cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d28j8
title: Data from: Ecophysiological limits to aerobic metabolism in hypoxia determine epibenthic distributions and energy sequestration in the northeast Pacific ocean

description: Expansion of oxygen deficient waters (hypoxia) in the northeast Pacific
 Ocean (NEP) will have marked impacts on marine life. The response of the
 resident communities will be a function of their ecophysiological
 constraints in low oxygen, although this remains untested in the NEP due
 to a lack of integrative studies. Here, we combine in situ surveys and
 lab-based respirometry experiments were conducted on three indicator
 species (spot prawn Pandalus platyceros, slender sole Lyopsetta exilis,
 squat lobster Munida quadrispina) of seasonally hypoxic systems in the NEP
 to test if metabolic constraints determine distributions and energy
 sequestration in a hypoxic setting. These experiments were integrated with
 a global review of critical oxygen levels ( math formula; lower threshold
 of aerobic metabolism) for crustaceans to determine if math formula-based
 hypoxia thresholds are different among ocean basins. Our results show that
 species-specific differences in math formula and standard metabolic rates
 (1) determine the lowest environmental oxygen ([O2]env) at which in situ
 populations occur, (2) result in disproportionate shifts in distributions
 among co-occurring species during summer hypoxia expansion events, and (3)
 characterize shifts in megafaunal community respiration rates due to
 marked spatio-temporal variability in [O2]env. Our results show that math
 formula-based hypoxia thresholds are significantly lower in the East
 Pacific Ocean relative to other major ocean basins, which suggests that
 the physiological response of local fauna to deoxygenation can be
 determined by the natural variability and oxygen exposure in a region. In
 order to establish realistic predictions on the biological consequences of
 marine deoxygenation, we suggest integrating metabolism-based traits to
 calculate hypoxia thresholds for marine ecosystems.
description: CHONe_EF-13_ChuJ_Data_LnO2016Data are from lab-based respirometry experiments designed to measure metabolic rates (oxygen consumption) and critical oxygen tensions (O2crit or Pcrit) for slender sole, spot prawn, and squat lobster. Data was collected as part of a PhD thesis (J.W.F. Chu).
DOI: 10.5061/dryad.dm437
title: Data from: Specific alleles at immune genes, rather than genome-wide heterozygosity, are related to immunity and survival in the critically endangered Attwater's prairie-chicken

description: The negative effects of inbreeding on fitness are serious concerns for
 populations of endangered species. Reduced fitness has been associated
 with lower genome-wide heterozygosity and immune gene diversity in the
 wild; however, it is rare that both types of genetic measures are included
 in the same study. Thus, it is often unclear whether the variation in
 fitness is due to the general effects of inbreeding, immunity-related
 genes or both. Here, we tested whether genome-wide heterozygosity (20 990
 SNPs) and diversity at nine immune genes were better predictors of two
 measures of fitness (immune response and survival) in the endangered
 Attwater's prairie-chicken (Tympanuchus cupido attwateri). We found
 that postrelease survival of captive-bred birds was related to alleles of
 the innate (Toll-like receptors, TLRs) and adaptive (major
 histocompatibility complex, MHC) immune systems, but not to genome-wide
 heterozygosity. Likewise, we found that the immune response at the time of
 release was related to TLR and MHC alleles, and not to genome-wide
 heterozygosity. Overall, this study demonstrates that immune genes may
 serve as important genetic markers when monitoring fitness in inbred
 populations and that in some populations specific functional genes may be
 better predictors of fitness than genome-wide heterozygosity.
description: Read Me file for the
 immune response data fileDescribes variables and
 models used to test the relationship between immune assays and genetic
 variationREAD ME for immune response
 analyses.txtAPC_immune_response_for_DryadImmune response and genetic data for 144 birds. For an explanation see "Read Me File for immune response data file"R code for APC survival analysesR scripts to analyze survival of prairie-chickens (Table 2 in manuscript)APCcoxme input (n=116)Input data file for analysis of survival (using the R scripts in the file "R code for APC survival analyses.txt")APCcoxme_input.csvJohnson_2787XFASTA file of reads from first 454 pyrosequencing runJohnson_2821XFASTA file of reads from second run of 454 pyrosequencingBarcode key for raw 454 readsExcel file with key to Barcodes of individuals in the 454 pyrosequencing filesMHC_I_counts_per_indivSummary of the alleles and reads for each individual at MHC class I (Excel file)MHC_II_counts_per_indivSummary of the alleles and reads for each individual at MHC class II
DOI: 10.5061/dryad.v0nb0
title: Data from: Antiherbivore defenses alter natural selection on plant reproductive traits

description: While many studies demonstrate that herbivores alter selection on plant
 reproductive traits, little is known about whether antiherbivore defenses
 affect selection on these traits. We hypothesized that antiherbivore
 defenses could alter selection on reproductive traits by altering trait
 expression through allocation trade-offs, or by altering interactions with
 mutualists and/or antagonists. To test our hypothesis, we used white
 clover, Trifolium repens, which has a Mendelian polymorphism for the
 production of hydrogen cyanide—a potent antiherbivore defense. We
 conducted a common garden experiment with 185 clonal families of T. repens
 that included cyanogenic and acyanogenic genotypes. We quantified
 resistance to herbivores, and selection on 6 floral traits and phenology
 via male and female fitness. Cyanogenesis reduced herbivory but did not
 alter the expression of reproductive traits through allocation trade-offs.
 However, the presence of cyanogenic defenses altered natural selection on
 petal morphology and the number of flowers within inflorescences via
 female fitness. Herbivory influenced selection on flowers and phenology
 via female fitness independently of cyanogenesis. Our results demonstrate
 that both herbivory and antiherbivore defenses alter natural selection on
 plant reproductive traits. We discuss the significance of these results
 for understanding how antiherbivore defenses interact with herbivores and
 pollinators to shape floral evolution.
description: Defense-Reproduction_DataData collected in the field experiment, and associated metadata, are included in the folder. For convenience, data for individual plants and data for clonal family averages are included as separate datasets.Defense-Reproduction R ScriptR code for all analyses and data figures included in the associated article.2016-03-18-FAE_R_script.R
DOI: 10.5061/dryad.15r51
title: Data from: Profound reversible seasonal changes of individual skull size in a mammal

description: Postnatal size changes in most vertebrates are unidirectional and finite
 once the individual reaches full size. In rare cases, changes of body
 length may occur in response to harsh environmental conditions. Such
 reactionary changes are distinct from seasonal, often anticipatory
 morphological changes, such as the reversible size change of some adult
 bird brains. A unique pattern of profound anatomical change known as
 Dehnel’s phenomenon has been described for the body, skull and brain size
 of red-toothed shrews and some mustelids. The seasonal 20% decrease and
 15% re-growth of the most common proxy, braincase height, were documented
 at population level from extracted skulls post-mortem. Quantifying
 intra-individual change had so far been methodologically prohibitive.
 Here, we followed the intra-individual change in skull size and body mass
 throughout the full cycle in wild recaptured shrews (Sorex araneus). Using
 X-ray images we showed that individuals decreased the size of their
 braincases in anticipation of winter by an average of 15.3%. Braincases
 then partially regrew in spring by 9.3%. Body mass decreased by 17.6% and
 then dramatically increased by 83.4% in spring. Thus, we demonstrate that
 the dramatic changes incurred by Dehnel’s phenomenon occur in the
 individual’s bone and other tissues.
description: Skull measurements from
 X-ray images in common shrewsMeasurements in absolute
 values (mm) of braincase height, skull length, braincase width and tooth
 row and corrected by tooth row (cor) from individual (id) shrews
 captured/recaptured at different times (date) along their
 lifespan.xray_data.xlsxSkull measurements for measurement errorRepeated skull measurements from X-ray images on 10 individuals used to calculate the technical measurement errorTechnical_measurement_error.xlsx
DOI: 10.5061/dryad.dg6jk
title: Data from: Ecological influences and morphological correlates of resting and maximal metabolic rates across teleost fish species

description: Rates of aerobic metabolism vary considerably across evolutionary
 lineages, but little is known about the proximate and ultimate factors
 that generate and maintain this variability. Using data for 131 teleost
 fish species, we performed a large-scale phylogenetic comparative analysis
 of how interspecific variation in resting and maximum metabolic rates (RMR
 and MMR, respectively) is related to several ecological and morphological
 variables. Mass- and temperature-adjusted RMR and MMR are highly
 correlated along a continuum spanning a 30- to 40-fold range. Phylogenetic
 generalized least squares models suggest RMR and MMR are higher in pelagic
 species and that species with higher trophic levels exhibit elevated MMR.
 This variation is mirrored at various levels of structural organization:
 gill surface area, muscle protein content, and caudal fin aspect ratio (a
 proxy for activity) are positively related with aerobic capacity. Muscle
 protein content and caudal fin aspect ratio are also positively correlated
 with RMR. Hypoxia-tolerant lineages fall at the lower end of the metabolic
 continuum. Different ecological lifestyles are associated with contrasting
 levels of aerobic capacity, possibly reflecting the interplay between
 selection for increased locomotor performance on one hand and tolerance to
 low resource availability, particularly oxygen, on the other. These
 results support the aerobic capacity model of the evolution of endothermy,
 suggesting elevated body temperatures evolved as correlated responses to
 selection for high activity levels.
description: Killen et al Am Nat
 Table S1Data used for the
 analysis by Killen et al. 2016, American Naturalist.Fish_PhylogenyPhylogeny used for the analysis by Killen et al. 2016, American Naturalist.
DOI: 10.5061/dryad.r8d10
title: Data from: Patterns and predictors of β-diversity in the fragmented Brazilian Atlantic forest: a multiscale analysis of forest specialist and generalist birds

description: 1. Biodiversity maintenance in human-altered landscapes (HALs) depends on
 the species turnover among localities, but the patterns and determinants
 of β-diversity in HALs are poorly known. In fact, declines, increases, and
 neutral shifts in β-diversity have all been documented, depending on the
 landscape, ecological group and spatial scale of analysis. 2. We shed some
 light on this controversy by assessing the patterns and predictors of bird
 β-diversity across multiple spatial scales considering forest specialist
 and habitat generalist bird assemblages. 3. We surveyed birds from 144
 point counts in 36 different forest sites across two landscapes with
 different amount of forest cover in the Brazilian Atlantic forest. We
 analysed β-diversity among points, among sites, and between landscapes
 with multiplicative diversity partitioning of Hill numbers. We tested
 whether β-diversity among points was related to within-site variations in
 vegetation structure, and if β-diversity among sites was related to site
 location and/or to differences among sites in vegetation structure and
 landscape composition (i.e. percent forest and pasture cover surrounding
 each site). 4. β-diversity between landscapes was lower than among sites
 and among points in both bird assemblages. In forest specialist birds, the
 landscape with less forest cover showed the highest β-diversity among
 sites (bird differentiation among sites), but generalist birds showed the
 opposite pattern. At the local scale, however, the less forested landscape
 showed the lowest β-diversity among points (bird homogenisation within
 sites), independently of the bird assemblage. β-diversity among points was
 weakly related to vegetation structure, but higher β-diversity values were
 recorded among sites that were more isolated from each other, and among
 sites with higher differences in landscape composition, particularly in
 the less forested landscape. 5. Our findings indicate that patterns of
 bird β-diversity vary across scales and are strongly related to landscape
 composition. Bird assemblages are shaped by both environmental filtering
 and dispersal limitation, particularly in less forested landscapes.
 Conservation and management strategies should therefore prevent
 deforestation in this biodiversity hotspot.
description: Data_Morante-Filho_etal_JAEBird communities and environmental data sampled in 36 forest sites in two landscapes in Brazilian Atlantic Forest.
DOI: 10.13144/lil-1065
title: Emploi du temps (version pour Eurostat) - 2009-2010

description: L'enquête Emploi du temps de 2009-2010 est la 5ème enquête d'une série initiée en 1967. Elle a pour objectif de collecter des données sur la façon dont les individus organisent leur temps. Elle est complétée, en France métropolitaine, par un module "Décisions dans le couple" consacré aux modes de décision au sein du ménage. L'enquête permet des analyses quantifiées des comportements dans le domaine des activités de la vie quotidienne, globalement (heures consacrées au travail professionnel ou domestique), ou pour des populations particulières (emplois du temps des actifs occupés, des chômeurs, des femmes au foyer, des personnes âgées, des étudiants etc.). Elle permet d'aborder des problèmes très généraux : aménagement du temps et de l'espace, organisation familiale (modes de garde des enfants ...), rapports entre loisirs et famille, loisirs et travail ou de traiter de questions plus spécifiques : rôle de la télévision, équipements ménagers et gain de temps, production domestique, impact de la réduction du temps de travail, etc. Suite à la publication du rapport de la Commission "Stiglitz-Sen-Fitoussi" (Commission sur la Mesure de la Performance Économique et du Progrès Social), un sur-échantillon a été ajouté avec pour objectif de mesurer le bien-être subjectif général et d'apprécier le caractère agréable des moments de la vie quotidienne. A la demande de la DEPP (Ministère de l'éducation nationale), l'enquête permet aussi d'appréhender le temps de travail des enseignants du primaire et du secondaire. Le module "décisions dans le couple" concerne des couples sélectionnés en fonction de leur activité professionnelle et de la composition du ménage. Ce module s'intéresse particulièrement aux arrangements financiers, à la gestion quotidienne dans la famille, au partage des responsabilités et des décisions, à l'indépendance dans les usages de l'argent et à l'organisation bancaire du couple. Comme les enquêtes précédentes, celle de 2009-2010 est une enquête à vagues, la collecte s'effectuant sur une durée d'un an. L'enquête a lieu en 6 vagues de 8 semaines. 12 000 ménages ont répondu à l'enquête Emploi du temps ; et 2000 couples au module complémentaire "Décisions dans le couple". La version pour Eurostat comprend 3 fichiers de données.
DOI: 10.18160/b31k-yfxq
title: Biogenic in-situ observations (L2), Munich Soil sensors, 2023-04-17–2024-12-31

description: Soil temperature and water content data from Munich, Germany. Details of the measurements, file contents etc are described in ICOS Cities deliverable report D3.13.
DOI: 10.5061/dryad.815rj
title: Data from: Unidirectional diploid–tetraploid introgression among British birch trees with shifting ranges shown by restriction site-associated markers

description: Hybridization may lead to introgression of genes among species.
 Introgression may be bidirectional or unidirectional, depending on factors
 such as the demography of the hybridizing species, or the nature of
 reproductive barriers between them. Previous microsatellite studies
 suggested bidirectional introgression between diploid Betula nana (dwarf
 birch) and tetraploid B. pubescens (downy birch) and also between B.
 pubescens and diploid B. pendula (silver birch) in Britain. Here, we
 analyse introgression among these species using 51 237 variants in
 restriction site-associated (RAD) markers in 194 individuals, called with
 allele dosages in the tetraploids. In contrast to the microsatellite
 study, we found unidirectional introgression into B. pubescens from both
 of the diploid species. This pattern fits better with the expected nature
 of the reproductive barrier between diploids and tetraploids. As in the
 microsatellite study, introgression into B. pubescens showed clear clines
 with increasing introgression from B. nana in the north and from B.
 pendula in the south. Unlike B. pendula alleles, introgression of B. nana
 alleles was found far from the current area of sympatry or allopatry
 between B. nana and B. pubescens. This pattern fits a shifting zone of
 hybridization due to Holocene reduction in the range of B. nana and
 expansion in the range of B. pubescens.
description: Genotyping method (mixed
 ploidy dataset)This script allows the
 genotyping of a mixed ploidy data set (including polyploids). It is based
 on read counts and average base quality. The algorithm calculates the most
 likely variant configuration at each locus using a log-likelihood
 model.genotyping.RBeta-binomial model for allelic ratiosFunction to model number of reads per SNP allele as a mixture of beta-binomial distributions. The data are censored to be between two cutoff values.betabinomial.RPlotting of figuresCollection of scripts used for plotting figures in the present study.plotting.RAnalyses used in present studyCollection of scripts used for analyses in the present study.analyses.RBetula RAD reference sequenceThese sequences were concatenated and used as a reference for the mapping of the 213 RAD individuals.Betula_RAD_reference.fasta.gzInput file for STRUCTURE analysisThis file was used to analyse the RAD data in STRUCTURE. The first row contains loci names, the first column individual names, the second column population identifiers, missing data is encoded as "-9", and the ploidy is four.structure_input.txtInput file for PCA etc.This R object is the basis of many of the analyses performed in the present study. E.g. the Principal Component Analysis and the calculation of Fst values.data_80p_genlight.rdata
DOI: 10.5061/dryad.q0h473vr
title: Data from: Latitudinal patterns in rodent metabolic flexibility

description: Macrophysiology is defined as the study of variation in physiological
 traits--including physiological trait flexibility--over large geographical
 and temporal scales, and the ecological implications of this variation. A
 classic example of a macrophysiological trend is the one emerging from the
 climatic variability hypothesis (CVH), which states that as the range of
 climatic fluctuation experienced by terrestrial animals increases with
 latitude, individuals at higher latitudes should be more plastic than
 individuals inhabiting lower latitudes. In this context, we evaluate the
 correlation between absolute metabolic scope during cold exposure (an
 instantaneous measure of metabolic flexibility) and different geographic
 and climatic variables for 48 rodent species. Conventional and
 phylogenetic informed analyses indicated a positive correlation between
 metabolic scope and geographic latitude. These findings, together with
 previous reports on latitudinal pattern in phenotypic flexibility, suggest
 that an increase in physiological flexibility with latitude may be hold
 for many phenotypic traits.
description: Naya_DatasetBasal and maximum metabolic rates for rodents
DOI: 10.5061/dryad.940m2
title: Data from: Invasive cane toads are unique in shape but overlap in ecological niche compared to Australian native frogs

description: Invasive species are an important issue worldwide but predicting
 invasiveness, and the underlying mechanisms that cause it, is difficult.
 There are several primary hypotheses to explain invasion success. Two main
 hypothesis based on niche spaces stand out as alternative, although not
 exclusive. The empty niche hypothesis states that invaders occupy a vacant
 niche space in the recipient community, and the niche competition
 hypothesis states that invaders overlap with native species in niche
 space. Studies on trait similarity/dissimilarity between the invader and
 native species can provide information on their niche overlap. Here, we
 use the highly invasive and well-studied cane toad (Rhinella marina) to
 test these two hypotheses in Australia, and assess its degree of overlap
 with native species in several niche dimensions. We compare extensive
 morphological and environmental data of this successful invader to 235
 species (97%) of native Australian frogs. Our study is the first to
 document the significant morphological differences between the invasive
 cane toad and a continent-wide frog radiation: despite significant
 environmental overlap, cane toads were distinct in body size and shape
 from most Australian frog species, suggesting that in addition to their
 previously documented phenotypic plasticity and wide environmental and
 trophic niche breadth, their unique shape also may have contributed to
 their success as an invasive species in Australia. Thus, the invasive
 success of cane toads in Australia may be explained through them
 successfully colonizing an empty niche among Australian anurans. Our
 results support that the cane toad's distinct morphology may have
 played a unique role in the invasiveness of this species in Australia,
 which coupled with a broad environmental niche breadth, would have boosted
 their ability to expand their distribution across Australia. We also
 propose RLLR (Relative limb length ratio) as a potentially useful measure
 of identifying morphological niche uniqueness and a potential measure of
 invasiveness potential in anuran amphibians.
description: Phylo_morpho_dataset_Vidal-Garcia_Keogh_EcolEvol2017Means_raw_morpho_dataset_Vidal-Garcia_Keogh_EcolEvol2017