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5,538 results for “Population data”
Data from: Bayesian estimates of male and female African lion mortality for future use in population management
The global population size of African lions is plummeting, and many small fragmented populations face local extinction. Extinction risks are amplified through the common practice of trophy hunting for males, which makes setting sustainable hunting quotas a vital task. Various demographic models evaluate consequences of hunting on lion population growth. However, none of the models use unbiased estimates of male age-specific mortality because such estimates do not exist. Until now, estimating mortality from resighting records of marked males has been impossible due to the uncertain fates of disappeared individuals: dispersal or death. We develop a new method and infer mortality for male and female lions from two populations that are typical with respect to their experienced levels of human impact. We found that mortality of both sexes differed between the populations and that males had higher mortality across all ages in both populations. We discuss the role that different drivers of lion mortality may play in explaining these differences and whether their effects need to be included in lion demographic models. Synthesis and applications. Our mortality estimates can be used to improve lion population management and, in addition, the mortality model itself has potential applications in demographically informed approaches to the conservation of species with sex-biased dispersal.
Data from: Effects of Poor Knights Islands Marine Reserve on demersal fish populations
PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN SUBSEQUENT PUBLICATIONS. PLEASE SEE Anderson et al. (2019) at https://doi.org/10.1002/ece3.4948 FOR MORE INFORMATION. We describe a new pathway for multivariate analysis of data consisting of counts of species abundances that includes two key components: copulas, to provide a flexible joint model of individual species, and dissimilarity-based methods, to integrate information across species and provide a holistic view of the community. Individual species are characterized using suitable (marginal) statistical distributions, with the mean, the degree of over-dispersion and/or zero-inflation being allowed to vary among a priori groups of sampling units. Associations among species are then modelled using copulas, which allow any pair of disparate types of variables to be coupled through their cumulative distribution function, while maintaining entirely the separate individual marginal distributions appropriate for each species. A Gaussian copula smoothly captures changes in an index of association that excludes joint-absences in the space of the original species variables. A permutation-based filter with exact family-wise error can optionally be used a priori to reduce the dimensionality of the copula estimation problem. We describe in detail an MCEM algorithm for efficient estimation of the copula correlation matrix with discrete marginal distributions (counts). The resulting fully parameterized copula models can be used to simulate realistic ecological community data under fully specified null or alternative hypotheses. Distributions of community centroids derived from simulated data can then be visualized in ordinations of ecologically meaningful dissimilarity spaces. Multinomial mixtures of data drawn from copula models also yield smooth power curves in dissimilarity-based settings. Our proposed analysis pathway provides new opportunities to combine model-based approaches with dissimilarity-based methods to enhance understanding of ecological systems. We demonstrate implementation of the pathway through an ecological example, where associations among fish species were found to increase after the establishment of a marine reserve.
Data from: The population genomic signature of environmental selection in the widespread insect-pollinated tree species Frangula alnus at different geographical scales
The evaluation of the molecular signatures of selection in species lacking an available closely related reference genome remains challenging, yet it may provide valuable fundamental insights into the capacity of populations to respond to environmental cues. We screened 25 native populations of the tree species Frangula alnus subsp. alnus (Rhamnaceae), covering three different geographical scales, for 183 annotated single-nucleotide polymorphisms (SNPs). Standard population genomic outlier screens were combined with individual-based and multivariate landscape genomic approaches to examine the strength of selection relative to neutral processes in shaping genomic variation, and to identify the main environmental agents driving selection. Our results demonstrate a more distinct signature of selection with increasing geographical distance, as indicated by the proportion of SNPs (i) showing exceptional patterns of genetic diversity and differentiation (outliers) and (ii) associated with climate. Both temperature and precipitation have an important role as selective agents in shaping adaptive genomic differentiation in F. alnus subsp. alnus, although their relative importance differed among spatial scales. At the 'intermediate' and 'regional' scales, where limited genetic clustering and high population diversity were observed, some indications of natural selection may suggest a major role for gene flow in safeguarding adaptability. High genetic diversity at loci under selection in particular, indicated considerable adaptive potential, which may nevertheless be compromised by the combined effects of climate change and habitat fragmentation.
Data from: Population of origin and environment interact to determine oomycete infections in spotted salamander populations
Spatial variation in disease risk in wild populations can depend both on environmental and genetic factors. Understanding the various contributions of each factor requires experimental manipulation of both the environment and genetic composition of populations under natural field conditions. We first examined natural patterns of oomycete composition and infection in the eggs of 13 populations of the spotted salamander Ambystoma maculatum. We then performed a fully factorial field transplant of the eggs of six populations to separate the contributions from population of origin and the environment on oomycete resistance in spotted salamanders. Among wild ponds, we found strong variation in oomycete infections in spotted salamander populations and differences in the composition of oomycete communities. In transplant experiments, salamander populations differed in their resistance to oomycete infections via a significant interaction between population of origin and environment. However, not all populations were locally adapted to local conditions. One population was significantly adapted to its home environment, and another one was significantly maladapted. These population effects could originate from differential adaptation of salamander populations to local oomycete communities or environmental conditions that mediate resistance, local adaptation and maladaptation of oomycetes to hosts, or from maternal transmission. Accounting for both environment and population of origin will often be necessary to understand disease dynamics in wild populations.
Data from: Conservation of old individual trees and small populations is integral to maintain species' genetic diversity of a historically fragmented woody perennial
Historically fragmented and specialised habitats such as granite outcrops are understudied globally unique hotspots of plant evolution. In contrast to predictions based on mainstream population genetics theory, some granite outcrop plants appear to have persisted as very small populations despite prolonged geographic and genetic isolation. Eucalyptus caesia Benth. is a long-lived lignotuberous tree endemic with a naturally fragmented distribution on granite outcrops in south-western Australia. To quantify population to landscape level genetic structure we employed microsatellite genotyping at 14 loci of all plants in 18 stands of E. caesia. Sampled stands were characterised by low levels of genetic diversity, small absolute population sizes, localised clonality and strong fine-scale genetic sub-division. There was no significant relationship between population size and levels of heterozygosity. At the landscape scale, high levels of population genetic differentiation were most pronounced among representatives of the two subspecies in E. caesia as originally circumscribed. Past genetic interconnection was evident between some geographical neighbours separated by up to 20 kilometres. Paradoxically, other pairs of neighbouring stands as little as 7 kilometres apart were genetically distinct. There was no consistent pattern of isolation by distance across the 280 km range of E. caesia. Low levels of gene flow, together with strong drift within stands, provides some explanation of the patterns of genetic differentiation we observed. Individual genet longevity via the ability to repeatedly re-sprout and expand from a lignotuber may enhance the persistence of some woody perennial endemic plants despite small population size, minimal genetic interconnection and low heterozygosity.
Data from: Partial support for the central–marginal hypothesis within a population: reduced genetic diversity but not increased differentiation at the range edge of an island endemic bird
Large-scale population comparisons have contributed to our understanding of the evolution of geographic range limits and species boundaries, as well as the conservation value of populations at range margins. The central–marginal hypothesis (CMH) predicts a decline in genetic diversity and an increase in genetic differentiation toward the periphery of species' ranges due to spatial variation in genetic drift and gene flow. Empirical studies on a diverse array of taxa have demonstrated support for the CMH. However, nearly all such studies come from widely distributed species, and have not considered if the same processes can be scaled down to single populations. Here, we test the CMH on a species composed of a single population: the Island Scrub-Jay (Aphelocoma insularis), endemic to a 250 km2 island. We examined microsatellite data from a quarter of the total population and found that homozygosity increased toward the island's periphery. However, peripheral portions of the island did not exhibit higher genetic differentiation. Simulations revealed that highly localized dispersal and small total population size, but not spatial variation in population density, were critical for generating fine-scale variation in homozygosity. Collectively, these results demonstrate that microevolutionary processes driving spatial variation in genetic diversity among populations can also be important for generating spatial variation in genetic diversity within populations.
Data from: Variation in age, body size, and reproductive traits among urban and rural amphibian populations
Although amphibians use human-created habitats in urban landscapes, few studies have investigated the quality of these habitats. To assess habitat quality of stormwater management ponds and adjacent urban uplands forwood frogs (Lithobates sylvaticus) and American toads (Anaxyrus americanus), we compared life history characteristics between populations breeding across an urbanization gradient. Specifically, we compared body size, ages of breeding adults, and female reproductive investment among urban, suburban, and rural populations in Baltimore County, Maryland, USA. Although there was variation in age at maturity among populations, ages of breeding adults did not differ among urban, suburban, and rural areas. Maternal body size strongly influenced reproductive investment in both species, but relationships did not vary among urban, suburban, and rural populations. Adult wood frogs and American toads from more urbanized landscapes were significantly smaller at age than conspecifics from rural landscapes; the magnitude of differences was similar across adult age classes. Our results suggest that in the urban and rural landscapes that we studied, adult habitats are similar in quality, but either larval or juvenile habitats may be of lower quality in urban areas.
Data from: Cross-taxa generalities in the relationship between population abundance and ambient temperatures
Identifying patterns in the effects of temperature on species' population abundances could help develop a general framework for predicting the consequences of climate change across different communities and realms. We used long-term population time series data from terrestrial, freshwater, and marine species communities within central Europe to compare the effects of temperature on abundance across a broad range of taxonomic groups. We asked whether there was an average relationship between temperatures in different seasons and annual abundances of species in a community, and whether species attributes (temperature range of distribution, range size, habitat breadth, dispersal ability, body size, and lifespan) explained interspecific variation in the relationship between temperature and abundance. We found that, on average, warmer winter temperatures were associated with greater abundances in terrestrial communities (ground beetles, spiders, and birds) but not always in aquatic communities (freshwater and marine invertebrates and fish). The abundances of species with large geographical ranges, larger body sizes, and longer lifespans tended to be less related to temperature. Our results suggest that climate change may have, in general, positive effects on species' abundances within many terrestrial communities in central Europe while the effects are less predictable in aquatic communities.
Data from: Genetic diversity and population structure of Trypanosoma brucei in Uganda: implications for the epidemiology of sleeping sickness and Nagana
Background: While Human African Trypanosomiasis (HAT) is in decline on the continent of Africa, the disease still remains a major health problem in Uganda. There are recurrent sporadic outbreaks in the traditionally endemic areas in south-east Uganda, and continued spread to new unaffected areas in central Uganda. We evaluated the evolutionary dynamics underpinning the origin of new foci and the impact of host species on parasite genetic diversity in Uganda. We genotyped 269 Trypanosoma brucei isolates collected from different regions in Uganda and southwestern Kenya at 17 microsatellite loci, and checked for the presence of the SRA gene that confers human infectivity to T. b. rhodesiense. Results: Both Bayesian clustering methods and Discriminant Analysis of Principal Components partition Trypanosoma brucei isolates obtained from Uganda and southwestern Kenya into three distinct genetic clusters. Clusters 1 and 3 include isolates from central and southern Uganda, while cluster 2 contains mostly isolates from southwestern Kenya. These three clusters are not sorted by subspecies designation (T. b. brucei vs T. b. rhodesiense), host or date of collection. The analyses also show evidence of genetic admixture among the three genetic clusters and long-range dispersal, suggesting recent and possibly on-going gene flow between them. Conclusions: Our results show that the expansion of the disease to the new foci in central Uganda occurred from the northward spread of T. b. rhodesiense (Tbr). They also confirm the emergence of the human infective strains (Tbr) from non-infective T. b. brucei (Tbb) strains of different genetic backgrounds, and the importance of cattle as Tbr reservoir, as confounders that shape the epidemiology of sleeping sickness in the region.
Data used for ALife 2016 paper "Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-Length Genomes"
<p>The results files in this directory contain the evolved critical mutation rates, exponential or quadratic curves produced by curve-fitting using the given data in R, and biological data used for comparison in the following paper:</p> <p>Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-Length Genomes, accepted for publication in ALife 2016: Proceedings of the 15th International Conference on the Synthesis and Simulation of Living Systems (ALIFE XV)</p>
Data_PlosOne_Too many is too bad: Long-term net negative effects of high density ungulate populations on a dominant Mediterranean shrub
<p>Dataset for Plos One Publication (2016): Too many is too bad: Long-term net negative effects of high density ungulate populations on a dominant Mediterranean shrub</p>
FIGURE 27. A–F in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status
FIGURE 27. A–F, lateral view of subrostral process. A, Aegla paulensis Schmitt, 1942 s. str., male topotype (MZUSP 34367). B, Aegla rosanae Campos Jr., 1998, male topotype (MZUSP 34369). C, Aegla vanini n. sp., male holotype (MZUSP 34371). D, Aegla japi n. sp., male paratype (MZUSP 34375). Aegla jaragua n. sp., male paratype (MZUSP 34377). F, Aegla jundiai n. sp., female holotype (MZUSP 13493). Bars: A, D = 1.0 mm; B, C, E, F = 0.5 mm.
FIGURE 23. Aegla jundiai n in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status
FIGURE 23. Aegla jundiai n. sp., female holotype (MZUSP 13493). A, lateral view of the anterior region of the cephalothorax. B, dorsal view of epibranchial area. C, third and fourth thoracic sternites. D, Telson, uropods and sixth abdominal segment. Note in A, the subrostral process (arrow). Bars: A, D = 2.0 mm; B = 0.25 mm; C = 1.0 mm.
FIGURE 19. Aegla japi n in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status
FIGURE 19. Aegla japi n. sp., male holotype (MZUSP 34374). A, lateral view of the anterior region of the cephalothorax. B, dorsal view of epibranchial area. C, third and fourth thoracic sternites. D, telson, uropods and sixth abdominal segment. Note in A, the subrostral process (arrow). Bars: A, C = 1.0 mm; B = 0.25 mm; D = 2.0 mm.
FIGURE 29. A–F in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status
FIGURE 29. A–F, Ventral view of third (St3) and fourth thoracic sternites. A, Aegla paulensis Schmitt, 1942 s. str., male topotype (MZUSP 34367). B, Aegla rosanae Campos Jr., 1998, male topotype (MZUSP 34369). C, Aegla vanini n. sp., male holotype (MZUSP 34371). D, Aegla japi n. sp., male paratype (MZUSP 34375). E, Aegla jaragua n. sp., male paratype (MZUSP 34377). F, Aegla jundiai n. sp., female holotype (MZUSP 13493). Note in A, St3 tapered distally; St3 abrupt in B; and St3 truncate in C–F. Bars = 0.5 mm.
FIGURE 17. Aegla vanini n in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status
FIGURE 17. Aegla vanini n. sp., male holotype (MZUSP 34371). A, lateral view of the anterior region of the cephalothorax. B, dorsal view of the right epibranchial area. C, third and fourth thoracic sternites. D, telson, uropods and sixth abdominal segment. Note in A, the subrostral process (arrow). Bars: A, D = 2.0 mm; B = 0.25 mm; C = 1.0 mm.
FIGURE 28. A–F in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status
FIGURE 28. A–F, dorsal view of epibranchial area. A, Aegla paulensis Schmitt, 1942 s. str., male topotype (MZUSP 34367). B, Aegla rosanae Campos Jr., 1998, male topotype (MZUSP 34369). C, Aegla vanini n. sp., male holotype (MZUSP 34371). D, Aegla japi n. sp., male paratype (MZUSP 34375). E, Aegla jaragua n. sp., male paratype (MZUSP 34377). F, Aegla jundiai n. sp., female holotype (MZUSP 13493). Bars: 0.2 mm.
FIGURE 15 in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status
FIGURE 15. Aegla lancinhas Bond-Buckup & Buckup in Santos et al., 2015, male topotype (MZUSP 34403). A, lateral view of the anterior region of the cephalothorax. B, lateral view of subrostral process (arrow). C, epibranchial area with small corneous scale on the anterolateral angle and lateral margin (arrows). D, anteromesial region of third thoracic sternite abruptshaped. E, chelipeds subequal and poorly inflated. F, telson, uropods and sixth abdominal segment Bars: A = 1.0 mm; B, D = 0.5 mm; C = 0.2 mm; E, F = 2.0 mm.
FIGURE 14 in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status
FIGURE 14. Aegla rosanae Campos Jr., 1998, female holotype (MZUSP 11162). A, ventral view of the posterior region of the cephalothorax and anterior region of the abdomen. B, lateral view of the anterior region of the cephalothorax. C, epibranchial area with small corneous scales on the anterolateral angle and lateral margin (arrows). D, anteromesial region of third thoracic sternite abrupt-shaped. Note in A, female gonopores and pleopods (arrows). Note in B, protogastric lobes (wide arrow), subrostral process (thin arrow) and rostrum nearly curved upward distally. Bars: A = 1.0 mm; B, D = 0.5 mm; C = 0.2 mm.
FIGURE 13 in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status
FIGURE 13. Aegla rosanae Campos Jr., 1998, male topotype (MZUSP 34369). A, lateral view of the anterior region of the cephalothorax. B, dorsal view of epibranchial area. C, third and fourth thoracic sternites. D, telson, uropods and sixth abdominal segment. Note in A, the subrostral process (arrow). Bars: A, D = 2.0 mm. B = 0.5 mm. C = 1.0 mm.
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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.