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212 results for “Data Drift”
Data from: Drift load in populations of small size and low density
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Data from: Influence of drift and admixture on population structure of American black bears (Ursus americanus) in the Central Interior Highlands, U.S.A. 50 years after translocation
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Data from: The roles of genetic drift and natural selection in quantitative trait divergence along an altitudinal gradient in Arabidopsis thaliana
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Data from: Swimming against the current: genetic structure, host mobility and the drift paradox in trematode parasites
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Data from: Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon
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Data from: Distribution and drift dispersal dynamics of a caddisfly grazer in response to resource abundance and its ontogeny
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Data from: Importance of biotic niches versus drift in a plant-inhabiting arthropod community depends on rarity and trophic group
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Data from: Frequency dependence and ecological drift shape coexistence of species with similar niches
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Data from: Do genetic drift and gene flow affect the geographic distribution of female plants in gynodioecious Lobelia siphilitica?
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Data for article: Normative drift and self-correction and self-regulation in scholarly publishing: The case of scholarly books published by academics at Makerere University
<p>University academics face multiple pressures to publish. These pressures emanate from contexts with different, often competing, social norms which result in academics publishing for reasons that may run counter to accepted scientific practice. This paper asks what decisions are being taken by academics when it comes to their choice of scholarly book publisher. An analysis of books selected from more than 2,500 self-reported scholarly publications produced by academics at Makerere University in Uganda from 2011 to 2017, reveals that 31 scholarly books were published. Of these books, more than half (54%) were published by publishers that do not follow accepted scholarly publishing practice. Findings also show that there was a sharp decline in books published with suspect publishers in the second half of the seven-year period. The article discusses possible reasons for the selection of suspect publishers and considers four factors that may account for the observable decline: (1) a cyclical downturn; (2) improved research management and reporting; (3) explication of the norms of science; and (4) self-correction.</p> <p><strong>METHODS</strong></p> <p>The specific interest of this study is the publication of scholarly books by academics at Makerere University. </p> <p>The sources of the publications data were the lists of research outputs published in Makerere University’s annual reports from 2011 to 2017. Digital copies of the annual reports in PDF format were downloaded from the university’s website. Data were scraped from the annual report PDFs by exporting the publication lists from the PDFs to MSWord, removing unnecessary line breaks and spacing to create a single publication per line, and copying the publication lists into MSExcel for cleaning and analysis. Data were cleaned to remove (1) duplicate entries (e.g. identical publications in the same annual report or a publication listed as ‘under review’ or ‘in press’ in one year and listed again as a publication in a following year); (2) publications listed as ‘submitted’, unpublished masters and PhD theses, speeches, lectures, responses or retractions; (3) incomplete entries (e.g. no article, book or journal title); and (4) publications prior to 2011 (e.g. a 2008 publication listed in the 2011 annual report).</p> <p>The cleaned data were then coded for ‘year of publication’ (2011 to 2017 inclusive), ‘college’ (any of the colleges at Makerere University to which the authors were affiliated), and ‘publication type’ (book chapter, journal article, edited volume, working paper, policy brief, monograph, conference paper, textbook, report, popular article, poster presentation, newsletter, essay, catalogue, poetry, handbook). Books or parts of books (i.e. ‘book chapter’, ‘edited volume’, ‘monograph’, ‘textbook’, ‘catalogue’, ‘poetry’ and ‘handbook’) were further coded for ‘publisher’ (name); ‘publisher location’ (city, country as indicated on the imprint page of the publication); and ‘URL’ (online reference to publisher or publication). In some cases, publications were listed by type in the annual reports. Where publication lists were not presented in this way, indicators such as ‘journal of’, ‘volume’, ‘issue’ and ISSNs were used to identify journals; conference names, ‘proceedings of’, dates and cities were used to identify conference papers and presentations; ‘news’, ‘magazine’, ISSNs and the absence of ‘journal of’ were used to identify periodicals; and place of publication, publisher and ISBNs were used to identify books. Where these indicators were insufficient to determine a publication type, an online search was done to find the missing data. </p> <p>A limitation of the adopted method is that it relies on self-reporting by the university colleges and the list can therefore not be assumed to be comprehensive. Without knowledge of the reporting guidelines, it is also not possible to know whether all colleges and schools used the same criteria when selecting what to submit for reporting purposes. For example, some colleges may have decided to include working papers, policy briefs or papers presented at conferences, while others may have decided not to do so. </p>
Data from: Sampling schemes and drift can bias admixture proportions inferred by STRUCTURE
<p><span>The interbreeding of individuals coming from genetically differentiated but incompletely isolated populations can lead to the formation of admixed populations, having important implications in ecology and evolution. In this simulation study, we evaluate how individual admixture proportions estimated by the software <span>structure</span> are quantitatively affected by different factors. Using various scenarios of admixture between two diverging populations, we found that unbalanced sampling from parental populations may seriously bias the inferred admixture proportions; moreover, proportionally large samples from the admixed population can also decrease the accuracy and precision of the inferences. As expected, weak differentiation between parental populations and drift after the admixture event strongly increase the biases caused by uneven sampling. We also show that admixture proportions are generally more biased when parental populations unequally contributed to the admixed population. Finally, with few exceptions, using a large number of markers reduces those biases, but using alternative priors for individual ancestry or the uncorrelated allele model only marginally affect the inference of admixture in most situations. We conclude that unbalanced sampling may cause important biases in the admixture proportions estimated by <span>structure</span>, especially when a small number of markers are used, and those biases can be worsened by the effect of drift and unequal genetic contribution of parental populations. Empirical studies should thus be careful with their sampling design and consider historical characteristics when using this software to estimate the ancestry of individuals from admixed populations.</span></p>
Data from: The effects of drift and selection on latitudinal genetic variation
<p>Clinal variation is paramount for understanding the factors shaping genetic diversity in space and time. During the last glacial maximum, northern Europe was covered by glacial ice that rendered the region uninhabitable for most taxa. Different evolutionary processes during and after the recolonisation of this area from different glacial refugia have affected the genetic landscape of the present-day European flora and fauna. In this study, we focus on the common toad (<i>Bufo bufo</i>) in Sweden and present evidence suggesting that these processes have resulted in two separate lineages of common toad, which colonised Sweden from two directions. Using ddRAD sequencing data for demographic modelling, structure analyses and analyses of molecular variance (AMOVA), we provide evidence of a contact zone located between Uppland and Västerbotten in central Sweden. Genetic diversity was significantly higher in southern Sweden compared to the north, in accordance with a pattern of decreased genetic diversity with increasing distance from glacial refugia. Candidate genes under putative selection are identified through outlier detection and gene-environment association methods. We provide evidence of divergent selection related to stress response and developmental processes in these candidate genes. The colonisation of Sweden by two separate lineages may have implications for how future conservation efforts should be directed by identifying management units and putative local adaptations.</p>
Data from: Comparing fitness and drift explanations of Neanderthal replacement
There is a general consensus among archaeologists that replacement of Neanderthals by anatomically modern humans in Europe occurred around 40K to 35K YBP. However, the causal mechanism for this replacement continues to be debated. Searching for specific fitness advantages in the archaeological record has proven difficult, as these may be obscured, absent, or subject to interpretation. Proposed models have therefore featured either fitness advantages in favor of anatomically modern humans, or invoked neutral drift under various preconditions. To bridge this gap, we rigorously compare the system-level properties of fitness- and drift-based explanations of Neanderthal replacement. Our stochastic simulations and analytical predictions show that, although both fitness and drift can produce replacement, they present important differences in 1) required initial conditions, 2) reliability, 3) time to replacement, and 4) path to replacement (population histories). These results present useful opportunities for comparison with archaeological and genetic data. We find far greater agreement between the available empirical evidence and the system-level properties of replacement by differential fitness, rather than by neutral drift.
Data from: Genetic drift during the spread phase of a biological invasion
Recent theoretical and experimental models have evidenced the role played by evolution during species spread, and particularly question the influence of genetic drift at range edges. By investigating the spread of an aquatic invader in patchy habitats, we quantified genetic drift and explored its consequences on genetic diversity and fitness. We examined the interplay of gene flow and genetic drift in 36 populations of the red swamp crayfish, Procambarus clarkii, in a relatively recently invaded wetland area (30 years, Brière, northwestern France). Despite the small spatial scale of our study (15 km²), populations were highly structured according to the strong barrier of land surfaces and revealed a clear pattern of colonisation through watercourses. Isolated populations exhibited small effective sizes and low dispersal rates that depended on water connectivity, suggesting that genetic drift dominated in the evolution of allele frequencies in these populations. We also observed a significant decrease in the genetic diversity of isolated populations over only a two-year period, but failed to demonstrate an associated fitness cost using fluctuating asymmetry. This study documents the possible strong influence of genetic drift during the spread of a species, and such findings provide critical insights in the current context of profound rearrangements in species distributions due to global change.
Data from: The action of stabilizing selection, mutation and drift on epistatic quantitative traits
For a quantitative trait under stabilizing selection, the effect of epistasis on its genetic architecture and on the changes of genetic variance caused by bottlenecking were investigated using theory and simulation. Assuming empirical estimates of the rate and effects of mutations and the intensity of selection, we assessed the impact of two-locus epistasis (synergistic/antagonistic) among linked or unlinked loci on the distribution of effects and frequencies of segregating loci in populations at the mutation-selection-drift balance. Strong pervasive epistasis did not modify substantially the genetic properties of the trait and, therefore, the most likely explanation for the low amount of variation usually accounted by the loci detected in genome-wide association analyses is that many causal loci will pass undetected. We investigated the impact of epistasis on the changes in genetic variance components when large populations were subjected to successive bottlenecks of different sizes, considering the action of genetic drift, operating singly (D), or jointly with mutation (MD) and selection (MSD). An initial increase of the different components of the genetic variance, as well as a dramatic acceleration of the between-line divergence, were always associated with synergistic epistasis but were strongly constrained by selection.
Data from: Reduced lifespan and increased ageing driven by genetic drift in small populations
Explaining the strong variation in lifespan among organisms remains a major challenge in evolutionary biology. Whereas previous work has concentrated mainly on differences in selection regimes and selection pressures, we hypothesize that differences in genetic drift may explain some of this variation. We develop a model to formalize this idea and show that the strong positive relationship between lifespan and genetic diversity predicted by this model indeed exists among populations of Daphnia magna, and that ageing is accelerated in small populations. Additional results suggest that this is due to increased drift in small populations rather than adaptation to environments favoring faster life histories: First, the correlation between genetic diversity and lifespan remains significant after statistical correction for potential environmental covariates. Second, no trade-offs are observed; rather, all investigated traits show clear signs of increased genetic load in the small populations. Third, hybrid vigor with respect to lifespan is observed in crosses between small but not between large populations. Together, these results suggest that the evolution of lifespan and ageing can be strongly affected by genetic drift, especially in small populations, and that variation in lifespan and ageing may often be non-adaptive, due to a strong contribution from mutation accumulation to this variation.
Data from: Inbreeding depression and drift load in small populations at demographic disequilibrium
Inbreeding depression is a major driver of mating system evolution and has critical implications for population viability. Theoretical and empirical attention has been paid to predicting how inbreeding depression varies with population size. Lower inbreeding depression is predicted in small populations at equilibrium, primarily due to higher inbreeding rates facilitating purging and/or fixation of deleterious alleles (drift load), but predictions at demographic and genetic disequilibrium are less clear. In this study, we experimentally evaluate how lifetime inbreeding depression and drift load, estimated by heterosis, vary with census (Nc) and effective (estimated as genetic diversity, He) population size across six populations of the biennial Sabatia angularis as well as present novel models of inbreeding depression and heterosis under varying demographic scenarios at disequilibrium (fragmentation, bottlenecks, disturbances). Our experimental study reveals high average inbreeding depression and heterosis across populations. Across our small sample, heterosis declined with He, as predicted, whereas inbreeding depression did not vary with He and actually decreased with Nc. Our theoretical results demonstrate that inbreeding depression and heterosis levels can vary widely across populations at disequilibrium despite similar He and highlight that joint demographic and genetic dynamics are key to predicting patterns of genetic load in nonequilibrium systems.
Data from: Genetic drift and rapid evolution of viviparity in insular fire salamanders (Salamandra salamandra)
Continental islands offer an excellent opportunity to investigate adaptive processes and to time microevolutionary changes that precede macroevolutionary events. We performed a population genetic study of the fire salamander (Salamandra salamandra), a species that displays unique intraspecific diversity of reproductive strategies, to address the microevolutionary processes leading to phenotypic and genetic differentiation of island, coastal and interior populations. We used eight microsatellite markers to estimate genetic diversity, population structure, and demographic parameters in viviparous insular populations and ovoviviparous coastal and interior populations. Our results show considerable genetic differentiation (FST range: 0.06 - 0.27), and no clear signs of gene flow among populations, except between the large and admixed interior populations. We find no support for island colonization by rafting or intentional/accidental anthropogenic introductions, indicating that rising sea levels were responsible for isolation of the island populations approximately 9,000 years ago. Our study provides evidence of rapid genetic differentiation among island and coastal populations, and rapid evolution of viviparity driven by climatic selective pressures on island populations, geographic isolation with genetic drift, or a combination of these factors. Studies of these viviparous island populations in early stages of divergence help us better understand the microevolutionary processes involved in rapid phenotypic shifts.
Data from: Sex chromosome turnovers and genetic drift: a simulation study
The recent advances of new genomic technologies has enabled to identify and characterize sex chromosomes in an increasing number of non-model species, revealing that many plants and animals undergo frequent sex chromosome turnovers. What evolutionary forces drive these turnovers remains poorly understood, but it was recently proposed that drift might play a more important role than generally assumed. We analyzed the dynamics of different types of turnovers using individual-based simulations, and show that when mediated by genetic drift, turnovers are usually easier to achieve than substitutions at neutral markers, but that their dynamics and relative likelihoods vary with the type of the resident and emergent sex chromosome system (XY and/or ZW), and the dominance relationships among the sex-determining factors. Focusing on turnovers driven by epistatically dominant mutations, we find that drift-mediated turnovers that preserve the heterogamety pattern are 2-4x more likely than those along which the heterogametic sex changes. This ratio nevertheless decreases along with effective population size, and can even reverse in case of extreme polygyny. This can be attributed to a "drift-induced" selective force, known to influence transitions between male and female heterogamety, but which according to our study, does not affect turnovers that preserve the heterogametic sex.
Data from: Gene flow and genetic drift in urban environments
Evidence is growing that human modification of landscapes has dramatically altered evolutionary processes. In urban population genetic studies, urbanization is typically predicted to act as a barrier that isolates populations of species, leading to increased genetic drift within populations and reduced gene flow between populations. However, urbanization may also facilitate dispersal among populations, leading to higher genetic diversity within and lower differentiation between urban populations. We reviewed the literature on non-adaptive urban evolution to evaluate the support for each of these urbanse urban fragmentation and facilitation models. In a review of the literature with supporting quantitative analyses of 167 published urban population genetics studies, we found a weak signature of reduced within-population genetic diversity, and no evidence of consistently increased between-population genetic differentiation associated with urbanization. In addition, we found that urban landscape features act as barriers or conduits to gene flow, depending on the species and city in question. Thus, we speculate that dispersal ability of species and environmental heterogeneity between cities contribute to the variation exhibited in our results. However, greater than 90% of published studies reviewed here showed an association of urbanization with genetic drift or gene flow, highlighting the strong impact of urbanization on non-adaptive evolution. It is clear that organism biology and city heterogeneity obscure patterns of genetic drift and gene flow in a quantitative analysis. Thus, we suggest that future research makes comparisons of multiple cities and nonurban habitats, and takes into consideration species' natural history, environmental variation, spatial modelling, and marker selection.
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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.