Find research datasets worth reusing

Pessimistic cognitive bias is associated with enhanced reproductive investment in female zebrafish

Optimistic and pessimistic cognitive biases have been described in many animals and are related to the perceived valence of the environment. We, therefore, hypothesize that such cognitive bias can be adaptive depending on environmental conditions. In reward rich environments an optimistic bias would be favored, whereas in harsh environments a pessimistic one would thrive. Here, we empirically investigated the potential adaptive value of such bias using zebrafish as a model. We first phenotyped female zebrafish in an optimistic/pessimistic axis using a previously validated judgment bias assay. Optimistic and pessimistic females were then exposed to an unpredictable chronic stress protocol for 17 days, after which fish were euthanized and the sectional area of the different ovarian structures was quantified in both undisturbed and stressed groups. Our results show that zebrafish ovarian development responded to chronic stress, and that judgment bias impacted the relative area of the vitellogenic developmental stage in the stress treatment, with pessimists showing higher vitellogenic areas as compared with optimists. These results suggest that pessimism maximize reproductive investment, through increased vitellogenesis, indicating a relationship between cognitive bias and life-history organismal decisions.

Simulated data for: The evolution of mating preferences for genetic attractiveness and quality in the presence of sensory bias

This repository contains simulated datasets relating to the publication: Henshaw JM, Fromhage L, Jones AG (2022) The evolution of mating preferences for genetic attractiveness and quality in the presence of sensory bias. Proc. Natl. Acad. Sci. USA (doi:10.1073/pnas.2206262119) In this paper, we simulate the evolution of female preferences for multiple male ornament types (e.g., 'Fisherian', 'handicap' and 'indicator' ornaments) that differ in their associations with genes for attractiveness and for general 'quality' (operationalized as the ability to acquire resources). We allowed for ornaments to differ in their saliency to females. We also analyze the causal mechanisms generating sexual selection (e.g., 'good genes' and 'sexy sons') using causal inference. Datasets are organised into ZIP files named after the corresponding figure in the publication. For further information see the publication and the file README.txt in this repository.

Data from: Sex-biased habitat selection by American marten in the Acadian forest

Differences in spatial ecology between the sexes are generally expected for mammalian carnivores because of physiological (e.g., sexual dimorphism) or behavioral (e.g., uniparental care of offspring) differences, but sex is rarely included in studies of occurrence or occupancy. We evaluated differences in landscape-scale occurrence, as a function of habitat amount and configuration, between male and female American martens in the heterogeneous, commercially-managed forests of northern Maine. Our analysis focused on resident adults; individuals that had survived to >1 year old, dispersed, and successfully established their home range.

Data for: Sensory biases in response to novel complex acoustic signals in male and female gray treefrogs, Hyla chrysoscelis

The sensory bias hypothesis proposes that female preferences for male sexual signaling traits evolved in contexts other than mating. Individuals of both sexes may experience similar selection pressures in these contexts, thus males may have similar biases to females for variation in signal traits. We tested this prediction in the gray treefrog, Hyla chrysoscelis, in which males produce simple advertisement calls, but females are more attracted to certain novel complex stimuli. We recorded males' responses to playbacks of both simple advertisement calls and complex calls consisting of the advertisement call with an acoustic appendage (filtered noise, or heterospecific call pulses) either leading or following the call. We tested females' preferences for the same stimuli in phonotaxis tests. We found evidence for a sensory bias in both sexes: males gave more aggressive calls in response to complex stimuli and females sometimes preferred complex over simple calls. These biases were not universal and depended on both temporal order and appendage characteristics, but how these effects manifested differed between the sexes. Ultimately, our approach of studying biases of both sexes in response to novel mating signals will shed light on the origin of mating preferences, and the mechanisms by which sensory biases operate.

Increasing efficiency and reducing bias in the detection of seed-dispersal interactions based on mist-netted birds

Efficient and unbiased sampling of ecological interactions is essential to our understanding of the functions they mediate. Seed dispersal by frugivorous birds is a key mutualism for plant regeneration and community dynamics. Mist-netting is one of the most widely used methods to sample avian seed dispersal through the identification of seeds in droppings of captured birds kept inside cloth bags. However, birds may drop seeds on the ground before being extracted from the net, leading to a fraction of missing information due to ineffective sampling. Worryingly, this fraction could be unevenly distributed across bird and plant species, leading to sampling biases. Here, we assess the effectiveness of using a 1- m wide mesh below mist nets to sample seeds dropped by entangled birds. We used data from birds mist-netted during one-year-round. We sampled nearly 50% of interaction events and 75% of dispersed seeds on the mesh band below the mist nets (i.e. lost information without this optimization). The proportion of seeds sampled on the mesh bands was not evenly distributed among bird species but strongly related to bird size, ranging from 57-63% in warblers to 84-94% in thrushes. Moreover, the proportion of seeds sampled on the mesh was negatively related to seed size, although this relationship was weaker. We also evaluated accumulation curves of species and pairwise interactions with increasing sampling effort, both with and without using the mesh bands. The number of seed species sampled increased by 21% when using the mesh bands and the number of pairwise interactions by 36%. Our findings provide strong evidence on how inefficient and biased traditional mist-netting can be for sampling community-wide seed-dispersal interactions. We thus urge the use of mesh bands in future studies to increase sampling effectiveness and avoid biases, which will ultimately improve our understanding of the seed dispersal function.

opencc-by-4.0Sep 2022View details →

Bias adjusted and statistically down-scaled ISIMIP3b for historical and hist-nat experiments over Central Asia

Downscaling and bias adjustment have been conducted by the BASD software. For a comprehensive description of version 1.0 of the methods see Lange (2019, <a href="https://doi.org/10.5194/gmd-12-3055-2019">doi:10.5194/gmd-12-3055-2019</a>). The models are: <ul> <li>  canesm5_r1i1p1f1 </li> <li>  cnrm-cm6-1_r1i1p1f2 </li> <li>  gfdl-esm4_r1i1p1f1 </li> <li>  ipsl-cm6a-lr_r1i1p1f1 </li> <li>  miroc6_r1i1p1f1 </li> <li>  mri-esm2-0_r1i1p1f1 </li> </ul> the variables are <ul> <li> tas- daily mean of near surface air temperature (K) </li> <li> pr - daily precipitation (kg m-2 s-1 ) </li> </ul> the final horizontal resolution is 0.25°  and the area covered longitude 44.125 -90.875 & latitude 33.125-56.375

opencc-by-4.0Sep 2022View details →

Biases in LWP adjustments, code and dataset

Code and source data to reproduce the figures in article: Antti Arola, Antti Lipponen, Pekka Kolmonen, Timo H. Virtanen, Nicolas Bellouin, Daniel P. Grosvenor, Edward Gryspeerdt, Johannes Quaas, and Harri Kokkola: Aerosol Effects on Clouds Are Concealed by Natural Cloud Heterogeneity and Satellite Retrieval Errors, submitted to Nature Communications, 2022.

opencc-zeroSep 2022View details →

Meta-analysis of Antarctic phylogeography reveals strong sampling bias and critical knowledge gaps

Much of Antarctica's highly endemic terrestrial biodiversity is found in small ice-free patches. Substantial genetic differentiation has been detected among populations across spatial scales. Sampling is, however, often restricted to commonly-accessed sites, and we therefore lack a comprehensive understanding of broad-scale biogeographic patterns, which could impede forecasts of the nature and impacts of future change. Here, we present a synthesis of published genetic studies across terrestrial Antarctica and the broader Antarctic region, aiming to identify current biogeographic patterns, environmental drivers of diversity, and future research priorities. A database of all published genetic research from terrestrial fauna and flora (excl. microbes) across the Antarctic region was constructed. This database was then filtered to focus on the most well-represented taxa and markers (mitochondrial COI for fauna, and nuclear ITS for flora). The final dataset comprised 7222 records, spanning 153 studies of 335 different species. There was strong taxonomic bias towards flowering plants (52% of all floral data sets) and springtails (54% of all faunal data sets), and geographic bias towards the Antarctic Peninsula and Victoria Land. Recent connectivity between the Antarctic continent and neighbouring landmasses, such as South America and the Southern Ocean Islands (SOIs), was inferred for some groups, but patterns observed for most taxa were strongly influenced by sampling biases. Above-ground wind speed and habitat heterogeneity were positively correlated with genetic diversity indices overall, though environment was a generally poor predictor of genetic diversity. The low resolution and variable coverage of data may also have reduced the power of our comparative inferences. In the future, higher-resolution data, such as genomic SNPs and environmental modelling, alongside targeting sampling of remote sites and under-sampled taxa, will address current knowledge gaps and greatly advance our understanding of evolutionary processes across the Antarctic region.

opencc-by-4.0Oct 2022View details →

JAG Bias Corrected SPP

This dataset belongs to the paper: Comparison of Bias-Corrected MultiSatellite Precipitation Products by Deep Learning Framework Daily dataset from 01/01/2016 to 12/2019

opencc-zeroOct 2022View details →

A paradoxical bias in knowledge about Norwegian freshwater fishes: Research efforts during 1980–2020

Norwegian freshwater systems are in general species-poor. That is particularly the case for freshwater fishes. Only 32 species are considered native, whereas an additional 12 species are non-native. Some of the non-native species are also considered to be invasive and have negative ecosystem effects. Freshwater fishes are exposed to numerous stressors throughout their life cycle, many of which are of anthropogenic origin. In order to manage and conserve the diversity of fish there is a need for basic knowledge and understanding. Here I make an effort to review the published research on all Norwegian freshwater fish species during the 1980–2020 period, based on a standardized search on the Web of Science. Over 2000 relevant articles were retrieved and evaluated following the search. The research activity has been highly biased, with most research activity directed at a few species of high economic and societal value. Most work was directed at Atlantic salmon Salmo salar and brown trout S. trutta, and in general towards species within the salmonid family. Extremely little attention was directed at species such as the lampreys (four species) and sculpins (three species). Also, many species that have been listed on the Norwegian Red List during various time periods have not been given any particular attention. This lack of attention was also evident for most of the non-native species. The strong bias in research activity and lack of attention given to many species will clearly lead to difficulties in making appropriate management decisions. This is unfortunate, in particular at a time when climate change may lead to numerous ecosystem-level changes.

opencc-by-4.0Oct 2017View details →

Biases of STRUCTURE software when exploring introduction routes: Datasets, STRUCTURE outputs, simulation and analysis pipeline

This archive is associated with the article “Biases of STRUCTURE software when exploring introduction routes of invasive species”. Authors: Eric Lombaert, Thomas Guillemaud & Emeline Deleury. The file contains the 22,500 simulated datasets, the corresponding 900,000 STRUCTURE outputs and the summary statistics files. It also contains SIM_STRUCT which is a home-made pipeline developed for the purpose of carrying out analyzes as described in the manuscript. It can be used to simulate and summarize datasets, and to perform STRUCTURE analyses in batch on those simulated datasets. It is currently based on several softwares such as DIYABC, ARLSUMSTAT and STRUCTURE, as well as on some home-made PERL scripts. A tutorial is included. See the Readme file for details.

opencc-by-4.0Jun 2017View details →

Data supplementing the article "Avoiding quantification bias in metabarcoding: application of a cell biovolume correction factor in diatom molecular biomonitoring" V. Vasselon, A. Bouchez, F. Rimet, S. Jacquet, R. Trobajo, M. Corniquel, K. Tapolczai, I. Domaizon submitted to Methods in Ecology and Evolution journal

These data supplement the article "Avoiding quantification bias in metabarcoding: application of a cell biovolume correction factor in diatom molecular biomonitoring" V. Vasselon, A. Bouchez, F. Rimet, S. Jacquet, R. Trobajo, M. Corniquel, K. Tapolczai, I. Domaizon submitted to Methods in Ecology and Evolution journal The directory contains the following files: 15 fastq files raw reads (5 mock communities, 3 replicates).rar - contains the 15 fastq files provided by the sequencing platform with demultiplexed DNA reads (raw data prior any bioinformatics treatments). 15 fastq files information.xlsx : - contains the information relative to the 15 fastq files corresponding to the PGM raw data of the 5 mock communities (sequenced with 3 replicates), including: the ID of the fastq files, the mock community name, the replicate number, the final sample Id and the number of raw reads per fastq file. - contains the information of the proportion of the 8 diatoms species (%) used to create the 5 mock communities (estimated from microscopy).

opencc-zeroApr 2024View details →

Data for: Inter-rater reliability of risk of bias tools for non-randomized studies

PURPOSE: Currently, there is limited knowledge about the reliability of risk of bias (ROB) tools for assessing internal validity in systematic reviews of exposure and frequency studies. We aimed to identify and then compare the inter-rater reliability (IRR) of six commonly used tools for frequency (Loney scale, Gyorkos checklist, American Academy of Neurology [AAN] tool) and exposure (Newcastle-Ottawa scale, SIGN50 checklist, AAN tool) studies. METHODS: Six raters independently assessed the ROB of 30 frequency and 30 exposure studies using the 3 respective ROB tools. Articles were rated on a 3-level summary measure of ROB (low, intermediate, or high). We calculated an intraclass correlation coefficient (ICC) for each tool and category of ROB tool. We compared the IRR between ROB tools and tool type by inspection of overlapping ICC 95% CIs and by comparing their coefficients after transformation to Fisher Z values. We assessed criterion validity of the AAN ROB tools by calculating an ICC for each rater in comparison with the original ratings from the AAN. RESULTS: All individual ROB tools had an IRR in the substantial range or higher (ICC point estimate = 0.61-0.80). The IRR was almost perfect (ICC point estimate > 0.80) for the AAN frequency tool and the SIGN50 checklist. All tools were comparable in IRR, except for the AAN frequency tool which had a significantly higher ICC than the Gyorkos checklist (p=0.021) and trended towards a higher ICC when compared to the Loney scale (p=0.085). When examined by category of ROB tool, scales and checklists had a substantial IRR, whereas the AAN tools had an almost perfect IRR. For the criterion validity of the AAN ROB tools, the average agreement between our raters and the original AAN ratings was moderate. CONCLUSION: All tools had substantial IRR except for the AAN frequency tool and the SIGN50 checklist, which both had an almost perfect IRR. The AAN ROB tools were the only category of ROB tool to demonstrate an almost perfect IRR. This category of ROB tool had fewer and more simple criteria. Overall, parsimonious tools with clear instructions, such as those from the AAN, may provide more reliable ROB assessments.

opencc-by-4.0Apr 2024View details →

Bias detection data

The dataset includes 30 interview questions to cover a variety of biases that are frequently present in interview settings and a set of 15 sampling methods that potentially yield either biased or unbiased samples.

opencc-by-4.0Apr 2024View details →

Global Cloud Biases in Optical Satellite Remote of Rivers - Accompanying Dataset

Open the record for dataset details and reuse information.

opencc-by-4.0May 2024View details →

Data and scripts (2) for Storkey et al, "Resolution dependence of interlinked Southern Ocean biases in global coupled HadGEM3 models", GMD (2024)

================================================================  Data and scripts for producing plots from Storkey et al (2024):  "Resolution dependence of interlinked Southern Ocean biases in  global coupled HadGEM3 models"  ================================================================ The plots in the paper consist of 10-year mean fields from the third  decade of the spin up and timeseries of scalar quantities for the first 150 years of the spin up. The data to produce these plots are stored in the MEANS_YEARS_21-30 and TIMESERIES_DATA directories respectively. Note that due to the size limit on records on Zenodo, the 10-year mean  output from the N216-ORCA12 integration has been stored as a separate record. Scripts to produce the plots are in SCRIPT, with section definitions in SECTIONS. Bespoke plotting scripts are included in SCRIPT. They use python 3 including the Matplotlib, Iris and Cartopy packages. The  plotting of the timeseries data used the Marine_Val VALSO-VALTRANS  package which is available here:  https://github.com/JMMP-Group/MARINE_VAL/tree/main/VALSO-VALTRANS  Much of the processing of the model output data was performed with the CDFTools package, which is available here:  https://github.com/meom-group/CDFTOOLS and the NCO package:  https://web.mit.edu/course/13/13.715/nco-2.8.1/doc/

opencc-zeroMay 2024View details →

Data coverage, biases, and trends in a global citizen-science resource for monitoring avian diversity

Aim: Understanding and addressing the global biodiversity crisis requires ecological information compiled continuously from across the globe. Data from citizen science initiatives are useful for quantifying species' ecological niches and geographical distributions but can be difficult to apply towards biodiversity monitoring. The presence of fixed geographical locations reduces the opportunistic nature of citizen science data, allowing for more reliable and nuanced trend estimation. The eBird citizen-science programs contains predefined locations whose bird assemblages are sampled across years ('hotspots'). For hotspots to function as a biodiversity monitoring resource, issues related to data coverage, biases, and trends need to be addressed. Location: Global. Methods: We estimated the survey completeness of species richness at 300,500 eBird hotspots during the years 2002 to 2022. We documented sampling biases at eBird hotspot and non-hotspot locations during 2022 based on protection status, temperature, precipitation, and landcover. Results: A total of 10,410 bird species (ca. 96.9% of total) were recorded at hotspots. The number hotspots and the quantity of data and unique participants and quality of species richness estimates has increased worldwide with the Nearctic containing the strongest and most consistent trends. Compared to non-hotspots, hotspots over sampled areas with higher protection status. Hotspots and non-hotspots over sampled warmer and wetter locations in the Antarctic, Nearctic, and Palearctic, and cooler locations in the Afrotropics, Australasia, and the Neotropics. Hotspots and especially non-hotspots over sampled urban areas. Hotspots and non-hotspots under sampled shrublands in Australasia. Hotspots and especially non-hotspots under sampled forests in the Afrotropics, Indomalaya, Neotropics, and Oceania. Main conclusions: Hotspots have captured a large component of the world's avian diversity but have done so inconsistently across space and time. Data quantity and quality are increasing in many regions, but the presence of sampling biases and spatial uncertainty needs to be addressed when applying the data.

opencc-zeroMay 2024View details →

Data from: Caste-biased patterns of brain investment in the subterranean termite Reticulitermes flavipes

Investment into neural tissue is expected to reflect the specific sensory and behavioral capabilities of a particular organism. Termites are eusocial insects that exhibit a caste system in which individuals can develop into one of several morphologically and behaviorally distinct castes. However, it is unclear to what extent these differences between castes are reflected in the anatomy of the brain. To address this question, we used deformation-based morphometry to conduct pairwise comparisons between the brains of different castes in the eastern subterranean termite, Reticulitermes flavipes. The dataset presented here consists of the confocal images of all the brains used in our analysis, separated by caste. Brains from five castes are presented - workers, soldiers, ergatoids, nymphs, and alates - which are further divided by sex.

opencc-by-4.0May 2024View details →

Replication of manuscript entitled "Multi-decadal climate variability and satellite biases have amplified model-observation discrepancies in tropical troposphere warming estimates"

Replication of manuscript entitled "Multi-decadal climate variability and satellite biases have amplified model-observation discrepancies in tropical troposphere warming estimates". This page contains datasets used to replicate figures in a manuscript entitled "Multi-decadal climate variability and satellite biases have amplified model-observation discrepancies in tropical troposphere warming estimates". These ascii or netcdf files can be easily read by NCL, Fortran and others.