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5,538 results for “Population data”
Data from: A high density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour
High density SNP microarrays ('SNP chips') are a rapid, accurate and efficient method for genotyping several hundred thousand polymorphisms in large numbers of individuals. While SNP chips are routinely used in human genetics and in animal and plant breeding, they are less widely used in evolutionary and ecological research. In this paper we describe the development and application of a high density Affymetrix Axiom chip with around 500 000 SNPs, designed to perform genomics studies of great tit (Parus major) populations. We demonstrate that the per-SNP genotype error rate is well below 1% and that the chip can also be used to identify structural or copy number variation (CNVs). The chip is used to explore the genetic architecture of exploration behaviour (EB), a personality trait that has been widely studied in great tits and other species. No SNPs reached genome-wide significance, including at DRD4, a candidate gene. However, EB is heritable and appears to have a polygenic architecture. Researchers developing similar SNP chips may note: (i) SNPs previously typed on alternative platforms are more likely to be converted to working assays, (ii) detecting SNPs by more than one pipeline, and in independent datasets, ensures a high proportion of working assays, (iii) allele frequency ascertainment bias is minimised by performing SNP discovery in individuals from multiple populations and (iv) samples with the lowest call rates tend to also have the greatest genotyping error rates.
Data from: A trait-based approach to predict population genetic structure in bees
Understanding population genetic structure is key to developing predictions about species susceptibility to environmental change, such as habitat fragmentation and climate change. It has been theorized that life-history traits may constrain some species in their dispersal and lead to greater signatures of population genetic structure. In this study, we use a quantitative comparative approach to assess if patterns of population genetic structure in bees are driven by three key species-level life-history traits: body size, sociality, and diet breadth. Specifically, we reviewed the current literature on bee population genetic structure, as measured by the differentiation indices Nei's GST, Hedrick's G`ST, and Jost's D. We then used phylogenetic generalised linear models to estimate the correlation between the evolution of these traits and patterns of genetic differentiation. Our analyses revealed a negative and significant effect of body size on genetic structure, regardless of differentiation index utilized. For Hedrick's G`ST and Jost's D, we also found a significant impact of sociality, where social species exhibited lower levels of differentiation than solitary species. We did not find an effect of diet specialization on population genetic structure. Overall, our results suggest that physical dispersal or other functions related to body size are among the most critical for mediating population structure for bees. We further highlight the importance of standardizing population genetic measures to more easily compare studies and to identify the most susceptible species to landscape and climatic changes.
Data from: Loci under selection during multiple range expansions of an invasive plant are mostly population-specific, but patterns are associated with climate
Identifying the genes underlying rapid evolutionary changes, describing their function and ascertaining the environmental pressures that determine fitness are the central elements needed for understanding of evolutionary processes and phenotypic changes that improve the fitness of populations. It has been hypothesized that rapid adaptive changes in new environments may contribute to the rapid spread and success of invasive plants and animals. As yet, studies of adaptation during invasion are scarce, as is knowledge of the genes underlying adaptation, especially in multiple replicated invasions. Here, we quantified how genotype frequencies change during invasions, resulting in rapid evolution of naturalized populations. We used six fully replicated common garden experiments in Brazil where Pinus taeda (loblolly pine) was introduced at the same time, in the same numbers, from the same seed sources, and has formed naturalized populations expanding outward from the plantations. We used a combination of nonparametric, population genetics and multivariate statistics to detect changes in genotype frequencies along each of the six naturalization gradients and their association with climate as well as shifts in allele frequencies compared to the source populations. Results show 25 genes with significant shifts in genotype frequencies. Six genes had shifts in more than one population. Climate explained 25% of the variation in the groups of genes under selection across all locations, but specific genes under strong selection during invasions did not show climate-related convergence. In conclusion, we detected rapid evolutionary changes during invasive range expansions, but the particular gene-level patterns of evolution may be population specific.
Data from: Contracting patterns of diversity and population differentiation at the innate immunity gene Toll-like receptor 2 (TLR2) in two sympatric rodent species
Comparing patterns of diversity and divergence between populations at immune genes and neutral markers can give insights into the nature and geographic scale of parasite-mediated selection. To date, studies investigating such patterns of selection in vertebrates have primarily focused on the acquired branch of the immune system, whereas it remains largely unknown how parasite-mediated selection shapes innate immune genes both within and across vertebrate populations. Here, we present a study on the diversity and population differentiation at the innate immune gene Toll-like receptor 2 (TLR2) across nine populations of yellow-necked mice (Apodemus flavicollis) and bank voles (Myodes glareolus) in southern Sweden. In yellow-necked mice, TLR2 diversity was very low, as was TLR2 population differentiation compared to neutral loci. In contrast, several TLR2 haplotypes co-occurred at intermediate frequencies within and across bank vole populations, and pronounced isolation by distance between populations was observed. The diversity and differentiation at neutral loci was similar in the two species. These results indicate that parasite-mediated selection has been acting in dramatically different ways on a given immune gene in ecologically similar and sympatric species. Furthermore, the finding of TLR2 population differentiation at a small geographical scale in bank voles highlights that vertebrate innate immune defence may be evolutionarily more dynamic than has previously been appreciated.
Data from: Evaluating population receptive field estimation frameworks in terms of robustness and reproducibility
Within vision research retinotopic mapping and the more general receptive field estimation approach constitute not only an active field of research in itself but also underlie a plethora of interesting applications. This necessitates not only good estimation of population receptive fields (pRFs) but also that these receptive fields are consistent across time rather than dynamically changing. It is therefore of interest to maximize the accuracy with which population receptive fields can be estimated in a functional magnetic resonance imaging (fMRI) setting. This, in turn, requires an adequate estimation framework providing the data for population receptive field mapping. More specifically, adequate decisions with regard to stimulus choice and mode of presentation need to be made. Additionally, it needs to be evaluated whether the stimulation protocol should entail mean luminance periods and whether it is advantageous to average the blood oxygenation level dependent (BOLD) signal across stimulus cycles or not. By systematically studying the effects of these decisions on pRF estimates in an empirical as well as simulation setting we come to the conclusion that a bar stimulus presented at random positions and interspersed with mean luminance periods is generally most favorable. Finally, using this optimal estimation framework we furthermore tested the assumption of temporal consistency of population receptive fields. We show that the estimation of pRFs from two temporally separated sessions leads to highly similar pRF parameters.
Data from: Conservation action based on threatened species capture taxonomic and phylogenetic richness in breeding and wintering populations of Central Asian birds
Although phylogenetic diversity has been suggested to be relevant from a conservation point of view, its role is still limited in applied nature conservation. Recently, the practice of investing conservation resources based on threatened species was identified as a reason for the slow integration of phylogenetic diversity in nature conservation planning. One of the main arguments is based on the observation that threatened species are not evenly distributed over the phylogenetic tree. However this argument seems to dismiss the fact that conservation action is a spatially explicit process, and even if threatened species are not evenly distributed over the phylogenetic tree, the occurrence of threatened species could still indicate areas with above average phylogenetic diversity and consequently could protect phylogenetic diversity. Here we aim to study the selection of important bird areas in Central Asia, which were nominated largely based on the presence of threatened bird species. We show that although threatened species occurring in Central Asia do not capture phylogenetically more distinct species than expected by chance, the current spatially explicit conservation approach of selecting important bird areas covers above average taxonomic and phylogenetic diversity of breeding and wintering birds. We conclude that the spatially explicit processes of conservation actions need to be considered in the current discussion of whether new prioritization methods are needed to complement conservation action based on threatened species.
Data from: Species delimitation with gene flow: a methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs
Accurately delimiting species boundaries is a non-trivial undertaking that can have significant effects on downstream inferences. We compared the efficacy of commonly-used species delimitation methods (SDMs) and a population genomics approach based on genome-wide single nucleotide polymorphisms (SNPs) to assess lineage separation in the Malaysian Torrent Frog Complex currently recognized as a single species (Amolops larutensis). First, we used morphological, mitochondrial DNA and genome-wide SNPs to identify putative species boundaries by implementing non-coalescent and coalescent-based SDMs (mPTP, iBPP, BFD*). We then tested the validity of putative boundaries by estimating spatiotemporal gene flow (fastsimcoal2, ABBA-BABA) to assess the extent of genetic isolation among putative species. Our results show that the A. larutensis complex runs the gamut of the speciation continuum from highly divergent, genetically isolated lineages (mean Fst = 0.9) to differentiating populations involving recent gene flow (mean Fst = 0.05; Nm > 5). As expected, SDMs were effective at delimiting divergent lineages in the absence of gene flow but overestimated species in the presence of marked population structure and gene flow. However, using a population genomics approach and the concept of species as separately evolving metapopulation lineages as the only necessary property of a species, we were able to objectively elucidate cryptic species boundaries in the presence of past and present gene flow. This study does not discount the utility of SDMs but highlights the danger of violating model assumptions and the importance of carefully considering methods that appropriately fit the diversification history of a particular system.
Data from: Geographical variation in species' population responses to changes in temperature and precipitation
Despite increasing concerns about the vulnerability of species' populations to climate change, there has been little overall synthesis of how individual population responses to variation in climate differ between taxa, with trophic level or geographically. To address this, we extracted data from 132 long-term (≥20 years) studies of population responses to temperature and precipitation covering 236 animal and plant species across terrestrial and freshwater habitats. Temperature tended to have a greater overall impact on populations than precipitation, although the effects of increased precipitation varied strongly with latitude, being most positive at low latitudes. Population responses to increased temperature were generally positive, but did not vary significantly with latitude. Studies reporting significant climatic trends through time tended to show more negative effects of temperature and more positive effects of precipitation upon populations than other studies. Our results identify likely geographical differences in the effects of climate change on populations and communities. Most studies of climate change impacts on biodiversity have focussed on temperature and are from middle to high northern latitudes; our results suggest their findings may be less applicable to low latitudes, where most species occur and where variation in precipitation under climate change may be more important in determining demographic responses.
Data from: Let's stay together? Intrinsic and extrinsic factors involved in pair bond dissolution in a recolonizing wolf population
For socially monogamous species, breeder bond dissolution has important consequences for population dynamics, but the extent to which extrinsic or intrinsic population factors causes pair dissolution remain poorly understood, especially among carnivores. Using an extensive life-history data set, a survival analysis and competing risks framework, we examined the fate of 153 different wolf (Canis lupus) pairs in the recolonizing Scandinavian wolf population, during 14 winters of snow tracking and DNA monitoring. Wolf pair dissolution was generally linked to a mortality event and was strongly affected by extrinsic (i.e. anthropogenic) causes. No divorce was observed, and among the pair dissolution where causes have been identified, death of one or both wolves was always involved. Median time from pair formation to pair dissolution was three consecutive winters (i.e. approximately 2 years). Pair dissolution was mostly human-related, primarily caused by legal control actions (36·7%), verified poaching (9·2%) and traffic-related causes (2·1%). Intrinsic factors, such as disease and age, accounted for only 7·7% of pair dissolutions. The remaining 44·3% of dissolution events were from unknown causes, but we argue that a large portion could be explained by an additional source of human-caused mortality, cryptic poaching. Extrinsic population factors, such as variables describing the geographical location of the pair, had a stronger effect on risk of pair dissolution compared to anthropogenic landscape characteristics. Population intrinsic factors, such as the inbreeding coefficient of the male pair member, had a negative effect on pair bond duration. The mechanism behind this result remains unknown, but might be explained by lower survival of inbred males or more complex inbreeding effects mediated by behaviour. Our study provides quantitative estimates of breeder bond duration in a social carnivore and highlights the effect of extrinsic (i.e. anthropogenic) and intrinsic factors (i.e. inbreeding) involved in wolf pair bond duration. Unlike the effects of intrinsic and extrinsic factors that are commonly reported on individual survival or population growth, here we provide quantitative estimates of their potential effect on the social unit of the population, the wolf pair.
Data from: Targeted agri-environment schemes significantly improve the population size of common farmland bumblebee species
Changes in agricultural practice across Europe and North America have been associated with range contractions and local extinction of bumblebees (Bombus spp.). A number of agri-environment schemes have been implemented to halt and reverse these declines, predominantly revolving around the provision of additional forage plants. Although it has been demonstrated that these schemes can attract substantial numbers of foraging bumblebees, it remains unclear to what extent they actually increase bumblebee populations. We used standardized transect walks and molecular techniques to compare the size of bumblebee populations between Higher Level Stewardship (HLS) farms implementing pollinator-friendly schemes and Entry Level Stewardship (ELS) control farms. Bumblebee abundance on the transect walks was significantly higher on HLS farms than ELS farms. Molecular analysis suggested maximum foraging ranges of 566 m for Bombus hortorum, 714 m for B. lapidarius, 363 m for B. pascuorum and 799 m for B. terrestris. Substantial differences in maximum foraging range were found within bumblebee species between farm types. Accounting for foraging range differences, B. hortorum (47 vs 13 nests/km2) and B. lapidarius (45 vs 22 nests/km2) were found to nest at significantly greater densities on HLS farms than ELS farms. There were no significant differences between farm type for B. terrestris (88 vs 38 nests/km2) and B. pascuorum (32 vs 39 nests/km2). Across all bumblebee species, HLS management had a significantly positive effect on bumblebee nest density. These results show that targeted agri-environment schemes that increase the availability of suitable forage can significantly increase the size of wild bumblebee populations.
Data from: Large-scale parentage analysis reveals reproductive patterns and heritability of spawn timing in a hatchery population of steelhead (Oncorhynchus mykiss)
Understanding life history traits is an important first step in formulating effective conservation and management strategies. The use of artificial propagation and supplementation as such a strategy can have numerous effects on the supplemented natural populations and minimizing life history divergence is crucial in minimizing these effects. Here, we use single nucleotide polymorphism (SNP) genotypes for large-scale parentage analysis and pedigree reconstruction in a hatchery population of steelhead, the anadromous form of rainbow trout. Nearly complete sampling of the broodstock for several consecutive years in two hatchery programmes allowed inference about multiple aspects of life history. Reconstruction of cohort age distribution revealed a strong component of fish that spawn at 2 years of age, in contrast to programme goals and distinct from naturally spawning steelhead in the region, which raises a significant conservation concern. The first estimates of variance in family size for steelhead in this region can be used to calculate effective population size and probabilities of inbreeding, and estimation of iteroparity rate indicates that it is reduced by hatchery production. Finally, correlations between family members in the day of spawning revealed for the first time a strongly heritable component to this important life history trait in steelhead and demonstrated the potential for selection to alter life history traits rapidly in response to changes in environmental conditions. Taken together, these results demonstrate the extraordinary promise of SNP-based pedigree reconstruction for providing biological inference in high-fecundity organisms that is not easily achievable with traditional physical tags.
Data from: Adaptation to local climate in a multi-trait space: evidence from silver fir (Abies alba Mill.) populations across a heterogeneous environment
Heterogeneous environments, such as mountainous landscapes, create spatially varying selection pressure that potentially affects several traits simultaneously across different life stages, yet little is known about the general patterns and drivers of adaptation in such complex settings. We studied silver fir (Abies alba Mill.) populations across Switzerland and characterized their mountainous landscape using downscaled historical climate data. We sampled 387 trees from 19 populations and genotyped them at 374 single-nucleotide polymorphisms (SNPs) to estimate their demographic distances. Seedling morphology, growth and phenology traits were recorded in a common garden, and a proxy for water use efficiency was estimated for adult trees. We tested whether populations have more strongly diverged at quantitative traits than expected based on genetic drift alone in a multi-trait framework, and identified potential environmental drivers of selection. We found two main responses to selection: (i) populations from warmer and more thermally stable locations have evolved towards a taller stature, and (ii) the growth timing of populations evolved towards two extreme strategies, "start early and grow slowly" or "start late and grow fast", driven by precipitation seasonality. Populations following the "start early and grow slowly" strategy had higher water use efficiency and came from inner Alpine valleys characterized by pronounced summer droughts. Our results suggest that contrasting adaptive life-history strategies exist in silver fir across different life stages (seedling to adult), and that some of the characterized populations may provide suitable seed sources for tree growth under future climatic conditions.
Data from: Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline
This study presents genetic evidence that whale sharks, Rhincodon typus, are comprised of at least two populations that rarely mix and is the first to document a population expansion. Relatively high genetic structure is found when comparing sharks from the Gulf of Mexico with sharks from the Indo-Pacific. If mixing occurs between the Indian and Atlantic Oceans, it is not sufficient to counter genetic drift. This suggests whale sharks are not all part of a single global meta-population. The significant population expansion we found was indicated by both microsatellite and mitochondrial DNA. The expansion likely happened during the Holocene, when tropical species could expand their range due to sea level rise eliminating dispersal barriers. However, the historic trend of population increase may have reversed recently. Declines in genetic diversity are found for 6 consecutive years at Ningaloo Reef in Australia. The declines in genetic diversity being seen now are likely due to commercial-scale harvesting of whale sharks and collision with boats in past decades in other countries in the Indo-Pacific. Whale shark hunting is banned in Australia but continues in other countries despite bans in places like China. The study findings have implications for models of population connectivity for whale sharks and advocate for continued focus on effective protection of the world's largest fish at multiple spatial scales.
Data from: Contrasting patterns of phenotype-dependent parasitism within and among populations of threespine stickleback
Variation in infection rate arises from variation in host exposure and resistance to parasites both within and among populations. All things being equal, phenotypes that increase exposure risk should covary positively with infection among individuals. It might therefore be expected that populations with mean phenotypes that increase exposure might also have higher rates of infection. However, such positive covariance between exposure and infection at the population level might be undermined by other factors such as geographic variation in parasite abundance or host resistance, negating or reversing in between-population comparisons. We studied rates of infection of two parasites among 18 populations of threespine stickleback (Gasterosteus aculeatus). As predicted, within populations, trophic morphology covaries with infection of two trophically transmitted parasites: individuals with benthic (or limnetic) phenotypes were more likely to be infected with a benthic (or limnetic) parasite. However, across populations, the relationship between morphology and infection rate was absent (limnetic parasite) or reversed (benthic parasite). Our results confirm the importance of phenotype-dependent exposure, but stress different factors or processes, such as the evolution of reduced susceptibility, might shape variation in infection at larger spatial scales.
Data from: Spatial patterns of neutral and functional genetic variation reveal patterns of local adaptation in raccoon (Procyon lotor) populations exposed to raccoon rabies
Local adaptation is necessary for population survival and depends on the interplay between responses to selective forces and demographic processes that introduce or retain adaptive and maladaptive attributes. Host-parasite systems are dynamic, varying in space and time, where both host and parasites must adapt to their ever-changing environment in order to survive. We investigated patterns of local adaptation in raccoon populations with varying temporal exposure to the raccoon rabies virus (RRV). RRV infects approximately 85% of the population when epizootic and has been presumed to be completely lethal once contracted; however, disease challenge experiments and varying spatial patterns of RRV spread suggest some level of immunity may exist. We first assessed patterns of local adaptation in raccoon populations along the eastern seaboard of North America by contrasting spatial patterns of neutral (microsatellite loci) and functional, major histocompatibility complex (MHC) genetic diversity and structure. We explored variation of MHC allele frequencies in light of temporal population exposure to RRV (0-60 years) and specific RRV strains in infected raccoons. Our results revealed high levels of MHC variation (66 DRB exon 2 alleles) and pronounced genetic structure relative to neutral microsatellite loci, indicative of local adaptation. We found a positive association linking MHC genetic diversity and temporal RRV exposure, but no association with susceptibility and resistance to RRV strains. These results have implications for landscape epidemiology studies seeking to predict the spread of RRV and present an example of how population demographics influence the degree to which populations adapt to local selective pressures.
Data from: Comparison of population genetic patterns in two widespread freshwater mussels with contrasting life histories in western North America
We investigate population genetic structuring in Margaritifera falcata, a freshwater mussel native to western North America, across the majority of its geographical range. We find shallow rangewide genetic structure, strong population-level structuring and very low population diversity in this species, using both mitochondrial sequence and nuclear microsatellite data. We contrast these patterns with previous findings in another freshwater mussel species group (Anodonta californiensis/A. nuttalliana) occupying the same continental region and many of the same watersheds. We conclude that differences are likely caused by contrasting life history attributes between genera, particularly host fish requirements and hermaphroditism. Further, we demonstrate the occurrence of a 'hotspot' for genetic diversity in both groups of mussels, occurring in the vicinity of the lower Columbia River drainage. We suggest that stream hierarchy may be responsible for this pattern and may produce similar patterns in other widespread freshwater species.
Data from: Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds
Recombination rate is heterogeneous across the genome of various species, and so are genetic diversity and differentiation as a consequence of linked selection. However, we still lack a clear picture of the underlying mechanisms for regulating recombination. Here we estimated fine-scale population recombination rate based on the patterns of linkage disequilibrium (LD) across the genomes of multiple populations of two closely related flycatcher species (Ficedula albicollis and F. hypoleuca). This revealed an overall conservation of the recombination landscape between these species at the scale of 200-kb, but we also identified differences in the local rate of recombination despite their recent divergence (<1 million years). Genetic diversity and differentiation were associated with recombination rate in a lineage-specific manner, indicating differences in the extent of linked selection between species. We detected 400-3,085 recombination hotspots per population. Location of hotspots was conserved between species, but the intensity of hotspot activity varied between species. Recombination hotspots were primarily associated with CpG islands (CGIs), regardless of whether CGIs were at promoter regions or away from genes. Recombination hotspots were also associated with specific transposable elements (TEs), but this association appears indirect due to shared preferences of the transposition machinery and the recombination machinery for accessible open chromatin regions. Our results suggest that CGIs are a major determinant of the localization of recombination hotspots, and we propose that both the distribution of TEs and fine-scale variation in recombination rate may be associated with the evolution of the epigenetic landscape.
Data from: Mature male parr contribution to the effective size of an anadromous Atlantic salmon (Salmo salar) population over 30 years
We describe temporal changes in the genetic composition of a small anadromous Atlantic salmon (Salmo salar) population from South Newfoundland, an area where salmon populations are considered threatened (COSEWIC 2010). We examined the genetic variability (13 microsatellite loci) in 869 out-migrating smolt and post-spawning kelt samples, collected from 1985 to 2011 for a total of 22 annual collections and a 30 year span of assigned cohorts. We estimated the annual effective number of breeders (Nb) and the generational effective population size (Ne) through genetic methods and demographically using the adult sex ratio. Comparisons between genetic and demographic estimates show that the adult spawners inadequately explain the observed Ne estimates, suggesting that mature male parr are significantly increasing Nb and Ne over the study period. Spawning as parr appears to be a viable and important strategy in the near absence of adult males.
Data from: Migratory divides and their consequences for dispersal, population size and parasite-host interactions
Populations of migratory birds differ in their direction of migration with neighboring populations often migrating in divergent directions separated by migratory divides. A total of 26% of 103 passerine bird species in Europe had migratory divides that were located disproportionately often along a longitudinal gradient in Central Europe, consistent with the assumption of a Quaternary glacial origin of such divides in the Iberian and Balkan peninsulas followed by re-colonization. Given that studies have shown significant genetic differentiation and reduced gene flow across migratory divides we hypothesized that an absence of migratory divides would result in elevated rates of gene flow and hence a reduced level of local adaptation. In a comparative study, species with migratory divides had larger population sizes and population densities and longer dispersal distances than species without migratory divides. Species with migratory divides tended to be habitat generalists. Bird species with migratory divides had higher richness of blood parasites and higher growth rates of Staphylococcus on their eggs during the incubation period. There was weaker cell-mediated immunity in adults and stronger cell lysis in species with migratory divides. These findings may suggest that migratory divides constitute barriers to dispersal with consequences for ecology and evolution of distributions, population sizes, habitats, and parasite-host interactions. They also suggest that migratory divides may play a role in local adaptation in host-parasite interactions.
Data from: Tracking the history and ecological changes of rising double-crested cormorant populations using pond sediments from islands in eastern Lake Ontario
In the Laurentian Great Lakes region, the double-crested cormorant (Phalacrocorax auritus) has seen a thousand-fold population increase in recent decades. These large colonies of birds now often conflict with socioeconomic interests, particularly due to perceived competition with fisheries and the destruction of terrestrial vegetation in nesting habitats. Here we use dated sediment cores from ponds on islands in eastern Lake Ontario that receive waste inputs from dense colonies of cormorants and ring-billed gulls (Larus delawarensis) to chronicle the population rise of these species and assess their long-term ecological impacts. Modern water chemistry sampling from these sites reveals drastically elevated nutrient and major ion concentrations compared to reference ponds not influenced by waterbirds. Geochemical tracers in dated sediment cores, particularly δ15N and chlorophyll-a concentrations, track waterbird influences over time. Fossil diatom assemblages were dominated by species tolerant of hyper-eutrophic and polluted systems, which is in marked contrast to assemblages in reference sites. In addition to establishing long-term ecological impacts, this multi-proxy paleoecological approach can be used to determine whether islands of concern have been long-term nesting sites or were only recently colonized by cormorant or ring-billed gull populations across the Great Lakes, facilitating informed management decisions about controversial culling programs.
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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.