cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1d0f3
title: Data from: Impact of nutrition and salinity changes on biological performances of green and white sturgeon

description: Green and white sturgeon are species of high conservational and economic
 interest, particularly in the San Francisco Bay Delta (SFBD) for which
 significant climate change-derived alterations in salinity and nutritional
 patterns are forecasted. Although there is paucity of information, it is
 critical to test the network of biological responses underlying the
 capacity of animals to tolerate current environmental changes. Through
 nutrition and salinity challenges, climate change will likely have more
 physiological effect on young sturgeon stages, which in turn may affect
 growth performance. In this study, the two species were challenged in a
 multiple-factor experimental setting, first to levels of feeding rate, and
 then to salinity levels for different time periods. Data analysis included
 generalized additive models to select predictors of growth performance
 (measured by condition factor) among the environmental stressors
 considered and a suite of physiological variables. Using structural
 equation modeling, a path diagram is proposed to quantify the main
 linkages among nutrition status, salinity, osmoregulation variables, and
 growth performances. Three major trends were anticipated for the growth
 performance of green and white sturgeon in the juvenile stage in the SFBD:
 (i) a decrease in prey abundance will be highly detrimental for the growth
 of both species; (ii) an acute increase in salinity within the limits
 studied can be tolerated by both species but possibly the energy spent in
 osmoregulation may affect green sturgeon growth within the time window
 assessed; (iii) the mechanism of synergistic effects of nutrition and
 salinity changes will be more complex in green sturgeon, with condition
 factor responding nonlinearly to interactions of salinity and nutrition
 status or time of salinity exposure. Green sturgeon merits special
 scientific attention and conservation effort to offset the effects of feed
 restriction and salinity as key environmental stressors in the SFBD.
description: Data for the analysis of
 Biological responses to nutritional changes2014_Vaz_etal_NutritionData.csvData for the analysis of Predictors of growth performance in sturgeons faced with nutritional and salinity changes2014_Vaz_etal_SalinityData.csv
DOI: 10.5061/dryad.84n16hg
title: Data from: Material composition of the mouthpart cuticle in a damselfly larva (Insecta: Odonata) and its biomechanical significance

description: Odonata larvae are key predators in their habitats. They catch prey with a
 unique and highly efficient apparatus, the prehensile mask. The mandibles
 and maxillae, however, play the lead in handling and crushing the food.
 The material composition of the cuticle in the biomechanical system of the
 larval mouthparts has not been studied so far. We used confocal laser
 scanning microscopy (CLSM) to detect material gradients in the cuticle by
 differences in autofluorescence. Our results show variations of materials
 in different areas of the mouthparts: (i) resilin-dominated pads within
 the membranous transition between the labrum and the anteclypeus, which
 support mobility and might provide shock absorption, an adaptation against
 mechanical damage; (ii) high degrees of sclerotisation in the incisivi of
 the mandibles, where high forces occur when crushing the prey's body
 wall. The interaction of the cuticle geometry, the material composition,
 and the related musculature determines the complex concerted movements of
 the mouthparts. The material composition influences the strength, mobility
 and durability of the cuticular components of the mouthparts. Applying
 CLSM for extracting information about material composition and material
 properties of arthropod cuticles will considerably help improve FEM
 studies.
description: LSM raw-data files from
 CLSM - ZIP1Zip-folder containg LSM
 raw-data files from CLSM, please use ZEN software (Carl Zeiss Microscopy
 GmbH; www.zeiss.de/mikroskopie) to open and visualizing the
 data.Buesse&Gorb-CLSM_Data.zip
DOI: 10.5061/dryad.vn52f
title: Data from: Inferring node dates from tip dates in fossil Canidae: the importance of tree priors

description: Tip-dating methods are becoming popular alternatives to traditional node
 calibration approaches for building time-scaled phylogenetic trees, but
 questions remain about their application to empirical datasets. We
 compared the performance of the most popular methods against a dated tree
 of fossil Canidae derived from previously published monographs. Using a
 canid morphology dataset, we performed tip-dating using BEAST v. 2.1.3 and
 MrBayes v. 3.2.5. We find that for key nodes (Canis, approx. 3.2 Ma,
 Caninae approx. 11.7 Ma) a non-mechanistic model using a uniform tree
 prior produces estimates that are unrealistically old (27.5, 38.9 Ma).
 Mechanistic models (incorporating lineage birth, death and sampling rates)
 estimate ages that are closely in line with prior research. We provide a
 discussion of these two families of models (mechanistic versus
 non-mechanistic) and their applicability to fossil datasets.
description: canidae_traceLogs_ALL_v2Trace plots of key variables for all 60 analyses.canidae_treeLogs_ALL_v2Plots of the MCC trees for all 60 analyses.expert_vs_estimated_node_agesLinear regressions showing the correlation between the expert tree and estimated node ages, for nodes shared between the expert tree and estimated trees. Caveats for these regressions are discussed in Supplemental Text.Canidae_expertThe "expert" tree, derived from digitization of the phylogenies of Canidae published in the monographs of Wang and Tedford, using TreeRogue.Table_S2_TipDate_runs_v3Summary of all 60 variant analyses (contains Supplemental Table S2, and some associated notes and file locations).Matzke_Wright_SuppData1A zipfile of all inputs, outputs, and scripts for all analyses. (pt 1/3)Matzke_Wright_SuppData2A zipfile of all inputs, outputs, and scripts for all analyses. (pt 2/3)Matzke_Wright_SuppData3A zipfile of all inputs, outputs, and scripts for all analyses. (pt 3/3)
DOI: 10.6084/m9.figshare.31155205
title: Neural Additive Model Code

description: The study develops a Ground Motion Model (GMM) for the Himalayan region to capture the source, path and site characteristics using the Neural Additive Model (NAM) framework.
DOI: 10.6084/m9.figshare.31155205.v1
title: Neural Additive Model Code

description: The study develops a Ground Motion Model (GMM) for the Himalayan region to capture the source, path and site characteristics using the Neural Additive Model (NAM) framework.
DOI: 10.5061/dryad.bq4t8
title: Data from: PCR-Free enrichment of mitochondrial DNA from human blood and cell lines for high quality next-generation DNA sequencing

description: Recent advances in sequencing technology allow for accurate detection of
 mitochondrial sequence variants, even those in low abundance at
 heteroplasmic sites. Considerable sequencing cost savings can be achieved
 by enriching samples for mitochondrial (relative to nuclear) DNA.
 Reduction in nuclear DNA (nDNA) content can also help to avoid false
 positive variants resulting from nuclear mitochondrial sequences (numts).
 We isolate intact mitochondrial organelles from both human cell lines and
 blood components using two separate methods: a magnetic bead binding
 protocol and differential centrifugation. DNA is extracted and further
 enriched for mitochondrial DNA (mtDNA) by an enzyme digest. Only 1 ng of
 the purified DNA is necessary for library preparation and next generation
 sequence (NGS) analysis. Enrichment methods are assessed and compared
 using mtDNA (versus nDNA) content as a metric, measured by using real-time
 quantitative PCR and NGS read analysis. Among the various strategies
 examined, the optimal is differential centrifugation isolation followed by
 exonuclease digest. This strategy yields &gt;35% mtDNA reads in blood
 and cell lines, which corresponds to hundreds-fold enrichment over
 baseline. The strategy also avoids false variant calls that, as we show,
 can be induced by the long-range PCR approaches that are the current
 standard in enrichment procedures. This optimization procedure allows
 mtDNA enrichment for efficient and accurate massively parallel sequencing,
 enabling NGS from samples with small amounts of starting material. This
 will decrease costs by increasing the number of samples that may be
 multiplexed, ultimately facilitating efforts to better understand
 mitochondria-related diseases.
description: 06_16_15-fastqs.tar.gz_replace06_16_15-fastqs.tar.gz
DOI: 10.5061/dryad.0kn60
title: Data from: A problem of bias and response heterogeneity, in Standing With Giants: A Collection of Public Health Essays in Memoriam to Dr. Elizabeth M. Whelan

description: There is extensive literature on the question, “Does air quality have
 health effects?” For example, Google Scholar gives 199,000 hits for
 (“mortality” and “air pollution”). See Health Effects Institute (2010) and
 editorial by Brauer and Mancini (2014), for example. One paper that
 appeared in 1993 has over 6,000 citations. The vast majority of these
 papers find a positive association between air quality health effects
 (death). A few papers make the case that if potential bias is carefully
 taken into account then there is no association between air quality and
 deaths, e.g. Chay et al. (2003), Enstrom (2005), Janes et al. (2007),
 Greven et al. (2011), Cox et al. (2013). Clearly the weight of evidence is
 for a positive association, but for any particular type of claim,
 logically it takes only one true negative to negate all the positives
 associations with respect to causation for that claim. A real, causative
 claim should always be detected in a well-designed and properly run
 experiment. What are some of the factors that lead to these discordant
 literature results?
description: Pope NEJM
 2009air quality, longevity
 and demographic variables for 211 US cities
DOI: 10.5061/dryad.bc65p
title: Data from: P53 gene discriminates two ecologically divergent sister species of pine voles

description: Genes with relevant roles in the differentiation of closely-related
 species are likely to have diverged simultaneously with the species and
 more accurately reproduce the species tree. The Lusitanian (Microtus
 lusitanicus) and Mediterranean (M. duodecimcostatus) pine voles are two
 recently separated sister species with fossorial lifestyles whose
 different ecological, physiological and morphological phenotypes reflect
 the better adaptation of M. duodecimcostatus to the underground habitat.
 Here we asked whether the differentiation of M. lusitanicus and M.
 duodecimcostatus involved genetic variations within the tumour suppressor
 p53 gene, given its role in stress-associated responses. We performed a
 population-genetic analysis through sequencing of exons and introns of p53
 in individuals from sympatric and allopatric populations of both the
 species in the Iberian Peninsula in which a unidirectional introgression
 of mitochondrial DNA was previously observed. We were able to discriminate
 the two species to a large extent. We show that M. duodecimcostatus is
 composed of one genetically unstructured group of populations sharing a
 P53 protein that carries a mutation in the DNA-binding region not observed
 in M. lusitanicus, raising the possibility that this mutation may have
 been central in the evolutionary history of M. duodecimcostatus. Our
 results provide suggestive evidence for the involvement of a master
 transcription factor in the separation of M. lusitanicus and M.
 duodecimcostatus during Microtus radiation in the Quaternary presumably
 via a differential adaptive role of the novel p53 in M. duodecimcostatus.
description: p53 haplotypes_Quina
 etalSequence information of
 the p53 haplotypes found in Microtus duodecimcostatus and Microtus
 lusitanicus (Quina et al, 2015).Samples Table_Quina
 etalInformation on species,
 sample ID, p53 genotype (with GenBank accession number) and respective
 cytb haplotype if known (with GenBank accession number) is provided for
 each specimen analysed in our study (Quina et al, 2015). Also included are
 sampling locality (country and location) for each specimen analysed and
 the source of published data.
DOI: 10.15468/dl.pefscm
title: Occurrence Download

description: A dataset containing 2435 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Betula platyphylla"
 ]
}

 The dataset includes 2435 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001153-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8rq18
title: Data from: Socially cued seminal fluid gene expression mediates responses in ejaculate quality to sperm competition risk

description: There is considerable evidence that males will increase the number of
 sperm ejaculated in response to sperm competition risk. However, whether
 they have the capacity to adjust seminal fluid components of the ejaculate
 has received less attention. Male crickets (Teleogryllus oceanicus) have
 been shown to adjust the viability of sperm in their ejaculate in response
 to sperm competition risk. Here we show that socially mediated plasticity
 in sperm viability is probably due, at least in part, to male adjustments
 in the protein composition of the seminal fluid. Seven seminal fluid
 protein genes were found to have an increased expression in males exposed
 to rival calls. Increased expression of these genes was correlated with
 increased sperm viability in whole ejaculates, and gene knockdown
 confirmed that at least one of these proteins promotes sperm viability.
 Our results lend support for recent theoretical models that predict
 complex responses in male allocation to seminal fluid composition in
 response to sperm competition risk.
description: Data from: Socially cued
 seminal fluid gene expression mediates responses in ejaculate quality to
 sperm competition riskGene expression data for
 11 seminal fluid proteins in males exposed to rival song or reared in
 acoustic isolation, and gene expression following RNA
 interferenceSimmonsProcB_sfps.xlsx
DOI: 10.5061/dryad.tq1f7
title: Data from: Shifts in North Sea forage fish productivity and potential fisheries yield

description: Forage fish populations support large scale fisheries and are key
 components of marine ecosystems across the world, linking secondary
 production to higher trophic levels. While climate-induced changes in the
 North Sea zooplankton community are described and documented in
 literature, the associated bottom-up effects and consequences for
 fisheries remain largely unidentified. We investigated the temporal
 development in forage fish productivity and the associated influence on
 fisheries yield of herring, sprat, Norway pout and sandeel in the North
 Sea. Using principal component analysis, we analysed 40 years of
 recruitment success and growth proxies to reveal changes in productivity
 and patterns of synchroneity across stocks (i.e. functional
 complementarity). The relationship between forage fish production and
 Calanus finmarchicus (an indicator of climate change) was also analysed.
 We used a population model to demonstrate how observed shifts in
 productivity affected total forage fish biomass and fisheries yield. The
 productivity of North Sea forage fish changed around 1993 from a higher
 average productivity to lower average productivity. During the higher
 productivity period, stocks displayed a covariance structure indicative of
 functional complementarity. Calanus finmarchicus was positively correlated
 to forage fish recruitment, however, for growth, the direction of the
 response differed between species and time periods. Maximum sustainable
 yield (MSY) and the associated fishing mortality (Fmsy) decreased by
 33%–68% and 26%–64%, respectively, between the higher and lower
 productivity periods. Synthesis and applications. The results demonstrate
 that fisheries reference points for short-lived planktivorous species are
 highly dynamic and respond rapidly to changes in system productivity.
 Furthermore, from an ecosystem-based fisheries management perspective, a
 link between functional complementarity and productivity, indicates that
 ecosystem resilience may decline with productivity. Based on this, we
 advise that system productivity, perhaps monitored as forage fish growth,
 becomes an integral part of management reference points; in both single
 species and ecosystem contexts. However, to retain social license of
 biological advice when fish catch opportunities are reduced, it is crucial
 that shifts in productivity are thoroughly documented and made apparent to
 managers and stakeholders.
description: Caclulating the
 finmarchicus index for Fig3Caclulating the
 finmarchicus index for Fig3Figure3Data used in Fig. 3Length_and_Recruitment_anomaly_data_Fig1_and_Fig2Data used in Figure 1 and 2
DOI: 10.5061/dryad.vj5np
title: Data from: The effects of synthetic estrogen exposure on pre-mating and post-mating episodes of selection in sex-role-reversed Gulf pipefish

description: Environmental estrogens have been shown to affect populations of aquatic
 organisms in devastating ways, including feminization of males,
 alterations in mating behaviors, and disruption of sexual selection.
 Studies have shown 17α-ethinylestradiol (EE2) exposure to induce
 female-like secondary sexual traits in male Gulf pipefish, changing how
 females perceive affected males. We aimed to understand the effects of EE2
 exposure on the sex-role-reversed mating system and the strength of
 selection in Gulf pipefish. We used artificial Gulf pipefish breeding
 aggregations and microsatellite-based parentage analysis to determine
 maternity. We then calculated the opportunity for selection and selection
 differentials on body size for both sexes during three consecutive
 episodes of selection. Exposure to EE2 did not affect the strength of
 selection, likely due to the unusual sex-role-reversed mating system found
 in this species. With respect to multiply mated females, EE2 exposed
 females produced more eggs with higher embryo survivorship than
 non-exposed females. Thus, short-term exposure to low concentrations (2.0
 ng/L) of EE2 in Gulf pipefish enhanced female reproductive success.
 However, higher EE2 concentrations (5.0 ng/L) caused complete reproductive
 failure in Gulf pipefish males. These results call for more work on the
 long-term effects of EE2 exposure in Gulf pipefish in artificial and
 natural populations.
description: Evo Ap Data Sheet
 7.3.13Male and Female data on
 separate worksheets for number of mates, number of eggs and
 offspring/failed eggs.
DOI: 10.5061/dryad.rg0s0
title: Data from: Within-individual plasticity explains age-related decrease in stress response in a short-lived bird

description: A crucial problem for every organism is how to allocate energy between
 competing life-history components. The optimal allocation decision is
 often state-dependent and mediated by hormones. Here, we investigated how
 age, a major state variable affects individuals' hormonal response to
 a standardized stressor: a trait that may reflect allocation between
 self-maintenance and reproduction. We caught free-living house sparrows
 and measured their hormonal (corticosterone) response to capture stress in
 consecutive years. Using a long-term ringing dataset, we determined the
 age of the birds, and we partitioned the variation into within- and
 among-individual age components to investigate the effects of plasticity
 versus selection or gene flow, respectively, on the stress response. We
 found large among-individual variation in the birds' hormone
 profiles, but overall, birds responded less strongly to capture stress as
 they grew older. These results suggest that stress responsiveness is a
 plastic trait that may vary within individuals in an adaptive manner, and
 natural selection may act on the reaction norms producing optimal
 phenotypic response in the actual environment and life-history stage.
description: DataThis file contains the
 data that was used in the analyses. The data was collected in the field in
 the Centre d'Études Biologiques de Chizé, France, between 2005 and
 2007.Analysis
 scriptThis file contains the R
 code for the analyses.FinalPaper_ESM_RScript.R
DOI: 10.5061/dryad.9v216
title: Data from: Heterozygosity and orange colouration are strongly associated in the guppy (Poecilia reticulata)

description: The good-genes-as-heterozygosity hypothesis predicts that more elaborate
 male sexual ornaments are associated with higher levels of heterozygosity.
 Recent theoretical work suggests that such associations are likely to
 arise in finite, structured populations. We investigated the correlation
 between multilocus heterozygosity (MLH), which was estimated using 13
 microsatellite loci, and male coloration in a wild population of guppies
 (Poecilia reticulata), a model species in sexual selection research. We
 found that MLH was a significant predictor of the relative area of orange
 spots, a trait that is subject to strong female preference in this
 species. Neither the relative area of black spots nor the number of black
 or orange spots was significantly correlated with MLH. We found no
 statistical support for local effects (i.e. strong effects of
 heterozygosity at specific markers), which suggests that relative orange
 spots area reflects genome-wide heterozygosity.
description: Casupo_13loci_1popgenotypes of 13 microsatellite loci; Venezuelan guppies; field data; genepop file formatphenotypic_traitsBody length, height, total area of orange spots measured on the right side of the body, multilocus heterozygosity (MLH) in 9 loci in Hardy-weinberg equilibrium and in all 13 loci, for each guppy male. Individuals in the same order as in the genepop file with genotypes.