cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30774632
title: Data for manuscript: "Gradients not needed: ML-driven propagation of nonadiabatic molecular dynamics without reference gradients"

description: Dataset containing ML-models as well as datasets described in the paper.Auxiliary data for CHD is split into 4 shards, due to the size of the dataset. The AIQM1/MRCI data for azobenzene is available at:<br>https://github.com/dralgroup/al-namd<br><br><br>
DOI: 10.6084/m9.figshare.30774632.v1
title: Data for manuscript: "Gradients not needed: ML-driven propagation of nonadiabatic molecular dynamics without reference gradients"

description: Dataset containing ML-models as well as datasets described in the paper.Auxiliary data for CHD is split into 4 shards, due to the size of the dataset. The AIQM1/MRCI data for azobenzene is available at:<br>https://github.com/dralgroup/al-namd<br><br><br>
DOI: 10.5061/dryad.n8n6k
title: Data from: Evidence for past and present hybridization in three Antarctic icefish species provides new perspectives on an evolutionary radiation

description: Determining the timing, extent, and underlying causes of inter-specific
 gene exchange during or following speciation is central to understanding
 species’ evolution. Antarctic notothenioid fish, thanks to the acquisition
 of antifreeze glycoproteins during Oligocene transition to polar
 conditions, experienced a spectacular radiation to &gt;100 species
 during Late Miocene cooling events. The impact of recent glacial cycles on
 this group is poorly known, but alternating warming and cooling periods
 may have affected species’ distributions, promoted ecological divergence
 into recurrently opening niches, and/or possibly brought allopatric
 species into contact. Using microsatellite markers and statistical methods
 including Approximate Bayesian Computation, we investigated genetic
 differentiation, hybridization and the possible influence of the last
 glaciation/deglaciation events in three icefish species of the genus
 Chionodraco. Our results provide strong evidence of contemporary and past
 introgression by showing that: i) a substantial fraction of contemporary
 individuals in each species has mixed ancestry; ii) evolutionary scenarios
 excluding hybridization or including it only in ancient times have small
 or zero posterior probabilities; iii) the data support a scenario of
 interspecific gene flow associated with the two most recent interglacial
 periods. Glacial cycles might therefore have had a profound impact on the
 genetic composition of Antarctic fauna, as newly available shelf areas
 during the warmer intervals might have favoured secondary contacts and
 hybridization between diversified groups. If our findings are confirmed in
 other notothenioids, they offer new perspectives for understanding
 evolutionary dynamics of Antarctic fish, and suggest a need for new
 predictions on the effects of global warming in this group.
description: Marino et al.
 genotypesMicrosatellite genotypes
 used in the paper. Full description reported in the ReadMe
 file.
DOI: 10.5061/dryad.t6n8h
title: Data from: Choosy wolves? Heterozygote advantage but no evidence of MHC-based disassortative mating

description: A variety of nonrandom mate choice strategies, including disassortative
 mating, are used by vertebrate species to avoid inbreeding, maintain
 heterozygosity and increase fitness. Disassortative mating may be mediated
 by the major histocompatibility complex (MHC), an important gene cluster
 controlling immune responses to pathogens. We investigated the patterns of
 mate choice in 26 wild-living breeding pairs of gray wolf (Canis lupus)
 that were identified through noninvasive genetic methods and genotyped at
 3 MHC class II and 12 autosomal microsatellite (STR) loci. We tested for
 deviations from random mating and evaluated the covariance of genetic
 variables at functional and STR markers with fitness proxies deduced from
 pedigree reconstructions. Results did not show evidences of MHC-based
 disassortative mating. Rather we found a higher peptide similarity between
 mates at MHC loci as compared with random expectations. Fitness values
 were positively correlated with heterozygosity of the breeders at both MHC
 and STR loci, whereas they decreased with relatedness at STRs. These
 findings may indicate fitness advantages for breeders that, while avoiding
 highly related mates, are more similar at the MHC and have high levels of
 heterozygosity overall. Such a pattern of MHC-assortative mating may
 reflect local coadaptation of the breeders, while a reduction in genetic
 diversity may be balanced by heterozygote advantages.
description: MHC DRB1, DQA1, DQB1
 genotypesMHC reconstructed
 genotypes for each of the 47 wolf (Canis lupus) breeders analyzed in this
 study. For each breeder, the name of the pack where it reproduced is
 indicated (with names as from Caniglia et al. 2014), together with its
 alleles at the three MHC class II loci DRB1, DQA1, and DQB1, as identified
 after phasing (details available in the Materials and Methods section in
 the paper). Allele names follow the official DLA nomenclature committee.
 GenBank accession numbers are also indicated and the corresponding records
 can be accessed by clicking on the hyperlinks in the text. In the breeder
 IDs, the letter ‘W’ stands for ‘wolf’ and is followed by the initials of
 the province where the animals were non-invasively sampled for the first
 time, by a numeric identifier and by the letter ‘F’ for females or ‘M’ for
 males.Galaverni_et_al_2015_MHC_genotypes.xlsx
DOI: 10.5281/zenodo.18371489
title: Satellite and Lidar Data
DOI: 10.5281/zenodo.18371490
title: Satellite and Lidar Data
DOI: 10.5061/dryad.kn21m
title: Data from: Predator exposure improves anti-predator responses in a threatened mammal

description: Incorporating an understanding of animal behaviour into conservation
 programmes can influence conservation outcomes. Exotic predators can have
 devastating impacts on native prey species and thwart reintroduction
 efforts, in part due to prey naïveté caused by an absence of co-evolution
 between predators and prey. Attempts have been made to improve the
 anti-predator behaviours of reintroduced native prey by conducting
 laboratory-based predator recognition training but results have been
 varied and have rarely led to improved survival in reintroduction
 programmes. We investigated whether in situ predator exposure could
 improve anti-predator responses of a predator-naïve mammal by exposing
 prey populations to low densities of introduced predators under controlled
 conditions. We reintroduced 352 burrowing bettongs to a 26-km2 fenced
 exclosure at the Arid Recovery Reserve in South Australia and exposed them
 to feral cats (density 0.03–0.15 cats/km2) over an 18-month period. At the
 same time, we translocated a different group of bettongs into an exclosure
 free of introduced predators, as a control. We compared three behaviours
 (flight initiation distances, trap docility and behaviour at feeding
 trays) of cat-exposed and control bettongs before the translocations, then
 at 6, 12 and 18 months post-translocation. Cat-exposed bettongs displayed
 changes in behaviour that suggested increased wariness, relative to
 control bettongs. At 18 months post-reintroduction, cat-exposed bettongs
 had greater flight initiation distances and approached feed trays more
 slowly than control bettongs. Cat-exposed bettongs also increased their
 trap docility over time. Synthesis and applications. Translocation is
 recommended as a conservation tool for many threatened species yet success
 rates are generally low. We demonstrate that controlled levels of in situ
 predator exposure can increase wariness in the behaviour of naïve prey.
 Our findings provide support for the hypothesis that in situ predator
 exposure could be used as a method to improve the anti-predator responses
 of predator-naïve threatened species populations.
description: Bettong behaviour
 dataContains three sheets
 with behaviour scores of burrowing bettongs in three tests 1. Trap
 docility 2. Flight initiation distances 3. Behaviour while
 foragingDryad
 data.xlsx
DOI: 10.5061/dryad.ch56t
title: Data from: Basking behavior predicts the evolution of heat tolerance in Australian rainforest lizards

description: There is pressing urgency to understand how tropical ectotherms can
 behaviorally and physiologically respond to climate warming. We examine
 how basking behavior and thermal environment interact to influence
 evolutionary variation in thermal physiology of multiple species of
 lygosomine rainforest skinks from the Wet Tropics of northeastern
 Queensland, Australia (AWT). These tropical lizards are behaviorally
 specialized to exploit canopy or sun, and are distributed across steep
 thermal clines in the AWT. Using phylogenetic analyses, we demonstrate
 that physiological parameters are either associated with changes in local
 thermal habitat or to basking behavior, but not both. Cold tolerance, the
 optimal sprint speed, and performance breadth are primarily influenced by
 local thermal environment. Specifically, montane lizards are more cool
 tolerant, have broader performance breadths, and higher optimum sprinting
 temperatures than their lowland counterparts. Heat tolerance, in contrast,
 is strongly affected by basking behavior: there are two evolutionary
 optima, with basking species having considerably higher heat tolerance
 than shade skinks, with no effect of elevation. These distinct responses
 among traits indicate the multiple selective pressures and constraints
 that shape the evolution of thermal performance. We discuss how behavior
 and physiology interact to shape organisms' vulnerability and
 potential resilience to climate change.
description: Phylogenetic data used
 for analysesAustralcombo.nex
DOI: 10.15468/dl.ectwkv
title: Occurrence Download

description: A dataset containing 210 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Alpinia oblongifolia"
 ]
}

 The dataset includes 210 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001331-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8804fn51
title: Data from: Parasitized mates increase infection risk for partners

description: Individuals can gain fitness benefits and costs through their mates.
 However, studies on sexual selection have tended to focus on genetic
 benefits. A potentially widespread cost of pairing with a parasitized mate
 is that it will increase an individual's parasite abundance. Such a
 cost has been overlooked in systems where parasites are indirectly
 transmitted. We manipulated the abundance of the nematode parasite
 Trichostrongylus tenuis, an indirectly transmitted parasite, within pairs
 of wild red grouse Lagopus lagopus scoticus in spring. Parasite levels
 were correlated within pairs before the experiment. We removed parasites
 from either males, females, or both members of the pair, and evaluated
 individual parasite uptake over the subsequent breeding period. At the end
 of the breeding season, an individual's parasite abundance was
 greater when its mate had not been initially purged of parasites. This
 cost appeared greater for males. We discuss the implications of our
 results in relation to the costs that parasites may have on sexual
 selection processes.
description: Parasitism risk within
 pairs. Lagopus lagopus scoticus.
DOI: 10.5061/dryad.hf7gg
title: Data from: Mesopredator suppression by an apex predator alleviates the risk of predation perceived by small prey

description: Predators can impact their prey via consumptive effects that occur through
 direct killing, and via non-consumptive effects that arise when the
 behaviour and phenotypes of prey shift in response to the risk of
 predation. Although predators' consumptive effects can have cascading
 population-level effects on species at lower trophic levels there is less
 evidence that predators' non-consumptive effects propagate through
 ecosystems. Here we provide evidence that suppression of abundance and
 activity of a mesopredator (the feral cat) by an apex predator (the dingo)
 has positive effects on both abundance and foraging efficiency of a desert
 rodent. Then by manipulating predators' access to food patches we
 further the idea that apex predators provide small prey with refuge from
 predation by showing that rodents increased their habitat breadth and use
 of ‘risky′ food patches where an apex predator was common but
 mesopredators rare. Our study suggests that apex predators'
 suppressive effects on mesopredators extend to alleviate both
 mesopredators' consumptive and non-consumptive effects on prey.
description: Gordon.et.al.2015_DataExcel file containing raw data used in analyses. The Experiment 1 tab holds data relating to the Experiment 1 section of the paper. The Experiment 2 tab holds data relating to the Experiment 2 section of the paper. The Abundance_SpotlightData tab holds data relating to the Dingo, fox, cat and N. fuscus abundance section of the paper.
DOI: 10.5061/dryad.r540f
title: Data from: Effects of protein malnutrition on tolerance to helminth infection

description: Infection tolerance is the ability of a host to limit the health effects
 of a given parasite load. A few recent studies have demonstrated genetic
 variation for tolerance, but little is known about how environmental
 factors affect tolerance. Here, we used the intestinal nematode
 Heligmosomoides polygyrus in laboratory mice to test for effects of
 protein malnutrition on tolerance. We performed an experiment where two
 different mouse strains (CBA and BALB/c) were fed either adequate-protein
 food or low-protein food, and trickle-infected with different doses of H.
 polygyrus larvae during four weeks. We found that protein malnutrition
 decreases tolerance measured as intestinal barrier function, but only in
 one of the strains (BALB/c); that is, there was a host
 genotype-by-environment interaction for tolerance. We conclude that
 nutritional status can affect tolerance and that sensitivity of tolerance
 to malnutrition may differ between host genotypes.
description: Hpolygyrus
 infectionFile contains data on
 mouse strain, diet, parasite dose, weight, worm load, and intestinal
 permeability to FD4.Hpoly_Jan2015.xlsx
DOI: 10.5061/dryad.n6c64
title: Data from: Building a beetle: how larval environment leads to adult performance in a horned beetle

description: The link between the expression of the signals used by male animals in
 contests with the traits which determine success in those contests is
 poorly understood. This is particularly true in holometabolous insects
 such as horned beetles where signal expression is determined during
 metamorphosis and is fixed during adulthood, whereas performance is
 influenced by post-eclosion feeding. We used path analysis to investigate
 the relationships between larval and adult nutrition, horn and body size
 and fitness-related traits such as strength and testes mass in the horned
 beetle Euoniticellus intermedius. In males weight gain post-eclosion had a
 central role in determining both testes mass and strength. Weight gain was
 unaffected by adult nutrition but was strongly correlated with by horn
 length, itself determined by larval resource availability, indicating
 strong indirect effects of larval nutrition on the adult beetle’s ability
 to assimilate food and grow tissues. Female strength was predicted by a
 simple path diagram where strength was determined by eclosion weight,
 itself determined by larval nutrition: weight gain post-eclosion was not a
 predictor of strength in this sex. Based on earlier findings we discuss
 the insulin-like signalling pathway as a possible mechanism by which
 larval nutrition could affect adult weight gain and thence traits such as
 strength.
description: Male
 dataPerformance, weight etc.
 data for male beetles. See supplementary information for full details of
 the analysis.maledata.txtFemale dataData on weight, performance etc. for female beetles. See supplementary information for details of the analysis.femaledata.txt
DOI: 10.5061/dryad.m1mj65t
title: Data from: Habitat preference and den characterization of Indian Pangolin (Manis crassicaudata) in a tropical lowland forested landscape of southwest Sri Lanka

description: The Indian pangolin (Manis crassicaudata) is under threat due to hunting
 for local consumption and illegal trafficking of scales and meat. The
 dearth of scientific studies on the ecology of the M. crassicaudata has
 impaired accurate assessments of its conservation needs. This study
 investigated the habitat preference and burrow characteristics of M.
 crassicaudata in a tropical lowland rainforest in southwest Sri Lanka. A
 total of 75 burrows (54 feeding burrows and 21 resting burrows) of M.
 crassicaudata in four different habitat types i.e. secondary forest,
 Pine-dominated forest, rubber cultivations and tea-dominated home gardens
 bordering forest were observed using fixed-width transects in order to
 characterize resting and feeding burrows of this species. The highest
 density of resting burrows was recorded from the secondary forest (4ha-1),
 followed by rubber cultivations (2.5ha-1) while no resting burrows were
 recorded in Pine-dominated forest and tea-dominated home gardens bordering
 forest. Feeding burrows were more abundant in Pine-dominated forest
 (5.7ha-1). The burrow depth, burrow opening height and width were
 significantly larger in resting burrows compared to feeding burrows.
 Resting burrows were located at higher elevations (75-100m) with
 moderately high slopes (450-600), dense canopy cover (&gt;75%) and
 away from human habitation. Feeding burrows showed a greater variability
 in terms of associated environmental features. The study further revealed
 that Indian pangolins exclusively prefer habitat with rocks and boulders
 under which they dig resting burrows while the location of feeding burrows
 largely overlaps with the distribution of prey species. The resting burrow
 design consisted of a bending tunnel that initially slopes downward and
 then gradually inclines at an angle between 20 and 300, leading to the
 resting chamber. Our study highlights the importance of conserving
 fragmented secondary natural forests in changing landscapes of the
 southwest lowlands of Sri Lanka as these habitats appear to be critical to
 sustaining populations of M. crassicaudata.
description: S1 Table : Burrow
 characteristics of resting and feeding burrowsS1 Table contain data
 set of the study on den characterization of Indian Pangolin (Manis
 crassicaudata) in a tropical lowland forested landscape of South-west Sri
 Lanka.S1
 Table.xlsx
DOI: 10.5061/dryad.1872r
title: Data from: Larval environment alters amphibian immune defenses differentially across life stages and populations

description: Recent global declines, extirpations and extinctions of wildlife caused by
 newly emergent diseases highlight the need to improve our knowledge of
 common environmental factors that affect the strength of immune defense
 traits. To achieve this goal, we examined the influence of acidification
 and shading of the larval environment on amphibian skin-associated innate
 immune defense traits, pre and post-metamorphosis, across two populations
 of American Bullfrogs (Rana catesbeiana), a species known for its
 wide-ranging environmental tolerance and introduced global distribution.
 We assessed treatment effects on 1) skin-associated microbial communities
 and 2) post-metamorphic antimicrobial peptide (AMP) production and 3) AMP
 bioactivity against the fungal pathogen Batrachochytrium dendrobatidis
 (Bd). While habitat acidification did not affect survival, time to
 metamorphosis or juvenile mass, we found that a change in average pH from
 7 to 6 caused a significant shift in the larval skin microbial community,
 an effect which disappeared after metamorphosis. Additionally, we found
 shifts in skin-associated microbial communities across life stages
 suggesting they are affected by the physiological or ecological changes
 associated with amphibian metamorphosis. Moreover, we found that
 post-metamorphic AMP production and bioactivity were significantly
 affected by the interactions between pH and shade treatments and
 interactive effects differed across populations. In contrast, there were
 no significant interactions between treatments on post-metamorphic
 microbial community structure suggesting that variation in AMPs did not
 affect microbial community structure within our study. Our findings
 indicate that commonly encountered variation in the larval environment
 (i.e. pond pH and degree of shading) can have both immediate and long-term
 effects on the amphibian innate immune defense traits. Our work suggests
 that the susceptibility of amphibians to emerging diseases could be
 related to variability in the larval environment and calls for research
 into the relative influence of potentially less benign anthropogenic
 environmental changes on innate immune defense traits.
description: Larval environment
 alters amphibian immune defenses differentially across life stages and
 populationsData includes:Larval
 survival (%), Larval duration, mass at sample collection, AMP production
 (BCA assay), AMP bioactivity as measured by the slope of the
 log-transformed growth curve, AMP bioactivity as measured by pathogen
 growth rate (r).Krynak_BF_datadryad.csv
DOI: 10.5061/dryad.qj812
title: Data from: Selection by parasitoid females among closely related hosts based on volatiles: Identifying relevant chemical cues

description: Parasitoid fitness is influenced by the ability to overcome host defense
 strategies and by the ability of parasitoid females to select high-quality
 host individuals. When females are unable to differentiate among hosts,
 their fitness will decrease with an increasing abundance of resistant
 hosts. To understand the effect of mixed host populations on female
 fitness, it is therefore necessary to investigate the ability of female
 parasitoids to select among hosts. Here, we used behavioral assays,
 headspace volatile collection, and electrophysiology to study the ability
 of Asecodes parviclava to use olfactory cues to select between a
 susceptible host (Galerucella calmariensis) and a resistant host
 (Galerucella pusilla) from a distance. Our studies show that parasitoid
 females have the capacity to distinguish the two hosts and that the
 selection behavior is acquired through experiences during earlier life
 stages. Further, we identified two volatiles (α-terpinolene and
 [E]-β-ocimene) which amounts differ between the two plant–herbivore
 systems and that caused behavioral and electrophysiological responses. The
 consequence of this selection behavior is that females have the capacity
 to avoid laying eggs in G. pusilla, where the egg mortality is higher due
 to much stronger immune responses toward A. parviclava than in larvae of
 G. calmariensis.
description: EAG_Asecodes
 parviclavaEAG responses of
 antennae from Asecodes parviclava females.EAG_Asecodes.xlsx
DOI: 10.15468/dl.gue63m
title: Occurrence Download

description: A dataset containing 408 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Bupleurum chinense",
 "Year 1975-2026"
 ]
}

 The dataset includes 408 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001333-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.