cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8kn7ng0
title: Data from: Predicting the thermal and allometric dependencies of disease transmission via the metabolic theory of ecology

description: The metabolic theory of ecology (MTE) provides a general framework of
 allometric and thermal dependence that may be useful for predicting how
 climate change will affect disease spread. Using Daphnia magna and a
 microsporidian gut parasite, we conducted two experiments across a wide
 thermal range and fitted transmission models that utilize MTE submodels
 for transmission parameters. We decomposed transmission into contact rate
 and probability of infection, and further decomposed probability of
 infection into a product of gut residence time (GRT) and per-parasite
 infection rate of gut cells. Contact rate generally increased with
 temperature and scaled positively with body size, whereas infection rate
 had a narrow hump-shaped thermal response and scaled negatively with body
 size. GRT increased with host size and was longest at extreme
 temperatures. GRT and infection rate inside the gut combined to create a
 3.5x higher probability of infection for the smallest relative to the
 largest individuals. Small temperature changes caused large differences in
 transmission. We also fit several alternative transmission models to data
 at individual temperatures. The more complex models, parasite antagonism
 or synergism and host heterogeneity, did not substantially improve the fit
 to the data. Our results show that transmission rate is the product of
 several distinct thermal and allometric functions that can be predicted
 continuously across temperature and host size using MTE.
description: Code and
 DataCode and
 DataAm_Nat_Code_and_Data.zip
DOI: 10.6084/m9.figshare.31158037
title: Data for ProtFinder

description: These are datasets for ProtFinder paper
DOI: 10.6084/m9.figshare.31158037.v1
title: Data for ProtFinder

description: These are datasets for ProtFinder paper
DOI: 10.5061/dryad.53885k7
title: Data from: Condition-dependent begging elicits increased parental investment in a wild bird population

description: The resolution of parent-offspring conflict has long been thought to
 involve offspring need driving begging and parental care, leaving other
 hypotheses underexplored. In a population of wild birds, we tested
 experimentally whether begging serves as a negatively condition-dependent
 signal of need or a positively condition-dependent signal of quality.
 Across multiple years, we food-supplemented nestling house wrens shortly
 after hatching, and simultaneously manipulated corticosterone levels to
 simulate the hunger-induced increase in glucocorticoids thought to mediate
 begging. This allowed us also to test whether begging is simply a
 proximate signal of hunger. Days after supplementation ended,
 food-supplemented nestlings were in better condition than non-supplemented
 nestlings and begged for food at an increased rate; their parents, in
 turn, increased provisioning to a greater extent than parents of
 non-supplemented young, as begging positively predicted provisioning.
 Food-supplemented nestlings, therefore, attained above-average condition,
 which predicted their recruitment as breeding adults in the local
 population. Glucocorticoids increased begging in the short-term, but this
 transient effect depended on nestling satiety. Thus, glucocorticoids
 promoted begging as a proximate response to hunger, whereas the
 longer-term changes in nestling condition, begging, and food provisioning
 suggest that begging ultimately signals offspring quality to elicit
 increased parental allocation, thereby enhancing offspring survival.
description: NESTS
DOI: 10.5061/dryad.445m9j4
title: Data from: Pervasive admixture between eucalypt species has consequences for conservation and assisted migration

description: Conservation management often uses information on genetic population
 structure to assess the importance of local provenancing for ecological
 restoration and reintroduction programs. For species that do not exhibit
 complete reproductive isolation, the estimation of population genetic
 parameters may be influenced by the extent of admixture. Therefore, to
 avoid perverse outcomes for conservation, genetically-informed management
 strategies must determine whether hybridisation between species is
 relevant, and the extent to which observed population genetic patterns are
 shaped by inter-specific versus intra-specific gene flow. We used
 genotyping-by-sequencing to identify over 2400 informative
 single-nucleotide polymorphisms across 18 populations of Eucalyptus
 regnans F. Muell., a foundation tree species of montane forests in
 south-eastern Australia. We used this data to determine the extent of
 hybridisation with another species, Eucalyptus obliqua L’Hér., and
 investigate how admixture influences genetic diversity parameters, by
 estimating metrics of genetic diversity and examining population genetic
 structure in datasets with and without admixed individuals. We found
 hybrid individuals at all sites, and two highly introgressed populations.
 Hybrid individuals were not distributed evenly across environmental
 gradients, with logistic regression identifying hybrids as being
 associated with temperature. Removal of hybrids resulted in increases in
 genetic differentiation (FST), expected heterozygosity, observed
 heterozygosity and the inbreeding coefficient, and different patterns of
 isolation-by-distance. After removal of hybrids and introgressed
 populations, mountain ash showed very little population genetic structure,
 with a small effect of isolation-by-distance, and very low global FST
 (0.03). Our study shows that, in plants, decisions around provenancing of
 individuals for restoration depend on knowledge of whether hybridisation
 is influencing population genetic structure. For species in which most
 genetic variation is held within populations, there may be little benefit
 in planning conservation strategies around environmental adaptation of
 seed sources. The possibility for adaptive introgression may also be
 relevant when species regularly hybridise.
description: Eucalyptus_genotypes_040518Eucalyptus regnans and Eucalyptus obliqua genotypesChromosome, site and concatenated locus namesThis file contains the Chromosome/scaffold, site #, and concatenated ChromoSite (called "locus") names of all 49622 lociChromoSiteLocus.csv
DOI: 10.5061/dryad.6bq1c1r
title: Data from: Rethinking the scale and formulation of indices assessing organism vulnerability to warmer habitats

description: Ecologists often use indices or proxies to communicate complex ecological
 entities. Indices commonly known as Thermal Safety Margin, Habitat Thermal
 Quality and Hours of Restriction describe species' vulnerability to
 climate change by comparing organisms' thermal limits or preferences
 to available habitat temperatures. Ready access to temperature data, from
 global gridded datasets or limited in situ measurements, has made these
 indices popular for vulnerability assessments across taxonomic groups and
 regions. However, such coarse descriptions of thermal landscape mask the
 spatio-temporal heterogeneity that organisms experience, compromising the
 value of these indices. Full understanding of how scale affects index
 estimates is lacking, leaving ecologists and conservation managers with
 little guidance for applying or interpreting indices. Here, we show that
 incomplete temperature sampling, in space or time, provides erroneous
 assessments of vulnerability. Gradually sub-sampling a long-term,
 fine-scale dataset of operative environmental temperature altered the
 index estimates for a lizard. Uncertainty associated with the selection of
 data increased with coarser scales, often leading to contrasting
 interpretations about the species' vulnerability to climate change
 depending on the data subset used. Compressing the environmental
 temperature data into central or extreme tendencies, as traditionally done
 to compute these indices, further masked the thermal variation that
 animals exploit to buffer warming. We suggest the use of improved index
 formulations that better describe temperature availability at scales that
 are appropriate to the study organism.
description: Garcia_Allen_Clusella-Trullas_indices_functionCode for computing indices of species' vulnerability to warming based on data of available operative environmental temperature (Te) and the species' thermal preference and tolerance. The function returns the values of the Habitat Thermal Quality, Thermal Safety Margin and Hours of Restriction indices as well as Te summary statistics.
DOI: 10.5061/dryad.np4vh0g
title: Data from: Within-generation consequences of post-settlement mortality for trait composition in wild populations: an experimental test

description: There is a critical need to understand patterns and causes of
 intraspecific variation in physiological performance in order to predict
 the distribution and dynamics of wild populations under natural- and
 human-induced environmental change. However, the usual explanation for
 trait differences, local adaptation, fails to account for the small-scale
 phenotypic and genetic divergence observed in fishes and other species
 with dispersive early life stages. We tested the hypothesis that
 local-scale variation in the strength of selective mortality in early life
 mediates the trait composition in later life stages. Through in situ
 experiments, we manipulated exposure to predators in the coral reef
 damselfish Dascyllus aruanus and examined consequences for subsequent
 growth performance under common garden conditions. Groups of 20
 recently-settled D. aruanus (mean ± SD standard length = 8.53 ± 0.450 mm)
 were outplanted to experimental coral colonies in Moorea lagoon and either
 exposed to natural predation mortality (52% mortality in three days) or
 protected from predators with cages for three days. Predator-exposed
 groups were shorter, while those with lower survival were in better
 condition, suggesting that predators removed the larger, thinner
 individuals. Growth of both treatment groups was subsequently compared
 under common conditions. We did not detect consequences of predator
 exposure for subsequent growth performance: growth over the following 37
 days was not affected by the prior predator treatment or survival.
 Genotyping at 10 microsatellite loci did indicate, however, that predator
 exposure significantly influenced the genetic composition of groups. We
 conclude that post-settlement mortality did not have carry-over effects on
 the subsequent growth performance of cohorts in this instance, despite
 evidence for directional selection during the initial mortality phase.
description: CiottiAndPlanes2019Data and R code for Ciotti and Planes (2019) "Within-generation consequences of post-settlement mortality for trait composition in wild populations: an experimental test", published in Ecology and Evolution.
DOI: 10.5061/dryad.2t547dd
title: Data from: Scent of death: evolution from sea to land of an extreme collective attraction to conspecific death

description: All living organisms must eventually die, though in some cases their death
 can bring life-giving opportunities. Few studies, however, have
 experimentally tested how animals capitalize on conspecific death and why
 this specialization would evolve. Here we conducted experiments on the
 phylogenetically most closely-related marine and terrestrial hermit crabs
 to investigate the evolution of responses to death during the sea-to-land
 transition. In the sea, death of both conspecifics and heterospecifics
 generates unremodeled shells needed by marine hermit crabs. In contrast,
 on land, terrestrial hermit crabs are specialized to live in
 architecturally remodeled shells, and the sole opportunity to acquire
 these essential resources is conspecific death. We experimentally tested
 these different species’ responsiveness to the scent of conspecific versus
 heterospecific death, predicting that conspecific death would have special
 attractive value for the terrestrial species. We found the terrestrial
 species was overwhelmingly attracted to conspecific death, rapidly
 approaching and forming social groupings around conspecific death sites
 that dwarfed those around heterospecific death sites. This differential
 responsiveness to conspecific versus heterospecific death was absent in
 marine species. Our results thus reveal that on land a reliance on
 resources associated exclusively with conspecifics has favored the
 evolution of an extreme collective attraction to conspecific death.
description: Scent of death_Ecology
 and Evolution_all raw Excel data (uploaded 2018-12-28 to
 Dryad)All data for both
 experiments in the paper (Experiments 1 and 2).
DOI: 10.15468/dl.ws52w4
title: Occurrence Download

description: A dataset containing 8871 records in GBIF matching the query:
SELECT
 '414' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 37.42857426825602
 AND decimalLatitude &lt;= 41.89415215079384
 AND decimalLongitude &gt;= 63.32053397346014
 AND decimalLongitude &lt;= 71.92889702835036
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 8871 records were derived from 149 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001540-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1sb340g
title: Data from: Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε

description: The most frequently recurring cancer-associated DNA polymerase ε (Pol ε)
 mutation is a P286R substitution in the exonuclease domain. While
 originally proposed to increase genome instability by disrupting
 exonucleolytic proofreading, the P286R variant was later found to be
 significantly more pathogenic than Pol ε proofreading deficiency per se.
 The mechanisms underlying its stronger impact remained unclear. Here we
 report the crystal structure of the yeast orthologue, Pol ε−P301R,
 complexed with DNA and an incoming dNTP. Structural changes in the protein
 are confined to the exonuclease domain, with R301 pointing towards the
 exonuclease site. Molecular dynamics simulations suggest that R301
 interferes with DNA binding to the exonuclease site, an outcome not
 observed with the exonuclease-inactive Pol ε−D290A,E292A variant lacking
 the catalytic residues. These results reveal a distinct mechanism of
 exonuclease inactivation by the P301R substitution and a likely basis for
 its dramatically higher mutagenic and tumorigenic effects.
description: MD simulation trajectory
 data and input filesInput files, topology
 files, starting structures, and representative snapshots from the
 simulations.DNA_PolE_MD_data.tar.gz
DOI: 10.7927/gadr-8q65
title: IPCC AR6 Synthesis Report LR Figure 2.5 (a): Global GHG emissions of modelled pathways

description: This panel shows global GHG emissions over 2015–2050 for four types of assessed modelled global pathways:

Trend from implemented policies: Pathways with projected near-term GHG emissions in line with policies implemented until the end of 2020 and extended with comparable ambition levels beyond 2030 (29 scenarios across categories C5–C7, WGIII Table SPM.2);
Limit to 2°C (&gt;67%) or return warming to 1.5°C (&gt;50%) after a high overshoot, NDCs until 2030: Pathways with GHG emissions until 2030 associated with the implementation of NDCs announced prior to COP26, followed by accelerated emissions reductions likely to limit warming to 2°C (C3b, WGIII Table SPM.2) or to return warming to 1.5°C with a probability of 50% or greater after high overshoot (subset of 42 scenarios from C2, WGIII Table SPM.2).
Limit to 2°C (&gt;67%) with immediate action: Pathways that limit warming to 2°C (&gt;67%) with immediate action after 2020 (C3a, WGIII Table SPM.2).
Limit to 1.5°C (&gt;50%) with no or limited overshoot: Pathways limiting warming to 1.5°C with no or limited overshoot (C1, WGIII Table SPM.2 C1).

All these pathways assume immediate action after 2020. Past GHG emissions for 2010–2015 used to project global warming outcomes of the modelled pathways are shown by a black line.
DOI: 10.5061/dryad.nf6b29v
title: Data from: Expansion of industrial plantations continues to threaten Malayan tiger habitat

description: Southeast Asia has some of the highest deforestation rates globally, with
 Malaysia being identified as a deforestation hotspot. The Malayan tiger, a
 critically endangered subspecies of the tiger endemic to Peninsular
 Malaysia, is threatened by habitat loss and fragmentation. In this study,
 we estimate the natural forest loss and conversion to plantations in
 Peninsular Malaysia and specifically in its tiger habitat between 1988 and
 2012 using the Landsat data archive. We estimate a total loss of 1.35 Mha
 of natural forest area within Peninsular Malaysia over the entire study
 period, with 0.83 Mha lost within the tiger habitat. Nearly half (48%) of
 the natural forest loss area represents conversion to tree plantations.
 The annual area of new plantation establishment from natural forest
 conversion increased from 20 thousand ha year−1 during 1988–2000 to 34
 thousand ha year−1 during 2001–2012. Large-scale industrial plantations,
 primarily those of oil palm, as well as recently cleared land, constitute
 80% of forest converted to plantations since 1988. We conclude that
 industrial plantation expansion has been a persistent threat to natural
 forests within the Malayan tiger habitat. Expanding oil palm plantations
 dominate forest conversions while those for rubber are an emerging threat.
description: Peninsular Malaysia
 Natural Forest and Natural Forest LossNatural forest (year
 1988) and natural forest loss (total for years 1988-2000) data for
 Peninsular Malaysia at 30 m x 30 m resolution from the research article
 ‘Expansion of Industrial Plantations Continues to Threaten Malayan Tiger
 Habitat’, which includes a full description of the data creation
 process.Shevade_et_al_2017_NaturalForestLoss.zip
DOI: 10.5061/dryad.1sd556t
title: Data from: Genotype-free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data

description: Restriction-site associated sequencing (RADSeq) facilitates rapid
 generation of thousands of genetic markers at relatively low cost;
 however, several sources of error specific to RADSeq methods often lead to
 biased estimates of allele frequencies and thereby to erroneous population
 genetic inference. Estimating the distribution of sample allele
 frequencies without calling genotypes was shown to improve population
 inference from whole genome sequencing data, but the ability of this
 approach to account for RADSeq-specific biases remains unexplored. Here we
 assess in how far genotype-free methods of allele frequency estimation
 affect demographic inference from empirical RADSeq data. Using the
 well-studied pied flycatcher (Ficedula hypoleuca) as a study system, we
 compare allele frequency estimation and demographic inference from whole
 genome sequencing data with that from RADSeq data matched for samples
 using both genotype-based and genotype free methods. The demographic
 history of pied flycatchers as inferred from RADSeq data was highly
 congruent with that inferred from WGS data when allele frequencies were
 estimated directly from the read data. In contrast, when allele
 frequencies were derived from called genotypes, RADSeq-based estimates of
 most model parameters fell outside the 95% confidence interval (CI) of
 estimates derived from WGS data. Notably, more stringent filtering of
 genotypes tended to increase the discrepancy between parameter estimates
 from WGS and RADSeq data, respectively. The results from this study
 demonstrate the ability of genotype-free methods to improve AFS-based
 demographic inference from RADSeq data and highlight the need to account
 for uncertainty in NGS data regardless of sequencing method.
description: dadi
 scriptsPython scripts to run
 dadi for the three models described in the paperdadi_scripts.zip
DOI: 10.5061/dryad.4j36s87
title: Data from: Vegetation phenology and nest survival: diagnosing heterogeneous effects through time

description: Birds should select nest sites that minimize predation risk, but
 understanding the influence of vegetation on nest survival has proven
 problematic. Specifically, the common practice of measuring vegetation on
 nest fate date can overestimate its effect on survival, simply because
 vegetation at hatched nests grows for a longer period of time than
 vegetation at nests that were depredated. Here, we sampled the literature
 to determine the prevalence of this bias in studies of duck breeding
 ecology. We then used survival data collected from ~2,800 duck nests to
 empirically evaluate evidence of bias in four different vegetation
 metrics: vegetation density measured when the nest was found, density when
 the nest was fated, and date-corrected regression residuals of these two.
 We also diagnosed the magnitude of vegetation effects on nest survival by
 restricting analysis to only nests which were fated contemporaneously
 (thereby removing potential bias in the timing of measurement). Finally,
 we examined whether systematic phenological differences exist between
 vegetation at hatched and depredated nests that have the potential to
 further obfuscate the relationship between vegetation and nest survival.
 We found evidence for a true positive effect of vegetation density on nest
 survival that appeared to be inflated when using raw vegetation
 measurements collected at fate date. However, taken in combination with
 the literature review, our results suggest that the majority of duck
 nesting studies have evaluated the role of vegetation on nest survival
 using a relatively less biased metric—vegetation density when the nest was
 found. Finally, we found that over the course of a nesting attempt,
 vegetation increased in density at successful nests, but decreased in
 density at depredated nests. This seasonal change potentially points to an
 important new metric for understanding predation risk, but further
 experimental research is required to fully eliminate potential biases in
 the timing of vegetation measurements.
description: North Dakota duck
 nesting datasetThese are survival data
 for duck nests in North Dakota. Column headers are described in the
 publication. Nest fate information follows that required by program MARK
 accessed through the package RMark (see description by Rotella on the CRAN
 site).robel_2018.06.15.csv