cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.87v26
title: Data from: Growth and development rates have different thermal responses

description: Growth and development rates are fundamental to all living organisms. In a
 warming world, it is important to determine how these rates will respond
 to increasing temperatures. It is often assumed that the thermal responses
 of physiological rates are coupled to metabolic rate and thus have the
 same temperature dependence. However, the existence of the
 "temperature-size rule" (TSR) suggests intraspecific growth and
 development are decoupled. Decoupling of these rates would have important
 consequences for individual species and ecosystems, yet this has not been
 tested systematically across a range of species. We conducted an analysis
 on growth and development rate data compiled from the literature for a
 well-studied group, marine pelagic copepods, and use an information
 theoretic approach to test which equations best describe these rates.
 Growth and development rates were best characterised by models with
 significantly different parameters: development has stronger temperature
 dependence than growth across all life stages. As such it is incorrect to
 assume these rates have the same temperature dependence. We used the best
 fit models for these rates to predict changes in organism mass to
 temperature. These predictions follow a concave relationship, which
 complicates attempts to model the impacts of increasing global
 temperatures on species body size.
description: Growth
 RatesLarval Development
 RatesEgg Development
 Rates
DOI: 10.15468/dl.9skfxm
title: Occurrence Download

description: A dataset containing 89559 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Platycladus"
 ]
}

 The dataset includes 89559 records from 628 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000698-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8tg194r
title: Data from: Difficult patient-doctor encounters in a Swiss university outpatient clinic: a cross-sectional study.

description: Introduction: Previous research has shown that multiple factors contribute
 to healthcare providers perceiving encounters as difficult, and are
 related to both medical and non-medical demands. Aim: To measure the
 prevalence and to identify predictors of encounters perceived as difficult
 by medical residents. Design and Setting: Cross-sectional study at the
 Department of Ambulatory Care and Community Medicine (DACCM), a university
 outpatient clinic with a long tradition of caring for vulnerable patients.
 Method: We identified difficult doctor-patient encounters using the
 validated Difficult Doctor-Patient Relationship Questionnaire (DDPRQ-10),
 and characterized patients using the Patient’s Vulnerability Grid, a
 validated questionnaire measuring 5 domains of vulnerability, both
 completed by medical residents after each encounter. We used a multiple
 linear regression model with the outcome variable as the DDPRQ-10 score,
 controlling for resident characteristics. Participants: We analyzed 527
 patient encounters performed by all 27 DACCM residents (17 women and 10
 men). We asked each medical resident to evaluate 20 consecutive
 consultations starting on the same date. Outcome: One hundred and
 fifty-seven encounters (29,8%) were perceived as difficult. Results: After
 adjusting for differences among residents, all five domains of the Patient
 Vulnerability Grid were independently associated with a difficult
 encounter: frequent health care user; psychological comorbidity; health
 comorbidity; risky behaviors and a precarious social situation.
 Conclusion: Nearly a third of encounters were perceived as difficult by
 medical residents in our university outpatient clinic that cares for a
 high proportion of vulnerable patients. This represents twice the average
 ratio of difficult encounters in general practice. All five domains of
 patient vulnerability appear to have partial explanatory power on medical
 residents’ perception of difficult patient encounters.
description: Difficult_patient_doctor_encounter_Lausanne_SwitzerlandData from medical residents self-perception of patient-doctor encounter.bbdd_difpatdoc_final_2.xlsx
DOI: 10.5061/dryad.f76f2
title: Data from: The network motif architecture of dominance hierarchies

description: The widespread existence of dominance hierarchies has been a central
 puzzle in social evolution, yet we lack a framework for synthesizing the
 vast empirical data on hierarchy structure in animal groups. We applied
 network motif analysis to compare the structures of dominance networks
 from data published over the past 80 years. Overall patterns of dominance
 relations, including some aspects of non-interactions, were strikingly
 similar across disparate group types. For example, nearly all groups
 exhibited high frequencies of transitive triads, whereas cycles were very
 rare. Moreover, pass-along triads were rare, and double-dominant triads
 were common in most groups. These patterns did not vary in any systematic
 way across taxa, study settings (captive or wild) or group size. Two
 factors significantly affected network motif structure: the proportion of
 dyads that were observed to interact and the interaction rates of the
 top-ranked individuals. Thus, study design (i.e. how many interactions
 were observed) and the behaviour of key individuals in the group could
 explain much of the variations we see in social hierarchies across
 animals. Our findings confirm the ubiquity of dominance hierarchies across
 all animal systems, and demonstrate that network analysis provides new
 avenues for comparative analyses of social hierarchies.
description: ShizukaMcDonald_dataCompressed file containing 172 data matrices. The cell values represent the number of times the row individual 'beat' the column individual.ShizukaMcDonald_Data.zipMetadataThis .csv file includes citation information and some basic data for each data matrix.
DOI: 10.5061/dryad.v4t42
title: Data from: A protocol for conducting and presenting results of regression-type analyses

description: Scientific investigation is of value only insofar as relevant results are
 obtained and communicated, a task that requires organizing, evaluating,
 analysing and unambiguously communicating the significance of data. In
 this context, working with ecological data, reflecting the complexities
 and interactions of the natural world, can be a challenge. Recent
 innovations for statistical analysis of multifaceted interrelated data
 make obtaining more accurate and meaningful results possible, but key
 decisions of the analyses to use, and which components to present in a
 scientific paper or report, may be overwhelming. We offer a 10-step
 protocol to streamline analysis of data that will enhance understanding of
 the data, the statistical models and the results, and optimize
 communication with the reader with respect to both the procedure and the
 outcomes. The protocol takes the investigator from study design and
 organization of data (formulating relevant questions, visualizing data
 collection, data exploration, identifying dependency), through conducting
 analysis (presenting, fitting and validating the model) and presenting
 output (numerically and visually), to extending the model via simulation.
 Each step includes procedures to clarify aspects of the data that affect
 statistical analysis, as well as guidelines for written presentation.
 Steps are illustrated with examples using data from the literature.
 Following this protocol will reduce the organization, analysis and
 presentation of what may be an overwhelming information avalanche into
 sequential and, more to the point, manageable, steps. It provides
 guidelines for selecting optimal statistical tools to assess data
 relevance and significance, for choosing aspects of the analysis to
 include in a published report and for clearly communicating information.
description: Baboon
 dataModified baboon data
 taken from Dryad Digital Repository: Sick C, Carter AJ, Marshall HH, Knapp
 LA, Dabelsteen T, Cowlishaw G (2014) Data from: Evidence for varying
 social strategies across the day in chacma baboons. Dryad Digital
 Repository. http://dx.doi.org/10.5061/dryad.n4k6pMonkeysV2.txtOwl dataThe meaning of the variables is self-explanatory.Owls2.txtOystercatcher dataOystercatcherData.txtR codeThis file contains all the R code used to generate the graphs and tables.ZuurIeno_MEE_2016_V5.R
DOI: 10.5061/dryad.08h3j
title: Data from: Antagonistic selection factors induce a continuous population divergence in a polymorphism

description: Understanding the relative importance of selection and stochastic factors
 in population divergence of adaptive traits is a classical topic in
 evolutionary biology. However, it is difficult to separate these factors
 and detect the effects of selection when two or more contrasting selective
 factors are simultaneously acting on a single locus. In the damselfly
 Ischnura senegalensis, females exhibit color dimorphism and morph
 frequencies change geographically. We here evaluated the role of selection
 and stochastic factors in population divergence of morph frequencies by
 comparing the divergences in color locus and neutral loci. Comparisons
 between population pairwise FST for neutral loci and for the color locus
 did not detect any stochastic factors affecting color locus. Although
 comparison between population divergence in color and neutral loci using
 all populations detected only divergent selection, we detected two
 antagonistic selective factors acting on the color locus, that is,
 balancing and divergent selection, when considering geographical distance
 between populations. Our results suggest that a combination of two
 antagonistic selective factors, rather than stochastic factors,
 establishes the geographic cline in morph frequency in this system.
description: MicrosatelliteData on microsatellite genenotypesmicro.txtmtDNAData on mtDNA genotypes
DOI: 10.5061/dryad.1159
title: Data from: A test of the "flexible stem" model of evolution: ancestral plasticity, genetic accommodation, and morphological divergence in the threespine stickleback radiation

description: If an ancestral stem group repeatedly colonizes similar environments,
 developmental plasticity specific to that group should consistently give
 rise to similar phenotypes. Parallel selection on those similar phenotypes
 could lead to the repeated evolution of characteristic ecotypes, a
 property common to many adaptive radiations. A key prediction of this
 "flexible stem" model of adaptive radiation is that patterns of
 phenotypic divergence in derived groups should mirror patterns of
 developmental plasticity in their common ancestor. The threespine
 stickleback radiation provides an excellent opportunity to test this
 prediction because the marine form is representative of the ancestral stem
 group, which has repeatedly given rise to several characteristic ecotypes.
 We examined plasticity of several aspects of shape and trophic morphology
 in response to diets characteristic of either the derived benthic or
 limnetic ecotypes. When marine fish were reared on alternative diets,
 plasticity of head and mouth shape paralleled phenotypic divergence
 between the derived ecotypes, supporting the flexible stem model. Benthic
 and limnetic fish exhibited patterns of plasticity similar to the marine
 population; however, some differences in population means were present, as
 well as subtle differences in shape plasticity in the benthic population,
 indicating a role for genetic accommodation in this system.
description: WUND_DRYAD_tpslandmarkdata.tpsThis text file is in a format compatible with F. James Rohlf’s TPS morphometrics programs (http://life.bio.sunysb.edu/morph/). The data are the raw x-y coordinates for all 147 specimens. “LM=16” indicates that 16 landmarks were scored. The left and right column of numbers reflects the x and y coordinates, respectively, in pixels. Multiply by the indicated scale factor to convert pixels to centimeters. The “ID” reflects fishID/treatment. Treatments can be discerned from the corresponding excel file, or by considering this “ID” field. The second number (after the slash) reflects treatment. 1: limnetic fish, Artemia diet; 2 limnetic fish, bloodworm diet; 3: benthic fish, Artemia diet; 4: benthic fish, bloodworm diet; 5: marine fish, Artemia diet; 6: marine fish, bloodworm diet.WUND_DRYAD_proclndmrks_rakers.xlsxThis data file contains two types of data. First are the lengths of the 3 longest gill rakers on the first gill arch of all specimens. Second are the Procrustes superimposed x-y coordinates for all specimens (see figure 2 in manuscript for landmark locations). Families are nested within populations, and fish are nested within families. The “TPS Picture #” column corresponds with the order of specimens in the accompanying TPS text file. Thus, if the excel data are sorted by this column, specimens will be in the same order as in the TPS file.
DOI: 10.5061/dryad.gj7hb
title: Data from: Heterogeneity in plant-soil feedbacks and resident population dynamics affect mutual invasibility

description: 1. Understanding the mechanisms governing coexistence is a central goal in
 ecology and has implications for conserving and restoring communities, yet
 the high diversity in many plant communities is difficult to explain.
 Theory suggests that plant-soil feedbacks (PSF) can lead to
 frequency-dependent coexistence by suppressing conspecifics more than
 heterospecifics, potentially helping to explain high-diversity plant
 communities. In addition, species-specific population dynamics, including
 the rate at which individuals are replaced in a population, or population
 turnover rate, may influence coexistence outcomes. 2. We have created a
 rigorous test of the coexistence predictions of theory by generating a
 soil heterogeneity experiment in the field and testing for mutual
 invasibility by establishing resident populations, then experimentally
 invading them. Experimental tests of mutual invasibility can demonstrate
 coexistence because, if species are able to invade one another's
 populations when at low density, they should exhibit long-term
 coexistence. We use pairs of congeners in this experiment that coexist at
 small spatial scales, sometimes within cm, at our field site. 3. We
 demonstrate that invader individuals established better in congener's
 soils than in conspecific soils, consistent with plant-soil feedback
 mediated coexistence. This effect was often mediated by competition with
 established resident plants. 4. Further, we show that soil heterogeneity
 interacted with the population turnover rate of the resident population to
 influence invasibility (P &lt; 0.10), consistent with the theoretical
 prediction that a plant's population dynamics will interact with
 heterogeneity to influence coexistence. 5. Synthesis - Plant-soil
 feedbacks can in theory lead to frequency-dependent coexistence, and
 reciprocally negative feedback effects in greenhouse experiments are often
 consistent with this prediction. We provide the first field test of mutual
 invasibility structured by PSF, demonstrating that PSF can lead to
 coexistence when they create a patchy, or heterogeneous, soil environment.
 This work suggests that understanding the influence of PSF on diversity
 necessitates understanding the spatial scale at which soil heterogeneity
 emerges in the field. Thus high diversity might be maintained in plant
 communities by heterogeneity created by plants' influence on the
 soil, and this outcome depends strongly on population dynamics.
description: Individual invader
 establishment for 2012 field season.Invader establishment
 data, for plots started in 2011. Data through the 2012 field
 season.Individual_invader_establishment_2011.csv
DOI: 10.5061/dryad.bf206
title: Data from: Enriched rearing environment and wild genetic background can enhance survival and disease resistance of salmonid fishes during parasite epidemics

description: The importance and volume of aquaculture is increasing world-wide. Rearing
 practices play a key role in determining growth rate, survival and disease
 resistance in aquaculture fishes. Recent evidence suggests that in
 comparison with a standard stimulus-poor rearing environment, an enriched
 or variable rearing environment has significant positive effects on
 several traits underlying growth and well-being of fish. However, the
 effect of enriched rearing on one of the most important threats for
 aquaculture development, occurrence of parasitic infections, remains
 unknown. We used surveillance data of experimental salmonid populations of
 wild and hatchery origin under semi-natural parasite exposure to explore
 effects of enriched rearing on outbreaks of important aquaculture
 pathogens and associated fish mortalities in production-scale fish
 densities. We also conducted controlled parasite exposures to investigate
 if enriched rearing reduces susceptibility of fish to infection in
 comparison with standard rearing conditions. We found evidence of enriched
 rearing influencing survival and disease resistance of aquaculture fish
 during parasite epidemics. Essentially, populations from enriched rearing
 had a higher survival rate, lower parasite occurrence and greater
 resistance to most infections compared to fish held in standard rearing
 conditions. Similarly, fish of wild genetic background had lower mortality
 during some of the epidemics compared to fish of hatchery origin. However,
 we also demonstrate significant variation in these patterns and in some
 cases a tendency for opposite effects of enriched rearing and genetic
 background depending on the fish species and nature of the epidemic.
 Synthesis and applications. Our results suggest that parasitic infections
 and epidemics can be managed through enriched rearing conditions. This may
 have important implications for economically and ecologically sustainable
 parasite and disease prevention strategies in aquaculture.
description: Atlantic salmon
 mortality dataThe Excel sheet contains
 mortality data of Atlantic salmon during epidemics of three
 disease-causing agents.I. multifiliis
 occurrence dataThe Excel sheet contains
 data on occurrence of I. multifiliis on Atlantic salmonExperimental Diplostomum
 exposure dataThe Excel sheet contains
 data on experimental exposure of landlocked Atlantic salmon and brown
 trout to Diplostomum pseudospathaceum parasite
DOI: 10.5061/dryad.94366
title: Data from: Long-term panmixia in a cosmopolitan Indo-Pacific coral reef fish and a nebulous genetic boundary with its broadly sympatric sister species

description: Phylogeographical studies have shown that some shallow-water marine
 organisms, such as certain coral reef fishes, lack spatial population
 structure at oceanic scales, despite vast distances of pelagic habitat
 between reefs and other dispersal barriers. However, whether these
 dispersive widespread taxa constitute long-term panmictic populations
 across their species ranges remains unknown. Conventional
 phylogeographical inferences frequently fail to distinguish between
 long-term panmixia and metapopulations connected by gene flow. Moreover,
 marine organisms have notoriously large effective population sizes that
 confound population structure detection. Therefore, at what spatial scale
 marine populations experience independent evolutionary trajectories and
 ultimately species divergence is still unclear. Here, we present a
 phylogeographical study of a cosmopolitan Indo-Pacific coral reef fish
 Naso hexacanthus and its sister species Naso caesius, using two mtDNA and
 two nDNA markers. The purpose of this study was two-fold: first, to test
 for broad-scale panmixia in N. hexacanthus by fitting the data to various
 phylogeographical models within a Bayesian statistical framework, and
 second, to explore patterns of genetic divergence between the two broadly
 sympatric species. We report that N. hexacanthus shows little population
 structure across the Indo-Pacific and a range-wide, long-term panmictic
 population model best fit the data. Hence, this species presently
 comprises a single evolutionary unit across much of the tropical Indian
 and Pacific Oceans. Naso hexacanthus and N. caesius were not reciprocally
 monophyletic in the mtDNA markers but showed varying degrees of population
 level divergence in the two nuclear introns. Overall, patterns are
 consistent with secondary introgression following a period of isolation,
 which may be attributed to oceanographic conditions of the mid to late
 Pleistocene, when these two species appear to have diverged.
description: hex_caeCOImtDNA (CO1) sequence alignments in Arlequin formathex_caeDloopmtDNA (control region) sequence alignment in Arlequin formathex_caeEnolDNA sequence alignments of the unkown enolase-like nuclear intron called EnolN, in Arlequin formathexcaeCKArlequin file containing restriction site polymorphism data from a Creatine Kinase intron. Two enzymes were used to acquire this data: DraI and BtsC1.
DOI: 10.5061/dryad.3vd89
title: Data from: Drivers of plant species’ potential to spread: the importance of demography versus seed dispersal

description: Understanding the ability of plants to spread is important for assessing
 conservation strategies, landscape dynamics, invasiveness and ability to
 cope with climate change. While long-distance seed dispersal is often
 viewed as a key process in population spread, the importance of
 inter-specific variation in demography is less explored. Indeed, the
 relative importance of demography vs seed dispersal in determining
 population spread is still little understood. We modelled species’
 potential for population spread in terms of annual migration rates for a
 set of species inhabiting dry grasslands of central Europe.
 Simultaneously, we estimated the importance of demographic (population
 growth rate) vs long-distance dispersal (99th percentile dispersal
 distance) characteristics for among-species differences in modelled
 population spread. In addition, we assessed how well simple proxy measures
 related to demography (the number and survival of seedlings, the survival
 of flowering individuals) and dispersal (plant height, terminal velocity
 and wind speed during dispersal) predicted modelled spread rates. We found
 that species’ demographic rates were the more powerful predictors of
 species’ modelled potential to spread than dispersal. Furthermore, our
 simple proxies were correlated with modelled species spread rates and
 together their predictive power was high. Our findings highlight that for
 understanding variation among species in their potential for population
 spread, detailed information on local demography and dispersal might not
 always be necessary. Simple proxies or assumptions that are based
 primarily on species demography could be sufficient.
description: Hemrova_ Drivers of
 species spread_DataData "Hemrova_
 Drivers of species spread_Data" consist of tables with primary data:
 1) Table 1 – The sixteen species selected for the study, the values of
 their dispersal and demographic characteristics and calculated wavespeeds
 (published also in main text of the paper: Drivers of plant species’
 potential to spread: the importance of demography vs seed dispersal). 2)
 Table A1 – The sixteen species selected for the study; their family, life
 history, dispersal structures on diaspores, start and end of seed release
 period, the number of matrices used for calculation of a mean matrix, the
 number of stages in the demographic matrix, presence of a clonal stage in
 the matrix, country in which the demography was measured, source of the
 demographic matrix (published also in Supplementary material Appendix 1).
 3) A1 – Demographic matrices of species under study used for wavespeed
 modelling and calculation of simple proxy measures related to demography
 (published also in Supplementary material Appendix 1).