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19,493 results for “Populism”
Data from: Drift happens: molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests
Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four river systems and two major watersheds in Wisconsin, USA. Floodplain forests and marshes provide a model system for assessing the effects of habitat fragmentation within agricultural/urban landscapes and for testing whether rivers act to genetically connect dispersed populations. We generated a panel of 12,856 single nucleotide polymorphisms and assessed genetic diversity, differentiation, gene flow, and drift. Clustering methods revealed strong population genetic structure with limited admixture and highly differentiated populations (mean multilocus FST = 0.32, FST' = 0.33). No signals of isolation by geographic distance or environment emerged, but alleles may flow along rivers given that genetic differentiation increased with river distance. Differentiation also increased in populations with fewer private alleles (R2 = 0.51) and higher local inbreeding (R2 = 0.22). Populations varied greatly in levels of local inbreeding (FIS = 0.2 to 0.9) and FIS declined in smaller, more isolated populations. These results suggest that genetic drift dominates other forces in structuring these Impatiens populations. In rapidly changing environments, species must migrate or genetically adapt. Habitat fragmentation limits both processes, potentially compromising the ability of species to persist in fragmented landscapes.
Data from: Long-term persistence of monotypic dengue transmission in small size isolated populations, French Polynesia, 1978-2014
<p>Understanding the transition of epidemic to endemic dengue transmission remains a challenge in regions where serotypes co-circulate and there is extensive human mobility. French Polynesia, an isolated group of 72 inhabited islands, distributed among five geographically separated subdivisions, has recorded mono-serotype epidemics since 1944, with long inter-epidemic periods of circulation. Laboratory confirmed cases have been recorded since 1978, enabling exploration of dengue epidemiology under monotypic conditions in an isolated, spatially structured geographical location. A database was constructed of confirmed dengue cases, geolocated to island for a 35-year period. Statistical analyses of viral establishment, persistence and fade-out as well as synchrony among subdivisions were performed. Seven monotypic and one heterotypic dengue epidemic occurred, followed by low-level viral circulation with a recrudescent epidemic occurring on one occasion. Incidence was asynchronous among the subdivisions. Complete viral die-out occurred on several occasions with invasion of a new serotype, but also in the absence of any novel serotype. Island population size had a strong impact on the establishment, persistence and fade-out of dengue cases and endemicity was estimated achievable only at a population size in excess of 175 000. Despite island remoteness and low population size, dengue cases were observed somewhere in French Polynesia almost constantly, in part due to the spatial structuration generating asynchrony among subdivisions. Long-term persistence of dengue virus in this group of island populations may be enabled by island hopping, although could equally be explained by a reservoir of sub-clinical infections on the most populated island, Tahiti.</p>
Data from: Natural selection on antihelminth antibodies in a wild mammal population
<p>An effective immune response is expected to confer fitness benefits through improved resistance to parasites but also energetic costs which negatively impact fitness-related traits such as reproduction. These fitness costs and benefits of an immune response are likely to depend on host age, sex, and levels of parasite exposure. Few studies have examined the full extent to which patterns of natural selection on immune phenotypes vary across demographic groups and environments in the wild. Here, we assessed natural selection on plasma levels of three functionally distinct isotypes (IgA, IgE and IgG) of antibodies against a prevalent nematode parasite measured in a wild Soay sheep population over 25 years. We found little support for environment-dependent selection or reproductive costs. However, antibody levels were negatively associated with parasite egg counts and positively associated with subsequent survival, albeit in a highly age- and isotype-dependent manner. Raised levels of anti-parasite IgA best predicted reduced egg counts but this did not predict survival in lambs, whilst in adult females increased anti-parasite IgG predicted reduced egg counts and improved survival. Our results highlight the potential importance of age-dependent selection on immune phenotypes in nature, and that patterns of selection can vary even amongst functionally-related immune markers.</p>
Run and output files from: Holocene population expansion of a tropical bee coincides with early human colonisation of Fiji rather than climate change
<p><span><span><span><span><span><span><span><span><span><span><span>There is substantial debate about the relative roles of climate change and human activities on biodiversity and species demographies over the Holocene. In some cases, these two factors can be resolved using fossil data, but for many taxa such data are not available. Inferring historical demographies of taxa has become common, but the methodologies are mostly recent and their shortcomings often unexplored. The bee genus <i>Homalictus</i> is developing into a tractable model system for understanding how native bee populations in tropical islands have responded to past climate change. We greatly expand on previous studies using sequences of the mitochondrial gene COI from 474 specimens and between 171 and 3,928 autosomal (DArTSeq) SNP loci from 19 specimens of the native Fijian bee, <i>Homalictus fijiensis</i> (Perkins & Cheesman, 1928), to explore its historical demography using coalescent and mismatch analyses. We ask whether past changes in demography were human- or climate-driven, while considering analytical assumptions. We show that inferred changes in population sizes are too recent to be explained by past climate change. Instead we find that a dramatic increase in population size for the main island of Viti Levu coincides with increasing occupation by humans and their modification of the environment. We found no corresponding change in bee population size for another major island, Kadavu, where human populations and agricultural activities have been historically very low. Our analyses indicate that molecular approaches can be used to disentangle the impacts of humans and climate change on a major tropical pollinator and that stringent analytical approaches are required for reliable interpretation of results. </span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Different genetic structures revealed resident populations of a specialist parasitoid wasp in contrast to its migratory host
Genetic comparisons of parasitoids and their hosts are expected to reflect ecological and evolutionary processes that influence the interactions between species. The parasitoid wasp, Cotesia vestalis, and its host diamondback moth (DBM), Plutella xylostella, provide opportunities to test whether the specialist natural enemy migrates seasonally with its host or occurs as resident population. We genotyped 17 microsatellite loci and two mitochondrial genes for 158 female adults of C. vestalis collected from 12 geographical populations, as well as nine microsatellite loci for 127 DBM larvae from six separate sites. The samplings covered both the likely source (southern) and immigrant (northern) areas of DBM from China. Populations of C. vestalis fell into three groups, pointing to isolation in northwestern and southwestern China and strong genetic differentiation of these populations from others in central and eastern China. In contrast, DBM showed much weaker genetic differentiation and high rates of gene flow. TESS analysis identified the immigrant populations of DBM as showing admixture in northern China. Genetic disconnect between C. vestalis and its host suggests that the parasitoid did not migrate yearly with its host but likely consisted of resident populations in places where its host could not survive in winter.
Data from: Sporadic genetic connectivity among small insular populations of the rare geoendemic plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower)
Globally, a small number of plants have adapted to terrestrial outcroppings of serpentine geology, which are characterized by soils with low levels of essential mineral nutrients (N, P, K, Ca, Mo) and toxic levels of heavy metals (Ni, Cr, Co). Paradoxically, many of these plants are restricted to this harsh environment. Caulanthus ampexlicaulis var. barbarae (Brassicaceae) is a rare annual plant that is strictly endemic to a small set of isolated serpentine outcrops in the coastal mountains of central California. The goals of the work presented here were to 1) determine the patterns of genetic connectivity among all known populations of Caulanthus ampexlicaulis var. barbarae, and 2) estimate contemporary effective population sizes (Ne), in order to inform ongoing genomic analyses of the evolutionary history of this taxon, and to provide a foundation upon which to model its future evolutionary potential and long-term viability in a changing environment. Eleven populations of this taxon were sampled, and population-genetic parameters were estimated using 11 nuclear microsatellite markers. Contemporary effective population sizes were estimated using multiple methods and found to be strikingly small (typically Ne < 10). Further, our data showed that a substantial component of genetic connectivity of this taxon is not at equilibrium, and instead showed sporadic gene flow. Several lines of evidence indicate that gene flow between isolated populations is maintained through long-distance seed dispersal (e.g. > 1 km), possibly via zoochory.
Varying genetic imprints of roads and human density in North American mammal populations
<p>Road networks and human density are major factors contributing to habitat fragmentation and loss, isolation of wildlife populations and reduced genetic diversity. Terrestrial mammals are particularly sensitive to road networks and encroachment by human populations. However, there are limited assessments of the impacts of road networks and human density on population-specific nuclear genetic diversity, and it remains unclear how these impacts are modulated by life history traits. Using generalized linear mixed models and microsatellite data from 1444 North American terrestrial mammal populations we show that taxa with large home range sizes, dense populations, and large body sizes had reduced nuclear genetic diversity with increasing road impacts and human density, but the overall influence of life history traits was generally weak. Instead, we observed a high degree of genus-specific variation in genetic responses to road impacts and human density. Human density negatively affected allelic diversity or heterozygosity more than road networks (13 versus 5-7 of 25 assessed genera, respectively); increased road networks and human density also positively affected allelic diversity and heterozygosity in 15 and 6-9 genera, respectively. Large bodied, human-averse species were generally more negatively impacted than small, urban-adapted species. Genus-specific responses to habitat fragmentation by ongoing road development and human encroachment likely depend on the specific capability to (i) navigate roads as either barriers or movement corridors, and (ii) exploit resource-rich urban environments. The non-uniform genetic response to roads and human density highlights the need to implement efforts to mitigate the risk of vehicular collisions, while also facilitating gene flow between populations of particularly vulnerable taxa.</p>
Convergent geographic patterns between grizzly bear population genetic structure and Indigenous language groups in coastal British Columbia
<p>Microsatellite loci calls, sex, and mean centre detection per individual (GrizzlyMicroLociMeanXY.csv) and code associated with the paper: "Convergent geographic patterns between grizzly bear population genetic structure and Indigenous language groups in coastal British Columbia". All code is from published R packages or GitHub repositories not created by the author. Code used is best described in these alternate resources. </p>
Population disruption: estimating changes in population distribution in the UK during the COVID-19 pandemic - Estimates for Local Authority Districts
<p><strong>Overview:</strong></p> <p>Population estimates from the publication: <em>Population disruption: estimating changes in population distribution in the UK during the COVID-19 pandemic.</em> </p> <p>Population estimates were aggregated to Local Authority Districts (LADs). </p> <p><strong>Methodology: </strong></p> <p>Population estimates were extracted from Bing Tiles (Zoom Level 12) to 2019 LADs by assigning tiles to LADs by their percent areal overlap. This method assumes constant population distribution across a single Bing Tile.</p> <p>2019 LAD boundaries are available from the <a href="https://geoportal.statistics.gov.uk/datasets/local-authority-districts-december-2019-boundaries-uk-bfc/explore">UK Government Open Geography Portal</a>.</p> <p> </p>
Simulation of freely-diffusing smFRET data of a static mixture of 2 populations
<p>Simulation data created with PyBroMo smFRET simulation software.</p>
FIGURE 30 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 30. Bayesian tree (TPM 2 uf + G) for Aegla species based on partial fragment of 16 S. Node numbers represent posterior probabilities (values <50 % are not shown), and divergence time in millions of years (my); * indicates the calibration points to molecular clock. The clade C proposed by Pérez-Losada et al. (2004) is highlighted in grey. The basin and sub-basin origin of the discussed species in this study are shown after the specific names.
FIGURE 24. A – L 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 24. A – L, proximal portion of fifth pereiopod showing coxa and sexual tube of long and narrow type. A – B, Aegla paulensis Schmitt, 1942 s. str., male topotype (MZUSP 34368). C – D, Aegla rosanae Campos Jr., 1998, male topotype (MZUSP 34369). E – F, Aegla vanini n. sp., male paratype (MZUSP 34372). G – H, Aegla japi n. sp., male paratype (MZUSP 34375). I – J, Aegla jaragua n. sp. male paratype (MZUSP 34378). K-L, Aegla jundiai n. sp., male paratype (MZUSP 13490). Bars: A – D, F – H, J = 200 µm; K, L = 100 µm; E, I = 500 µm.
FIGURE 8 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 8. Types of Aegla Leach, 1820 male sexual tubes. A, long and narrow (A. lancinhas Bond-Buckup & Buckup in Santos et al., 2015, MZUSP 34403). B, short and wide (A. leptochela Bond-Buckup & Buckup, 1994, MZUSP 34491).
FIGURE 1 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 1. Distribution of the species of Aegla in four main hydrographic basins of southern Brazil: Rio Grande, Rio Tietê (Upper Paraná system), Rio Paraíba do Sul and Ribeira de Iguape. Indications L 1 through L 7 refer to the locations mentioned under “ sampling area ” in the Material & Methods section.
Fig. 5. All reported populations for the following species. A. Uronema marinum Dujardin, 1841. B in Seven scuticociliates (Protozoa, Ciliophora) from Alabama, USA, with descriptions of two parasitic species isolated from a freshwater mussel Potamilus purpuratus
Fig. 5. All reported populations for the following species. A. Uronema marinum Dujardin, 1841. B. Pseudocohnilembus hargisi Evans & Thompson, 1964. C. Metanophrys similis Song et al., 2002. D. Pleuronema setigerum Calkins, 1902. E. Uronemita filificum Kahl, 1931.
High density genotypes of French Sheep populations
<p>Genotypes of 27 French sheep populations on the Illumina Ovine HD SNP chip.</p> <p>Dataset and results are presented in the preprint:</p> <p><strong>High density genome scan for selection signatures in French sheep reveals allelic heterogeneity and introgression at adaptive loci. </strong>Christina Marie Rochus, Flavie Tortereau, Florence Plisson-Petit, Gwendal Restoux, Carole Moreno-Romieux, Gwenola Tosser-Klopp, Bertrand Servin. bioRxiv 103010; doi: https://doi.org/10.1101/103010</p>
Overcoming the Dichotomy: New Insights into the Genomic Diversity of Open and Isolated European Populations
<p>The dataset includes autosomal data of 227 individuals of 9 Italian populations (Aosta, Benetutti, Carloforte, Lessinia Cimbrians, North Sardinia, Sappada, Sauris, Sulcis Iglesiente and Timau) genotyper with the GenoChip 2.0.</p>
Disease Spread in Age Structured Populations with Maternal Age Effects
<p>Fundamental ecological processes, such as extrinsic mortality, determine population age structure. This influences disease spread when individuals of different ages differ in susceptibility or when maternal age determines offspring susceptibility. We show that Daphnia magna offspring born to young mothers are more susceptible than those born to older mothers, and consider this alongside previous observations that susceptibility declines with age in this system. We used a susceptible- infected compartmental model to investigate how age-specific susceptibility and maternal age effects on offspring susceptibility interact with demographic factors affecting disease spread. Our results show a scenario where an increase in extrinsic mortality drives an increase in transmission potential. Thus, we identify a realistic context in which age effects and maternal effects produce conditions favouring disease transmission. </p> <p>epi model R script.R</p> <p>This is the script for the SIR model as well as the associated script for life history data. </p> <p>main.body size.csv</p> <p>This is the data for the body size data collected in the main experiment. This was measured using imageJ, was recorded in pixels and converted into millimetres. </p> <p>main.exposed.csv</p> <p>This is the proportion of infected/not infected individuals from an exposed treatment group. This was a subset of individuals from the entire experiment. This was the result of the exposures from the main experiment. </p> <p>main.reproduction.csv</p> <p>This document records reproduction for individuals from old or young mothers. It is a count of the offspring born at each reproductive event, which occurs generally every three days, though variation in interclutch interval increases with age. This was from the main experiment. Only those who were unexposed to the parasite, where used for this portion of the experimental work. </p> <p>sm.body size.csv</p> <p>This records body size similarly to above, and was an independent replication of the main experiment. </p> <p>sm.infection status.csv</p> <p>This is infection outcomes of exposures carried out as above, in an independent replication of the main experiment. </p> <p>sm.total babies.csv</p> <p>This is the reproductive output, carried out similarly to above, but in an independent replication of the main experiment. </p>
Figure 9b. from: A first integrative study of the identity and origins of the British Dwarf Pill Millipede populations, Trachysphaera cf. lobata (Diplopoda, Glomerida, Glomeridae) - Biodiversity Data Journal 3: e5176 (09 June 2015) https://doi.org/10.3897/BDJ.3.e5176
Figure 9b. - Taxonomically informative character examples. Abbreviations: AS = anal shield; T10 = tergite 10; c8 = male tergite 10, posterior margin, number of rows of large bacilli; c12 = male anal shield, shape. For more information on characters and states see Table 2.Figure 9a.TW30: T.lobata, male, South Wales (MBsID: 852824). Character states: two rows of bacilli on posterior edge of T10 (c8/1) and well-rounded anal shield (c12/0). This set of character states is (in our sample) unique for T.lobata.Figure 9b.GL07: T.cf.rousseti, male, Spain (MBsID: 852825). Character states: one row of bacilli on posterior edge of T10 (c8/0) and anal shield with special protuberance (c12/1). This set of character states is (in our sample) shared by T.pyrenaica, T.cf.rousseti, and T.cf.drescoi. <br>
Figure 9a. from: A first integrative study of the identity and origins of the British Dwarf Pill Millipede populations, Trachysphaera cf. lobata (Diplopoda, Glomerida, Glomeridae) - Biodiversity Data Journal 3: e5176 (09 June 2015) https://doi.org/10.3897/BDJ.3.e5176
Figure 9a. - Taxonomically informative character examples. Abbreviations: AS = anal shield; T10 = tergite 10; c8 = male tergite 10, posterior margin, number of rows of large bacilli; c12 = male anal shield, shape. For more information on characters and states see Table 2.Figure 9a.TW30: T.lobata, male, South Wales (MBsID: 852824). Character states: two rows of bacilli on posterior edge of T10 (c8/1) and well-rounded anal shield (c12/0). This set of character states is (in our sample) unique for T.lobata.Figure 9b.GL07: T.cf.rousseti, male, Spain (MBsID: 852825). Character states: one row of bacilli on posterior edge of T10 (c8/0) and anal shield with special protuberance (c12/1). This set of character states is (in our sample) shared by T.pyrenaica, T.cf.rousseti, and T.cf.drescoi. <br>
ScienceDex guides
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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.