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.
1,940
datasets available to search
ShareScore release 0.9.0
Dataset results
1,940 results for “data sample”
Data from: Mate sampling and choosiness in the sand goby
To date, mate choice studies have mostly focused on establishing which mates are chosen or how the choices are performed. Here, we combined these two approaches by empirically testing how latency to mate is affected by various search costs, variation in mate quality and female quality in the sand goby (Pomatoschistus minutus). Our results show that females adjust their mating behaviour according to the costs and benefits of the choice situation. Specifically, they mated sooner when access to males was delayed and when the presence of other females presented a mate sampling cost. We also found a positive link between size variation among potential mating partners and spawning delay in some (but not all) experimental conditions. By contrast, we did not find the number of available males or the females' own body size ('quality') to affect mating latency. Finally, female mating behaviour varied significantly between years. These findings are notable for demonstrating that (i) mate sampling time is particularly sensitive to costs and, to a lesser degree, to variation among mate candidates, (ii) females' mating behaviour is sensitive to qualitative rather than to quantitative variation in their environment, and (iii) a snapshot view may describe mate sampling behaviour unreliably.
Data from: Accounting for kin sampling reveals genetic connectivity in Tasmanian and New Zealand school sharks, Galeorhinus galeus
Fishing represents a major problem for conservation of chondrichthyans, with a quarter of all species being overexploited. School sharks, Galeorhinus galeus, are targeted by commercial fisheries in Australia and New Zealand. The Australian stock has been depleted to below 20% of its virgin biomass, and the species is recorded as Conservation Dependent within Australia. Individuals are known to move between both countries, but it is disputed whether the stocks are reproductively linked. Accurate and unbiased determination of stock and population connectivity is crucial to inform effective management. In this study, we assess the genetic composition and population connectivity between Australian and New Zealand school sharks using genome‐wide SNPs, while accounting for non‐random kin sampling. Between 2009 and 2013, 88 neonate and juvenile individuals from Tasmanian and New Zealand nurseries were collected and genotyped. Neutral loci were analyzed to detect fine‐scale signals of reproductive connectivity. Seven full‐sibling groups were identified and removed for unbiased analysis. Based on 6,587 neutral SNPs, pairwise genetic differentiation from Tasmanian and New Zealand neonates was non‐significant (FST = 0.0003, CI95 = [−0.0002, 0.0009], p = 0.1163; Dest = 0.0006 ± 0.0002). This pattern was supported by clustering results. In conclusion, we show a significant effect of non‐random sampling of kin and identify fine‐scale reproductive connectivity between Australian and New Zealand school sharks.
Data from: Monitoring the effective population size of a brown bear (Ursus arctos) population using new single-sample approaches
The effective population size (Ne) could be the ideal parameter for monitoring populations of conservation concern as it conveniently summarizes both the evolutionary potential of the population and its sensitivity to genetic stochasticity. However, tracing its change through time is difficult in natural populations. We applied four new methods for estimating Ne from a single sample of genotypes to trace temporal change in Ne for bears in the Northern Dinaric Mountains. We genotyped 510 bears using 20 microsatellite loci, and determined their age. The samples were organized into cohorts with regard to the year when the animals were born and yearly samples with age categories for every year when they were alive. We used the Estimator by Parentage Assignment (EPA) to directly estimate both Ne and generation interval for each yearly sample. For cohorts, we estimated the effective number of breeders (Nb) using Linkage Disequilibrium, Sibship Assignment and Approximate Bayesian Computation methods, and extrapolated these estimates to Ne using the generation interval. The Ne estimate by EPA is 276 (183-350 95% CI), meeting the inbreeding-avoidance criterion of Ne > 50 but short of the long-term minimum viable population goal of Ne > 500. The results obtained by the other methods are highly consistent with this result, and all indicate a rapid increase in Ne probably in the late 1990s and early 2000s. The new single-sample approaches to estimation of Ne provide efficient means for including Ne in monitoring frameworks, and will be of great importance for future management and conservation.
Data from: Predator-guided sampling reveals biotic structure in the bathypelagic
We targeted habitat used differentially by deep-diving, air-breathing predators to empirically sample their prey's distributions off southern California. Fine-scale measurements of the spatial variability of potential prey animals from the surface to 1200 m were obtained using conventional fisheries echosounders aboard a surface ship and uniquely integrated into a deep-diving autonomous vehicle. Significant spatial variability in the size, composition, total biomass, and spatial organization of biota was evident over all spatial scales examined and was consistent with the general distribution patterns of foraging Cuvier's beaked whales (Ziphius cavirostris) observed in separate studies. Striking differences were found in prey characteristics between regions at depth, however, did not reflect differences observed in surface layers. These differences in deep pelagic structure horizontally and relative to surface structure, absent clear physical differences, change our long-held views of this habitat as uniform. The revelation that animals deep in the water column are so spatially heterogeneous at scales from 10 m to 50 km critically affects our understanding of the processes driving predator-prey interactions, energy transfer, biogeochemical cycling and other ecological processes in the deep sea, and the connections between the productive surface mixed layer and the deep water column.
Data from: MicroRNA stability in FFPE tissue samples: dependence on GC content
MicroRNAs (miRNAs) are small non-coding RNAs responsible for fine-tuning of gene expression at post-transcriptional level. The alterations in miRNA expression levels profoundly affect human health and often lead to the development of severe diseases. Currently, high throughput analyses, such as microarray and deep sequencing, are performed in order to identify miRNA biomarkers, using archival patient tissue samples. MiRNAs are more robust than longer RNAs, and resistant to extreme temperatures, pH, and formalin-fixed paraffin-embedding (FFPE) process. Here, we have compared the stability of miRNAs in FFPE cardiac tissues using next-generation sequencing. The mode read length in FFPE samples was 11 nucleotides (nt), while that in the matched frozen samples was 22 nt. Although the read counts were increased 1.7-fold in FFPE samples, compared with those in the frozen samples, the average miRNA mapping rate decreased from 32.0% to 9.4%. These results indicate that, in addition to the fragmentation of longer RNAs, miRNAs are to some extent degraded in FFPE tissues as well. The expression profiles of total miRNAs in two groups were highly correlated (0.88
Data from: A pipeline for metabarcoding and diet analysis from fecal samples developed for a small semi-aquatic mammal
Metabarcoding allows the genetic analysis of pooled samples of various sources. It is becoming popular in the study of animal diet, especially because it allows the analysis of the composition of feces without the need of handling animals. In this work, we studied the diet of the Pyrenean desman (Galemys pyrenaicus), a small semi-aquatic mammal endemic to the Iberian Peninsula and the Pyrenees, by sequencing COI minibarcodes from feces using next-generation sequencing techniques. For the identification of assembled sequences, we employed a tree-based identification method that used a reference tree of sequences of freshwater organisms. The comparison of freshly collected fecal samples and older samples showed that fresh samples produced significantly more sequencing reads. They also rendered more operational taxonomical units (OTUs), but not significantly. Our analyses of 41 samples identified 224 OTUs corresponding to species of the reference tree. Ephemeroptera, Diptera excl. Chironomidae, and Chironomidae were the most highly represented groups in terms of reads as well as samples. Other groups of freshwater organisms detected were Plecoptera, Trichoptera, Neuropteroida, Coleoptera, Crustacea, and Annelida. Our results are largely in line with previous morphological and genetic studies on the diet of the Pyrenean desman, but allowed the identification of a higher diversity of OTUs in each sample. Additionally, the bioinformatic pipeline we developed for deep sequencing of fecal samples will enable the quantitative analysis of the diet of this and other species, which can be highly useful to determine their ecological requirements.
Data from: Estimating feral cat densities using distance sampling in an urban environment
1. Estimating feral cat population densities in urban environments can be difficult due to lack of public space and human interference. The purpose of this study was to use distance sampling in a citywide landscape to determine population size and areas of high abundance to inform trap-neuter-release management programs. 2. Line transect distance sampling was used to estimate density of the feral cat population in Windsor, Ontario from June to July 2014. Windsor has a human population of 217,188 and is about 146 km2 in size. Most transects were placed along local roads. 3. Density was estimated at about 13.3 (95% CI 9.7 – 18.1) cats per km2, and an estimated population size of 1858 cats (95% CI 1361 – 2537) with the highest relative density occurring in West and Central Windsor. 4. Urban wildlife managers could utilize these methods to monitor feral cat populations and evaluate the effectiveness of trap-neuter-release programs.
Data from: Multiple loci and complete taxonomic sampling resolve the phylogeny and biogeographic history of tenrecs (Mammalia: Tenrecidae) and reveal higher speciation rates in Madagascar's humid forests
The family Tenrecidae (tenrecs) is one of only four extant terrestrial mammal lineages to have colonized and diversified on Madagascar. Over the past 15 years, several studies have disagreed on relationships among major tenrec lineages, resulting in multiple reinterpretations of the number and timing of historical transoceanic dispersal events between Africa and Madagascar. We reconstructed the phylogeny of Tenrecidae using multiple loci from all recognized extant species and estimated divergence timing using six fossil calibrations within Afrotheria. All phylogenetic analyses strongly support monophyly of the Malagasy tenrecs, and our divergence timing analysis places their colonization of the island at 30-56 Ma. Our comprehensive phylogeny supports three important taxonomic revisions that reflect the evolutionary history of tenrecs: (1) we formally elevate the African otter shrews to their own family Potamogalidae, thereby rendering extant Tenrecidae entirely endemic to Madagascar, (2) we subsume the semiaquatic genus Limnogale within the shrew-tenrec genus Microgale, and (3) we re-elevate the two largest-bodied shrew tenrecs, Microgale dobsoni and M. talazaci, to the genus Nesogale Thomas 1918. Finally, we use recently summarized habitat data to test the hypothesis that diversification rates differ between humid and arid habitats on Madagascar, and we compare three common methods for ancestral biogeographic reconstruction. These analyses suggest higher speciation rates in humid habitats and reveal a minimum of three and more likely five independent transitions to arid habitats. Our results resolve the relationships among previously recalcitrant taxa, illuminate the timing and mechanisms of major biogeographic patterns in an extraordinary example of an island radiation, and permit the first comprehensive, phylogenetically consistent taxonomy of Madagascar's tenrecs.
Data from: Return of a giant: DNA from archival museum samples helps to identify a unique cutthroat trout lineage formerly thought to be extinct
Currently one small, native population of the culturally and ecologically important Lahontan cutthroat trout (Oncorhynchus clarkii henshawi, LCT, Federally listed) remains in the Truckee River watershed of northwestern Nevada and northeastern California. The majority of populations in this watershed were extirpated in the 1940's due to invasive species, overharvest, anthropogenic water consumption and changing precipitation regimes. In 1977, a population of cutthroat trout discovered in the Pilot Peak Mountains in the Bonneville basin of Utah, was putatively identified as the extirpated LCT lacustrine lineage native to Pyramid Lake in the Truckee River basin based upon morphological and meristic characters. Our phylogenetic and Bayesian genotype clustering analyses of museum specimens collected from the large lakes (1872-1913) and contemporary samples collected from populations throughout the extant range provide evidence in support of a genetically distinct Truckee River basin origin for this population. Analysis of museum samples alone identified three distinct genotype clusters and historical connectivity among water bodies within the Truckee River basin. Baseline data from museum collections indicate that the extant Pilot Peak strain represents a remnant of the extirpated lacustrine lineage. Given the limitations on high quality data when working with a sparse number of preserved museum samples, we acknowledge that, in the end, this may be a more complicated story. However, the paucity of remnant populations in the Truckee River watershed in combination with data on the distribution of morphological, meristic and genetic data for Lahontan cutthroat trout, suggest that recovery strategies, particularly in the large lacustrine habitats should consider this lineage as an important part of the genetic legacy of this species.
Data from: Counting cats: spatially explicit population estimates of cheetah (Acinonyx jubatus) using unstructured sampling data
Many ecological theories and species conservation programmes rely on accurate estimates of population density. Accurate density estimation, especially for species facing rapid declines, requires the application of rigorous field and analytical methods. However, obtaining accurate density estimates of carnivores can be challenging as carnivores naturally exist at relatively low densities and are often elusive and wide-ranging. In this study, we employ an unstructured spatial sampling field design along with a Bayesian sex-specific spatially explicit capture-recapture (SECR) analysis, to provide the first rigorous population density estimates of cheetahs (Acinonyx jubatus) in the Maasai Mara, Kenya. We estimate adult cheetah density to be between 1.22 ± 0.301 and 1.28 ± 0.322 individuals/100km2 across four candidate models specified in our analysis. Our spatially explicit approach revealed 'hotspots' of cheetah density, highlighting that cheetah are distributed heterogeneously across the landscape. The SECR models incorporated a movement range parameter which indicated that male cheetah moved four times as much as females, possibly because female movement was restricted by their reproductive status and/or the spatial distribution of prey. We show that SECR can be used for spatially unstructured data to successfully characterise the spatial distribution of a low density species and also estimate population density when sample size is small. Our sampling and modelling framework will help determine spatial and temporal variation in cheetah densities, providing a foundation for their conservation and management. Based on our results we encourage other researchers to adopt a similar approach in estimating densities of individually recognisable species.
Data from: Effects of sample size and full sibs on genetic diversity characterization: a case study of three syntopic Iberian pond-breeding amphibians
Accurate characterization of genetic diversity is essential for understanding population demography, predicting future trends and implementing efficient conservation policies. For that purpose, molecular markers are routinely developed for nonmodel species, but key questions regarding sampling design, such as calculation of minimum sample sizes or the effect of relatives in the sample, are often neglected. We used accumulation curves and sibship analyses to explore how these 2 factors affect marker performance in the characterization of genetic diversity. We illustrate this approach with the analysis of an empirical dataset including newly optimized microsatellite sets for 3 Iberian amphibian species: Hyla molleri, Bufo calamita, and Pelophylax perezi. We studied 17–21 populations per species (total n = 547, 652, and 516 individuals, respectively), including a reference locality in which the effect of sample size was explored using larger samples (77–96 individuals). As expected, FIS and tests for Hardy–Weinberg equilibrium and linkage disequilibrium were affected by the presence of full sibs, and most initially inferred disequilibria were no longer statistically significant when full siblings were removed from the sample. We estimated that to obtain reliable estimates, the minimum sample size (potentially including full sibs) was close to 20 for expected heterozygosity, and between 50 and 80 for allelic richness. Our pilot study based on a reference population provided a rigorous assessment of marker properties and the effects of sample size and presence of full sibs in the sample. These examples illustrate the advantages of this approach to produce robust and reliable results for downstream analyses.
Data from: Comparing the prediction of joint species distribution models with respect to characteristics of sampling data
Biotic interactions have been rarely included in traditional species distribution models, wherein Joint Species Distribution Models (JSDMs) emerge as a feasible approach to incorporate environmental factors and interspecific interactions simultaneously, making it a powerful tool for analyzing the structure and assembly processes of biotic communities. However, the predictability and statistical robustness of JSDMs are largely unknown because of the lack of research efforts for those newly developed models. This study systematically evaluated the performances of five JSDMs in predicting the occurrence and biomass of multiple species, with a particular focus on diverse characteristics of sampling data, including type of response variables, number of sampling sites, and the number of species included in models. In general, most models yielded satisfactory performances on fitting to observed data and on the estimation of environmental effects; however, they showed less well performances in evaluating species associations, and their predictability had large variations. The JSDMs showed inconsistent performances between the goodness-of-fit and predictability in cross-validation, and the Boral model was relatively robust than others. The predictability of JSDMs was less influenced by sample sizes and substantially improved by incorporating rare species. This study contributes to an appropriate model selection and application of JSDMs.
Data from: Comparing convenience and probability sampling for urban ecology applications
1. Urban forest ecosystems confer multiple ecosystem services. There is thus a need to quantify ecological characteristics in terms of community structure and composition so that benefits can be better understood in ecosystem service models. Efficient sampling and monitoring methods are crucial in this process. 2. Full tree inventories are scarce due to time and financial constraints, thus a variety of sampling methods exist. Modern vegetation surveys increasingly use stratified-random plot-based sampling to reduce the bias associated with convenience sampling, even though the latter can save time and increase species richness scores. The urban landscape, with a high degree of conspecific clustering and high species diversity, provides a unique biogeographical case for comparing these two methodological approaches. 3. We use two spatially extensive convenience samples of the urban forest of Meran (Italy) and compare the community structure, tree characteristics and ecosystem service provision with 200 random circular plots. 4. The convenience sampling resulted in a higher species diversity, incorporating more rare species. This is a result of covering more area per unit sampling time. Pseudorandom sub-plots were compared to the random plots revealing similar Shannon diversity and sampling comparability indices. Measured tree variables (diameter at breast height, height, tree-crown width, height to crown base) were similar between the two methods, as were ecosystem service model outputs. 5. Synthesis and applications. The results suggest that convenience sampling may be a time and money saving alternative to random sampling as long as stratification by land-use type is incorporated into the design. The higher species richness can potentially improve the accuracy of urban ecological models, which rely on species-specific functional traits.
Data from: Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics.
The systematics and speciation literature is rich with discussion relating to the potential for gene tree/species tree discordance. Numerous mechanisms have been proposed to generate discordance, including differential selection, long-branch attraction, gene duplication, genetic introgression, and/or incomplete lineage sorting. For speciose clades in which divergence has occurred recently and rapidly, recovering the true species tree can be particularly problematic due to incomplete lineage sorting. Unfortunately, the availability of multi-locus or "phylogenomic" data sets does not simply solve the problem, particularly when the data are analyzed with standard concatenation techniques. In our study, we conduct a phylogenetic study for a nearly complete species sample of the dwarf and mouse lemur clade, Cheirogaleidae. Mouse lemurs (genus, Microcebus) have been intensively studied over the past decade for reasons relating to their high level of cryptic species diversity, and although there has been emerging consensus regarding the evolutionary diversity contained within the genus, there is no agreement as to the inter-specific relationships within the group. We attempt to resolve cheirogaleid phylogeny, focusing especially on the mouse lemurs, by employing a large multi-locus data set. We compare the results of Bayesian concordance methods with those of standard gene concatenation, finding that though concatenation yields the strongest results as measured by statistical support, these results are found to be highly misleading. By employing an approach where individual alleles are treated as OTUs, we show that phylogenetic results are substantially influenced by the selection of alleles in the concatenation process.
Data from: Multi-year stigmatic pollen-load sampling reveals temporal stability in interspecific pollination of flowers in a subalpine meadow
Co-flowering plants may commonly experience interspecific pollination. It remains unknown, however, whether interspecific pollination is a largely stochastic process or consistent enough over years to exert selection for traits that can reduce interspecific pollination or ameliorate its deleterious effects on reproduction. To assess the likelihood of this precondition being met, stigmatic pollen loads on 17 to 34 insect-pollinated plant species over 3 consecutive years were scored in a subalpine meadow in southwestern China. Plant species varied significantly in the amount and proportion of heterospecific pollen (HP) on stigmas. Both the number of HP species and the proportion of the pollen load that was HP for each recipient species correlated positively between years (reflected in pairwise correlations for all year-by-year combinations). Although inter-annual variation was smaller for conspecific pollen (CP) than for HP loads, species tended to experience either consistently high or consistently low HP proportions across years. We found that species with higher stigmatic HP proportions generally experienced lower proportional variation in stigmatic HP, an unexpected result if high HP loads are the result of rare stochastic events. The novel finding of between-year consistency in stigmatic loads of heterospecific pollen suggests that adaption to stigmatic loads of HP is possible, and two divergent strategies may have evolved: HP avoidance and HP tolerance. The observation of temporally consistent differences among species in levels of HP supports the idea that natural selection may be operating either to increase tolerance or to minimize arrival of heterospecific pollen on stigmas in co-flowering plants. Such adaptations may be important for the maintenance of high levels of local plant diversity in biodiversity hotspots such as our study area.
Data from: Breaking down the lithification bias: the effect of preferential sampling of larger specimens on the estimate of species richness, evenness, and average specimen size
Lithification, the transition of unconsolidated sediments to fully indurated rocks, can potentially bias estimates of species richness, evenness, and body size distribution derived from fossil assemblages. Fossil collections made from well-indurated rocks consistently exhibit lower species richness, lower evenness, and a specimen size distribution skewed towards larger specimens relative to collections made from unconsolidated sediments, even when collections are drawn from the same assemblage. This phenomenon is known as the lithification bias. While the bias itself has been demonstrated empirically, much less attention has been paid to its causes. Proposed causes include taphonomic processes (e.g., destruction of small specimens during early diagenesis) or methodological differences (e.g., sieving vs. counting specimens on outcrops, bedding surfaces, or mechanically split surfaces). Here we investigate the potential effects of preferential intersection that could also result in a methodologically related bias: the preferential sampling of larger specimens relative to smaller ones when fossils are counted on rock surfaces. We used an analog model to simulate preferential intersection (fossil collection via splitting fossiliferous rock) and compare the results to a random draw model that approximates the effects of sieving. The model was parameterized using nine different combinations of species abundance and species size distributions. The results show that, with rare exceptions, species richness is 5–23% lower, evenness 5-25% lower, and average specimen size 24–150% higher in preferential intersection than in random draw simulations. We conclude that preferential intersection can impose a significant bias independent of other mechanisms (e.g., preferential destruction of smaller specimens during diagenetic or sampling processes), that the magnitude of this bias is partially dependent on the species abundance and size distributions, and that this bias alone does not fully account for empirically observed lithification bias on species richness (i.e., other sources of bias are also at work).
Data from: Accounting for observation processes across multiple levels of uncertainty improves inference of species distributions and guides adaptive sampling of environmental DNA
Understanding factors that influence observation processes is critical for accurate assessment of underlying ecological processes. When indirect methods of detection, such as environmental DNA, are used to determine species presence, additional levels of uncertainty from observation processes need to be accounted for. We conducted a field trial to evaluate observation processes of a terrestrial invasive species (wild pigs- Sus scrofa) from DNA in water bodies. We used a multi-scale occupancy analysis to estimate different levels of observation processes (detection, p): the probability DNA is available per sample (θ), the probability of capturing DNA per extraction (γ), and the probability of amplification per qPCR run (δ). We selected four sites for each of three water body types and collected 10 samples per water body during two months (September and October 2016) in central Texas. Our methodology can be used to guide sampling adaptively to minimize costs while improving inference of species distributions. Using a removal sampling approach was more efficient than pooling samples, and was unbiased. Availability of DNA varied by month, was considerably higher when water pH was near neutral, and was higher in ephemeral streams relative to wildlife guzzlers and ponds. To achieve a cumulative detection probability greater than 90% (including availability, capture, and amplification), future studies should collect 20 water samples per site, conduct at least 2 extractions per sample, and conduct 5 qPCR replicates per extraction. Accounting for multiple levels of uncertainty of observation processes improved estimation of the ecological processes and provided guidance for future sampling designs.
Data from: Optimizing the trade-off between spatial and genetic sampling efforts in patchy populations: towards a better assessment of functional connectivity using an individual-based sampling scheme
Genetic data are increasingly used in landscape ecology for the indirect assessment of functional connectivity, i.e. the permeability of landscape to movements of organisms. Among available tools, matrix correlation analyses (e.g. Mantel tests or mixed models) are commonly used to test for the relationship between pairwise genetic distances and movement costs incurred by dispersing individuals. When organisms are spatially clustered, a population-based sampling scheme (PSS) is usually performed, so that a large number of genotypes can be used to compute pairwise genetic distances on the basis of allelic frequencies. Because of financial constraints, this kind of sampling scheme implies a drastic reduction in the number of sampled aggregates, thereby reducing sampling coverage at the landscape level. We used matrix correlation analyses on simulated and empirical genetic datasets to investigate the efficiency of an individual-based sampling scheme (ISS) in detecting isolation-by-distance and isolation-by-barrier patterns. Provided that pseudo-replication issues are taken into account (e.g. through restricted permutations in Mantel tests), we showed that the use of inter-individual measures of genotypic dissimilarity may efficiently replace inter-population measures of genetic differentiation: the sampling of only three or four individuals per aggregate may be sufficient to efficiently detect specific genetic patterns in most situations. The ISS proved to be a promising methodological alternative to the more conventional PSS, offering much flexibility in the spatial design of sampling schemes and ensuring an optimal representativeness of landscape heterogeneity in data, with few aggregates left unsampled. Each strategy offering specific advantages, a combined use of both sampling schemes is discussed.
Data from: The scale-of-choice effect and how estimates of assortative mating in the wild can be biased due to heterogeneous samples
The mode in which sexual organisms choose mates is a key evolutionary process, as it can have a profound impact on fitness and speciation. One way to study mate choice in the wild is by measuring trait correlation between mates. Positive assortative mating is inferred when individuals of a mating pair display traits that are more similar than those expected under random mating while negative assortative mating is the opposite. A recent review of 1134 trait correlations found that positive estimates of assortative mating were more frequent and larger in magnitude than negative estimates. Here we describe the scale-of-choice effect (SCE), which occurs when mate choice exists at a smaller scale than that of the investigator's sampling, while simultaneously the trait is heterogeneously distributed at the true scale-of-choice. We demonstrate the SCE by Monte Carlo simulations and estimate it in two organisms showing positive (Littorina saxatilis) and negative (L. fabalis) assortative mating. Our results show that both positive and negative estimates are biased by the SCE by different magnitudes, typically towards positive values. Therefore, the low frequency of negative assortative mating observed in the literature may be due to the SCE's impact on correlation estimates, which demands new experimental evaluation.
Data from: A survey of palaeontological sampling biases in fishes based on the phanerozoic record of Great Britain
Fishes represent more than half of all living vertebrate species, but patterns of fish diversity remain little explored in the fossil record. A compendium of fossil occurrences from Great Britain was assembled in order to address a series of questions concerning the palaeontological record of fishes. There are broad similarities between British richness trajectories and those compiled from global data, including an initial peak in the mid-Palaeozoic (Devonian or Carboniferous, depending on the compilation), with a late Palaeozoic trough followed by a sharp rise in diversity in the Late Cretaceous and Paleogene. The British dataset is too small to reveal any significant differences in richness between time bins using subsampling, but a modeling approach based on sampling and geological proxies consistently shows lower-than-predicted richness in the Silurian-Devonian and higher-than-predicted richness in the Late Cretaceous and Eocene. This positive excursion is robust to the exclusion of data from the early Eocene London Clay Lagerstätte. Chondrichthyans (sharks, rays, and ratfishes) and osteichthyans (ray-finned and lobe-finned fishes) show contrasting relationships with geological and sampling proxies, possibly reflecting different taphonomic profiles or idiosyncratic variation in the relative proportion of freshwater and marine deposits over the British Phanerozoic.
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.