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5,153 results for “Genetic data”
Data from: Creating small food-habituated groups might alter genetic diversity in the endangered Yunnan snub-nosed monkey. https://doi.org/10.1016/j.gecco.2020.e01422
<p>Ecotourism is increasing worldwide for financial, educational and social purposes. Organized viewing of wildlife, especially at feeding sites where wildlife is “ready-to-view”, increases the opportunities for tourists to observe animals in the wild. However, feeding sites might retain only a subsample of wild populations. We thus hypothesized that such human intervention could induce population subdivisions and alter random mating by artificially creating small groups. The endangered Yunnan snub-nosed monkey (Rhinopithecus bieti) is an emblematic example reflecting the contradictions between conservation and ecotourism. In Gehuaqing/Xiangguqing (Yunnan, China), some individuals are maintained at feeding sites, while the rest of the monkey subpopulation wanders in a large surrounding area. Using faecal sampling and molecular analyses, we showed that this subpopulation is genetically structured into two moderately differentiated subgroups. The fed subgroup exhibited lower genetic diversity and higher relatedness than the rest of the subpopulation. Simulation model results indicated that a single translocation probably would not restore genetic diversity in fed individuals. Thus, feeding sites implementation and associated management practices might rapidly induce founder effects. We discuss the possibilities of conciliating ecotourism and the conservation of endangered animal species from this viewpoint.</p>
Data from: Genomic data reveal deep genetic structure but no support for current taxonomic designation in a grasshopper species complex
<p>Taxonomy has traditionally relied on morphological and ecological traits to interpret and classify biological diversity. Over the last decade, technological advances and conceptual developments in the field of molecular ecology and systematics have eased the generation of genomic data and changed the paradigm of biodiversity analysis. Here we illustrate how traditional taxonomy has led to species designations that are supported neither by high throughput sequencing data nor by the quantitative integration of genomic information with other sources of evidence. Specifically, we focus on <em>Omocestus antigai </em>and<em> O. navasi</em>, two montane grasshoppers from the Pyrenean region that were originally described based on quantitative phenotypic differences and distinct habitat associations (alpine vs. Mediterranean-montane habitats). To validate current taxonomic designations, test species boundaries, and understand the factors that have contributed to genetic divergence, we obtained phenotypic (geometric morphometrics) and genome-wide SNP data (ddRADSeq) from populations covering the entire known distribution of the two taxa. Coalescent-based phylogenetic reconstructions, integrative Bayesian model-based species delimitation, and landscape genetic analyses revealed that populations assigned to the two taxa show a spatial distribution of genetic variation that do not match with current taxonomic designations and is incompatible with ecological/environmental speciation. Our results support little phenotypic variation among populations and a marked genetic structure that is mostly explained by geographic distances and limited population connectivity across the abrupt landscapes characterizing the study region. Overall, this study highlights the importance of integrative approaches to identify taxonomic units and elucidate the evolutionary history of species.</p>
Data from: Genetic diversity in widespread species is not congruent with species richness in alpine plant communities
The Convention on Biological Diversity (CBD) aims at the conservation of all three levels of biodiversity, i.e. ecosystems, species and genes. Genetic diversity represents evolutionary potential and is important for ecosystem functioning. Unfortunately, genetic diversity in natural populations is hardly considered in conservation strategies because it is difficult to measure and has been hypothesized to co-vary with species richness. This means that species richness is taken as a surrogate of genetic diversity in conservation planning, though their relationship has not been properly evaluated. We tested whether the genetic and species levels of biodiversity co-vary, using a large-scale and multi-species approach. We chose the high-mountain flora of the Alps and the Carpathians as study systems and demonstrate that species richness and genetic diversity are not correlated. Species richness thus cannot act as a surrogate for genetic diversity. Our results have important consequences for implementing the CBD when designing conservation strategies.
Data from: Drift happens: molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests
Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four river systems and two major watersheds in Wisconsin, USA. Floodplain forests and marshes provide a model system for assessing the effects of habitat fragmentation within agricultural/urban landscapes and for testing whether rivers act to genetically connect dispersed populations. We generated a panel of 12,856 single nucleotide polymorphisms and assessed genetic diversity, differentiation, gene flow, and drift. Clustering methods revealed strong population genetic structure with limited admixture and highly differentiated populations (mean multilocus FST = 0.32, FST' = 0.33). No signals of isolation by geographic distance or environment emerged, but alleles may flow along rivers given that genetic differentiation increased with river distance. Differentiation also increased in populations with fewer private alleles (R2 = 0.51) and higher local inbreeding (R2 = 0.22). Populations varied greatly in levels of local inbreeding (FIS = 0.2 to 0.9) and FIS declined in smaller, more isolated populations. These results suggest that genetic drift dominates other forces in structuring these Impatiens populations. In rapidly changing environments, species must migrate or genetically adapt. Habitat fragmentation limits both processes, potentially compromising the ability of species to persist in fragmented landscapes.
Data from: Genetic and morphological evidence of a geographically widespread hybrid zone between two crocodile species, Crocodylus acutus and Crocodylus moreletii
<p>Hybrid zones represent natural laboratories to study gene flow, divergence and the nature of species boundaries between closely related taxa. We evaluated the level and extent of hybridization between <em>Crocodylus moreletii </em>and<em> C. acutus </em>using genetic and morphological data on 300 crocodiles from 65 localities. To our knowledge, this is the first genetic study that includes the entire historic range and sympatric zone of the two species. Contrary to expectations, Bayesian admixture proportions and maximum likelihood estimates of hybrid indexes revealed that most sampled crocodiles were admixed and that the hybrid zone is geographically extensive, extending well beyond their historical region of sympatry. We identified a few geographically isolated, non-admixed populations of both parental species. Hybrids do not appear to be F<sub>1</sub>s or recent backcrosses, but rather are more likely later-generation hybrids, suggesting that hybridization has been going on for several to many generations and is mostly the result of natural processes. <em>C. moreletii </em>is not the sister species of <em>C. acutus,</em> suggesting that the hybrid zone formed from secondary contact rather than primary divergence. Non-admixed individuals from the two species were distinguishable based on morphological characters, whereas hybrids had a complex mosaic of morphological characters that hinders identification in the wild. Very few non-admixed <em>C. acutus</em> and <em>C. moreletii</em> populations exist in the wild. Consequently, the last non-admixed <em>C. moreletii</em> populations have become critically endangered. Indeed, not only the parental species but also the naturally occurring hybrids should be considered for their potential conservation value.</p>
Data from: Association genetics of growth and adaptive traits in loblolly pine (Pinus taeda L.) using whole-exome-discovered polymorphisms
In the United States, forest genetics research began over 100 years ago and loblolly pine breeding programs were established in the 1950s. However, the genetics underlying complex traits of loblolly pine remains to be discovered. To address this, adaptive and growth traits were measured and analyzed in a clonally tested loblolly pine (Pinus taeda L.) population. Over 2.8 million single nucleotide polymorphism (SNP) markers detected from exome sequencing were used to test for single locus associations, SNP-SNP interactions and correlation of individual heterozygosity with phenotypic traits. A total of 36 SNP-trait associations were found for specific leaf area (5 SNPs), branch angle (2), crown width (3), stem diameter (4), total height (9), carbon isotope discrimination (4), nitrogen concentration (2), and pitch canker resistance traits (7). Eleven SNP-SNP interactions were found to be associated with branch angle (1 SNP-SNP interaction), crown width (2), total height (2), carbon isotope discrimination (2), nitrogen concentration (1), and pitch canker resistance (3). Non-additive effects imposed by dominance and epistasis account for a large fraction of the genetic variance for the quantitative traits. Genes that contain the identified SNPs have a wide spectrum of functions. Individual heterozygosity positively correlated with water use efficiency and nitrogen concentration. In conclusion, multiple effects identified in this study influence the performance of loblolly pines, provide resources for understanding the genetic control of complex traits, and have potential value for assessing with breeding through marker assisted selection and genomic selection.
Data from: Discordant patterns of genetic and phenotypic differentiation in five grasshopper species co-distributed across a microreserve network
<p>Conservation plans can be greatly improved when information on the evolutionary and demographic consequences of habitat fragmentation is available for several co-distributed species. Here, we study spatial patterns of phenotypic and genetic variation among five grasshopper species that are co-distributed across a network of microreserves but show remarkable differences in dispersal-related morphology (body size and wing length), degree of habitat specialization and extent of fragmentation of their respective habitats in the study region. In particular, we tested the hypothesis that species with preferences for highly fragmented microhabitats show stronger genetic and phenotypic structure than co-distributed generalist taxa inhabiting a continuous matrix of suitable habitat. We also hypothesized a higher resemblance of spatial patterns of genetic and phenotypic variability among species that have experienced a higher degree of habitat fragmentation due to their more similar responses to the parallel large-scale destruction of their natural habitats. In partial agreement with our first hypothesis, we found that genetic structure, but not phenotypic differentiation, was higher in species linked to highly fragmented habitats. We did not find support for congruent patterns of phenotypic and genetic variability among any studied species, indicating that they show idiosyncratic evolutionary trajectories and distinctive demographic responses to habitat fragmentation across a common landscape. This suggests that conservation practices in networks of protected areas require detailed ecological and evolutionary information on target species in order to focus management efforts on those taxa that are more sensitive to the effects of habitat fragmentation.</p>
Data from: Different genetic structures revealed resident populations of a specialist parasitoid wasp in contrast to its migratory host
Genetic comparisons of parasitoids and their hosts are expected to reflect ecological and evolutionary processes that influence the interactions between species. The parasitoid wasp, Cotesia vestalis, and its host diamondback moth (DBM), Plutella xylostella, provide opportunities to test whether the specialist natural enemy migrates seasonally with its host or occurs as resident population. We genotyped 17 microsatellite loci and two mitochondrial genes for 158 female adults of C. vestalis collected from 12 geographical populations, as well as nine microsatellite loci for 127 DBM larvae from six separate sites. The samplings covered both the likely source (southern) and immigrant (northern) areas of DBM from China. Populations of C. vestalis fell into three groups, pointing to isolation in northwestern and southwestern China and strong genetic differentiation of these populations from others in central and eastern China. In contrast, DBM showed much weaker genetic differentiation and high rates of gene flow. TESS analysis identified the immigrant populations of DBM as showing admixture in northern China. Genetic disconnect between C. vestalis and its host suggests that the parasitoid did not migrate yearly with its host but likely consisted of resident populations in places where its host could not survive in winter.
Data from: Adaptive genetic variation distinguishes Chilean blue mussels (Mytilus chilensis) from different marine environments
Chilean mussel populations have been thought to be panmictic with limited genetic structure. Genotyping-by-sequencing approaches have enabled investigation of genome-wide variation that may better distinguish populations that have evolved in different environments. We investigated neutral and adaptive genetic variation in Mytilus from six locations in southern Chile with 1,240 SNP obtained with RAD-seq. Differentiation among locations with 891 neutral SNPs was low (FST = 0.005). Higher differentiation was obtained with a panel of 58 putative outlier SNPs (FST = 0.114) indicating the potential for local adaptation. This panel identified clusters of genetically related individuals and demonstrated that much of the differentiation (~92%) could be attributed to the three major regions and environments: extreme conditions in Patagonia, inner bay influenced by aquaculture (Reloncaví́), and outer bay (Chiloé Island). Patagonia samples were most distinct, but additional analysis carried out excluding this collection also revealed adaptive divergence between inner and outer bay samples. The four locations within Reloncaví́ area were most similar with all panels of markers, likely due to similar environments, high gene flow by aquaculture practices and low geographic distance. However, fine scale structure could be detected when analyses included only this zone. Our results and the SNP markers developed will be a powerful tool supporting management and programs of this harvested species.
Data from: Sporadic genetic connectivity among small insular populations of the rare geoendemic plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower)
Globally, a small number of plants have adapted to terrestrial outcroppings of serpentine geology, which are characterized by soils with low levels of essential mineral nutrients (N, P, K, Ca, Mo) and toxic levels of heavy metals (Ni, Cr, Co). Paradoxically, many of these plants are restricted to this harsh environment. Caulanthus ampexlicaulis var. barbarae (Brassicaceae) is a rare annual plant that is strictly endemic to a small set of isolated serpentine outcrops in the coastal mountains of central California. The goals of the work presented here were to 1) determine the patterns of genetic connectivity among all known populations of Caulanthus ampexlicaulis var. barbarae, and 2) estimate contemporary effective population sizes (Ne), in order to inform ongoing genomic analyses of the evolutionary history of this taxon, and to provide a foundation upon which to model its future evolutionary potential and long-term viability in a changing environment. Eleven populations of this taxon were sampled, and population-genetic parameters were estimated using 11 nuclear microsatellite markers. Contemporary effective population sizes were estimated using multiple methods and found to be strikingly small (typically Ne < 10). Further, our data showed that a substantial component of genetic connectivity of this taxon is not at equilibrium, and instead showed sporadic gene flow. Several lines of evidence indicate that gene flow between isolated populations is maintained through long-distance seed dispersal (e.g. > 1 km), possibly via zoochory.
Data and modeling results for publication: Landscape genetics indicate recently increased habitat fragmentation in African forest-associated chafers
<ul> <li>DNA sequences: <em>cox1</em> and ITS1 alignments</li> <li>spatial records (in hypervolume archive)</li> <li>spatial principal component 1-3 used for <em>hypervolume</em> models (in hypervolume archive)</li> <li>Present and past species distribution models (SDMs): <ul> <li><em>biomod2</em> ensemble SDMs <ul> <li>Present</li> <li>Holocene Altithermal</li> <li>Last Glacial Maximum</li> </ul> </li> <li><em>biomod2</em> SDMs for single PMIP3 models <ul> <li>Present</li> <li>Holocene Altithermal</li> <li>Last Glacial Maximum</li> </ul> </li> <li><em>hypervolume</em> SDMs</li> </ul> </li> <li>landscape connectivity models <ul> <li>circuitscape (for F0, F1, and F2)</li> <li>least cost corridors and paths (for F0, F1, and F2)</li> </ul> </li> </ul>
Raw data used for COI delineation of the Eupolybothrus species: Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
<p>Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar</p>
Raw Genotyping data from: Variation in recombination rate and its genetic determinism in sheep populations from combining multiple genomewide datasets
<p>Data supporting :</p> <p><strong>Variation in recombination rate and its genetic determinism in sheep populations from combining multiple genomewide datasets</strong></p> <p>Morgane Petit, Jean-Michel Astruc, Julien Sarry, Laurence Drouilhet, Stephane Fabre, Carole Moreno, Bertrand Servin</p> <p>http://doi.org/10.1534/genetics.117.300123</p> <p><strong>Abstract</strong></p> <p>Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and datasets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified about 50,000 crossover hotspots on the genome and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting inter-individual variation in recombination rate in Lacaune, including the <em>RNF212</em> and<em> HEI10</em> genes and possibly 2 other loci of smaller effects including the <em>KCNJ15</em> and <em>FSHR</em> genes. Finally, we compared our results to those obtained previously in a distantly related population of domestic sheep, the Soay. This comparison revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome and that the two datasets can be combined to create more precise male meiotic recombination maps in sheep. Despite their similar recombination maps, we show that Soay and Lacaune males exhibit different heritabilities and QTL effects for inter-individual variation in genome-wide recombination rates.</p> <p> </p> <p>Data files are provided in Plink format ( https://www.cog-genomics.org/plink2 ).</p> <p> </p>
Georeferenced data for the study Environmental suitability throughout the late Quaternary explains population genetic diversity
<p>Data filtered from GBIF (datasetKey: 50c9509d-22c7-4a22-a47d-8c48425ef4a7) Contains 150 records of the <i>Sciurus aberti </i>squirrel filtered in latitudinal windows of 5 degrees from 20 to 45 degrees N. </p>
Data from: The genetic basis of traits associated with the evolution of serpentine endemism in monkeyflowers
<p>The floras on chemically and physically challenging soils, such as gypsum, shale, and serpentine, are characterized by narrowly endemic species. The evolution of edaphic endemics may be facilitated or constrained by genetic correlations among traits contributing to adaptation and reproductive isolation across soil boundaries. The yellow monkeyflowers in the <em>Mimulus guttatus</em> species complex are an ideal system in which to examine these evolutionary patterns. To determine the genetic basis of adaptive and prezygotic isolating traits, we performed genetic mapping experiments with F2 hybrids derived from a cross between a serpentine endemic, <em>M. nudatus</em>, and its close relative <em>M. guttatus</em>. Few large effect and many small effect QTL contribute to interspecific divergence in life history, floral and leaf traits, and a history of directional selection contributed to trait divergence. Loci contributing to adaptive traits and prezygotic reproductive isolation overlap, and their allelic effects are largely in the direction of species divergence. These loci contain promising candidate genes regulating flowering time and plant organ size. Together our results suggest that genetic correlations among traits can facilitate the evolution of adaptation and speciation and may be a common feature of the genetic architecture of divergence between edaphic endemics and their widespread relatives.</p>
Data from: How density dependence, genetic erosion, and the extinction vortex impact evolutionary rescue
<p>Following severe environmental change that reduces mean population fitness below replacement, populations must adapt to avoid eventual extinction, a process called evolutionary rescue. Models of evolutionary rescue demonstrate that initial size, genetic variation, and degree of maladaptation influence population fates. However, many models feature populations that grow without negative density dependence or with constant genetic diversity despite precipitous population decline, assumptions likely to be violated in conservation settings. We examined the simultaneous influences of density-dependent growth and erosion of genetic diversity on populations adapting to novel environmental change using stochastic, individual-based simulations. Density dependence decreased the probability of rescue and increased the probability of extinction, especially in large and initially well-adapted populations that previously have been predicted to be at low risk. Increased extinction occurred shortly following environmental change, as populations under density dependence experienced more rapid decline and reached smaller sizes. Populations that experienced evolutionary rescue lost genetic diversity through drift and adaptation, particularly under density dependence. Populations that declined to extinction entered an extinction vortex, where small size increased drift, loss of genetic diversity, and the fixation of maladaptive alleles, hindered adaptation, and kept populations at small densities where they were vulnerable to extinction via demographic stochasticity.</p>
Data for: Genetic structuring and species boundaries in the Atlantic stony coral Favia (Scleractinia, Faviidae)
<p class="MsoNormal">Scleractinian corals are the main modern builders of coral reefs, dynamic ecosystems that are hot spots of marine biodiversity. Southern Atlantic reef corals are understudied compared to their Caribbean and Indo-Pacific counterparts and many hypotheses about their population dynamics demand further testing. We employed thousands of single nucleotide polymorphisms (SNPs) recovered via ezRAD to characterize genetic population structuring and species boundaries in the amphi-Atlantic hard coral genus <em>Favia</em>. Coalescent-based species delimitation (BFD* - Bayes factor delimitation) recovered <em>F. fragum </em>and <em>F. gravida </em>as separate species. Although our results agree with depth-related genetic structuring in <em>F.</em><em> frag</em><em>um</em><em>,</em><em> </em>they did not support incipient speciation of the "tall" and "short" morphotypes. The preferred scenario revealed a split between two main lineages of <em>F. gravida</em>, one from Ascension Island and the other from Brazil. The Brazilian lineage is further divided into a species that occurs throughout the Northeastern coast and another that ranges from the Abrolhos Archipelago to the state of Espírito Santo. BFD* scenarios were supported by analysis of datasets with varying levels of missing data. Our results challenge current notions about Atlantic reef corals because they uncovered surprising genetic diversity in <em>Favia</em><em> </em>and<em> </em>rejected the long-standing hypothesis that Abrolhos Archipelago may have served as a Pleistocenic refuge during the last glaciations. </p>
Data from: harnessing the power of regional baselines for broad-scale genetic stock identification: a multistage, integrated, and cost-effective approach
<p>In mixed-stock fishery analyses, genetic stock identification (GSI) estimates the contribution of each population to a mixture and is typically conducted at a regional scale using genetic baselines specific to the stocks expected in that region. Often these regional baselines cannot be combined to produce broader geographical baselines due to non-overlapping populations and genetic markers. In cases where the mixture contains stocks spanning across a wide area, a broad-scale baseline is created, but often at the cost of resolution. Here, we introduce a new GSI method to harness the resolution capabilities of baselines developed for regional applications in the analysis of mixtures containing individuals from a broad geographic range. This method employs a multistage framework that allows disparate baselines to be used in a single integrated process that produces estimates along with the propagated errors from each stage. All individuals in the mixture sample are required to be genotyped for all genetic markers in the baselines used by this model, but the baselines do not require overlap in genetic markers or populations representing the broad-scale or regional baselines.</p> <p>We demonstrate our integrated multistage GSI model using a synthesized data set made up of Chinook salmon, <em>Oncorhynchus tshawytscha</em>, from the North Bering Sea of Alaska. The data set is designed to be run using R package, Ms.GSI, and it does not represent the composition of the real fishery. The results show an improved accuracy for estimates using an integrated multistage framework, compared to the conventional framework of using separate hierarchical steps. The integrated multistage framework allows GSI of a wide geographic area without first developing a large scale, high-resolution genetic baseline or dividing a mixture sample into smaller regions beforehand. This approach is more cost-effective than updating range-wide baselines with all regionally important markers.</p>
Naked mole rats have distinctive cardiometabolic and genetic adaptations to their underground low-oxygen lifestyles (non-genetic data)
<p>The naked mole-rat <em>Heterocephalus glaber</em> is a eusocial mammal exhibiting extreme longevity (37-year lifespan), extraordinary resistance to hypoxia and absence of cardiovascular disease. To identify the mechanisms behind these exceptional traits, metabolomics and RNAseq of cardiac tissue from naked mole-rats were compared to other African mole-rat genera. We identified metabolic and genetic adaptations unique to naked mole-rats including elevated glycogen, thus enabling glycolytic ATP generation during cardiac ischemia. Elevated normoxic expression of HIF-1α was observed while downstream hypoxia-responsive genes were down-regulated, suggesting adaptation to low-oxygen environments. Naked mole-rat hearts showed reduced succinate build-up during ischemia and negligible tissue damage following ischemia-reperfusion injury. These adaptive evolutionary traits reflect a unique hypoxic and eusocial lifestyle that collectively may contribute to their longevity and health span.</p>
Data from: Dominance reversals and the maintenance of genetic variation
<p>Beneficial reversals of dominance reduce the costs of genetic trade-offs and can enable selection to maintain genetic variation for fitness. Beneficial dominance reversals are characterized by the beneficial allele for a given context (<em>e.g.</em> habitat, developmental stage, trait, or sex) being dominant in that context but recessive where deleterious. This context-dependence at least partially mitigates the fitness consequence of heterozygotes carrying one non-beneficial allele for their context and can result in balancing selection that maintains alternative alleles. Dominance reversals are theoretically plausible and are supported by mounting empirical evidence. Here we highlight the importance of beneficial dominance reversals as a mechanism for the mitigation of genetic conflict and review the theory and empirical evidence for them. We identify some areas in need of further research and development and outline three methods (dominance ordination, allele-specific expression, and allele-specific ATAC-Seq) that could facilitate the identification of antagonistic genetic variation. There is ample scope for the development of new empirical methods as well as reanalysis of existing data through the lens of dominance reversals. A greater focus on this topic will expand our understanding of the mechanisms that resolve genetic conflict and whether they maintain genetic variation.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.