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.
141
datasets available to search
ShareScore release 0.9.0
Dataset results
141 results for “MHC class I”
Data from: No evidence for MHC class I based disassortative mating in a wild population of great tits
Genes of the major histocompatibility complex (MHC) are regarded as a potentially important target of mate choice due to the fitness benefits that may be conferred to the offspring. According to the complementary genes hypothesis, females mate with MHC dissimilar males to enhance the immunocompetence of their offspring or to avoid inbreeding depression. Here, we investigate whether selection favours a preference for maximally dissimilar or optimally dissimilar MHC class I types, based on MHC genotypes, average amino acid distances and the functional properties of the antigen-binding sites (MHC supertypes); and whether MHC type dissimilarity predicts relatedness between mates in a wild great tit population. In particular, we explore the role that MHC class I plays in female mate choice decisions while controlling for relatedness and spatial population structure, and examine the reproductive fitness consequences of MHC compatibility between mates. We find no evidence for the hypotheses that females select mates on the basis of either maximal or optimal MHC class I dissimilarity. A weak correlation between MHC allele sharing and relatedness, and between MHC supertype sharing and relatedness suggests that MHC dissimilarity at functional variants may not provide an effective index of relatedness. Moreover the reproductive success of pairs did not vary with MHC dissimilarity. Our results provide no support for the suggestion that selection favours, or that mate choice realises, a preference for complimentary MHC types.
Data from: No evidence for MHC class II-based non-random mating at the gametic haplotype in Atlantic salmon
Genes of the major histocompatibility complex (MHC) are a likely target of mate choice because of their role in inbreeding avoidance and potential benefits for offspring immunocompetence. Evidence for female choice for complementary MHC alleles among competing males exists both for the pre- and the postmating stages. However, it remains unclear whether the latter may involve non-random fusion of gametes depending on gametic haplotypes resulting in transmission ratio distortion or non-random sequence divergence among fused gametes. We tested whether non-random gametic fusion of MHC-II haplotypes occurs in Atlantic salmon Salmo salar. We performed in vitro fertilizations that excluded interindividual sperm competition using a split family design with large clutch sample sizes to test for a possible role of the gametic haplotype in mate choice. We sequenced two MHC-II loci in 50 embryos per clutch to assess allelic frequencies and sequence divergence. We found no evidence for transmission ratio distortion at two linked MHC-II loci, nor for non-random gamete fusion with respect to MHC-II alleles. Our findings suggest that the gametic MHC-II haplotypes play no role in gamete association in Atlantic salmon and that earlier findings of MHC-based mate choice most likely reflect choice among diploid genotypes. We discuss possible explanations for these findings and how they differ from findings in mammals.
Data from: Patterns of genetic differentiation at MHC class I genes and microsatellites identify conservation units in the giant panda
Background: Evaluating patterns of genetic variation is important to identify conservation units (i.e., evolutionarily significant units [ESUs], management units [MUs], and adaptive units [AUs]) in endangered species. While neutral markers could be used to infer population history, their application in the estimation of adaptive variation is limited. The capacity to adapt to various environments is vital for the long-term survival of endangered species. Hence, analysis of adaptive loci, such as the major histocompatibility complex (MHC) genes, is critical for conservation genetics studies. Here, we investigated 4 classical MHC class I genes (Aime-C, Aime-F, Aime-I, and Aime-L) and 8 microsatellites to infer patterns of genetic variation in the giant panda (Ailuropoda melanoleuca) and to further define conservation units. Results: Overall, we identified 24 haplotypes (9 for Aime-C, 1 for Aime-F, 7 for Aime-I, and 7 for Aime-L) from 218 individuals obtained from 6 populations of giant panda. We found that the Xiaoxiangling population had the highest genetic variation at microsatellites among the 6 giant panda populations and higher genetic variation at Aime-MHC class I genes than other larger populations (Qinling, Qionglai, and Minshan populations). Differentiation index (FST)-based phylogenetic and Bayesian clustering analyses for Aime-MHC-I and microsatellite loci both supported that most populations were highly differentiated. The Qinling population was the most genetically differentiated. Conclusions: The giant panda showed a relatively higher level of genetic diversity at MHC class I genes compared with endangered felids. Using all of the loci, we found that the 6 giant panda populations fell into 2 ESUs: Qinling and non-Qinling populations. We defined 3 MUs based on microsatellites: Qinling, Minshan-Qionglai, and Daxiangling-Xiaoxiangling-Liangshan. We also recommended 3 possible AUs based on MHC loci: Qinling, Minshan-Qionglai, and Daxiangling-Xiaoxiangling-Liangshan. Furthermore, we recommend that a captive breeding program be considered for the Qinling panda population.
Data from: Specific MHC class I supertype associated with parasite infection and colour morph in a wild lizard population
The major histocompatibility complex (MHC) is a large gene family that plays a central role in the immune system of all jawed vertebrates. Non-avian reptiles are under-represented within the MHC literature and little is understood regarding the mechanisms maintaining MHC diversity in this vertebrate group. Here, we examined the relative roles of parasite-mediated selection and sexual selection in maintaining MHC class I diversity of a colour polymorphic lizard. We discovered evidence for parasite-mediated selection acting via rare-allele advantage or fluctuating selection as ectoparasite load was significantly lower in the presence of a specific MHC supertype (functional clustering of alleles); supertype four. Based on comparisons between ectoparasite prevalence and load, and assessment of the impact of ectoparasite load on host fitness, we suggest that supertype four confers quantitative resistance to ticks or an intracellular tick-borne parasite. We found no evidence for MHC-associated mating in terms of pair genetic distance, number of alleles or specific supertypes . An association was uncovered between supertype four and male throat colour morph. However, it is unlikely that male throat colouration acts as a signal of MHC genotype to conspecifics because we found no evidence to suggest that male throat colouration predicts male mating status. Overall, our results suggest that parasite-mediated selection plays a role in maintaining MHC diversity in this population via rare allele advantage and/or fluctuating selection. Further work is required to determine whether sexual selection also plays a role in maintaining MHC diversity in agamid lizards.
Data from: Very high MHC Class IIB diversity without spatial differentiation in the Mediterranean population of Greater Flamingos
Background: Selective pressure from pathogens is thought to shape the allelic diversity of major histocompatibility complex (MHC) genes in vertebrates. In particular, both local adaptation to pathogens and gene flow are thought to explain a large part of the intraspecific variation observed in MHC allelic diversity. To date, however, evidence that adaptation to locally prevalent pathogens maintains MHC variation is limited to species with limited dispersal and, hence, reduced gene flow. On the one hand high gene flow can disrupt local adaptation in species with high dispersal rates, on the other hand such species are much more likely to experience spatial variation in pathogen pressure, suggesting that there may be intense pathogen mediated selection pressure operating across breeding sites in panmictic species. Such pathogen mediated selection pressure operating across breeding sites should therefore be sufficient to maintain high MHC diversity in high dispersing species in the absence of local adaptation mechanisms. We used the Greater Flamingo, Phoenicopterus roseus, a long-lived colonial bird showing a homogeneous genetic structure of neutral markers at the scale of the Mediterranean region, to test the prediction that higher MHC allelic diversity with no population structure should occur in large panmictic populations of long-distance dispersing birds than in other resident species. Results: We assessed the level of allelic diversity at the MHC Class IIB exon 2 from 116 individuals born in four different breeding colonies of Greater Flamingo in the Mediterranean region. We found one of the highest allelic diversity (109 alleles, 2 loci) of any non-passerine avian species investigated so far relative to the number of individuals and loci genotyped. There was no evidence of population structure between the four major Mediterranean breeding colonies. Conclusion: Our results suggest that local adaptation at MHC Class IIB in Greater Flamingos is constrained by high gene flow and high MHC diversity appears to be maintained by population wide pathogen-mediated selection rather than local pathogen-mediated selection. Further understanding of how pathogens vary across space and time will be crucial to further elucidate the mechanisms maintaining MHC diversity in species with large panmictic populations and high dispersal rates.
An mRNA-encoded, long-lasting Interleukin-2 restores CD8+ T cell neoantigen immunity in MHC class I-deficient cancers
<ul> <li><strong><span>Cd45Summit-IntgrAllgroups_finalUMAP_simplified_colorordered.RData </span></strong><span>contains all final result of the workflow (data integration and annotation) without subsetting the cell types into the different treatment groups.</span></li> <li><strong><span>Cd45Summit-IntgrAllgroups_finalUMAP_Only_CD8Tcells_subsetted.RData </span></strong><span>contains combined dataset of all present CD8+ T cell types (final UMAP, all annotated), which are subsetted into the four treatment groups.</span></li> <li><strong><span>Cd45Summit-IntgrAllgroups_finalUMAP_Only_ProlifMacros_subsetted.RData </span></strong><span>contains only the proliferating CD8+ T cells, which are subsetted into the four different treatment groups.</span></li> <li><strong><span>Cd45Summit-IntgrAllgroups_forJan_Macors_Gr1to4.RData </span></strong><span>contains only the combined macrophages of the dataset, subsetted into the four treatment groups.</span></li> </ul>
Data from: MHC class II diversity of koala (Phascolarctos cinereus) populations across their range
Major histocompatibility complex class II (MHCII) genes code for proteins that bind and present antigenic peptides and trigger the adaptive immune response. We present a broad geographical study of MHCII DA β1 (DAB) and DB β1 (DBB) variants of the koala (Phascolarctos cinereus; n=191) from 12 populations across eastern Australia, with a total of 13 DAB and 7 DBB variants found. We identified greater MHCII variation and, possibly, additional gene copies in koala populations in the north (Queensland and New South Wales) relative to the south (Victoria), confirmed by STRUCTURE analyses and genetic differentiation using analysis of molecular variance. The higher MHCII diversity in the north relative to south could potentially be attributed to (i) significant founder effect in Victorian populations linked to historical translocation of bottlenecked koala populations and (ii) increased pathogen-driven balancing selection and/or local genetic drift in the north. Low MHCII genetic diversity in koalas from the south could reduce their potential response to disease, although the three DAB variants found in the south had substantial sequence divergence between variants. This study assessing MHCII diversity in the koala with historical translocations in some populations contributes to understanding the effects of population translocations on functional genetic diversity.
16S V4 raw read count data; 16S reads metadata; new MHC class II allele sequences
<p>Pathogen-mediated selection at the major histocompatibility complex (MHC) is thought to promote MHC-based mate choice in vertebrates. Mounting evidence implicates odour in conveying MHC genotype, but the underlying mechanisms remain uncertain. MHC effects on odour may be mediated by odour-producing symbiotic microbes whose community structure is shaped by MHC genotype. In birds, preen oil is the primary source of body odour and similarity at MHC predicts similarity in preen oil composition. Hypothesizing that this relationship is mediated by symbiotic microbes, we characterized MHC genotype, preen gland microbial communities, and preen oil chemistry of song sparrows (<i>Melospiza melodia</i>). Consistent with the microbial mediation hypothesis, pairwise similarity at MHC predicted similarity in preen gland microbiota. Overall microbial similarity did not predict chemical similarity of preen oil, counter to this hypothesis. However, permutation testing identified a maximally predictive set of microbial taxa that best reflect MHC genotype, and another set of taxa that best predict preen oil chemical composition. The relative strengths of relationships between MHC and microbes, microbes and preen oil, and MHC and preen oil suggest that MHC may affect host odour both directly and indirectly. Thus, birds may assess MHC genotypes based on both host-associated and microbially-mediated odours.</p>
Figure 3. Bayesian phylogenetic reconstruction for MHC class II in Diversity of MHC class II DRB alleles in the Eurasian population of the least weasel, Mustela nivalis (Mustelidae: Mammalia)
Figure 3. Bayesian phylogenetic reconstruction for MHC class II DRB alleles from Mustela nivalis and other species in Mustelidae, Felidae, and Canidae. Numbers near nodes are posterior probability values. Sequences from M. nivalis obtained in this study are in bold. GenBank accession numbers of previously published nucleotide sequences are in parentheses. Clades in Mustelidae are indicated by capital letters (A–G) to the right of the tree. The scale bar at the bottom shows branch length in substitutions per site. Abbreviations for species names are as follows: Cafa, Canis familiaris; Cala, Canis latrans; Calu, Canis lupus; Enlu, Enhydra lutris; Febi, Felis silvestris bieti; Feca, Felis catus; Fesi, Felis silvestris; Gugu, Gulo gulo; Meme, Meles meles; Muit, Mustela itatsi; Mulu, Mustela lutreola; Musi, Mustela sibirica; Nevi, Neovison vison; Tata, Taxidea taxus; Zaca, Zalophus californianus.
Figure 2 in Diversity of MHC class II DRB alleles in the Eurasian population of the least weasel, Mustela nivalis (Mustelidae: Mammalia)
Figure 2. Amino acid sequences deduced from the nucleotide sequences of part of Mustela nivalis MHC class II DRB exon 2. Identity with allele Muni-DRB*01 is indicated by dots. Numbers above the top sequence indicate codon positions in the β1-domain. Grey shading shows the antigen-binding site (ABS) predicted from data on the human gene HLA-DR1 (Brown et al., 1993). Asterisks indicate codons corresponding to sites under positive selection calculated from the mixed-effects model evolution (MEME) analysis. A triangle shows the recombination break point with the single break point recombination (SBP) method (see the text).
Figure 1 in Diversity of MHC class II DRB alleles in the Eurasian population of the least weasel, Mustela nivalis (Mustelidae: Mammalia)
Figure 1. Map of Eurasia showing collecting localities (black circles) for 35 specimens of Mustela nivalis in this study. The sample size at each locality is indicated in parentheses.
Data from: MHC class II diversity of koala (Phascolarctos cinereus) populations across their range
Open the record for dataset details and reuse information.
Data from: Patterns of genetic differentiation at MHC class I genes and microsatellites identify conservation units in the giant panda
Open the record for dataset details and reuse information.
Data from: Extreme MHC class I diversity in the sedge warbler (Acrocephalus schoenobaenus); selection patterns and allelic divergence suggest that different genes have different functions
Open the record for dataset details and reuse information.
16S V4 raw read count data; 16S reads metadata; new MHC class II allele sequences
Open the record for dataset details and reuse information.
Data from: MHC class I expression dependent on bacterial infection and parental factors in whitefish embryos (Salmonidae)
Open the record for dataset details and reuse information.
Data from: No evidence for MHC class II-based non-random mating at the gametic haplotype in Atlantic salmon
Open the record for dataset details and reuse information.
Data from: MHC class II DRB diversity predicts antigen recognition and is associated with disease severity in California sea lions naturally infected with Leptospira interrogans
Open the record for dataset details and reuse information.
Data from: Extra-pair mating in a passerine bird with highly duplicated MHC class II: Preference for the golden mean
Open the record for dataset details and reuse information.
Data from: Genetic variation at MHC class II loci influences both olfactory signals and scent discrimination in ring-tailed lemurs
Open the record for dataset details and reuse information.
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.