cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4r7b7hg1
title: Data from: Marine-freshwater transitions are associated with the evolution of dietary diversification in terapontid grunters (Teleostei: Terapontidae)

description: The ecological opportunities associated with transitions across the
 marine-freshwater interface are regarded as an important catalyst of
 diversification in a range of aquatic taxa. Here, we examined the role of
 these major habitat transitions and trophic diversification in a radiation
 of Australasian fishes using a new molecular phylogeny incorporating 37
 Terapontidae species. A combined mitochondrial and nuclear gene analysis
 yielded a well supported tree with most nodes resolved. Ancestral
 terapontids appear to have been euryhaline in habitat affiliation, with a
 single transition to freshwater environments producing all Australasian
 freshwater species. Mapping of terapontid feeding modes onto the molecular
 phylogeny predicted carnivorous dietary habits were displayed by ancestral
 terapontids, which subsequently diversified into a range of additional
 carnivorous, omnivorous, herbivorous and detritivorous dietary modes upon
 transition to freshwater habitats. Comparative analyses suggested that
 following the freshwater invasion, the single freshwater clade has
 exhibited an increased rate of diversification at almost three times the
 background rate evident across the rest of the family. The
 marine-freshwater transition within Terapontidae appears to have resulted
 in substantial dietary radiation in freshwater environments, as well as
 increased lineage diversification rates relative to euryhaline-marine
 habitats.
description: tera.cb.rag1.2.concatFasta formatted file containing the sequence alignment used for all analyses.terapontidae.diet.contentThis table contains the proportion of different food items in the diet of each Terapontidae species included. The source of this information is contained in the supplementary material published with the paper.
DOI: 10.5061/dryad.3hh96v4
title: Data from: Natural selection drives parallel divergence in the mountain plant Heliosperma pusillum s.l.

description: (1) The evolution of species or ecotypes can occur gradually through
 neutral and adaptive genetic changes. To explore the influence of natural
 selection during early phases of divergence, morphological and ecological
 discontinuity and its adaptive significance were investigated in six pairs
 of alpine and independently evolved montane populations of Heliosperma
 pusillum .; the latter are usually taxonomically recognised at the species
 rank in spite of their highly doubtful debatable taxonomic value. (2) We
 tested whether environmental conditions – characterised by Landolt
 indicator values from vegetation surveys and temperature measurements –
 and morphology of alpine and montane populations differ discretely and in
 parallel across six population pairs. By reciprocal transplantation
 experiments in natural environments in two population pairs and in climate
 chambers for five population pairs we compared fitness of native vs.
 non-native individuals. (3) Alpine and montane populations differed in
 environmental conditions and morphology within each pair. Morphological
 differentiation occurred in parallel and correlated with environmental,
 but not with genetic distances. In both environments, native individuals
 had higher establishment success and plant size. (4) Differentiation of
 the independently evolved montane populations is driven by natural
 selection and parallel, independent adaptation in response to drought,
 lower irradiance and higher, less fluctuating temperatures in montane and
 alpine populations, respectively. Our study system exemplifies rapid,
 parallel evolution leading to morphologically and ecologically strongly
 divergent, though fully interfertile, ecotypes.
description: Ecological
 DifferentiationAccompanying vegetation
 and the attributed Landolt indicator valuesDataNiche.csvMorphological differentiationcharacter values of morphologyheliosperma_morphometry_CB.csvTransplantsMonitoringFitness Monitoring in natural populationsTransplants SurvivalNumber of seedlings recorded in natural populationsTransplantsNumberSeedlings.csvGermination and Fitness recorded in climate chambersKeimungFitnessKlimaschrank.csv
DOI: 10.5061/dryad.9b37gv4
title: Data from: Costs of injury for scent signalling in a strepsirrhine primate

description: Honesty is crucial in animal communication when signallers are conveying
 information about their condition. Condition dependence implies a cost to
 signal production; yet, evidence of such cost is scarce. We examined the
 effects of naturally occurring injury on the quality and salience of
 olfactory signals in ring-tailed lemurs (Lemur catta). Over a decade, we
 collected genital secretions from 23 (13 male, 10 female) adults across 34
 unique injuries, owing primarily to intra-group fights. Using gas
 chromatography-mass spectrometry, we tested for differences in the
 chemical composition of secretions across pre-injury, injury, and
 recovery, in animals that did and did not receive antibiotics. Lemur
 genital secretions were significantly dampened and altered during injury,
 with patterns of change varying by sex, season, and antibiotics. Using
 behavioural bioassays (excluding odorants from antibiotic-treated
 animals), we showed that male ‘recipients’ discriminated injury status
 based on scent alone, directing more competitive counter marking towards
 odorants from injured vs. uninjured male ‘signallers.’ That injured
 animals could not maintain their normal signatures provides rare evidence
 of the energetic cost to signal production. That conspecifics detected
 olfactory-encoded ‘weakness’ suggests added behavioural costs: By
 influencing the likelihood of intra- or inter-sexual conflict,
 condition-dependent signals could have important implications for
 socio-reproductive behaviour.
description: Behavioural bioassays on
 captive ring-tailed lemurs (Lemur catta)Results of behavioural
 bioassays conducted in October 2016 at the Duke Lemur Center in Durham,
 North Carolina. All animals were captive born adults, housed socially in
 single or mixed-sex social groups. All bioassays were videotaped and
 animal behaviour recorded using a published ethogram (see manuscript
 Supplementary Material). Each bioassay is represented by two data lines
 (one for each dowel used in each trial).SREP-18-10168A_bioassays.csvGC-MS odorant dataOdorant chemical data for 99 scent secretion samples collected from adult, captive-born ring-tailed lemurs housed at the Duke Lemur Center in Durham, North Carolina, USA. Odorant data derived from GC-MS analyses of scent secretions on cotton swabs, all samples collected between 2007-2016. Datafile includes 12 metadata columns and 318 dependent variable columns (retention times of individual chemical compound peaks given in the column headings).SREP-18-10168A_ GCMS.csv
DOI: 10.5061/dryad.177g0
title: Data from: Functional identity and diversity of animals predict ecosystem functioning better than species-based indices

description: Drastic biodiversity declines have raised concerns about the deterioration
 of ecosystem functions and have motivated much recent research on the
 relationship between species diversity and ecosystem functioning. A
 functional trait framework has been proposed to improve the mechanistic
 understanding of this relationship, but this has rarely been tested for
 organisms other than plants. We analysed eight datasets, including five
 animal groups, to examine how well a trait-based approach, compared with a
 more traditional taxonomic approach, predicts seven ecosystem functions
 below- and above-ground. Trait-based indices consistently provided greater
 explanatory power than species richness or abundance. The frequency
 distributions of single or multiple traits in the community were the best
 predictors of ecosystem functioning. This implies that the ecosystem
 functions we investigated were underpinned by the combination of trait
 identities (i.e. single-trait indices) and trait complementarity (i.e.
 multi-trait indices) in the communities. Our study provides new insights
 into the general mechanisms that link biodiversity to ecosystem
 functioning in natural animal communities and suggests that the observed
 responses were due to the identity and dominance patterns of the trait
 composition rather than the number or abundance of species per se.
description: Bees-Field beans
 dataMetadataBees-Oilseed rape dataBees-Strawberries dataNematodes dataEarthworms dataDung beetles dung removal dataDung beetles seed removal dataCarabids aphid biocontrol dataCarabids seed As dataCarabids seed Ca dataCarabids seed Ga dataCarabids seed Pt data
DOI: 10.5061/dryad.366j4
title: Data from: Monte Carlo Strategies for selecting parameter values in simulation experiments

description: Simulation experiments are used widely throughout evolutionary biology and
 bioinformatics to compare models, promote methods, and test hypotheses.
 The biggest practical constraint on simulation experiments is the
 computational demand, particularly as the number of parameters increases.
 Given the extraordinary success of Monte Carlo methods for conducting
 inference in phylogenetics, and indeed throughout the sciences, we
 investigate ways in which Monte Carlo framework can be used to carry out
 simulation experiments more efficiently. The key idea is to sample
 parameter values for the experiments, rather than iterate through them
 exhaustively. Exhaustive analyses become completely infeasible when the
 number of parameters gets too large, whereas sampled approaches can fare
 better in higher dimensions. We illustrate the framework with applications
 to phylogenetics and genetic archaeology.
description: Scripts and sources for
 Case study 2Our C++ implementation
 of the plant domestication model described in Allaby et al (2008)
 referenced in our manuscript, along with the Python scripts used to
 demonstrate our MCMC/importance sampling approach with this
 model.CaseStudyTwo.tar.bz2UPGMA/NJ comparison Python scriptsScripts used to perform MCMC/importance sampling to compare UPGMA and NJ tree inference methods. The scripts used to compare these methods using a grid search approach, and at random points sampled uniformly from the prior distribution are also included, as well as scripts to compare the grid search/prior sampling to our MCMC+IS method.CaseStudyOne.tar.bz2supplement_LeighBryant2015Updated supplementary information, including details of case study simulations.
DOI: 10.5061/dryad.5081qr5
title: Data from: Populations with greater flexibility in floral traits modify mating system in response to the pollinator environment

description: 1. Mixed mating and variation in outcrossing rate among populations of the
 same species are common. Outcrossing can be affected by pollinator
 activity and floral traits that facilitate or impede autonomous
 self-fertilization. However, the relative contribution of pollen
 limitation and evolved differences in the ability to self fertilize to
 variation in the mating system is poorly understood and can only be
 disentangled using an experimental approach. 2. We placed arrays of plants
 from eight Campanula americana populations that varied in autonomous
 selfing ability (hereafter "autonomy") in sun and shade habitats
 to create high- and low-pollination environments. Floral visitors were
 observed and pollen limitation, dichogamy, herkogamy, and pollen
 persistence within the flower were measured. Outcrossing rate was
 estimated for a subset of the arrays. 3. Pollen limitation was over
 three-times higher in the shade than the sun due to differences in
 pollinator visitation. Populations with high levels of autonomy displayed
 greater pollen persistence and dichogamy in the more pollen-limited
 environments than in the high-pollination environments. In these
 high-autonomy populations, outcrossing rates were tightly associated with
 pollen limitation, with reduced outcrossing under strong pollen
 limitation. In contrast, populations with intermediate autonomy levels had
 less plastic floral traits and their outcrossing rates changed little with
 pollen limitation.4. Mating system was shaped by both the pollination
 environment and the magnitude of plasticity in floral traits. The
 experimental approach used here revealed that plasticity in floral traits
 provides the ability to adjust mating system in response to limited
 potential for outcrossing. The lack of plasticity in some populations
 could explain mismatches between pollinator activity and mating system in
 natural populations. Finally, flexibility in the mating system may help
 explain the prevalence of mixed mating.
description: Pollinator-data-Table-1Pollinator visitation to experimental arraysHerkogamy-data-Table-2Herkogamy data for arrays of Campanula americana from high and medium autogamy populations in placed in sun and shade environments.Male-traits-Table-2Male traits (dichogamy and pollen persistence) for arrays of Campanula americana from high and medium autogamy populations in placed in sun and shade environmentsPollen-limitation-Table-2Pollen limitation for arrays of Campanula americana from high and medium autogamy populations in placed in sun and shade environmentsOutcrossing-Table-3Outcrossing rates for arrays of Campanula americana from high and medium autogamy populations that experience a range of pollen limitation.
DOI: 10.5061/dryad.8pq6c
title: Data from: Stress hormone receptors change as range expansion progresses in house sparrows

description: As ranges expand, individuals encounter different environments at the
 periphery than at the centre of the range. Previously, we have shown that
 glucocorticoids (GCs) vary with range expansion: individuals at the range
 edge release more GCs in response to restraint. Here, we measured
 hippocampal mRNA expression of GC receptors (mineralocorticoid, MR and
 glucocorticoid, GR) in eight house sparrow (Passer domesticus) populations
 varying in age. We found that individuals closest to the range edge had
 the lowest expression of MR relative to GR; in all likelihood, this
 relationship was driven by a marginal reduction of MR mRNA at the range
 edge. Reduced MR (relative to GR) might allow enhanced GC binding to GR,
 the lower affinity receptor that would enhance a rapid physiological and
 behavioural response to stressors. The insights gained from this study are
 not only enlightening to introduced species, but may also predict how
 certain species will react as their ranges shift owing to anthropogenic
 changes.
description: DissectionIndividual mass, tarsus, wing cord values as well as cDNA concentrations for each sample.Gene expression ValuesRaw values from qPCR output, standard curves from each plate; quantity of each gene for each individualqPCR all plates.xlsx
DOI: 10.5061/dryad.d69r2
title: Data from: Combined structural, biochemical and cellular evidence demonstrates that both FGDF motifs in alphavirus nsP3 are required for efficient replication

description: Recent findings have highlighted the role of the Old World alphavirus
 non-structural protein 3 (nsP3) as a host defence modulator that functions
 by disrupting stress granules, subcellular phase-dense RNA/protein
 structures formed upon environmental stress. This disruption mechanism was
 largely explained through nsP3-mediated recruitment of the host G3BP
 protein via two tandem FGDF motifs. Here, we present the 1.9 Å resolution
 crystal structure of the NTF2-like domain of G3BP-1 in complex with a
 25-residue peptide derived from Semliki Forest virus nsP3 (nsP3-25). The
 structure reveals a poly-complex of G3BP-1 dimers interconnected through
 the FGDF motifs in nsP3-25. Although in vitro and in vivo binding studies
 revealed a hierarchical interaction of the two FGDF motifs with G3BP-1,
 viral growth curves clearly demonstrated that two intact FGDF motifs are
 required for efficient viral replication. Chikungunya virus nsP3 also
 binds G3BP dimers via a hierarchical interaction, which was found to be
 critical for viral replication. These results highlight a conserved
 molecular mechanism in host cell modulation.
description: MST data for Figure
 3MSTdata.zip
DOI: 10.5061/dryad.320h5
title: Data from: Do brachiopods show substrate-related phenotypic variation? A case study from the Burgess Shale

description: As sessile, benthic filter feeders, brachiopods share an intimate
 relationship with their chosen substrate. Individuals of Micromitra
 burgessensis in the Burgess Shale Formation are preserved in life
 position, attached to a range of hard substrates, including skeletal
 debris, conspecific brachiopods, sponges and enigmatic tubes. Here we
 investigate the phenotypic variability of M. burgessensis associated with
 differing substrate attachments. We apply geometric morphometrics to test
 for variation by plotting landmarks on the exterior of ventral and dorsal
 valves of M. burgessensis specimens that are preserved attached to
 different substrates. Using principal component, canonical variate
 analyses and anova, we determine that there is some variation in shape
 related to substrate. Canonical variate analyses, for ventral valves and
 dorsal valves, indicate that specimens attached to the same substrate are
 recognizable in shape from specimens attached to other substrate types.
 The strength of differentiation however, is not robust and combined with
 our discriminate analysis of separate populations suggests that there is
 the potential for substrates to exercise only weak control over the
 morphology of Brachiopoda.
description: Topper et al. Raw
 coordinates used in ventral valve analysesRaw landmark coordinates
 used in ventral valve analyses exported directly from MorphoJ. This data
 has not been transformed using Generalized Procrustes
 Analysis.Topper et al. Dryad Ventral
 Valves.xlsxTopper et al. Raw
 coordinates for dorsal valvesRaw landmark coordinates
 used in dorsal valve analyses exported directly from MorphoJ. This data
 has not been transformed using Generalized Procrustes
 Analysis.Topper et al. Dryad Dorsal
 Valves.xlsxTable
 S1Table S1 Details of
 Micromitra burgessensis specimens included in the analysis, including
 information regarding attachments, locality and individual measurements.
 WQ denotes the Walcott Quarry Shale Member, RQ denotes, the slightly
 younger Raymond Quarry Shale Member and Ta refers to material collected as
 talus.Table
 S2Table S1 Details of
 Micromitra burgessensis dorsal valve specimens included in the analysis,
 including information regarding attachments, locality and individual
 measurements. WQ denotes the Walcott Quarry Shale Member and RQ denotes,
 the slightly younger Raymond Quarry Shale Member.Table
 S3Table S3 CVA results of
 valve shape variation in the ventral valves of M. burgessensis. In the
 results of the CVA, significant p values are indicated by light blue
 boxes.Table
 S4Table S3 CVA results of
 valve shape variation in the dorsal valves of M. burgessensis. In the
 results of the CVA, significant p values are indicated by light blue
 boxes.
DOI: 10.5061/dryad.4bp16g2
title: Data from: Ecological and phylogenetic predictors of mobbing behavior in a tropical dry forest

description: Mobbing represents a well-known anti-predatory behavior, where potential
 prey display aggressively against a predator. Despite considerable
 experimental and descriptive work, no models predict species participation
 in mobbing assemblages. Here, we aimed to understand why some bird species
 engage in this behavior, while others do not, and what factors can be used
 to predict mobbing engagement within an avian community. We investigated
 whether certain functional traits, such as body size, foraging guild,
 foraging mode, and strata, as well species abundance and evolutionary
 relatedness, are important mobbing predictors. To address these goals, we
 simulated the presence of the Ferruginous Pygmy-Owl (Glaucidium
 brasilianum) by broadcasting its voice in 230 experiments conducted in 115
 points, systematically distributed in a dry forest of northeastern Brazil.
 We compared these results to 162 avian surveys (point counts) conducted in
 the same area. Our avian surveys detected 108 bird species (local avian
 community), whereas our playback experiments attracted 72 species (mobbing
 assemblage). In general, small, canopy insectivorous or frugivorous birds
 dominated the mobs. The best mobbing predictors were body mass and guild,
 whereas species abundance, foraging mode, and strata were not retained in
 the best models. We found a strong phylogenetic component in body mass and
 mobbing propensity (almost 90% of the species and individuals
 participating in the mobs were passerines). At the community level, we
 found significant differences in the functional and phylogenetic structure
 of the mobbing assemblage in relation to the avian community. Our results
 suggest that mobbing behavior is tightly associated to predation risk and
 the capacity of individual species to find and detect predators, and that
 functional and phylogenetic features can predict species participation in
 this complex animal behavior.
description: Supplementary material
 Appendix_Lima et al 2018Supplementary material
 Appendix, Table A1. Shows all bird species known to participate in mobbing
 behavior against the Ferruginous Pygmy-Owl (Glaucidium brasilianum) in the
 Neotropics. Species in bold were attracted to the sound of the Pygmy-Owl
 in this study. The references represent previous studies where each
 species was detected. Species in bold that lack previous references
 represent a novel mobbing record obtained by this study. The supplementary
 material Appendix, Table A2. Shows a list of bird species recorded at the
 Fazenda Pau d’Arco, at the Chapada do Araripe, Ceará, Brazil, and their
 respective functional traits used in this study. In bold, the species
 attracted to the broadcast of the sound of the Ferruginous Pygmy-Owl
 (Glaucidium brasilianum), as a stimulus to mobbing in the study
 areaSupplementary
 material_Lima_et_al_2018.zip
DOI: 10.5061/dryad.9f878
title: Data from: Clonal reproduction shapes evolution in the lizard malaria parasite Plasmodium floridense

description: The preponderant clonal evolution hypothesis (PCE) predicts that frequent
 clonal reproduction (sex between two clones) in many pathogens capable of
 sexual recombination results in strong linkage disequilibrium and the
 presence of discrete genetic subdivisions characterized by occasional gene
 flow. We expand on the PCE and predict that higher rates of clonal
 reproduction will result in: (1) morphologically cryptic species that
 exhibit (2) low within-species variation and (3) recent between-species
 divergence. We tested these predictions in the Caribbean lizard malaria
 parasite Plasmodium floridense using 63 single-infection samples in
 lizards collected from across the parasite's range, and sequenced
 them at two mitochondrial, one apicoplast, and five nuclear genes. We
 identified 11 provisionally cryptic species within P. floridense, each of
 which exhibits low intraspecific variation and recent divergence times
 between species (some diverged ∼110000 years ago). Our results are
 consistent with the hypothesis that clonal reproduction can profoundly
 affect diversification of species capable of sexual recombination, and
 suggest that clonal reproduction may have led to a large number of
 unrecognized pathogen species. The factors that may influence the rates of
 clonal reproduction among pathogens are unclear, and we discuss how
 prevalence and virulence may relate to clonal reproduction.
description: Adsl_alignmentAtub_alignmentclpC_alignmentcoxI_alignmentcytB_alignmentEF2_alignmentHisH3_alignmentHSP70_alignment