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.
457
datasets available to search
ShareScore release 0.7.1
Dataset results
457 results for “Inbreeding”
Data for: Elevated inbreeding in Heliconia tortuosa is determined by tropical forest stand age, isolation, and loss of hummingbird functional diversity
<p>Forest conversion and habitat loss are major threats to biological diversity. Forest regeneration can mitigate the negative effects of old growth forest loss on species diversity, but less is known about the extent to which forest loss reduces genetic diversity in remnant populations and whether secondary forests play a role in the maintenance of genetic diversity. We quantified genetic diversity in a tropical hummingbird-pollinated understory herb, <em>Heliconia tortuosa</em>, across a landscape mosaic of primary and secondary forest regrowth. Using microsatellite genotypes from >850 adult and juvenile plants within 33 forest patches and extensive bird surveys, we examined the effect of contemporary and historical landscape features including forest age (primary vs. secondary forest), stand isolation, and pollinator assemblages on genetic diversity and levels of inbreeding in <em>H. tortuosa</em>. We found that inbreeding was up to 3x higher in secondary forest, and this effect was amplified with reductions in primary forest in the surrounding landscape through reduced observed heterozygosity in isolated fragments. Inbreeding in forest patches was negatively correlated with the local frequency of specialist long-distance foraging traplining hummingbirds. Traplining hummingbirds therefore appear to facilitate mating among unrelated plants - an inference we tested using empirically parameterized simulations. Higher levels of inbreeding in <em>H. tortuosa</em> are therefore associated with reduced functional diversity of hummingbirds in secondary forests and forest patches isolated from primary forests. Our findings suggest a cryptic consequence of primary forest loss and secondary forest regeneration through the disruption of mutualistic interactions resulting in the erosion of genetic diversity in a common understory plant.</p>
High levels of inbreeding with spatial and host-associated structure in lice of an endangered freshwater seal
<p>Host-specialist parasites of endangered large vertebrates are in many cases more endangered than their hosts. In particular, low host population densities and reduced among-host transmission rates are expected to lead to inbreeding within parasite infrapopulations living on single host individuals. Furthermore, spatial population structures of directly-transmitted parasites should be concordant with those of their hosts. Using population genomic approaches, we investigated inbreeding and population structure in a host-specialist seal louse (<em>Echinophthirius horridus</em>) infesting the Saimaa ringed seal (<em>Phoca hispida saimensis</em>), which is endemic to Lake Saimaa in Finland and is one of the most endangered pinnipeds in the world. We conducted genome resequencing of pairs of lice collected from 18 individual Saimaa ringed seals throughout the Lake Saimaa complex. Our analyses showed high genetic similarity and inbreeding between lice inhabiting the same individual seal host, indicating low among-host transmission rates. Across the lake, genetic differentiation among individual lice was correlated with their geographic distance, and assignment analyses revealed a marked break in the genetic variation of the lice in the middle of the lake, indicating substantial population structure. These findings indicate that movements of Saimaa ringed seals across the main breeding areas of the fragmented Lake Saimaa complex may in fact be more restricted than suggested by previous population-genetic analyses of the seals themselves.</p>
Environmentally associated variation in dispersal distance affects inbreeding risk in a stream salamander
<p>Avoiding inbreeding is considered a key driver of dispersal evolution, and dispersal distances should be especially important in mediating inbreeding risk because the likelihood of mating with relatives decreases with dispersal distance. However, a lack of direct data on dispersal distances has limited empirical tests of this prediction, particularly in the context of the multiple selective forces that can influence dispersal. Using a headwater salamander system, we tested whether spatial variation in environmental conditions leads to differences in dispersal distances, resulting in spatial variation in the effect of dispersal on inbreeding risk. Using capture-recapture and population genomic data from 5 streams, we found that dispersal distances were greater in downstream reaches than upstream reaches. Inbreeding risk was lower for dispersers than non-dispersers in downstream reaches, but not in upstream reaches. Furthermore, stream reaches did not differ in spatial patterns of individual relatedness, indicating that variation in inbreeding risk was in fact due to differences in dispersal distances. These results demonstrate that environmentally associated variation in dispersal distances can cause the inbreeding consequences of dispersal to vary at fine spatial scales. They also show that selective pressures other than inbreeding avoidance maintain phenotypic variation in dispersal, underscoring the importance of addressing alternative hypotheses in dispersal research.</p>
Can age-related changes in parental care modulate inbreeding depression? A test using the burying beetle, Nicrophorus orbicollis
<p>Parental care has been shown to reduce the magnitude of inbreeding depression in some species with facultative care. However, parents often vary in the quality or amount of care they provide to their offspring and it is less clear whether this variation also impacts the magnitude of inbreeding depression. Here, we tested whether age related changes in parental care modulate the expression of inbreeding depression in the burying beetle, Nicrophorus orbicollis. Consistent with previous studies, we found that older parents produced larger broods of offspring than younger parents without sacrificing mean larval mass. Inbreeding depression was evident in several fitness-related traits: brood size at dispersal, the proportion of the brood that survived to eclosion, and mean age at death were all reduced in inbred broods compared to outbred broods. Surprisingly, inbred offspring were heavier at dispersal than outbred offspring. This was likely due to reduced sibling competition in inbred broods. Despite evidence for age related changes in parental investment and the existence of inbreeding depression, there was no evidence that an interaction between the two influenced any of the traits we measured. Our results suggest that age-related changes in parental care may be too slight to influence the expression of inbreeding depression.</p>
Effects of inbreeding and elevated rearing temperatures on strategic sperm investment
<p>Males often strategically adjust the number of available sperm based on the social context (i.e., sperm priming response), but it remains unclear how environmental and genetic factors shape this adjustment. In freshwater ecosystems, high ambient temperatures often lead to isolated pools of hotter water in which inbreeding occurs. Higher water temperatures and inbreeding can impair fish development, potentially disrupting sperm production. We used guppies (<em>Poecilia reticulata</em>) to investigate how developmental temperature (26 °C, 30 °C) and male inbreeding status (inbred, outbred) influence their sperm priming response. We also tested if sperm priming was affected by whether the female was a relative (sister), and whether she was inbred or outbred.</p> <p>We ran two separate analyses to address our research questions. First, we ran a linear mixed model (LMM) to investigate the effects of male inbreeding status (inbred, outbred), rearing temperature (warm, control), and social environment (no female, unrelated outbred female, related female) and all three two-way interactions on sperm priming response (i.e., the total number of sperm produced in 7 days). Second, we noted that inbred males might produce fewer sperm than outbred males in the presence of a related female due to their sister being inbred and therefore of lower quality (e.g., less fecund). To test whether the observed effect of male inbreeding status was confounded by the related female's inbreeding status, we ran an additional LMM exclusively for inbred males. We separated the effects of inbreeding status of the female and her genetic relatedness to the male by considering three types of female (inbred related, inbred unrelated, outbred unrelated) that inbred males encountered. </p> <p>There was no effect of rearing temperature; male inbreeding status alone determined the number of available sperm in response to female presence, her inbreeding status and her relatedness. Inbred males produced significantly more sperm in the presence of an unrelated, outbred female than when no female was present. Conversely, outbred males did not alter the number of sperm available in response to female presence or relatedness. Moreover, inbred males produced marginally more sperm when exposed to an unrelated female that was outbred rather than inbred, but there was no difference when exposed to an inbred female that was unrelated versus related. Together, a sperm priming response was only observed in inbred males when exposed to an outbred female. Outbred females in our study were larger than inbred females, suggesting that inbred males strategically allocated ejaculate resources towards females in better condition.</p>
Data from: Heterosis is common and inbreeding depression absent in natural populations of Arabidopsis thaliana
The importance of genetic drift in shaping patterns of adaptive genetic variation in nature is poorly known. Genetic drift should drive partially recessive deleterious mutations to high frequency, and inter‐population crosses may therefore exhibit heterosis (increased fitness relative to intra‐population crosses). Low genetic diversity and greater genetic distance between populations should increase the magnitude of heterosis. Moreover, drift and selection should remove strongly deleterious recessive alleles from individual populations, resulting in reduced inbreeding depression. To estimate heterosis, we crossed 90 independent line pairs of Arabidopsis thaliana from 15 pairs of natural populations sampled across Fennoscandia, and crossed an additional 41 line pairs from a subset of 4 of these populations to estimate inbreeding depression. We measured lifetime fitness of crosses relative to parents in a large outdoor common garden (8448 plants in total) in central Sweden. To examine the effects of genetic diversity and genetic distance on heterosis, we genotyped parental lines for 869 SNPs. Overall, genetic variation within populations was low (median expected heterozygosity = 0.02), and genetic differentiation was high (median FST = 0.82). Crosses between 10 of 15 population pairs exhibited significant heterosis, with magnitudes of heterosis as high as 117%. We found no significant inbreeding depression, suggesting that the observed heterosis is due to fixation of mildly deleterious alleles within populations. Widespread and substantial heterosis indicates an important role for drift in shaping genetic variation, but there was no significant relationship between fitness of crosses relative to parents and genetic diversity or genetic distance between populations.
Supplementary tables for "Comparative inbreeding analyses in cattle"
<p>Supplementary Tables for the manuscript "Comparative analysis of inbreeding parameters and runs of homozygosity islands in two Italian autochthonous cattle breeds mainly raised in the Parmigiano-Reggiano cheese production region"</p>
Data and R scripts for: Effects of hunting on genetic diversity, inbreeding and dispersal in Finnish black grouse (Lyrurus tetrix)
<p>While intensive hunting activities, such as commercial fishing and trophy hunting, can have profound influences on natural populations, less intensive recreational hunting can also have more subtle effects on animal behaviour, habitat use and movement, with implications for population persistence. Lekking species such as the black grouse (<em>Lyrurus</em> <em>tetrix</em>) may be especially prone to hunting as leks are temporally and spatially predictable, making them easy targets. Furthermore, inbreeding in black grouse is mainly avoided through female-biased dispersal, so any disruptions to dispersal caused by hunting could lead to changes in gene flow, leading to an increasing risk of inbreeding. We therefore investigated the impact of hunting on genetic diversity, inbreeding and dispersal on a metapopulation of black grouse in Central Finland. We genotyped 1,065 adult males and 813 adult females from twelve lekking sites (six hunted, six unhunted) and 200 unrelated chicks from seven sites (two hunted, five unhunted) at up to thirteen microsatellite loci. Our initial confirmatory analysis of sex-specific fine-scale population structure revealed little genetic structure in the metapopulation. Levels of inbreeding did not differ significantly between hunted and unhunted sites in both adults and chicks. However, immigration rates into hunted sites were significantly higher among adults compared to immigration into unhunted sites. We conclude that the influx of migrants into hunted sites may compensate for the loss of harvested individuals, thereby increasing gene flow and mitigating inbreeding. Given the absence of any obvious potential barriers to gene flow in Central Finland, a spatially heterogeneous matrix of hunted and unhunted regions may be crucial to ensure sustainable harvests into the future.</p>
Genetic assessment reveals inbreeding, possible hybridization, and low levels of genetic structure in a declining goose population
<p>The population numbers of taiga bean goose (<i>Anser fabalis fabalis</i>) have halved during recent decades. Since this subspecies is hunted throughout most of its range, the decline is of management concern. Knowledge of the genetic population structure and diversity is important for guiding management and conservation efforts. Genetically unique subpopulations might be hunted to extinction if not managed separately, and any inbreeding depression or lack of genetic diversity may affect the ability to adapt to changing environments and increase extinction risk. We used microsatellite and mitochondrial DNA markers to study the genetic population structure and diversity among taiga bean geese breeding within the Central flyway management unit using non-invasively collected feathers. We found some genetic structuring with the maternally inherited mitochondrial DNA between four geographic regions (<i>ɸ</i><sub>ST</sub> = 0.11-0.20) but none with the nuclear microsatellite markers (all pairwise <i>F</i><sub>ST</sub>-values 0.002- 0.005). These results could be explained by female natal philopatry and male-biased dispersal, which completely homogenizes the nuclear genome. Therefore, the population could be managed as a single unit. Genetic diversity was still at a moderate level (average <i>H</i><sub>E</sub> = 0.69) and there were no signs of past population size reductions, although significantly positive inbreeding coefficients in all sampling sites (<i>F</i><sub>IS</sub> = 0.05-0.10) and high relatedness values (<i>r </i>= 0.60-0.86) between some individuals could indicate inbreeding. In addition, there was evidence of either incomplete lineage sorting or introgression from the pink-footed goose (<i>A. brachyrhynchus</i>). The current population is not under threat by genetic impoverishment but monitoring in the future is desirable.</p>
Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird
<p>Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations. Across island systems, contemporary patterns of genetic diversity reflect complex population demography, including colonisation events, bottlenecks, gene flow and genetic drift. Here, we investigate whether island founder events have prolonged effects on genome-wide diversity and runs of homozygosity (ROH) distributions, using whole genome resequencing from six populations across three archipelagos of Berthelot's pipit (<em>Anthus</em> <em>berthelotii</em>) – a passerine which has undergone island speciation relatively recently. Pairwise sequential Markovian coalescent (PSMC) analyses estimated divergence from its sister species approximately two million years ago. Results indicate that all Berthelot's pipit populations had shared ancestry until approximately 50,000 years ago, when the Madeiran archipelago populations were founded, while the Selvagens were colonised within the last 8,000 years. We identify extensive long ROH (>1 Mb) in genomes in the most recently colonised populations of Madeira and Selvagens which have experienced sequential island founder events and population crashes. Population expansion within the last 100 years may have eroded long ROH in the Madeiran archipelago, resulting in a prevalence of short ROH (<1 Mb). Extensive long and short ROH in the Selvagens reflects strong recent inbreeding, small contemporary effective population size and past bottleneck effects, with as much as 37.7% of the autosomes comprised of ROH >250 kb in length. These findings highlight the importance of demographic history, as well as selection and genetic drift, in shaping contemporary patterns of genomic diversity across diverging populations. </p>
Using inbreeding to test the contribution of non-additive genetic effects to additive genetic variance: A case study in Drosophila serrata
<p>Additive genetic variance, <em>V<sub>A</sub></em>, is the key parameter for predicting adaptive and neutral phenotypic evolution. Changes in demography (e.g., increased close-relative inbreeding) can alter <em>V<sub>A</sub></em>, but how depends on the, typically unknown, gene action and allele frequencies across many loci. For example, <em>V<sub>A</sub></em> increases proportionally with the inbreeding coefficient when allelic effects are additive, but larger (or smaller) increases can occur when allele frequencies are unequal at causal loci with dominance effects. Here, we describe an experimental approach to assess the potential for rare, recessive alleles to inflate <em>V<sub>A</sub></em> under inbreeding. Applying a powerful paired pedigree design in <em>Drosophila serrata</em>, we measured 11 wing traits on half-sibling families bred via either random or sibling mating, differing only in homozygosity (not allele frequency). Despite close inbreeding and substantial power to detect small <em>V<sub>A</sub></em>, we detected no deviation from the expected additive effect of inbreeding on genetic (co)variances. Our results suggest the average dominance coefficient is very small relative to the additive effect, or that allele frequencies are relatively equal at loci affecting wing traits. We outline the further opportunities for this paired pedigree approach to reveal the characteristics of <em>V<sub>A</sub></em>, providing insight into historical selection and future evolutionary potential.</p>
Data for: Multiple mechanisms for inbreeding avoidance used simultaneously in a wild ape
<p class="MsoNormal">Mating with close kin can have considerable negative fitness consequences, which are expected to result in selective pressure for inbreeding avoidance mechanisms, such as dispersal, mate choice and postcopulatory biases. Captive studies have suggested that inbreeding avoidance through mate choice is far less widespread than expected and may be absent where other mechanisms already limit inbreeding. However, few studies have examined multiple mechanisms of inbreeding avoidance simultaneously, particularly in the wild. We use 13 years of detailed dispersal, copulation, and paternity data from mountain gorillas to examine inbreeding avoidance. We find that partial dispersal of both sexes results in high kinship in multimale groups, but that copulations between close kin occur 40% less than expected. We find strong kin discrimination in mate choice, with significant avoidance of maternal kin but more limited avoidance of paternal kin. We find no evidence for post-copulatory inbreeding avoidance. Our analyses support familiarity-based mechanisms of kin identification and age-based avoidance that limits mating between fathers and daughters in their natal group. Our findings demonstrate that multiple complementary mechanisms for inbreeding avoidance can evolve in a single species and suggest that inbreeding avoidance through mate choice may enable more flexible dispersal systems to evolve.</p>
Severe inbreeding depression is predicted by the “rare allele load” in Mimulus guttatus
Open the record for dataset details and reuse information.
Using inbreeding to test the contribution of non-additive genetic effects to additive genetic variance: A case study in Drosophila serrata
Open the record for dataset details and reuse information.
Data from: Heterosis is common and inbreeding depression absent in natural populations of Arabidopsis thaliana
Open the record for dataset details and reuse information.
Inbreeding depression in a sexually selected weapon and the homologue in females
Open the record for dataset details and reuse information.
Inbreeding and disease avoidance in a free‐ranging koala population
Open the record for dataset details and reuse information.
Data from: Sexually-selected male weapon is associated with lower inbreeding load but higher gender load in the bulb mite
Open the record for dataset details and reuse information.
Assessment of inbreeding depression on progeny of Afrocarpus gracilior
Open the record for dataset details and reuse information.
Data for: Genomic insights into inbreeding and adaptive divergence of trout populations to inform genetic rescue
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.