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1,659 results for “structured population”
Data from: Genomics reveals the role of admixture in the evolution of structure among sperm whale populations within the Mediterranean Sea
<p>In oceanic ecosystems, the nature of barriers to gene flow, and the processes by which populations may become isolated are different from the terrestrial environment, and less well understood. In this study, we investigate a highly mobile species (the sperm whale, <em>Physeter macrocephalus</em>) that is genetically differentiated between an open North Atlantic population and the populations in the Mediterranean Sea. We apply high-resolution single nucleotide polymorphisms (SNP) analysis to study the nature of barriers to gene flow in this system, comparing gene flow across the putative boundary into the Mediterranean (Strait of Gibraltar and Alboran Sea region) with novel analyses on structuring among sperm whale populations within the Mediterranean basin. Our data support a recent founding of the Mediterranean, around the time of the last glacial maximum, and shows concerted historical demographic profiles in both the Atlantic and the Mediterranean. In each region, there is evidence for a population decline around the time of the founder event, more extreme within the Mediterranean Sea where effective population size is substantially lower. While differentiation is strongest at the Atlantic/Mediterranean boundary, there is also significant differentiation between the Eastern and Western basins of the Mediterranean Sea. We propose, however, that the mechanisms are different. While post-founding gene flow was reduced between the Mediterranean and Atlantic populations, within the Mediterranean an important factor differentiating the basins is likely a greater degree of admixture between the Western basin and the North Atlantic.</p>
Data for: Amazonian birds in more dynamic habitats have less population genetic structure and higher gene flow
<p>Understanding the factors that govern variation in genetic structure across species is key to the study of speciation and population genetics. Genetic structure has been linked to several aspects of life history, such as foraging strategy, habitat association, migration distance, and dispersal ability, all of which might influence dispersal and gene flow. Comparative studies of population genetic data from species with differing life histories provide opportunities to tease apart the role of dispersal in shaping gene flow and population genetic structure. Here, we examine population genetic data from sets of bird species specialized on a series of Amazonian habitat types hypothesized to filter for species with dramatically different dispersal abilities: stable upland forest, dynamic floodplain forest, and highly dynamic riverine islands. Using genome-wide markers, we show that habitat type has a significant effect on population genetic structure, with species in upland forest, floodplain forest, and riverine islands exhibiting progressively lower levels of structure. Although morphological traits used as proxies for individual-level dispersal ability did not explain this pattern, population genetic measures of gene flow are elevated in species from more dynamic riverine habitats. Our results suggest that the habitat in which a species occurs drives the degree of population genetic structuring via its impact on long-term fluctuations in levels of gene flow, with species in highly dynamic habitats having particularly elevated gene flow. These differences in genetic variation across taxa specialized in distinct habitats may lead to disparate responses to environmental change or habitat-specific diversification dynamics over evolutionary time scales.</p>
Figs 1–2 in The population structure of Leptoiulus proximus (Nĕmec, 1896) (Diplopoda, Julidae) in floodplain forests after summer flooding
Figs 1–2. Changes in abundance of individual stadia in the population of L. proximus. 1. Changes in epigeic activity (numbers of individuals per 18 pitfall traps) at four-week intervals over the four years after flooding. 2. Changes in density (individuals/m2) at four-week intervals over the four years after flooding (animals extracted from soil samples by Tullgren funnels).
Temporal population structure, a genetic dating method for ancient Eurasian genomes from the past 10,000 years
<p>Radiocarbon dating is the gold standard in archeology to estimate the age of skeletons, a key to studying their origins. Many published ancient genomes lack reliable and direct dates, which results in obscure and contradictory reports. Here, we developed the Temporal Population Structure (TPS), the first DNA-based dating method for ancient genomes ranging from the Late Mesolithic to modern-days, and applied it to 3,591 ancient and 1,307 modern Eurasians. We show that TPS predictions align with their known dates and correctly account for kin relationships. TPS dating of poorly dated Eurasian samples resolved conflicting reports in the literature, as illustrated by one test case. We demonstrated how TPS improved the ability to study phenotypic traits over time.</p>
Figure 4 in The spatial structure of а snow leopard population (Panthera uncia, Felidae, Carnivora) in east Kyrgyzstan
Figure 4. Relationship between the males of the Sarychat-Ertash Reserve (as inferred from the DNA microsatellite profiles).
Figure 3 in The spatial structure of а snow leopard population (Panthera uncia, Felidae, Carnivora) in east Kyrgyzstan
Figure 3. Relationship between the females of the Sarychat–Ertash Reserve (as inferred from the DNA microsatellite profiles).
Figure 2. Sections 1–3 in The spatial structure of а snow leopard population (Panthera uncia, Felidae, Carnivora) in east Kyrgyzstan
Figure 2. Sections 1–3 of different intensity of marking activity of the snow leopard. For a description, see text (polygons A, B, C).
Figure 1 in The spatial structure of а snow leopard population (Panthera uncia, Felidae, Carnivora) in east Kyrgyzstan
Figure 1. Areas of snow leopard study in the East Kyrgyzstan. Blue squares-surveyed areas; red points, traces of snow leopard activity.
National forest inventory data for a size-structured forest population model
<p>In forest communities, light competition is a key process for community assembly. Species' differences in seedling and sapling tolerance to shade cast by overstory trees is thought to determine species composition at late-successional stages. Most forests are distant from these late-successional equilibria, impeding a formal evaluation of their potential species composition. To extrapolate competitive equilibria from short-term data, we therefore introduce the JAB model, a parsimonious dynamic model with interacting size-structured populations, which focuses on sapling demography including the tolerance to overstory competition. We apply the JAB model to a two-"species" system from temperate European forests, i.e. the shade-tolerant species Fagus sylvatica L. and the group of all other competing species. Using Bayesian calibration with prior information from external Slovakian national forest inventory (NFI) data, we fit the JAB model to short timeseries from the German NFI. We use the posterior estimates of demographic rates to extrapolate that F. sylvatica will be the predominant species in 94% of the competitive equilibria, despite only predominating in 24% of the initial states. We further simulate counterfactual equilibria with parameters switched between species to assess the role of different demographic processes for competitive equilibria. These simulations confirm the hypothesis that the higher shade-tolerance of F. sylvatica saplings is key for its long-term predominance. Our results highlight the importance of demographic differences in early life stages for tree species assembly in forest communities.</p>
Figure 5 Nav kdr 1016 and 1534 in Genetic study in Aedes (Stegomyia) aegypti (Linnaeus, 1762) from Londrina (Paraná State, Brazil): an approach to population structure and pyrethroid resistance
Figure 5 Nav kdr 1016 and 1534 site allele frequencies in UEL. Collection site locations were distributed in the three regions of the campus.
Figure 4 in Genetic study in Aedes (Stegomyia) aegypti (Linnaeus, 1762) from Londrina (Paraná State, Brazil): an approach to population structure and pyrethroid resistance
Figure 4 Allele frequencies of Nav kdr 1016 and 1534 genotyping distributed in the five different regions of Londrina.
Figure 3 in Genetic study in Aedes (Stegomyia) aegypti (Linnaeus, 1762) from Londrina (Paraná State, Brazil): an approach to population structure and pyrethroid resistance
Figure 3 Haplotypic network obtained through specimens collected in UEL. The circles are proportional to the number of specimens observed in each haplotype.
Figure 2 in Genetic study in Aedes (Stegomyia) aegypti (Linnaeus, 1762) from Londrina (Paraná State, Brazil): an approach to population structure and pyrethroid resistance
Figure 2 Haplotype network observed in five regions of Londrina. The circles are proportional to the number of specimens observed in each haplotype. The haplotypes observed are in bold. The numbers represent nucleotide change positions.
Figure 1 in Genetic study in Aedes (Stegomyia) aegypti (Linnaeus, 1762) from Londrina (Paraná State, Brazil): an approach to population structure and pyrethroid resistance
Figure 1 Collection sites in Londrina. The red line is a boundary between the five regions of the city. The yellow ones represent the streets and avenues of the city. Only the urban area was evaluated in the study.
Fig. 7 in Comparative analysis of the population structure of Crematogaster subdentata and Lasius neglectus in the primary and secondary ranges (Hymenoptera: Formicidae)
Fig. 7 – Comparison of the sizes of foraging areas of polycalic colonies and supercolonies of Crematogaster subdentata and Lasius neglectus in the primary and secondary ranges: a, Crimea, b, – Rostov-on-Don, c, Tashkent.
Fig. 6 in Comparative analysis of the population structure of Crematogaster subdentata and Lasius neglectus in the primary and secondary ranges (Hymenoptera: Formicidae)
Fig. 6 – Average values of the average size of the foraging areas of Crematogaster subdentata (a) and Lasius neglectus (b) in the primary and secondary ranges. C – Crimea, T – Tashkent, R – Rostov-on-Don.
Fig. 5 in Comparative analysis of the population structure of Crematogaster subdentata and Lasius neglectus in the primary and secondary ranges (Hymenoptera: Formicidae)
Fig. 5 – Relation of tree and shrub species visited by Crematogaster subdentata (a, Crimea, b, Rostov-on-Don, c, Tashkent) and Lasius neglectus (d, – Crimea, e, – Rostov-on-Don, f, – Tashkent). Trees: Ac – Acer sp., Ah – Aesculus hippocastanum, Aj – Albizia julibrissin, Al – Ailanthus altissima, An – Acer negundo, Cl – Cedrus libani, Co – Cydonia oblonga, Cs – Cupressus sempervirens, Ea – Elaeagnus angustifolia, Fe – Fraxinus excelsior, Fr – Fraxinus sp., Gl – Gleditsia triacanta, Jr – Juglans regia, M – Morus sp., Md – Malus domestica, Mn – Morus nigra, Pa – Prunus americana, Pb - Pinus brutia, Pc – Prunus cerasus, Pd – Prunus domestica, Pi – Pinus pallasiana, Pp – Populus niger, Po – Populus alba, Pr – Prunus cerasifera, Ps – Prunus spinosa, Py - Populus pyramidalis, Ra – Robinia pseudoacacia, Sa – Salix sp., Sj – Styphnolobium japonicum, Tl – Tilia sp., Ul – Ulmus sp., Us – Ulmus laevis.
Fig. 1 in Comparative analysis of the population structure of Crematogaster subdentata and Lasius neglectus in the primary and secondary ranges (Hymenoptera: Formicidae)
Fig. 1 – Distribution of Crematogaster subdentata and Lasius neglectus in Tashkent C. subdentata, polycalic colonies, C. subdentata, monocalic colonies, L. neglectus,> 20 nests per 100 m, L. neglectus, 10-20 nests per 100 m, L. neglectus, <10 nests per 100 m.
Fig. 2 in Comparative analysis of the population structure of Crematogaster subdentata and Lasius neglectus in the primary and secondary ranges (Hymenoptera: Formicidae)
Fig. 2 – Scheme of the foraging areas of Lasius neglectus in Rostov-on-Don species; trees: Pc – Prunus cerasus, Ps – Prunus spinosa, Ul – Ulmus sp.
Fig. 4 in Comparative analysis of the population structure of Crematogaster subdentata and Lasius neglectus in the primary and secondary ranges (Hymenoptera: Formicidae)
Fig. 4 – Scheme of the foraging areas of Crematogaster subdentata in Crimea (A) and Tashkent (B) large accessible nests of C. subdentata in buildings and outside; inaccessible nests of C. subdentata in buildings; trees: Co – Cydonia oblonga, Jr – Juglans regia, M – Morus sp., Md – Malus domestica, Mn – Morus nigra, Pa – Prunus americana, Pd – Prunus domestica.
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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.