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4,480 results for “hybrid”
Mantis shrimp locomotion: coordination and variation of hybrid metachronal swimming
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Signatures of hybridization in Trypanosoma brucei
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Hybrid evolution repeats itself across environmental contexts in Texas sunflowers (Helianthus)
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Data from: Hybrid incompatibility between D. virilis and D. lumei is stronger in the presence of transposable elements
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Correlated nanoimaging of structure and dynamics of cation-polaron coupling in hybrid perovskites
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Yeast 1-hybrid screens for upstream regulators of A. thaliana AGO1, AGO7, and AGO10: raw data and R code
<p>These files document a yeast 1-hybrid experiments and associated analyses described in a paper by Hoyer et al. (2019): <a href="https://doi.org/10.1002/pld3.102">https://doi.org/10.1002/pld3.102</a></p> <p>This release corresponds to the fourth version of the Zenodo record. None of the code or data files changed from record 1472704 (the version linked in the paper); I simply added a link to the <a href="https://doi.org/10.1002/pld3.102">Plant Direct paper</a> to the ReadMe file.</p>
Enhanced reforming of mixed biomass tar model compounds using a hybrid gliding arc plasma catalytic process
<p>Datasheet for the paper; DOI: 10.1016/j.cattod.2019.05.046</p>
Data from: First evidence for allotriploid hybrids between Juniperus thurifera and J. sabina in a sympatric area in the French Alps
<p>At Saint Crépin location (French Alps), where sympatry between the tetraploid <i>Juniperus thurifera</i> and the diploid <i>Juniperus sabina</i> occurs, three individuals with an atypical morphology<i>,</i> have been observed. AFLP markers were used to unravel hybridization and potential introgression events in this population. In total, 147 polymorphic loci remained after the process of peak selection. This dataset demonstrates hybrids originated from a cross between <i>J. sabina</i> and <i>J. thurifera</i> and suggests that back-cross at least to <i>J. thurifera </i>is possible. This study shed light on a rare case of hybridization of two <i>Juniperus</i> species with different ploidy levels in natural sympatric population.</p>
The Effects of Upper-Hybrid Waves on Energy Conversion in the Electron Diffusion Region
<p>The data from the simulations of upper-hybrid waves near the electron diffusion region. </p> <p>Read 'note.txt' for the description about the data. </p>
Data from: Allopatric divergence and hybridization within Cupressus chengiana (Cupressaceae), a threatened conifer in the northern Hengduan Mountains of western China
<p class="CxSpFirst">Having a comprehensive understanding of population structure, genetic differentiation and demographic history is important for the conservation and management of threatened species. High‐throughput sequencing (HTS) provides exciting opportunities to address a wide range of factors for conservation genetics. Here, we generated HTS data and identified 266,884 high‐quality single nucleotide polymorphisms from 82 individuals of <i>Cupressus chengiana </i>, to assess population genomics across the species' full range, comprising the Daduhe River (DDH), Minjiang River (MJR) and Bailongjiang River (BLJ) catchments in western China. admixture , principal components analysis and phylogenetic analyses indicated that each region contains a distinct lineage, with high levels of differentiation between them (DDH, MJR and BLJ lineages). MJR was newly distinguished compared to previous surveys, and evidence including coalescent simulations supported a hybrid origin of MJR during the Quaternary. Each of these three lineages should be recognized as an evolutionarily significant unit (ESU), due to isolation, differing genetic adaptations and different demographic history. Currently, each ESU faces distinct threats, and will require different conservation strategies. Our work shows that population genomic approaches using HTS can reconstruct the complex evolutionary history of threatened species in mountainous regions, and hence inform conservation efforts, and contribute to the understanding of high biodiversity in mountains.</p>
Data from: The contribution of hybridization to range‐wide population genetic structure in a Pacific coastal dune plant
<p>Premise of the study: Interspecific hybridization can cause genetic structure across species ranges if the mating system and degree of sympatry/parapatry with close relatives varies geographically. The coastal dune endemic <em>Camissoniopsis cheiranthifolia</em> (Onagraceae) exhibits genetic subdivisions across its range, some of which are associated with shifts in mating system from outcrossing to selfing, while others are not. For instance, strong differentiation between large-flowered, self-incompatible (LF-SI) and large-flowered, self-compatible (LF-SC) populations occurs without much reduction in outcrossing or obvious barriers to gene flow. We hypothesized that LF-SI diverged from LF-SC via hybridization with the predominantly inland SI sister species <em>C. bistort</em>a.</p> <p>Methods: We analyzed spatial proximity using 1460 herbarium records, and genetic variation at 12 microsatellites assayed for 805 and 404 individuals from 32 <em>C. cheiranthifolia</em> and 18 <em>C. bistorta</em> populations, respectively. We also assayed nine chloroplast microsatellites for 124 and 111 individuals from 27 and 19 populations, respectively. </p> <p>Key results: Closer parapatry was associated with unexpectedly high genetic continuity between LF-SI <em>C. cheiranthifolia</em> and <em>C. bistorta</em>. LF-SI genotypes clustered with <em>C. bistorta</em> exclusive of other <em>C. cheiranthifolia</em> genotypes. Similarly, pairwise FST among SI <em>C. cheiranthifolia</em> and <em>C. bistorta</em>, adjusted for geographic proximity, was not higher between heterospecific than conspecific populations. </p> <p>Conclusions: The lack of genetic differentiation between LF-SI <em>C. cheiranthifolia</em> and <em>C. bistorta</em> populations, even those located away from the zone of parapatry, suggests that LF-SI <em>C. cheiranthifolia</em> instead of hybridizing with <em>C. bistorta</em> is rather an ecotype of <em>C. bistorta</em> that has adapted to coastal dune habitat independent of other lineages in <em>C. cheiranthifolia</em> proper.</p>
Data from: Overlap of spatial and temporal spawning distributions of spring and summer Chinook Salmon results in hybridization in the upper Columbia River
<p>The upper Columbia River in Washington State (main-stem and tributary habitat between McNary and Chief Joseph dams) is inhabited by two major lineages of Chinook Salmon (<i>Oncorhynchus tshawytscha</i>); endangered spring Chinook Salmon and summer Chinook Salmon which are not ESA listed. The lineages are highly genetically divergent from one another and historically spatial and temporal isolating mechanisms maintained these genetic differences. Both lineages occur in the Entiat River, a system where anthropogenic activity has changed habitat, flows, species composition, and the distribution of the two lineages over the past century. We examined the spatial and temporal overlap in spawning distributions between Entiat River spring and summer Chinook Salmon and we used genetic markers to assess the level of introgression between lineages. Redd surveys were conducted from 2003 to 2017 to describe spatial and temporal spawning patterns of both lineages. We genotyped sub-yearling juvenile Chinook Salmon captured in the Entiat River from 2009–2014 at 90 SNP loci to determine lineage and hybridization status. There was temporal overlap in spawning between lineages in several years and considerable spatial overlap in redd locations annually. Genetic analysis revealed hybridization between lineages does occur, albeit at relatively low rates (2.6% of sub-yearling juveniles genotyped). We detected hybrids each year samples were collected and they were distributed throughout the Entiat River basin. Hybridization between lineages of Chinook Salmon could result in introgression and a loss of genetic diversity between the lineages, and/or, a loss of production by ESA-listed spring Chinook Salmon. The presence of hybrids warrants concern for ESA-listed spring Chinook Salmon in both the Entiat River system and throughout the upper Columbia River basin.</p>
Loss of ecologically important genetic variation in late generation hybrids reveals links between adaptation and speciation
Adaptation to contrasting environments occurs when advantageous alleles accumulate in each population, but it remains largely unknown whether these same advantageous alleles create genetic incompatibilities that can cause intrinsic reproductive isolation leading to speciation. Identifying alleles that underlie both adaptation and reproductive isolation is further complicated by factors such as dominance and genetic interactions among loci, which can affect both processes differently and obscure potential links between adaptation and speciation. Here, we use a combination of field and glasshouse experiments to explore the connection between adaptation and speciation while accounting for dominance and genetic interactions. We created a hybrid population with equal contributions from four contrasting ecotypes of Senecio lautus (Asteraceae), which produced hybrid genomes both before (F1 hybrid generation) and after (F4 hybrid generation) recombination among the parental ecotypes. In the glasshouse, plants in the second generation (F2 hybrid generation) showed reduced fitness as a loss of fertility, but fertility was recovered in subsequent generations suggesting that genetic variation underlying fertility reduction was lost in subsequent generations. To quantify the effects of losing genetic variation at the F2 generation on the fitness of later generation hybrids, we used a reciprocal transplant to test for fitness differences between parental ecotypes, and F1 and F4 hybrids in all four parental habitats. Compared to the parental ecotypes and F1 hybrids, variance in F4 hybrid fitness was lower, and lowest in habitats that showed stronger native-ecotype advantage, suggesting that stronger natural selection for the native ecotype reduced fitness variation in the F4 hybrids. Fitness trade-offs that were present in the parental ecotypes and F1 hybrids were absent in the F4 hybrid. Together, these results suggest that the genetic variation lost after the F2 generation was likely associated with both adaptation and intrinsic reproductive isolation among populations adapted to contrasting environments.
Dynamic shifts in social network structure and composition within a breeding hybrid population
1. Mating behavior and the timing of reproduction can inhibit genetic exchange between closely related species; however, these reproductive barriers are challenging to measure within natural populations. Social network analysis provides promising tools for studying the social context of hybridization, and the exchange of genetic variation, more generally. 2. We test how social networks within a hybrid population of California (Callipepla californica) and Gambel's quail (Callipepla gambelii) change over discrete periods of a breeding season. We assess patterns of phenotypic and genotypic assortment, and ask whether altered associations between individuals (association rewiring), or changes to the composition of the population (individual turnover) drive network dynamics. We use genetic data to test whether social associations and relatedness between individuals correlate with patterns of parentage within the hybrid population. 3. To achieve these aims, we combine RFID association data, phenotypic data, and genomic measures with social network analyses. We adopt methods from the ecological network literature to quantify shifts in network structure and to partition changes into those due to individual turnover and association rewiring. We integrate genomic data into networks as node-level attributes (ancestry) and edges (relatedness, parentage) to test links between social and parentage networks. 4. We show that rewiring of associations between individuals that persist across network periods, rather than individual turnover, drives the majority of the changes in network structure throughout the breeding season, and that the traits involved in phenotypic/genotypic assortment were highly dynamic over time. Social networks were randomly assorted based upon genetic ancestry, suggesting weak behavioral reproductive isolation within this hybrid population. Finally, we show that the strength of associations within the social network, but not levels of genetic relatedness, predict patterns of parentage. 5. Social networks play an important role in population processes such as the transmission of disease and information, yet there has been less focus on how networks influence the exchange of genetic variation. By integrating analyses of social structure, phenotypic assortment, and reproductive outcomes within a hybrid zone, we demonstrate the utility of social networks for analyzing links between social context and gene flow within wild populations. 08-Jul-2020
Disentangling sources of gene tree discordance in phylogenomic datasets: testing ancient hybridizations in Amaranthaceae s.l.
<p>Gene tree discordance in large genomic datasets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The dataset included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations.</p>
Hybrid nanoplasmonic porous biomaterial scaffold for liquid biopsy diagnostics using extracellular vesicles: data and media
<p>Raw datasets and media accompanying the manuscript: <strong>Hybrid nanoplasmonic porous biomaterial scaffold for liquid biopsy diagnostics using extracellular vesicles</strong>, published in ACS Sensors</p>
Hybrid-electric passenger car energy utilization and emissions: Relationships for real-world driving conditions that account for road grade
<p>Past research showed on-road emissions patterns unique to hybrid electric vehicles (HEVs), indicating the need to account for them in emissions models as projected HEV sales increase over the coming decades. This work defines and characterizes a variable that quantifies HEV operating behavior to inform future development of new HEV emissions models based on current knowledge of conventional vehicle (CV) emissions patterns. Instantaneous hybridization factor (IHF), was quantified using on-road data collected from a 2010 Toyota Camry HEV. IHF is the ratio of electric system power to total system power and accounts for energy storage in the high voltage battery (IHF ranges from −1 to +1). Relationships between IHF and vehicle specific power (VSP), road type and road grade were examined. Negative VSP resulted in regenerative braking operation (IHF = −0.01 to −1) 90% of the time. IHF identified the VSP range where HEV operation was highly variable (VSP = −1 to 8 kW/ton) when driving at speeds below the ICE-off threshold (42 mph). VSP and IHF together account for 76–86% of the variability in HEV CO<sub>2</sub> emissions in this study. CO<sub>2</sub> model results using VSP computed with the measured real-world road grade (R<sup>2</sup> = 0.86) gave improved fits over the no-grade VSP model (R<sup>2</sup> = 0.69). This study establishes one framework for calculating the instantaneous HEV power split, confirms the need to include road grade in VSP for accurate modeling of vehicle emissions, and identified the need for significant improvements in on-board diagnostic (OBD) scantool measurement requirements for HEVs in three areas: (1) temporal resolution (sub-second to capture transient events such as ICE restarts); (2) simultaneous data logging capability for multiple controller area networks (i.e., engine and HEV parameters together); and (3) improved data precision.</p>
Breaking ecological barriers: anthropogenic disturbance leads to habitat transitions, hybridization, and high genetic diversity
<p>Genetic diversity is expected to erode in disturbed habitats through strong selection, local extinctions, and recolonization associated with genetic bottlenecks and restricted gene flow. Despite this general prediction and over three decades of population genetics studies, our understanding of the long-term effect of environmental disturbance on local and regional genetic diversity remains limited. We conducted a population genetic survey of the microcrustacean <i>Daphnia</i> across a landscape subject to anthropogenic stressors from a century of industrial mining. At the local scale we found moderate genetic diversity (i.e., low clonal diversity), characteristic of habitat-specific selective sweeps and local extinctions, but high diversity and strong genetic structure at the regional scale despite the shared watershed of many lakes and exceptional dispersal ability of daphniids. Many habitats experienced changes in species assemblages, with the obligate asexual <i>Daphnia pulex</i> lineages—known only to inhabit ponds—dominating disrupted urban lakes. This habitat transition (pond to lake) was likely facilitated by the disruption of ecological barriers maintaining the genomic separation of these young species. Thus, disrupted habitats can exhibit complex and unexpected genetic patterns of local extinctions and recolonizations, followed by habitat transitions, hybridization and potential speciation events that are difficult to predict and should not be underestimated.</p>
Research data for "Understanding the geometric diversity of inorganic and hybrid frameworks through structural coarse-graining"
<p>This dataset supports the paper: "Understanding the geometric diversity of inorganic and hybrid frameworks through structural coarse-graining", available at the following DOI: 10.1039/d0sc03287e.</p> <p>The cleaned-up, coarse-grained, and re-scaled structures are provided here in both XYZ and CIF format. The data presented in the journal publication is also included; namely, MDS coordinates, T densities, and A-site heterogeneities for each structure in the dataset. T densities -- defined as: metals per unit volume (nm-3) -- are calculated using the re-scaled structures.</p>
Migratory divides coincide with reproductive barriers across replicated avian hybrid zones above the Tibetan Plateau
<p>Migratory divides are proposed to be catalysts for speciation across a diversity of taxa. However, it is difficult to test the relative contributions of migratory behavior vs. other divergent traits to reproductive isolation. Comparing hybrid zones with and without migratory divides offers a rare opportunity to directly examine the contribution of divergent migratory behavior to reproductive barriers. We show that across replicate sampling transects of two pairs of barn swallow (Hirundo rustica) subspecies, strong reproductive isolation coincided with a migratory divide spanning 20 degrees of latitude. A third subspecies pair exhibited no evidence for a migratory divide and hybridized extensively. Within migratory divides, overwintering habitats were associated with assortative mating, implicating a central contribution of divergent migratory behavior to reproductive barriers. The remarkable geographic coincidence between migratory divides and genetic breaks supports a longstanding hypothesis that the Tibetan Plateau is a substantial barrier contributing to the diversity of Siberian avifauna.</p>
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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.