cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.653q97g
title: Data from: Gene expression in the phenotypically plastic Arctic charr (Salvelinus alpinus): a focus on growth and ossification at early stages of development

description: Gene expression during development shapes the phenotypes of individuals.
 Although embryonic gene expression can have lasting effects on
 developmental trajectories, few studies consider the role of maternal
 effects, such as egg size, on gene expression. Using qPCR, we characterize
 relative expression of 14 growth and/or skeletal promoting genes across
 embryonic development in Arctic charr (Salvelinus alpinus). We test to
 what extent their relative expression is correlated with egg size and size
 at early life‐stages within the study population. We predict smaller
 individuals to have higher expression of growth and skeletal promoting
 genes, due to less maternal resources (i.e., yolk) and prioritization of
 energy toward ossification. We found expression levels to vary across
 developmental stages and only three genes (Mmp9, Star, and Sgk1)
 correlated with individual size at a given developmental stage. Contrary
 to our hypothesis, expression of Mmp9 and Star showed a non‐linear
 relationship with size (at post fertilization and hatching, respectively),
 whilst Sgk1 was higher in larger embryos at hatching. Interestingly, these
 genes are also associated with craniofacial divergence of Arctic charr
 morphs. Our results indicate that early life‐stage variation in gene
 expression, concomitant to maternal effects, can influence developmental
 plasticity and potentially the evolution of resource polymorphism in
 fishes.
description: 2019Beck-ArcticCharrEmbryonicGeneExpression_dataAll data collected for this study can be found in this file
DOI: 10.5061/dryad.wh70rxwx1
title: Water availability regulates abrupt shifts in global terrestrial vegetation productivity by reducing resilience

description: Abrupt shifts in vegetation productivity induced by environmental change
 profoundly affect ecosystem functions and services, such as carbon
 sequestration, biodiversity maintenance, and climate regulation, yet their
 long-term global patterns and underlying drivers remain insufficiently
 understood. In this study, abrupt shifts in vegetation
 productivity were identified using two independent long-term satellite
 datasets, and early warning signals were assessed through ecosystem
 resilience. The main drivers of resilience decline were further examined
 across land cover, climate, and human-activity dimensions. The results
 showed that negative abrupt shifts were predominantly concentrated in high
 northern latitudes and equatorial regions, and that both negative and
 positive abrupt shifts displayed distinct increasing trends after 2002. A
 sharp decline in ecosystem resilience was also detected during the
 four years preceding abrupt shifts. Changes in water
 availability were identified as the primary factor contributing
 to the reduced resilience of global ecosystems, as evidenced
 by the driver trajectory, generalized additive models, and
 convergent cross-mapping methods. This study provides insight
 into the pervasive occurrence of abrupt shifts in vegetation productivity
 and the discernible impact of climate change. When projecting
 vegetation dynamics under future climate change, it is essential to
 consider the significant uncertainties associated with abrupt shifts.
description: # Water availability regulates abrupt shifts in global terrestrial
 vegetation productivity by reducing resilience
 [https://doi.org/10.5061/dryad.wh70rxwx1](https://doi.org/10.5061/dryad.wh70rxwx1) The dataset contains all of the original data, as well as all of the data and code for the graphs that produced the main text. ## Description of the data and file structure The data processing and plotting are done using NCL (NCAR Command Language, [https://www.ncl.ucar.edu/](https://www.ncl.ucar.edu/)) and R ([https://www.r-project.org/](https://www.r-project.org/)), with NCL being the primary tool and R serving as a supplementary tool. The missing value for all data is -32767.0. ## Sharing/Access information Data was derived from the sources: The raw data can be found in our article. Detailed methods for all figures and for data processing can be found in the Supplementary_Data.zip, and each file contains a README (as README.pdf) corresponding to its content. Please refer to the contents of Supplementary_Data.zip for details. ## Code/Software All code requires NCL (NCAR Command Language, [https://www.ncl.ucar.edu/](https://www.ncl.ucar.edu/)) or R ([https://www.r-project.org/](https://www.r-project.org/)) to run.
DOI: 10.5061/dryad.vg6jp14
title: Data from: Real-world study of efficacy, risk management and reasons for discontinuation of natalizumab for treatment of multiple sclerosis in Russia

description: Background. NTZ is approved in Russia for the treatment of highly active
 relapsing remitting multiple sclerosis and is reimbursed via federal
 budget program. However, no data about NTZ treatment in Russia and the
 effect of federal reimbursement have been performed so far. Objective. To
 characterize the population of patients receiving natalizumab and assess
 the efficacy and risk-management plan (RMP) implementation of NTZ therapy
 in routine clinical practice in Russia. Methods. We analyzed data for 334
 patients, who received at least one infusion of NTZ. Relapse rate, MRI
 activity, NEDA-3 status after 2 years were assessed. Anti-JC virus
 antibodies status and RMP implementation were evaluated. Drop-out rate and
 reasons for therapy discontinuation were analyzed. Results. Patients
 switched to natalizumab in Russia are mainly female (63%), with median
 EDSS score of 3.5 and high disease activity: 93% had at least 1 relapse
 and 58% had both T1Gd+ and new T2 lesion an year before therapy
 initiation. Introduction of federal reimbursement allowed to start therapy
 with natalizumab for patients with less relapses. The only predictor of
 6-month progression was EDSS score at the baseline of therapy (HR=2.1375,
 95%CI 1.0026 – 4.5570, p=0.0492). 82% patients reached NEDA-3 at 24 month
 of therapy. 25% of patients discontinued NTZ for reasons: tolerability
 (14.5%), JCV antibody status (61%), and patient’s decision (17%). RMP was
 implemented in only 36% patients. Conclusion. Natalizumab appeared to have
 high efficacy in Russian clinical practice. Federal reimbursement allowed
 less active patients to start natalizumab. More efforts should be done to
 improve RMP implementation.
description: All
 data_English
DOI: 10.5061/dryad.b1866n0
title: Data from: Marking mosquitoes in their natural larval sites using 2H-enriched water: a promising approach for tracking over extended temporal and spatial scales

description: 1. Background. Tracking mosquitoes using current methods of
 mark-release-recapture are limited to small spatial and temporal scales
 exposing major gaps in understanding long-range movements and extended
 survival. Novel approaches to track mosquitoes may yield fresh insights
 into their biology which improves intervention activities to reduce
 disease transmission. Stable isotope enrichment of natural mosquito
 breeding sites allows large-scale marking of wild mosquitoes absent human
 handling. Mosquito larvae that develop in 2H-enriched water are expected
 to be detectable for over four months using tissue mass-fraction 2H
 measurements, providing opportunities for long-term mark-capture studies
 on a large scale. 2. Approach. A laboratory study followed by a field
 experiment of mosquito larval habitat 2H-enrichment was conducted in Mali,
 to evaluate potential labeling of wild mosquitoes. Twelve natural larval
 sites were enriched using [2H]-Deuterium-oxide (D2O, 99%). Enrichment
 level was maintained by supplementation following dilution by rains.
 Availability of 2H to mosquito larvae was enhanced by locally collected
 and cultured microorganisms (i.e. protozoa, algae and bacteria) reared in
 deuterated water, and provided as larval diet. Putative natural predators
 were removed from the larval sites and first instar larvae Anopheles
 gambiae s.l. larvae were added every other day. Emergence traps enabled
 collection of eclosing adults. Adult mosquitoes were kept at laboratory
 conditions for analysis of label attrition with age. 3. Results. Deuterium
 enrichment of wild mosquitoes above background levels (maximum = 143.1
 ppm) became apparent 5-6 days after initial exposure, after which 2H
 values increased steadily until ~24 days later (to a mean of approx. 220
 ppm). Anopheles and Culex mosquitoes showed significantly different 2H
 values (211 and 194.2 ppm respectively). Both genera exhibited exponential
 label attrition (e(-x)) amounting to 21.6% by day 30 post emergence, after
 which attrition rate continuously decreased. Males of both taxa exhibited
 a higher mean 2H value compared to females. 4. Conclusions.
 Deuterium-oxide proved useful in marking mosquitoes in their natural
 larval sites and although costly, may prove valuable for studies of
 mosquitoes and other aquatic insects. Based on our field study, we provide
 a protocol for marking mosquito larval sites using deuterium-oxide.
description: Faiman_etal_MarkingMosquitoesDeuteriumDataExcel database with separate tabs for Laboratory, Field and Control deuterium enrichment data of mosquitoesFaiman_etal_DeuteriumData.xlsx
DOI: 10.5281/zenodo.18391615
title: Three Worlds: Resolving the Black Hole Information Paradox with Cosmic Rebirth

description: The black hole information paradox arises from the apparent conflict between unitary quantum evolution and the thermal nature of Hawking radiation. We resolve this tension by recognizing that spacetime itself bifurcates into three causally autonomous domains during gravitational collapse: (I) the exterior universe, (II) the black hole interior, and (III) a new expanding spacetime born from the singularity. Within this “Three Worlds” framework, information is not lost but partitioned: it enters World II, where tidal forces erase all structure until entropy vanishes at the singularity, thereby seeding a low-entropy Big Bang in World III. Crucially, the second law of thermodynamics holds independently in each world when formulated within causal diamonds. The model predicts a testable observational signature: anisotropic dark energy fluctuations around sites of former low-spin black holes, with magnitude inversely proportional to the square of the black hole mass and spatial scale growing as the cube root of cosmic time. Upcoming surveys (Euclid, Roman, SKA) can probe this signal within the next decade. By linking black hole physics to cosmic origins, the framework explains both the information paradox and the low-entropy initial condition of our universe—without firewalls, remnants, or holographic duality—offering a minimal, falsifiable, and cosmologically rich resolution.
DOI: 10.5061/dryad.8sk4367
title: Data from: A link between heritable parasite resistance and mate choice in dung beetles

description: Parasites play a central role in the adaptiveness of sexual reproduction.
 Sexual selection theory suggests a role for parasite resistance in the
 context of mate choice, but the evidence is mixed. The parasite-mediated
 sexual selection (PMSS) hypothesis derives a number of predictions, among
 which that resistance to parasites is heritable, and that female choice
 favours parasite resistance genes in males. Here we tested the PMSS
 hypothesis using the dung beetle Onthophagus taurus, a species that can be
 heavily parasitised by Macrocheles merdarius mites, which are known to
 affect adult survival. We investigated the heritability of resistance to
 M. merdarius, as well as whether female O. taurus impose a mating bias
 against males susceptible to mite infestation. Female choice for parasite
 resistance is difficult to disentangle from the possibility that females
 are simply choosing less parasitised males due to naturally selected
 benefits of avoiding contracting those parasites. This is especially
 likely for ectoparasites, such as mites. We tackled this problem by
 performing a mate choice trial first, and then measuring a male’s
 resistance to mite infestation. Resistance to mite infestation exhibited
 significant levels of additive genetic variance. Although we found no
 relationship between mating success and parasite resistance, males with
 greater resistance to infestation mated for longer. If females control
 copula duration, given that short copulations often result in mating
 failure, female choice could act on parasite resistance.
description: Buzatto et al 2019 Behav
 EcolThis data file has two
 tabs. The first tab contains data for the heritability of mite resistance
 (to the mite Macrocheles merdarius) in the dung beetle Onthophagus taurus.
 The first column has the individual ID, the second column the ID of their
 father, and the third column the ID of their mother, which together
 comprise the pedigree information for a nested paternal half-sib/full-sib
 breeding design. The number of mites found on males after experimental
 exposure and the pronotum width of each male (in mm) are also presented.
 The second tab has information from another experiment about mate choice
 and its relationship to a subsequent resistance to parasites (also under
 experimental exposure). This tab has information on male ID, their latency
 to court females (seconds between being exposed to a female and starting
 to court), number of courting bouts (see MS), mating success (1 when
 mated, 0 when failed to mate), mating latency (seconds between starting to
 court and mating), and mating duration (in seconds). This information can
 be used to calculate courtship rate (see MS). Finally, this tab also
 contains information on the number of mites found on males after the
 subsequent (after the mate choice trial) experimental exposure to these
 parasites, and the identity of the block.
DOI: 10.5061/dryad.md87fk1
title: Data from: The effects of microhabitat specialization on mating communication in a wolf spider

description: Animal signals experience selection for detectability, which is determined
 in large part by the signal transmission properties of the habitat.
 Understanding the ecological context in which communication takes place is
 therefore critical to understanding selection on the form of communication
 signals. In order to determine the influence of environmental
 heterogeneity on signal transmission, we focus on a wolf spider species
 native to central Florida, Schizocosa floridana, in which males court
 females using a substrate-borne vibratory song. We test the hypothesis
 that S. floridana is a substrate specialist by (i) assessing substrate use
 by females and males in the field, (ii) quantifying substrate-specific
 vibratory signal transmission in the laboratory, and (iii) determining
 substrate-specific mating success in the laboratory. We predict a priori
 that (a) S. floridana restricts its signaling to oak litter, (b) oak
 litter best transmits their vibratory signal, and (c) S. floridana mates
 most readily on oak litter. We find that S. floridana is almost
 exclusively found on oak litter, which was found to attenuate vibratory
 courtship signals the least. Spiders mated with equal frequency on oak and
 pine, but did not mate at all on sand. Additionally, we describe how S.
 floridana song contains a novel component, chirps, which attenuate more
 strongly than its other display components on pine and sand, but not on
 oak, suggesting that the ways in which the environment relaxes
 restrictions on signal form may be as important as the ways in which it
 imposes them.
description: transmission_datasubstrate vibratory transmission dataset - all other raw data is available in the full manuscript
DOI: 10.5061/dryad.dc036n6
title: Data from: Equilibrium and non-equilibrium phases in the radiation of Hakea and the drivers of diversity in Mediterranean-Type Ecosystems

description: Mediterranean-Type ecosystems (MTEs) contain exceptional plant diversity.
 Explanations for this diversity are usually classed as either
 “equilibrium”, with elevated MTE diversity resulting from greater
 ecological carrying capacities, or “non-equilibrium”, with MTEs having a
 greater accumulation of diversity over time. These models have typically
 been considered as mutually exclusive. Here we present a trait-based
 explanatory framework that incorporates both equilibrium and
 non-equilibrium dynamics. Using a large continental Australian plant
 radiation (Hakea) as a case study, we identify traits associated with
 niche partitioning in co-occurring species (α traits) and with
 environmental filtering (β traits), and reconstruct the mode and relative
 timing of diversification of these traits. Our results point to a
 radiation with an early, non-equilibrium phase marked by divergence of β
 traits as Hakea diversified exponentially and expanded from the southwest
 Australian MTE into biomes across the Australian continent. This was
 followed from 7Mya by an equilibrium phase, marked by diversification of α
 traits and a slowdown in lineage diversification as the MTE niches became
 saturated. These results suggest that processes consistent with both
 equilibrium and non-equilibrium models have been important during
 different stages of the radiation of Hakea, and together they provide a
 richer explanation of present-day diversity patterns.
description: community_survey_latlonsLatitude and Longitude values for floristic surveys used in this study to identify local-scale species interactionscommunity_survey_presence_absencePresence/Absence data for hakea species in each floristic survey used in this studyecoregion_dataEcoregion-level data: species richness, phylogenetic clustering (MPDses), functional dispersion of alpha and beta traits, 4 environmental PC axes and the environmental variables used to produce them.ecoregion_presence_absencePresence / absnece data of hakea species across ecoregions in Australia
DOI: 10.5061/dryad.14rf353
title: Data from: A key metabolic gene for recurrent freshwater colonization and radiation in fishes

description: Colonization of new ecological niches has triggered large adaptive
 radiations. Although some lineages have made use of such opportunities,
 not all do so. The factors causing this variation among lineages are
 largely unknown. Here, we show that deficiency in docosahexaenoic acid
 (DHA), an essential ω-3 fatty acid, can constrain freshwater colonization
 by marine fishes. Our genomic analyses revealed multiple independent
 duplications of the fatty acid desaturase gene Fads2 in stickleback
 lineages that subsequently colonized and radiated in freshwater habitats,
 but not in close relatives that failed to colonize. Transgenic
 manipulation of Fads2 in marine stickleback increased their ability to
 synthesize DHA and survive on DHA-deficient diets. Multiple freshwater
 ray-finned fishes also show a convergent increase in Fads2 copies,
 indicating its key role in freshwater colonization.
description: DHA meta-analysis
 dataPercentage of DHA in
 total fatty acid were obtained from literatures. DHA contents in algae and
 consumers from marine and freshwater habitats were
 analyzed.DHA.csv
DOI: 10.5061/dryad.q0ht491
title: Data from: Conservation of the threatened species Pulsatilla vulgaris Mill. (pasqueflower) is aided by reproductive system and polyploidy

description: Population loss due to habitat disturbance is a major concern in
 biodiversity conservation. Here we investigate the genetic causes of the
 demographic decline observed in English populations of Pulsatilla vulgaris
 and the consequences for conservation. Using ten nuclear microsatellite
 markers, we compare genetic variation in wild populations with restored
 and seed-regenerated populations (674 samples). Emergence of genetic
 structure and loss of allelic variation in natural populations is not as
 evident as expected from demographic trends. Restored populations show
 genetic variation comparable to their source populations and, in general,
 to the wild ones. Genetic homogeneity is observed in regeneration trials,
 although some alleles not captured in source populations are detected. We
 infer that polyploidy, longevity and clonal reproduction have provided P.
 vulgaris with the standing genetic variation necessary to make the species
 resilient to the effects of demographic decline, suggesting that the use
 of multiple sources for reintroduction may be beneficial to mimic natural
 gene flow and the availability of multiple allele copies typical of
 polyploid species.
description: Microsatellite
 datasetDataset_microsats.txtRecoded datasetDataset recoded in Polysat (function recodeAllopoly)Recoded_dataset.txtAlleles in derived populationsAlleles in restored/regenerated populations not occurring in wild-origin population samples. Occurrences are expressed by their De Silva frequency.Allelic captureAlleles occurring in wild origin populations which were also captured in restored/regenerated populations. Occurrences are expressed by their De Silva frequencies.De Silva Frequencies
DOI: 10.5061/dryad.d117b3k
title: Data from: Statistical comparison of trait-dependent biogeographical models indicates that Podocarpaceae dispersal is influenced by both seed cone traits and geographical distance

description: The ability of lineages to disperse long distances over evolutionary
 timescales may be influenced by the gain or loss of traits adapted to
 enhance local, ecological dispersal. For example, some species in the
 southern conifer sister families Podocarpaceae and Araucariaceae have
 fleshy cones that encourage bird dispersal, but it is unknown how this
 trait has influenced the clade’s historical biogeography, or its
 importance compared to other predictors of dispersal such as the
 geographic distance between regions. We answer these questions
 quantitatively by using a dated phylogeny of 197 species of southern
 conifers to statistically compare standard, trait-independent biogeography
 models with new BioGeoBEARS models where an evolving trait can influence
 dispersal probability, and trait history, biogeographical history, and
 model parameters are jointly inferred. We validate the method with
 simulation-inference experiments. Comparing all models, those that include
 trait-dependent dispersal accrue 87.5% of the AICc model weight. Averaged
 across all models, lineages with non-fleshy cones had a dispersal
 probability multiplier of 0.49 compared to lineages with fleshy cones.
 Distance is included as a predictor of dispersal in all credible models
 (100% model weight). However, models with changing geography earned only
 22.0% of the model weight, and models submerging New Caledonia/New Zealand
 earned only 0.01%. The importance of traits and distance suggests that
 long-distance dispersal over macroevolutionary timespans should not be
 thought of as a highly unpredictable chance event. Instead, long-distance
 dispersal can be modelled, allowing statistical model comparison to
 quantify support for different hypotheses.
description: Supplementary_Materialsupplemental text, list of taxa, dataset, settings, simmulation test resuls, examplesKlaus_Matzke_2019_SysBio_Supplemental_Textsupplemental text