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1,659 results for “structured population”
Data from: Effects of brooding and broadcasting reproductive modes on the population genetic structure of two Antarctic gastropod molluscs
Life-history characteristics exert a profound influence upon the population structure of many marine organisms. However, relatively few genetic studies have compared direct with indirect-developing species in the same ecosystem or geographic region, and none to our knowledge within an Antarctic setting. To address this issue we have collected novel Amplified Fragment Length Polymorphism (AFLP) data from the direct-developing top shell Margarella antarctica to form a comparison with previously published data for the broadcast-spawning Antarctic limpet Nacella concinna. We scored 270 loci in 240 M. antarctica individuals sampled from five populations spanning the full length of the Antarctic Peninsula. Profound differences were identified in the strength and pattern of population structure between the two species, consistent with gene flow being highly restricted in M. antarctica relative to N. concinna.
Data from: Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing
Sweet potato, Ipomoea batatas (L.) Lam., is an important food crop that is cultivated worldwide. However, no genome-wide assessment of the genetic diversity of sweet potato has been reported to date. In the present study, the population structure and genetic diversity of 197 sweet potato accessions most of which were from China were assessed using 62,363 SNPs. A model-based structure analysis divided the accessions into three groups: group 1, group 2 and group 3. The genetic relationships among the accessions were evaluated using a phylogenetic tree, which clustered all the accessions into three major groups. A principal component analysis (PCA) showed that the accessions were distributed according to their population structure. The mean genetic distance among accessions ranged from 0.290 for group 1 to 0.311 for group 3, and the mean polymorphic information content (PIC) ranged from 0.232 for group 1 to 0.251 for group 3. The mean minor allele frequency (MAF) ranged from 0.207 for group 1 to 0.222 for group 3. Analysis of molecular variance (AMOVA) showed that the maximum diversity was within accessions (89.569%). Using CoreHunter software, a core set of 39 accessions was obtained, which accounted for approximately 19.8% of the total collection. The core germplasm set of sweet potato developed will be a valuable resource for future sweet potato improvement strategies.
Data from: Using DNA metabarcoding for simultaneous inference of common vampire bat diet and population structure
Metabarcoding diet analysis has become a valuable tool in animal ecology; however, co-amplified predator sequences are not generally used for anything other than to validate predator identity. Exemplified by the common vampire bat we demonstrate the use of metabarcoding to infer predator population structure alongside diet assessments. Growing populations of common vampire bats impact human, livestock and wildlife health in Latin America through transmission of pathogens, such as lethal rabies infections. Techniques to determine large scale variation in vampire bat diet and bat population structure would empower locality- and species-specific projections of disease transmission risks. However, previously used methods are not cost-effective and efficient for large scale applications. Using blood meal and faecal samples from common vampire bats from coastal, Andean and Amazonian regions of Peru, we showcase metabarcoding as a scalable tool to assess vampire bat population structure and feeding preferences. Dietary metabarcoding was highly effective, detecting vertebrate prey in 93.2% of the samples. Bats predominantly preyed on domestic animals, but fed on tapirs at one Amazonian site. In addition, we identified arthropods in 9.3% of samples, likely reflecting consumption of ectoparasites. Using the same data, we document mitochondrial geographic population structure in the common vampire bat in Peru. Such simultaneous inference of vampire bat diet and population structure can enable new insights into the interplay between vampire bat ecology and disease transmission risks. Importantly, the methodology can be extrapolated to metabarcoding diet studies of other animals to couple information on diet and population structure.
Data from: Network-scale effects of invasive species on spatially-structured amphibian populations
<p>Understanding the factors affecting the dynamics of spatially-structured populations (SSP) is a central topic of conservation and landscape ecology. Invasive alien species are increasingly important drivers of the dynamics of native species. However, the impacts of invasives are often assessed at the patch scale, while their effects on SSP dynamics are rarely considered. We used long-term abundance data to test whether the impact of invasive crayfish on subpopulations can also affect the whole SSP dynamics, through their influence on source populations. From 2010 to 2018, we surveyed a network of 58 ponds and recorded the abundance of Italian agile frog clutches, the occurrence of an invasive crayfish, and environmental features. Using Bayesian hierarchical models, we assessed relationships between frog abundance in ponds and a) environmental features; b) connectivity within the SSP; c) occurrence of invasive species at both the patch- and the SSP-levels. If spatial relationships between ponds were overlooked, we did not detect effects of crayfish presence on frog abundance or trends. When we jointly considered habitat, subpopulation, and SSP features, processes acting at all these levels affected frog abundance. At the subpopulation scale, frog abundance in a year was related to habitat features, but was unrelated to crayfish occurrence at that site during the previous year. However, when we considered the SSP level, we found a strong negative relationship between frog abundance in a given site and crayfish frequency in surrounding wetlands during the previous year. Hence, SSP-level analyses can identify effects that would remain unnoticed when focussing on single patches. Invasive species can affect population dynamics even in not invaded patches, through the degradation of subpopulation networks. Patch-scale assessments of the impact of invasive species can thus be insufficient: predicting the long-term interplay between invasive and native populations requires landscape-level approaches accounting for the complexity of spatial interactions.</p>
Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas)
Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies to evaluate the genetic health of the exploited populations. The present work is based on a set of 10 nuclear markers amplified in 331 individuals from 10 different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and showed a large and stable historical effective size instead. This result could be accounted for by specific life history traits (reproduction and longevity) and the limitations of molecular markers in covering very recent timescales for non temporal samples. Our study emphasizes the necessity of integrating information on effective population sizes and life history parameters when evaluating population connectivity levels from genetic data.
Data from: Resolving patterns of population genetic and phylogeographic structure to inform control and eradication initiatives for brown rats Rattus norvegicus on South Georgia
The control and eradication of invasive species is a common management strategy to protect or restore native biodiversity. On South Georgia in the Southern Ocean, the brown rat Rattus norvegicus was brought onto the island with the onset of whaling and sealing activity in the 1800s and has had a significant detrimental impact on key bird species of conservation concern. Efforts to eradicate rats from South Georgia using poisoned bait are ongoing. Despite the South Georgia rat eradication programme being the geographically largest and most ambitious eradication initiative to date, its success is facilitated by the potential that rat populations are effectively isolated by glacial barriers. This allows for localized eradication effort at manageable scales, leading to sequential eradication of individual populations with minimal risk of incursion from neighbouring areas. Here, we use the levels of population genetic divergence estimated from 299 single nucleotide polymorphism (SNP) loci and DNA sequence variation across 993 base pairs of the mitochondrial DNA cytochrome B locus to examine whether rat populations from nine glacially isolated areas on South Georgia are genetically distinct and so can be treated as independent eradication units. Bayesian clustering of individuals based on SNP similarity identified seven different genetic groups, which were confirmed using analyses based on pairwise genetic distance estimates and ordination of individuals using principal coordinate analysis. From a management perspective, these seven groups represent individual targets in baiting operations. Two mtDNA haplotypes were resolved across South Georgia, with a distinct geographical separation between the north-western and south-eastern populations. Approximate Bayesian computation (ABC) was used to identify that this divergence was a consequence of two separate historical colonization events. Synthesis and applications. We illustrate that molecular markers are a valuable tool in species management and pest eradication given that the spatial distribution of genetic diversity can: (i) identify demographically and genetically independent populations on which local eradication effort can be focussed, (ii) distinguish between incomplete eradication and immigration in situations where individuals remain after eradication has been attempted and (iii) identify the source of migrants when dispersal occurs over large spatial scales.
Population structure, landscape genomics, and genetic signatures of adaptation to exotic disease pressure in Cornus florida L. – insights from GWAS and GBS data
<p>Understanding the consequences of exotic diseases on native forests is important to evolutionary ecology and conservation biology because exotic pathogens have drastically altered US eastern deciduous forests. Cornus florida L. (flowering dogwood tree) is one such species facing heavy mortality. Characterizing the genetic structure of C. florida populations and identifying the genetic signature of adaptation to dogwood anthracnose (an exotic pathogen responsible for high mortality) remains vital for conservation efforts. By integrating genetic data from genotype-by-sequencing (GBS) of 289 trees across the host species range and distribution of disease, we evaluated the spatial patterns of genetic variation and population genetic structure of C. florida and compared the pattern to the distribution of dogwood anthracnose. Using GWAS and gradient forest analysis, we identified genetic loci under selection and associated with ecological and diseased regions. The results revealed signals of weak genetic differentiation of three or more subgroups nested within two clusters—explaining up to 2-6% of genetic variation. The groups largely corresponded to the regions within and outside the eastern Hot-Continental ecoregion, which also overlapped with areas within and outside the main distribution of dogwood anthracnose. The fungal sequences contained in the GBS data of sampled trees bolstered visual records of disease at sampled locations and were congruent with the reported range of D. destructiva, suggesting fungal sequences within host genomic data were informative for detecting or predicting disease. The genetic diversity between populations at diseased vs. disease-free sites across the range of C. florida showed no significant difference. We identified 72 SNPs from 68 loci putatively under selection, some of which exhibited abrupt turnover in allele frequencies along the borders of the Hot-Continental ecoregion and the range of dogwood anthracnose. One such candidate SNP was independently identified in two prior studies as a possible L-type lectin-domain containing receptor kinase. While diseased and disease-free areas do not significantly differ in genetic diversity, overall there are slight trends to indicate marginally smaller amounts of genetic diversity in disease-affected areas. Our results were congruent with previous studies that were based on a limited number of genetic markers in revealing high genetic variation and weak population structure in C. florida.</p>
Data from: Does population structure predict the rate of speciation? A comparative test across Australia's most diverse vertebrate radiation
Population divergence is the first step in allopatric speciation, as has long been recognized in both theoretical models of speciation and empirical explorations of natural systems. All else being equal, lineages with substantial population differentiation should form new species more quickly than lineages that maintain range-wide genetic cohesion through high levels of gene flow. However, there have been few direct tests of the extent to which population differentiation predicts speciation rates as measured on phylogenetic trees. Here, we explicitly test the links between organismal traits, population-level processes, and phylogenetic speciation rates across a diverse clade of Australian lizards that shows remarkable variation in speciation rate. Using genome-wide ddRAD data from 892 individuals, we generated a comparative dataset on isolation-by-distance and population differentiation across 104 putative species-level lineages (OTUs). We find that species show substantial variation in the extent of population differentiation, and this variation is predicted by organismal traits that are thought to be proxies for dispersal and deme size. However, variation in population structure does not predict variation in speciation rate. Our results suggest that population differentiation is not the rate-limiting step in species formation and that other ecological and historical factors are primary determinants of speciation rates at macroevolutionary scales.
Data from: Comparing direct and indirect selfing rate estimates: when are population-structure estimates reliable?
The rate of self-fertilization (that is, selfing) is a key evolutionary parameter in hermaphroditic species, yet obtaining accurate estimates of selfing rates in natural populations can be technically challenging. Most published estimates are derived from population-level heterozygote deficiency (that is, FIS) or identity disequilibria (for example, the software RMES (robust multilocus estimate of selfing)). These indirect methods can be applied to population genetic survey data, whereas direct methods using progeny arrays require much larger data sets that are often difficult to collect in natural populations or even require captive breeding. Unfortunately, indirect methods rely on assumptions that can be problematic, such as negating biparental inbreeding, inbreeding disequilibrium and (for FIS) the presence of null alleles. The performance of indirect estimates against progeny-array estimates is still largely unknown. Here we used both direct progeny-array and indirect population-level methods to estimate the selfing rate in a single natural population of the simultaneously hermaphroditic freshwater snail Radix balthica throughout its reproductive lifespan using 10 highly polymorphic microsatellites. We found that even though progeny arrays (n=1034 field-collected embryos from 60 families) did not reveal a single selfed embryo, FIS-based selfing rates (n=316 adults) were significantly positive in all 6 sequential population samples. Including a locus with a high frequency of null alleles further biased FIS-based estimates. Conversely, RMES-based estimates were very similar to progeny-array estimates and proved insensitive to null alleles. The assumptions made by RMES were thus either met or irrelevant in this particular population, making RMES a valid, cost-efficient alternative to progeny arrays.
Data from: Genetic structure in a dynamic baboon hybrid zone corroborates behavioral observations in a hybrid population
Behavior and genetic structure are intimately related: mating patterns and patterns of movement between groups or populations influence the movement of genetic variation across the landscape and from one generation to the next. In hybrid zones, the behavior of the hybridizing taxa can also have an important impact on the incidence and outcome of hybridization events. Hybridization between yellow baboons and anubis baboons has been well-documented in the Amboseli basin of Kenya, where more anubis-like individuals tend to experience maturational and reproductive advantages. However, it is unknown whether these advantages are reflected in the genetic structure of populations surrounding this area. Here, we used nuclear microsatellite genotype data to evaluate the geographic structure and composition of baboon populations in southern Kenya, up to the border of Tanzania. Our results indicate that, unlike for mitochondrial DNA, microsatellite-based measures of genetic structure are in concordance with phenotypically based taxonomic distinctions, and that the currently active hybrid zone is relatively narrow. Interestingly, isolation with migration analysis revealed asymmetric gene flow in this region from anubis populations into yellow populations, in support of the anubis-biased phenotypic advantages observed in Amboseli. Populations that are primarily yellow but that are the recipients of anubis gene flow exhibit higher levels of genetic diversity than yellow populations far from the introgression front. Our results support previous work that indicates a long history of hybridization and male-mediated genetic introgression among East African baboons. In particular, it suggests that anubis baboons are in the process of gradual range expansion into the historic range of yellow baboon populations, a pattern that could be mechanistically explained by behavioral and life history advantages that correlate with anubis ancestry.
Data from: Ecology and life history affect different aspects of the population structure of 27 high-alpine plants
A plant species' genetic population structure is the result of a complex combination of its life history, ecological preferences, position in the ecosystem, and historical factors. As a result, many different statistical methods exist that measure different aspects of species' genetic structure. However, little is known about how these methods are interrelated and how they are related to a species' ecology and life history. In this study, we used the IntraBioDiv AFLP-dataset from 27 high-alpine species to calculate eight genetic summary statistics that we jointly correlate to a set of six ecological and life-history traits. We found that there is a large amount of redundancy among the calculated summary statistics and that there is a significant association with the matrix of species traits. In a multivariate analysis, two main aspects of population structure were visible among the 27 species. The first aspect is related to the species' dispersal capacities and the second is most likely related to the species' postglacial recolonisation of the Alps. Furthermore, we found that some summary statistics, most importantly Mantel's r and Jost's D, show different behaviour than expected based on theory. We therefore advise caution in drawing too strong conclusions from these statistics.
Data from: ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America
Recently evolved species typically share genetic variation across their genomes due to incomplete lineage sorting and/or ongoing gene flow. Given only subtle allele frequency differences at most loci and the expectation that divergent selection may affect only a tiny fraction of the genome, distinguishing closely related species based on multi‐locus data requires substantial genomic coverage. In this study, we used ddRAD‐seq to sample the genomes of five recently diverged, New World "mallards" (Anas spp.), a group of dabbling duck species characterized by diagnosable phenotypic differences but minimal genetic differentiation. With increased genomic sampling, we aimed to characterize population structure within this group and identify genomic regions that may have experienced divergent selection during speciation. We analyzed 3,017 autosomal ddRAD‐seq loci and 177 loci from the Z‐chromosome. In contrast to previous studies, the ddRAD‐seq data were sufficient to assign individuals to their respective species or subspecies and to generate estimates of gene flow in a phylogenetic framework. We find limited evidence of contemporary gene flow between the dichromatic mallard and several monochromatic taxa, but find evidence for historical gene flow between some monochromatic species pairs. We conclude that the overall genetic similarity of these taxa likely reflects retained ancestral polymorphism rather than recent and extensive gene flow. Thus, despite recurring cases of hybridization in this group, our results challenge the current dogma predicting the genetic extinction of the New World monochromatic dabbling ducks via introgressive hybridization with mallards. Moreover, ddRAD‐seq data were sufficient to identify previously unknown outlier regions across the Z‐chromosome and several autosomal chromosomes, regions that may have been involved in the diversification of species in this recent radiation.
Data from: The program STRUCTURE does not reliably recover the correct population structure when sampling is uneven: sub-sampling and new estimators alleviate the problem
Inferences of population structure and more precisely the identification of genetically homogeneous groups of individuals are essential to the fields of ecology, evolutionary biology, and conservation biology. Such population structure inferences are routinely investigated via the program STRUCTURE implementing a Bayesian algorithm to identify groups of individuals at Hardy-Weinberg and linkage equilibrium. While the method is performing relatively well under various population models with even sampling between subpopulations, the robustness of the method to uneven sample size between subpopulations and/or hierarchical levels of population structure has not yet been tested despite being commonly encountered in empirical datasets. In this study, I used simulated and empirical microsatellite datasets to investigate the impact of uneven sample size between subpopulations and/or hierarchical levels of population structure on the detected population structure. The results demonstrated that uneven sampling often leads to wrong inferences on hierarchical structure and downward biased estimates of the true number of subpopulations. Distinct subpopulations with reduced sampling tended to be merged together, whilst at the same time, individuals from extensively sampled subpopulations were generally split, despite belonging to the same panmictic population. Four new supervised methods to detect the number of clusters were developed and tested as part of this study and were found to outperform the existing methods using both evenly and unevenly sampled datasets. Additionally, a sub-sampling strategy aiming to reduce sampling unevenness between subpopulations is presented and tested. These results altogether demonstrate that when sampling evenness is accounted for, the detection of the correct population structure is greatly improved.
Data from: Genetic structure in a fragmented Northern Hemisphere rainforest: large effective sizes and high connectivity among populations of the epiphytic lichen Lobaria pulmonaria
An extraordinary diversity of epiphytic lichens is found in the boreal rainforest of central Norway, the highest-latitude rainforest in the world. These rainforest relicts are located in ravine systems, and clear cutting has increased the distance between remaining patches. We hypothesized that the relatively small lichen populations in the remaining forest stands have suffered a depletion of genetic diversity through bottlenecks and founder events. In order to test this hypothesis we assessed genetic diversity and structure in populations of the tripartite lichen Lobaria pulmonaria using eight SSR loci. We sampled thalli growing on Picea abies branches and propagules deposited in snow at three localities. Contrary to expectations, we found high genetic diversity in lichen and snow samples, and high effective sizes of the studied populations. Also, limited genetic differentiation between populations, high historical migration rates, and a high proportion of first generation immigrants were estimated, implying high connectivity across distances <30 km. Almost all genetic variation was due to variation within sites; spatial genetic structures within populations were absent or appeared on small scales (5–10 m). The high genetic diversity in the remaining old boreal rainforests shows that even relict forest patches might be suitable for conservation of genetic diversity.
Data from: Environmental extremes drive population structure at the northern range limit of Atlantic salmon in North America
Conservation of exploited species requires an understanding of both genetic diversity and the dominant structuring forces, particularly near range limits, where climatic variation can drive rapid expansions or contractions of geographic range. Here, we examine population structure and landscape associations in Atlantic salmon (Salmo salar) across a heterogeneous landscape near the northern range limit in Labrador, Canada. Analysis of two amplicon-based data sets containing 101 microsatellites and 376 single nucleotide polymorphisms (SNPs) from 35 locations revealed clear differentiation between populations spawning in rivers flowing into a large marine embayment (Lake Melville) compared to coastal populations. The mechanisms influencing the differentiation of embayment populations were investigated using both multivariate and machine-learning landscape genetic approaches. We identified temperature as the strongest correlate with genetic structure, particularly warm temperature extremes and wider annual temperature ranges. The genomic basis of this divergence was further explored using a subset of locations (n=17) and a 220K SNP array. SNPs associated with spatial structuring and temperature mapped to a diverse set of genes and molecular pathways, including regulation of gene expression, immune response, and cell development and differentiation. The results spanning molecular marker types and both novel and established methods clearly show climate-associated, fine-scale population structure across an environmental gradient in Atlantic salmon near its range limit in North America, highlighting valuable approaches for predicting population responses to climate change and managing species sustainability.
Data from: Dispersal syndromes can impact ecosystem functioning in spatially structured freshwater populations
Dispersal can strongly influence ecological and evolutionary dynamics. Besides the direct contribution of dispersal to population dynamics, dispersers often differ in their phenotypic attributes from non-dispersers, which leads to dispersal syndromes. The consequences of such dispersal syndromes have been widely explored at the population and community level, however, to date, ecosystem-level effects remain unclear. Here, we examine whether dispersing and resident individuals of two different aquatic keystone invertebrate species have different contributions to detrital processing, a key function in freshwater ecosystems. Using experimental two-patch systems, we found no difference in leaf consumption rates with dispersal status of the common native species Gammarus fossarum. In Dikerogammarus villosus, however, a Ponto-Caspian species now expanding throughout Europe, dispersers consumed leaf litter at roughly three times the rate of non-dispersers. Furthermore, this put the contribution of dispersing D. villosus to leaf litter processing on par with native G. fossarum, after adjusting for differences in organismal size. Given that leaf litter decomposition is a key function in aquatic ecosystems, and the rapid species turnover in freshwater habitats with range expansions of non-native species, this finding suggests that dispersal syndromes may have important consequences for ecosystem functioning.
Data from: Spatial population genetic structure of a bacterial parasite in close coevolution with its host
Knowledge of a species' population genetic structure can provide insight into fundamental ecological and evolutionary processes including gene flow, genetic drift, and adaptive evolution. Such inference is of particular importance for parasites, as an understanding of their population structure can illuminate epidemiological and coevolutionary dynamics. Here we describe the population genetic structure of the bacterium Pasteuria ramosa, a parasite that infects planktonic crustaceans of the genus Daphnia. This system has become a model for investigations of host-parasite interactions and represents an example of coevolution via negative frequency-dependent selection (a.k.a. 'Red Queen' dynamics). To sample P. ramosa, we experimentally infected a panel of Daphnia hosts with natural spore banks from the sediments of 25 ponds throughout much of the species range in Europe and Western Asia. Using 12 polymorphic VNTR loci, we identified substantial genetic diversity both within and among localities that was structured geographically among ponds. Genetic diversity was also structured among host genotypes within ponds, though this pattern varied by locality, with P. ramosa at some localities partitioned into distinct host-specific lineages, and other localities where recombination had shuffled genetic variation among different infection phenotypes. Across the sample range, there was a pattern of isolation-by-distance, and principal components analysis coupled with Procrustes rotation identified congruence between patterns of genetic variation and geography. Our findings support the hypothesis that Pasteuria is an endemic parasite coevolving closely with its host. These results provide important context for previous studies of this model system and inform hypotheses for future research.
Data from: EB Ford revisited: assessing the long-term stability of wing-spot patterns and population genetic structure of the meadow brown butterfly on the Isles of Scilly
Understanding selection in the wild remains a major aim of evolutionary ecology and work by Ford and colleagues on the meadow brown butterfly Maniola jurtina did much to ignite this agenda. A great deal of their work was conducted during the 1950s on the Isles of Scilly. They documented island-specific wing-spot patterns that remained consistent over about a decade, but patterns on some islands changed after environmental perturbation. It was suggested that these wing-spot patterns reflected island-specific selection and that there was little migration between islands. However, genetic studies to test the underlying assumption of restricted migration are lacking and it is also unknown whether the originally described wing-spot patterns have persisted over time. We therefore collected female butterflies from five of Ford's original study locations, including three large islands (St Mary's, St Martin's and Tresco) and two small islands (Tean and St Helen's). Wing-spot patterns had not changed appreciably over time on three of the islands (two large and one small), but were significantly different on the other two. Furthermore, analysis of 176 amplified fragment length polymorphisms revealed significant genome-wide differentiation among the five islands. Our findings are consistent with Ford's conclusions that despite the close proximity of these islands, there is restricted gene flow among them.
Data from: Genetic diversity and population structure in South African, French and Argentinian Angora Goats from genome-wide SNP data
The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have been kept geographically and genetically distinct. Due to country-specific selection and breeding strategies, there is a need to characterize the populations on a genetic level. In this study we analysed genetic variability of Angora goats from three distinct geographical regions using the standardized 50k Goat SNP Chip. A total of 104 goats (AR: 30; FR: 26; SA: 48) were genotyped. Heterozygosity values as well as inbreeding coefficients across all autosomes per population were calculated. Diversity, as measured by expected heterozygosity (HE) ranged from 0.371 in the SA population to 0.397 in the AR population. The SA goats were the only population with a positive average inbreeding coefficient value of 0.009. After merging the three datasets, standard QC and LD-pruning, 15 105 SNPs remained for further analyses. Principal component and clustering analyses were used to visualize individual relationships within and between populations. All SA Angora goats were separated from the others and formed a well-defined, unique cluster, while outliers were identified in the FR and AR breeds. Apparent admixture between the AR and FR populations was observed, while both these populations showed signs of having some common ancestry with the SA goats. LD averaged over adjacent loci within the three populations per chromosome were calculated. The highest LD values estimated across populations were observed in the shorter intervals across populations. The Ne for the Angora breed was estimated to be 149 animals ten generations ago indicating a declining trend. Results confirmed that geographic isolation and different selection strategies caused genetic distinctiveness between the populations.
Data from: Assessing polar bear (Ursus maritimus) population structure in the Hudson Bay region using SNPs
Defining subpopulations using genetics has traditionally used data from microsatellite markers to investigate population structure; however, single-nucleotide polymorphisms (SNPs) have emerged as a tool for detection of fine-scale structure. In Hudson Bay, Canada, three polar bear (Ursus maritimus) subpopulations (Foxe Basin (FB), Southern Hudson Bay (SH), and Western Hudson Bay (WH)) have been delineated based on mark–recapture studies, radiotelemetry and satellite telemetry, return of marked animals in the subsistence harvest, and population genetics using microsatellites. We used SNPs to detect fine-scale population structure in polar bears from the Hudson Bay region and compared our results to the current designations using 414 individuals genotyped at 2,603 SNPs. Analyses based on discriminant analysis of principal components (DAPC) and STRUCTURE support the presence of four genetic clusters: (i) Western—including individuals sampled in WH, SH (excluding Akimiski Island in James Bay), and southern FB (south of Southampton Island); (ii) Northern—individuals sampled in northern FB (Baffin Island) and Davis Strait (DS) (Labrador coast); (iii) Southeast—individuals from SH (Akimiski Island in James Bay); and (iv) Northeast—individuals from DS (Baffin Island). Population structure differed from microsatellite studies and current management designations demonstrating the value of using SNPs for fine-scale population delineation in polar bears.
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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.