cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g4p92
title: Data from: Abiotic, biotic and evolutionary control of the distribution of C and N isotopes in food webs

description: Ecosystem functioning depends on nutrient cycles and their responses to
 abiotic and biotic determinants, with the influence of evolutionary
 legacies being generally overlooked in ecosystem ecology. Along a broad
 elevation gradient characterized by shifting climatic and grazing
 environments, we addressed clines of plant N and C∶N content and of δ13C
 and δ15N in producers (herbs) and in primary (grasshoppers) and secondary
 (birds) consumers, both within and between species in phylogenetically
 controlled scenarios. We found parallel and significant intra- and
 interspecific trends of isotopic variation with elevation in the three
 groups. In primary producers, nutrient and isotope distributions had a
 detectable phylogenetic signal that constrained their variation along the
 environmental gradient. The influence of the environment could not be
 ascribed to any single factor, and both grazing and climate had an effect
 on leaf stoichiometry and, thus, on the resources available to consumers.
 Trends in consumers matched those in plants but often became
 nonsignificant after controlling for isotopic values of their direct
 resources, revealing direct bottom-up control and little phylogenetic
 dependence. By integrating ecosystem and mechanistic perspectives, we
 found that nutrient dynamics in food webs are governed at the base by the
 complex interaction between local determinants and evolutionary factors.
description: Data set for the paper
 Laiolo et al_AmNat_MS55531Here we report the
 abundances of C and N isotopes of individual plants, grasshopper and birds
 of this study. The nutrient content of plants (%N, C:N ratios) are also
 shown. These variables are accompanied by geographic coordinates, year of
 sampling, elevation and sex-age (birds) or sex (grasshoppers) of each
 sample.Data_Laiolo et
 al_AmNat_MS55531.xlsx
DOI: 10.5061/dryad.q3hs1
title: Data from: Early replication dynamics of sex-linked mitochondrial DNAs in the doubly uniparental inheritance species Ruditapes philippinarum (Bivalvia Veneridae)

description: Mitochondrial homoplasmy, which is maintained by strictly maternal
 inheritance and a series of bottlenecks, is thought to be an adaptive
 condition for metazoans. Doubly uniparental inheritance (DUI) is a unique
 mode of mitochondrial transmission found in bivalve species, in which two
 distinct mitochondrial genome (mtDNA) lines are present, one inherited
 through eggs (F) and one through sperm (M). During development, the two
 lines segregate in a sex- and tissue-specific manner: females lose M
 during embryogenesis, whereas males actively segregate it in the germ
 line. These two pivotal events are still poorly characterized. Here we
 investigated mtDNA replication dynamics during embryogenesis and
 pre-adulthood of the venerid Ruditapes philippinarum using real-time
 quantitative PCR. We found that both mtDNAs do not detectably replicate
 during early embryogenesis, and that the M line might be lost from females
 around 24 h of age. A rise in mtDNA copy number was observed before the
 first reproductive season in both sexes, with the M mitochondrial genome
 replicating more than the F in males, and we associate these boosts to the
 early phase of gonad production. As evidence indicates that DUI relies on
 the same molecular machine of mitochondrial maternal inheritance that is
 common in most animals, our data are relevant not only to DUI but also to
 shed light on how differential segregations of mtDNA variants, in the same
 nuclear background, may be controlled during development.
description: Guerra2015HDY_qPCRThis Excel file contains the Cq values obtained for every target in each sample analyzed. From the Cq values, ratios for each target were obtained using relative quantification methods (please refer to the ReadMe file for details).
DOI: 10.5061/dryad.7r682
title: Data from: Evolutionary inferences from the analysis of exchangeability

description: Evolutionary inferences are usually based on statistical models that
 compare mean genotypes and phenotypes (or their frequencies) among
 populations. An alternative is to use the actual distribution of genotypes
 and phenotypes to infer the “exchangeability” of individuals among
 populations. We illustrate this approach by using discriminant functions
 on principal components to classify individuals among paired lake and
 stream populations of threespine stickleback in each of six independent
 watersheds. Classification based on neutral and non-neutral microsatellite
 markers was highest to the population of origin and next-highest to
 populations in the same watershed. These patterns are consistent with the
 influence of historical contingency (separate colonization of each
 watershed) and subsequent gene flow (within but not between watersheds).
 In comparison to this low genetic exchangeability, ecological (diet) and
 morphological (trophic and armor traits) exchangeability was relatively
 high – particularly among populations from similar habitats. These
 patterns reflect the role of natural selection in driving parallel changes
 adaptive changes when independent populations colonize similar habitats.
 Importantly, however, substantial non-parallelism was also evident. Our
 results show that analyses based on exchangeability can confirm inferences
 based on statistical analyses of means or frequencies, while also refining
 insights into the drivers of – and constraints on – evolutionary
 diversification.
description: Ecological_dataData on stomach contents (benthic versus limnetic) and stable isotopes for individual stickleback collected from 12 populations (six lake-stream pairs) on Vancouver Island, British Columbia, Canada.Genotype_dataData on microsatellite genotypes for individual stickleback collected from 12 populations (six lake-stream pairs) on Vancouver Island, British Columbia, Canada.Morphological_dataData on morphological traits for individual stickleback collected from 12 populations (six lake-stream pairs) on Vancouver Island, British Columbia, Canada.
DOI: 10.5061/dryad.rg8mb
title: Data from: Test of synergistic interactions among deleterious mutations in bacteria

description: Identifying the forces responsible for the origin and maintenance of
 sexuality remains one of the greatest unsolved problems in biology. The
 mutational deterministic hypothesis postulates that sex is an adaptation
 that allows deleterious mutations to be purged from the genome; it
 requires synergistic interactions, which means that two mutations would be
 more harmful together than expected from their separate effects. We
 generated 225 genotypes of Escherichia coli carrying one, two or three
 successive mutations and measured their fitness relative to an unmutated
 competitor. The relationship between mutation number and average fitness
 is nearly log-linear. We also constructed 27 recombinant genotypes having
 pairs of mutations whose separate and combined effects on fitness were
 determined. Several pairs exhibit significant interactions for fitness,
 but they are antagonistic as often as they are synergistic. These results
 do not support the mutational deterministic hypothesis for the evolution
 of sex.
description: Raw data for Figure
 2Results of competition
 experiments. Colony counts and fitness estimates for each clon isolated
 from each genotype.Raw data for Figure
 3Results of competition
 experiments for double mutants generated for the second test of
 epistasis.
DOI: 10.5061/dryad.3k8m3
title: Data from: Temperature drives epidemics in a zooplankton-fungus disease system: a trait-driven approach points to transmission via host foraging

description: Climatic warming will likely have idiosyncratic impacts on infectious
 diseases, causing some to increase while others decrease or shift
 geographically. A mechanistic framework could better predict these
 different temperature-disease outcomes. However, such a framework remains
 challenging to develop, due to the non-linear and (sometimes) opposing
 thermal responses of different host and parasite traits, and due to the
 difficulty of validating model predictions with observations and
 experiments. We address these challenges in a zooplankton-fungus (Daphnia
 dentifera-Metschnikowia bicuspidata) system. We test the hypothesis that
 warmer temperatures promote disease spread and produce larger epidemics.
 In lakes, epidemics that start earlier and warmer in autumn grow much
 larger. In a mesocosm experiment, warmer temperatures produced larger
 epidemics. A mechanistic model parameterized with trait assays revealed
 that this pattern arose primarily from the temperature-dependence of
 transmission rate (β), governed by the increasing foraging (and hence
 parasite exposure) rate of hosts (f). In the trait assays, parasite
 production seemed sufficiently responsive to shape epidemics as well;
 however, this trait proved too thermally insensitive in the mesocosm
 experiment and lake survey to matter much. Thus, in warmer environments,
 increased foraging of hosts raised transmission rate, yielding bigger
 epidemics through a potentially general, exposure-based mechanism for
 ectotherms. This mechanistic approach highlights how a trait-based
 framework will enhance predictive insight into responses of infectious
 disease to a warmer world.
description: All Code and
 DataAll Code and
 DataFinal
 Code and Data.zip
DOI: 10.5061/dryad.59jp0
title: Data from: From integrative taxonomy to species description: one step beyond

description: Integrative taxonomy has emerged as a methodologically sound method for
 discovering new taxa. By coupling different sources of information (e.g.
 molecular and morphological data) and by combining analytical approaches
 (e.g. multivariate analyses, phylogenetics), systematists have the tools
 to uncover cryptic diversity and draw more reliable species hypotheses.
 Integratively-delimited taxa may be more prone to formal description
 compared to taxa delimited with a single source of information, because
 more detailed species hypotheses can be drawn. Integrative taxonomy has
 therefore the potential to reduce the so-called “taxonomic impediment”
 (i.e. the gap between the number of taxa that remain to be described and
 the number of taxa that are formally named). However, bridging fields such
 as molecular systematics and morphological taxonomy may remain
 challenging, as it either requires the training of versatile scientists,
 or the establishment of collaborations among scientists from these fields.
 We therefore asked ourselves whether integratively-delimiting species
 necessarily led to formal taxonomic descriptions. We reviewed the
 “integrative taxonomy” literature of the past five years to estimate the
 ratio of studies delimiting species (without describing them) over studies
 describing species, and tested whether this ratio was dependent on the
 types and numbers of characters used for delimitation. Based on a sample
 of 361 studies claiming an integrative approach to species delimitation,
 68% used at least two characters for species delimitation, and 32% were
 based on a single character (most often DNA sequences), restricting their
 integrative approach to including different types of data analyses.
 Overall, 46% of studies delimit without describing, and a majority of
 those do not provide a justification for the absence of formal
 descriptions. Authors that do provide a justification mention lack of
 data, forthcoming publications with formal descriptions, or find
 nomenclatural rules too complex. Integrative taxonomy is, based on our
 sample, not an efficient solution to the “taxonomic impediment.”
description: Online appendix
 1List
 of the 494 articles reviewed and data extracted.Online appendix
 2List
 of the journals in which new species were delineated. Editorial policies
 on including formal taxonomic descriptions to articles and impact factors
 were investigated before 2005, between 2005-2010, and 2011-2014. Y=Yes,
 N=No, NA=Not Available and IF=Impact Factor.
DOI: 10.5061/dryad.8856h
title: Data from: Phytochemical traits underlie genotypic variation in susceptibility of quaking aspen (Populus tremuloides) to browsing by a keystone forest ungulate

description: 1.Overbrowsing by ungulates is a major cause of poor aspen stand
 regeneration across North America and Eurasia. In general, factors driving
 ungulate browser preferences include concentrations of plant secondary
 compounds and the nutritional composition (non-structural carbohydrates,
 protein, and minerals) of foliage. While each of these phytochemical
 factors has been shown to independently influence ungulate preference, the
 relative impact of each factor is unknown, as no study to date has
 examined them simultaneously. 2.Plant fitness depends not only on the
 capacity of plants to resist browsing, but also on their capacity to
 tolerate browsing once it has occurred. Little is known of aspen tolerance
 to browsing, which inflicts a different form of damage than insect
 herbivory. 3.We employed multiple aspen genotypes, replicate trees of
 which were subjected to different soil nutrient treatments, to
 investigate: 1) the effects of aspen genotype, nutrient treatment, and
 genotype x nutrient interactions on susceptibility to browsing by
 white-tailed deer, 2) the phytochemical basis for the patterns observed in
 (1), and 3) the effects of genotype, soil nutrients, and their interaction
 on short-term tolerance to deer browsing. 4.Aspen genotypes varied
 markedly in their vernal susceptibility to deer browsing. Genetic
 variation in early season levels of non-structural carbohydrates (sugars),
 protein, and multiple macro- and trace minerals had the strongest
 influence on tree susceptibility to browsing. In contrast, levels of
 phytochemical defenses had minimal effects, although the range of levels
 expressed in this study was small. Soil nutrient availability did not
 significantly influence deer preference. 5.The extent of browsing affected
 post-browse tolerance across genotypes. Soil nutrient treatment had little
 differential effect on tolerance, and, for the most part, genotypes did
 not display differential tolerance to browsing, regardless of which soil
 nutrient treatment they experienced. 6.Synthesis: Genetic variation for
 susceptibility to browsing indicates that ungulate browsers have the
 potential to be agents of selection in aspen populations. In contrast with
 previous studies in aspen highlighting the importance of phytochemical
 defenses in shaping preferences of browsing mammals, our results indicate
 that the nutritional composition of foliage (sugars, protein, and mineral
 concentrations) can have sizable effects on preference. The observed lack
 of influence of soil nutrient availability on tree browsing tolerance
 contrasts with predictions of the limiting resource model, the prevailing
 model for plant tolerance.
description: ToleranceTolerance dataBrowsing measures and secondary compoundsBrowsing and secondary compoundsBrowsing measures and Secondary compounds.xlsxMineral AnalysesMineral analyses
DOI: 10.5061/dryad.m247bg66
title: Data from: Imprints from genetic drift and mutation imply relative divergence times across marine transition zones in a pan-European small pelagic fish (Sprattus sprattus)

description: Geographic distributions of most temperate marine fishes are affected by
 post-glacial recolonisation events which have left complex genetic
 imprints on populations of marine species. This study investigated
 population structure and demographic history of European sprat (Sprattus
 sprattus L.) by combining inference from both mtDNA and microsatellite
 genetic markers throughout the species distribution. We compared effects
 from genetic drift and mutation for both genetic markers in shaping
 genetic differentiation across four transition zones. Microsatellite
 markers revealed significant isolation by distance and a complex
 population structure across the species' distribution (overall θST =
 0.038, p &lt; 0.01). Across transition zones markers indicated larger
 effects of genetic drift over mutations in the northern distribution of
 sprat contrasting a stronger relative impact of mutation in the species
 southern distribution in the Mediterranean region. These results were
 interpreted to reflect more recent divergence times between northern
 populations in accordance with previous findings. This study demonstrates
 the usefulness of comparing inference from different markers and
 estimators of divergence for phylogeographic and population genetic
 studies in species with weak genetic structure, as is the case in many
 marine species.
description: Limborg et al.
 2012_Sprattus sprattus_microsatellite dataMicrosatellite data for
 eight loci and 17 samples of Sprattus sprattus.
DOI: 10.5061/dryad.hm756
title: Data from: CRISPR-induced null alleles show that Frost protects Drosophila melanogaster reproduction after cold exposure

description: The ability to survive and reproduce after cold exposure is important in
 all kingdoms of life. However, even in a sophisticated genetic model
 system like Drosophila melanogaster, few genes have been identified as
 functioning in cold tolerance. The accumulation of the Frost (Fst) gene
 transcript increases after cold exposure, making it a good candidate for a
 gene that has a role in cold tolerance. However, despite extensive RNAi
 knockdown analysis, no role in cold tolerance has been assigned to Fst.
 CRISPR is an effective technique for completely knocking down genes, and
 less likely to produce off-target effects than GAL4-UAS RNAi systems. We
 have used CRISPR-mediated homologous recombination to generate Fst null
 alleles, and these Fst alleles uncovered a requirement for FST protein in
 maintaining female fecundity following cold exposure. However, FST does
 not have a direct role in survival following cold exposure. FST mRNA
 accumulates in the Malpighian tubules, and the FST protein is a highly
 disordered protein with a putative signal peptide for export from the
 cell. Future work is needed to determine whether FST is exported from the
 Malpighian tubules and directly interacts with female reproductive tissues
 post-cold exposure, or if it is required for other repair/recovery
 functions that indirectly alter energy allocation to reproduction.
description: Quantitative Data
 ResubmissionRaw data for Fat
 CRISPR-induced alleles.QuantitativeData
 Resubmission.xlsx
DOI: 10.15468/dl.k97evb
title: Occurrence Download

description: A dataset containing 199451 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "GadmGid is USA.26_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sialia sialis",
 "Year 2010-2025"
 ]
}

 The dataset includes 199451 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000737-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.667g2
title: Data from: Do ecological niche models accurately identify climatic determinants of species ranges?

description: Defining species’ niches is central to understanding their distributions
 and is thus fundamental to basic ecology and climate change projections.
 Ecological niche models (ENMs) are a key component of making accurate
 projections and include descriptions of the niche in terms of both
 response curves and rankings of variable importance. In this study, we
 evaluate Maxent’s ranking of environmental variables based on their
 importance in delimiting species’ range boundaries by asking whether these
 same variables also govern annual recruitment based on long-term
 demographic studies. We found that Maxent-based assessments of variable
 importance in setting range boundaries in the California tiger salamander
 (Ambystoma californiense; CTS) correlate very well with how important
 those variables are in governing ongoing recruitment of CTS at the
 population level. This strong correlation suggests that Maxent’s ranking
 of variable importance captures biologically realistic assessments of
 factors governing population persistence. However, this result holds only
 when Maxent models are built using best-practice procedures and variables
 are ranked based on permutation importance. Our study highlights the need
 for building high-quality niche models and provides encouraging evidence
 that when such models are built, they can reflect important aspects of a
 species’ ecology.
description: LocalitiesList of 1627 localities used to generate the Maxent models in "Do ecological niche models accurately identify climatic determinants of species ranges?" Provided data include the longitude and latitude for each locality and bioclimatic variables ('bio1' to 'bio19'), as extracted from the 'WorldClim' database (for definitions see: http://www.worldclim.org/bioclim). Further information about WorldClim at Hijmans, R.J., S.E. Cameron, J.L. Parra, P.G. Jones and A. Jarvis, 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25: 1965-1978. http://dx.doi.org/10.1002/joc.1276
DOI: 10.5061/dryad.sm4tj6t
title: Data from: NMDA receptor antagonists and pain relief: a meta-analysis of experimental trials

description: OBJECTIVES: We conducted a meta-analysis of controlled trials that used
 experimental models of acute pain and hyperalgesia to examine the
 analgesic effects of N-methyl-D-aspartate receptor (NMDAR) antagonists.
 METHODS: Six major databases were systematically searched (to 03/2018) for
 studies using human evoked pain models to compare NMDAR antagonists with
 no-intervention controls. Pain outcome data were analyzed with
 random-effects meta-analysis. RESULTS: Searches identified 70 eligible
 trials (N=1069). Meta-analysis found that low-dose ketamine (&lt;1
 mg/kg) produced a decrease in the size of hyperalgesic area (Standardized
 Mean Difference=0.54, CI95[0.34, 0.74], p&lt;.001), and a 1.2-point
 decrease (CI95[0.88, 1.44], p&lt;.001) in pain ratings from 4.6 to 3.4
 on a 0-10 scale (a 26% reduction). Similar analgesia was observed for
 acute and hyperalgesic models and was constant across the dosing range
 (0.03-1.00 mg/kg). Moderate-high variability in effect size was observed
 and mild side effects (e.g. sedation, sensory disturbance) were common. No
 effects of dextromethorphan were found. CONCLUSIONS: Findings provide
 robust evidence for analgesic and anti-hyperalgesic effects of ketamine,
 supporting its utility for acute and chronic pain management. However,
 pain relief was modest, suggesting ketamine may potentially be most useful
 when opioids are contraindicated, rapid analgesia is required or for pain
 resistant to conventional medication.
description: Table 1. Characteristics
 of included studiesAppendix 2. Search
 strategyAppendix 3. Study
 validity criteriaAppendix 4. Reference
 list of studies included in meta-analysis