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788 results for “genotypic data”
Data from: Competitive consequences determined by phenotypic but not genetic distance: a study with asexual Daphnia genotypes
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Data from: Nitrogen availability and plant-plant interactions drive leaf silicon concentration in wheat genotypes
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Field data and microsatellite genotypes of Cercidiphyllum japonicum
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Data from: Progeny contribution scores in offense double-matings of different genotypes for the Sdic region
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Data from: More affordable and effective noninvasive SNP genotyping using high-throughput amplicon sequencing
<p>Non-invasive genotyping methods have become key elements of wildlife research over the last two decades, but their widespread adoption is limited by high costs, low success rates, and high error rates. <span>The information lost when genotyping success is low may lead to decreased precision in animal population densities, which could misguide conservation and management actions.</span> <span>Single nucleotide polymorphisms (SNPs) provide a promising alternative to traditionally used microsatellites as SNPs allow amplification of shorter DNA fragments, are less prone to genotyping errors, and produce results that are easily shared among laboratories.</span> Here, we outline a detailed protocol for cost-effective and accurate noninvasive SNP genotyping using multiplexed amplicon sequencing optimized for degraded DNA. <span>We validated this method for individual identification by genotyping 216 scats, 18 hairs and 15 tissues from coyotes (<i>Canis latrans</i>) using 26 SNPs. </span><a name="_Hlk33181599">Our genotyping success rate for scat samples was 93%, and 100% for hair and tissue, representing a substantial increase compared to previous microsatellite-based studies while remaining at a low cost of under $5 per PCR replicate (excluding labor). </a>The accuracy of the genotypes was further corroborated in that genotypes from scats matching known, GPS-collared coyotes were always located within the territory of the known individual. We also show that different levels of multiplexing produced similar results, but that PCR product cleanup strategies can have substantial effects on genotyping success. By making noninvasive genotyping more affordable, accurate, and efficient, this research may allow for a substantial increase in the use of noninvasive methods to monitor and conserve free-ranging wildlife populations.</p>
Selected data for Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling
<p>TF1 cell line (Figure 3) and CRC cancer (Figure 4) data from the "Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling" work. </p>
Data from: Variant files for genotypic and sex-reversed males
<p>X and Y chromosomes are usually derived from a pair of homologous autosomes, which then diverge from each other over time. Although Y-specific features have been characterized in sex chromosomes of various ages, the earliest stages of Y chromosome evolution remain elusive. In particular, we do not know whether early stages of Y chromosome evolution consist of changes to individual genes or happen via chromosome-scale divergence from the X. To address this question, we quantified divergence between young proto-X and proto-Y chromosomes in the house fly, <i>Musca domestica</i>. We compared proto-sex chromosome sequence and gene expression between genotypic (XY) and sex-reversed (XX) males. We find evidence for sequence divergence between genes on the proto-X and proto-Y, including five genes with mitochondrial functions. There is also an excess of genes with divergent expression between the proto-X and proto-Y, but the number of genes is small. This suggests that individual proto-Y genes, but not the entire proto-Y chromosome, have diverged from the proto-X. We identified one gene, encoding an axonemal dynein assembly factor (which functions in sperm motility), that has higher expression in XY males than XX males because of a disproportionate contribution of the proto-Y allele to gene expression. The up-regulation of the proto-Y allele may be favored in males because of this gene's function in spermatogenesis. The evolutionary divergence between proto-X and proto-Y copies of this gene, as well as the mitochondrial genes, is consistent with selection in males affecting the evolution of individual genes during early Y chromosome evolution.</p>
Data from: Ecology shapes epistasis in a genotype-phenotype-fitness map for stick insect colour
<p>Genetic interactions such as epistasis are widespread in nature and can shape evolutionary dynamics. Epistasis occurs due to non-linearity in biological systems, which can arise via cellular processes that convert genotype to phenotype and via selective processes that connect phenotype to fitness. Few studies in nature have connected genotype to phenotype to fitness for multiple potentially interacting genetic variants. Thus, the causes of epistasis in the wild remain poorly understood. Here, we show that epistasis for fitness is an emergent and predictable property of non-linear selective processes. We do so by measuring the genetic basis of cryptic colouration and survival in a field experiment with stick insects. We find that colouration exhibits a largely additive genetic basis, but with some effects of epistasis that enhance differentiation between colour morphs. In terms of fitness, different combinations of loci affecting colouration confer high survival in one host-plant treatment. Specifically, non-linear correlational selection for specific combinations of colour traits in this treatment drives the emergence of pairwise and higher-order epistasis for fitness at loci underlying colour. In turn, this results in a rugged fitness landscape for genotypes. In contrast, fitness epistasis was dampened in another treatment, where selection was weaker. Patterns of epistasis that are shaped by ecologically based selection could be common, and central to understanding fitness landscapes, the dynamics of evolution, and potentially other complex systems.</p>
Genotype data and analysis code for HDY-20-A0076RR
<p>Selection pressure from parasites is thought to be a major force shaping the extreme polymorphism of the major histocompatibility complex (MHC) genes, but the modes and consequences of selection remain unclear. Here, we analyse MHC class II and microsatellite diversity in 16 guppy (<i>Poecilia reticulata</i>) populations from two islands (Trinidad and Tobago) that have been separated for at least 10 ky. Within-population MHC diversity was high, but allele sharing was limited within islands and even lower between islands, suggesting relatively fast turnover of alleles. Allelic lineages strongly supported in phylogenetic analyses tended to be island-specific, suggesting rapid lineage sorting, and an expansion of an allelic lineage private to Tobago was observed. New alleles appear to be generated locally at a detectably high frequency. We did not detect a consistent signature of local adaptation, but F<sub>ST</sub> outlier analysis suggested that balancing selection may be the more general process behind spatial variation in MHC allele frequencies in this system, particularly within Trinidad. We found no evidence for divergent allele advantage within populations, or for decreased genetic structuring of MHC supertypes compared to MHC alleles. The dynamic and complex nature of MHC evolution we observed in guppies, coupled with some evidence for balancing selection shaping MHC allele frequencies, are consistent with Red Queen processes of host-parasite coevolution.</p>
Taxus genotype data for "Trunk perimeter correlates with genetic bottleneck intensity and the level of genetic diversity in populations of Taxus baccata L."
<p>The data set contains microsatellite genotypes (18 loci) of Taxus baccata trees, together with the information about sampling sites.</p>
Data from: Spontaneous hybridization and introgression between walleye (Sander vitreus) and sauger (S. canadensis) in two large reservoirs: insights from genotyping-by-sequencing
<p>Anthropogenic activities may facilitate undesirable hybridization and genomic introgression between fish species. Walleye (<i>Sander vitreus</i>) and sauger (<i>Sander canadensis</i>) are economically valuable freshwater species that can spontaneously hybridize in areas of sympatry. Levels of genomic introgression between walleye and sauger may be increased by modifications to waterbodies (e.g., reservoir development) and inadvertent propagation of hybrids in stocking programs. We used genotyping by sequencing (GBS) to examine 217 fish from two large reservoirs with mixed populations of walleye and sauger in Saskatchewan, Canada (Lake Diefenbaker, Tobin Lake). Analyses with 20,038 (r90) and 478 (r100) SNPs clearly resolved walleye and sauger, and classified hybrids with high confidence. F<sub>1</sub>, F<sub>2</sub>, and multi-generation hybrids were detected in Lake Diefenbaker, indicating potentially high levels of genomic introgression. In contrast, only F<sub>1</sub> hybrids were detected in Tobin Lake. Field classification of fish was unreliable; 7% of fish were misidentified based on broad species categories. Important for activities such as brood stock selection, 12/173 (7%) fish field-identified as pure walleye, and 1/24 (4%) identified as pure sauger were actually hybrids. In addition, 2/15 (13%) field-identified hybrids were actually pure walleye or sauger. We conclude that hybridization and introgression are occurring in Saskatchewan reservoirs, and that caution is warranted when using these populations in stocking programs. GBS offers a powerful and flexible tool for examining hybridization without pre-identification of informative loci, eliminating some of the key challenges associated with other marker types.</p>
Microsatellite genotype data from seven loci for a phylogeographic/population genetic study of the South African endemic freshwater crab Potamonautes lividus sampled from eight localities in the KwaZulu-Natal and Eastern Cape provinces in South Africa
<ol> <li>During the present study, the phylogeography of the only southern African IUCN Red Listed vulnerable (VU) freshwater crab, <i>Potamonautes lividus</i> was investigated by surveying several localities in the Eastern Cape and KwaZulu-Natal provinces in South Africa. Both nuclear and mitochondrial DNA markers were used, and it was hypothesized, that marked genetic differentiation should be present, while niche modeling was undertaken to explore the distribution of the species along the east coast of South Africa. <span><span>Further, the shortfalls in the present approach to IUCN Red Listing, as illustrated by a vulnerable species of crabs are discussed</span></span>.</li> <li>Results from the mtDNA revealed the presence of two haploclades confined to specimens from the two provinces respectively and the general absence of maternal dispersal; a fact that was further validated by the marked <i>F</i><sub>ST</sub> data and high F<sub>ST</sub>. Within the Eastern Cape haploclade, low frequency maternal dispersal occurred, corroborated by the low F<sub>ST</sub>. In contrast, no haplotypes were shared in the KwaZulu-Natal haploclade a fact corroborated by marked F<sub>ST</sub> differences. </li> <li>The microsatellite data demonstrated the presence of higher frequency, possibly paternally biased dispersal of specimens between the Eastern Cape and KwaZulu-Natal provinces. Our results suggest that presence of two distinct management units within <i>P. lividus</i>. Divergence time estimation suggest a late Pleistocene cladogenesis between the Eastern Cape and KwaZulu-Natal haploclades. </li> <li>Considering the presence of <i>P. lividus</i> in several newly collected nature conservation areas in both provinces, and its potential presence in the intermediary area based on the MAXENT niche modeling, our data suggest the species IUCN Red Listing status should be downgraded to LC.</li> <li>A comparison of all the EN, VU and CR IUCN Red Listed freshwater crabs for the entire Afrotropical region reveals the lack of recent sampling in the three biodiversity hotspots in West, Central and East Africa, with mountainous areas containing a disproportionate number of species with most species being devoid of phylogeographic study. </li> </ol>
Genotype, spatial and morphological data of adults and progeny in a natural population of Leucadendron rubrum
<p>We provide a dataset containing data on both female and male plants measured in a natural population of <em>Leucadendron rubrum</em> about plant architecture, and leaf morphology, thus informing about sexual dimorphism in this species. Genotypes of these males and females on eight microsatellites combined with corresponding genotype data in their progeny permits to undertake parentage analyses. Finally, the spatial distribution of both parents and juveniles allows to account for potential spatial biases in sampling juveniles in parentage analyses.</p>
Data from: What drives selection on flowering time? An experimental manipulation of the inherent correlation between genotype and environment
The optimal timing of the seasonal switch from somatic growth to reproduction can depend on an individual's condition at reproduction, the quality of the environment in which it will reproduce, or both. In annual plants, vegetative size (a function of age at flowering) affects resources available for seed production, while exposure to mutualists, antagonists, and abiotic stresses in the environment (functions of Julian date of flowering), influences success in converting resources into offspring. The inherent tight correlation between age, size, and environment obscures their independent fitness contributions. We isolated the fitness effects of these factors by experimentally manipulating the correlation between age at flowering and date of flowering in Brassica rapa. We staggered the planting dates of families with differing ages at flowering to produce experimental populations in which age at flowering and date of flowering were positively-, negatively-, or uncorrelated. In all populations, plants with an early date of flowering produced more seed than those flowering late, regardless of age or size at flowering onset. The temporal environment was thus the principal driver of selection on flowering time, but its importance relative to that of age and size varied with the presence/absence of herbivores and seed predators.
Data from: Estimations of linkage disequilibrium, effective population size and ROH-based inbreeding coefficients in Spanish Churra sheep using imputed high-density SNP genotypes
In this study, the availability of the Ovine HD SNP BeadChip (HD-chip) and the development of an imputation strategy provided an opportunity to further investigate the extent of linkage disequilibrium (LD) at short distances in the genome of the Spanish Churra dairy sheep breed. A population of 1686 animals, including 16 rams and their half-sib daughters, previously genotyped for the 50K-chip, was imputed to the HD-chip density based on a reference population of 335 individuals. After assessing the imputation accuracy for beagle v4.0 (0.922) and fimpute v2.2 (0.921) using a cross-validation approach, the imputed HD-chip genotypes obtained with beagle were used to update the estimates of LD and effective population size for the studied population. The imputed genotypes were also used to assess the degree of homozygosity by calculating runs of homozygosity and to obtain genomic-based inbreeding coefficients. The updated LD estimations provided evidence that the extent of LD in Churra sheep is even shorter than that reported based on the 50K-chip and is one of the shortest extents compared with other sheep breeds. Through different comparisons we have also assessed the impact of imputation on LD and effective population size estimates. The inbreeding coefficient, considering the total length of the run of homozygosity, showed an average estimate (0.0404) lower than the critical level. Overall, the improved accuracy of the updated LD estimates suggests that the HD-chip, combined with an imputation strategy, offers a powerful tool that will increase the opportunities to identify genuine marker-phenotype associations and to successfully implement genomic selection in Churra sheep.
Data from: Quantifying genotype x environment effects in long-term common wheat yield trials from an agroecologically diverse production region
Multienvironment trials (METs) are used to investigate the performance of crop genotypes. To efficiently generate reliable performance estimates, the magnitude and patterns of genotype × environment interaction (G×E) in MET data must be known. We quantified G×E in fall-planted common wheat (Triticum aestivum L.) in California, with the goal of increasing the reliability and efficiency of statewide variety testing activities. Linear mixed models and the genotype main effects plus G×E interaction effects (GGE) biplot method were used to analyze MET data for 211 common wheat genotypes, the MET consisted of 9 locations and 14 seasons. The representativeness and discriminating power of the MET locations were tested, and estimates of the optimum number of test locations were made. The analyses did not find evidence for significant, repeatable, crossover G×E. The genotype and G×E effects were of a similar magnitude, and the G×E effects were relatively strong compared with other sources of variance but were dominated by seasonal effects, with potentially repeatable genotype-by-location (G×L) effects being relatively weak. The GGE analyses did not detect repeatable G×L patterns across seasons. As a result, we conclude that the cereal production regions of California consist of a single, but unstable, mega-environment for common wheat grain yield. The test location evaluation found few significant differences between test locations in terms of how well they represent the target production environment. We estimate that the number of test locations could be reduced while maintaining trial accuracy, which would improve the resource use efficiency of statewide trial activities without sacrificing information about variety-specific common wheat yield performance.
Data from: The architecture of an empirical genotype-phenotype map
Recent advances in high-throughput technologies are bringing the study of empirical genotype-phenotype (GP) maps to the fore. Here, we use data from protein binding microarrays to study an empirical GP map of transcription factor (TF) binding preferences. In this map, each genotype is a DNA sequence. The phenotype of this DNA sequence is its ability to bind one or more TFs. We study this GP map using genotype networks, in which nodes represent genotypes with the same phenotype, and edges connect nodes if their genotypes differ by a single small mutation. We describe the structure and arrangement of genotype networks within the space of all possible binding sites for 525 TFs from three eukaryotic species encompassing three kingdoms of life (animal, plant, and fungi). We thus provide a high-resolution depiction of the architecture of an empirical GP map. Among a number of findings, we show that these genotype networks are "small-world" and assortative, and that they ubiquitously overlap and interface with one another. We also use polymorphism data from Arabidopsis thaliana to show how genotype network structure influences the evolution of TF binding sites in vivo. We discuss our findings in the context of regulatory evolution.
Data from: Susceptibility of Macrosiphum euphorbiae to the parasitoid Aphidius ervi: larval development depends on host aphid genotype
The potato aphid, Macrosiphum euphorbiae Thomas (Hemiptera: Aphididae: Macrosiphini), is a common polyphagous aphid in Europe and North America. However, the factors influencing potato aphid dynamics and susceptibility to natural enemies are largely undescribed, particularly in relation to facultative endosymbiotic bacteria, which can provide protection against parasitism and disease in some aphid species. This study investigated whether potato aphid susceptibility to one of its principal natural enemies, the parasitoid Aphidius ervi Haliday (Hymenoptera: Braconidae: Aphidiinae), varied in relation to aphid genotype and/or endosymbiont presence. Parasitism and aphid fitness assays were conducted on clonal lineages of aphids, harbouring their natural endosymbiont infections, collected over 3 years from separate geographic locations. Parasitized aphids were dissected to quantify parasitoid oviposition, larval development, and mummification. Amongst the 19 clonal lines of M. euphorbiae tested, seven aphid genotypes were identified, and 11 lines harboured one or both of the facultative endosymbionts Hamiltonella defensa Moran et al. and Regiella insecticola Moran et al.; H. defensa infections were associated exclusively with two of the seven M. euphorbiae genotypes. Parasitism resistance was detected in clonal lines belonging to a single aphid genotype and resulted from failure of parasitoid eggs to develop into larvae rather than failure of the parasitoid to oviposit. Contrary with studies of several other aphid species, there was little evidence that H. defensa provided strong protection to M. euphorbiae from parasitism by A. ervi. Furthermore, there were no clear fitness costs to the aphid associated with parasitism resistance or with H. defensa infection. The two M. euphorbiae genotypes in which H. defensa occurred, which included the resistant genotype, exhibited faster development, higher survival, and greater fecundity than the other five aphid genotypes. These findings suggest that biological control of M. euphorbiae using A. ervi alone could exacerbate pest problems by selecting for the fittest parasitism-resistant genotypes.
Data from: Phenotypic but not genotypic selection for earlier flowering in a perennial herb
1. Timing of reproduction affects the outcome of interactions between plants and their pollinators, grazers and seed predators, as well as with their local abiotic environment. In seasonal environments, phenotypic selection has often been shown to favor early flowering. Yet, we still know little about the agents driving selection in natural populations and whether observed phenotypic selection corresponds to genotypic selection – a prerequisite for evolutionary change. 2. In this study, we experimentally assessed phenotypic and genotypic selection for flowering time in a natural population of the perennial herb Lathyrus vernus. We transplanted sibling individuals, obtained through controlled crosses, to their source population and found net phenotypic selection for earlier flowering in the field. 3. Despite a higher susceptibility to roe deer grazing, early-flowering plants had higher fruit set and more seeds per fruit than late-flowering plants. We found no support for genotypic selection on flowering time, and heritability for first flowering day was very low. 4. Synthesis: Our results suggest that commonly observed patterns of higher fitness in early-flowering plants do not always correspond to selection on genotypic values and are thus not necessarily expected to result in evolutionary change even if the relationship between flowering time and fitness is causal. This finding should be important to understand how species phenology might respond to changing environmental conditions.
Data from: Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters
Phylogeographic inferences about gene flow are strengthened through comparison of co-distributed taxa, but also depend on adequate genomic sampling. Amplified Fragment Length Polymorphisms (AFLP) provide a rapid and inexpensive source of multilocus allele frequency data for making genomically robust inferences. Every AFLP study initially generates markers with a range of locus-specific genotyping error rates and applies criteria to select a subset for analysis. However, there has been very little empirical evaluation of the best tradeoff between culling all but the lowest-error loci to minimize overall genotyping error versus the potential for increasing population genetic signal by retaining more loci. Here, we used AFLPs to compare population structure in co-distributed broadcast spawning (Crassostrea virginica) and brooding (Ostrea equestris) oyster species. Using existing methods for almost entirely automated marker selection and scoring, genotyping error tradeoffs were evaluated by comparing results across a nested series of datasets with mean mismatch errors of 0, 1, 2, 3, 4 and >4%. Artifactual population structure was diagnosed in high-error datasets and we assessed the low-error point at which expected population substructure signal was lost. In both species we identified substructure patterns deemed to be inaccurate at error rates {less than or equal to}2% and >4%. In the species comparison, the optimum datasets showed higher gene flow for the brooding oyster with more oceanic salinity tolerances. AFLP tradeoffs may differ among studies, but our results suggest that important signal may be lost in the pursuit of 'acceptable' error levels and our procedures provide a general method for empirically exploring these tradeoffs.
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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.