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227 results for “demographic history”
Data from: Contrasting population structure and demographic history of cereal aphids in different environmental and agricultural landscapes
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Population genomic analyses reveal hybridization and marked differences in genetic structure and demographic history of Scurria limpet sister species with parapatric distributions across the southeastern pacific
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Population genetic structure and demographic history of Rhodeus atremius suigensis, an endangered bitterling in Japan
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Data from: Population structure, connectivity and demographic history of an apex marine predator, the bull shark Carcharhinus leucas
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Data from: Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus)
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Data from: Genomic divergence, demographic histories, and male territorial response reveal asymmetric reproductive barriers in allopatric eastern versus western Nashville warbler subspecies (<em>Leiothlypis ruficapilla</em>)
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Data from: Genetic structure and demographic history of house mice in Western Europe inferred using whole genome sequences
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Data from: Demographic history and inbreeding in two declining sea duck species inferred from whole genome sequence data
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Genetic diversity, genetic differentiation and demographic history of Cryptomeria (Cupressaceae), a Tertiary relict plant in East Asia based on RAD sequencing
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Population genetics, demographic and evolutionary history of the Dudley’s lousewort, a rare redwood forest specialist (Pedicularis dudleyi)
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Data from: Demographic history and genomic diversity and divergence in blue tit populations across heterogeneous environments
<p>Understanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio-temporal variation in population demography and variation in recombination rate and diversity along the genome. Here, we investigated these parameters in blue tit populations inhabiting deciduous <i>versus</i> evergreen forests and insular <i>versus</i> mainland areas, in the context of a previously described strong phenotypic differentiation. Neighboring population pairs of deciduous and evergreen habitats were weakly genetically differentiated (<i>F</i><sub>ST</sub> = 0.004 on average), nevertheless with a statistically significant effect of habitat type on the overall genetic structure. This low differentiation was consistent with the strong and long-lasting gene flow between populations, inferred by demographic modeling. In turn, insular and mainland populations were moderately differentiated (<i>F</i><sub>ST</sub> = 0.08 on average), in line with the inference of moderate ancestral migrations, followed by isolation since the end of the last glaciation. Effective population sizes were overall large, yet smaller on the island than on the mainland. Weak and non-parallel footprints of divergent selection between deciduous and evergreen populations were consistent with their high connectivity and the probable polygenic nature of local adaptation in these habitats. In turn, stronger footprints of divergent selection were identified between long isolated insular <i>versus</i> mainland birds, and were more often found in regions of low recombination as expected from theory. Lastly, we identified a genomic inversion on the mainland, spanning 2.8Mb. These results provide insights into the demographic history and genetic architecture of local adaptation in blue tit populations at multiple geographic scales.</p>
Population genetic structure and demographic history of the lone star tick, Amblyomma americanum (Ixodida: Ixodidae): new evidence supporting old records
Range expansions are a potential outcome of climate change. Population genetic structure and demography can be used as tools to evaluate hypotheses on changes in geographic distribution. In this study we explored the genetic variability, population genetic structure, demographic history, and habitat suitability of Amblyomma americanum, a North American tick species that is a known vector of several pathogenic microorganisms. We used a novel double digestion restriction site-associated DNA sequencing (dd-RAD seq), and we discovered 8181 independent single nucleotide polymorphisms (SNPs) from 189 ticks from across the geographic range of the species. Overall, genetic diversity was lower than expected. Further, the edge populations did not have a statistically significant lower diversity than core populations, and hypotheses of range expansion are not supported by a test based on genetic data. Nonetheless, moderate levels of population structure were detected among geographic regions, with the northeast cluster the least variable. Demographic and species distribution models support a scenario where A. americanum was present in more northern locations in the past, underwent a bottleneck, and is now recovering. These findings highlight the importance of demographic modeling and genomic data in assessing the recent history and genetic structure of pathogen vectors.
Data from: Genetic diversity and demographic history of introduced sika deer on the Delmarva Peninsula
The introduction of non-native species can have long-term effects on native plant and animal communities. Introduced populations are occasionally not well understood and offer opportunities to evaluate changes in genetic structure through time and major population changes such as bottleneck and or founder events. Invasive species can often evolve rapidly in new and novel environments, which could be essential to their long-term success. Sika deer are native to East Asia, and their introduction and establishment to the Delmarva Peninsula, USA is poorly documented, but probably involved ≥1 founder and/or bottleneck events. We quantified neutral genetic diversity in the introduced population and compared genetic differentiation and diversity to the presumed source population from Yakushima Island, Japan, and a captive population of sika deer in Harrington, Delaware, USA. Based on data from 10 microsatellite DNA loci, we observed reduced genetic variation attributable to founder events, support for historic hybridization events, and evidence that the population did originate from Yakushima Island stocks. Estimates of population structure through Bayesian clustering and demographic history derived from Approximate Bayesian Computation (ABC), were consistent with the hypothesized founder history of the introduced population in both timing and effective population size (approximately 5 effective breeding individuals, an estimated 36 generations ago). Our ABC results further supported a single introduction into the wild happening before sika deer spread throughout the Delmarva. We conclude that free-ranging sika deer on Delmarva are descended from ca. 5 individuals introduced about 100 years ago from captive stocks of deer maintained in the United Kingdom. Free-ranging sika deer on Delmarva have lost neutral diversity due to founder and bottleneck events, yet populations have expanded in recent decades and show no evidence of abnormalities associated with inbreeding. We suggest management practices including increasing harvest areas and specifically managing sika deer outside of Maryland.
Study on the correlation of prevalence of ocular disease to different demographic variables, medical history and concomitant diseases.
<p>Random blood sugar, cholesterol, and triglycerides were analyzed by taking the blood sample from each patient. The average of the parameters was recorded, and the standard deviation (SD) was calculated. The parameters have been presented in the study as mean± SD. Blood sample analysis revealed that the average random blood glucose level (mg/dl) was 113.3±26.9 (Mean ±SD). The average cholesterol level was 189.35± 49.7 mg/dl, and the average triglycerides level was 124.25±50.0 mg/dl. Average systolic and diastolic blood pressure was found to be 126.0 ± 15.5 mmHg and 81.43 ± 8.0 mmHg, respectively. The patients were examined by the dermatologist. The dermatologists observed the signs, and the patients were asked about the presence of the symptoms to evaluate the severity of psoriasis and psoriatic arthropathy. The patients were asked about the duration for which they had been suffering from psoriasis. On average, a patient was found to be suffering from psoriasis for 11.4 ±9.9 years (the duration ranged from a minimum of 1 year to a maximum of 45 years). The doctor screened the patients for the number of sites involved and evaluated the severity of psoriasis via psoriasis area and severity index (PASI) score. Average Psoriasis Area and Severity Index (PASI) for the patients, as recorded by the dermatologists, was found to be 5.94 ± 6.8. </p>
Data from: Lack of genetic isolation by distance, similar genetic structuring but different demographic histories in a fig-pollinating wasp mutualism
Historical abiotic factors such as climatic oscillations and extreme climatic events as well as biotic factors have shaped the structuring of species' genetic diversity. In obligate species-specific mutualisms, the biogeographic histories of the interacting species are tightly linked. This could be particularly true for nuclear genes in the Ficus-pollinating wasp mutualistic association as the insects disperse pollen from their natal tree. In this study we compare spatial genetic structure of plant and pollinator for the Ficus hirta-Valisia javana association throughout South-East China including Hainan Island, for both nuclear and cytoplasmic markers. We show that dispersal of the insect leads to plant and insect presenting similar signatures of lack of genetic isolation by distance for nuclear genes on the continent over a distance of 1000 km. But we also show that the demographic histories of plant and insect are strikingly different. This is in agreement with extreme climatic events leading to transient regional extinctions of the insects, associated with local survival of the plants. We also evidence genetic differentiation for both wasps and fig-tree between the continent and Hainan Island, although the Qiongzhou Strait is only on average 30 km wide suggesting that geographic isolation by itself has not been sufficient to generate this differentiation. Hence, our results suggest that in highly dispersive mutualistic systems, isolation by dispersal limitation across a geographic barrier could be supplemented by isolation by adaptation, and maybe by coevolution, allowing further genetic divergence. In such systems, species may frequently be composed of a single population.
Data from: Speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a species of conservation concern
The North America deserts were impacted by both Neogene plate tectonics and Quaternary climatic fluctuations, yet it remains unclear how these events influenced speciation in this region. We tested published hypotheses regarding the timing and mode of speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a sand dune specialist endemic to the Mojave Desert of California and Arizona. We sampled 109 individual lizards representing 22 insular dune localities, obtained DNA sequences for 14 nuclear loci, and found that U. scoparia has low genetic diversity relative to the U. notata species complex, comparable to that of chimpanzees and southern elephant seals. Analyses of genotypes using Bayesian clustering algorithms did not identify discrete populations within U. scoparia. Using Isolation-with-Migration (IM) models and a novel coalescent-based hypothesis testing approach, we estimated that U. scoparia diverged from U. notata in the Pleistocene epoch. The Likelihood Ratio Test and the Akaike Information Criterion consistently rejected nested speciation models that included parameters for migration and population growth of U. scoparia. We reject the Neogene vicariance hypothesis for the speciation of U. scoparia, and define this species as a single evolutionarily significant unit for conservation purposes.
Data from: Demographic history inferred from genome-wide data reveals two lineages of sheldgeese endemic to a glacial refugium in the southern Atlantic
Aim: The Malvinas/Falkland Islands (MFI) constitute the largest archipelago in the southern Atlantic, and harbour endemic lineages that presumably evolved after sea-level rise, associated with glacial periods, isolated ancestral populations. We investigate the role of the MFI in isolating populations from continental counterparts of two highly vagile species: the sheldgeese Chloephaga picta and Chloephaga rubidiceps. Location: Patagonia and the Malvinas/Falkland Islands. Methods: We sampled C. picta and C. rubidiceps on the continent and MFI. Using a reduced-representation genomic approach, we quantified the genetic differentiation between insular and continental populations of both species, and used coalescent-based analyses to model their demography. Results: The MFI harbour independently evolving lineages of C. picta and C. rubidiceps, which diverged from their continental counterparts during the Middle-Late Pleistocene and have since experienced negligible gene flow. Main conclusions: The c. 450 km that separate the archipelago from the continent are sufficient to isolate populations of these putatively highly vagile species. Ancestral lineages may have reached the MFI refugium during glacial cycles. Without conservation measures, the drastic decline of the morphologically, behaviourally and ecologically distinct continental population of C. rubidiceps, to < 1000 individuals, may lead to the extinction of an independently evolving taxon.
Data from: Post-Pleistocene demographic history of the North Atlantic endemic Irish moss Chondrus crispus: glacial survival, spatial expansion and gene flow
Range expansions and gene flow as micro-evolutionary processes played a leading role in the population demographic history of marine organisms. Herein, we sequenced partial mtDNA Cox1 gene from 26 assigned geographic populations in order to understand how Irish moss (Chondrus crispus) responded to severe climatic oscillations during the Pleistocene glaciations and contemporary forces such as gene flow. Phylogeographic patterns indicated that haplotype frequency distributions were strongly skewed, with nearly half found only in single samples and thus restricted to a single population. Analysis of molecular variance revealed that most of the variation was within populations with no significant genetic structuring on either side of the Atlantic. Demographic analyses indicated that ISI (Irish Sea and Ireland) and NS (the North Sea) areas experienced a slight trend of increase in population size over time, whereas EC (the English Channel) area experienced expansion beginning approximately 170,000-360,000 BP. The observed complex genetic pattern of C. crispus is consistent with a scenario of multiple unrelated founding events by survival of this species in at least three putative Pleistocene refugia along the European coastline, and subsequent trans-Atlantic dispersal combined with contiguous northward population expansion predating the LGM and geographically gene flow.
Data from: Genetic diversity, demographical history and conservation aspects of the endangered yew tree Taxus contorta (syn. Taxus fuana) in Pakistan
Western Himalayan yew (Taxus contorta Griffith, synonym T. fuana Nan Li & R.R. Mill), one of the highly prized tree species for its anticancer properties is experiencing severe reduction in populations across its range in Pakistan. We examined a chloroplast DNA region (trnL-F) and ten nuclear microsatellite loci variations among seven populations to investigate the levels of genetic diversity and demographical history of T. contorta in Pakistan. Low haplotype diversity (HT = 0.182), moderate level of microsatellite diversity (HE = 0.526 ± 0.034), significant population differentiation (FST = 0.106) and high level of inbreeding (FIS = 0.222-0.418) was found in T. contorta compared with its congeners. Results of mismatch distribution analysis, neutrality tests and data on glacial chronologies of western Himalaya indicated that demographic expansion of T. contorta in Pakistan predates extensive glaciations that occurred during late Pleistocene (140.06 thousand years ago (kya), and the spatial expansion most likely happened very recently in the Holocene (6.71 kya). An unprecedented level of habitat disturbances since past few decades coupled with the severe historic climate may have played an important role on an extant population structure of T. contorta. We have discussed a range of sustainable management measures for the ecological restoration of remnant populations as well as to exploit high economic benefits that can be obtained from this species.
Data from: Comparing genetic diversity and demographic history in co-distributed wild South American camelids
Vicuñas and guanacos are two species of wild South American camelids that are key ruminants in the ecosystems where they occur. Although closely related, these species feature differing ecologies and life history characters, which are expected to influence both their genetic diversity and population differentiation at different spatial scales. Here, using mitochondrial and microsatellite genetic markers, we show that vicuña display lower genetic diversity within populations than guanaco but exhibit more structure across their Peruvian range, which may reflect a combination of natural genetic differentiation linked to geographic isolation and recent anthropogenic population declines. Coalescent based demographic analyses indicate that both species have passed through a strong bottleneck, reducing their effective population sizes from over 20,000 to less than 1,000 individuals. For vicuña this bottleneck is inferred to have taken place ~3,300 years ago, but to have occurred more recently for guanaco at ~2,000 years ago. These inferred dates are considerably later than the onset of domestication (when the alpaca was domesticated from the vicuña while the llama was domesticated from the guanaco), coinciding instead with a major human population expansion following the mid-Holocene cold period. As importantly, they imply earlier declines than the well-documented Spanish conquest, where major mass mortality events were recorded for Andean human and camelid populations. We argue that underlying species' differences and recent demographic perturbations have influenced genetic diversity in modern vicuña and guanaco populations, and these processes should be carefully evaluated in the development and implementation of management strategies for these important genetic resources.
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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.