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.
64
datasets available to search
ShareScore release 0.9.0
Dataset results
64 results for “population size estimation”
Data from: Estimating population size in the presence of temporary migration using a joint analysis of telemetry and capture recapture data
1.Temporary migration – where individuals can leave and re-enter a sampled population – is a feature of many capture–mark–recapture (CMR) studies of mobile populations which, if unaccounted for, can lead to biased estimates of population capture probabilities and consequently biased estimates of population abundance. 2. We present a method for incorporating radiotelemetry data within a CMR study to eliminate bias due to temporary migration using a Bayesian state-space model. 3. Our results indicate that using a relatively small number of telemetry tags, it is possible to greatly reduce bias in estimates of capture probabilities using telemetry data to model transition probabilities in and out of the sampling area. In a capture–recapture data set for trout Cod in the Murray river, Australia, accounting for temporary migration led to overall higher estimates of capture probabilities than models assuming permanent or zero migration. Also, individual heterogeneity in detectability can be managed through explicit modelling. We show how accounting for temporary migration when estimating capture probabilities can be used to estimate the abundance and size distribution of a population as though it were closed. 4. Our model provides a basis for more complex models that might integrate telemetry data into other CMR scenarios, thus allowing for greater precision in estimates of vital rates that might otherwise be biased by temporary migration. Our results highlight the importance of accounting for migration in survey design and parameter estimation, and the potential scope for supplementing large-scale CMR data sets with a subset of auxiliary data that provide information on processes that are hidden to primary sampling processes.
Data from: A model-derived short-term estimation method of effective size for small populations with overlapping generations
If not actively managed, small and isolated populations lose their genetic variability and the inbreeding rate increases. Combined, these factors limit the ability of populations to adapt to environmental changes, increasing their risk of extinction. The effective population size (Ne) is proportional to the loss of genetic diversity and therefore of considerable conservation relevance. However, estimators of Ne that account for demographic parameters in species with overlapping generations require sampling of populations across generations, which is often not feasible in long-lived species. We created an individual-based model that allows calculation of Ne based on demographic parameters that can be obtained in a time period much shorter than a generation. It can be adapted to every life-history parameter combination. The model is freely available as an r-package NEff. The model was first used in a simulation experiment observing changes in Ne in response to different degrees of generational overlap. Results showed that increased generational overlap slowed annual rates of heterozygosity loss, resulting in higher annual effective sizes (Ny) but decreased Ne per generation. Adding the effect of different recruitment rates only affected Ne for populations with low generational overlap. The model was further tested using real population data of the Australian arboreal gecko Gehyra variegata. Simulation results were compared to genetic analyses and matched estimates of the real population very well. Unlike other estimation methods of Ne, NEff neither requires long time series of population monitoring nor genetic analyses of changes in gene frequencies. Thus, it seems to be the first method for calculating Ne within short time periods and comparably low costs facilitating the use of Ne in applied conservation and management.
Data from: Heritability estimates from genome wide relatedness matrices in wild populations: application to a passerine, using a small sample size
Genomic developments have empowered the investigation of heritability in wild populations directly from genome wide relatedness matrices (GRM). Such GRM based approaches can in particular be used to improve or substitute approaches based on social pedigree (PED-social). However, measuring heritability from GRM in the wild has not been widely applied yet, especially using small samples and in non-model species. Here, we estimated heritability for four quantitative traits (tarsus length, wing length, bill length and body mass), using PED-social and a pedigree corrected by genetic data (PED-corrected) and GRM from a small sample (n = 494) of blue tits from natural populations in Corsica genotyped at nearly 50,000 filtered SNPs derived from RAD-seq. We also measured genetic correlations among traits and we performed chromosome partitioning. Heritability estimates were slightly higher when using GRM compared to PED-social, and PED-corrected yielded intermediate values, suggesting a minor underestimation of heritability in PED-social due to incorrect pedigree links, including extra-pair paternity, and to lower information content than the GRM. Genetic correlations among traits were similar between PED-social and GRM but credible intervals were very large in both cases, suggesting a lack of power for this small dataset. Although a positive linear relationship was found between the number of genes per chromosomes and the chromosome heritability for tarsus length, chromosome partitioning similarly showed a lack of power for the three other traits. We discuss the usefulness and limitations of the quantitative genetic inferences based on genomic data in small samples from wild populations.
Data from: Accounting for heterogeneity when estimating stopover duration, timing and population size of red knots along the Luannan Coast of Bohai Bay, China
1. To successfully perform their long-distance migrations, migratory birds require sites along their migratory routes to rest and refuel. Monitoring the use of so-called stopover and staging sites provides insights into (1) the timing of migration and (2) the importance of a site for migratory bird populations. A recently developed Bayesian superpopulation model that integrates mark-recapture data and ring density data enabled the estimation of stopover timing, duration and population size. Yet, this model did not account for heterogeneity in encounter (p) and staying (ϕ) probabilities. 2. Here we extended the integrated superpopulation model by implementing finite mixtures to account for heterogeneity in p and ϕ. We used simulations and real data on red knots Calidris canutus staging in Bohai Bay, China, during spring migration to (1) show the importance of accounting for heterogeneity in encounter and staying probabilities to get unbiased estimates of stopover timing, duration and numbers of migratory birds at staging sites and (2) get accurate stopover parameter estimates for a migratory bird species at a key staging site that is threatened by habitat destruction. 3. Our simulations confirmed that heterogeneity in p affected stopover parameter estimates more than heterogeneity in ϕ. Bias was particularly severe when most birds had both low ϕ and p. Bias was largest for population size, intermediate for stopover duration and negligible for stopover timing. 4. 50,000-100,000 red knots were estimated to annually stop for 5-9 days in Bohai Bay between 10 and 30 May. This shows the key importance of this staging site for this declining species. There were no clear changes in stopover parameters over time. 5. Our study shows the importance of accounting for heterogeneity in both encounter and staying probabilities for accurately estimating stopover duration and population size and provides an appropriate modelling framework.
Data from: Hierarchical distance sampling to estimate population sizes of common lizards across a desert ecoregion
1) Multi-species wildlife monitoring across large geographical regions is important for effective conservation planning in response to expected impacts from climate change and land use. Unlike many species of birds, mammals, and amphibians which can be efficiently sampled using automated sensors including cameras and sound recorders, reptiles are often much more challenging to detect, in part because of their typically cryptic behavior and generally small body sizes. Although many lizard species are more active during the day which makes them easier to detect using visual encounter surveys, they may be unavailable for sampling during certain periods of the day or year due to their sensitivity to temperature. 2) In recognition of these sampling challenges, we demonstrate application of a recent innovation in distance sampling that adjusts for temporary emigration between repeat survey visits. We used transect surveys to survey lizards at 229 sites throughout the Mojave Desert in California, USA, 2016. 3) We estimated a total population size of 80 million (90% CI: 64–97 million) for the three most common species of lizards across this 66,830 km2 ecoregion. We mapped how density at the 1-km2 scale was predicted to vary with vegetation cover and human development. We validated these results against independent surveys from the southern portion of our study area. 4) Our methods and results demonstrate how multi-species monitoring programs spanning arid ecoregions can better incorporate information about reptiles.
How to better count elusive birds? Comparing non-invasive monitoring methods to estimate population size of the endangered Pin-tailed sandgrouse (Pterocles alchata)
<p>Data to run analyses for manuscript comparing non-invasive monitoring methods to estimate Pin-tailed sandgrouse abundance</p>
Data from: Effective population size of natural populations of Drosophila buzzatii, with a comparative evaluation of nine methods of estimation
Allozyme and microsatellite data from numerous populations of Drosophila buzzatii have been used (i) to determine to what degree Ne varies among generations within populations, and among populations, and (ii) to evaluate the congruence of four temporal and five single sample estimators of Ne. Effective size of different populations varied over two orders of magnitude, most populations are not temporally stable in genetic composition, and Ne showed large variation over generations in some populations. Short term Ne estimates from the temporal methods were highly correlated, but the smallest estimates were the most precise for all four methods, and the most consistent across methods. Except for one population, Ne estimates were lower when assuming gene flow than when assuming populations were closed. However, attempts to jointly estimate Ne and immigration rate were of little value because the source of migrants was unknown. Correlations among the estimates from the single sample methods generally were not significant although, as for the temporal methods, estimates were most consistent when they were small. These single sample estimates of current Ne are generally smaller than the short term temporal estimates. Nevertheless, population genetic variation is not being depleted, presumably due to past or ongoing migration. A clearer picture of current and short term effective population sizes will only follow with better knowledge of migration rates between populations. Different methods are not necessarily estimating the same Ne, they are subject to different bias, and the biology, demography and history of the population(s) may affect different estimators differently.
Distribution. Now restricted to the Channel Country of SW Queensland and the Lake Eyre Basin in NE South Australia. Descriptive notes. Head-body 95-120 mm, tail 105-160 mm, ear 23-29 mm, hindfoot 32-37 mm; weight 30-50 g. The Fawn Hopping Mouse has body form typical of hopping mice, with very long hindfeet, long tail with distal brush of longer hairs, very long ears, and large protruberant eyes. Dorsal fur is of variable color, from pale pinkish fawn to gray; ventral fur white. Unlike most other hopping mice, it has no throat pouch, but males have a glandular area of naked skin on the chest. Habitat. Occurs in low shrublands and tussock grasslands on stony ("gibber") plains and claypans. Shows marked habitat segregation from the Dusky Hopping Mouse (N. fuscus), which is closely associated with sandy substrates. Food and Feeding. The Fawn Hopping Mouse is mostly granivorous, but also eats other plant material (stems, leaves) and occasionally invertebrates. It uses succulent, salt-adapted plants around edges of claypans as a source of water. Breeding. Reproduction is probably largely opportunistic and aseasonal, with high reproductive output from near-continuous breeding after periods of high rainfall; reported littersize is 1-5, most commonly three; gestation period 38-43 days for nonlactating females. Females may mature later than other hopping mice, with reproductive maturity reached at about six months. Activity patterns. Terrestrial and nocturnal. Fawn Hopping Mice shelter during day in burrow systems that are typically simpler and shallower than those of other hopping mice. Movements, Home range and Social organization. Fawn Hopping Mice generally live singly or in small groups; typically uncommon within range, but population density may increase by an order of magnitude following periods of high rainfall. Status and Conservation. Classified as Near Threatened on The IUCN Red List. The Fawn Hopping Mouse has shown marked decline in range (estimated at greater than 50%), and presumably population size, since European settlement of Australia. This is mostlikely due to predation by the introduced house cat and Red Fox (Vulpes vulpes), and to habitat degradation associated with pastoralism. Bibliography. Brazenor (1934), Burbidge et al. (2008), Finlayson (1939), Gould (1853), Jackson & Groves (2015), Murray et al. (1999), Ogilby (1892), Thomas (1921h), Van Dyck & Strahan (2008), Waite (1898), Watts & Aslin (1981), Woinarski et al. (2014), Wood Jones (1925). in Muridae
Distribution. Now restricted to the Channel Country of SW Queensland and the Lake Eyre Basin in NE South Australia. Descriptive notes. Head-body 95-120 mm, tail 105-160 mm, ear 23-29 mm, hindfoot 32-37 mm; weight 30-50 g. The Fawn Hopping Mouse has body form typical of hopping mice, with very long hindfeet, long tail with distal brush of longer hairs, very long ears, and large protruberant eyes. Dorsal fur is of variable color, from pale pinkish fawn to gray; ventral fur white. Unlike most other hopping mice, it has no throat pouch, but males have a glandular area of naked skin on the chest. Habitat. Occurs in low shrublands and tussock grasslands on stony ("gibber") plains and claypans. Shows marked habitat segregation from the Dusky Hopping Mouse (N. fuscus), which is closely associated with sandy substrates. Food and Feeding. The Fawn Hopping Mouse is mostly granivorous, but also eats other plant material (stems, leaves) and occasionally invertebrates. It uses succulent, salt-adapted plants around edges of claypans as a source of water. Breeding. Reproduction is probably largely opportunistic and aseasonal, with high reproductive output from near-continuous breeding after periods of high rainfall; reported littersize is 1-5, most commonly three; gestation period 38-43 days for nonlactating females. Females may mature later than other hopping mice, with reproductive maturity reached at about six months. Activity patterns. Terrestrial and nocturnal. Fawn Hopping Mice shelter during day in burrow systems that are typically simpler and shallower than those of other hopping mice. Movements, Home range and Social organization. Fawn Hopping Mice generally live singly or in small groups; typically uncommon within range, but population density may increase by an order of magnitude following periods of high rainfall. Status and Conservation. Classified as Near Threatened on The IUCN Red List. The Fawn Hopping Mouse has shown marked decline in range (estimated at greater than 50%), and presumably population size, since European settlement of Australia. This is mostlikely due to predation by the introduced house cat and Red Fox (Vulpes vulpes), and to habitat degradation associated with pastoralism. Bibliography. Brazenor (1934), Burbidge et al. (2008), Finlayson (1939), Gould (1853), Jackson & Groves (2015), Murray et al. (1999), Ogilby (1892), Thomas (1921h), Van Dyck & Strahan (2008), Waite (1898), Watts & Aslin (1981), Woinarski et al. (2014), Wood Jones (1925).
Figure 1 in Using short-term surveys and mark-recapture to estimate diversity and population size of orchid bees in forest formations of the Brazilian savanna
Figure 1. Marking method used in the study of euglossine populations. (a) During all populational estimatives. Each geometric shape corresponds to the day when the PTT was collected. Square = 1st day; circle = 2nd day; pentagon = 3rd day; triangle = 4th day; diamond = 5th day. (b) During the samplings occurred simultaneously in seasonal semi-deciduous (ssf) and gallery forest (ssf). Square = 1st day; circle = 2nd day; pentagon = 3rd day; square combined with spot on the wing = 4th day; circle combined with spot on the wing = 5th day.
Estimation of worker population size-density by nest counting in the Asian weaver ant, Oecophylla smaragdina (Hymenoptera: Formicidae) and it's dynamic in oil palm plantations industry
<p>Supplementary material-information supporting the article of research related to the Asian weaver ant population size-density in the oil palm plantations. The findings suggested an abundant numerical amount of individual workers per colony. The weaver ant were self-sustainable surviving during long years i.e. more than 20 years. This is the first study carried out on a large scale in oil palm plantation directly in the field by gathering only empirical data and monitor the population dynamic on a long term basis. </p>
Data from: Beyond abundance: The impact of sampling design on effective population size estimates in capercaillie
Open the record for dataset details and reuse information.
Data from: Estimating population size in the presence of temporary migration using a joint analysis of telemetry and capture recapture data
Open the record for dataset details and reuse information.
Data from: Short-term genetic changes: evaluating effective population size estimates in a comprehensively described brown trout (Salmo trutta) population
Open the record for dataset details and reuse information.
Data from: Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 1. Insights from the estimation of effective population sizes
Open the record for dataset details and reuse information.
Data from: Estimating demographic contributions to effective population size in an age-structured wild population experiencing environmental and demographic stochasticity
Open the record for dataset details and reuse information.
Data from: Assessing conservation risks to populations of an anadromous Arctic salmonid, the northern Dolly Varden (Salvelinus malma malma), via estimates of effective and census population sizes and approximate Bayesian computation
Open the record for dataset details and reuse information.
Data from: Interannual variation in effective number of breeders and estimation of effective population size in long-lived iteroparous lake sturgeon (Acipenser fulvescens)
Open the record for dataset details and reuse information.
Data from: Quantifying population size of migrant birds at stopover sites: combining count data with stopover length estimated from stable isotope analysis
Open the record for dataset details and reuse information.
Data from: Techniques for estimating the size of low density gopher tortoise populations
Open the record for dataset details and reuse information.
Data from: Effective population size of natural populations of Drosophila buzzatii, with a comparative evaluation of nine methods of estimation
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.