cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k6djh9wb4
title: Mediterranean underwater fish visual census surveys data

description: The positive effect of fully protected Marine Protected Areas (MPAs) on
 marine biodiversity, specifically on fishes, has been widely documented.
 In contrast, the potential of MPAs to mitigate the impact of adverse
 climatic conditions has seldom been investigated. Here, we assessed the
 effectiveness of MPAs, quantified as increasing fish biomass, across wide
 geographic and environmental gradients across the Mediterranean Sea. We
 performed underwater visual surveys within and outside MPAs to
 characterize fish assemblages in 52 rocky reef sites across an extent of
 over 3,300 km. We used the steep spatial temperature gradient across the
 Mediterranean as a ‘space-for-time’ substitution to infer climate-driven
 temporal changes. We found that, as expected, Mediterranean MPAs increased
 fish biomass. At the same time, higher seawater temperatures are
 associated with decreased fish biomass, changes in species composition,
 and shifts towards more thermophilic species. Importantly, we found that
 the rate of decrease in fish biomass with temperature was similar between
 protected and fished sites. Taken together, these results suggest that the
 capacity of MPAs to harbor higher fish biomass, compared to surrounding
 areas, is maintained across a broad temperature range. At the same time,
 MPAs will not be able to offset larger-scale biotic alterations associated
 with climate change. Policy implications: Our results suggest that
 sustained warming will likely reduce fish biomass in the Mediterranean Sea
 and shift community structure, requiring more conservative targets for
 fishery regulations. At the same time, protection from fishing will remain
 an important management tool even with future high-water temperatures, and
 MPAs are expected to continue to provide local-scale benefits to
 conservation and fisheries.
DOI: 10.6078/d1fq42
title: Data from: The influence of human activity on predator-prey spatiotemporal overlap

description: Despite growing evidence of widespread impacts of humans on animal
 behavior, our understanding of how humans reshape species interactions
 remains limited. Here, we present a framework that draws on key concepts
 from behavioral and community ecology to outline four primary pathways by
 which humans can alter predator-prey spatiotemporal overlap. We suggest
 that predator-prey dyads can exhibit similar or opposite responses to
 human activity with distinct outcomes for predator diet, predation rates,
 population demography, and trophic cascades. We demonstrate how to assess
 these behavioral response pathways with hypothesis testing, using temporal
 activity data for 178 predator-prey dyads from published camera trap
 studies on terrestrial mammals. We found evidence for each of the proposed
 pathways, revealing multiple patterns of human influence on predator-prey
 activity and overlap. Our framework and case study highlight current
 challenges, gaps, and advances in linking human activity to animal
 behavior change and predator-prey dynamics. By using a hypothesis-driven
 approach to estimate the potential for altered species interactions, we
 can anticipate the ecological consequences of human activities on whole
 communities.
description: Contains: Temporal activity and functional trait data for 178
 predator-prey dyads from 19 published camera trap studies of terrestrial
 mammals in paired settings of high and low human use. For information on
 how this dataset was compiled and the included datatypes, please review
 the enclosed README.md and metadata files. Includes R scripts, which
 produced Figures 2 and 3 of the case study, to assess how human activity
 can influence predator-prey activity and overlap.
DOI: 10.25338/b8363m
title: Developing a vehicle cost calculator to promote electrical vehicle adoption among transportation network company (TNC) drivers

description: This research developed EV Explorer 2.0, an online vehicle cost calculator
 (VCC) to meet the requirements of transportation network company (TNC)
 drivers considering acquiring an electric vehicle (EV). The tool was built
 to also support the needs of other users considering an EV, including
 other types of gig economy drivers as well as the general population of
 non-professional drivers. EV Explorer 2.0 includes several important
 features and functionalities to support the TNC driver use case that are
 not found in any other available tool: (1) It allows users to estimate TCO
 for used vehicles as well as new (others only estimate TCO for new
 vehicles); (2) Outputs include ridehail-driving income estimates,
 accounting for EV trip bonuses offered by Uber, net driving costs; (3)
 Estimates of total cost of driving (TCD) include charging network
 membership fees and charging session fees (in addition to electricity
 prices). It also includes key features found in other leading tools, such
 as presenting and tailoring EV purchase/lease incentive estimates (based
 on a database we developed), and innovative features to benefit all users,
 such as animations conveying the social and environmental impacts of
 vehicle choice. Design features were informed and validated in user
 testing with TNC drivers who had expressed interest in EV adoption.
description: Federal incentives sourced from fueleconomy.gov
 State and local incentives sourced from AFDC.energy.gov
 Maintenance itemized costs sourced from
 afleet.es.anl.gov Lyft upgraded ride-eligible PEVs
 sourced from
 help.lyft.com/hc/en-us/all/articles/115012923147-Lyft-Lux-Lux-Black-and-Lux-Black-XL-rides-for-drivers#eligible Uber upgraded ride-eligible PEVs sourced from uber.com/global/en/eligible-vehicles/?city=san-francisco; NOTE: Uber provides vehicle eligibility by city, so we used those eligible in San Francisco, CA, as the reference.
DOI: 10.5061/dryad.7pvmcvdxs
title: The effect of polyphenol compounds on Helicobacter pylori eradication: a systematic review with meta-analysis

description: Objectives: Polyphenol compounds are classified as organic
 compounds with phenolic units exhibiting a variety of biological
 functions. This meta-analysis aims to assess the efficacy and safety of
 polyphenol compounds (curcumin, cranberry, garlic, licorice, and broccoli)
 in eradicating Helicobacter pylori. Design: Systematic review and
 meta-analysis. Data sources: These include PubMed, Embase, The
 Cochrane Library, Web of Science, Medline, Chinese National Knowledge
 Infrastructure database , Chinese Scientific Journal Database , and Wan
 Fang database from inception to January 2022. Study
 selection: All randomized controlled trials comparing polyphenol
 compounds with the placebo or used as an adjunct treatment are included in
 this meta-analysis. Data synthesis: The treatment effect for
 dichotomous outcomes were assessed using risk ratio, while for
 continuous outcomes, mean differences (MDs) both with 95% CIs, were used.
 Subgroup analyses were carried out for different treatment schemes and
 polyphenol compound species.   Results: 12
 trials were included in the meta-analysis. The total eradication rate of
 H.pylori in the polyphenol compounds group was higher than in the
 group without polyphenol compounds. Statistical significance was also
 observed (RR 1.19, 95% CI:1.03 to 1.38, P=0.02). The most frequent adverse
 effects of polyphenol compounds included diarrhea, headache, and vomiting.
 However, there were no differences regarding side effects between the two
 groups (RR 1.47, 95% CI: 0.83 to 2.58, P=0.18). In
 subgroup analyses, the H.pylori eradication rate regimens with
 polyphenols therapy was superior to that of regimens without polyphenols
 therapy in the polyphenols versus placebo subgroup (RR 4.23, 95% CI:1.38
 to 12.95, P=0.01), polyphenols plus triple therapy versus triple therapy
 subgroup (RR 1.11, 95% CI: 1.01 to 1.22, P=0.03). Conclusion: Polyphenol
 compounds can improve H.pylori eradication rates. Polyphenol compounds
 plus standard triple therapy can significantly improve the eradication.
 However, no evidence of a higher incidence of side effects could
 be found. PROSPERO registration number: CRD42022307477
description: A systematic search was performed in the following
 eight databases with a restriction of time from inception to January 2022
 to filter the eligible studies: PubMed, Embase, The Cochrane Library, Web
 of Science, Medline, Chinese National Knowledge Infrastructure database
 (CNKI), Chinese Scientific Journal Database (VIP), and Wan Fang
 database.Two reviewersindependently extracted data from the included
 studies using a pre-designed data extraction tool. Any disagreements
 were resolved by negotiation and discussion. Any additional disagreements
 were arbitrated by a third reviewer.
DOI: 10.15468/dl.9je9cc
title: Occurrence Download

description: A dataset containing 4280 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "DatasetKey is Taxon occurrence data for the FungalRoot database",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 4280 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003415-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7m0cfxpzm
title: Patterns of morphological variation highlight the effect of natural selection on eyespots modularity in the butterfly Morpho telemachus - Dataset

description: Morphological correlations can stem from developmental constraints but
 also from selective pressures. Butterfly eyespots are repeated wing color
 pattern elements, widespread across species. As developmental serial
 homologues, they are controlled by similar developmental pathways imposing
 correlations among eyespots: selection on a single eyespot may induce
 correlated responses in all eyespots. We study the variations in the
 ventral eyespots of Morpho telemachus, where two different selective
 regimes are likely to act: while most eyespots are always-visible, two
 eyespots are conditionally-displayed: hidden at rest, they can be exposed
 when the butterflies are threatened, or during sexual interactions. We
 investigate how such contrasted selection across eyespots can alter the
 covariations imposed by their shared developmental origin. We quantified
 eyespots' co-variations within a large population of M. telemachus
 and compared the observed patterns to those found in M. helenor, where all
 eyespots are always-visible and thus probably affected by a similar
 selection regime. We found that M. telemachus conditionally-displayed
 eyespots are less variable than always-visible eyespots and that these two
 eyespots form a separate variational module in this species, in contrast
 to M. helenor. Our results suggest that eyespots' covariations were
 shaped by selection, highlighting how natural selection may promote the
 evolution of modularity.
description: These files contain data used in the three sections of Materials
 & Methods, in order: Estimating eyespot
 conspicuousness_ reflectance spectrum:   
 1) <em>helenor</em> spectra -
 Reflectance spectra (.RFL8 files) from (n=10) <em>M</em>.
 <em>helenor</em>, Yellow ring + Black ring
 - "Spectra IDH.csv" = referende files for
 <em>helenor</em> spectra, indicating the butterfly ID, the
 eyespot ID and the side of each reflectance spectra. 
 Example "PBM_0664_O1L" = spectrum measured on the
 butterfly "PBM_0664", on the eyespot "O1" on the Left
 side.    2)
 <em>telemachus</em> spectra - Reflectance
 spectrum (.RFL8 files) from (n=10) <em>M</em>.
 <em>telemachus</em>, Yellow ring + Black ring
 - "Spectra IDT.csv" = reference files, indicating the
 butterfly ID, the eyespot ID and the side of each reflectance
 spectra.  3) "spectra_code.R" = R code for
 spectra (.RFL8) analysis   Photos_butterflies: 1) Photo_telemachus : 740 photos (dorsal and ventral side, noted "d" and "v" respectively) of the 370 sampled males <em>Morpho</em> <em>telemachus</em> from a single emergence bloom collected in 1995 in Bolivia, in the province of Chapare (Department of Cochabamba CBBA; Gilbert Lachaume, pers. com.). 2) Photo_helenor : 62 photos (dorsal and ventral side, noted "d" and "v" respectively) of the 31 males <em>Morpho</em> <em>helenor</em> from MNHN's collections + reference file "ID_helenor" indicating the sub-species and localities of catching of all <em>helenor</em> individuals.
DOI: 10.5061/dryad.g79cnp5tg
title: Evolutionary radiation in canids following continental colonizations

description: Colonization of a new environment may trigger a remarkable radiation
 process, defined as an accelerated accumulation of species in a short
 period of time. However, how often colonization events trigger such
 radiations is still an open question. We studied the worldwide dispersal
 of the subfamily Caninae to investigate whether the invasion of new
 continents resulted in a great increase in species diversification. We
 used a combination of phylogenetic analyses and ancestral area
 reconstructions to estimate ancestral ranges of 56 extant and extinct
 species of Caninae, as well as variation in speciation and extinction
 rates through time and across clades. Our findings indicate that canids
 experienced a remarkable radiation event when lineages were able to reach
 Eurasia and South America around 11 million years ago. This large number
 of species arising in a short period of time suggests that canids
 experienced ecological opportunity events within the new areas, implying
 that the differences in the ecological settings between continents, and
 size variation among Canidae and other carnivores may be responsible for
 the variation in clade dynamics. We suggest that the advance of grasslands
 and the new herbivorous fauna that came with it were the major forces
 responsible for the diversification of wolves in North America. On the
 other hand, empty niches and the absence of competitors can explain the
 success of canids in Africa and South America. We argue that interaction
 with other carnivores probably also affected the diversification dynamics
 of canids.
DOI: 10.5061/dryad.pvmcvdnqd
title: RGB and HSL pixel-mean colors of ant specimen head images from AntWeb.org

description: Our dataset consists of color data extracted from ~50,000 images of ant
 heads acquired from the database AntWeb.org. The .csv file contains the
 pixel-mean RGB and HSL values of image segments extracted from the ant
 head images, in addition to the existing metadata for these 50,000
 specimens.
description: The data was collected from AntWeb.org, a database containing
 records and metadata for ant specimens housed in museums. Around ~50,000
 of these specimens have images of their heads included in the database.
 Our dataset consists of color data extracted from these ant head images
 attached to the existing metadata from these 50,000 specimens. This color
 data consists of the mean RGB and HSL values of all pixels of image
 segments extracted from the ant head images. Segments were obtained using
 a DeepLabV3 segmentation model trained with transfer learning on 50 ant
 head images - the training set and training and inference code can be
 found in the project folder on GitHub.
description: The data is in .csv format and can be opened using a spreadsheet
 editor like Excel or a statistical environment like RStudio.
DOI: 10.5061/dryad.dz08kps1n
title: Data from: Cryptic recessive lethality of a supergene controlling social organization in ants

description: Supergenes are clusters of linked loci that control complex phenotypes,
 such as alternate forms of social organization in ants. Explaining the
 long-term maintenance of supergenes is challenging, particularly when the
 derived haplotype lacks homozygous lethality and causes gene drive. In the
 Alpine silver ant, Formica selysi, a large and ancient social supergene
 with two haplotypes, M and P, controls colony social organization.
 Single-queen colonies only contain MM females, while multi-queen colonies
 contain MP and PP females. The derived P haplotype, found only in
 multi-queen colonies, selfishly enhances its transmission through maternal
 effect killing, which could have led to its fixation. A population genetic
 model showed that a stable social polymorphism can only be maintained
 under a narrow set of conditions, which includes partial assortative
 mating by social form (which is known to occur in the wild), and low
 fitness of PP queens. With a combination of field and laboratory
 experiments, we show that the P haplotype has deleterious effects on
 female fitness. The survival rate of PP queens and workers was around half
 the one of other genotypes. Moreover, P-carrying queens had lower
 fertility and fecundity compared to other queens. We discuss how cryptic
 lethal effects of the P haplotype help stabilize this ancient
 polymorphism.
DOI: 10.5061/dryad.2z34tmpqn
title: Supplementary files: Social learning of innovations in dynamic predator-prey systems

description: We investigate social transmission of behavioral innovations between
 predators in two classic predator-prey models. We assume that innovations
 increase predator attack rates or conversion efficiencies, or that
 innovations reduce predator mortality or prey handling time. We find that
 a common outcome of innovations is the destabilization of the system.
 Destabilizing effects include increasing oscillations or limit cycles.
 Particularly, in systems where prey are self-limiting and predators have a
 Type II functional response, destabilization occurs due to
 overexploitation of the prey. Whenever instability increases the risk of
 extinction, innovations that benefit individual predators may not have
 positive long-term effects on predator populations. An additional
 consequence of instability is the maintenance of behavioral variability
 among predators. Interestingly, when predator populations are low despite
 coexisting with prey populations near their carrying capacity, innovations
 that could help predators better exploit their prey are least likely to
 spread. Precisely how unlikely this is depends on whether or not naïve
 individuals need to observe an informed individual interact with prey to
 learn the innovation. Our results offer perspective on the potential role
 of innovation in biological invasions, urban colonization, and the
 maintenance of behavioral polymorphisms.
DOI: 10.5281/zenodo.18401434
title: GCM output (diagfi) from Early Mars simulation without ocean heat transport (NOHT)

description:  This dataset contains the diagfi output file from a 3D Global Climate Model (Generic-PCM ) simulation of early Mars performed without ocean heat transport (OHT disabled).

The simulation explores early Mars surface and atmospheric conditions under a dense CO₂–H₂ atmosphere, consistent with scenarios proposed to allow transient liquid water. In this configuration, ocean-covered grid cells are still thermodynamically coupled to the atmosphere via a slab ocean representation, but no lateral ocean heat transport is permitted. This setup isolates the role of the atmosphere in redistributing heat and serves as a control experiment for assessing the climatic impact of ocean dynamics.
DOI: 10.5061/dryad.1c59zw402
title: Data from: Wallace 2: A shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions

description: These are the occurrence locality datasets used in the example provided in
 "wallace 2: a shiny app for modeling species niches and distributions
 redesigned to facilitate expansion via module contributions"
 published in Ecography (DOI: 10.1111/ecog.06547). The analysis workflow is
 displayed in the Supporting information of the paper (Fig. S1), and these
 data are also used in the wallace 2 vignette
 (https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html).
description: This data was downloaded from the Global Biodiversity Information
 Facility (GBIF) in 2021 using the R package occCite, implemented in the
 shiny app for the R package wallace. It contains georeferenced occurrences
 of Bassaricyon alleni (eastern lowland olingo) and Bassaricyon neblina
 (olinguito) in South America. All fields are standard GBIF data
 fields.
description: The files are in .csv form and can be opened with spreadsheet
 software or using programming languages.
DOI: 10.5281/zenodo.18401433
title: GCM output (diagfi) from Early Mars simulation without ocean heat transport (NOHT)

description:  This dataset contains the diagfi output file from a 3D Global Climate Model (Generic-PCM ) simulation of early Mars performed without ocean heat transport (OHT disabled).

The simulation explores early Mars surface and atmospheric conditions under a dense CO₂–H₂ atmosphere, consistent with scenarios proposed to allow transient liquid water. In this configuration, ocean-covered grid cells are still thermodynamically coupled to the atmosphere via a slab ocean representation, but no lateral ocean heat transport is permitted. This setup isolates the role of the atmosphere in redistributing heat and serves as a control experiment for assessing the climatic impact of ocean dynamics.
DOI: 10.5061/dryad.9kd51c5n4
title: Species of fast bulk-soil nutrient cycling have lower rhizosphere effects: A nutrient spectrum of rhizosphere effects

description: Tree roots not only acquire readily-usable soil nutrients but also affect
 microbial decomposition and manipulate nutrient availability in their
 surrounding soils, i.e., rhizosphere effects (REs). Thus, REs challenge
 the basic understanding how plants adapt to environment and co-exist with
 other species. Yet, how REs vary among species in response to
 species-specific bulk soil nutrient cycling is not well-known. Here we
 studied how plant-controlled microbial decomposition activities in
 rhizosphere soils respond to those in their corresponding bulk soils and
 whether these relations depend on species-specific nutrient cycling in the
 bulk soils. We targeted 55 woody species of different clades and
 mycorrhizal types in three contrasting biomes, namely a temperate forest,
 a subtropical forest and a tropical forest. We found that microbial
 decomposition activities in rhizosphere soils responded linearly to those
 in their corresponding bulk soils at the species level. Thereafter, we
 found that REs (parameters in rhizosphere soils minus those in
 corresponding bulk soils) of microbial decomposition activities had
 negative linear correlations with microbial decomposition activities in
 corresponding bulk soils. A multiple factor analysis revealed that soil
 organic carbon, total nitrogen and soil water content favored bulk soil
 decomposition activities in all three biomes, showing that the magnitude
 of REs varied along a fast-slow nutrient cycling spectrum in bulk soils.
 The species of fast nutrient cycling in their bulk soils tended to have
 smaller or even negative REs. Therefore, woody plants commonly utilize
 both positive and negative REs as a nutrient-acquisition strategy. Based
 on the trade-offs between REs and other nutrient-acquisition strategies,
 we proposed a push and pull conceptual model which can bring plant
 nutrient-acquisition cost and plant carbon economics spectrum together in
 the future. This model will facilitate not only the carbon and nutrient
 cycling but also the mechanisms of species co-existence in forest
 ecosystems.