cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.280gb5mrw
title: Niche conservatism limits the distribution of Medicago in the tropics

description: The increase in species number from poles to the equator is one of the
 most fundamental patterns in ecology. Although several hypotheses have
 been proposed, there is a lack of consensus on the mechanisms underlying
 this pattern. While most hypotheses provide plausible explanation for high
 tropical diversity of tropical clades, it is unclear if similar mechanisms
 drive the diversity of extra-tropical clades. Here, we investigated the
 environmental drivers influencing the diversity pattern of a Mediterranean
 plant genus Medicago and dissect their effects across continents and
 biomes. We compiled a comprehensive dataset on the distribution of all
 Medicago species and mapped their distribution at the spatial resolution
 of 100 × 100 km2. We used generalized linear models to quantify the
 relative effects of environmental factors on the richness patterns of
 Medicago and its two life forms. Next, using geographically weighted
 regression, we explored the variation in richness-environment relationship
 across latitude. We found that Quaternary climate change and environmental
 energy were important explanatory variables, and their effects were
 consistent at global, continental and biome scales. However, we found
 contrasting effect of environmental energy in temperate and tropical
 regions, with species richness increasing with energy in the temperate and
 decreasing in the tropics. We also found strong affinity of Medicago
 species to its ancestral Mediterranean climatic niche. Our results suggest
 that the spatial variation in Medicago richness patterns may be strongly
 influenced by heat tolerance as opposed to the tropical clades that depend
 upon cold tolerance. This dependency on heat tolerance can be attributed
 to strong niche conservatism exhibited by Medicago species. Our findings
 provide new insights into the richness-energy hypothesis and suggest that
 high environmental energy may not necessarily yield high species diversity
 but may also lower species diversity, especially of extra-tropical clades
 towards the tropics.
DOI: 10.5061/dryad.dfn2z354h
title: Close kin dyads indicate intergenerational dispersal and barriers

description: The movement of individuals through continuous space is typically
 constrained by dispersal ability and dispersal barriers. A range of
 approaches have been developed to investigate these.
 Kindisperse is a new approach that infers intergenerational
 dispersal (σ) from close kin dyads, and appears particularly useful for
 investigating taxa that are difficult to observe individually. This study,
 focusing on the mosquito Aedes aegypti, shows how the same close
 kin data can also be used for barrier detection. We empirically
 demonstrate this new extension of the method using genome-wide sequence
 data from 266 Ae. aegypti. First, we use the spatial distribution
 of full-sib dyads collected within one generation to infer past movements
 of ovipositing female mosquitoes. These dyads indicated the relative
 barrier strengths of two roads, and performed favourably against
 alternative genetic methods for detecting barriers. The difference in
 variance between the sib and first cousin spatial distributions was used
 to infer movement over the past two generations, providing estimates of
 intergenerational dispersal (σ = 81.5-197.1 m.gen-1/2) and density (ρ =
 833-4864 km-2). Dispersal estimates showed general agreement with those
 from mark-release-recapture studies. Barriers, σ, ρ, and neighbourhood
 size (331-526) can inform forthcoming releases of
 dengue-suppressing Wolbachia bacteria into this mosquito
 population.
description: Aedes aegypti mosquitoes were sampled from Jeddah, Saudi Arabia,
 in 2020. Genome-wide sequence data was generated from 266 mosquitoes using
 ddRADseq. Data were processed in the Stacksv2.0 pipeline. Specifics are
 listed in: https://doi.org/10.1101/2022.01.18.476819
description: All information is listed in the README and in the paper: https://doi.org/10.1101/2022.01.18.476819 Access to bam files used in these analyses is through NCBI SRA, accession numbers: PRJNA837703, PRJNA542421, SRP118883, PRJNA684450
DOI: 10.57707/fmi-b2share.dm32x-3jw28
title: Data and code for the manuscript "Future snow scenarios for Northern Europe  based on Coupled Model Intercomparison Project Phase 6 data" by Petri Räisänen et al.

description: This dataset contains analyses of changes in snow conditions in Northern Europe (land areas between 4-40 E, 50-72N) simulated by the latest CMIP6 generation of global climate models. Also provided are fortran programs and GrADS and R scripts employed to generate the results in the manuscript (Räisänen et al. 2025, International Journal of Climatology; revised version in January 2025).

REFERENCE TO THE MANUSCRIPT (please refer to the final accepted version if/when the paper will be accepted):

Räisänen, P., Luomaranta, A., and Jylhä, K. (2025): Future snow scenarios for Northern Europe based on Coupled Model Intercomparison Project phase 6 data. International Journal of Climatology, revised.
description: The starting point for the analysis was daily snow water equivalent (SWE) data for CMIP6 models for years 1951-2100, where historical experiments extending to year 2014 were combined with Shared Socieconomic Pathways scenarios SSP126, SSP245, SSP370 and SSP585 for years 2015-2100. A single ensemble member (i.e., model run) was analyzed for 15-17 CMIP6 models, depending on the scenario. In addition, large single-model ensembles (40-50 parallel runs) were analyzed for three CMIP6 models (ACCESS-ESM1-5, CanESM5 and MIROC6) for the SSP245 scenario. Based on these data, several snow season metrics were first computed for each "snow year" (from 1 Sep of the previous year to 31 Aug) in the period 1951-2100. These metrics included (but are not limited to) the maximum SWE in winter and the length, start date and end date of the longest continuous snow period. Based on these yearly metrics, trends over the periods 1951-2023 and 2023-2100 and 20-year running-mean changes compared to the reference period 1981-2010 were further computed and analyzed. Similar analysis was also performed for ERA5-Land reanalysis data (years 1951-2023).
description: The contents of the data files are described in the file "README_data.txt". The contents of the file containing code ("code_and_scripts.zip") are described in "README_code.txt" as well as in README files included in the zip file. The terms of use for the data and the code are given in the files "License_data.txt" and "License_code.txt", respectively.
DOI: 10.57707/fmi-b2share.wsgnt-8ee91
title: Data and code for the manuscript "Future snow scenarios for Northern Europe  based on Coupled Model Intercomparison Project Phase 6 data" by Petri Räisänen et al.

description: This dataset contains analyses of changes in snow conditions in Northern Europe (land areas between 4-40 E, 50-72N) simulated by the latest CMIP6 generation of global climate models. Also provided are fortran programs and GrADS and R scripts employed to generate the results in the manuscript (Räisänen et al. 2025, International Journal of Climatology; revised version in January 2025).

REFERENCE TO THE MANUSCRIPT (please refer to the final accepted version if/when the paper will be accepted):

Räisänen, P., Luomaranta, A., and Jylhä, K. (2025): Future snow scenarios for Northern Europe based on Coupled Model Intercomparison Project phase 6 data. International Journal of Climatology, revised.
description: The starting point for the analysis was daily snow water equivalent (SWE) data for CMIP6 models for years 1951-2100, where historical experiments extending to year 2014 were combined with Shared Socieconomic Pathways scenarios SSP126, SSP245, SSP370 and SSP585 for years 2015-2100. A single ensemble member (i.e., model run) was analyzed for 15-17 CMIP6 models, depending on the scenario. In addition, large single-model ensembles (40-50 parallel runs) were analyzed for three CMIP6 models (ACCESS-ESM1-5, CanESM5 and MIROC6) for the SSP245 scenario. Based on these data, several snow season metrics were first computed for each "snow year" (from 1 Sep of the previous year to 31 Aug) in the period 1951-2100. These metrics included (but are not limited to) the maximum SWE in winter and the length, start date and end date of the longest continuous snow period. Based on these yearly metrics, trends over the periods 1951-2023 and 2023-2100 and 20-year running-mean changes compared to the reference period 1981-2010 were further computed and analyzed. Similar analysis was also performed for ERA5-Land reanalysis data (years 1951-2023).
description: The contents of the data files are described in the file "README_data.txt". The contents of the file containing code ("code_and_scripts.zip") are described in "README_code.txt" as well as in README files included in the zip file. The terms of use for the data and the code are given in the files "License_data.txt" and "License_code.txt", respectively.
DOI: 10.5061/dryad.pvmcvdnp6
title: Resurrection ecology in Viola arvensis

description: Premise of the study: As part of global change, climate warming and
 pollinator decline are expected to affect plant phenology and
 plant-pollinator interactions. This paper aims at characterizing rapid
 evolution of life history traits and floral traits over two decades in the
 wild pansy (Viola arvensis), a common weed in agrosystems. Methods: We
 used a resurrection ecology approach with genotypes sampled in 1991 and
 2012 from a population in Burgundy (France). The species has a mixed
 mating system (hereafter: mixed selfer) and presents a floral
 polymorphism. In order to correct for maternal effects, plant traits were
 measured in the second generation in a common garden (after a refreshing
 generation) to characterize plant evolution during the two decades. In
 addition, historical population selfing rates in the 1991 and 2012 were
 inferred from microsatellites markers through heterozygote deficiency and
 identity disequilibrium. Key results: Phenotypic data revealed a
 significant advance in flowering date, reduced flower sizes and a higher
 propensity of plant to set seed by autonomous selfing. Moreover, we
 detected a change in color morph frequency with an increase of the pale
 morph frequency. In accordance with phenotypic data, the neutral genetic
 data revealed in increase in historical selfing rates from s=0.68 in 1991
 to s=0.86 in 2012. Conclusions: Taken together, such data suggest that the
 wild pansy, as mixed selfer, is evolving a selfing syndrome that may be
 the consequence of reduced pollinator activity in agrosystems.
description: Seeds come from botanical garden and field sampling. phenotypic
 meausrements were done in common garden in Montpellier (South of
 France)
DOI: 10.5281/zenodo.18400488
title: LINF_320012000

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.5281/zenodo.18400487
title: LINF_320012000

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.5061/dryad.wwpzgmsmt
title: SDM env predictor comparison dataset

description: Identifying the environmental drivers of the global distribution of
 succulent plants using the crassulacean acid metabolism pathway of
 photosynthesis has previously been investigated through ensemble-modelling
 of species delimiting the realised niche of the natural succulent biome.
 An alternative approach, which may provide further insight into the
 fundamental niche of succulent plants in the absence of dispersal
 limitation, is to model the distribution of selected species that are
 globally widespread and have become naturalised far beyond their native
 habitats.  This could be of interest, for example, in defining
 areas that may be suitable for cultivation of alternative crops resilient
 to future climate change. We therefore explored the performance of
 climate-only species distribution models in predicting the drivers and
 distribution of two widespread CAM plants, Opuntia ficus-indica and
 Euphorbia tirucalli.  Using two different algorithms and five
 predictor sets, we created distribution models for these examplar species
 and produced an updated map of global inter-annual rainfall
 predictability. No single predictor set produced markedly more accurate
 models, with the basic bioclim-only predictor set marginally
 out-performing combinations with additional predictors. Minimum
 temperature of the coldest month was the single most important variable in
 determining spatial distribution, but additional predictors such as
 precipitation and inter-annual precipitation variability were also
 important in explaining the differences in spatial predictions between
 SDMs. When compared against previous projections, an a posteriori approach
 correctly does not predict distributions in areas of ecophysiological
 tolerance yet known absence (e.g. due to biotic competition). An updated
 map of inter-annual rainfall predictability has successfully identified
 regions known to be depauperate in succulent plants. High model
 performance metrics suggest that the majority of potentially suitable
 regions for these species are predicted by these models with a limited
 number of climate predictors, and there is no benefit in expanding model
 complexity and increasing the potential for overfitting.
description: R code and additional raster datasets attached for recreating the
 data, models and results presented in Buckland et al. (2022) - Ecol
 & Evolution. Save the additional raster
 datasets to the working directory, and update the file pathways in the R
 code to the relevant directory locations. Please refer to README file for
 futher information, or contact the corresponding author:
 catherine.buckland@ouce.ox.ac.uk
DOI: 10.34740/kaggle/dsv/14649625
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.57724/hes_20250113_microant_mn
title: Microplastics in neuston, 2025
DOI: 10.5061/dryad.wm37pvmqd
title: Genetic characterization of potential venom resistance proteins in California ground squirrels (Otospermophilus beecheyi) using transcriptome analyses

description: Understanding the molecular basis of adaptations in coevolving species
 requires identifying the genes that underlie reciprocally selected
 phenotypes, such as those involved in venom in snakes and resistance to
 venom in their prey. In this regard, California ground squirrels (CGS;
 Otospermophilus beecheyi) are eaten by northern Pacific rattlesnakes
 (Crotalus oreganus oreganus), but individual squirrels may still show
 substantial resistance to venom and survive bites. A recent study using
 proteomics identified venom interactive proteins (VIPs) in the blood serum
 of CGS.  These VIPs represent possible resistance proteins, but
 the sequences of genes encoding them are unknown despite the value of such
 data to molecular studies of coevolution. To address this issue, we
 analyzed a de novo assembled transcriptome from CGS liver tissue—where
 many plasma proteins are synthesized—and other tissues from this species.
 We then examined VIP sequences in terms of three characteristics that
 identify them as possible resistance proteins: evidence for positive
 selection, high liver expression, and nonsynonymous variation across CGS
 populations. Based on these characteristics, we identified five VIPs
 (i.e., alpha-2-macroglobulin, alpha-1-antitrypsin-like protein GS55-LT,
 apolipoprotein A-II, hibernation-associated plasma protein HP-20, and
 hibernation-associated plasma protein HP-27) as the most likely candidates
 for resistance proteins among VIPs identified to date. Four of these
 proteins have been previously implicated in conferring resistance to venom
 in mammals, validating our approach. When combined with the detailed
 information available for rattlesnake venom proteins, these results set
 the stage for future work focused on understanding coevolutionary
 interactions at the molecular level between these species.
DOI: 10.15468/dl.a3bbd8
title: Occurrence Download

description: A dataset containing 623 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Dioscorea multiflora"
 ]
}

 The dataset includes 623 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003126-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.xsj3tx9hx
title: Common guillemots in the Baltic Sea studied with video surveillance and object detection: raw data, annotations, model, and model outputs

description: The data comes from common guillemots studied at Stora Karlsö, Sweden
 between 2019 and 2021. The common guillemots breed at an artificial cliff,
 and has been filmed continusly from above over three breeding seasons.
 Using the video material, a YOLOv5 model has been trained to detect adult
 birds, chicks and eggs. The dataset contains annotations (bounding boxes)
 used for training the model, the model itself, and outputs from the model
 (object detections). The data can be used and shared freely.
description: The raw data is videos in <em>.avi</em> format,
 recorded with a Avtech AVH8516 Network Video Recorder (NVR) connected to a
 2 megapixel IP camera (Avtech AVM543P) operating at 25 frames per second
 (FPS). From the videos, single frames have been picked out and annotated
 with bounding boxes with three classes: adult bird (0), chick (1) and egg
 (2). Using these annotations, a YOLOv5 model has been trained. The videos
 have then been downsampled to 1 FPS and Object detection has been run on
 the whole material, and the output has been stored in a SQLite
 database coordinates for each detected object.
description: <strong>The dataset contains:</strong>
 Annotations (images and bounding box coordinates).
 The format is "YOLO Darknet TXT", described in detail
 here: https://roboflow.com/formats/yolo-darknet-txt  The YOLOV5 model, 2 files: <em>.cfg</em> and <em>.weights</em> Inference from the YOLO model (bounding boxes) in SQlite format (.db)  The videos themselves are several Tb (approx 1 Gb per H of film) and therefore not possible to share at this moment at a reasonable cost. Sample videos (downsampled to 1 FPS) are provided as .avi files. Python code for training and running Yolov5 is available at: https://github.com/BalticSeabird/SeabirdDetections R code for post-processing the model outputs including the generation of figures is available at https://github.com/BalticSeabird/ObjectDetectionInferences
DOI: 10.5061/dryad.fttdz08vz
title: Temperature regime during embryogenesis alters subsequent behavioural phenotypes of juvenile brown trout

description: Climate warming imposes a serious threat, especially to freshwater
 ecosystems in temperate and (sub)polar regions, which are often dominated
 by cold-adapted ectotherms. Although relatively intense warming during
 winter is common across the climatic regions, comparably little focus has
 been put on the organismal impacts of winter warming. Embryonic
 development, which is exceptionally susceptible to ambient temperature,
 occurs during winter in various freshwater ectotherms. Yet, our knowledge
 of the effects of increased temperature during embryogenesis on later life
 stages is limited. Using brown trout (Salmo trutta), we examined how a
 1.5°C temperature increase from fertilisation to hatching affects various
 traits at the onset of the free-swimming stage (i.e., a comparison between
 3.5°C or 5.0°C treatments). Although all hatchlings were kept at the same
 temperature (7.0°C) from hatching to the onset of the
 free-swimming stage for about two months, the temperature increase during
 embryogenesis substantially reduced key ecological
 behaviours, i.e., activity and exploration levels, at the onset of the
 free-swimming stage despite only marginal temperature effects on
 morphological and physiological traits at this stage. Given the importance
 of behavioural traits in early growth and survival, our study suggests a
 likely pathway through which subtle changes in mean winter temperature
 affect early fitness.
DOI: 10.57707/fmi-b2share.2a14e-cea38
title: Derived data products analyzed and presented in the manuscript "Ter-diurnal Atmospheric Tide on Mars"

description: There are altogether 29 files including the all the data of the results. The filenames are self-explaining, because they refer to the figures in the publication.
DOI: 10.5061/dryad.hdr7sqvkt
title: Beyond bold versus shy: Zebrafish exploratory behavior falls into several behavioral clusters and is influenced by strain and sex

description: Individual differences in exploratory behavior have been found across a
 range of taxa and are thought to contribute to evolutionary fitness.
 Animals that explore more of a novel environment and visit areas of high
 predation risk are considered bold, whereas animals with the opposite
 behavioral pattern are shy. Here, we determined whether this bimodal
 characterization of bold versus shy adequately captures the breadth of
 behavioral variation in zebrafish or if there are more than these two
 subtypes. To identify behavioral categories, we applied unsupervised
 machine to three-dimensional swim traces from over 400 adult zebrafish
 across four strains (AB, TL, TU, and WIK) and both sexes. We found that
 behavior stratified into four distinct clusters: previously described bold
 and shy behavior and two new behavioral types we call wall-huggers and
 active explorers. Clusters were stable across time and influenced by
 strain and sex where we found that TLs were shy, female TU fish were bold,
 male TU fish were active explorers, and male ABs were wall-huggers. Our
 work suggests that zebrafish exploratory behavior has greater complexity
 than previously recognized and lays the groundwork for the use of
 zebrafish in understanding the biological basis of individual differences
 in behavior.