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351 results for “functional genetics”
Data from: A genome-wide functional genomics approach uncovers genetic determinants of immune phenotypes in type 1 diabetes
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Genetic analysis of SnRK1β3 subunit of peach and the functional identification of overexpression transformed tomato
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Microsatellite exploration in the climbing hydrangea (Hydrangea petiolaris Siebold & Zucc.) transcriptome: A resource for population genetics and functional genomics
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Raw data: Association and functional analysis of angiotensin-converting enzyme 2 gene genetic variants with the pathogenesis of pre-eclampsia
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Data from: Tree species and genetic diversity increase productivity via functional diversity and trophic feedbacks
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Data from: Incomplete loss of a conserved trait: function, latitudinal cline, and genetic constraints
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Quantitative trait locus mapping reveals an independent genetic basis for joint divergence in leaf function, life-history, and floral traits between scarlet monkeyflower (Mimulus cardinalis) populations
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The genetic basis of coordinated plasticity across functional units in a Lake Malawi cichlid mapping population
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The relationship between genetic diversity, function, and stability in marine foundation species
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Reference genome resources associated with the project: Functional genetic diversity is correlated with intensity of genetic drift in populations of an endangered rattlesnake
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Data from: Association and function analysis of genetic variants and the risk of gestational diabetes mellitus in a southern Chinese population
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Probabilistic inference of the genetic architecture of functional enrichment of complex traits
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Data from: Functional vertebrate group diversity, tick-borne pathogen ecology and genetic diversity
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Archived data for: Balancing selection, genetic drift, and human mediated-introgression interplay to shape MHC (functional) diversity in Mediterranean brown trout
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Plant intraspecific functional trait variation is related to within-habitat heterogeneity and genetic diversity in Trifolium montanum L.
<p>Intraspecific trait variation (ITV), based on available genetic diversity, is one of the major means plant populations can respond to environmental variability. The study of functional trait variation and diversity has become popular in ecological research, e.g. as a proxy for plant performance influencing fitness. Up to now, it is unclear which aspects of intraspecific functional trait variation (iFDCV) can be attributed to the environment or genetics under natural conditions. Here, we examined 260 individuals from 13 locations of the rare (semi-)dry calcareous grassland species Trifolium montanum L. in terms of iFDCV, within-habitat heterogeneity, and genetic diversity. The iFDCV was assessed by measuring functional traits (releasing height, biomass, leaf area, specific leaf area, leaf dry matter content, Fv/Fm, performance index, stomatal pore surface, and stomatal pore area index). Abiotic within-habitat heterogeneity was derived from altitude, slope exposure, slope, leaf area index, soil depth, and further soil factors. Based on microsatellites, we calculated expected heterozygosity (He) because it best-explained, among other indices, iFDCV. We performed multiple linear regression models quantifying relationships among iFDCV, abiotic within-habitat heterogeneity and genetic diversity, and also between separate functional traits and abiotic within-habitat heterogeneity or genetic diversity. We found that abiotic within-habitat heterogeneity influenced iFDCV twice as strong compared to genetic diversity. Both aspects together explained 77% of variation in iFDCV (Radj² = 0.77, F2, 10 = 21.66, p < 0.001). The majority of functional traits (releasing height, biomass, specific leaf area, leaf dry matter content, Fv/Fm and performance index) were related to abiotic habitat conditions indicating responses to environmental heterogeneity. In contrast, morphology-related functional traits (releasing height, biomass and leaf area) were only related to genetics. Our results suggest that both within-habitat heterogeneity and genetic diversity affect iFDCV, and are thus crucial to consider when aiming to understand or predict changes of plant species performance under changing environmental conditions.</p>
Functional genetic diversity of domestic and wild American mink (Neovison vison )
<p>The release of domestic organisms to the wild threatens biodiversity because the introduction of domestic genes through interbreeding can negatively impact wild conspecifics via outbreeding depression. In North America, farmed American mink (<i>Neovison vison</i>) frequently escape captivity, yet the impact of these events on functional genetic diversity of wild mink populations is unclear. We characterized domestic and wild mink in Ontario at 17 microsatellites located in functional genes and in a promoter region that is non-coding but thought to be associated with traits affected by domestication. We found low functional genetic diversity in both mink types, as only 4 of 17 genes were variable, and the number of alleles per locus were generally lower in captive mink than in wild mink. To determine if allele frequencies of wild populations were affected by domestic release events, we performed redundancy analysis and spatial analysis of principal components on four polymorphic loci (AR, ATN1, IGF-1, and TOB1). We found evidence to suggest domestic release events are affecting the functional genetic diversity of wild mink, as sPCA showed clear distinctions between wild individuals near mink farms and those located in areas without mink farms. This is further substantiated through RDA, where spatial location was associated with genetic variation of AR, ATN1, and IGF1.</p>
Functional and genetic diversity changes through time in a cloud forest ant assemblage
<p>Climate change in the Neotropics is causing upslope range shifts. We used arrays of ant species collected in a cloud forest at 1,500 m in Área de Conservación Guanacaste (ACG), northwestern Costa Rica, collected in two time periods (1998-2000 and 2008-2011) to measure changes in species richness and diversity over a decade. Using metrics of community structure, we found that the species assemblage in the collections from the 1990s were significantly phylogenetically clustered and functionally less diverse as compared to collections from the early 2000's. At both time points, the assemblages were significantly phylogenetically clustered and while the difference in functional diversity between the time points was not significant, the ant assemblage has become lighter in color (on average) over time. When individual species are considered the overall pattern of replacement is consistent with the cloud forest ant assemblage being colonized by arrivals from lower-elevation forests. The invertebrate communities on cloud forested mountain tops are especially vulnerable to a changing climate as there are two factors working together; no higher terrain to which they can move and the invasion of more and more taxa from lower downslope. This vulnerability is already measurable.</p>
Assessing the genetic diversity in Argopecten nucleus (Bivalvia: Pectinidae), a functional hermaphrodite species with extremely low population density and self-fertilization: effect of null alleles
<p>Argopecten nucleus is a functional hermaphroditic pectinid species that exhibits self-fertilization, whose natural populations have usually very low densities. In the present study, the genetic diversity of a wild population from Neguanje Bay, Santa Marta (Colombia), was estimated using microsatellite markers, and the effect of the presence of null alleles on this estimation was assessed. A total of 8 microsatellite markers were developed, the first described for this species, and their amplification conditions were standardized. They were used to determine the genotype of 48 wild individuals from Naguanje Bay, and 1010 individuals derived from the offspring of 38 directed crosses. For each locus, the frequencies of the identified alleles, including null alleles, were estimated using the statistical package Micro-Checker, and the parental genotypes were confirmed using segregation analysis. Three to 8 alleles per locus with frequencies from 0.001 to 0.632 were detected. The frequencies of null alleles ranged from 0.10 to 0.45, with Ho from 0.0 to 0.79 and He from 0.53 to 0.80. All loci were in H-W disequilibrium. The null alleles frequencies values were high, with lower estimations using segregation analysis than estimated using Micro-Checker. The present results show high levels of population genetic diversity, and indicate that null alleles were not the only cause of deviation from HW equilibrium in all loci, suggesting that the wild population under study presents signs of inbreeding and Wahlun effect.</p>
Data from: Adding landscape genetics and individual traits to the ecosystem function paradigm reveals the importance of species functional breadth
Animal pollination mediates both reproduction and gene flow for the majority of plant species across the globe. However, past functional studies have focused largely on seed production; although useful, this focus on seed set does not provide information regarding species-specific contributions to pollen-mediated gene flow. Here we quantify pollen dispersal for individual pollinator species across more than 690 ha of tropical forest. Specifically, we examine visitation, seed production, and pollen-dispersal ability for the entire pollinator community of a common tropical tree using a series of individual-based pollinator-exclusion experiments followed by molecular-based fractional paternity analyses. We investigate the effects of pollinator body size, plant size (as a proxy of floral display), local plant density, and local plant kinship on seed production and pollen-dispersal distance. Our results show that while large-bodied pollinators set more seeds per visit, small-bodied bees visited flowers more frequently and were responsible for more than 49% of all long distance (beyond 1 km) pollen-dispersal events. Thus, despite their size, small-bodied bees play a critical role in facilitating long-distance pollen-mediated gene flow. We also found that both plant size and local plant kinship negatively impact pollen dispersal and seed production. By incorporating genetic and trait-based data into the quantification of pollination services, we highlight the diversity in ecological function mediated by pollinators, the influential role that plant and population attributes play in driving service provision, and the unexpected importance of small-bodied pollinators in the recruitment of plant genetic diversity.
Data from: A function-valued trait approach to estimating the genetic basis of size at age and its potential role in fisheries induced evolution
Natural selection is inherently a multivariate phenomenon. The selection pressure on size (natural and artificial) and the age at which selection occurs is likely to induce evolutionary changes in growth rates across the entire life history. However, the covariance structure that will determine the path of evolution for size-at-age has been studied in only a few fish species. We therefore estimated the genetic covariance function for size throughout ontogeny using Atlantic silversides (Menidia menidia) as the model system. Over a 3-year period, a total of 542 families were used to estimate the genetic covariance in length at age from hatch through maturity. The function-valued trait approach was employed to estimate the genetic covariance functions. A Bayesian hierarchical model was used to account for the unbalanced design, unequal measurement intervals, unequal sample sizes, and family-aggregated data. To improve mixing, we developed a two-stage sampler using a Gibbs sampler to generate the posterior of a well-mixing approximate model followed by an importance sampler to draw samples from posterior of the completely specified model. We found that heritability of length is age-specific and there are strong genetic correlations in length across ages that last 30d or more. We used these estimates in a hypothetical model predicting the evolutionary response to harvesting following a single generation of selection under both sigmoidal and unimodal patterns of gear selectivity to illustrate the potential outcomes of ignoring the genetic correlations. In these scenarios genetic correlations were found to have a strong effect on both the direction and magnitude of the response to harvest selection.
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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.
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.