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.
13,117
datasets available to search
ShareScore release 0.9.0
Dataset results
13,117 results for “Maps”
Data from: Proteomic analysis of barley mapping population subjected to drought identifies proteins with genotype×environment interaction and pQTLs
Drought is one of the major abiotic stresses negatively influencing crop yield and is a serious issue in modern agriculture. To achieve further substantial crop improvements in terms of drought resistance it is necessary to incorporate scientific results into breeding strategies. However, most of the data on plant drought responses arises mostly from small-scale studies and, therefore, its use in breeding programs is very limited. Here, we present the results of the large-scale proteomic analysis performed on barley recombinant inbred lines (RILs) and their parental genotypes subjected to drought, applied shortly before tillering. The conducted proteomic analyses enabled us to monitor drought-induced proteome changes in leaf and root tissue, and to identify proteins that responded to drought in a genotype-specific manner, for instance Rubisco activase, luminal binding protein, phosphoglycerate mutase, glutathione S-transferase, heat shock proteins as well as enzymes involved in phenylpropanoid biosynthesis. We also demonstrated feasibility of incorporating proteomic data resulting from large-scale study into genetic linkage analysis, which constitutes a fundament in biotechnology-driven breeding strategies.
Data from: Homing of invasive Burmese pythons in South Florida: evidence for map and compass senses in snakes
Navigational ability is a critical component of an animal's spatial ecology and may influence the invasive potential of species. Burmese pythons (Python molurus bivittatus) are apex predators invasive to South Florida. We tracked the movements of 12 adult Burmese pythons in Everglades National Park, six of which were translocated 21–36 km from their capture locations. Translocated snakes oriented movement homeward relative to the capture location, and five of six snakes returned to within 5 km of the original capture location. Translocated snakes moved straighter and faster than control snakes and displayed movement path structure indicative of oriented movement. This study provides evidence that Burmese pythons have navigational map and compass senses and has implications for predictions of spatial spread and impacts as well as our understanding of reptile cognitive abilities.
Data from: Sex-determining chromosomes and sexual dimorphism: insights from genetic mapping of sex expression in a natural hybrid Fragaria × ananassa subsp. cuneifolia
We studied the natural hybrid (Fragaria × ananassa subsp. cuneifolia) between two sexually dimorphic octoploid strawberry species (Fragaria virginiana and Fragaria chiloensis) to gain insight into the dynamics of sex chromosomes and the genesis of sexual dimorphism. Male sterility is dominant in both the parental species and thus will be inherited maternally, but the chromosome that houses the sex-determining region differs. Thus, we asked whether (1) the cytotypic composition of hybrid populations represents one or both maternal species, (2) the sex-determining chromosome of the hybrid reflects the location of male sterility within the maternal donor species and (3) crosses from the hybrid species show less sexual dimorphism than the parental species. We found that F. × ananassa subsp. cuneifolia populations consisted of both parental cytotypes but one predominated within each population. Genetic linkage mapping of two crosses showed dominance of male sterility similar to the parental species, however, the map location of male sterility reflected the maternal donor in one cross, but not the other. Moreover, female function mapped to a single region in the first cross, but to two regions in the second cross. Aside from components of female function (fruit set and seed set), other traits that have been found to be significantly sexually dimorphic in the pure species were either not dimorphic or were dimorphic in the opposite direction to the parental species. These results suggest that hybrids experience some disruption of dimorphism in secondary sexual traits, as well as novel location and number of quantitative trait locus (QTL) affecting sex function.
Data from: Mapping and explaining wolf recolonization in France using dynamic occupancy models and opportunistic data
While large carnivores are recovering in Europe, assessing their distributions can help to predict and mitigate conflicts with human activities. Because they are highly mobile, elusive and live at very low density, modeling their distributions presents several challenges due to i) their imperfect detectability, ii) their dynamic ranges over time and iii) their monitoring at large scales consisting mainly of opportunistic data without a formal measure of the sampling effort. Here, we focused on wolves (Canis lupus) that have been recolonizing France since the early 90's. We evaluated the sampling effort a posteriori as the number of observers present per year in a cell based on their location and professional activities. We then assessed wolf range dynamics from 1994 to 2016, while accounting for species imperfect detection and time- and space-varying sampling effort using dynamic site-occupancy models. Ignoring the effect of sampling effort on species detectability led to underestimating the number of occupied sites by more than 50% on average. Colonization appeared to be negatively influenced by the proportion of a site with an altitude higher than 2500m and positively influenced by the number of observed occupied sites at short and longdistances , forest cover, farmland cover and mean altitude. The expansion rate, defined as the number of occupied sites in a given year divided by the number of occupied sites in the previous year, decreased over the first years of the study, then remained stable from 2000 to 2016. Our work shows that opportunistic data can be analyzed with species distribution models that control for imperfect detection, pending a quantification of sampling effort. Our approach has the potential for being used by decisionmakers to target sites where large carnivores are likely to occur and mitigate conflicts.
Data from: SNP-skimming: a fast approach to map loci generating quantitative variation in natural populations
Genome-wide association mapping (GWAS) is a method to estimate the contribution of segregating genetic loci to trait variation. A major challenge for applying GWAS to non-model species has been generating dense genome-wide markers that satisfy the key requirement that marker data is error-free. Here we present an approach to map loci within natural populations using inexpensive shallow genome sequencing. This 'SNP skimming' approach involves two steps: an initial genome-wide scan to identify putative targets followed by deep sequencing for confirmation of targeted loci. We apply our method to a test dataset of floral dimension variation in the plant Penstemon virgatus, a member of a genus that has experienced dynamic floral adaptation that reflects repeated transitions in primary pollinator. The ability to detect SNPs that generate phenotypic variation depends on population genetic factors such as population allele frequency, effect size, and epistasis as well as sampling effects contingent on missing data and genotype uncertainty. However, both simulations and the Penstemon data suggest that the most significant tests from the initial SNP skim are likely to be true positives – loci with subtle but significant quantitative effects on phenotype. We discuss the promise and limitations of this method and consider optimal experimental design for a given sequencing effort. Simulations demonstrate that sampling a larger number of individual at the expense of average read depth per individual maximizes the power to detect loci.
Data from: Genetic mapping identifies a major locus spanning P450 clusters associated with pyrethroid resistance in kdr-free Anopheles arabiensis from Chad
Prevention of malaria transmission throughout much of Africa is dependent on bednets that are impregnated with pyrethroid insecticides. Anopheles arabiensis is the major malaria vector in Chad and efforts to control this vector are threatened by the emergence of pyrethroid resistance. WHO bioassays revealed that An. arabiensis from Ndjamena is resistant to pyrethroids and dichlorodiphenyltrichloroethane (DDT) but fully susceptible to carbamates and organophosphates. No 1014F or 1014S kdr alleles were detected in this population. To determine the mechanisms that are responsible for resistance, genetic crosses were established between the Ndja strain and an insecticide susceptible population from Mozambique. Resistance was inherited as an autosomal trait and quantitative trait locus (QTL) mapping identified a single major locus on chromosome 2R, which explained 24.4% of the variance in resistance. This QTL is enriched in P450 genes including 25 cytochrome P450s in total. One of these, Cyp6p4 is 22-fold upregulated in the Ndja strain compared with the susceptible. Piperonyl butoxide (PBO) synergist and biochemical assays further support a role for P450s in conferring pyrethroid resistance in this population.
Data from: Genome-wide association mapping of phenotypic traits subject to a range of intensities of natural selection in Timema cristinae
The genetic architecture of adaptive traits can reflect the evolutionary history of populations and also shape divergence among populations. Despite this central role in evolution, relatively little is known regarding the genetic architecture of adaptive traits in nature, particularly for traits subject to known selection intensities. Here we quantitatively describe the genetic architecture of traits that are subject to known intensities of differential selection between host plant species in Timema cristinae stick insects. Specifically, we used phenotypic measurements of 10 traits and 211,004 single-nucleotide polymorphisms (SNPs) to conduct multilocus genome-wide association mapping. We identified a modest number of SNPs that were associated with traits and sometimes explained a large proportion of trait variation. These SNPs varied in their strength of association with traits, and both major and minor effect loci were discovered. However, we found no relationship between variation in levels of divergence among traits in nature and variation in parameters describing the genetic architecture of those same traits. Our results provide a first step toward identifying loci underlying adaptation in T. cristinae. Future studies will examine the genomic location, population differentiation, and response to selection of the trait-associated SNPs described here.
Data from: Admixture mapping of male nuptial color and body shape in a recently formed hybrid population of threespine stickleback
Despite recent progress, we still know relatively little about the genetic architecture that underlies adaptation to divergent environments. Determining whether the genetic architecture of phenotypic adaptation follows any predictable patterns requires data from a wide variety of species. However, in many organisms, genetic studies are hindered by the inability to perform genetic crosses in the laboratory or by long generation times. Admixture mapping is an approach that circumvents these issues by taking advantage of hybridization that occurs between populations or species in the wild. Here, we demonstrate the utility of admixture mapping in a naturally occurring hybrid population of threespine sticklebacks (Gasterosteus aculeatus) from Enos Lake, British Columbia. Until recently, this lake contained two species of sticklebacks adapted to divergent habitats within the lake. This benthic-limnetic species pair diverged in a number of phenotypes, including male nuptial coloration and body shape, which were previously shown to contribute to reproductive isolation between them. However, recent ecological disturbance has contributed to extensive hybridization between the species, and there is now a single, admixed population within Enos Lake. We collected over 500 males from Enos Lake and found that most had intermediate nuptial color and body shape. By genotyping males with nuptial color at the two extremes of the phenotypic distribution, we identified seven genomic regions on three chromosomes associated with divergence in male nuptial color. These genomic regions are also associated with variation in body shape, suggesting that tight linkage and/or pleiotropy facilitated adaptation to divergent environments in this benthic-limnetic species pairs.
Data from: QTL mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower
The wild North American sunflowers Helianthus annuus and H. debilis are participants in one of the earliest identified examples of adaptive trait introgression, and the exchange is hypothesized to have triggered a range expansion in H. annuus. However, the genetic basis of the adaptive exchange has not been examined. Here, we combine quantitative trait locus (QTL) mapping with field measurements of fitness to identify candidate H. debilis QTL alleles likely to have introgressed into H. annuus to form the natural hybrid lineage H. a. texanus. Two 500-individual BC1 mapping populations were grown in central Texas, genotyped for 384 single nucleotide polymorphism (SNP) markers and then phenotyped in the field for two fitness and 22 herbivore resistance, ecophysiological, phenological and architectural traits. We identified a total of 110 QTL, including at least one QTL for 22 of the 24 traits. Over 75% of traits exhibited at least one H. debilis QTL allele that would shift the trait in the direction of the wild hybrid H. a. texanus. We identified three chromosomal regions where H. debilis alleles increased both female and male components of fitness; these regions are expected to be strongly favoured in the wild. QTL for a number of other ecophysiological, phenological and architectural traits colocalized with these three regions and are candidates for the actual traits driving adaptive shifts. G × E interactions played a modest role, with 17% of the QTL showing potentially divergent phenotypic effects between the two field sites. The candidate adaptive chromosomal regions identified here serve as explicit hypotheses for how the genetic architecture of the hybrid lineage came into existence.
Data from: Is evolution predictable? quantitative genetics under complex genotype-phenotype maps
<p>A fundamental aim of post-genomic 21st century biology is to understand the genotype-phenotype map (GPM) or how specific genetic variation relates to specific phenotypic variation. Quantitative genetics approximates such maps using linear models, and has developed methods to predict the response to selection in a population. The other major field of research concerned with the GPM, developmental evolutionary biology or evo-devo, has found the GPM to be highly nonlinear and complex. Here we quantify how the predictions of quantitative genetics are affected by the complex, nonlinear maps found in developmental biology. We found that the disagreements between predicted and observed responses to selection are common, roughly in a third of generations, systematic and due to nonlinear nature of the genotype-phenotype map. They occur at all time scales, even from one generation to the next. Our results are a step towards integrating the fields studying the GPM.</p>
Data from: Input matters matter: bioclimatic consistency to map more reliable species distribution models
1. Accuracy of global bioclimatic databases is essential to understand biodiversity-environment relationships. Many studies have explored biases and uncertainties related to species distribution models (SDMs) but the effect of choosing a specific database among the different alternatives has not been previously assessed. 2. The lack of bioclimatic congruence (degree of agreement) between different databases is a main concern in distribution modelling and it is critical in single-source models, for which the database choice is decisive. In order to prevent unreliable predictions derived from distorted input data, SDMs accuracy can be assessed by mapping model predictions according to a bioclimatic congruence measure derived from the comparison of multiple databases, which can be achieved with the bioclimatic consistency maps that we propose in this study. Here, i) we present the first global-scale bioclimatic congruence map to analyse environmental mismatches between recently updated bioclimatic databases. We also test the importance of input matters on the reliability of distribution models of sixteen mammals, by addressing ii) inconsistencies among species response curves (temperature and precipitation), and iii) discrepancies among SDMs predictions depending on the chosen bioclimatic database. Finally, iv) we propose a strategy to assess bioclimatic consistency of model predictions, showing its application to the specific case of Litocranius walleri. 3. Our results confirm that the single-source modelling approach greatly influences the estimation of species-environment relationship and consequently, bias spatial predictions derived from SDMs. This is especially true for studies conducted in polar and mountainous regions which showed the smallest bioclimatic congruence. We show that by adding bioclimatic congruence to SDMs projections, we can build a bioclimatic consistency map that enables the detection of both risky and consistent areas, as revealed for the case of L. walleri. 4. Assessing uncertainty in bioclimatic input data is key to avoid erroneous conclusions in macroecological and biogeographical studies. The spatial characterisation of bioclimatic consistency provides an adequate empirical framework which effectively illustrates bioclimatic data limitations. We strongly recommend that this new strategy should be formally and systematically incorporated into distribution modelling to build more reliable SDMs, which are essential to develop successful biodiversity conservation programmes.
Data from: Resource-Area-Dependence Analysis: inferring animal resource needs from home-range and mapping data
An animal's home-range can be expected to encompass the resources it requires for surviving or reproducing. Thus, animals inhabiting a heterogeneous landscape, where resource patches vary in size, shape and distribution, will naturally have home-ranges of varied sizes, so that each home-range encompasses a minimum required amount of a resource. Home-range size can be estimated from telemetry data, and often key resources, or proxies for them such as the areas of important habitat types, can be mapped. We propose a new method, Resource-Area-Dependence Analysis (RADA), which uses a sample of tracked animals and a categorical map to i) infer in which map categories important resources are accessible, ii) within which home range cores they are found, and iii) estimate the mean minimum areas of these map categories required for such resource provision. We provide three examples of applying RADA to datasets of radio-tracked animals from southern England: 15 red squirrels Sciurus vulgaris, 17 gray squirrels S. carolinensis and 114 common buzzards Buteo buteo. The analyses showed that each red squirrel required a mean (95% CL) of 0.48 ha (0.24-0.97) of pine wood within the outermost home-range, each gray squirrel needed 0.34 ha (0.11-1.12) ha of mature deciduous woodland and 0.035-0.046 ha of wheat, also within the outermost home-range, while each buzzard required 0.54 ha (0.35-0.82) of rough ground close to the home-range center and 14 ha (11-17) of meadow within an intermediate core, with 52% of them also relying on 0.41 ha (0.29-0.59) of suburban land near the home-range center. RADA thus provides a useful tool to infer key animal resource requirements during studies of animal movement and habitat use.
Data from: Mapping the imprint of biotic interactions on β-diversity
Investigating how trophic interactions influence the β-diversity of meta-communities is of paramount importance to understanding the processes shaping biodiversity distribution. Here, we apply a statistical method for inferring the strength of spatial dependencies between pairs of species groups. Using simulated community data generated from a multi-trophic model, we showed that this method can approximate biotic interactions in multi-trophic communities based on β-diversity patterns across groups. When applied to soil multi-trophic communities along an elevational gradient in the French Alps, we found that fungi make a major contribution to the structuring of β-diversity across trophic groups. We also demonstrated that there were strong spatial dependencies between groups known to interact specifically (e.g. plant-symbiotic fungi, bacteria-nematodes) and that the influence of environment was less important than previously reported in the literature. Our method paves the way for a better understanding and mapping of multi-trophic communities through space and time.
Construction of genetic linkage map based on SNP markers, QTL mapping and detection of candidate genes of growth-related traits in Pacific abalone using genotyping-by-sequencing
<p><a name="_Hlk72585736"><span>Pacific abalone (<i>Haliotis discus hannai</i>) is a commercially important high valued molluscan species. Its wild population has decreased in recent years. Pacific abalone is widely cultured in Korea. Traditional breeding programs have been implemented for hatchery production of abalone seeds. To obtain more genetic information for the molecular breeding program, a high-density linkage map and quantitative trait locus (QTL) for three growth-related traits was constructed for Pacific abalone. F1 cross population with two parents were sampled to construct the linkage map using genotyping by sequencing (GBS). A total of 664,630,534 clean reads and 56,686 SNPs were generated. In sum, 3,345 segregating SNPs were used to construct a consensus linkage map. The map spanned 1,747.023 cM with 18 linkage groups and an average interval of 0.55 cM. QTL analysis revealed two significant QTL in LG10 on the consensus linkage map in each growth-related trait. Both the QTLs are located in the telomere region of the chromosome. Moreover, four potential candidate genes for growth-related traits were identified in the QTL region. Expression analysis revealed that identified genes are involved in growth regulation of abalone. The newly constructed genetic linkage map, growth-related QTLs and potential candidate genes identified in the present study can be used as valuable genetic resources and will be useful for marker-assisted selection (MAS) of Pacific abalone in molecular breeding program.</span></a></p>
Data from: Linkage mapping reveals strong chiasma interference in sockeye salmon: implications for interpreting genomic data
Meiotic recombination is fundamental for generating new genetic variation and for securing proper disjunction. Further, recombination plays an essential role during the rediploidization process of polyploid-origin genomes because crossovers between pairs of homeologous chromosomes retain duplicated regions. A better understanding of how recombination affects genome evolution is crucial for interpreting genomic data; unfortunately, current knowledge mainly originates from a few model species. Salmonid fishes provide a valuable system for studying the effects of recombination in nonmodel species. Salmonid females generally produce thousands of embryos, providing large families for conducting inheritance studies. Further, salmonid genomes are currently rediploidizing after a whole genome duplication and can serve as models for studying the role of homeologous crossovers on genome evolution. Here, we present a detailed interrogation of recombination patterns in sockeye salmon (Oncorhynchus nerka). First, we use RAD sequencing of haploid and diploid gynogenetic families to construct a dense linkage map that includes paralogous loci and location of centromeres. We find a nonrandom distribution of paralogs that mainly cluster in extended regions distally located on 11 different chromosomes, consistent with ongoing homeologous recombination in these regions. We also estimate the strength of interference across each chromosome; results reveal strong interference and crossovers are mostly limited to one per arm. Interference was further shown to continue across centromeres, but metacentric chromosomes generally had at least one crossover on each arm. We discuss the relevance of these findings for both mapping and population genomic studies.
Data from: Admixture mapping identifies introgressed genomic regions in North American canids
Hybrid zones typically contain novel gene combinations that can be tested by natural selection in a unique genetic context. Parental haplotypes that increase fitness can introgress beyond the hybrid zone, into the range of parental species. We used the Affymetrix canine SNP genotyping array to identify genomic regions tagged by multiple ancestry informative markers that are more frequent in an admixed population than expected. We surveyed a hybrid zone formed in the last 100 years as coyotes expanded their range into eastern North America. Concomitant with expansion, coyotes hybridized with wolves and some populations became more wolflike, such that coyotes in the northeast have the largest body size of any coyote population. Using a set of 3102 ancestry informative markers, we identified 60 differentially introgressed regions in 44 canines across this admixture zone. These regions are characterized by an excess of exogenous ancestry and, in northeastern coyotes, are enriched for genes affecting body size and skeletal proportions. Further, introgressed wolf-derived alleles have penetrated into Southern US coyote populations. Because no wolves currently exist in this area, these alleles are unlikely to have originated from recent hybridization. Instead, they probably originated from intraspecific gene flow or ancient admixture. We show that grey wolf and coyote admixture has far-reaching effects and, in addition to phenotypically transforming admixed populations, allows for the differential movement of alleles from different parental species to be tested in new genomic backgrounds.
Data from: Mapping the four-horned locus and testing the polled locus in three Chinese sheep breeds
Four-horned sheep are an ideal animal model for illuminating the genetic basis of horn development. The objective of this study was to locate the genetic region responsible for the four-horned phenotype and to verify a previously reported polled locus in three Chinese breeds. A genome-wide association study (GWAS) was performed using 34 two-horned and 32 four-horned sheep from three Chinese indigenous breeds: Altay, Mongolian and Sishui Fur sheep. The top two significant single nucleotide polymorphisms (SNPs) associated with the four-horned phenotype were both located in a region spanning positions 132.6 to 132.7 Mb on sheep chromosome 2. Similar locations for the four-horned trait were previously identified in Jacob, Navajo-Churro, Damara and Sishui Fur sheep, suggesting a common genetic component underlying the four-horned phenotype. The two identified SNPs were both downstream of the metaxin 2 (MTX2) gene and the HOXD gene cluster. For the top SNP—OAR2:g.132619300G>A—the strong associations of the AA and AG genotypes with the four-horned phenotype and the GG genotype with the two-horned phenotype indicated the dominant inheritance of the four-horned trait. No significant SNPs for the polled phenotype were identified in the GWAS analysis, and a PCR analysis for the detection of the 1.8-kb insertion associated with polled sheep in other breeds failed to verify the association with polledness in the three Chinese breeds. This study supports the hypothesis that two different loci are responsible for horn existence and number. This study contributes to the understanding of the molecular regulation of horn development and enriches the knowledge of qualitative traits in domestic animals.
Data from: Utility of pooled sequencing for association mapping in non-model organisms
High density genome-wide sequencing increases the likelihood of discovering genes of major effect and genomic structural variation in organisms. While there is an increasing availability of reference genomes across broad taxa, the greatest limitation to whole-genome sequencing of multiple individuals continues to be the costs associated with sequencing. To alleviate excessive costs, pooling multiple individuals with similar phenotypes and sequencing the homogenized DNA (Pool-Seq) can achieve high genome coverage, but at the loss of individual genotypes. Although Pool-Seq has been an effective method for association mapping in model organisms, it has not been frequently utilized in natural populations. To extend bioinformatic tools for rapid implementation of Pool-Seq data in non-model organisms, we developed a pipeline called PoolParty and illustrate its effectiveness in genetic association mapping. Alignment expectations based on five pooled Chinook salmon (Oncorhynchus tshawytscha) libraries showed that approximately 48% genome coverage per library could be achieved with reasonable sequencing effort. We additionally examined male and female O. tshawytscha libraries to illustrate how Pool-Seq techniques can successfully map known genes associated with functional differences among sexes such as growth hormone 2. Finally, we compared pools of individuals of different spawning ages for each sex to discover novel genes involved with age at maturity in O. tshawytscha such as opsin4 and transmembrane protein19. While not appropriate for every system, Pool-Seq data processed by the PoolParty pipeline is a practical method for identifying genes of major effect in non-model organisms when high genome coverage is necessary and cost is a limiting factor.
Data from: Mapping the expansion of coyotes (Canis latrans) across North and Central America
The geographic distribution of coyotes (Canis latrans) has dramatically expanded since 1900, spreading across much of North America in a period when most other mammal species have been declining. Although this considerable expansion has been well documented at the state/provincial scale, continent-wide descriptions of coyote spread have portrayed conflicting distributions for coyotes prior to the 1900s, with popularly referenced anecdotal accounts showing them restricted to the great plains, and more obscure, but data-rich accounts suggesting they ranged across the arid west. To provide a scientifically credible map of the coyote's historical range (10,000 – 300 BP) and describe their range expansion from 1900 to 2016, we synthesized archaeological and fossil records, museum specimens, peer-reviewed reports, and records from wildlife management agencies. Museum specimens confirm that coyotes have been present in the arid west and California throughout the Holocene, well before European colonization. Their range in the late 1800s was undistinguishable from earlier periods, and matched the distribution of non-forest habitat in the region. Coyote expansion began around 1900 as they moved north into taiga forests, east into deciduous forests, west into costal temperate rain forests, and south into tropical rainforests. Forest fragmentation and the extirpation of larger predators probably enabled these expansions. In addition, hybridization with wolves (C. lupus, C. lycaon, and/or C. rufus) and/or domestic dogs has been documented in the east, and suspected in the south. Our detailed account of the original range of coyotes and their subsequent expansion provides the core description of a large scale ecological experiment that can help us better understand the predator-prey interactions, as well as evolution through hybridization.
Data from: Association mapping of genetic risk factors for chronic wasting disease in wild deer
Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy affecting North American cervids. We assessed the feasibility of association mapping CWD genetic risk factors in wild white-tailed deer (Odocoileus virginianus) and mule deer (Odocoileus hemionus) using a panel of bovine microsatellite markers from three homologous deer linkage groups predicted to contain candidate genes. These markers had a low cross-species amplification rate (27.9%) and showed weak linkage disequilibrium (<1 cM). Markers near the prion protein and the neurofibromin 1 (NF1) genes were suggestively associated with CWD status in white-tailed deer (P = 0.006) and mule deer (P = 0.02), respectively. This is the first time an association between the NF1 region and CWD has been reported.
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.