc-zeroNov 2020View details →
dryad36/100

Data from: Are acute and acclimated thermal effects on metabolic rate modulated by cell size? A comparison between diploid and triploid zebrafish larvae

Being composed of small cells may carry energetic costs related to maintaining ionic gradients across cell membranes as well as benefits related to diffusive oxygen uptake. Here we test the hypothesis that these costs and benefits of cell size in ectotherms are temperature dependent. To study the consequences of cell size for whole-organism metabolic rate we compared diploid and triploid zebrafish larvae differing in cell size. A fully factorial design was applied combining three different rearing and test temperatures that allowed us to distinguish acute from acclimated thermal effects. Individual oxygen consumption rates of diploid and triploid larvae across declining levels of oxygen availability were measured. We found that both acute and acclimated thermal effects affected the metabolic response. In comparison to triploids, diploids responded more strongly to acute temperatures, especially when reared at the highest temperature. These observations support the hypothesis that animals composed of smaller cells (i.e. diploids) are less vulnerable to oxygen limitation in warm aquatic habitats. Furthermore, we found slightly improved hypoxia tolerance in diploids. By contrast, warm-reared triploids had higher metabolic rates when they were tested at acute cold temperature, suggesting that being composed of larger cells may provide metabolic advantages in the cold. We offer two mechanisms as a potential explanation of this result, related to homeoviscous adaptation of membrane function and the mitigation of developmental noise. Our results suggest that being composed of larger cells provides metabolic advantages in cold water, while being composed of smaller cells provides metabolic advantages in warm water.

opencc-zeroDec 2020View details →
dryad36/100

The evolutionary advantage of fitness-dependent recombination in diploids: a deterministic mutation–selection–balance model

<p>Recombination's omnipresence in nature is one of the most intriguing problems in evolutionary biology. The question of why recombination exhibits certain general features is no less interesting than that of why it exists at all. One such feature is recombination's fitness dependence (FD). The so far developed population-genetics models have focused on the evolution of FD recombination mainly in haploids, although the empirical evidence for this phenomenon comes mostly from diploids. Using numerical analysis of modifier models for infinite panmictic populations, we show here that FD recombination can be evolutionarily advantageous in diploids subjected to purifying selection. We ascribe this advantage to the differential rate of disruption of lower- vs higher-fitness genotypes, which can be manifested in selected systems with at least three loci. We also show that if the modifier is linked to such selected system, it can additionally benefit from modifying this linkage in a fitness-dependent manner. The revealed evolutionary advantage of FD recombination appeared robust to crossover interference within the selected system, either positive or negative. Remarkably, FD recombination was often favored in situations where any constant non-zero recombination was evolutionarily disfavored, implying a relaxation of the rather strict constraints on major parameters (e.g., selection intensity and epistasis) required for the evolutionary advantage of non-zero recombination formulated by classical models.</p>

opencc-zeroJan 2021View details →
dryad36/100

A first complete phylogenomic hypothesis for diploid blueberries (Vaccinium section Cyanococcus)

<p><strong>The premise of the study: </strong>The true blueberries, (<em>Vaccinium</em> sect. <em>Cyanococcus</em>; Ericaceae), endemic to North America, have been intensively studied for over a century. However, with species estimates ranging from 9 to 24 and much confusion regarding species boundaries, this ecologically and economically valuable group remains inadequately understood at a basic evolutionary and taxonomic level. As a first step toward understanding the evolutionary history and taxonomy of this species complex, we present the first phylogenomic hypothesis of the known diploid blueberries.</p> <p><strong>Methods</strong>: We used flow cytometry to verify the ploidy of putative diploid taxa and a target-enrichment approach to obtain a genomic dataset for phylogenetic analyses.</p> <p><strong>Results</strong>: Despite evidence of gene flow, we found that a primary phylogenetic signal is present. Monophyly for all morphospecies was recovered, with two notable exceptions: one sample of <em>V. boreale</em> was consistently nested in the V<em>. myrtilloides</em> clade, and <em>V. caesariense</em> was nested in the <em>V. fuscatum</em> clade. One diploid taxon, <em>Vaccinium pallidum</em>, is implicated as having a homoploid hybrid origin.</p> <p><strong>Conclusions</strong>: This foundational study represents the first attempt to elucidate evolutionary relationships of the true blueberries of North America with a phylogenomic approach and sets the stage for multiple avenues of future study such as a taxonomic revision of the group, the verification of a homoploid hybrid taxon, and the study of polyploid lineages within the context of a diploid phylogeny.</p>

opencc-zeroOct 2023View details →
dryad36/100

Divergence in cold tolerance promotes niche differentiation between diploid and polyploid kiwifruits along an altitudinal gradient in Southwest China

<p>Polyploidization is hypothesized to improve the freezing resistance of plants in cold regions. However, adaptive strategies and key physiological mechanisms involved in the freezing resistant ability of polyploids remain unclear. In <em>Actinidia chinensis</em> (kiwifruits), the tetraploids and hexaploids occupy higher altitude habitats with colder climates than the diploids, providing a study system to investigate mechanisms responsible for differentiation in freezing resistance between cytotypes. We characterized environmental conditions of their natural distribution areas, and measured leaf-level traits of cold damages and water relations at typical sites of each cytotype along an altitudinal gradient. Polyploids showed lower semi-lethal temperature (LT<sub>50</sub>) than ice nucleation temperature (INT), reflecting a tolerance strategy to cope with freezing events in the plateau regions. More negative turgor loss points and larger cell elastic modulus of polyploids could help to alleviate damages from freezing-induced cell dehydration, thus strengthening their tolerance to lower subzero temperatures (lower LT<sub>50</sub>). The increased supercooling capacity of polyploids (lower INT) might correlate with less extracellular ice formation due to lower osmotic potential at full turgor, apoplastic water fraction and tissue capacitance. Our study uncovers a greater cold tolerance in polyploid kiwifruits than diploids, and suggests the potential linkage between freezing tolerance and water relations. Taken together, such a divergence in stress resistance may underlie the niche shift of polyploid plants towards harsh environments.</p>

opencc-zeroDec 2023View details →
dryad36/100

Striking variation in chromosome structure within Musa acuminata and its diploid cultivars

<p>The majority of cultivated bananas originated from inter- and intra(sub)specific crosses between two wild diploid species, <em>Musa acuminata</em> and <em>Musa balbisiana</em>. Hybridization and polyploidization events during the evolution of bananas led to the formation of clonally propagated cultivars characterized by a high level of genome heterozygosity and reduced fertility. The combination of low fertility of edible clones and differences in the chromosome structure among <em>M. acuminata</em> subspecies greatly hampers the breeding of improved banana cultivars. Using comparative oligo painting we investigated large chromosomal rearrangements in a set of wild <em>M. acuminata</em> subspecies and cultivars that originated by natural crosses. Additionally, we analyzed chromosome structure of F1 progeny that resulted from crosses between Mchare bananas and wild <em>M. acuminata </em>'Calcutta 4' genotype. Analysis of chromosome structure within <em>M. acuminata</em> revealed the presence of a large number of chromosomal rearrangements showing a correlation with banana speciation. Chromosome painting of F1 hybrids was complemented by Illumina resequencing, which enabled to identify the contribution of parental subgenomes to the diploid hybrid clones. Balanced presence of both parental genomes was revealed in all F1 hybrids with the exception of one clone, which contained only Mchare specific SNPs, and thus most probably originated from an unreduced diploid gamete of Mchare.</p>

opencc-zeroApr 2024View details →
dryad36/100

Data for genetic characterization and curation of diploid a-genome wheat species

<p>Diploid A-genome relatives of wheat comprises <i>T</i>. <i>urartu</i>, <i>T</i>. <i>monococcum</i> subsp. <i>monococcum</i> (domesticated einkorn) and <i>T</i>. <i>monococcum</i> subsp. <i>aegilopoides</i> (wild einkorn). About 930 accessions of A-genome diploid wheat species preserved in the gene bank of the Wheat Genetics Resource Center (WGRC) at Kansas State University were genotyped using genotyping-by-sequencing (GBS). We constructed four pooled GBS libraries (384- and 288-plex) using restriction enzymes (Pst1-Msp1) combinations and the libraries were sequenced on the Illumina platform. The sequence data was processed using Tassel 5 GBS v2 pipeline and identified thousands of single nucleotide polymorphisms (SNPs) for downstream genetic and genomic dissections of the tested population. We have used <i>T</i>. <i>urartu</i> pseudomolecule (Tu2.0) as a reference genome to detect the genetic markers. Four fastq files with raw sequence reads information can be obtained at the National Center for Biotechnology Information (NCBI) SRA database with the BioProject accession PRJNA744683 (<a href="https://www.ncbi.nlm.nih.gov/sra/PRJNA744683" rel="noopener noreferrer">https://www.ncbi.nlm.nih.gov/sra/PRJNA744683</a>). Provided key file has information for demultiplexing including flowcell, lane number, barcodes and sample names to replicate the analysis. This experiment led us to curate the gene bank through identification of genetically duplicated accessions, miss-classified accessions and miss-classified non-diploid accessions. We were able to observe the unique genetic and evolutionary relationships among the diploid A-genome wheat species along with the unique population structures per species and sub-species. </p>

opencc-zeroDec 2021View details →
dryad36/100

The genetic diversity of triploid Celtis pumila and its diploid relatives C. occidentalis and C. laevigata (Cannabaceae)

<p>The genus <i>Celtis</i> in eastern North America shows puzzling patterns of variation. While three species are generally recognized, many authors have suggested hybridization may be blurring the boundaries among them. Suspected hybridization between <i>C. occidentalis</i> and <i>C. pumila</i> has hampered conservation planning for the latter, which is a Threatened species in Canada. Using microsatellite markers and flow cytometry, we assessed the relationship between genetic diversity, ploidy, and morphology in this group. We confirmed the presence of two diploid species, <i>C. occidentalis</i> and <i>C. laevigata</i>, and that they do hybridize where they co-occur in southern Missouri and Illinois. We found two triploid genetic groups. These groups had distinct geographic ranges, but were morphologically very similar, corresponding to <i>C. pumila</i>. Furthermore, the triploid groups were characterized by a small number of heterozygous multi-locus genotypes. A single genotype dominated populations across Ontario, Michigan, Ohio and Pennsylvania, indicating apomictic reproduction is common in these groups. While the triploid clusters were distinct from each other, they did have strong associations with sympatric diploid species, and also with the western triploid species <i>C. reticulata</i>. The triploid <i>Celtis pumila</i> demonstrates remarkable phenotypic plasticity, with the same genotype variously presenting as dwarf shrubs in xeric, exposed sites, and subcanopy tree in mesic forests.</p>

opencc-zeroJan 2022View details →
zenodo36/100

Haploid Diploid optimization data from eCS (EVONANO)

<p>Data-set produced by and depicted in https://arxiv.org/abs/1911.07302</p>

opencc-by-4.0Nov 2019View details →
dryad36/100

Elevated O3 inhibited isoprene emission of a diploid and a triploid genotype of Populus tomentosa by different mechanisms

<p>Ozone (O<sub>3</sub>) pollution affects plant growth and isoprene (ISO) emission. However, the response mechanism of isoprene emission rate (ISO<sub>rate</sub>) to elevated O<sub>3</sub> (EO<sub>3</sub>) remains poorly understood. ISO<sub>rate</sub> was investigated in two genotypes (diploid and triploid) of Chinese white poplar (<em>Populus tomentosa</em> Carr.) exposed to EO<sub>3</sub> in an open top chamber (OTC) system. The triploid genotype had higher photosynthesis rate (A) and stomatal conductance (g<sub>s</sub>) than the diploid one. EO<sub>3</sub> significantly decreased A, g<sub>s</sub>, and ISO<sub>rate</sub> of middle and lower leaf positions in both genotypes. In the diploid genotype, the reduction of ISO<sub>rate</sub> was caused by a systematic decrease related to ISO synthesis capacity, as indicated by decreased contents of isoprene precursor dimethylallyl diphosphate (DMADP) and isoprene synthase (ISPS) protein and activity of ISPS. On the other hand, the negative effect of O<sub>3</sub> on ISO<sub>rate</sub> of the triploid genotype did not result from inhibited ISO synthesis capacity, but from increased ISO oxidative loss within the leaf. Our findings will be useful for breeding poplar genotypes with high-yield and lower ISO<sub>rate</sub>, depending on local atmospheric VOC/NO<sub>x</sub> ratio, to cope with both the rising O<sub>3</sub> concentrations and increasing biomass demand. They can also enlighten the incorporation of O<sub>3</sub> effects into process-based models of isoprene emission.</p>

opencc-zeroMay 2022View details →
zenodo36/100

Differentially methylated genes involved in reproduction and ploidy levels in recent diploidized and tetraploidized Eragrostis curvula genotypes

<p>Epigenetics studies changes in gene activity without changes in the DNA sequence. Methylation is an epigenetic mechanism important in many pathways, such as biotic and abiotic stresses, cell division, and reproduction.&nbsp;<em>Eragrostis curvula</em>&nbsp;is a grass species reproducing by apomixis, a clonal reproduction by seeds. This work employed the MCSeEd technique to identify deferentially methylated positions, regions, and genes in the CG, CHG, and CHH contexts in&nbsp;<em>E</em>.&nbsp;<em>curvula</em> genotypes with similar genomic backgrounds but with different reproductive modes and ploidy levels. In this way, we focused the analysis on the cvs. Tanganyika INTA (4x, apomictic), Victoria (2x, sexual), and Bahiense (4x, apomictic). Victoria was obtained from the diploidization of Tanganyika INTA, while Bahiense was produced from the tetraploidization of Victoria. This study showed that polyploid/apomictic genotypes had more differentially methylated positions and regions than the diploid sexual ones. Interestingly, it was possible to observe fewer differentially methylated positions and regions in CG than in the other contexts, meaning CG methylation is conserved across the genotypes regardless of the ploidy level and reproductive mode. In the comparisons between sexual and apomictic genotypes, we identified differentially methylated genes involved in the reproductive pathways, specifically in meiosis, cell division, and fertilization. Another interesting observation was that several differentially methylated genes between the diploid and the original tetraploid genotype recovered their methylation status after tetraploidization, suggesting that methylation is an important mechanism involved in reproduction and ploidy changes.</p>

opencc-by-4.0Dec 2023View details →
zenodo36/100

From tetraploid to diploid, a pangenomic approach to identify genes lost during synthetic diploidization of Eragrostis curvula

<p><strong>Introduction:</strong>&nbsp;In&nbsp;<em>Eragrostis curvula</em>, commonly known as weeping lovegrass, a synthetic diploidization event of the facultative apomictic tetraploid Tanganyika INTA cv. originated from the sexual diploid Victoria cv. Apomixis is an asexual reproduction by seeds in which the progeny is genetically identical to the maternal plant.</p> <p><strong>Methods:</strong>&nbsp;To assess the genomic changes related to ploidy and to the reproductive mode occurring during diploidization, a mapping approach was followed to obtain the first&nbsp;<em>E. curvula</em>&nbsp;pangenome assembly. In this way, gDNA of Tanganyika INTA was extracted and sequenced in 2x250 Illumina pair-end reads and mapped against the Victoria genome assembly. The unmapped reads were used for variant calling, while the mapped reads were assembled using Masurca software.</p> <p><strong>Results:</strong> The length of the assembly was 28,982,419 bp distributed in 18,032 contigs, and the variable genes annotated in these contigs rendered 3,952 gene models. Functional annotation of the genes showed that the reproductive pathway was differentially enriched. PCR amplification in gDNA and cDNA of Tanganyika INTA and Victoria was conducted to validate the presence/absence variation in five genes related to reproduction and ploidy. The polyploid nature of the Tanganyika INTA genome was also evaluated through the variant calling analysis showing the single nucleotide polymorphism (SNP) coverage and allele frequency distribution with a segmental allotetraploid pairing behavior.</p>

opencc-by-4.0Mar 2023View details →
dryad36/100

An efficient CRISPR-mediated genome editing system in diploid and polyploid Tragopogon (Asteraceae) enables functional studies of complex phenotypes and polyploid genome evolution

<p>Polyploidy or whole-genome duplication (WGD) is a significant evolutionary force, especially in angiosperms. However, the underlying mechanisms governing polyploid genome evolution remain unclear, limited largely by a lack of functional analysis tools in organisms that best exemplify the earliest stages of WGD. <em>Tragopogon</em> (Asteraceae) includes an evolutionary model system for studying the immediate consequences of polyploidy. In this study, we significantly improved the genetic transformation of <em>Tragopogon</em> and obtained genome-edited <em>T. porrifolius</em> (2<em>x</em>) and <em>T. mirus</em> (4<em>x</em>) primary generation (T<sub>0</sub>) individuals. Using CRISPR/Cas9, we knocked out the dihydroflavonol 4-reductase (<em>DFR</em>) gene, which controls anthocyanin synthesis, in both <em>T. porrifolius</em> and <em>T. mirus</em>. All transgenic allotetraploid <em>T. mirus</em> individuals had at least one mutant <em>DFR</em> allele and 71.4% of the plants had all four <em>DFR</em> alleles (from both homeologs) edited, indicating a high efficiency of the CRISPR system in polyploid <em>Tragopogon</em>. The anticipated absence of the anthocyanin was observed in both leaf and floral tissues from <em>T. porrifolius</em> and <em>T. mirus</em> mutants. In addition, the mutations were inherited in the T<sub>1</sub> generation. This study demonstrates a highly efficient CRISPR platform producing genome-edited <em>Tragopogon</em> individuals that have successfully completed their life cycle. The approaches used and challenges faced in building the CRISPR system in <em>Tragopogon</em> provide a framework for building similar systems in other nongenetic models. Genome editing in <em>Tragopogon</em> paves the way for novel functional biology studies of polyploid genome evolution and the consequences of WGD on complex traits, which holds enormous potential for both basic and applied research.</p>

opencc-zeroJun 2024View details →
dryad36/100

Data from: Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)

Hybridization is a frequent and important force in plant evolution. Next-generation sequencing (NGS) methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We reconstructed the phylogeny of diploid representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa plus 5 outgroups. Additionally, we obtained alignments for 39 loci through an automated assembly algorithm. These data were analyzed with diverse phylogenetic methods, including concatenation, coalescence-based species tree estimation, Bayesian concordance analysis, and network reconstructions, to provide insights into the evolutionary relationships of Hippeastreae. Causes for gene tree heterogeneity and cytonuclear discordance were examined through a Bayesian posterior predictive approach (JML) and coalescent simulations. Two major clades were found, Hippeastrinae and Traubiinae, as previously reported. Our results suggest the presence of two major nuclear lineages in Hippeastrinae characterized by different chromosome numbers: 1) Tocantinia and Hippeastrum with 2n = 22, and 2) Eithea, Habranthus, Rhodophiala, and Zephyranthes mostly with 2n = 12, 14, and 18. Strong cytonuclear discordance was confirmed in Hippeastrinae, and a network scenario with at least six hybridization events is proposed to reconcile nuclear and plastid signals, along a backbone that may also have been affected by incomplete lineage sorting at the base of each major subclade.

opencc-zeroDec 2016View details →
dryad36/100

Is there hybridisation between diploid and tetraploid Euphrasia in a secondary contact zone?

<p>• Premise of the study: Hybridisation between species with contrasting ploidy is usually considered rare in nature due to strong ploidy related postzygotic reproductive isolating barriers. However, genomic sequencing has revealed previously overlooked examples of natural cross-ploidy hybridisation, suggesting this phenomenon may be more common than once thought. Here, we investigate potential cross-ploidy hybridisation in British eyebrights (Euphrasia, Orobanchaceae), a group where thirteen putative cross-ploidy hybrid combinations have been reported based on morphology.   • Methods: We analysed a contact zone between diploid E. rostkoviana and tetraploid E. arctica in Wales. We sequenced part of the internal transcribed spacer of nuclear ribosomal DNA (ITS1) and used Genotyping by Sequencing (GBS) to look for evidence of cross-ploidy hybridisation and introgression. • Key results: All variant sites in the ITS1 region were fixed between diploids and tetraploids, indicating a strong barrier to hybridisation. Clustering analyses of 356 SNPs generated using GBS clearly separated samples by ploidy and revealed strong genetic structure (FST = 0.44). However, the FST distribution across all SNPs was bimodal, indicating potential differential selection on loci between diploids and tetraploids. Demographic inference with dadI suggested potential gene flow – with this limited to around one or fewer migrants per generation. • Conclusions: Our results suggest recent cross-ploidy hybridisation is rare or absent in a site of secondary contact in Euphrasia. While a strong ploidy barrier prevents hybridisation over ecological time-scales, such hybrids may form in stable populations over evolutionary time-scales and may allow for cross-ploidy introgression to take place.</p>

opencc-zeroOct 2022View details →
zenodo36/100

Dataset for "Polyploidy impacts population growth and competition with diploids: Multigenerational experiments reveal key life history tradeoffs"

<p>Datasets associated with the manuscript &quot;Polyploidy impacts population growth and competition with diploids: Multigenerational experiments reveal key life history tradeoffs&quot;.</p>

opencc-by-3.0-usOct 2022View details →

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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.

allen-brain-atlas
neuroscienceopenDocumentation, web resources, and API references are available online.
Last verified 2026-04-30Open record

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.

abode-home-cage
behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.
Last verified 2026-04-30Open record

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.

dandi-nwb
electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.
Last verified 2026-04-30Open record

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.

ibl
behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.
Last verified 2026-04-29Open record

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.

openneuro
neuroscienceopenPublished datasets are available on demand over the internet.
Last verified 2026-04-29Open record