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1,663 results for “BIAS”
Mate-finding dispersal reduces local mate limitation and sex bias in dispersal
<p>1. Sex-biased dispersal (SBD) often skews the local sex ratio in a population. This can result in a shortage of mates for individuals of the less-dispersive sex. Such mate limitation can lead to Allee effects in populations that are small or undergoing range expansion, consequently affecting their survival, growth, stability and invasion speed.</p> <p>2. Theory predicts that mate shortage can lead to either an increase or a decrease in the dispersal of the less-dispersive sex. However, neither of these predictions have been empirically validated.</p> <p>3. To investigate how SBD-induced mate limitation affects dispersal of the less-dispersive sex, we used Drosophila melanogaster populations with varying dispersal propensities. To rule out any mate-independent density effects, we examined the behavioral plasticity of dispersal in presence of mates as well as same-sex individuals with differential dispersal capabilities.</p> <p>4. In the presence of high-dispersive mates, the dispersal of both male and female individuals was significantly increased. However, the magnitude of this increase was much larger in males than in females, indicating that the former show greater mate-finding dispersal. Moreover, the dispersal of either sex did not change when dispersing alongside high- or low-dispersive individuals of the same sex. This suggested that the observed plasticity in dispersal was indeed due to mate-finding dispersal, and not mate-independent density effects.</p> <p>5. Strong mate-finding dispersal can diminish the magnitude of sex bias in dispersal. This can modulate the evolutionary processes that shape range expansions and invasions, depending on the population size. In small populations, mate-finding dispersal can ameliorate Allee effects. However, in large populations, it can dilute the effects of spatial sorting. 28-May-2020</p>
Supplementary Data to Dual clumped isotope thermometry resolves kinetic biases in carbonate formation temperatures
<p>In this dataset, we provide analytical and model data to <em>Dual clumped isotope thermometry resolves kinetic biases in carbonate formation temperatures</em> by Bajnai et al. (2020). Also deposited here is the R code that we used to calculate the equations and generate the figures in the manuscript.</p>
Common field data limitations can substantially bias sexual selection metrics
<p>Sexual selection studies widely estimate several metrics, but values may be inaccurate because standard field methods for studying wild populations produce limited data (e.g., incomplete sampling, inability to observe copulations directly). We compared four selection metrics (Bateman gradient, opportunity for sexual selection, opportunity for selection, and <em>s'<sub>max</sub></em>) estimated with simulated complete and simulated limited data for 15 socially monogamous songbird species with extra-pair paternity (4-54% extra-pair offspring). Inferring copulation success from offspring parentage creates non-independence between these variables and systematically underestimates copulation success. We found that this introduces substantial bias for the Bateman gradient, opportunity for sexual selection, and <em>s'<sub>max</sub></em>. Notably, 47.5% of detected Bateman gradients were significantly positive for females, suggesting selection on females to copulate with multiple males, though the true Bateman gradient was zero. Bias generally increased with the extent of other sources of data limitations tested (nest predation, male infertility, and unsampled floater males). Incomplete offspring sampling introduced bias for all metrics except the Bateman gradient, while incomplete sampling of extra-pair sires did not introduce additional bias when sires were a random subset of breeding males. Overall, our findings demonstrate how biases due to field data limitations can strongly impact the study of sexual selection.</p>
Artificial night light helps account for observer bias in citizen science monitoring of an expanding large mammal population
1. The integration of citizen scientists into ecological research is transforming how, where, and when data are collected, and expanding the potential scales of ecological studies. Citizen-science projects can provide numerous benefits for participants, while educating and connecting professionals with lay audiences, potentially increasing acceptance of conservation and management actions. However, for all the benefits, collection of citizen-science data is often biased towards areas that are easily accessible (e.g. developments and roadways), and thus data are usually affected by issues typical of opportunistic surveys (e.g. uneven sampling effort). These areas are usually illuminated by artificial light at night (ALAN), a dynamic sensory stimulus that alters the perceptual world for both humans and wildlife. 2. Our goal was to test whether satellite-based measures of ALAN could improve our understanding of the detection process of citizen scientist-reported sightings of a large mammal. 3. We collected observations of American black bears (Ursus americanus; n = 1,315) outside their primary range in Minnesota, USA, as part of a study to gauge population expansion. Participants from the public provided sighting locations of bears on a website. We used an occupancy modelling framework to determine how well ALAN accounted for observer metrics when compared to other commonly used metrics (e.g. housing density). 4. Citizen scientists reported 17% of bear sightings were under artificially-lit conditions and monthly ALAN estimates did the best job accounting for spatial bias in detection of all observations, based on AIC values and effect sizes (β ^ = 0.81, 0.71 – 0.90 95% CI). Bear detection increased with elevated illuminance; relative abundance was positively associated with natural cover, closer proximity to primary bear range and lower road density. Although the highest counts of bear sightings occurred in the highly illuminated suburbs of the Minneapolis-St. Paul metropolitan region, we estimated substantially higher bear abundance in another region with plentiful natural cover and low ALAN (up to 275% increased predicted relative abundance) where observations were sparse. 5. We demonstrate the importance of considering ALAN radiance when analyzing citizen scientist-collected data, and we highlight the ways that ALAN data provides a dynamic snapshot of human activity. 31-Jul-2020
S2P3Rv2.0 bias data
<p>Annual mean (taken over 2000-2019) SST data from ECMWF ERA5 driven simulation of S2P3Rv2.0 in waters between 10 and 100m depth between 65 S and 65 N.</p> <p>Data provided as netcdf (NETCDF4) and CSV files</p>
Data presented in: Walking Drosophila navigate complex plumes using stochastic decisions biased by the timing of odor encounters
<p>How insects navigate complex odor plumes, where the location and timing of odor packets are uncertain, remains unclear. Here, we imaged complex odor plumes simultaneously with freely-walking flies, quantifying how behavior is shaped by encounters with individual odor packets. We found that navigation was stochastic, and did not rely on the continuous modulation of speed or orientation. Instead, flies turned stochastically with stereotyped saccades, whose direction was biased upwind by the timing of prior odor encounters, while the magnitude and rate of saccades remained constant. Further, flies used the timing of odor encounters to modulate the transition rates between walks and stops. In more regular environments, flies continuously modulate speed and orientation, even though encounters can still occur randomly due to animal motion. We find that in less predictable environments, where encounters are random in both space and time, walking flies instead navigate with random walks biased by encounter timing.</p>
data sets and trees for the Rasplus et al paper "Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)" Cladistics (2020)
<p>Data sets and trees for the Rasplus <em>et al</em>. paper "Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus <em>Ficus</em> (Moraceae)" Cladistics (2020). Preprint = https://www.biorxiv.org/content/10.1101/2020.04.15.042259v1</p> <p><strong>*.phy = Data sets (phylip format) [see Table 2 of the paper for more details].</strong></p> <p>- <strong>mergeR1R2.phy</strong> : complete data set (530 RAD loci shared by 75% of the samples + assembly of forward & reverse reads)<br> - <strong>mergeR1R2_GCinfmean.phy</strong> : loci with GC content inferior or equal to mean GC content<br> - <strong>mergeR1R2_GCsupmean.phy</strong> : loci with GC content strictly superior to mean GC content<br> - <strong>mergeR1R2_LS3.phy</strong> : loci that evolve at a homogeneous rate across clades of interest (Clade1= sect. Pharmacosycea; Clade2=subg. Urostigma, Clade3=sect. Oreosycea, Clade4= "gynodioecious clade")<br> - <strong>mergeR1R2_PCA.phy</strong> : loci for which difference between Long Branch (LB) scores for sect. Pharmacosycea and other ingroups was not significant according to our custom iterative PCA approach</p> <p> <br> <strong>Fig*.nwk : Trees (newick format) that were obtained for the different data sets.</strong></p> <p>Trees are also included as Figures or Supplementary Figures of the paper. Note that you may visualize these nwk trees in FigTree (open FigTree. Upload the FigS1A_RAxML_mergeR1R2_inclfigtreeannot.nex first and then open the other trees - do not close FigTree in between !- Annotations included in the first file will be automatically used to annotate other trees). </p> <p><strong>Appendix S2 : Morphological matrix + morphological tree + 4 competing molecular trees. </strong></p> <p>This file can be opened in Mesquite to get reconstruction of ancestral character states</p>
Hemipteran defensive odors trigger predictable color biases in jumping spider predators
<p>Multimodal warning displays often pair one signal modality (odor) with a second modality (color) to avoid predation. Experiments with bird predators suggest these signal components interact synergistically, with aversive odors triggering otherwise hidden aversions to particular prey colors. In a recent study, this phenomenon was found in a jumping spider (<em>Habronattus trimaculatus</em>), with the defensive odor from a coreid bug (<em>Acanthocephala femorata</em>) triggering an aversion to red. Here, we explore how generalizable this phenomenon is by giving <em>H. trimaculatus</em> the choice between red or black prey in the presence or absence of defensive odors secreted from (1) eastern leaf-footed bugs (<em>Leptoglossus phyllopus</em>, Hemiptera), (2) grass stinkbugs (<em>Mormidea pama</em>, Hemiptera), (3) Asian ladybird beetles (<em>Harmonia axyridis</em>, Coleoptera), and (4) eastern lubber grasshoppers (<em>Romalea microptera</em>, Orthoptera). As expected, in the presence of the hemipteran odors, spiders were less likely to attack red prey (compared to no odor). Unexpectedly, the beetle and grasshopper odors did not bias spiders away from red. Our results with the hemipteran odors were unique to red; follow-up experiments indicated that these odors did not affect biases for/against green prey. We discuss our findings in the context of generalized predator foraging behavior and the functions of multimodal warning displays. </p>
Code and data used in thesis Chapter 2 of 'Determining the biases and consistencies in the evidence for conservation'
<p>Code and data used in thesis Chapter 2 of 'Determining the biases and consistencies in the evidence for conservation'.</p>
Short-Tandem-Repeat (STR) marker set for Eurasian lynx for article: Genetic analysis indicates spatial-dependent patterns of sex-biased dispersal in Eurasian lynx in Finland
<p>Conservation and management of large carnivores requires knowledge of female and male dispersal. Such information is crucial to evaluate the population's status and thus management actions. This knowledge is challenging to obtain, often incomplete and contradictory at times. The size of the target population and the methods applied can bias the results. Also, population history and biological or environmental influences can affect dispersal on different scales within a study area. We have genotyped Eurasian lynx (180 males and 102 females, collected 2003-2017) continuously distributed in southern Finland (~23,000 km<sup>2</sup>) using 21 short tandem repeats (STR) loci and compared statistical genetic tests to infer local and sex-specific dispersal patterns within and across genetic clusters as well as geographic regions. We tested for sex-specific substructure with individual-based Bayesian assignment tests and spatial autocorrelation analyses. Differences between the sexes in genetic differentiation, relatedness, inbreeding, and diversity were analysed using population-based AMOVA, F-statistics, and assignment indices. Our results showed two different genetic clusters that were spatially structured for females but admixed for males. Similarly, spatial autocorrelation and relatedness was significantly higher in females than males. However, we found weaker sex-specific patterns for the Eurasian lynx when the data were separated in three geographical regions than when divided in the two genetic clusters. Overall, our results suggest male-biased dispersal and female philopatry for the Eurasian lynx in Southern Finland. The female genetic structuring increased from west to east within our study area. In addition, detection of male-biased dispersal was dependent on analytical methods utilized, on whether subtle underlying genetic structuring was considered or not, and the choice of population delineation. Conclusively, we suggest using multiple genetic approaches to study sex-biased dispersal in a continuously distributed species in which population delineation is difficult.</p>
The apparent exponential radiation of Phanerozoic land vertebrates is an artefact of spatial sampling biases
There is no consensus about how terrestrial biodiversity was assembled through deep time, and in particular whether it has risen exponentially over the Phanerozoic. Using a database of 38,711 fossil occurrences, we show that the spatial extent of the 'global' terrestrial tetrapod fossil record itself expands exponentially through the Phanerozoic, and that this spatial variation explains around 75% of the variation in known fossil species counts. Controlling for this bias, we find that regional-scale terrestrial tetrapod diversity was constrained over timespans of tens to hundreds of millions of years, and similar patterns are recovered for major subgroups, such as dinosaurs, mammals and squamates. The Cretaceous/Paleogene mass extinction, 66 million years ago, fundamentally disrupted terrestrial ecosystems, catalysing an abrupt increase in its aftermath. Nevertheless, this was followed by general stasis and recent diversity levels do not exceed those of the Paleogene. These findings parallel those recovered in analyses of local community-level richness, suggesting that tetrapod beta diversity has also not shown a general increase through time. Taken together, our findings strongly contradict past studies that suggested unbounded diversity increases over the last 100 million years.
Data from: Does sex-biased dispersal account for the lack of geographic and host-associated differentiation in introduced populations of an aphid parasitoid?
Host recognition and use in female parasitoids strongly relies on host fidelity, a plastic behavior which can significantly restrict the host preferences of parasitoids, thus reducing the gene flow between parasitoid populations attacking different insect hosts. However, the effect of migrant males on the genetic differentiation of populations has been frequently ignored in parasitoids, despite its known impact on gene flow between populations. Hence, we studied the extent of gene flow mediated by female and male parasitoids by assessing sibship relationships among parasitoids within and between populations, and its impact on geographic and host-associated differentiation in the aphid parasitoid Aphidius ervi. We report evidences of a high gene flow among parasitoid populations on different aphid hosts and geographic locations. The high gene flow among parasitoid populations was found to be largely male mediated, suggested by significant differences in the distribution of full-sib and paternal half-sib dyads of parasitoid populations.
Geolocators lead to better measures of timing and renesting in Black-tailed Godwits and reveal the bias of traditional observational methods
<p>Long‐term population studies can identify changes in population dynamics over time. However, to realize meaningful conclusions, these studies rely on accurate measurements of individual traits and population characteristics. Here, we evaluate the accuracy of the observational methods used to measure reproductive traits in individually marked black‐tailed godwits (<i>Limosa limosa limosa</i>). By comparing estimates from traditional methods with data obtained from light‐level geolocators, we provide an accurate estimate of the likelihood of renesting in godwits and the repeatability of the lay dates of first clutches. From 2012 – 2018, we used periods of shading recorded on the light‐level geolocators carried by 68 individual godwits to document their nesting behaviour. We then compared these estimates to those simultaneously obtained by our long‐term observational study. We found that among recaptured geolocator‐carrying godwits, all birds renested after a failed first clutch, regardless of the date of nest loss or the number of days already spent incubating. We also found that 43% of these godwits laid a second replacement clutch after a failed first replacement, and that 21% of these godwits renested after a hatched first clutch. However, the observational study correctly identified only 3% of the replacement clutches produced by geolocator‐carrying individuals and designated as first clutches a number of nests that were actually replacement clutches. Additionally, on the basis of the observational study, the repeatability of lay date was 0.24 (95% CI 0.17 – 0.31), whereas it was 0.54 (95% CI 0.28 – 0.75) using geolocator‐carrying individuals. We use examples from our own and other godwit studies to illustrate how the biases in our observational study discovered here may have affected the outcome of demographic estimates, individual‐level comparisons, and the design, implementation, and evaluation of conservation practices. These examples emphasize the importance of improving and validating field methodologies and show how the addition of new tools can be transformational.</p>
Impact of increased resolution on long-standing biases in HighResMIP-PRIMAVERA climate models
<p>This contains the data and plot scripts to reproduce the figures of the manuscript: <em>Impact of increased resolution on long-standing biases in HighResMIP-PRIMAVERA climate models</em>.</p> <p><strong>Authors:</strong></p> <p>Eduardo Moreno-Chamarro<sup>1*</sup>, Louis-Philippe Caron<sup>1,2</sup>, Saskia Loosveldt Tomas<sup>1</sup>, Oliver Gutjahr<sup>3,4</sup> , Marie-Pierre Moine<sup>5</sup>, Dian Putrasahan<sup>3</sup> , Christopher D. Roberts<sup>6</sup>, Malcolm J. Roberts<sup>7</sup>, Retish Senan<sup>6</sup>, Laurent Terray<sup>5</sup>, Etienne Tourigny<sup>1</sup>, Pier Luigi Vidale<sup>8</sup></p> <p><br> <sup>1 Barcelona Supercomputing Center (BSC), Barcelona, Spain.</sup></p> <p><sup>2 Ouranos, Montreal, H3A 1B9, Canada.</sup></p> <p><sup>3 Max Planck Institute for Meteorology. Hamburg, Germany.</sup></p> <p><sup>4 Now at Institut für Meereskunde, Universität Hamburg, Hamburg, Germany.</sup></p> <p><sup>5 CECI, Université de Toulouse, CERFACS/CNRS, Toulouse, France.</sup></p> <p><sup>6 ECMWF European Centre for Medium-Range Weather Forecasts, Reading, United Kingdom.</sup></p> <p><sup>7 Met Office, Exeter EX1 3PB, United Kingdom.</sup></p> <p><sup>8 NCAS-Climate, Department of Meteorology, University of Reading, Reading, United Kingdom.</sup></p> <p><sup>Correspondence to: Eduardo Moreno-Chamarro (eduardo.moreno@bsc.es)</sup></p> <p><strong>Abstract. </strong>We examine the impacts of increased resolution on four long-standing biases using five different climate models developed within the PRIMAVERA project. Atmospheric resolution is increased from ~100–200 km to ~25–50 km, and ocean resolution is increased from ~1° (i.e., eddy-parametrized) to ~0.25° (i.e., eddy-present). For one model, ocean resolution is also increased to 1/12° (i.e., eddy-rich). Fully-coupled general circulation models and their atmosphere-only versions are compared with observations and reanalysis of near-surface temperature, precipitation, cloud cover, net cloud radiative effect, and zonal wind over the period 1980–2014. Both the ensemble mean and the individual models are analyzed. Increased resolution especially in the atmosphere helps reduce the surface warm bias over the tropical upwelling regions in the coupled models, with further improvements in the cloud cover and precipitation biases over the tropical Atlantic particularly. Related to this and to the improvement in the precipitation distribution over the western tropical Pacific, the double ITCZ bias also weakens with resolution. Overall, increased ocean resolution from 1° to 0.25° offers limited improvements or even bias degradation in some models, although an eddy-rich ocean resolution seems beneficial to reduce the North Atlantic cold bias and the Gulf Stream path. Despite the improvements, however, large biases in precipitation and cloud cover persist over the whole tropics as well as in the upper-troposphere zonal winds at mid-latitudes in both coupled and atmosphere-only models at higher resolutions. The SO warm bias also worsens or persists in some coupled models. And a new warm bias emerges in the Labrador Sea in all the high-resolution coupled models. The analysis of the PRIMAVERA models therefore suggests that, to reduce biases, i) increased atmosphere resolution up to ~25–50 km alone might not be sufficient and ii) an eddy-rich ocean resolution might be needed. The study thus adds to evidence that further improved model physics and tuning might be necessary in addition to increased resolution to mitigate biases.</p>
Accounting for imperfect detection in data from museums and herbaria when modeling species distributions: Combining and contrasting data-level versus model-level bias correction
The digitization of museum collections as well as an explosion in citizen science initiatives has resulted in a wealth of data that can be useful for understanding the global distribution of biodiversity, provided that the well-documented biases inherent in unstructured opportunistic data are accounted for. While traditionally used to model imperfect detection using structured data from systematic surveys of wildlife, occupancy models provide a framework for modelling the imperfect collection process that results in digital specimen data. In this study, we explore methods for adapting occupancy models for use with biased opportunistic occurrence data from museum specimens and citizen science platforms using 7 species of Anacardiaceae in Florida as a case study. We explored two methods of incorporating information about collection effort to inform our uncertainty around species presence: (1) filtering the data to exclude collectors unlikely to collect the focal species and (2) incorporating collection covariates (collection type, time of collection, and history of previous detections) into a model of collection probability. We found that the best models incorporated both the background data filtration step as well as collector covariates. Month, method of collection and whether a collector had previously collected the focal species were important predictors of collection probability. Efforts to standardize meta-data associated with data collection will improve efforts for modeling the spatial distribution of a variety of species.
Dataset for article: Perakakis, P., Taylor, M., Martinez-Nieto, E., Revithi, I., Vila, J. (2009). Breathing Frequency Bias in Fractal Analysis of Heart Rate Variability. Biological Psychology, 82(1), pp. 82-88
<p>Dataset for article:</p> <p>Perakakis, P., Taylor, M., Martinez-Nieto, E., Revithi, I., Vila, J. (2009). Breathing Frequency Bias in Fractal Analysis of Heart Rate Variability. Biological Psychology, 82(1), pp. 82-88</p>
Breathing frequency bias in fractal analysis of heart rate variability (datasets)
<p>data form the article:</p> <p>Perakakis, P., Taylor, M., Martinez-Nieto, E., Revithi, I., Vila, J. (2009). Breathing Frequency Bias in Fractal Analysis of Heart Rate Variability. Bi- ological Psychology, 82(1), pp. 82-88 </p>
Supporting information: Analysis of attentional bias towards attractive and unattractive body regions among overweight males and females: An eye-movement study.
<p>This is the data set as supporting information, provided as .csv file.</p> <p>Further information is available on request.</p>
Age-dependent positivity bias in children's perception of emotion terms
<p>Data set of Bahn, D., Vesker, M., Garcia Alanis, J. C., Schwarzer, G., & Kauschke, C. (in press). Age-dependent positivity bias in children’s perception of emotion terms. <em>Frontiers in Psychology</em>. doi: 10.3389/fpsyg.2017.01268</p>
ParaMask, a new method to identify multicopy genomic regions, corrects major biases in whole-genome sequencing data. Additional Datasets.
<p>Data supporting the main figures of the "ParaMask, a new method to identify multicopy genomic regions, corrects major biases in whole-genome sequencing data" manuscript and a copy of the ParaMask software and scripts for analysis, and SV calls from longreads. README files are included.</p>
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