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788 results for “genotypic data”
Data from: Phenological and fitness responses to climate warming depend upon genotype and competitive neighborhood in Arabidopsis thaliana
1. Increasing temperatures during climate change are known to alter the phenology across diverse plant taxa, but the evolutionary outcomes of these shifts are poorly understood. Moreover, plant temperature-sensing pathways are known to interact with competition-sensing pathways, yet there remains little experimental evidence for how genotypes varying in temperature responsiveness react to warming in realistic competitive settings. 2. We compared flowering time and fitness responses to warming and competition for two near isogenic lines (NILs) of <i>Arabidopsis thaliana</i> transgressively segregating temperature-sensitive and -insensitive alleles for major-effect flowering time genes. We grew focal plants of each genotype in intraspecific and interspecific competition in four treatments contrasting daily temperature profiles in summer and fall under contemporary and warmed conditions. We measured phenology and fitness of focal plants to quantify plastic responses to season, temperature, and competition and the dependence of these responses on flowering time genotype. 3. The temperature-insensitive NIL was constitutively early-flowering and less fit, except in a future-summer climate in which its fitness was higher than the later flowering, temperature-sensitive NIL in low competition. The late-flowering NIL showed accelerated flowering in response to intragenotypic competition and to increased temperature in the summer but delayed flowering in the fall. However, its fitness fell with rising temperatures in both seasons, and in the fall its marginal fitness gain from decreasing competition was diminished in the future. 4. Functional alleles at temperature-responsive genes were necessary for plastic responses to season, warming, and competition. However, the plastic genotype was not the most fit in every experimental condition, becoming less fit than the temperature-canalized genotype in the warm summer treatment. 5. Climate change is often predicted to have deleterious effects on plant populations, and our results show how increased temperatures can act through genotype-dependent phenology to decrease fitness. Furthermore, plasticity is not necessarily adaptive in rapidly changing environments since a non-plastic genotype proved fitter than a plastic genotype in a warming climate treatment.
Data from: Effects of genotype on rates of substitution during experimental evolution
Rates of molecular evolution may vary widely between populations, yet the causes of this variation are still incompletely understood. Genetic differences between populations may make an important contribution to variation in rates of evolution, owing to differences in fitness, population size, mutation rates, or in the distribution of fitness effects (DFE) of available beneficial mutations. By whole genome sequencing of Escherichia coli populations experimentally evolved in the presence of a quinolone antibiotic, we found that rates of substitution varied by genotype, with evidence for a contribution from a genotype's starting fitness. Subsequent targeted sequencing showed that genotypes with high average substitution rates were more likely to undergo the simultaneous fixation of several mutations, consistent with theoretical models of multiple mutation dynamics. Moreover, patterns of substitution were indicative of epistatic relationships between known resistance mutations.
Data from: Bulk genotyping of biopsies can create spurious evidence for heterogeneity in mutation content
When multiple samples are taken from the neoplastic tissues of a single patient, it is natural to compare their mutation content. This is often done by bulk genotyping of whole biopsies, but the chance that a mutation will be detected in bulk genotyping depends on its local frequency in the sample. When the underlying mutation count per cell is equal, homogenous biopsies will have more high-frequency mutations, and thus more detectable mutations, than heterogeneous ones. Using simulations, we show that bulk genotyping of data simulated under a neutral model of somatic evolution generates strong spurious evidence for non-neutrality, because the pattern of tissue growth systematically generates differences in biopsy heterogeneity. Any experiment which compares mutation content across bulk-genotyped biopsies may therefore suggest mutation rate or selection intensity variation even when these forces are absent. We discuss computational and experimental approaches for resolving this problem.
Data from: Large-scale genotyping of highly polymorphic loci by next generation sequencing: how to overcome the challenges to reliably genotype individuals?
Studying the different roles of adaptive genes is still a challenge in evolutionary ecology and requires reliable genotyping of large numbers of individuals. Next-generation sequencing (NGS) techniques enable such large-scale sequencing, but stringent data processing is required. Here, we develop an easy to use methodology to process amplicon-based NGS data and we apply this methodology to reliably genotype four major histocompatibility complex (MHC) loci belonging to MHC class I and II of Alpine marmots (Marmota marmota). Our post-processing methodology allowed us to increase the number of retained reads. The quality of genotype assignment was further assessed using three independent validation procedures. A total of 3069 high-quality MHC genotypes were obtained at four MHC loci for 863 Alpine marmots with a genotype assignment error rate estimated as 0.21%. The proposed methodology could be applied to any genetic system and any organism, except when extensive copy-number variation occurs (that is, genes with a variable number of copies in the genotype of an individual). Our results highlight the potential of amplicon-based NGS techniques combined with adequate post-processing to obtain the large-scale highly reliable genotypes needed to understand the evolution of highly polymorphic functional genes.
Data from: Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana)
Picea mariana is a widely distributed boreal conifer across Canada and the subject of advanced breeding programs for which population genomics and genomic selection approaches are being developed. Targeted sequencing was achieved after capturing P. mariana exome with probes designed from the sequenced transcriptome of Picea glauca, a distant relative. A high capture efficiency of 75.9% was reached although spruce has a complex and large genome including gene sequences interspersed by some long introns. The results confirmed the relevance of using probes from congeneric species to perform successfully interspecific exome capture in the genus Picea. A bioinformatics pipeline was developed including stringent criteria that helped detect a set of 97 075 highly reliable in silico SNPs. These SNPs were distributed across 14 909 genes. Part of an Infinium iSelect array was used to estimate the rate of true positives by validating 4267 of the predicted in silico SNPs by genotyping trees from P. mariana populations. The true positive rate was 96.2%, for in silico SNPs compared to a genotyping success rate of 96.7% for a set 1115 P. mariana control SNPs recycled from previous genotyping arrays. These results indicate the high success rate of the genotyping array and the relevance of the selection criteria used to delineate the new P. mariana in silico SNP resource. Furthermore, in silico SNPs were generally of medium to high frequency in natural populations, thus providing high informative value for future population genomics applications.
Data from: Identification of multiple QTL hotspots in sockeye salmon (Oncorhynchus nerka) using genotyping-by-sequencing and a dense linkage map
Understanding the genetic architecture of phenotypic traits can provide important information about the mechanisms and genomic regions involved in local adaptation and speciation. Here, we used genotyping-by-sequencing and a combination of previously published and newly generated data to construct sex-specific linkage maps for sockeye salmon (Oncorhynchus nerka). We then used the denser female linkage map to conduct quantitative trait locus (QTL) analysis for 4 phenotypic traits in 3 families. The female linkage map consisted of 6322 loci distributed across 29 linkage groups and was 4082 cM long, and the male map contained 2179 loci found on 28 linkage groups and was 2291 cM long. We found 26 QTL: 6 for thermotolerance, 5 for length, 9 for weight, and 6 for condition factor. QTL were distributed nonrandomly across the genome and were often found in hotspots containing multiple QTL for a variety of phenotypic traits. These hotspots may represent adaptively important regions and are excellent candidates for future research. Comparing our results with studies in other salmonids revealed several regions with overlapping QTL for the same phenotypic trait, indicating these regions may be adaptively important across multiple species. Altogether, our study demonstrates the utility of genomic data for investigating the genetic basis of important phenotypic traits. Additionally, the linkage map created here will enable future research on the genetic basis of phenotypic traits in salmon.
Data from: The interaction between genotype and juvenile and adult density environment in shaping multidimensional reaction norms of behaviour
1. Both juvenile (Ej) and adult (Ea) environment can alter developmental trajectories, independently or interactively (as environment by environment interaction; Ej×Ea), to shape behaviour in later life. However, within a population, the developmental response of behaviours to environments can vary among genotypes (G×E×E, multidimensional behavioural plasticity). 2. Here we use a full-sibling, split-brood experimental design and random regression model to study genetic variation in behavioural plasticity across juvenile/adult density conditions in four behavioural traits of male water striders Tenagogerris euphrosyne: exploration, dispersal, same-sex sexual behaviour and remounting attempts. 3. Our results showed that both juvenile and adult density affected the expression of behaviours, and that there was modest level of genetic variation in all behaviour traits. In contrast, there was little genetic variation in behavioural plasticity across density conditions at different life stages (G×Ej, G×Ea or G×Ej×Ea) observed in all traits other than same-sex sexual behaviour. 4. We suggest that experiences at different life stages can interact to affect behavioural expression, but the magnitude of G×Ej, G×Ea or G×Ej×Ea interactions depends on the specific traits. 5. Lack of genetic variation in multidimensional behavioural plasticity may be due to strong selection across environments, high prevalence of environmental heterogeneity and/or modest genetic variance. 6. Our results highlight the complex ways in which plasticity shapes the behaviours and life-histories of organisms.
Data from: Genome assembly improvement and mapping convergently evolved skeletal traits in sticklebacks with genotyping-by-sequencing
Marine populations of the threespine stickleback (Gasterosteus aculeatus) have repeatedly colonized and rapidly adapted to freshwater habitats, providing a powerful system to map the genetic architecture of evolved traits. Here, we developed and applied a binned genotyping-by-sequencing (GBS) method to build dense genome-wide linkage maps of sticklebacks using two large marine by freshwater F2 crosses of more than 350 fish each. The resulting linkage maps significantly improve the genome assembly by anchoring 78 new scaffolds to chromosomes, reorienting 40 scaffolds, and rearranging scaffolds in 4 locations. In the revised genome assembly, 94.6% of the assembly was anchored to a chromosome. To assess linkage map quality, we mapped quantitative trait loci (QTL) controlling lateral plate number, which mapped as expected to a 200-kb genomic region containing Ectodysplasin, as well as a chromosome 7 QTL overlapping a previously identified modifier QTL. Finally, we mapped eight QTL controlling convergently evolved reductions in gill raker length in the two crosses, which revealed that this classic adaptive trait has a surprisingly modular and nonparallel genetic basis.
Data from: The mouse universal genotyping array: from substrains to subspecies
Genotyping microarrays are an important resource for genetic mapping, population genetics, and monitoring of the genetic integrity of laboratory stocks. We have developed the third generation of the Mouse Universal Genotyping Array (MUGA) series, GigaMUGA, a 143,259-probe Illumina Infinium II array for the house mouse (Mus musculus). The bulk of the content of GigaMUGA is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations, and for substrain-level identification of laboratory mice. In addition to 141,090 single nucleotide polymorphism probes, GigaMUGA contains 2006 probes for copy number concentrated in structurally polymorphic regions of the mouse genome. The performance of the array is characterized in a set of 500 high-quality reference samples spanning laboratory inbred strains, recombinant inbred lines, outbred stocks, and wild-caught mice. GigaMUGA is highly informative across a wide range of genetically diverse samples, from laboratory substrains to other Mus species. In addition to describing the content and performance of the array, we provide detailed probe-level annotation and recommendations for quality control.
Data from: Partial genotyping at polymorphic markers can improve heritability estimates in sibling groups
Accurate estimates of heritability (h²) are necessary to assess adaptive responses of populations and evolution of fitness-related traits in changing environments. For plants, h² estimates generally rely on maternal progeny designs, assuming that offspring are either half-sibs or unrelated. However, plant mating systems often depart from half-sib assumptions, this can bias h² estimates. Here, we investigate how to accurately estimate h² in non-model species through the analysis of sibling designs with a moderate genotyping effort. We performed simulations to investigate how microsatellite marker information available for only a subset of offspring can improve h² estimates based on maternal progeny designs in presence of non-random mating, inbreeding in the parental population or maternal effects. We compared the basic family method, considering or not adjustments based on average relatedness coefficients, and methods based on the animal model. The animal model was used with average relatedness information, or with hybrid relatedness information: associating one-generation pedigree and family assumptions, or associating one-generation pedigree and average relatedness coefficients. Our results highlighted that methods using marker-based relatedness coefficients performed as well as pedigree-based methods in presence of non-random mating (i.e. unequal male reproductive contributions, selfing), offering promising prospects to investigate in situ heritabilities in natural populations. In presence of maternal effects, only the use of pairwise relatednesses through pedigree information improved the accuracy of h² estimates. In that case the amount of father-related offspring in the sibling design is the most critical. Overall, we showed that the method using both one-generation pedigree and average relatedness coefficients was the most robust to various ecological scenarios.
Data from: Inferring the potentially complex genetic architectures of adaptation, sexual dimorphism, and genotype by environment interactions by partitioning of mean phenotypes.
Genetic architecture fundamentally affects the way that traits evolve. However, the mapping of genotype to phenotype includes complex interactions with the environment or even the sex of an organism that can modulate the expressed phenotype. Line cross analysis is a powerful quantitative genetics method to infer genetic architecture by analyzing the mean phenotype value of two diverged strains and a series of subsequent crosses and backcrosses. However, it has been difficult to account for complex interactions with the environment or sex within this framework. We have developed extensions to line cross analysis that allow for gene by environment and gene by sex interactions. Using extensive simulations studies and reanalysis of empirical data, we show that our approach can account for both unintended environmental variation when crosses cannot be reared in a common garden and can be used to test for the presence of gene by environment or gene by sex interactions. In analyses that fail to account for environmental variation between crosses we find that line cross analysis has low power and high false positive rates. However, we illustrate that accounting for environmental variation allows for the inference of adaptive divergence, and that accounting for sex differences in phenotypes allows practitioners to infer the genetic architecture of sexual dimorphism.
Data from: Polyploidy and microsatellite variation in the relict tree Prunus lusitanica L.: how effective are refugia in preserving genotypic diversity of clonal taxa?
Refugia are expected to preserve genetic variation of relict taxa, especially in polyploids, because high gene dosages could prevent genetic erosion in small isolated populations. However, other attributes linked to polyploidy, such as asexual reproduction, may strongly limit the levels of genetic variability in relict populations. Here, ploidy levels and patterns of genetic variation at nuclear microsatellite loci were analysed in Prunus lusitanica, a polyploid species with clonal reproduction that is considered a paradigmatic example of a Tertiary relict. Sampling in this study considered a total of 20 populations of three subspecies: mainland lusitanica (Iberian Peninsula and Morocco), and island azorica (Azores) and hixa (Canary Islands and Madeira). Flow cytometry results supported an octoploid genome for lusitanica and hixa, whereas a 16-ploid level was inferred for azorica. Fixed heterozygosity of a few allele variants at most microsatellite loci resulted in levels of allelic diversity much lower than those expected for a high-order polyploid. Islands as a whole did not contain higher levels of genetic variation (allelic or genotypic) than mainland refuges, but island populations displayed more private alleles and higher genotypic diversity in old volcanic areas. Patterns of microsatellite variation were compatible with the occurrence of clonal individuals in all but two island populations, and the incidence of clonality within populations negatively correlated with the estimated timing of colonization. Our results also suggest that gene flow has been very rare among populations, and thus population growth following founder events was apparently mediated by clonality rather than seed recruitment, especially in mainland areas. This study extends to clonal taxa the idea of oceanic islands as important refugia for biodiversity, since the conditions for generation and maintenance of clonal diversity (i.e. occasional events of sexual reproduction, mutation and/or seed immigration) appear to have been more frequent in these enclaves than in mainland areas.
Data from: Insect mating signal and mate preference phenotypes covary among host plant genotypes
Sexual selection acting on small initial differences in mating signals and mate preferences can enhance signal-preference co-divergence and reproductive isolation during speciation. However, the origin of initial differences in sexual traits remains unclear. We asked whether biotic environments, a source of variation in sexual traits, may provide a general solution to this problem. Specifically, we asked whether genetic variation in biotic environments provided by host plants can result in signal-preference phenotypic covariance in a host-specific, plant-feeding insect. We used a member of the Enchenopa binotata species complex of treehoppers (Hemiptera: Membracidae) to assess patterns of variation in male mating signals and female mate preferences induced by genetic variation in host plants. We employed a novel implementation of a quantitative genetics method, rearing field-collected treehoppers on a sample of naturally-occurring replicated host plant clone lines. We found remarkably high signal-preference covariance among host plant genotypes. Thus, genetic variation in biotic environments influences the sexual phenotypes of organisms living on those environment in a way that promotes assortative mating among environments. This consequence arises from conditions likely to be common in nature (phenotypic plasticity and variation in biotic environments). It therefore offers a general answer to how divergent sexual selection may begin.
Data from: Male-benefit sexually antagonistic genotypes show elevated vulnerability to inbreeding
Background: There is theoretical and empirical evidence for strong sexual selection in males having positive effects on population viability by serving to purify the genome of its mutation load at a low demographic cost. However, there is also theoretical and empirical evidence for negative effects of sexual selection on female fitness, and therefore population viability, known as the gender load. This can take the form of sexually antagonistic (SA) genetic variation where alleles with a selective advantage in males pose a detriment to female fitness, and vice versa. Here, using seed beetles, we shed light on a previously unexplored manifestation of the gender load: the effect of SA genetic variation on tolerance to inbreeding. Results: We found that genotypes encoding high male, but low female fitness exhibited significantly greater rates of extinction upon enforced inbreeding relative to genotypes encoding high female but low male fitness. Also, genotypes encoding low fitness in both sexes exhibited greater rates of extinction relative to generally high-fitness genotypes (though marginally non-significant), an expected finding attributable to variation in mutation load across genotypes. Despite follow-up investigations aiming to identify the mechanism(s) underlying these findings, it remains unclear whether the gender load and the mutation load have independent consequences for tolerance to inbreeding, or whether these two types of genetic architecture interact epistatically to render male-benefit genetic variation relatively intolerant to inbreeding. Conclusions: Regardless of the underlying mechanism(s), our results show that male-benefit/female-detriment SA genetic variation poses a previously unseen detriment to population viability due to its elevated vulnerability to inbreeding/homozygosity. This suggests that sexual selection in the context of SA genetic variance for fitness may enhance the gender load on population viability more than previously appreciated, due to selecting for male-benefit SA genetic variation that engenders lineages to extinction upon inbreeding. We note that our results imply that SA alleles that are sexually selected for in males may be underrepresented or even lacking in panels of inbred lines.
Data from: High-throughput genotyping for species identification and diversity assessment in germplasm collections
Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming species in germplasm collections, as well as providing valuable genetic diversity data. We genotyped 180 Brassicaceae samples sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP array. Of these, 76 were provided on the basis of suspected misclassification and another 104 were sourced independently from the germplasm collection. Presence of the A- and C-genomes combined with principle components analysis clearly separated Brassica rapa, B. oleracea, B. napus, B. carinata and B. juncea samples into distinct species groups. Several lines were further validated using chromosome counts. Overall, 18% of samples (32/180) were misclassified on the basis of species. Within these 180 samples, 23/76 (30%) supplied on the basis of suspected misclassification were misclassified, and 9/105 (9%) of the samples randomly sourced from the Australian Grains Genebank were misclassified. Surprisingly, several individuals were also found to be the product of interspecific hybridization events. The SNP (single nucleotide polymorphism) array proved effective at confirming species, and provided useful information related to genetic diversity. As similar genomic resources become available for different crops, high-throughput molecular genotyping will offer an efficient and cost-effective method to screen germplasm collections worldwide, facilitating more effective use of these valuable resources by breeders and researchers.
Data from: Thermal plasticity in postembryonic life history traits of a widely distributed Collembola: Effects of macroclimate and microhabitat on genotypic differences
Life history traits in many ectotherms show complex patterns of variation among conspecific populations sampled along wide latitudinal or climatic gradients. However, few studies have assessed whether these patterns can be explained better by thermal reaction norms of multiple life history traits, covering major aspects of the life cycle. In this study, we compared five populations of a Holarctic, numerically dominant soil microarthropod species, Folsomia quadrioculata, sampled from a wide latitudinal gradient (56–81°N), for growth, development, fecundity, and survival across four temperatures (10, 15, 20, and 25°C) in common garden experiments. We evaluated the extent to which macroclimate could explain differences in thermal adaptation and life history strategies among populations. The common garden experiments revealed large genotypic differences among populations in all the traits, which were little explained by latitude and macroclimate. In addition, the life history strategies (traits combined) hardly revealed any systematic difference related to latitude and macroclimate. The overall performance of the northernmost population from the most stochastic microclimate and the southernmost population, which remains active throughout the year, was least sensitive to the temperature treatments. In contrast, performance of the population from the most predictable microclimate peaked within a narrow temperature range (around 15°C). Our findings revealed limited support for macroclimate-based predictions, and indicated that local soil habitat conditions related to predictability and seasonality might have considerable influence on the evolution of life history strategies of F. quadrioculata. This study highlights the need to combine knowledge on microhabitat characteristics, and demography, with findings from common garden experiments, for identifying the key drivers of life history evolution across large spatial scales, and wide climate gradients. We believe that similar approaches may substantially improve the understanding of adaptation in many terrestrial ectotherms with low dispersal ability.
FIGURES 1‒3 in A revision of the genus Lepidobrya Womersley (Collembola: Entomobryidae) based on morphology and sequence data of the genotype
FIGURES 1‒3. Colour pattern of two individuals in Lepidobrya mawsoni. Scale bars: 1 mm.
Genotype data for ECG traits prediction
Open the record for dataset details and reuse information.
Phenotypic and genotypic data of genomic selection study of spring frost tolerance of Norway spruce
Open the record for dataset details and reuse information.
Data from: Genotyping-in-Thousands by sequencing of archival fish scales reveals maintenance of genetic variation following a severe demographic contraction in kokanee salmon
<p>Historical DNA analysis of archival samples has added new dimensions to population genetic studies, enabling spatiotemporal approaches for reconstructing population histories and informing conservation management. Here we tested the efficacy of Genotyping-in-Thousands by sequencing (GT-seq) for collecting targeted single nucleotide polymorphism (SNP) genotypic data from archival scale samples, and demonstrate its application to a study of kokanee salmon (<i>Oncorhynchus nerka</i>) in Kluane National Park and Reserve (KNPR; Yukon, Canada) that underwent a severe 12-year population decline followed by a rapid rebound. We genotyped archival scales sampled pre-crash and contemporary fin clips collected post-crash, revealing high coverage (>90% average genotyping across all individuals) and low genotyping error (<0.01% within-libraries, 0.60% among-libraries) despite the relatively poor quality of recovered DNA. We observed slight decreases in expected heterozygosity, allelic diversity, and effective population size post-crash, but none were significant, suggesting genetic diversity was retained despite the severe demographic contraction. Genotypic data also revealed the genetic distinctiveness of a now extirpated population just outside of KNPR, revealing biodiversity loss at the northern edge of the species distribution. More broadly, we demonstrate GT-seq as a valuable tool for genome-wide data collection from archival samples to address basic questions in ecology and evolution, and inform applied research in wildlife conservation and fisheries management.</p>
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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.