cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.68s75
title: Data from: Metabolic rate is canalized in the face of variable life history and nutritional environment

description: Despite its central importance in organismal physiology, we have poor
 understanding of how metabolic rate is influenced by two key factors –
 food nutritional content and an organism's physiological
 characteristics. We examined how variation in nutrients and physiological
 aspects of life history affect standard metabolic rate in Gryllus firmus
 cricket morphs that differ dramatically in flight capability and early-age
 fecundity. Newly moulted female morphs were fed one of 13 diets that
 differed in concentrations of protein and carbohydrate. Carbon dioxide
 production, respiratory exchange ratios (RERs), nutrient intake and mass
 and lipid levels were measured. CO2 production and RERs increased to a
 similar degree in both morphs as food macronutrient content increased. In
 contrast, no difference in whole-organism O2 consumption was observed
 across the protein–carbohydrate landscape or between morphs. Both morphs
 similarly increased food intake as nutrient concentration – particularly
 protein – decreased, but differed in mass and lipid gains, across the
 diets. Modulation of the substrate used for respiration coupled with
 compensating aspects of morph-specific metabolism appears to buffer the
 effects of variable nutrient intake and life history on standard metabolic
 rate. That is, respiration rate can be highly canalized in the face of
 dramatic variation in both the external nutritional environment and
 internal aspects of intermediary metabolism.
description: CricketDataPlease refer to the ReadMe file for a detailed description of the data.
DOI: 10.15468/dl.abhdhx
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ningaui yvonnae"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001266-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.740
title: Data from: A phylogenetic analysis of geese and swans (Anseriformes: Anserinae), including selected fossil species

description: A phylogenetic analysis of modern and selected fossil geese and swans was
 performed using 165 characters of the skeleton, trachea, and natal and
 definitive integument. Five shortest trees were found (length = 318;
 consistency index for informative characters = 0.634), which differed only
 in details of relationships among three species of Branta. The trees
 supported (1) +Cnemiornis as sister group to other taxa analyzed; (2) a
 sister group relationship between the moa-nalos of Hawaii and other geese
 and swans; (3) Cereopsis as sister group of Anser, Branta, Coscoroba, and
 Cygnus (contra Livezey, 1986, Auk 103:737--754); (4) monophyly of Anser,
 Branta, and +Geochen and confirmation of generic monophyly of each; and
 (5) Coscoroba as sister group to Cygnus. Selective exclusion of fossil
 taxa from the analysis variably affected inferred relationships and had
 substantial impacts on computational efficiency. Some nodes were not
 robust to bootstrapping: (1) nodes relating species groups within Anser,
 Cygnus, and +Thambetochen and (2) the node uniting Anser, Branta,
 Coscoroba, and Cygnus relative to Cereopsis. Bremer (decay) indices
 indicated similar differences in relative support for nodes. Skeletal
 characters were comparatively important in establishing higher order
 relationships, whereas integumentary characters were critical for lower
 order inferences. Constrained analyses revealed that other proposed
 phylogenetic hypotheses entailed variable penalities in parsimony. The
 shortest tree(s) was considered with respect to selected ecomorphological
 attributes (e.g., body mass, sexual size dimorphism, clutch size) and
 biogeography, and a revised phylogenetic classification of the geese and
 swans is proposed.
description: Livezey Data
 SetAnserMatrix.htm
DOI: 10.5061/dryad.n6g99
title: Data from: Phylogeographic analysis reveals northerly refugia for the riverine amphibian Triturus dobrogicus (Caudata: Salamandridae)

description: We investigated the recent evolutionary history of the Danube crested
 newt, Triturus dobrogicus through reconstructions of: (1) the number and
 position of refugia at the last glacial maximum, (2) the role of major
 central European rivers in pattern of post-glacial dispersal, and (3) the
 present-day distribution pattern. We analysed sequences of mitochondrial
 DNA (ND2, 1065 bp) and six microsatellite loci in 363 T. dobrogicus
 individuals from 58 populations covering the range of the species. Our
 analyses suggested that T. dobrogicus survived the last glacial maximum in
 two separate refugia positioned in northwestern Pannonia and in Southern
 Pannonia from where its range expanded along the Danube and Tisza Rivers.
 Our findings also confirmed that rivers played an important role in
 shaping the evolutionary history of amphibian species in Central Europe.
 We compared the T. dobrogicus range with another lowland amphibian, the
 fire-bellied toad Bombina bombina, using species distribution modelling.
 In line with these models, the isolated mountains inside Pannonia are
 occupied not by B. bombina, but by its mountain-dwelling sister-species B.
 variegata. However, in contrast to the model, crested newts (including T.
 dobrogicus) are absent from these mountains. We attribute this
 biogeographical discrepancy to the positioning of the species’ refugia at
 the last glacial maximum.
description: Tdobrogicus_input_filesInput files for PopArt, Arlequin, BAPS, Geneland, Genepop and Structure.
DOI: 10.5061/dryad.322bb
title: Data from: Pain and pessimism: dairy calves exhibit negative judgement bias following hot-iron disbudding

description: Pain is defined as an unpleasant sensory and emotional experience
 associated with actual or potential tissue damage, but emotional states
 are difficult to directly assess in animals. Researchers have assessed
 pain using behavioural and physiological measures, but these approaches
 are limited to understanding the arousal rather than valence of the
 emotional experience. Cognitive bias tasks show that depressed humans
 judge ambiguous events negatively and this technique has been applied to
 assess emotional states in animals. However, limited research has examined
 how pain states affect cognitive processes in animals. Here we present the
 first evidence of cognitive bias in response to pain in any non-human
 species. In two experiments, dairy calves (n = 17) were trained to respond
 differentially to red and white video screens and then tested with
 unreinforced ambiguous colours in two or three test sessions before and
 two sessions after the routine practice of hot-iron disbudding. After
 disbudding calves were more likely to judge ambiguous colours as negative.
 This ‘pessimistic’ bias indicates that post-operative pain following
 hot-iron disbudding results in a negative change in emotional state.
description: Calf approach responses
 in the cognitive bias taskCalf approach responses
 to each screen for each session before and after disbudding (%). Approach
 responses have been averaged across trials (23 each of positive and
 negative screens; 5 of each ambigous screen) within each
 sessionDRYAD_Table 1_Calf
 responses.docx
DOI: 10.5061/dryad.7q571d1
title: Data from: Reconciling multiple impacts of nitrogen enrichment on soil carbon: plant, microbial, and geochemical controls

description: Impacts of reactive nitrogen (N) inputs on ecosystem carbon (C) dynamics
 are highly variable, and the underlying mechanisms remain unclear. Here,
 we proposed a new conceptual framework that integrates plant, microbial,
 and geochemical mechanisms to reconcile diverse and contrasting impacts of
 N on soil C. This framework was tested using long-term N enrichment and
 acid addition experiments in a Mongolian steppe grassland. Distinct
 mechanisms could explain effects of N on particulate and
 mineral-associated soil C pools, potentially explaining discrepancies
 among previous N addition studies. While plant production predominated
 particulate C changes, N-induced soil acidification strongly affected
 mineral-associated C through decreased microbial growth and pH-sensitive
 associations between iron and aluminum minerals and C. Our findings
 suggest that effects of N-induced acidification on microbial respiration
 and geochemical properties should be included in Earth system models that
 predict ecosystem C budgets under future N deposition/input scenarios.
description: Reconciling multiple
 impacts of nitrogen enrichment on soil carbon: plant, microbial, and
 geochemical controlsData.xlsx
DOI: 10.5061/dryad.gn44qh6
title: Data from: Anatomy of the vegetative organs, inflorescence axis and pedicel in the Neoregelia bahiana complex (Bromeliaceae): taxonomic and ecological importance

description: Delimitation of Bromeliaceae into genera or species is often problematic,
 as observed for the Neoregelia bahiana complex, distributed throughout the
 rocky fields of Espinhaço Range, Brazil. Considering that the anatomical
 characterisation of different organs is potentially important for
 taxonomic and ecological interpretation of this complex, we analysed
 roots, stems (stolon), leaves, inflorescence axes (peduncle), and pedicels
 in individuals from different populations. In all the studied individuals,
 the roots are composed of velamen, a heterogeneous cortex, and a polyarch
 vascular cylinder with sclerenchymatous pith. The stolon features a
 parenchymatous cortex and collateral vascular bundles randomly distributed
 in the vascular cylinder. This organ may increase in diameter by the
 formation of new vascular bundles and a multi-layered cork. The leaf blade
 has epidermal cells with U-shaped thickened walls and peltate scales occur
 on the adaxial surface. The mesophyll consists of mechanical and
 water-storage hypodermis and a heterogeneous chlorenchyma. The
 inflorescence axis and the pedicel have a parenchymatous cortex and
 vascular bundles randomly distributed in an aerenchyma. Some variable leaf
 characters, such as presence of air lacunae in the mesophyll, are related
 to the size of the individuals and were interpreted as phenotypic
 variations related mainly to sunlight incidence. Leaf characters such as
 lamina shape, distribution of the peltate scales, and number of cell
 layers forming the water-storage hypodermis distinguish the populations of
 the Serra do Cabral and one population of the Diamantina (Minas Gerais)
 from the remaining studied populations, suggesting the existence of more
 than one taxon.
description: Studied populations of
 the Neoregelia bahiana complex.Average size of
 individuals from different populations of Neoregelia
 bahiana.N.bahiana populations_Average
 size of individuals.xls
DOI: 10.5061/dryad.7rp566h7
title: Data from: Tragedy of the commons among antibiotic resistance plasmids

description: As social interactions are increasingly recognized as important
 determinants of microbial fitness, sociobiology is being enlisted to
 better understand the evolution of clinically relevant microbes and,
 potentially, to influence their evolution to aid human health. Of special
 interest are situations in which there exists a “tragedy of the commons”,
 where natural selection leads to a net reduction in fitness for all
 members of a population. Here I demonstrate the existence of a tragedy of
 the commons among antibiotic resistance plasmids of bacteria. In serial
 transfer culture, plasmids evolved a greater ability to superinfect
 already-infected bacteria, increasing plasmid fitness when evolved
 genotypes were rare. Evolved plasmids, however, fell victim to their own
 success, reducing the density of their bacterial hosts when they became
 common and suffering reduced fitness through vertical transmission. Social
 interactions can thus be an important determinant of evolution for the
 molecular endosymbionts of bacteria. These results also identify an avenue
 of evolution that reduces proliferation of both antibiotic resistance
 genes and their bacterial hosts.
description: data-forStatsData used for statistical analyses. Fitness calculations described in paper.data-hostDensityRaw data (cfu/ml) for assays of host population density.data-invasionRaw data (cfu/ml) for plasmid fitness assays against differently-marked ancestral competitor. ____.inital = density immediately after serial passage. _____.final = density after one day incubation.data-populationDynamicsRaw data (cfu/ml) for assays of plasmid population dynamics (Fig. 1 in the paper).data-vsResistantRaw data (cfu/ml) for plasmid fitness assays against plasmid-resistant host strain. ____.inital = density immediately after serial passage. _____.final = density after one day incubation.
DOI: 10.5061/dryad.v2n81
title: Data from: A new exceptionally preserved Cambrian priapulid from the Chengjiang Lagerstätte

description: A fossil priapulid, Eximipriapulus globocaudatus new genus new species, is
 described from the Cambrian Chengjiang Lagerstätte of Yunnan, China. The
 exceptional preservation of the animal reveals morphological details that
 allow direct comparison with extant priapulids. The body is divisible into
 a partially eversible pharynx, a smooth collar, a scalid-bearing
 introvert, a neck with triangular scalids, an unsegmented trunk with
 annulations, and a distinctly expanded terminal region. Several
 specialized regions of the alimentary canal are recognized: a pharynx
 (lined by cuticle and bearing teeth), esophagus, midgut, hindgut, and a
 terminal anus. The sample includes a putative juvenile. The animal is
 inferred to have been an active burrower using a double-anchor strategy,
 practicing both deposit feeding and carnivory. Inclusion of Eximipriapulus
 in the most recent character matrix for cladistic analysis of fossil and
 Recent priapulids resolves the new genus within the priapulid crown group.
description: Data
 matrixData matrix for the
 phylegenetic analysis in the manuscript
DOI: 10.5061/dryad.66qh9
title: Data from: Megalaria allenae (Ramalinaceae), a new sorediate species from southeastern North America previously confused with M. pulverea

description: Megalaria allenae, a blue-gray to green-blue sterile sorediate crustose
 lichen containing atranorin, fumarprotocetraric acid and zeorin, is
 described as new to science. It is corticolous on deciduous trees and
 endemic to swamp forests of the Atlantic Coastal Plain of southeastern
 North America. As sexual reproductive structures are unknown in the
 species, the generic placement and relationship with M. pulverea were
 determined using molecular phylogenetic analyses of ITS and mtSSU sequence
 data.
description: Megalaria_data_packetOriginal data file in nexus format, data file for bayesian inference, data file for maximum likelihood analyses, and data file for ITS distance calculations
DOI: 10.5061/dryad.336n3gt0
title: Data from: Global patterns of leaf defenses in oak species

description: Plant defensive traits drive patterns of herbivory and herbivore diversity
 among plant species. Over the past 30 years, several prominent hypotheses
 have predicted the association of plant defenses with particular abiotic
 environments or geographic regions. We used a strongly supported phylogeny
 of oaks to test whether defensive traits of 56 oak species are associated
 with particular components of their climatic niche. Climate predicted both
 the chemical leaf defenses and the physical leaf defenses of oaks, whether
 analyzed separately or in combination. Oak leaf defenses were higher at
 lower latitudes, and this latitudinal gradient could be explained entirely
 by climate. Using phylogenetic regression methods, we found that plant
 defenses tended to be greater in oak species that occur in regions with
 low temperature seasonality, mild winters, and low minimum precipitation,
 and that plant defenses may track the abiotic environment slowly over
 macroevolutionary time. The pattern of association we observed between oak
 leaf traits and abiotic environments was consistent with a combination of
 a seasonality gradient, which may relate to different herbivore pressures,
 and the resource availability hypothesis, which posits that herbivores
 exert greater selection on plants in resource-limited abiotic
 environments.
description: oak_defense_archiveA species-level data frame describing oak leaf traits (standardized as z-scores), latitude (as decimal degrees), and climatic associations (using Worldclim codes e.g. "BIO14"). The 56 oak species are referred to by specific epithet. Trait data was collected from trees in a common garden at the UC Davis Shields Oaks Grove.
DOI: 10.5061/dryad.jv463
title: Data from: Age-related sex differences in body condition and telomere dynamics of red-sided garter snakes

description: Life-history strategies vary dramatically between the sexes, which may
 drive divergence in sex-specific senescence and mortality rates. Telomeres
 are tandem nucleotide repeats that protect the ends of chromosomes from
 erosion during cell division. Telomeres have been implicated in senescence
 and mortality because they tend to shorten with stress, growth and age. We
 investigated age-specific telomere length in female and male red-sided
 garter snakes, Thamnophis sirtalis parietalis. We hypothesized that
 age-specific telomere length would differ between males and females given
 their divergent reproductive strategies. Male garter snakes emerge from
 hibernation with high levels of corticosterone, which facilitates energy
 mobilization to fuel mate-searching, courtship and mating behaviours
 during a two to four week aphagous breeding period at the den site.
 Conversely, females remain at the dens for only about 4 days and seem to
 invest more energy in growth and cellular maintenance, as they usually
 reproduce biennially. As male investment in reproduction involves a yearly
 bout of physiologically stressful activities, while females prioritize
 self-maintenance, we predicted male snakes would experience more
 age-specific telomere loss than females. We investigated this prediction
 using skeletochronology to determine the ages of individuals and qPCR to
 determine telomere length in a cross-sectional study. For both sexes,
 telomere length was positively related to body condition. Telomere length
 decreased with age in male garter snakes, but remained stable in female
 snakes. There was no correlation between telomere length and growth in
 either sex, suggesting that our results are a consequence of divergent
 selection on life histories of males and females. Different selection on
 the sexes may be the physiological consequence of the sexual dimorphism
 and mating system dynamics displayed by this species.
description: Garter snake telomeres
 and conditionGarter snake dataset TELOMERES
 and age.xlsx
DOI: 10.5061/dryad.t78gv
title: Data from: Dodging silver bullets: good CRISPR gene-drive design is critical for eradicating exotic vertebrates

description: Self-replicating gene drives that can spread deleterious alleles through
 animal populations have been promoted as a much needed but controversial
 ‘silver bullet’ for controlling invasive alien species. Homing-based
 drives comprise an endonuclease and a guide RNA that are replicated during
 meiosis via homologous recombination. However, their efficacy for
 controlling wild populations is threatened by inherent polymorphic
 resistance and the creation of resistance alleles via non-homologous
 end-joining (NHEJ) mediated DNA repair. We used stochastic
 individual-based models to identify realistic gene-drive strategies
 capable of eradicating vertebrate pest populations (mice, rats and
 rabbits) on islands. One popular strategy, a sex-reversing drive that
 converts heterozygous females into sterile males, failed to spread and
 required the ongoing deployment of gene-drive carriers to achieve
 eradication. Multiplexed guide RNAs could overcome inherent polymorphic
 resistance and were required for eradication success even when the
 probability of NHEJ was low. Strategies causing homozygotic embryonic
 non-viability or homozygotic female sterility produced high probabilities
 of eradication and were robust to NHEJ-mediated deletion of DNA sequence
 between multiplexed endonuclease recognition sites. The latter two
 strategies also purged the gene drive when eradication failed, therefore
 posing lower long-term risk should animals escape beyond target islands.
 Multiplexing guide RNAs will be necessary if this technology is to be
 useful for insular extirpation attempts; however, precise knowledge of
 homing rates will be required to design low-risk gene drives with high
 probabilities of eradication success.
description: R code for simulating
 pest populations inoculated with gene-drive carriersR code for: (1) a
 function for simulating pest population dynamics assuming different
 gene-drive strategies and species' demographies; (2) running the
 function for different parameter inputs and plotting the
 resultsgene_drive_base.R
DOI: 10.5061/dryad.qn4kq
title: Data from: Multi-species genetic connectivity in a terrestrial habitat network

description: Background: Habitat fragmentation reduces genetic connectivity for
 multiple species, yet conservation efforts tend to rely heavily on
 single-species connectivity estimates to inform land-use planning. Such
 conservation activities may benefit from multi-species connectivity
 estimates, which provide a simple and practical means to mitigate the
 effects of habitat fragmentation for a larger number of species. To test
 the validity of a multi-species connectivity model, we used neutral
 microsatellite genetic datasets of Canada lynx (Lynx canadensis), American
 marten (Martes americana), fisher (Pekania pennanti), and southern flying
 squirrel (Glaucomys volans) to evaluate multi-species genetic connectivity
 across Ontario, Canada. Results: We used linear models to compare
 node-based estimates of genetic connectivity for each species to
 point-based estimates of landscape connectivity (current density) derived
 from circuit theory. To our knowledge, we are the first to evaluate
 current density as a measure of genetic connectivity. Our results depended
 on landscape context: habitat amount was more important than current
 density in explaining multi-species genetic connectivity in the northern
 part of our study area, where habitat was abundant and fragmentation was
 low. In the south however, where fragmentation was prevalent, genetic
 connectivity was correlated with current density. Contrary to our
 expectations however, locations with a high probability of movement as
 reflected by high current density were negatively associated with gene
 flow. Subsequent analyses of circuit theory outputs showed that high
 current density was also associated with high effective resistance,
 underscoring that the presence of pinch points is not necessarily
 indicative of gene flow. Conclusions: Overall, our study appears to
 provide support for the hypothesis that landscape pattern is important
 when habitat amount is low. We also conclude that while current density is
 proportional to the probability of movement per unit area, this does not
 imply increased gene flow, since high current density tends to be a result
 of neighbouring pixels with high cost of movement (e.g., low habitat
 amount). In other words, pinch points with high current density appear to
 constrict gene flow.
description: Microsatellite
 dataMicrosatellite genotypes
 for 702 Canada lynx and 278 southern flying squirrels sampled in Ontario,
 Canada. Genotypes are sampled at sites uniquely identified by the variable
 NodeID. Each row is a unique individual.Data.zip