cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m097580
title: Data from: Male responses to sperm competition risk when rivals vary in their number and familiarity

description: Males of many species adjust their reproductive investment to the number
 of rivals present simultaneously. However, few studies have investigated
 whether males sum previous encounters with rivals, and the total level of
 competition has never been explicitly separated from social familiarity.
 Social familiarity can be an important component of kin recognition and
 has been suggested as a cue that males use to avoid harming females when
 competing with relatives. Previous work has succeeded in independently
 manipulating social familiarity and relatedness among rivals, but
 experimental manipulations of familiarity are confounded with
 manipulations of the total number of rivals that males encounter. Using
 the seed beetle Callosobruchus maculatus we manipulated three factors:
 familiarity among rival males, the number of rivals encountered
 simultaneously, and the total number of rivals encountered over a 48-hour
 period. Males produced smaller ejaculates when exposed to more rivals in
 total, regardless of the maximum number of rivals they encountered
 simultaneously. Males did not respond to familiarity. Our results
 demonstrate that males of this species can sum the number of rivals
 encountered over separate days, and therefore the confounding of
 familiarity with the total level of competition in previous studies should
 not be ignored.
description: Lymbery et al 2018 Full
 datasetContains all the data
 used in the statistical analyses for the associated manuscript. The file
 contains two spreadsheets: one containing the data and one containing a
 legend relating to column titles.Lymbery et al Full
 Dataset.xlsxLymbery et al 2018
 Reduced dataset 1Contains data used in
 the attached manuscript following the removal of three outliers for the
 purposes of data distribution, as described in the associated R code. The
 file contains two spreadsheets: one containing the data and one containing
 a legend relating to column titles.Lymbery et al Reduced Dataset
 After 1st Round of Outlier
 Removal.xlsxLymbery et al 2018
 Reduced dataset 2Contains the data used
 in the statistical analyses for the associated manuscript, after the
 removal of all outliers stated in the manuscript and associated R code.
 The file contains two spreadsheets: one containing the data and one
 containing a legend relating to column titles.Lymbery et al Reduced Dataset
 After Final Outlier Removal.xlsxLymbery et al 2018 R
 ScriptContains all the R code
 used for statistical analysis in this manuscript, with annotations to aid
 interpretation.
DOI: 10.5061/dryad.7cr21
title: Data from: Experimentally evolved and phenotypically plastic responses to enforced monogamy in a hermaphroditic flatworm

description: Sexual selection is considered a potent evolutionary force in all sexually
 reproducing organisms, but direct tests in terms of experimental evolution
 of sexual traits are still lacking for simultaneously hermaphroditic
 animals. Here, we tested how evolution under enforced monogamy affected a
 suite of reproductive traits (including testis area, sex allocation,
 genital morphology, sperm morphology and mating behaviour) in the
 outcrossing hermaphroditic flatworm Macrostomum lignano, using an assay
 that also allowed the assessment of phenotypically plastic responses to
 group size. The experiment comprised 32 independent selection lines that
 evolved under either monogamy or polygamy for 20 generations. While we did
 not observe an evolutionary shift in sex allocation, we detected effects
 of the selection regime for two male morphological traits. Specifically,
 worms evolving under enforced monogamy had a distinct shape of the male
 copulatory organ and produced sperm with shorter appendages. Many traits
 that did not evolve under enforced monogamy showed phenotypic plasticity
 in response to group size. Notably, individuals that grew up in larger
 groups had a more male-biased sex allocation and produced slightly longer
 sperm than individuals raised in pairs. We conclude that, in this
 flatworm, enforced monogamy induced moderate evolutionary but substantial
 phenotypically plastic responses.
description: Janicke_et_al_2016_JEvolBiol_DATAFile encompasses three data sheets including (i) morphological data, (ii) behavioural data and (iii) per capita estimates of female fecundity.
DOI: 10.5061/dryad.1k8m6p2
title: Data from: Predicting drug-induced liver injury using ensemble learning methods and molecular fingerprints

description: Drug-induced liver injury (DILI) is a major safety concern in the
 drug-development process, and various methods have been proposed to
 predict the hepatotoxicity of compounds during the early stages of drug
 trials. In this study, we developed an ensemble model using three machine
 learning algorithms and 12 molecular fingerprints from a dataset
 containing 1,241 diverse compounds. The ensemble model achieved an average
 accuracy of 71.1±2.6%, sensitivity of 79.9±3.6%, specificity of 60.3±4.8%,
 and area under the receiver operating characteristic curve (AUC) of
 0.764±0.026 in five-fold cross-validation and an accuracy of 84.3%,
 sensitivity of 86.9%, specificity of 75.4%, and AUC of 0.904 in an
 external validation dataset of 286 compounds collected from the Liver
 Toxicity Knowledge Base (LTKB). Compared with previous methods, the
 ensemble model achieved relatively high accuracy and sensitivity. We also
 identified several substructures related to DILI. In addition,
description: Supplementary_Table_1Details of the training dataset.Supplementary_Table_2Details of the external validation dataset.Supplementary_Table_3The results of the 35 ensemble models in five-fold cross-validationSupplementary_Table_4The results of the 35 ensemble models in the external validation.
DOI: 10.5061/dryad.8257
title: Data from: Analysis of expressed sequence tags from the placenta of the live-bearing fish Poeciliopsis (Poeciliidae)

description: Matrotrophic fish in the genus Poeciliopsis (Poeciliidae) have a
 placenta-like structure used in post-fertilization maternal provisioning
 of the developing embryo. To understand better the structure and function
 of the Poeciliopsis placenta we derived cDNA libraries from the maternal
 follicular placenta of two matrotrophic Poeciliopsis sister species, P.
 turneri and P. presidionis. These species inherited their placenta from a
 common ancestor and represent one of three independent origins of
 placentas in Poeciliopsis. Expressed sequence tags were generated and
 putative function was determined using BLASTX homology searches and Gene
 Ontology annotation. Reverse transcriptase-PCR was used to verify placenta
 tissue expression of a putative candidate gene, alpha-2 macroglobulin.
 1956 (71.5% of the total submitted ESTs) and 924 (71.0% of the total
 submitted ESTs) unique transcripts were identified for the P. turneri and
 P. presidionis placenta, respectively. Homology search and Gene Ontology
 annotation revealed putative genes whose products may be involved in
 specific transport functions of the maternal follicle. These putative
 genes are excellent candidates for future research on the evolution of the
 placenta. We discuss our results in light of the parent-offspring conflict
 theory of placental evolution and in terms of the Poeciliid placenta
 structure and function.
description: Panhuisetal_Supplementary Table 1_Evalueranges_subThis is a supplementary table of the BLASTX results presented as the number of unique transcripts represented in a specific E-value range. The total number of P. turneri and P. presidionis unique sequences was 1956 and 924, respectively.
DOI: 10.5061/dryad.b31g6
title: Data from: The evolutionary fate of heterogeneous gene duplications: a precarious overdominant equilibrium between environment, sublethality and complementation.

description: Gene duplications occur at a high rate. Although most appear detrimental,
 some homogeneous duplications (identical gene copies) can be selected for
 beneficial increase in produced proteins. Heterogeneous duplications,
 which combine divergent alleles of a single locus, are seldom studied due
 to the paucity of empirical data. We investigated their role in an ongoing
 adaptive process at the ace-1 locus in Culex pipiens mosquitoes. We
 assessed the worldwide diversity of the ace-1 alleles (single-copy,
 susceptible S and insecticide-resistant R, and duplicated D that pair one
 S and one R copy), analyzed their phylogeography, and measured their
 fitness to understand their early dynamics using population genetics
 models. It provides a coherent and comprehensive evolutionary scenario. We
 show that D alleles are present in most resistant populations, and display
 a higher diversity than R alleles (27 vs. 4). Most appear to result from
 independent unequal crossing-overs between local single-copy alleles,
 suggesting a recurrent process. Most duplicated alleles have a limited
 geographic distribution, probably resulting from their homozygous
 sublethality (HS phenotype). In addition, heterozygotes carrying different
 HS D alleles showed complementation, indicating different recessive lethal
 mutations. Due to mosaic insecticide control practices, balancing
 selection (overdominance) plays a key role in the early dynamics
 heterogeneous duplicated alleles; it also favors a high local polymorphism
 of HS D alleles in natural populations (overdominance reinforced by
 complementation). Overall our study shows that the evolutionary fate of
 heterogeneous duplications (and their long-term role) depends on finely
 balanced selective pressures due to the environment and to their genomic
 structure.
description: Complete
 dataComplete_data.xlsxR script for the evolution experiment (cf. Fig. 3)Script_D_fitness_estimations.RR model for the invasion dynamics of homozygous-sublethal (HS) D alleles (cf. Fig. 4)Script_HS_D_invasion_dynamics.Race-1 sequences Intron2 - partial Exon3 (cf. Fig2)Seq2.txt
DOI: 10.5061/dryad.1nq6m
title: Data from: Testing a “genes-to-ecosystems” approach to understanding aquatic-terrestrial linkages

description: A ‘genes-to-ecosystems’ approach has been proposed as a novel avenue for
 integrating the consequences of intraspecific genetic variation with the
 underlying genetic architecture of a species in order to shed light on the
 relationships among hierarchies of ecological organization (genes
 [RIGHTWARDS ARROW] individuals [RIGHTWARDS ARROW] communities [RIGHTWARDS
 ARROW] ecosystems). However, attempts to identify genes with major effect
 on the structure of communities and/or ecosystem processes have been
 limited and a comprehensive test of this approach has yet to emerge. Here,
 we present an interdisciplinary field study that integrated a common
 garden containing different genotypes of a dominant, riparian tree,
 Populus trichocarpa, and aquatic mesocosms to determine how intraspecific
 variation in leaf litter alters both terrestrial and aquatic communities
 and ecosystem functioning. Moreover, we incorporate data from extensive
 trait screening and genome-wide association studies estimating the
 heritability and genes associated with litter characteristics. We found
 that tree genotypes varied considerably in the quality and production of
 leaf litter, which contributed to variation in phytoplankton abundances,
 as well as nutrient dynamics and light availability in aquatic mesocosms.
 These ‘after-life’ effects of litter from different genotypes were
 directly comparable to the responses of terrestrial communities associated
 with the living foliage. We found that multiple litter traits
 corresponding with aquatic community and ecosystem responses differed in
 their heritability. Moreover, the underlying genetic architecture of these
 traits was complex, and many genes contributed only a small portion to
 phenotypic variation. Our results provide further evidence that genetic
 variation is a key component of aquatic-terrestrial linkages, but
 challenges the ability to predict community or ecosystem responses based
 on the actions of one or a few genes.
description: Crutsinger et
 al.Excel format showing
 individual, community, and ecosystem data from mesocosm experiment sorted
 by the identity of the Populus trichocarpa genotype.Structural Equation
 Model R scriptmolecolLARS_SEM.rStructural Equation Model data filepop_dat.csv
DOI: 10.5061/dryad.t3q41
title: Data from: The power of evolutionary rescue is constrained by genetic load

description: Extinction risk of small isolated populations in changing environments can
 be reduced by rapid adaptation and subsequent growth to larger, less
 vulnerable sizes. Whether this process, called evolutionary rescue, is
 able to reduce extinction risk and sustain population growth over multiple
 generations is largely unknown. To understand the consequences of adaptive
 evolution as well as maladaptive processes in small isolated populations,
 we subjected experimental Tribolium castaneum populations founded with 10
 or 40 individuals to novel environments, one more favorable, and one
 resource poor, and either allowed evolution, or constrained it by
 replacing individuals one-for-one each generation from a non-adapting
 large population to minimize both adaptive and non-adaptive evolutionary
 processes. Replacement individuals spent one generation in the target
 novel environment before use to standardize effects due to the parental
 environment. After 8 generations we mixed a subset of surviving
 populations to facilitate admixture, allowing us to estimate drift load by
 comparing performance of mixed to unmixed groups. Evolving populations had
 reduced extinction rates, and increased population sizes in the first four
 to five generations compared to populations where evolution was
 constrained. Performance of evolving populations subsequently declined.
 Admixture restored their performance, indicating high drift load that may
 have overwhelmed the beneficial effects of adaptation in evolving
 populations. Our results indicate that evolution may quickly reduce
 extinction risk and increase population sizes, but suggest that relying
 solely on adaptation from standing genetic variation may not provide
 long-term benefits to small isolated populations of diploid sexual
 species, and that active management facilitating gene flow may be
 necessary for longer-term persistence.
description: Population size
 dataPopulation sizes,
 treatment variables, and extinction data for experimentally observed
 populations of Tribolium castaneum.All_Data_EcoEvo_Final.xlsx
DOI: 10.5061/dryad.pm29d
title: Data from: Low functional diversity promotes niche changes in natural island pollinator communities

description: Functional diversity loss among pollinators has rapidly progressed across
 the globe and is expected to influence plant–pollinator interactions in
 natural communities. Although recent findings suggest that the
 disappearance of a certain pollinator functional group may cause niche
 expansions and/or shifts in other groups, no study has examined this
 prediction in natural communities with high plant and pollinator
 diversities. By comparing coastal pollination networks on continental and
 oceanic islands, we examined how community-level flower visit patterns are
 influenced by the relative biomass of long-tongued pollinators (RBLP). We
 found that RBLP significantly correlated with pollinator functional
 diversity and was lower in oceanic than in continental islands. Pollinator
 niches shifted with decreasing RBLP, such that diverse species with
 various proboscis lengths, especially short-tongued species, increasingly
 visited long-tubed flowers. However, we found no conspicuous negative
 impacts of low RBLP and the consequent niche shifts on pollinator visit
 frequencies to flowers in oceanic island communities. Notably, fruit set
 significantly decreased as RBLP decreased in a study plant species. These
 results suggest that niche shifts by other functional groups can generally
 compensate for a decline in long-tongued pollinators in natural
 communities, but there may be negative impacts on plant reproduction.
description: primary_dataPlant-pollinator interaction data of the studies used in the analysis.
DOI: 10.5061/dryad.qn54m
title: Data from: Comprehensive diagnosis of PCDD/F emission from three hazardous waste incinerators

description: Comprehensive diagnosis of polychlorinated dibenzo-p-dioxin and
 dibenzofuran (PCDD/F) emissions was systematically conducted on three
 hazardous waste incinerators (HWIs.) Results indicated that PCDD/F mainly
 existed in the solid phase before the bag filter. This was especially true
 for higher chlorinated dioxin and furan congeners (hexa-, hepta- and
 octa-.) The aged bag filters tended to increase the gas-phase PCDD/F.
 Emissions also increased due to PCDD/F desorption from circulated
 scrubbing solution and plastic packing media used in the wet scrubber. The
 PCDD/F concentrations were elevated during start-up process, reaching up
 to 5.4 times higher than those measured during the normal operating
 period. The ratios of PCDFs/PCDDs revealed that the surface-catalyzed de
 novo synthesis was the dominant pathway of PCDD/F formation. Installation
 of more efficient fabric filters, intermittent replacement of circulated
 scrubbing solution will result in reduced PCDD/F emission. Additionally,
 2,3,4,7,8-PeCDF correlated well with the international toxic equivalent
 quantity (I-TEQ) value, which suggests that 2,3,4,7,8-PeCDF could act as
 an I-TEQ indicator.
description: Comprehensive Diagnosis
 of PCDDF Emission from Three Hazardous Waste Incinerators
 dataIt contains the mass
 concentration and I-TEQ of 17 I-TEQ weighted PCDD/F congeners. The data
 are categorized by different waste incinerators as well as different
 sampling points. For some samples, the vapor and solid phase
 concentrations are analyzed separately.
DOI: 10.5061/dryad.km42m
title: Data from: A review of riverine ecosystem service quantification: research gaps and recommendations

description: 1.Increasing demand for benefits provided by riverine ecosystems threatens
 their sustainable provision. The ecosystem service concept is a promising
 avenue to inform riverine ecosystem management, but several challenges
 have prevented the application of this concept. 2.We quantitatively assess
 the field of riverine ecosystem services’ progress in meeting these
 challenges. We highlight conceptual and methodological gaps, which have
 impeded integration of the ecosystem service concept into management.
 3.Across 89 relevant studies, 33 unique riverine ecosystem services were
 evaluated, for a total of 404 ecosystem service quantifications. Studies
 quantified between one and 23 ecosystem services, although the majority
 (55%) evaluated three or less. Among studies that quantified more than one
 service, 58% assessed interactions between services. Most studies (71%)
 did not include stakeholders in their quantification protocols, and 34%
 developed future scenarios of ecosystem service provision. Almost half
 (45%) conducted monetary valuation, using 16 methods. Only 9% did not
 quantify or discuss uncertainties associated with service quantification.
 The indicators and methods used to quantify the same type of ecosystem
 service varied. Only 3% of services used indicators of capacity, flow, and
 demand in concert. 4.Our results suggest indicators, data sources, and
 methods for quantifying riverine ecosystem services should be more clearly
 defined and accurately represent the service they intend to quantify.
 Furthermore, more assessments of multiple services across diverse spatial
 extents and of riverine service interactions are needed, with better
 inclusion of stakeholders. Addressing these challenges will help riverine
 ecosystem service science inform river management. 5.Synthesis and
 applications. The ecosystem service concept has great potential to inform
 riverine ecosystem management and decision making processes. However, this
 review of riverine ecosystem service quantification uncovers several
 remaining research gaps, impeding effective use of this tool to manage
 riverine ecosystems. We highlight these gaps and point to studies
 showcasing methods that can be used to address them.
description: Review of riverine
 ecosystem service quantification studiesThis file contains a
 database of studies that quantified riverine ecosystem services prior to
 April 2016, as well as quantitative data on the location of each study,
 the types and numbers of ecosystem services evaluated, and the methods
 used to quantify services.Hanna_Riverine ES Review
 Database.xlsx
DOI: 10.5061/dryad.dc068
title: Data from: Heritability of behavioural tolerance to high CO2 in a coral reef fish is masked by non-adaptive phenotypic plasticity

description: Previous studies have demonstrated limited potential for acclimation of
 adversely affected olfactory behaviours in reef fishes under elevated CO2,
 indicating that genetic adaptation will be required to maintain
 behavioural performance in the future. Adaptation depends on the presence
 of heritable phenotypic variation in the trait, which may differ between
 populations and environments. We used parent-offspring regressions to
 estimate the heritability (h2) of variation in behavioural tolerance to
 high CO2 (754 μatm) in both field-collected and laboratory-reared families
 of Acanthochromis polyacanthus. Tolerance to elevated CO2 was measured by
 determining the behavioural response of individuals to chemical alarm
 cues. Both populations exhibited high heritability of olfactory behaviour
 phenotype (father-midoffspring h2 = 0.56 & 0.65, respectively)
 when offspring were acutely exposed to high CO2 for 4 days. However, there
 was no heritability in the behavioural phenotype when juveniles were
 chronically exposed to high CO2 for 6 weeks in the laboratory-reared
 families. Parental exposure to high CO2 during the breeding season did not
 alter this relationship between heritability and length of juvenile
 exposure to high CO2. These results demonstrate that variation in
 behavioural tolerance to high CO2 is heritable, but adaptive potential may
 be constrained by a loss of phenotypic variation when juveniles
 permanently experience a high CO2 environment, as will occur with rising
 CO2 levels in the ocean.
description: Heritability of
 behavioural tolerance to high CO<sub>2</sub> in a coral reef
 fish is masked by non-adaptive phenotypic plasticityThis file contains data
 for parental and juvenile olfactory behaviours as well as water chemistry
 parameters at both James Cook University and Lizard Island Research
 Station.Welch and Munday Evol App 2017
 Data.xlsx