cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.50kn1p0
title: Data from: Landscape context and farm uptake limit effects of bird conservation in the Swedish Volunteer & Farmer Alliance

description: 1. In Europe, agri-environmental schemes (AES) have been unsuccessful in
 halting biodiversity declines to any great extent. Two particular
 shortcomings of AES include the low farm uptake and the modest efficacy of
 many AES options. Partly in response to these shortcomings, initiatives
 encouraging farmers to take an active role in biodiversity conservation
 have gained in popularity. However, almost no evaluations of such
 initiatives exist. 2. We evaluated uptake of conservation advice on farms
 in the Swedish Volunteer & Farmer Alliance, a BirdLife
 Sweden-coordinated project aimed at farmland bird conservation, and the
 response of farmland birds to those actions using farm-level survey data,
 in a before-after implementation assessment. 3. Uptake was higher for
 unsubsidised (i.e. non-AES) measures than for AES options, and depended on
 farmers’ interest in nature, farm size (higher uptake on larger farms) and
 production type (higher on organic farms). 4. In general, abundances of
 non-crop nesting and field-nesting bird species declined between inventory
 years (median interval 3 years). Decreases were more marked in
 agriculturally marginal regions than in more arable-dominated regions, and
 declines were stronger on organic than conventional farms. 5. Negative
 abundance trends among non-crop nesting species were reduced by an
 increasing number of conservation measures at the farm, but only in the
 more arable-dominated landscapes. Changes in other non-crop species and in
 field-nesting species did not significantly relate to implemented
 measures, but the power to detect such effects was generally small due to
 the small sample size of high-uptake farms as well as high inter-farm
 variability. 6. Implications: Our results suggest that Volunteer Farmer
 Alliances and the addition of unsubsidised measures may be successful in
 changing the local number of non-crop nesting farmland birds at the farm
 level, and especially so in intensively managed agricultural landscapes.
 Thus, unsubsidised measures can be a useful addition to the set of
 agri-environment tools, although their effects on breeding bird numbers
 are (as with AES) dependent on landscape context, as well as on ensuring
 high on-farm uptake of different interventions.
description: Complete data
 setData on farm-level
 structural variables, farmland bird inventory data, and uptake of
 conservation measures, collected through the Swedish Volunteer &
 Farmer Alliance. A Readme, including explanations for each column, is
 found in the second tab of the xlsx-file.Josefssonetal_svfa-data.xlsx
DOI: 10.5061/dryad.2v54j
title: Data from: Genetic differentiation associated with host plants and geography among six widespread species of South American Blepharoneura fruit flies (Tephritidae)

description: Tropical herbivorous insects are astonishingly diverse and many are highly
 host-specific. Much evidence suggests that herbivorous insect diversity is
 a function of host-plant diversity; yet, the diversity of some lineages
 exceeds the diversity of plants. Although most species of herbivorous
 fruit flies in the Neotropical genus Blepharoneura are strongly
 host-specific (they deposit their eggs in a single host plant species and
 flower sex), some species are collected from multiple hosts or flowers and
 these may represent examples of lineages that are diversifying via changes
 in host use. Here, we investigate patterns of diversification within six
 geographically widespread Blepharoneura species that have been collected
 and reared from at least two host-plant species or host-plant parts. We
 use microsatellites to: 1) test for evidence of local genetic
 differentiation associated with different sympatric hosts (different plant
 species or flower sexes); and 2) examine geographic patterns of genetic
 differentiation across multiple South American collection sites. In four
 of the six fly species, we find evidence of local genetic differences
 between flies collected from different hosts. All six species show
 evidence of geographic structure, with consistent differences between
 flies collected in the Guianan Shield and flies collected in Amazonia.
 Continent-wide analyses reveal - in all but one instance - that
 genetically differentiated flies collected in sympatry from different host
 species or different sex flowers are not one another's closest
 relatives, indicating that genetic differences often arise in allopatry
 before, or at least coincident with, the evolution of novel host use.
description: Raw microsatellite
 genotype scores for 6 Blepharoneura speciesThis file contains raw
 microsatellite genotype data for six species of Blepharoneura fly. The
 first column of each sheet contains specimen names corresponding to those
 in mtCOI trees in the supplemental materials of the paper. The second
 column of each sheet contains plant tissue information (fGA = female
 Gurania acuminata; mGA = male G. acuminata; fGS = female Gurania
 spinulosa; mGS = male G. spinulosa). The second column also contains
 collection site information, the codes for which may be found in the main
 paper and its supplement. Numbers in the first row refer to microsatellite
 locus names, with the diploid genotypes for each locus located in the
 column below each name as well as in the column to the right of the locus
 name. Genotypes are given as fragment lengths. A score of "-9"
 indicates missing data.Ottens et al
 Dryad.xlsx
DOI: 10.5061/dryad.282f6
title: Data from: The effect of diet and time after bacterial infection on fecundity, resistance, and tolerance in Drosophila melanogaster

description: Mounting and maintaining an effective immune response in the face of
 infection can be costly. The outcome of infection depends on two host
 immune strategies: resistance and tolerance. Resistance limits pathogen
 load, while tolerance reduces the fitness impact of an infection. While
 resistance strategies are well studied, tolerance has received less
 attention, but is now considered to play a vital role in host–pathogen
 interactions in animals. A major challenge in ecoimmunology is to
 understand how some hosts maintain their fitness when infected while
 others succumb to infection, as well as how extrinsic, environmental
 factors, such as diet, affect defense. We tested whether dietary
 restriction through yeast (protein) limitation affects resistance,
 tolerance, and fecundity in Drosophila melanogaster. We predicted that
 protein restriction would reveal costs of infection. Because infectious
 diseases are not always lethal, we tested resistance and tolerance using
 two bacteria with low lethality: Escherichia coli and Lactococcus lactis.
 We then assayed fecundity and characterized bacterial infection pathology
 in individual flies at two acute phase time points after infection. As
 expected, our four fecundity measures all showed a negative effect of a
 low-protein diet, but contrary to predictions, diet did not affect
 resistance to either bacteria species. We found evidence for diet-induced
 and time-dependent variation in host tolerance to E. coli, but not to L.
 lactis. Furthermore, the two bacteria species exhibited remarkably
 different infection profiles, and persisted within the flies for at least
 7 days postinfection. Our results show that acute phase infections do not
 necessarily lead to fecundity costs despite high bacterial loads. The
 influence of intrinsic variables such as genotype are the prevailing
 factors that have been studied in relation to variation in host tolerance,
 but here we show that extrinsic factors should also be considered for
 their role in influencing tolerance strategies.
description: Models 1a,b & 2,
 Fig.2Data file corresponding
 to Model numbers 1 a,b and 2, Figure 2, Table 1.Models_1ab_2.csvModel 3a, Fig. 3aData corresponding to Model 3a, Figure 3a and Table 2.Model3a_Fig3a.csvModel 3b, Fig. 3bData corresponding to Model 3b, Figure 3b and Table 2.Model3b_Fig3b.csvModel 4a, Fig. 4aData corresponding to Model 4a, Figure 4a and Table 3.Model4a_Fig4a.csvModel 4b, Fig. 4bData corresponding to Model 4b, Figure 4b and Table 3Model4b_Fig4b.csvModel 5, Fig. 5Data corresponding to Model 5, Figure 5 and Table 4.Model5_Fig5.csvModel 6a, Fig. 3Data corresponding to Model 6a, Figure 3 and Table 4.Model6a_Fig3.csvModel 6b, Fig. 3Data corresponding to Model 6b, Figure 3, Table 4.Model6b_Fig3.csvFig. S1, S2 & Appendix S1Data corresponding to Figures S1 & S2 and mating data in Appendix S1.FigS1_S2_AppS1.csvFig. S3Survival data corresponding to Fig. S3.FigS3.csv
DOI: 10.5061/dryad.d52n0
title: Data from: Evaluation of the bladder stimulation technique to collect midstream urine in infants in a pediatric emergency department

description: Objective: Midstream clean-catch urine is an accepted method to diagnose
 urinary tract infection but is impracticable in infants before potty
 training. We tested the bladder stimulation technique to obtain a
 clean-catch urine sample in infants. Materials and methods: We included
 142 infants under walking age who required a urine sample in a cross-
 sectional study carried out during a 3-months period, from September to
 November 2014, in the emergency department of the University Children’s
 Hospital of Nice (France). A technique based on bladder stimulation and
 lumbar stimulation maneuvers, with at least two attempts, was tested by
 four trained physicians. The success rate and time to obtain urine sample
 within 3 minutes were evaluated. Discomfort (EVENDOL score ≥4/15) was
 measured. We estimated the risk factors in the failure of the technique.
 Chi-square test or Fisher’s exact test were used to compare frequencies.
 T-test and Wilcoxon test were used to compare quantitative data according
 to the normality of the distribution. Risk factors for failure of the
 technique were evaluated using a multivariate logistic regression model.
 Results: We obtained midstream clean-catch urine in 55.6% of infants with
 a median time of 52.0 s (10.0; 110.0). The success rate decreased with age
 from 88.9% (newborn) to 28.6% (&gt;1 y) (p=0.0001) and with weight,
 from 85.7% (&lt;4kg) to 28.6% (&gt;10kg) (p=0.0004). The success
 rate was 60.8% for infants without discomfort (p&lt;0.0001). Heavy
 weight and discomfort were associated with failure, with adjusted ORs of
 1.47 [1.04-2.31] and 6.65 [2.85-15.54], respectively. Conclusion: Bladder
 stimulation seems to be efficient in obtaining midstream urine with a
 moderate success rate in our study sample. This could be an alternative
 technique for infants before potty training but further randomized
 multicenter studies are needed to validate this procedure.
description: Evaluation of the
 bladder stimulation technique in infants (Data)This data set contains
 all data that are statistically readable. No abbreviation. No additional
 user guidance is needed
DOI: 10.5061/dryad.5kv17
title: Data from: Direct and trans-generational effects of male and female gut microbiota in Drosophila melanogaster

description: There is increasing evidence of the far-reaching effects of gut bacteria
 on physiological and behavioural traits, yet the fitness-related
 consequences of changes in the gut bacteria composition of sexually
 interacting individuals remain unknown. To address this question, we
 manipulated the gut microbiota of fruit flies, Drosophila melanogaster, by
 monoinfecting flies with either Acetobacter pomorum (AP) or Lactobacillus
 plantarum (LP). Re-inoculated individuals were paired in all treatment
 combinations. LP-infected males had longer mating duration and induced
 higher short-term offspring production in females compared with
 AP-infected males. Furthermore, females of either re-inoculation state
 mated with AP-infected males were more likely to have zero offspring after
 mating, suggesting a negative effect of AP on male fertility. Finally, we
 found that the effects of male and female gut bacteria interacted to
 modulate their daughters', but not sons' body mass, revealing a
 new trans-generational effect of parental gut microbiota. In conclusion,
 this study shows direct and trans-generational effects of the gut
 microbiota on mating and reproduction.
description: Morimotoetal2016-gutmicrobiota-BehaviouraldataBehavioural data of the manipulation of the gut bacteria on mating and reproductive parameters. Tab 2 contains the data for the offspring body mass.Morimotoetal2016-gutmicrobiota.xls
DOI: 10.5061/dryad.0vm0s
title: Data from: Do males form social associations based on sexual attractiveness in a fission-fusion fish society?

description: Recent theory predicts that males should choose social environments that
 maximize their relative attractiveness to females by preferentially
 associating with less attractive rivals, so as to enhance their mating
 success. Using the Trinidadian guppy (Poecilia reticulata), a highly
 social species, we tested for non-random social associations among males
 in mixed-sex groups based on two phenotypic traits (body length and
 coloration) that predict relative sexual attractiveness to females and
 sexual (sperm) competitiveness. Based on a well-replicated laboratory
 dichotomous-choice test of social group preference, we could not reject
 the null hypothesis that focal males chose randomly between a mixed-sex
 group that comprised a female and a rival male that was less sexually
 attractive than themselves and another mixed-sex group containing a
 sexually more attractive male. The same conclusion was reached when
 females were absent from the two groups. As might be expected from these
 laboratory findings, free-ranging males in the field were not assorted by
 either body length or colour in mixed-sex shoals. The apparent lack of an
 evolved and expressed preference in wild male guppies from our study
 population to form social associations with other males based on their
 relative sexual attractiveness and competitiveness might be due to the
 fission-fusion dynamics of guppy shoals in nature. Such social dynamics
 likely places constraints on the formation of stable phenotype-based
 social associations among males. This possibility is supported by a
 simulation model which assumes group departure rules based on relative
 body size and coloration in males.
description: Figure 2
 dataExcel data file for
 results depicted in Figure 2 of Auge et al. (2016)
 paper.Figure 3
 dataExcel data file
 supporting the results depicted in Figure 3 of Auge et al. (2016)
 paper.Figure 4
 dataExcel data file
 supporting the results depicted in Figure 4 of Auge et al. (2016)
 paper.Figure 5
 dataExcel data file
 supporting the results depicted in Figure 5 of Auge et al. (2016)
 paper.Table 1
 dataExcel data file
 supporting the results depicted in Table 1 of Auge et al. (2016)
 paper.
DOI: 10.5061/dryad.dm05n
title: Data from: Patterns and drivers of aquatic invertebrate diversity across an arid biome

description: Managing and restoring faunal diversity across large areas requires an
 understanding of the roles of connectivity and dispersal in driving
 community patterns. We sought to determine the influence of connectivity,
 water regime, water source, geographical location, and dispersal traits on
 patterns of aquatic invertebrate diversity across a continent-wide arid
 biome. We compiled data on freshwater invertebrate assemblages from sites
 spanning the breadth of arid Australia. Univariate analyses (analysis of
 variance and rarefaction) revealed that alpha and gamma diversity across
 sites decreased as latitude increased. Multivariate analyses (ordination
 and analysis of similarity) revealed that community composition had
 considerable fidelity to geographic regions. Hydrological connectivity was
 strongly associated with riverine community composition although water
 rarely flowed (often less than annually). Hydrologically isolated sites
 (springs and rockholes) supported communities that were markedly
 dissimilar to hydrologically connected sites, and to each other. We
 investigated the influence of dispersal on diversity patterns by examining
 Distance Decay Relationships for each of four dispersal trait groups
 (obligate aquatic and passive, weak, and strong aerial dispersers) on the
 basis of geodesic (shortest path) distances between pairs of sites and
 Mantel tests. We did not detect clear differences between dispersal traits
 and distance decay relationships at the continental scale, even for the
 two groups with the lowest dispersal ability (obligate aquatics and
 passive dispersers.) Our results suggest that the loss of hydrological
 connectivity from water developments in arid lands (for example, the
 impoundment of intermittent rivers) is likely to affect
 macroinvertebrates. However, the exact flow mechanisms underlying such
 changes remain to be determined.
description: Appendix S3-Australian
 freshwater invertebrate families & dispersal traitsAppendix S3 provides a
 list of the dispersal traits associated with freshwater invertebrate
 families collected from sampling sites across the Australian arid
 zoneAppendix
 S3.csvAppendix S1- Site
 dataAppendix S1 provides
 environmental information, including water source (groundwater or surface
 water), water regime (permanent or temporary) and connectivity (within
 river network or isolated) for all sites included in the analysis of
 patterns of freshwater invertebrate community composition across the
 Australian arid zone.Appendix S1
 .csv
DOI: 10.5061/dryad.1285
title: Data from: Sixty years of anthropogenic pressure: a spatio-temporal genetic analysis of brown trout populations subject to stocking and population declines

description: Analyses of historical samples can provide invaluable information on
 changes to the genetic composition of natural populations resulting from
 human activities. Here, we analyze 21 microsatellite loci in historical
 (archived scales from 1927-1956) and contemporary samples of brown trout
 (Salmo trutta) from six neighbouring rivers in Denmark, to compare the
 genetic structure of wild populations before and after population declines
 and stocking with non-local strains of hatchery trout. We show that all
 populations have been strongly affected by stocking, with admixture
 proportions ranging from 14 to 64%. Historical population genetic
 structure was characterized by isolation-by-distance and by positive
 correlations between historical effective population sizes and habitat
 area within river systems. Contemporary population genetic structure still
 showed isolation-by-distance, but also reflected differences among
 populations in hatchery trout admixture proportions. Despite significant
 changes to the genetic composition within populations over time, dispersal
 rates among populations were roughly similar before and after stocking. We
 also assessed whether population declines or introgression by hatchery
 strain trout should be the most significant conservation concern in this
 system. Based on theoretical considerations, we argue that population
 declines have had limited negative effects for the persistence of adaptive
 variation, but admixture with hatchery trout may have resulted in reduced
 local adaptation. Collectively, our study demonstrates the usefulness of
 analyzing historical samples for identifying the most important
 consequences of human activities on the genetic structure of wild
 populations.
description: Brown trout
 microsatellite dataThe file contains
 microsatellite data (21 loci) from six wild brown trout populations in
 Western Jutland, Denmark, along with samples from two hatchery strains
 used for stocking the rivers. The samples from the wild populations
 consist of contemporary samples (2000-2006) and historical pre-stocking
 samples (1927-1956), the latter obtained by analyzing DNA from archived
 scale samples. See Hansen et al. (2009) for further details on the data
 and study. The file format is MSA [Dieringer D, Schlotterer C (2003)
 Microsatellite Analyser (msa): a platform independent analysis tool for
 large microsatellite data sets. Molecular Ecology Notes, 3,
 167–169].Hansen et al 2009
 MEC.xlsx
DOI: 10.5061/dryad.h9j67
title: Data from: Fossil grebes from the Truckee Formation (Miocene) of Nevada and a new phylogenetic analysis of Podicipediformes (Aves)

description: Podicipediformes is a cosmopolitan clade of foot-propelled diving birds
 that, despite inhabiting marine and lacustrine environments, have a poor
 fossil record. In this contribution, we describe three new grebe fossils
 from the diatomite beds of the Late Miocene Truckee Formation (10.2 ± 0.2
 Ma) of Nevada (USA). Two postcranial skeletons and an associated set of
 wing elements indicate that at least two distinct grebe species occupied
 the large, shallow Lake Truckee during the Miocene. Phylogenetic analysis
 of morphological data supports a basal divergence between a clade uniting
 the dabchicks (Tachybaptus, Limnodytes, Poliocephalus) and a clade uniting
 Podilymbus, Rollandia, Podiceps and Aechmophorus. Missing data, combined
 with a paucity of informative skeletal characters, make it difficult to
 place the Truckee grebes within either of these major clades. Given the
 weak projection of the cnemial crests compared with extant grebes, it also
 remains plausible that these specimens represent stem lineage grebes.
 Although more material is needed to resolve the phylogenetic position of
 the Truckee grebes, our analysis offers insight into the tempo of grebe
 evolution by placing the Miocene taxon Thiornis sociata within the
 dabchick clade. Thiornis sociata provides a minimum age calibration of 8.7
 Ma for the basal divergence among dabchicks. Based on the recovery of a
 nonmonophyletic Tachybaptus and placement of the Western Hemisphere
 ‘Tachybaptus’ dominicus as the basal member of the otherwise exclusively
 Eastern Hemisphere dabchick clade, we resurrect the genus Limnodytes for
 this extant species (Limnodytes dominicus). Our results also nest the
 large, long-necked Aechmophorus grebes within the genus Podiceps, as the
 sister taxon to Podiceps major.
description: Ksepka et al.
 Podicipediformes MatrixNexus file containing
 phylogenetic matrix.KsepkaetalGrebes.nexusKsepka et al. Character ListList of morphological characters used in phylogenetic analysis, with list of specimens examined for codings.
DOI: 10.5061/dryad.t1sg6
title: Data from: Onset of fights and mutual assessment in ant founding queens

description: In animals, the progress and outcomes of contests can be influenced by an
 individual's own condition, its opponent's condition or a
 combination of both. The use of chemical information to assess the quality
 of rivals has been underestimated despite its central role in the
 regulation of social interactions in many taxa. Here, we studied pairwise
 contests between founding queens of the ant Lasius niger to investigate
 whether the decision to engage in agonistic interactions relies on self or
 mutual assessment. Queens modulated their aggressive behaviours depending
 both on their own status and their opponent's status. We showed no
 influence of lipid stores or size on the onset of fights. However,
 differences in cuticular chemical signatures linked to fertility status
 accurately predicted the probability of behaving aggressively in pairs.
 Our study thus suggests that ant queens could rely on mutual assessment
 via chemical cues to make informed decisions about fight initiation.
description: Mutual_assessment_queensRaw data including size, mass, relative abundance of cuticular hydrocarbons and score of aggression. Raw data are provided in the spreadsheet "DATA" and explanations for each each column are provided in the spreadsheet "LEGEND".