cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0p2ngf1xk
title: Data from: Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass

description: Germplasm from perennial ryegrass (Lolium perenne L.) natural populations
 is useful for breeding because of its adaptation to a wide range of
 climates. Climate-adaptive genes can be detected from associations between
 genotype, phenotype and climate but an integrated framework for the
 analysis of these three sources of information is lacking. We used two
 approaches to identify adaptive loci in perennial ryegrass and their
 effect on phenotypic traits. First, we combined Genome-Environment
 Association (GEA) and GWAS analyses. Then, we implemented a new test based
 on a Canonical Correlation Analysis (CANCOR) to detect adaptive loci.
 Furthermore, we improved the previous perennial ryegrass gene set by de
 novo gene prediction and functional annotation of 39,967 genes. GEA-GWAS
 revealed eight outlier loci associated with both an environmental variable
 and a phenotypic trait. CANCOR retrieved 633 outlier loci associated with
 two climatic gradients, characterized by cold-dry vs mild-wet winter and
 long rainy season vs long summer, and pointed out traits putatively
 conferring adaptation at the extremes of these gradients. Our CANCOR test
 also revealed the presence of both polygenic and oligogenic climatic
 adaptations. Our gene annotation revealed that 374 of the CANCOR outlier
 loci were positioned within or close to a gene. Co-association networks of
 outlier loci revealed a potential utility of CANCOR for investigating the
 interaction of genes involved in polygenic adaptations. The CANCOR test
 provides an integrated framework to analyze adaptive genomic diversity and
 phenotypic responses to environmental selection pressures that could be
 used to facilitate the adaptation of plant species to climate change.
DOI: 10.5061/dryad.4tmpg4f6z
title: Data from: Synergistic effects of nitrogen and CO2 enrichment on alpine grassland biomass and community structure

description: Global environmental change is altering Earth’s ecosystems.
 However, much research has focused on ecosystem-level responses, and
 we know substantially less about community-level responses to
 global change stressors. Here we conducted a 6-year field experiment in a
 high-altitude (4600 m above sea level) alpine grassland on the Tibetan
 Plateau to explore the effects of nitrogen (N) addition and
 rising atmospheric CO2 concentration on plant communities. Our
 results showed that N and CO2 enrichment had synergistic effects
 on alpine grassland communities. Adding nitrogen or CO2 alone did
 not alter total community biomass, species diversity, or
 community composition, whereas adding both resources together increased
 community biomass, reduced species diversity, and altered
 community composition. The observed decline in species diversity under
 simultaneous N and CO2 enrichment was associated with
 greater community biomass and lower soil water content, and driven by the
 loss of species characterized simultaneously by tall stature and
 small specific leaf area. Our findings point to the co-limitation of
 alpine plant community biomass and structure by nitrogen and CO2,
 emphasizing the need for future studies to consider multiple
 aspects of global environmental change together to gain a more complete
 understanding of their ecological consequences.
description: The data were collected through plant community surveys.
DOI: 10.5061/dryad.3xsj3txcx
title: Anopheles stephensi occurrence data 1985 - 2019

description: In 2012, an unusual outbreak of malaria occurred in Djibouti City followed
 by increasingly severe annual outbreaks. Investigations revealed the
 presence of an Asian mosquito species; Anopheles stephensi, which thrives
 in urban environments. Anopheles stephensi has since been identified in
 Ethiopia and Sudan. By combining data for An. stephensi across its full
 range (Asia, Arabian Peninsula, Horn of Africa) with spatial models that
 identify the species’ preferred habitat, we provide evidence-based maps
 predicting the possible African locations where An. stephensi could
 establish if allowed to spread.  
description: A two year data collation
 process was conducted as part of the HumBug Project to build on the
 existing MAP database of global occurrence data for the Asian DVS of human
 malaria. Using the MAP data abstraction protocol additional searches of
 the published literature (PubMed, Web of Science and Scopus) were
 conducted extending the occurrence data from 2010 to 2016 and where
 possible, disaggregated sibling species data from the existing data across
 the full time period (1985 – 2016). Only those records with reliable
 reported identification methods (i.e. molecular methods distinguishing
 siblings) were included. Additional searches were conducted to include
 specific reports of <em>An. stephensi</em> in
 Africa.
description: The data is ready to use for niche modelling. It includes all
 citations to the original data source.
DOI: 10.5281/zenodo.11433426
title: DIVINE: Andalusia Agroclimatic Information Network Historic Datasets - GRANADA - (June 23 - May 24)

description: This dataset contains high-resolution daily agroclimatic data from the RIA (Red de Información Agroclimática de Andalucía) the andalusian agroclimatic information network, managed by IFAPA. The data has been collected as part of the DIVINE project to support research in precision agriculture, water management, and climate adaptation in Southern Spain.

The dataset covers the period from June 1, 2023, to May 31, 2024, providing key parameters such as temperature (mean, max, min), humidity, wind speed, solar radiation, precipitation, and calculated ETo (Evapotranspiration) using the Penman-Monteith method.

Geographic Coverage and Station Distribution: The dataset includes part of the processed records from 123 monitoring stations distributed across the 8 provinces of Andalusia. In this case the data includes the ones in Granada:

Data Format:





Format: JSON (JavaScript Object Notation).




Naming Convention: 34 [Province_ID] [Station_ID] DIVINE [Station_Name] ([Province]).json




Coordinate System: WGS84 (included within the metadata of individual station files).



Source: Data retrieved from the official IFAPA RIAWS API (Junta de Andalucía).
DOI: 10.5281/zenodo.11433427
title: DIVINE: Andalusia Agroclimatic Information Network Historic Datasets - GRANADA - (June 23 - May 24)

description: This dataset contains high-resolution daily agroclimatic data from the RIA (Red de Información Agroclimática de Andalucía) the andalusian agroclimatic information network, managed by IFAPA. The data has been collected as part of the DIVINE project to support research in precision agriculture, water management, and climate adaptation in Southern Spain.

The dataset covers the period from June 1, 2023, to May 31, 2024, providing key parameters such as temperature (mean, max, min), humidity, wind speed, solar radiation, precipitation, and calculated ETo (Evapotranspiration) using the Penman-Monteith method.

Geographic Coverage and Station Distribution: The dataset includes part of the processed records from 123 monitoring stations distributed across the 8 provinces of Andalusia. In this case the data includes the ones in Granada:

Data Format:





Format: JSON (JavaScript Object Notation).




Naming Convention: 34 [Province_ID] [Station_ID] DIVINE [Station_Name] ([Province]).json




Coordinate System: WGS84 (included within the metadata of individual station files).



Source: Data retrieved from the official IFAPA RIAWS API (Junta de Andalucía).
DOI: 10.5061/dryad.nzs7h44p6
title: Data from: Oxidative stress mediates rapid compensatory growth and its costs

description: 1. While oxidative stress has been hypothesized to function both as a
 constraint on and a cost of growth, its mediatory role in shaping life
 history is still highly debated. Empirical studies about the role of
 oxidative stress in shaping growth responses and the associated costs are
 scarce and the two hypotheses have never been combined in one study. 2. By
 directly manipulating oxidative stress we tested its role in determining
 compensatory growth responses and the associated costs in the damselfly
 Lestes viridis. We reduced oxidative stress levels using the mitochondrial
 uncoupler 2,4-dinitrophenol (DNP). To induce a compensatory growth
 response, half of the larvae in each oxidant treatment was exposed to a
 transient starvation period, after which food was present ad libitum. 3.
 As expected, the transient starvation period induced a compensatory growth
 response, which was associated with increased oxidative damage and costs
 in terms of performance (reduced escape swimming speed) and physiology
 (reduced fat content). As expected, DNP exposure reduced oxidative stress
 and this resulted in the strongest compensatory growth response without
 any apparent costs and no increase in oxidative damage. 4. By directly
 downregulating oxidative stress, our results are consistent with the
 hypothesis that the level of oxidative stress predictably determines the
 degree of the compensatory growth response and its associated costs. Our
 data therefore suggest a mediatory role of oxidative stress in shaping
 life history.
description: Data were collected from experimental work including life history
 data from living animals and physiological analyses
DOI: 10.5061/dryad.1g1jwstsj
title: Modernizing health information technology: lessons from healthcare delivery systems

description: Abstract Objective To identify recurrent themes, insights, and process
 recommendations from stakeholders in US organizations during the health
 information technology (HIT) modernization of an existing electronic
 health record (EHR) to a commercial-off-the-shelf product in both
 resource-plentiful settings and in a resource-constrained environment, the
 US Indian Health Service. Materials and Methods Thirteen qualitative
 interviews with stakeholders in various organizations were conducted about
 HIT modernization efforts. Using a Theory of Change framework, recurring
 themes were identified and analyzed. Results The interviewees emphasized
 the importance of organizational and process revision during
 modernization, converting historical data, and clinical and leadership
 involvement. HIT implementation required technological and infrastructure
 redesign, additional training, and workflow reconfiguration. Motivations
 for modernization included EHR usability dissatisfaction, revenue
 enhancements, and improved clinical operations. Decision-making
 strategies, primarily during HIT selection, included meetings with
 stakeholders. Successful modernization resulted in improvements in
 clinical operations, patient experience, and financial outlay. Discussion
 Existing implementation frameworks fail to provide experiential feedback,
 such as implementation challenges, like data conversion, regulatory,
 functionality, and interoperability requirements. Regardless of the
 healthcare environment, HIT modernization requires the engagement of
 leadership and end-users during HIT selection and through all stages of
 the implementation to prepare people, processes, and technology.
 Organizations must iteratively define the technological, infrastructure,
 organizational, and workflow changes required for a successful HIT
 modernization effort. Conclusions HIT modernization is an opportunity for
 organizational and technological change. Successful modernization requires
 a comprehensive, intentional, well-communicated, and multidisciplinary
 approach. Resource-constrained environments have the additional challenges
 of financial burdens, limited staffing, and unstable infrastructure.
DOI: 10.5061/dryad.xgxd254dd
title: Data from: When to stay and when to leave? Proximate causes of dispersal in an endangered social carnivore

description: 1. Reliable estimates of birth, death, emigration, and immigration rates
 are fundamental to understanding and predicting the dynamics of wild
 populations and, consequently, inform appropriate management actions.
 However, when individuals disappear from a focal population, inference on
 their fate is often challenging. 2. Here we used 30 years of
 individual-based mark-recapture data from a population of free-ranging
 African wild dogs (Lycaon pictus) in Botswana and a suite of individual,
 social, and environmental predictors to investigate factors affecting the
 decision to emigrate from the pack. We subsequently used this information
 to assign an emigration probability to those individuals that were no
 longer sighted within their pack (i.e. missing individuals). 3. Natal
 dispersal (i.e. emigration from the natal pack) showed seasonal patterns
 with female dispersal peaking prior to the mating season and male
 dispersal peaking at the beginning of the wet season. For both sexes,
 natal dispersal rate increased in the absence of unrelated individuals of
 the opposite sex in the pack. Male natal dispersal decreased with
 increasing number of pups in the pack and increased in larger packs.
 Female natal dispersal decreased with increasing number of pups in larger
 packs, but increased with increasing number of pups in smaller packs.
 Individuals of both sexes were less likely to exhibit secondary dispersal
 (i.e. emigration from a pack other than the natal pack) if they were
 dominant and if many pups were present in the pack. 4. Our models
 predicted that 18% and 25% of missing females and males, respectively, had
 likely dispersed from the natal pack, rather than having died. A
 misclassification of this order of magnitude between dispersal and
 mortality can have far-reaching consequences in the evaluation and
 prediction of population dynamics and persistence, and potentially mislead
 conservation actions. 5. Our study showed that the decision to disperse is
 context-dependent and that the effect of individual, social, and
 environmental predictors differs between males and females and between
 natal and secondary dispersal related to different direct and indirect
 fitness consequences. Furthermore, we demonstrated how a thorough
 understanding of the proximate causes of dispersal can be used to assign a
 dispersal probability to missing individuals. Knowledge of causes of
 dispersal can then be used within an integrated framework to more reliably
 estimate mortality rates.
DOI: 10.5061/dryad.b8gtht79d
title: Molecular underpinning of intracellular pH regulation on TMEM16F

description: TMEM16F, a dual functional phospholipid scramblase and ion channel, is
 important in blood coagulation, skeleton development, HIV infection and
 cell fusion. Despite advances in understanding its structure and
 activation mechanism, how TMEM16F is regulated by intracellular factors
 remains largely elusive. Here we report that TMEM16F lipid scrambling and
 ion channel activities are strongly influenced by intracellular pH (pHi).
 We found that low pHi attenuates, whereas high pHi potentiates, TMEM16F
 channel and scramblase activation under physiological concentrations of
 intracellular Ca2+ ([Ca2+]i). We further demonstrate that TMEM16F pHi
 sensitivity depends on [Ca2+]i and exhibits a bell-shaped relationship
 with [Ca2+]i: TMEM16F channel activation becomes increasingly pHi
 sensitive from the resting [Ca2+]i to micromolar [Ca2+]i, but when [Ca2+]i
 increases beyond 15µM, the pHi sensitivity gradually diminishes. The
 mutation of a Ca2+-binding residue that markedly reduces TMEM16F Ca2+
 sensitivity (E667Q), maintains the bell-shaped relationship between pHi
 sensitivity and Ca2+ but causes a dramatic shift of the peak [Ca2+]i from
 15µM to 3 mM. Our biophysical characterizations thus pinpoints that the
 pHi regulatory effects on TMEM16F stem from the competition between Ca2+
 and proton for the primary Ca2+-binding residues in the pore. Within the
 physiological [Ca2+]i range, the protonation state of the primary
 Ca2+-binding sites influences Ca2+ binding and regulates TMEM16F
 activation. Our findings thus uncover a regulatory mechanism of TMEM16F by
 pHi and shine light on our understanding of the pathophysiological roles
 of TMEM16F in diseases with dysregulated pHi including cancer.
DOI: 10.15468/dl.fayb4x
title: Occurrence Download

description: A dataset containing 91 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-98.4486 19.12295,-98.40797 19.14095,-98.40797 19.20556,-98.42891 19.23209,-98.44917 19.23097,-98.45986 19.22872,-98.47111 19.211,-98.49389 19.20228,-98.50515 19.18399,-98.52062 19.18343,-98.52484 19.15389,-98.50205 19.12351,-98.4486 19.12295))",
 "OccurrenceStatus is Present",
 "TaxonKey is Chordata"
 ]
}

 The dataset includes 91 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002421-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j9kd51c8r
title: Pervasive effects of Wolbachia on host temperature preference

description: Heritable symbionts can modify a range of ecologically important host
 traits, including behavior. About half of all insect species are infected
 with maternally transmitted Wolbachia, a bacterial endosymbiont
 known to alter host reproduction, nutrient acquisition, and virus
 susceptibility. Here, we broadly test the hypothesis
 that Wolbachia modify host behavior by assessing the
 effects of eight different Wolbachia strains on the
 temperature preference of six Drosophila melanogaster-subgroup
 species. Four of the seven host genotypes infected with
 A-group Wolbachia strains (wRi in D.
 simulans, wHa in D. simulans, wSh
 in D. sechellia, and wTei in D. teissieri)
 prefer significantly cooler temperatures relative to uninfected genotypes.
 Contrastingly, when infected with divergent
 B-group wMau, D. mauritiana prefer a warmer
 temperature. For most strains, changes to host temperature preference do
 not alter Wolbachia titer. However, males infected
 with wSh and wTei experience an increase in titer when
 shifted to a cooler temperature for 24 hours, suggesting
 that Wolbachia-induced changes to host behavior may promote
 bacterial replication and
 influence Wolbachia transmission rates. Modifications to
 host temperature preference likely influence host thermoregulation, and
 understanding the fitness consequences of these effects is crucial for
 predicting evolutionary outcomes of host-symbiont interactions, including
 how Wolbachia spread to become common.
DOI: 10.5061/dryad.hmgqnk9dh
title: Assigning occurrence data to cryptic taxa improves climatic niche assessments: biodecrypt, a new tool tested on European butterflies

description: Aim Occurrence data are fundamental to macroecology, but accuracy is often
 compromised when multiple units are lumped together (e.g. in recently
 separated cryptic species or citizen science records). Using amalgamated
 data leads to inaccuracy in species mapping, to biased beta-diversity
 assessments and to potentially erroneously predicted responses to climate
 change. We provide a set of R functions (biodecrypt) to objectively
 attribute undetermined occurrences to the most probable taxon based on a
 subset of identified records. Innovation Biodecrypt assumes that unknown
 occurrences can only be attributed at certain distances from areas of
 sympatry. The function draws concave hulls based on the subset of
 identified records; subsequently, based on hull geometry, it attributes
 (or not) unknown records to a given taxon. Concavity can be imposed with
 an alpha value and sea or land areas can be excluded. A cross-validation
 function tests attribution reliability and another function optimizes the
 parameters (alpha, buffer, distance ratio between hulls). We applied the
 procedure to 16 European butterfly complexes recently separated into 33
 cryptic species for which most records were amalgamated. We compared niche
 similarity and divergence between cryptic taxa, and we re-calculated and
 contributed updated CLIMBER variables for climatic preferences. Main
 conclusions Biodecrypt showed a cross-validated correct attribution of
 known records always ≥98% and attributed more than 80% of unknown records
 to the most likely taxon in parapatric species. The functions determined
 where records can be assigned even for largely sympatric species, and
 highlighted areas where further sampling is required. All the cryptic taxa
 showed significantly diverging climatic niches, reflected in different
 values of mean temperature and precipitation compared to the values
 originally provided in the CLIMBER database. The substantial fraction of
 cryptic taxa existing across different taxonomic groups and their
 divergence in climatic niches highlights the importance of using reliably
 assigned occurrence data in macroecology.
description: The script "Script.R" contains all the scrpts to run
 examples and the analyses to carry out separation of occurrence data among
 cryptic taxa. The "biodecrypt.R" file
 contains the functions The "Total_data.txt"
 file contains the data used for the analyses without duplicates for each
 cell The "all_data.txt" file contains all the
 occurrence data (also duplicated data) with indications for geographic
 locations, BOLD and genbank IDs The
 "Appendix_S2.txt" file contains the new CLIMBER data
DOI: 10.5061/dryad.fxpnvx0p9
title: Irreversible habitat specialization does not constrain diversification in hypersaline water beetles

description: Specialization to extreme environments is often considered an evolutionary
 dead-end, leading to irreversible adaptations and reduced evolvability.
 There is, however, mixed evidence of this macroevolutionary pattern, and
 limited data from speciose lineages. Here, we tested the effect of habitat
 specialization to hypersaline waters in the diversification rates of
 aquatic beetles of the genus Ochthebius (Coleoptera, Hydraenidae), using a
 molecular phylogeny with more than 50% of the 546 recognized species,
 including representatives of all subgenus and species groups but one.
 Phylogenies were built combining mitochondrial and nuclear genes, with the
 addition of 42 mitochondrial genomes. Using Bayesian methods of character
 reconstruction, we show that hypersaline tolerance is an irreversible
 ecological specialization that arose multiple times independently. Two
 lineages of Ochthebius experienced a significant increase in
 diversification rates, one of them inhabiting hypersaline waters, but
 there was no overall correlation with habitat or any significant decrease
 in diversification rates despite the irreversibility of the hypersaline
 tolerance. Our study tested for the first time the impact of hypersaline
 habitat specialization on diversification rates, without support of being
 an evolutionary dead-end. On the contrary, multiple and ancient lineages
 fully adapted to these extreme osmotic conditions seem able to diversify
 over long evolutionary periods.
description: See attached README.pdf for additional information.