cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k1jt9
title: Data from: Trait means, trait plasticity and trait differences to other species jointly explain species performances in grasslands of varying diversity

description: Functional traits may help to explain the great variety of species
 performances in plant communities, but it is not clear whether the
 magnitude of trait values of a focal species or trait differences to
 co-occurring species are key for trait-based predictions. In addition,
 trait expression within species is often plastic, but this variation has
 been widely neglected in trait-based analyses. We studied functional
 traits and plant biomass of 59 species in 66 experimental grassland
 mixtures of varying species richness (Jena Experiment). We related mean
 species performances (species biomass and relative yield RY) and their
 plasticities along the diversity gradient to trait-based pedictors
 involving mean species traits (Tmean), trait plasticities along the
 diversity gradient (Tslope), extents of trait variation across communities
 (TCV; coefficient of variation) and hierarchical differences (Tdiff) and
 trait distances (absolute values of trait differences Tdist) between focal
 and co-occurring species. Tmean (30–55%) and Tdiff (30–33%) explained most
 variation in mean species performances and their plasticities, but Tslope
 (20–25%) was also important in explaining mean species performances. The
 mean species traits and the trait differences between focal species and
 neighbors with the greatest explanatory power were related to plant size
 and stature (shoot length, mass:height ratios) and leaf photosynthetic
 capacity (specific leaf area, stable carbon isotopes and leaf nitrogen
 concentration). The contribution of trait plasticities in explaining
 species performances varied in direction (positive or negative) and
 involved traits related to photosynthetic capacity, nitrogen acquisition
 (nitrogen concentrations and stable isotopes) as well as structural
 stability (shoot carbon concentrations). Our results suggest that
 incorporating plasticity in trait expression as well as trait differences
 to co-occurring species is critical for extending trait-based analyses to
 understand the assembly of plant communities and the contribution of
 individual species in structuring plant communities.
description: trait-based
 predictorsThis file contains
 trait-based indices derived from measurements of plant traits in the
 mixtures of the Jena Experiment for 60 grassland species. All
 abbreviations of variable names are explained in the data file as well as
 in the related publication. Abbreviations of species names are explained
 in the READ me file.data-traitBasedPredictors.xlsSpecies performance measuresThis file contains measures of species performance (population-level biomass, relative yields, performance plasticities) for 60 study species based on aboveground biomass harvested in the mixtures of the Jena Experiment at estimated peak canopy development (late May) in the study years 2005-2009. All abbreviations of variables are explained in the data file; abbreviations of species names are explained in the READ me file.data-SpeciesBiomass.xls
DOI: 10.5061/dryad.tq480
title: Data from: Association of rule of law and health outcomes: an ecological study

description: Objectives: To explore whether the rule of law is a foundational
 determinant of health that underlies other socioeconomic, political and
 cultural factors that have been associated with health outcomes. Setting:
 Global project. Participants: Data set of 96 countries, comprising 91% of
 the global population. Primary and secondary outcome measures: The
 following health indicators, infant mortality rate, maternal mortality
 rate, life expectancy, and cardiovascular disease and diabetes mortality
 rate, were included to explore their association with the rule of law. We
 used a novel Rule of Law Index, gathered from survey sources, in a
 cross-sectional and ecological design. The Index is based on eight
 subindices: (1) Constraints on Government Powers; (2) Absence of
 Corruption; (3) Order and Security; (4) Fundamental Rights; (5) Open
 Government; (6) Regulatory Enforcement, (7) Civil Justice; and (8)
 Criminal Justice. Results: The rule of law showed an independent
 association with infant mortality rate, maternal mortality rate, life
 expectancy, and cardiovascular disease and diabetes mortality rate, after
 adjusting for the countries’ level of per capita income, their
 expenditures in health, their level of political and civil freedom, their
 Gini measure of inequality and women's status (p&lt;0.05). Rule
 of law remained significant in all the multivariate models, and the
 following adjustment for potential confounders remained robust for at
 least one or more of the health outcomes across all eight subindices of
 the rule of law. Findings show that the higher the country's level of
 adherence to the rule of law, the better the health of the population.
 Conclusions: It is necessary to start considering the country's
 adherence to the rule of law as a foundational determinant of health.
 Health advocates should consider the improvement of rule of law as a tool
 to improve population health. Conversely, lack of progress in rule of law
 may constitute a structural barrier to health improvement.
description: Rule of law and public
 health indicatorsWe used a novel Rule of
 Law Index, gathered from survey sources, in a crosssectional and
 ecological design. We obtained all statistical data used in this study
 from previously published sources for the most recent year (between
 2009-2012), using UN sources for health and economic data, supplemented
 with data and political freedom and the rule of law from Freedom House and
 the World Justice Project, respectively. The limitations of the individual
 sources allowed for a merged database of complete data in 96 countries,
 comprising 91% of global population.2015BMJOpen.dta
DOI: 10.5061/dryad.2v4m067
title: Data from: Body mass as a supertrait linked to abundance and behavioural dominance in hummingbirds: a phylogenetic approach

description: Body mass has been considered one of the most critical organismal traits,
 and its role in many ecological processes has been widely studied. In
 hummingbirds body mass has been linked to ecological features like
 foraging performance, metabolic rates, and cost of flying, among others.
 We used an evolutionary approach to test if body mass is a good predictor
 of two of the main ecological features of hummingbirds: their abundances
 and behavioural dominance. To determine whether a species was abundant
 and/or behaviourally dominant, we used information from the literature on
 249 hummingbird species. For abundance we classified a species as
 “plentiful” if it was described as the most abundant species in at least
 part of its geographic distribution, while we deemed a species to be
 “behaviourally dominant” when it was described as pugnacious (notably
 aggressive). We found that plentiful hummingbird species had intermediate
 body masses and were more phylogenetically related to each other than
 expected by chance. Conversely, behaviourally dominant species tended to
 have larger body mass and showed a random pattern of distribution in the
 phylogeny. Additionally, small-bodied hummingbird species were not
 considered plentiful by our definition and did not exhibit behavioural
 dominance. These results suggest a link between body mass, abundance, and
 behavioural dominance in hummingbirds. Our findings indicate the existence
 of a body mass range associated with the capacity of hummingbird species
 to be plentiful, behaviourally dominant, or to show both traits. The
 mechanisms behind these relationships are still unclear; however, our
 results provide support for the hypothesis that body mass is a supertrait
 that explains abundance and behavioural dominance in hummingbirds.
description: Appendix
 AMorphological,
 behavioural and ecological characteristics of hummingbird
 species.Appendix
 BSpecies names, genebank
 accession number and genes used to construct the hummingbird phylogeny
 used in this study.
DOI: 10.5061/dryad.cp486
title: Data from: Low levels of hybridization in two species of African driver ants

description: Hybridization in ants can have consequences different from those observed
 in most other species, with many of the potential deleterious effects
 being mitigated due to haplodiploidy and eusociality. In some species
 where colonies are either headed by multiple queens or single queens that
 mate with many males, hybridization is associated with genetic caste
 determination, where hybrids develop into workers and purebred individuals
 develop into queens. A previous study suggested that hybridization occurs
 between two Dorylus army ant species with multiply mate queens. However,
 the extent and exact pattern of hybridization has remained unclear, and
 its possible effect on caste determination has not been investigated. In
 this study we aimed to determine the extent and direction of hybridization
 by measuring how frequently hybrids occur in colonies of both species, and
 to investigate the possibility of genetic caste determination. We show
 that hybridization is bidirectional and occurs at equal rates in both
 species. Hybrid workers make up only 1-2% of the population, and
 interspecific matings represent approximately 2% of all matings in both
 species. This shows that, while interspecific matings that give rise to
 worker offspring occur regularly, they are much rarer than intraspecific
 mating. Finally, we find no evidence of an association between
 hybridization and genetic caste determination in this population. This
 means that genetic caste determination is not a necessary outcome of
 hybridization in ants, even in species where queens mate with multiple
 males.
description: Microsatellite data for
 samples of Dorylus molestus and D. wilverthi in Kakamega
 ForestColony samples from 50
 colonies collected in Kakamega Forest, Kenya in 2012. Samples are
 genotyped at 12 microsatellite loci.Microsatellitedata.xlsx
DOI: 10.15468/dl.xmttxq
title: Occurrence Download

description: A dataset containing 586307 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Insect Species Occurrence Data from Multiple Projects Worldwide with Focus on Bees and Wasps in North America"
 ]
}

 The dataset includes 586307 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000695-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1mg27
title: Data from: The stratigraphy of mass extinction

description: Patterns of last occurrences of fossil species are often used to infer the
 tempo and timing of mass extinction, even though last occurrences
 generally precede the time of extinction. Numerical simulations with
 constant extinction demonstrate that last occurrences are not randomly
 distributed, but tend to cluster at subaerial unconformities, surfaces of
 forced regression, flooding surfaces and intervals of stratigraphical
 condensation, all of which occur in predictable stratigraphical positions.
 This clustering arises not only from hiatuses and non-deposition, but also
 from changes in water depth. Simulations with intervals of elevated
 extinction cause such clusters of last occurrences to be enhanced within
 and below the interval of extinction, suggesting that the timing and
 magnitude of extinctions in these instances could be misinterpreted. With
 the possible exception of the end-Cretaceous, mass extinctions in the
 fossil record are characterized by clusters of last occurrences at these
 sequence stratigraphical horizons. Although these clusters of last
 occurrences may represent brief pulses of elevated extinction, they are
 equally likely to form by stratigraphical processes during a protracted
 period (more than several hundred thousand years) of elevated extinction
 rate. Geochemical proxies of extinction causes are also affected
 similarly, suggesting that many local expressions of mass extinction
 should be re-evaluated for the timing of extinction and its relation to
 environmental change. We propose three tests for distinguishing pulses of
 extinction from clusters of last occurrences produced by stratigraphical
 processes.
description: Code for simulating
 basins and last occurrencesUnzip this data file.
 The sedflux folder contains the files used to recreate the basin
 simulation used in the models. Read the documentation supplied for Sedflux
 for how to use these files. The file extinctionStratigraphy.R contains the
 R modeling code for simulating last occurrences within the stratigraphy
 produced by Sedflux.stratigraphyMassExtinction.zip
DOI: 10.5061/dryad.db800
title: Data from: Where have all the tadpoles gone? Individual genetic tracking of amphibian larvae until adulthood.

description: Reliably marking larvae and reidentifying them after metamorphosis is a
 challenge that has hampered studies on recruitment, dispersal, migration
 and survivorship of amphibians for a long time, as conventional tags are
 not reliably retained through metamorphosis. Molecular methods allow
 unique genetic fingerprints to be established for individuals. Although
 microsatellite markers have successfully been applied in mark–recapture
 studies on several animal species, they have never been previously used in
 amphibians to follow individuals across different life cycle stages. Here,
 we evaluate microsatellites for genetic across-stages mark–recapture
 studies in amphibians and test the suitability of available software
 packages for genotype matching. We sampled tadpoles of the dendrobatid
 frog Allobates femoralis, which we introduced on a river island in the
 Nature Reserve ‘Les Nouragues’ in French Guiana. In two subsequent
 recapture sessions, we searched for surviving juveniles and adults,
 respectively. All individuals were genotyped at 14 highly variable
 microsatellite loci, which yielded unique genetic fingerprints for all
 individuals. We found large differences in the identification success of
 the programs tested. The pairwise-relatedness-based approach, conducted
 with the programs kingroup or ML-Relate, performed best with our data set.
 Matching ventral patterns of juveniles and adult individuals acted as a
 control for the reliability of the genetic identification. Our results
 demonstrate that microsatellite markers are a highly powerful tool for
 studying amphibian populations on an individual basis. The ability to
 individually track amphibian tadpoles throughout metamorphosis until
 adulthood will be of substantial value for future studies on amphibian
 population ecology and evolution.
description: dryad_full
 datasetgenepop format of all
 individual genotypes at all 14 microsatellite loci
DOI: 10.5061/dryad.ss427
title: Data from: Molecular characterisation of trophic ecology within an island radiation of insect herbivores (Curculionidae: Entiminae: Cratopus).

description: The phytophagous beetle family Curculionidae is the most species-rich
 insect family known, with much of this diversity having been attributed to
 both co-evolution with food plants and host-shifts at key points within
 the early evolutionary history of the group. Less well understood is the
 extent to which patterns of host use vary within or among related species,
 largely because of the technical difficulties associated with quantifying
 this. Here we develop a recently characterised molecular approach to
 quantify diet within and between two closely related species of weevil
 occurring primarily within dry forests on the island of Mauritius. Our aim
 is to quantify dietary variation across populations and assess adaptive
 and non-adaptive explanations for this, and to characterise the nature of
 a trophic shift within an ecologically distinct population within one of
 the species. We find that our study species are polyphagous, consuming a
 much wider range of plants than would be suggested by the literature. Our
 data suggest that local diet variation is largely explained by food
 availability, and locally specialist populations consume food plants that
 are not phylogenetically novel, but do appear to represent a novel
 preference. Our results demonstrate the power of molecular methods to
 unambiguously quantify dietary variation across populations of insect
 herbivores, providing a valuable approach to understanding trophic
 interactions within and among local plant and insect herbivore
 communities.
description: Alignment of all phased
 ITS2 individualsSample names are in the
 following format: indentifier_species_(collection site). The letters a and
 b suffixed to the identifier denote the alleles for the same individual.
 Homozygotes are entered twice. Individuals were phased using a combination
 of the program PHASE 2.1 as implemented in DNASP v5 and Indelligent v1.2
 (available from:
 imperialis.inhs.illinois.edu/dmitriev/indel.asp‎).ITS2_dryad.fastaGenbank accession numbersA table of genbank accession numbers for all specimens collected during this study. Additional columns are included indicating the species and sampling site for each specimen.Kitson et al Genbank refs.xlsxPlant trnL references and beetle derived variantsA fasta file of plant sequences amplified for this paper. Sequences are not aligned globally but beetle variants are aligned to each plant reference. The description section of each fasta sequence explains whether a beetle derived sequence was identified by comparison to a reference sequence or using SAP.Plant references and beetle variants.fasta
DOI: 10.5061/dryad.gp5km40
title: Data from: Parasitic wasp-associated symbiont affects plant-mediated species interactions between herbivores

description: Microbial mutualistic symbiosis is increasingly recognised as a hidden
 driving force in the ecology of plant–insect interactions. Although
 plant‐associated and herbivore‐associated symbionts clearly affect
 interactions between plants and herbivores, the effects of symbionts
 associated with higher trophic levels has been largely overlooked. At the
 third‐trophic level, parasitic wasps are a common group of insects that
 can inject symbiotic viruses (polydnaviruses) and venom into their
 herbivorous hosts to support parasitoid offspring development. Here, we
 show that such third‐trophic level symbionts act in combination with venom
 to affect plant‐mediated interactions by reducing colonisation of
 subsequent herbivore species. This ecological effect correlated with
 changes induced by polydnaviruses and venom in caterpillar salivary glands
 and in plant defence responses to herbivory. Because thousands of
 parasitoid species are associated with mutualistic symbiotic viruses in an
 intimate, specific relationship, our findings may represent a novel and
 widespread ecological phenomenon in plant–insect interactions.
description: Oviposition choice-test,
 transcript levels in caterpillar’s salivary glands and in plant defence
 responses to herbivoryCusumano et al. 2018 Ecology
 Letters data.zip
DOI: 10.5061/dryad.mq5ct
title: Data from: Secondary evolution of a self-incompatibility locus in the Brassicaceae genus Leavenworthia

description: Self-incompatibility (SI) is the flowering plant reproductive system in
 which self pollen tube growth is inhibited, thereby preventing
 self-fertilization. SI has evolved independently in several different
 flowering plant lineages. In all Brassicaceae species in which the
 molecular basis of SI has been investigated in detail, the product of the
 S-locus receptor kinase (SRK) gene functions as receptor in the initial
 step of the self pollen-rejection pathway, while that of the S-locus
 cysteine-rich (SCR) gene functions as ligand. Here we examine the
 hypothesis that the S locus in the Brassicaceae genus Leavenworthia is
 paralogous with the S locus previously characterized in other members of
 the family. We also test the hypothesis that self-compatibility in this
 group is based on disruption of the pollen ligand-producing gene. Sequence
 analysis of the S-locus genes in Leavenworthia, phylogeny of S alleles,
 gene expression patterns, and comparative genomics analyses provide
 support for both hypotheses. Of special interest are two genes located in
 a non-S locus genomic region of Arabidopsis lyrata that exhibit domain
 structures, sequences, and phylogenetic histories similar to those of the
 S-locus genes in Leavenworthia, and that also share synteny with these
 genes. These A. lyrata genes resemble those comprising the A. lyrata S
 locus, but they do not function in self-recognition. Moreover, they appear
 to belong to a lineage that diverged from the ancestral Brassicaceae
 S-locus genes before allelic diversification at the S locus. We
 hypothesize that there has been neo-functionalization of these
 S-locus-like genes in the Leavenworthia lineage, resulting in evolution of
 a separate ligand-receptor system of SI. Our results also provide support
 for theoretical models that predict that the least constrained pathway to
 the evolution of self-compatibility is one involving loss of pollen gene
 function.
description: Lal2/SRK alignment for
 entire coding sequenceNexus-formatted
 alignment of the full coding sequence for SRK and Lal2 sequences included
 in Figure 2-A. Includes commands used for phylogenetic inference in
 mrbayes.lal2_srk_all.nexLal2/SRK alignment for S-domain coding sequenceNexus-formatted alignment of the S-domain coding sequence for SRK and Lal2 sequences included in Figure S3-A. Includes commands used for phylogenetic inference in mrbayes.lal2_srk_sdom.nexLal2/SRK alignment for coding sequence excluding S-domainNexus-formatted alignment of the coding sequence excluding the S-domain for SRK and Lal2 sequences included in Figure S3-B. Includes commands used for phylogenetic inference in mrbayes.lal2_srk_rest.nex
DOI: 10.5061/dryad.ks633
title: Data from: Geographical barriers and dispersal propensity interact to limit range expansions of Himalayan birds

description: Range expansions are limited by two key factors. These are (1) dispersal,
 which includes a species’ intrinsic mobility, geographical barriers, and
 their interaction; and (2) the ability of a species to persist beyond its
 current range. I evaluate the role of these in affecting bird species
 distributions across the Himalayas, under a hypothesis that many species
 have recently expanded their range out of an eastern Pleistocene refuge. I
 measured wing shape as a proxy for dispersal ability and topographic
 complexity across the Himalayas as a proxy for dispersal barriers. As a
 factor affecting the potential for persistence in novel locations, I
 compared similarity of a species’ climatic envelope in the east, the
 hypothesized historical refuge, and the west, the location of recent
 colonization. Climatic similarity, wing shape, and the interaction of
 topographic complexity with wing shape all contribute significantly to the
 range extent of a given species. The result highlights the important
 interaction between morphological and landscape factors in affecting
 successful range expansions. The two dispersal-related parameters together
 explain two times the variance explained by climate, but I present
 additional evidence that other factors besides climate—notably biotic
 interactions—affect the ability of a species to persist beyond its range.
description: Data
 SupplementExcel spreadsheet
 containing wing shape, elevational and geographic range limits, habitat
 affinity, and foraging stratum for 444 species of Himalayan birds. Super
 species designation is indicated. Climate similarity and landscape
 complexity encountered by each species is also included, and measurements
 from Field Museum of Natural History specimens are on a separate
 tab.AEWhite_Am_Nat_2016_Data_Supp.xls