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.
502
datasets available to search
ShareScore release 0.9.0
Dataset results
502 results for “natural populations”
Data from: Bayesian quantification of ecological determinants of outcrossing in natural plant populations: computer simulations and the case study of biparental inbreeding in English yew
Open the record for dataset details and reuse information.
Data from: Stage- and thermal-specific genetic architecture for preadult viability in natural populations of Drosophila melanogaster
Studying the processes affecting variation for preadult viability is essential to understand the evolutionary trajectories followed by natural populations. This task requires focusing on the complex nature of the phenotype-genotype relationship by taking into account usually neglected aspects of the phenotype and recognizing the modularity between different ontogenetic stages. Here we describe phenotypic variability for viability during the larval and pupal stages in lines derived from three natural populations of Drosophila melanogaster, as well as the variability for phenotypic plasticity and canalization at two different rearing temperatures. The observed phenotypic differences between populations can be attributed both to adaptation to environmental conditions and lack of gene flow between them. According to our results, different aspects of the phenotype (means, plasticity, canalization, plasticity of canalization) are affected by different genetic bases underlying changes in viability in a stage- and environment-specific manner. These findings explain the generalized maintenance of genetic variability for this fitness trait.
Dataset and scripts from: Predicting temperature mortality and selection in natural Drosophila populations
<p>The study develops and validates a theoretical model to predict thermal mortality under natural conditions, based on measurements of mortality performed in the laboratory at multiple constant temperatures. The theoretical model first fits a thermal tolerance landscape, which describes how survival probability is affected by both temperature and exposure time, to the empirical measurements of mortality obtained in the laboratory under controlled conditions. Then, employing a numerical approximation to the analytical solution based on differential calculus, it combines this tolerance landscape with ambient temperature records in natural settings to predict the survival probability curve under these thermal conditions. These predictions were validated by contrasting predicted and observed mortality curves in 11 Drosophila species under three different warming rates, reported in the literature, which were virtually indistinguishable. Having validated the model, the study then examines how mortality should be affected by climate change in a natural population of Drosophila subobscura from Santiago, Chile, employing temperature records for this location during 1984 - 1991 and 2014 - 2018. The cumulative mortality predicted from temperature records closely resemble the periods of population collapse recorded for this population during the Austral summer and, according to the model, warming temperatures in the past 30 years may have advanced this period by almost a month. This methodology is highly general and can in principle be employed to predict temperature mortality in small ectotherms under any varying thermal regime. </p>
Male reproductive traits among natural populations of P. guentheri
<p>Ejaculate traits vary extensively among individuals and species, but little is known about their variation among populations of the same species. Here, we investigated patterns of intraspecific variation in male reproductive investment in the terrestrial-breeding frog <i>Pseudophryne guentheri</i>. Like most anurans, breeding activity in <i>P. guentheri</i> is cued by precipitation, and therefore the timing and duration of breeding seasons differ among geographically separated populations, potentially leading to differences in the level of sperm competition. We therefore anticipated local adaptation in sperm traits that reflect these phenological differences among populations. Our analysis of six natural populations across a rainfall gradient revealed significant divergence in testes and ejaculate traits that correspond with annual rainfall and rainfall seasonality; males from the northern and drier edge of the species range had significantly smaller testes <span>containing fewer, smaller and less motile sperm compared to those from mesic central populations. These findings may reflect spatial variation in the strength of postcopulatory sexual selection, likely driven by</span><span> local patterns of precipitation.</span></p>
Parentage analyses identify local dispersal events and sibling aggregations in a natural population of Millepora hydrocorals, a free-spawning marine invertebrate
<p><span><span><span><span><span><span><span><span><span><span><span>Dispersal is a critical process for the persistence and productivity of marine populations. For many reef species, there is increasing evidence that local demography and self-recruitment have major consequences on their genetic diversity and adaptation to environmental change. Yet empirical data of dispersal patterns in reef-building species remain scarce. Here, we document the first genetic estimates of self-recruitment and dispersal distances in a free-spawning marine invertebrate, the hydrocoral <i>Millepora platyphylla</i>. Using twelve microsatellite markers, we gathered genotypic information from 3,160 georeferenced colonies collected over 9,000 m<sup>2</sup> of a single reef in three adjacent habitats in Moorea, French Polynesia; the mid slope, upper slope, and back reef. Although the adult population was predominantly clonal (85% were clones), our parentage analysis revealed a moderate self-recruitment rate with 8 to 37% of sexual propagules produced locally. Assigned offspring often settled at less than 10 meters from their parents and dispersal events decrease with increasing geographic distance. There were no discrepancies between the dispersal distances of offspring assigned to parents belonging to clonal <i>versus</i> non-clonal genotypes. Inter-habitat dispersal events via cross-reef transport were also detected for sexual and asexual propagules. Sibship analysis showed that full siblings recruit together on the reef (more than 40% settled at < 30 m), resulting in sibling aggregations. Our findings highlight the importance of self-recruitment together with clonality in stabilizing population dynamics, which may ultimately enhance local sustainability and resilience to disturbance.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: An integrated population model for estimating the relative effects of natural and anthropogenic factors on a threatened population of steelhead trout
<p>This collection includes data on the abundance, age composition, and harvest of adult steelhead trout, as well as the numbers of juveniles released from a hatchery, for steelhead trout (<em>Oncorhyncus mykiss</em>) from the Skagit River in Washington, USA. It also includes estimates of the marine survival of hatchery-origin steelhead.</p>
Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population
<p>Hybridization between divergent lineages generates new allelic combinations. One mechanism that can hinder the formation of hybrid populations is mitonuclear incompatibility, i.e. dysfunctional interactions between proteins encoded on the nuclear and mitochondrial genomes (mitogenomes) of diverged lineages. Theoretically, selective pressure due to mitonuclear incompatibility can affect genotypes in a hybrid population in which nuclear genomes and mitogenomes from divergent lineages admix. To directly and thoroughly observe this key process, we <i>de novo</i> sequenced the 747 Mb genome of the coastal goby, <i>Chaenogobius annularis</i>, and investigated its integrative genomic phylogeographics using RNA‐sequencing, RAD‐sequencing, genome re‐sequencing, whole mitogenome sequencing, amplicon‐sequencing, and small RNA‐sequencing. <i>Chaenogobius annularis</i> populations have been geographically separated into Pacific Ocean (PO) and Sea of Japan (SJ) lineages by past isolation events around the Japanese archipelago. Despite the divergence history and potential mitonuclear incompatibility between these lineages, the mitogenomes of the PO and SJ lineages have coexisted for generations in a hybrid population on the Sanriku Coast. Our analyses revealed accumulation of nonsynonymous substitutions in the PO‐lineage mitogenomes, including two convergent substitutions, as well as signals of mitochondrial lineage‐specific selection on mitochondria‐related nuclear genes. Finally, our data implied that a microRNA gene was involved in resolving mitonuclear incompatibility. Our integrative genomic phylogeographic approach revealed that mitonuclear incompatibility can affect genome evolution in a natural hybrid population.</p>
Data from: Mitochondrial gene diversity associated with the atp9 stop codon in natural populations of wild carrot (Daucus carota ssp. carota)
Mitochondrial genomes extracted from wild populations of Daucus carota have been used as a genetic resource by breeders of cultivated carrot, yet little is known concerning the extent of their diversity in nature. Of special interest is a SNP in the putative stop codon of the mitochondrial gene atp9 that has been associated previously with male-sterile and male-fertile phenotypic variants. In this study either sequence or PCR/RFLP genotypes were obtained from the mitochondrial genes atp1, atp9 and cox1 found in D. carota individuals collected from 24 populations in the eastern U.S. More than half of the 128 individuals surveyed had a CAA or AAA, rather than TAA, genotype at the position usually thought to function as an atp9 stop codon in this species. We also found no evidence for mitochondrial RNA editing (Cytosine to Uridine) of the CAA stop codon in either floral or leaf tissue. Evidence for intra-genic recombination, as opposed the more common inter-genic recombination in plant mitochondrial genomes, in our data set is presented. Indel and SNP variants elsewhere in atp9, and in the other two genes surveyed, were non-randomly associated with the three atp9 stop codon variants, though further analysis suggested that multi-locus genotypic diversity had been enhanced by recombination. Overall the mitochondrial genetic diversity was only modestly structured among populations with an Fst of 0.34.
Data from: Rapid buildup of genetic diversity in founder populations of the gynodioecious plant species Origanum vulgare after semi-natural grassland restoration
In most landscapes the success of habitat restoration is largely dependent on spontaneous colonization of plant species. This colonization process, and the outcome of restoration practices, can only be considered successful if the genetic makeup of founding populations is not eroded through founder effects and subsequent genetic drift. Here we used 10 microsatellite markers to investigate the genetic effects of recent colonization of the long-lived gynodioecious species Origanum vulgare in restored semi-natural grassland patches. We compared the genetic diversity and differentiation of fourteen recent populations with that of thirteen old, putative source populations, and we evaluated the effects of spatial configuration of the populations on colonization patterns. We did not observe decreased genetic diversity in recent populations, or inflated genetic differentiation among them. Nevertheless, a significantly higher inbreeding coefficient was observed in recent populations, although this was not associated with negative fitness effects. Overall population genetic differentiation was low (FST = 0.040). Individuals of restored populations were assigned to on average 6.1 different source populations (likely following the 'migrant pool' model). Gene flow was, however, affected by the spatial configuration of the grasslands, with gene flow into the recent populations mainly originating from nearby source populations. This study demonstrates how spontaneous colonization after habitat restoration can lead to viable populations in a relatively short time, overcoming pronounced founder effects, when several source populations are nearby. Restored populations can therefore rapidly act as stepping stones and sources of genetic diversity, likely increasing overall metapopulation viability of the study species.
Data from: Natural selection favors a larger eye in response to increased competition in natural populations of a vertebrate
1.Eye size varies notably across taxa. Much work suggests that this variation is driven by contrasting ecological selective pressures. However, evaluations of the relationship between ecological factors and shifts in eye size have largely occurred at the macroevolutionary scale. Experimental tests in nature are conspicuously absent. 2.Trinidadian killifish, Rivulus hartii, are found across fish communities that differ in predation intensity. We recently showed that increased predation is associated with the evolution of a smaller eye. Here, we test how divergent predatory regimes alter the trajectory of eye size evolution using comparative mark‐recapture experiments in multiple streams. 3.We found that increases in eye size are associated with enhanced survival, irrespective of predation intensity. More importantly, eye size is associated with enhanced growth in communities that lack predators, while this trend is absent when predators are present. 4.Such results argue that increased competition for food in sites that lack predators is the key driver of eye size evolution.
Data from: Structural diversity of naturally regenerating Chinese yew (Taxus wallichiana var. mairei) populations in an ex situ conservation
The Chinese yew (Taxus wallichiana var. mairei) is ranked among the first class of important wild endangered plants in China. However, due to its overexploitation, it now occurs scattered in the forest undergrowth along the Yangtze River Valley. To improve this tree's conservation management, we used structural indices to investigate the structural diversity of naturally regenerating yew populations that have established via ex situ conservation. The results show that most yews had larger non-yew tree neighbors; these were 30–70% larger than their reference trees. Collectively, the average distances between the yews and the three nearest-neighboring trees were short (<3 m). This result suggests that the yews likely face strong interspecific competition from neighbors. In these two forest stands, most of the pole-sized yews are found beneath a single tall neighboring tree (height ≥10 m), and their growth was enhanced under a single neighboring tree but not under two, three or zero neighboring trees. Finally, we recommend simple silvicultural treatments to reduce interspecific competition; specifically, the cutting or pruning of branches of large neighboring trees in tandem with the thinning of canopy trees growing next to the mother yews.
Data from: Fine-scale spatial covariation between infection prevalence and susceptibility in a natural population
The prevalence of infection varies dramatically on a fine spatial scale. Many evolutionary hypotheses are founded on the assumption that this variation is due to host genetics, such that sites with a high frequency of alleles conferring susceptibility are associated with higher infection prevalence. This assumption is largely untested and may be compromised at finer spatial scales where gene flow between sites is high. We put this assumption to the test in a natural snail-trematode interaction in which host susceptibility is known to have a strong genetic basis. A decade of field sampling revealed substantial spatial variation in infection prevalence between 13 sites around a small lake. Laboratory assays replicated over 3 years demonstrate striking variation in host susceptibility among sites in spite of high levels of gene flow between sites. We find that mean susceptibility can explain more than one-third of the observed variation in mean infection prevalence among sites. We estimate that variation in susceptibility and exposure together can explain the majority of variation in prevalence. Overall, our findings in this natural host-parasite system argue that spatial variation in infection prevalence covaries strongly with variation in the distribution of genetically based susceptibility, even at a fine spatial scale.
Data from: Association of polyandry and sex-ratio drive prevalence in natural populations of Drosophila neotestacea
Selfish genetic elements bias their own transmission to the next generation, even at the expense of the fitness of their carrier. Sex-ratio (SR) meiotic drive occurs when an X-chromosome causes Y-bearing sperm to die during male spermatogenesis, so that it is passed on to all of the male's offspring, which are all daughters. How SR is maintained as a stable polymorphism in the absence of genetic suppressors of drive is unknown. Here, we investigate the potential for the female remating rate to affect SR dynamics in natural populations, using the fly Drosophila neotestacea. In controlled laboratory conditions, females from populations where SR is rare mate more often than females from populations where SR is common. Furthermore, only when males mate multiply does the average fertility of SR males relative to wild-type males decrease to a level that can prevent SR from spreading. Our results suggest that differences in the female mating rate among populations may contribute to SR dynamics in the wild, and thus also affect the outcome of this intragenomic conflict. In line with this, we also present evidence of a localized population crash due to SR that may have resulted from habitat fragmentation along with a reduced mating rate.
Data from: Genetic resources of teak (Tectona grandis Linn. f.) – strong genetic structure among natural populations
Twenty-nine provenances of teak (Tectona grandis Linn. f.) representing the full natural distribution range of the species were genotyped with microsatellite DNA markers to analyse genetic diversity and population genetic structure. Provenances originating from the semi-moist east coast of India had the highest genetic diversity while provenances from Laos showed the lowest. In the eastern part of the natural distribution area, comprising Myanmar, Thailand and Laos, there was a strong clinal decrease in genetic diversity the further east the provenance was located. Overall, the pattern of genetic diversity supports the hypothesis that teak has its centre of origin in India, from where it spread eastwards. The analysis of molecular variance (AMOVA) gave an overall highly significant F st value of 0.227—population pairwise F st values were in the range 0.01–0.48. Applying the G″st differentiation parameter, the estimated overall differentiation was 0.632, implying a strong genetic structure among populations. A neighbour-joining (NJ) tree, using the pairwise population matrix of G″st values as input, contained three distinct groups: (1) the eight provenances from Thailand and Laos, (2) the Indian provenances from the dry interior and the moist west coast and (3) the provenances from northern Myanmar. The provenances from southern Myanmar were placed close to the root of the tree together with the three provenances from the semi-moist east coast of India. A Bayesian cluster analysis using the STRUCTURE software gave very similar results, with three main clusters, each containing two sub-clusters, while Bayesian cluster analysis in the Geneland software, exploiting the spatial coordinates of the provenances, resulted in five clusters in accordance with the former results. The implications of the findings for conservation and use of genetic resources of the species are discussed.
Data from: Individual inversions or their combinations: which is the main selective target in a natural population of Drosophila subobscura?
It is generally accepted that chromosomal inversions have been key elements in adaptation and speciation processes. In this context, D. subobscura has been, and still is, an excellent model species due to its rich chromosomal polymorphism. In this species, many analyses from natural populations have demonstrated the adaptive potential of individual inversions (and their overlapped combinations, the so called arrangements). However, little information is available on the evolutionary role of combinations generated by inversions located in homologous and non-homologous chromosomes. The aim of this research is to ascertain whether these combinations are also a target for natural selection. For this objective, we have studied the inversion composition of homologous and non-homologous chromosomes from a D. subobscura sample collected in a well-studied population, Mount Avala (Serbia). No significant deviation from H-W expectations was detected, and when comparing particular karyotypic combinations, likelihood ratios close to 1 were obtained. Thus, it seems that for each pair of homologous chromosomes inversions no deviation from randomness was detected. Finally, no linkage disequilibrium was observed between inversions located in different chromosomes of the karyotype. For all these reasons it can be assumed that, at the cytological level, the individual inversions rather than their combinations in different chromosomes are the main target of selection.
Data from: Cytonuclear evidence for hybridogenetic reproduction in natural populations of the Australian carp gudgeon (Hypseleotris: Eleotridae).
Although most vertebrates reproduce sexually, a small number of fishes, amphibians, and reptiles are known in which reproduction is asexual i.e. without meiotic recombination. In fishes, these so-called "unisexual" lineages usually comprise only females, and utilize co-occurring males of a related sexual species to reproduce via gynogenesis or hybridogenesis. Here we examine patterns of microsatellite and mitochondrial DNA (mtDNA) variation in a widespread group of freshwater fishes (carp gudgeons; Hypseleotris spp.) to investigate a long-standing proposal that this group includes unisexual forms. We show that the mtDNA genome of most carp gudgeons in tributaries of the Goulburn River belong in one of two deeply divided clades (~10% cyt b divergence) and that nuclear variation divides the same individuals into four distinct groups. Group 1 exhibits the genotypic proportions of a random mating population and has a 1:1 sex ratio. Two other groups are extremely sex-biased (98% male, 96% female), exhibit excess heterozygosity at most loci and share at least one allele per locus with group 1. We propose that these two groups represent "unisexual" hybridogenetic lineages, and that both utilize co-occurring group 1 as sexual host. Interestingly, the fourth distinct group appears to represent hybrid offspring of the two putative hybridogenetic lineages. The propagation of clonal haploid genomes by both males and females and the ability of these clones to unite and form sexually mature diploid hybrid offspring may represent a novel mechanism that contributes to the dynamics of coexistence between hybridogenetic lineages and their sexual hosts.
Data from: Heterosis and outbreeding depression in crosses between natural populations of Arabidopsis thaliana
Understanding the causes and architecture of genetic differentiation between natural populations is of central importance in evolutionary biology. Crosses between natural populations can result in heterosis if recessive or nearly recessive deleterious mutations have become fixed within populations because of genetic drift. Divergence between populations can also result in outbreeding depression because of genetic incompatibilities. The net fitness consequences of between-population crosses will be a balance between heterosis and outbreeding depression. We estimated the magnitude of heterosis and outbreeding depression in the highly selfing model plant Arabidopsis thaliana, by crossing replicate line pairs from two sets of natural populations (C↔R, B↔S) separated by similar geographic distances (Italy↔Sweden). We examined the contribution of different modes of gene action to overall differences in estimates of lifetime fitness and fitness components using joint scaling tests with parental, reciprocal F1 and F2, and backcross lines. One of these population pairs (C↔R) was previously demonstrated to be locally adapted, but locally maladaptive quantitative trait loci were also found, suggesting a role for genetic drift in shaping adaptive variation. We found markedly different genetic architectures for fitness and fitness components in the two sets of populations. In one (C↔R), there were consistently positive effects of dominance, indicating the masking of recessive or nearly recessive deleterious mutations that had become fixed by genetic drift. The other set (B↔S) exhibited outbreeding depression because of negative dominance effects. Additional studies are needed to explore the molecular genetic basis of heterosis and outbreeding depression, and how their magnitudes vary across environments.
Mitonuclear mismatch alters performance and reproductive success in naturally-introgressed populations of a montane leaf beetle
Coordination between nuclear and mitochondrial genomes is critical to metabolic processes underlying animals' ability to adapt to local environments, yet consequences of mitonuclear interactions have rarely been investigated in populations where individuals with divergent mitochondrial and nuclear genomes naturally interbreed. Genetic variation in the leaf beetle <i>Chrysomela aeneicollis</i> was assessed along a latitudinal thermal gradient in California's Sierra Nevada. Variation at mitochondrial <i>cytochrome oxidase II</i> (<i>COII</i>) and the nuclear gene <i>phosphoglucose isomerase</i> (<i>PGI</i>) shows concordance and was significantly greater along a 65 km transect than 10 other loci. STRUCTURE analyses using neutral loci identified a southern and northern subpopulation, which interbreed in the central drainage Bishop Creek. <i>COII</i> and <i>PGI</i> were used as indicators of mitochondrial and nuclear genetic variation in field and laboratory experiments conducted on beetles from this admixed population. Fecundity, larval development rate, running speed and male mating frequency were higher for beetles with geographically 'matched' than 'mismatched' mitonuclear genotypes. Effects of mitonuclear mismatch were largest for individuals with northern nuclear genotypes possessing southern mitochondria and were most pronounced after heat treatment or at high elevation. These findings suggest that mitonuclear incompatibility diminishes performance and reproductive success in nature, effects that could intensify at environmental extremes.
Data from: SNP-skimming: a fast approach to map loci generating quantitative variation in natural populations
Genome-wide association mapping (GWAS) is a method to estimate the contribution of segregating genetic loci to trait variation. A major challenge for applying GWAS to non-model species has been generating dense genome-wide markers that satisfy the key requirement that marker data is error-free. Here we present an approach to map loci within natural populations using inexpensive shallow genome sequencing. This 'SNP skimming' approach involves two steps: an initial genome-wide scan to identify putative targets followed by deep sequencing for confirmation of targeted loci. We apply our method to a test dataset of floral dimension variation in the plant Penstemon virgatus, a member of a genus that has experienced dynamic floral adaptation that reflects repeated transitions in primary pollinator. The ability to detect SNPs that generate phenotypic variation depends on population genetic factors such as population allele frequency, effect size, and epistasis as well as sampling effects contingent on missing data and genotype uncertainty. However, both simulations and the Penstemon data suggest that the most significant tests from the initial SNP skim are likely to be true positives – loci with subtle but significant quantitative effects on phenotype. We discuss the promise and limitations of this method and consider optimal experimental design for a given sequencing effort. Simulations demonstrate that sampling a larger number of individual at the expense of average read depth per individual maximizes the power to detect loci.
Data from: How populations differentiate despite gene flow: sexual and natural selection drive phenotypic divergence within a land fish, the Pacific leaping blenny
Background: Divergence between populations in reproductively important features is often vital for speciation. Many studies attempt to identify the cause of population differentiation in phenotype through the study of a specific selection pressure. Holistic studies that consider the interaction of several contrasting forms of selection are more rare. Most studies also fail to consider the history of connectivity among populations and the potential for genetic drift or gene flow to facilitate or limit phenotypic divergence. We examined the interacting effects of natural selection, sexual selection and the history of connectivity on phenotypic differentiation among five populations of the Pacific leaping blenny (Alticus arnoldorum), a land fish endemic to the island of Guam. Results: We found key differences among populations in two male ornaments—the size of a prominent head crest and conspicuousness of a coloured dorsal fin—that reflected a trade-off between the intensity of sexual selection (male biased sex ratios) and natural selection (exposure to predators). This differentiation in ornamentation has occurred despite evidence suggesting extensive gene flow among populations, which implies that the change in ornament expression has been recent (and potentially plastic). Conclusions: Our study provides an early snapshot of divergence in reproductively important features that, regardless of whether it reflects genetic or plastic changes in phenotype, could ultimately form a reproductive barrier among populations.
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.