cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1cd62
title: Data from: Plasmid stability is enhanced by higher-frequency pulses of positive selection

description: Plasmids accelerate bacterial adaptation by sharing ecologically important
 traits between lineages. However, explaining plasmid stability in
 bacterial populations is challenging due to their associated costs.
 Previous theoretical and experimental studies suggest that pulsed positive
 selection may explain plasmid stability by favouring gene mobility and
 promoting compensatory evolution to ameliorate plasmid cost. Here we test
 how the frequency of pulsed positive selection affected the dynamics of a
 mercury resistance plasmid, pQBR103, in experimental populations of
 Pseudomonas fluorescens SBW25. Plasmid dynamics varied according to the
 frequency of Hg2+ positive selection: in the absence of Hg2+ plasmids
 declined to low frequency whereas pulses of Hg2+ selection allowed
 plasmids to sweep to high prevalence. Compensatory evolution to ameliorate
 the cost of plasmid carriage was widespread across the entire range of
 Hg2+ selection regimes, including both constant and pulsed Hg2+ selection.
 Consistent with theoretical predictions, gene mobility via conjugation
 appeared to play a greater role in promoting plasmid stability under
 low-frequency pulses of Hg2+ selection. However, upon removal of Hg2+
 selection, plasmids which had evolved under low-frequency pulse selective
 regimes declined over time. Our findings suggest that temporally variable
 selection environments, such as those created during antibiotic
 treatments, may help to explain the stability of mobile plasmid-encoded
 resistance.
description: CaglaStevenson.RawData
DOI: 10.5061/dryad.3vj3d
title: Data from: Patterns of earthworm, enchytraeid and nematode diversity and community structure in urban soils of different ages

description: Annelids (Lumbricidae and Enchytraeidae) and nematodes are common soil
 organisms and play important roles in organic matter decomposition,
 nutrient cycling and creation of soil structure and porosity. However,
 these three groups have rarely been studied together and only few studies
 exist for urban soils. We studied the diversity and community composition
 of annelids and nematodes in soils spanning more than two centuries of
 urban soil development in Neuchâtel (Switzerland) and assessed the
 relationships 1) among these three groups and 2) between each group and
 environmental (physical, chemical and functional) characteristics of soils
 and soil age. While the groups of environmental variables were correlated
 (Mantel tests) no correlation was found between pairs of soil fauna groups
 and between each soil fauna group and environmental variables. More
 specifically, redundancy analyses showed that earthworm assemblages were
 best correlated with soil bulk density and with soil depth, the latter
 being positively correlated with soil age. Enchytraeid assemblages and the
 proportion of enchytraeid r-strategists were respectively best correlated
 with soil carbonate content and negatively correlated with soil age.
 Nematodes assemblages were best correlated with soil water content.
 Moreover, relationships between pairs of soil biota groups, and between
 each group and environmental (physical, chemical and functional)
 variables, varied along the soil age gradient (moving window analysis).
 This study provides new knowledge on urban soil biodiversity and how
 environmental conditions can influence soil diversity and community
 patterns in the urban context. The contrasted community patterns of
 earthworms, enchytraeids and nematodes in urban soils of different ages
 and their different ecological roles suggest that they represent potential
 complementary indicators of soil quality and functioning such as soil
 formation and organic matter dynamics.
description: Earthworms_dataEnchytraeids_dataNematodes_dataPhysicochemical_dataSites_geographical_coordinates
DOI: 10.5061/dryad.n9r31
title: Data from: The wake of hovering flight in bats

description: Hovering means stationary flight at zero net forward speed, which can be
 achieved by animals through muscle powered flapping flight. Small bats
 capable of hovering typically do so with a downstroke in an inclined
 stroke plane, and with an aerodynamically active outer wing during the
 upstroke. The magnitude and time history of aerodynamic forces should be
 reflected by vorticity shed into the wake. We thus expect hovering bats to
 generate a characteristic wake, but this has until now never been studied.
 Here we trained nectar-feeding bats, Leptonycteris yerbabuenae, to hover
 at a feeder and using time-resolved stereoscopic particle image
 velocimetry in conjunction with high-speed kinematic analysis we show that
 hovering nectar-feeding bats produce a series of bilateral stacked vortex
 loops. Vortex visualizations suggest that the downstroke produces the
 majority of the weight support, but that the upstroke contributes
 positively to the lift production. However, the relative contributions
 from downstroke and upstroke could not be determined on the basis of the
 wake, because wake elements from down- and upstroke mix and interact. We
 also use a modified actuator disc model to estimate lift force, power and
 flap efficiency. Based on our quantitative wake-induced velocities, the
 model accounts for weight support well (108%). Estimates of aerodynamic
 efficiency suggest hovering flight is less efficient than forward flapping
 flight, while the overall energy conversion efficiency (mechanical power
 output/metabolic power) was estimated at 13%.
description: Data from: The wake of
 hovering flight in batsInduced power, flap
 efficiency, induced power factor, make angle and kinematic data of
 hovering batsHovering data Leptonycteris
 yerbabuenae.xls
DOI: 10.5061/dryad.7gp80
title: Data from: Ecotypic differentiation under farmers’ selection: molecular insights into the domestication of Pachyrhizus Rich. ex DC. (Fabaceae) in the Peruvian Andes

description: Understanding the distribution of crop genetic diversity in relation to
 environmental factors can give insights into the eco-evolutionary
 processes involved in plant domestication. Yam beans (Pachyrhizus Rich. ex
 DC.) are leguminous crops native to South and Central America that are
 grown for their tuberous roots but are seed-propagated. Using a landscape
 genetic approach, we examined correlations between environmental factors
 and phylogeographic patterns of genetic diversity in Pachyrhizus landrace
 populations. Molecular analyses based on chloroplast DNA sequencing and a
 new set of nuclear microsatellite markers revealed two distinct lineages,
 with strong genetic differentiation between Andean landraces (lineage A)
 and Amazonian landraces (lineage B). The comparison of different
 evolutionary scenarios for the diversification history of yam beans in the
 Andes using Approximate Bayesian Computation (ABC) suggests that P. ahipa
 and P. tuberosus share a progenitor-derivative relationship, with
 environmental factors playing an important role in driving selection for
 divergent ecotypes. The new molecular data call for a revision of the
 taxonomy of Pachyrhizus but are congruent with palaeoclimatic and
 archaeological evidence, and suggest that selection for determinate growth
 was part of ecophysiological adaptations associated with the
 diversification of the P. tuberosus–P. ahipa complex during the
 Mid-Holocene.
description: Table_S1Metadata for Table S1 Passport information, genetic data and occurrence data for accessions used in analyses. The file contains three sections: a) Geographic origin, genotypes, voucher specimen and accession numbers of Pachyrhizus accessions used in molecular and landscape genetic analyses; b) Genotypic data for the 244 accessions characterized at 14 nuclear microsatellite markers. Alleles at nuclear SSR loci are coded as number of repeats (for details on markers see Delêtre et al. 2013); c) Additional occurrence data for landscape genetic analyses.GESTE_env_dataMean values for the eight bioclimatic variables (ALT, BIO1, BIO3, BIO7, BIO12, BIO15, LON, LAT) retained for GESTE analyses. Means are based on 169 unique occurrence points representing 11 out of the 16 subpopulations identified. Wild populations (TW, PW), Jacatupe (Ja) and Yushpe (Yp) were not included (see Material and Methods for details).
DOI: 10.5061/dryad.q54rp
title: Data from: Using camera trapping and hierarchical occupancy modelling to evaluate the spatial ecology of an African mammal community

description: Emerging conservation paradigms have shifted from single to multi-species
 approaches focused on sustaining biodiversity. Multi-species hierarchical
 occupancy modelling provides a method for assessing biodiversity while
 accounting for multiple sources of uncertainty. We analysed camera
 trapping data with multi-species models using a Bayesian approach to
 estimate the distributions of a terrestrial mammal community in northern
 Botswana and evaluate community, group, and species-specific responses to
 human disturbance and environmental variables. Groupings were based on two
 life-history traits: body size (small, medium, large and extra-large) and
 diet (carnivore, omnivore and herbivore). We photographed 44 species of
 mammals over 6607 trap nights. Camera station-specific estimates of
 species richness ranged from 8 to 27 unique species, and species had a
 mean occurrence probability of 0·32 (95% credible interval = 0·21–0·45).
 At the community level, our model revealed species richness was generally
 greatest in floodplains and grasslands and with increasing distances into
 protected wildlife areas. Variation among species’ responses was explained
 in part by our species groupings. The positive influence of protected
 areas was strongest for extra-large species and herbivores, while
 medium-sized species actually increased in the non-protected areas. The
 positive effect of grassland/floodplain cover, alternatively, was
 strongest for large species and carnivores and weakest for small species
 and herbivores, suggesting herbivore diversity is promoted by habitat
 heterogeneity. Synthesis and applications. Our results highlight the
 importance of protected areas and grasslands in maintaining biodiversity
 in southern Africa. We demonstrate the utility of hierarchical Bayesian
 models for assessing community, group and individual species’ responses to
 anthropogenic and environmental variables. This framework can be used to
 map areas of high conservation value and predict impacts of land-use
 change. Our approach is particularly applicable to the growing number of
 camera trap studies world-wide, and we suggest broader application
 globally will likely result in reduced costs, improved efficiency and
 increased knowledge of wildlife communities.
description: Camera trap and
 covariate dataFile includes camera
 trap locations, species detections at the respective camera traps,
 probability of detection covariates, probability of occupancy covariates,
 and species names as well as diet and body size
 classificationsRich_data.xlsx
DOI: 10.5061/dryad.q5b10
title: Data from: Begging blue tit nestlings discriminate between the odour of familiar and unfamiliar conspecifics

description: 1. Offspring often solicit, and compete for, limited parental care by
 elaborate begging behaviour. Kin selection theory predicts that competing
 offspring should modify the intensity of their begging depending on the
 degree of relatedness to their nest- or litter mates. 2. Empirical
 evidence in birds, which are a key model in the study of parent-offspring
 interactions, indeed indicates that a lower level of relatedness between
 offspring in the nest correlates with more intense begging (i.e. more
 ‘selfish’ behaviour). This implies that competing nestlings can recognize
 kin, but the mechanism underlying such discrimination is unclear. Birds
 have long been thought to mainly rely on visual and auditory cues in their
 social communication, but there is now growing evidence for the importance
 of olfactory cues too. 3. To assess the potential importance of olfactory
 cues in modulating nestling begging behaviour, we experimentally tested in
 a free-living bird, the blue tit Cyanistes caeruleus, if nestlings
 discriminate and adjust their begging behaviour depending on their
 familiarity with a conspecific nestling odour stimulus. 4. We found that
 individuals responded with longer and more intense begging bouts to an
 unfamiliar compared to a familiar odour stimulus. 5. Our findings provide
 first evidence for a role of olfaction in modulating offspring begging
 behaviour in a wild bird population. Although our experiment cannot
 differentiate between the effects of familiarity and relatedness, it
 raises the interesting possibility that blue tit nestlings may also
 discriminate between odours of kin and non-kin, and adjust their begging
 behaviour accordingly. This hypothesis requires further testing.
description: Nestling begging
 responses to familiar versus unfamiliar odour stimuliThis data file was used
 to analyse the likelihood, duration and intensity of nestling begging
 responses to familiar versus unfamiliar odour stimuli, while controlling
 for several additional predictor variables.Rossi_FunctEcol_BeggingExperiment.csvNestling mass and survivalThis data file was used to analyse the effect of the olfactory discrimination test trials on nestling mass and survival as observed on day 15 after hatching.Rossi_FunctEcol_NestlingMassSurvival.csv
DOI: 10.5061/dryad.6vb73
title: Data from: Social control of reproduction and breeding monopolization in the eusocial snapping shrimp Synalpheus elizabethae

description: Understanding why individuals within altruistic societies forego
 reproduction to raise others' offspring has fascinated scientists
 since Darwin. Although worker polymorphism is thought to have evolved only
 in sterile workers, worker subcastes appear to be common among social
 invertebrates and vertebrates. We asked whether sterility accompanies
 eusociality and morphological differentiation in snapping shrimps
 (Synalpheus) - the only known marine eusocial group. We show that workers
 in S. elizabethae are reproductively totipotent, and that female — but not
 male — gonadal development and mating are mediated by the presence of a
 queen, apparently without physical aggression. In queenless experimental
 colonies, a single immature female worker typically became ovigerous, and
 no female workers matured in colonies with a resident queen. Thus,
 eusocial shrimp workers retain reproductive totipotency despite signs of
 morphological specialization. The failure of most female workers to mature
 is instead facultative and mediated by the presence of the queen, ensuring
 her reproductive monopoly.
description: Table A1. Sex and
 maturation status of adult workers.Sex and maturation
 status of adult workers from five S. elizabethae colonies from the
 demosponge Lissodendoryx colombiensis collected from Bocas del Toro,
 Panama.AMN
 final table A1.xlsxTable A2. Gonadal
 development of workersGonadal development of
 the worker that had the most advanced development in each group under
 three experimental treatments. 1Q/6W: one queen and six workers; 0Q/6W:
 queenless with six workers (0Q/6W); and 0Q/1W: one worker only. Numbers in
 the table represent counts of groups. We have excluded 10, 10 and 4 groups
 from treatments 0Q/1W, 1Q/6W and 0Q/6W respectively, because either
 workers had initial gonadal development, the queen died, the group had
 only male workers, or the group had only female
 workers.AMN
 final table A2.xlsxTable A3. Gonadal
 development of workers with initial gonadal developmentGonadal development of
 the worker that had the most advanced development in each group under
 three experimental treatments where workers had initial gonadal
 developmentAMN final table
 A3.xlsxNumber of queens and
 colony size in the eusocial shrimps Synalpheus elizabethae in Bocas del
 Toro, PanamaData include 72 colonies
 collected from Bocas del Toro, Panama between 2007 and
 2013BDT
 queen regression data.xlsx
DOI: 10.5061/dryad.cj27s
title: Data from: Environmental variability and acoustic signals: A multilevel approach in songbirds

description: Among songbirds, growing evidence suggests that acoustic adaptation of
 song traits occurs in response to habitat features. Despite extensive
 study, most research supporting acoustic adaptation has only considered
 acoustic traits averaged for species or populations, overlooking
 intraindividual variation of song traits, which may facilitate effective
 communication in heterogeneous and variable environments. Fewer studies
 have explicitly incorporated sexual selection, which, if strong, may
 favour variation across environments. Here, we evaluate the prevalence of
 acoustic adaptation among 44 species of songbirds by determining how
 environmental variability and sexual selection intensity are associated
 with song variability (intraindividual and instraspecific) and short-term
 song complexity. We show that variability in precipitation can explain
 short-term song complexity among taxonomically diverse songbirds and that
 precipitation seasonality and the intensity of sexual selection are
 related to intraindividual song variation. Our results link song
 complexity to environmental variability, something previously found for
 mockingbirds (family Mimidae). Perhaps more importantly, our results
 illustrate that individual variation in song traits may be shaped by both
 environmental variability and strength of sexual selection.
description: Phylogenetic
 hypothesisPhylogeny based on
 Barker et al. (2004) with additional phylogenetic information from three
 other sources (Ohlson et al. 2008; Murray et al. 1994; Jonsson &
 Fjeldsa 2006). Because several sources were used to construct this
 phylogeny, we used Grafen’s (1989) method of setting branch lengths such
 that the distance from nodes to tips is equal to the number of taxa in the
 clade minus one. We initially based species pairs on the work of Bonier et
 al. (2007), which provided species pairs that differed in their elevation
 and latitudinal ranges, indicative of differences in tolerances to
 environmental features. Additional species were added based on these same
 criteria, but using pairs previously identified by Hu and Cardoso (2009).
 See the electronic supplementary material of the paper describing these
 data for full reference details.Medina&Francis_tree.nexMedina&Francis_BiolLett_data
DOI: 10.5061/dryad.h14kk
title: Data from: An experimental analysis of the heritability of variation in glucocorticoid concentrations in a wild avian population

description: Glucocorticoid hormones (CORT) are predicted to promote adaptation to
 variable environments, yet little is known about the potential for CORT
 secretion patterns to respond to selection in free-living populations. We
 assessed the heritable variation underlying differences in hormonal
 phenotypes using a cross-foster experimental design with nestling North
 American barn swallows (Hirundo rustica erythrogaster). Using a bivariate
 animal model, we partitioned variance in baseline and stress-induced CORT
 concentrations into their additive genetic and rearing environment
 components and estimated their genetic correlation. Both baseline and
 stress-induced CORT were heritable with heritability of 0.152 and 0.343,
 respectively. We found that the variation in baseline CORT was best
 explained by rearing environment, whereas the variation in stress-induced
 CORT was contributed to by a combination of genetic and environmental
 factors. Further, we did not detect a genetic correlation between these
 two hormonal traits. Although rearing environment appears to play an
 important role in the secretion of both types of CORT, our results suggest
 that stress-induced CORT levels are underlain by greater additive genetic
 variance compared with baseline CORT levels. Accordingly, we infer that
 the glucocorticoid response to stress has a greater potential for
 evolutionary change in response to selection compared with baseline
 glucocorticoid secretion patterns.
description: NestlingBarnSwallowCORT2010-HeritabilityMSContains data for USGS-banded nestling North American barn swallows (Hirundo rustica erythrogaster) collected at day 12 between May and July 2010. Data includes site and nest location, date banded, brood size manipulation treatment, age at data collection, sex, brood number (based on breeding adult pair), clutch size, brood size, mass, presence of mites, DNA extraction number, social and genetic assignments of parents, date and time information for baseline and stress-induced corticosterone (CORT) samples, CORT concentrations, and plumage color scoresNestlingCORT2010-HeritabilityMS.Dryad_28May2014.csvPedigree3_070114A text file containing pedigree that includes the genetic parent(s) of the nestlings that was used to determine the additive genetic variance component for calculating heritability.CORT3_070114Text file containing all pertinent data for the bivariate animal model we ran to assess heritability of variation in baseline and stress-induced corticosterone (CORT) concentrations in nestling barn swallows. This file is similar to the excel file available in this datafile but in a format more easily accessible to R statistical program.
DOI: 10.5061/dryad.tn0250c
title: Data from: Outcomes after ischemic stroke caused by intracranial atherosclerosis versus dissection

description: Objective To compare the outcomes between patients with non-traumatic
 intracranial arterial dissection (ICAD) and intracranial atherosclerotic
 stenosis (ICAS) using high-resolution MRI (HR-MRI). Methods We conducted a
 prospective study using HR-MRI in patients with acute symptomatic
 cerebrovascular disease due to intracranial occlusive disease and no
 dissection on luminal images. Patients were followed-up for 27.9 ± 19.3
 months. We compared the functional outcome, recurrence, and changes in
 vascular status between patients with ICAD (dissection and no plaque on
 HR-MRI) and ICAS (atherosclerosis plaque on HR-MRI). Results We included
 312 patients (mean age, 59.0 ± 14.2 years; men, 58.3%), of whom 113 had
 ICAD and 199 had ICAS. The functional outcome (as measured by modified
 Rankin score) on the 90th day after symptom onset was not different
 between the groups, after adjusted for other factors (P = 0.095). However,
 recurrent ischemic cerebrovascular disease on the relevant vascular
 territory was lower in the ICAD group (7 patients, 6.2%) than in the ICAS
 group (37 patients, 18.6%). ICAD was a significant independent determinant
 of disease recurrence (hazard ratio, 0.43; 95% CI, 0.19–0.98). Improvement
 in vascular stenosis on follow-up vascular studies was more frequently
 observed in ICAD (50.7%) than in ICAS (11.6%). ICAD was an independent
 determinant of vascular improvement (odds ratio, 7.94; 95% CI,
 3.32–19.01). Conclusion Considering the high prevalence of ICAD in the
 patients with presumed ICAS and the differential outcomes between ICAD and
 ICAS, HR-MRI may be a useful diagnostic tool in this population.
description: Supplemental
 MaterialSupplemental data of the
 study.04
 Supplemental Material.docx