cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b0hs8gr
title: Data from: Extensive reduction of the nuclear pore complex in nucleomorphs

description: The nuclear pore complex (NPC) is a large macromolecular assembly situated
 within the pores of the nuclear envelope. Through interactions between its
 subcomplexes and import proteins, the NPC mediates the transport of
 molecules into and out of the nucleus and facilitates dynamic chromatin
 regulation and gene expression. Accordingly, the NPC constitutes a highly
 integrated nuclear component that is ubiquitous and conserved amongst
 eukaryotes. Potential exceptions to this are nucleomorphs: highly reduced,
 relict nuclei that were derived from green and red algae following their
 endosymbiotic integration into two lineages, the chlorarachniophytes and
 the cryptophyceans. A previous investigation failed to identify NPC genes
 in nucleomorph genomes suggesting that these genes have either been
 relocated to the host nucleus or lost. Here we sought to investigate the
 composition of the NPC in nucleomorphs by using genomic and transcriptomic
 data to identify and phylogenetically classify NPC proteins in
 nucleomorph-containing algae. Although we found NPC proteins in all
 examined lineages, most of those found in chlorarachniophytes and
 cryptophyceans were single copy, host-related proteins that lacked signal
 peptides. Two exceptions were Nup98 and Rae1, which had clear
 nucleomorph-derived homologues. However, these proteins alone are likely
 insufficient to structure a canonical NPC and previous reports revealed
 that Nup98 and Rae1 have other nuclear functions. Ultimately, these data
 indicate that nucleomorphs represent eukaryotic nuclei without a canonical
 NPC, raising fundamental questions about their structure and function.
description: Nucleomorph Nuclear Pore
 DataA
 zipped folder containing all the alignments (which contain newly
 identified nucleoporins and reference proteins), the phylogenetic trees
 (used to infer figures 1 and 2), the HMM models used for the search,
 signal peptide predictions for all the proteins in the alignments, and a
 text file with the phylogenetic models used for each tree (as selected in
 IQTree using ModelFinder).nuclear_pore_data_dryad.zip
DOI: 10.5061/dryad.tg142pt
title: Data from: A survey of risk tolerance to multiple sclerosis therapies

description: Objective: To determine tolerance to various risk scenarios associated
 with current MS therapies. Methods: People with MS from the North American
 Research Committee on Multiple Sclerosis (NARCOMS) Registry’s online
 cohort and the National Multiple Sclerosis Society were invited to
 complete a questionnaire on tolerance to real-world risks associated with
 a hypothetical therapy. Multiple risks levels were presented including,
 skin rash, infection, kidney injury, thyroid injury, liver injury, and
 PML. Results: Both progressive multifocal leukoencephalopathy (PML) and
 kidney injury had lowest risk tolerance at 1:1,000,000 and thyroid and
 infection risks had highest tolerance at 1:1,000. Males, younger age and
 participants with greater disability reported a higher tolerance to all
 risk scenarios. Those that were currently taking a MS therapy reported
 higher tolerance than those not taking any therapy. Participants taking
 infusion therapies reported high tolerance to all risks and those taking
 injectables reported a lower tolerance. Conclusion: People with MS
 displayed a wide range of RT for MS therapies. Our study identified sex,
 age, disability and current DMT use to be associated with RT.
description: Supplementary
 TablesSupplementary
 TablesRT
 main manuscript, Supp Tables,
 8-9-2018.pdf
DOI: 10.5061/dryad.n11h95s
title: Data from: Annual environmental variation influences host tolerance to parasites

description: When confronted with a parasite or pathogen, hosts can defend themselves
 by resisting or tolerating the attack. While resistance can be diminished
 when resources are limited, it is unclear how robust tolerance is to
 changes in environmental conditions. Here we investigate the sensitivity
 of tolerance in a single host population living in a highly variable
 environment. We manipulated the abundance of an invasive parasitic fly,
 Philornis downsi, in nests of Galápagos mockingbirds (Mimus parvulus) over
 four field seasons and measured host fitness in response to parasitism.
 Mockingbird tolerance to P. downsi varied significantly among years and
 decreased when rainfall was limited. Video observations indicate that
 parental provisioning of nestlings appears key to tolerance: in drought
 years, mockingbirds likely do not have sufficient resources to compensate
 for the effects of P. downsi. These results indicate that host tolerance
 is a labile trait and suggest that environmental variation plays a major
 role in mediating the consequences of host-parasite interactions.
description: McNewetal_dryad_nestlingmeasurementsCondition and size of nestlings in study. Each row is a nestling. Nestlings were measured multiple times (see methods).McNewetal_dryad_behaviorData on nestling provisioning used in the study. Each row is a video observation period, recorded at an individual nest.McNewetal_dryad_allnestsData on reproductive success of nests in the study. Each row is a nest.
DOI: 10.5061/dryad.r20qm4j
title: Data from: Species asynchrony and response diversity determine multifunctional stability of natural grasslands

description: 1. A growing body of empirical evidence has suggested that biodiversity
 affects the simultaneous performance of multiple ecosystem functions (that
 is, ecosystem multifunctionality). Given increasing environmental
 variability and uncertainty under global change, an emerging question is
 how biodiversity influences the stability of multiple functions (that is,
 multifunctional stability). We currently know little, however, about the
 determinants and mechanisms of multifunctional stability, which is of
 practical importance for ensuring the sustainable provision of multiple
 functions. 2. Here we examined mechanisms contributing to stability
 (quantified as the ratio of the mean to the standard deviation) of
 multiple functions related to ecosystem productivity and carbon
 sequestration, including plant aboveground and belowground productivity,
 litter production, gross primary productivity, and ecosystem respiration,
 in a large grassland biodiversity experiment in Inner Mongolia. 3. We
 found that community-wide species asynchrony was a strong driver to
 stabilize multiple functions. Community-wide asynchrony mediated the
 positive effects of species richness and response diversity (describing
 how species with similar effects on ecosystem function respond differently
 to environmental change) on multifunctional stability. However, species
 richness had a negative direct effect on multifunctional stability
 because, although it increased the averaged temporal mean of multiple
 functions, it strongly increased the averaged temporal standard deviation
 of multiple functions. The overall effects of species richness on
 multifunctional stability were thus negative, whereas those of response
 diversity were positive. 4. Synthesis. The studied ecosystem functions
 related to ecosystem productivity and carbon sequestration are important
 in natural grasslands across the world. We conclude that species
 asynchrony and response diversity, rather than species richness, are key
 to the ecosystem multifunctional stability. The loss of response diversity
 and compensatory mechanisms would likely reduce the long-term
 sustainability of grasslands in the face of global change.
description: Multifunctional
 stability_data_Sasaki_JEcol2019Original data
 file
DOI: 10.5061/dryad.c5rs958
title: Data from: Habitat explains patterns of population decline for an invasive crayfish

description: Invasive non-indigenous species are defined by their impacts: they
 substantially change native communities or ecosystems. Accordingly,
 invasive species might transform their habitats in ways that eventually
 become unfavorable to them, causing population declines or even
 extirpations. Here we use over 40 years of systematically collected data
 on the abundance of the invasive rusty crayfish Faxonius rusticus from 17
 lakes in northern Wisconsin, USA to explore if population declines of this
 invader are related to the prevalence of rocky habitat, which shelters
 crayfish from predators and is unchanged by crayfish. We predicted that
 lakes with rock-dominated substrates would be resistant to F. rusticus
 population declines, whereas lakes lacking rock-dominated substrates would
 experience F. rusticus declines due to crayfish destruction of
 shelter-providing macrophytes. We found that in nearly half (47%) of the
 study lakes, F. rusticus experienced population declines over the study
 time period, and these lakes had significantly lower proportions of rock
 substrate than lakes that did not experience population declines. We
 recommend that more studies should investigate the potential for invasive
 species-mediated community or ecosystem feedbacks to eventually contribute
 to their own population declines.
description: Rusty crayfish CPUE
 through time and trap locationsWorksheet 1: Study lakes
 with proportion rock and mean catch-per-unit effort of male Faxonius
 rusticus by year. Missing values are years where the lake was not sampled.
 Worksheet 2: Trap locations (WGS84 decimal degrees) for study lakes from
 baited trapping for rusty crayfish Faxonius rusticus.Larson_etal_Data.xlsx
DOI: 10.5061/dryad.4b14m4r
title: Data from: Variable effects on growth and defence traits for plant ecotypic differentiation and phenotypic plasticity along elevation gradients

description: Along ecological gradients, phenotypic differentiation can arise through
 natural selection on trait diversity and magnitude, and environment-driven
 plastic changes. The magnitude of ecotypic differentiation versus
 phenotypic plasticity can vary depending on the traits under study. Using
 reciprocal transplant-common gardens along steep elevation gradients, we
 evaluated patterns of ecotypic differentiation and phenotypic plasticity
 of several growth and defence-related traits for two coexisting but
 unrelated plant species, Cardamine pratensis and Plantago major. For both
 species, we observed ecotypic differentiation accompanied by plasticity in
 growth related traits. Plants grew faster and produced more biomass when
 placed at low elevation. In contrast, we observed fixed ecotypic
 differentiation for defence and resistance traits. Generally, low
 elevation ecotypes produced higher chemical defences regardless of the
 growing elevation. Yet, some plasticity was observed for specific
 compounds, such as indole glucosinolates. The results of this study may
 suggest that ecotypic differentiation in defence traits is maintained by
 costs of chemical defence production, while plasticity in growth traits is
 regulated by temperature driven growth response maximization.
description: Growth-, resistance-,
 and chemical-related trait measurement of C. pratensis and P major
 plantThe data file consists
 into an excel document divided in three worksheets; the first two named
 "C_pratensis" and P_major" contain data about the
 treatments, measurements of plant growth and plant secondary metabolites
 and the herbivore performance (one file for each species used in the
 study); the third worksheet called "Unit and Info About
 Variables" contains info and measuring units about treatments and
 dependent variables used in the study.Raw_data.xlsx
DOI: 10.5061/dryad.55mc74q
title: Data from: Mechanisms of a locally adaptive shift in allocation among growth, reproduction, and herbivore resistance in Mimulus guttatus

description: Environmental gradients can drive adaptive evolutionary shifts in plant
 resource allocation among growth, reproduction, and herbivore resistance.
 However, few studies have attempted to connect these adaptations to
 underlying physiological and genetic mechanisms. Here, we evaluate
 potential mechanisms responsible for a coordinated locally adaptive shift
 between growth, reproduction, and herbivore defense in the yellow
 monkeyflower, Mimulus guttatus. Through manipulative laboratory
 experiments we found that gibberellin (GA) growth hormones may play a role
 in the developmental divergence between perennial and annual ecotypes of
 M. guttatus. Further, we detected an interaction between a locally
 adaptive chromosomal inversion, DIV1, and GA addition. This finding is
 consistent with the inversion contributing to the evolutionary divergence
 between inland annual and coastal perennial ecotypes by reducing GA
 biosynthesis/activity in perennials. Finally, we found evidence that the
 DIV1 inversion is partially responsible for a coordinated shift in the
 divergence of growth, reproduction, and herbivore resistance traits
 between coastal perennial and inland annual M. guttatus. The inversion has
 already been established to have a substantial impact on the life-history
 shift between long-term growth and rapid reproduction. Here, we
 demonstrate that the DIV1 inversion also has sizable impacts on both the
 total abundance and composition of phytochemical compounds involved in
 herbivore resistance.
description: GA Population Accession
 ExperimentThis is a spreadsheet of
 the results from the greenhouse gibberellin experiment with population
 accessions and basis for the PC analysis in Figure 2 and Figure
 S2.GA_Experiment_All_Traits_InlandPs_11_15_18.xlsxGA NIL ExperimentThis is a spreadsheet of results of the gibberellin addition experiment with the near isogenic lines and parental lines. It is the basis of Figure 3.GA_NILs_All_Traits_Parents&coastal_background_1_7_19.xlsxNIL PPG ExperimentThis spreadsheet contains the data from the experiment to evaluate the concentration of defensive phenylpropanoid glycoside (PPG) compounds in near isogenic and parental lines. It is the basis for Figure 4.NIL_PPG_Experiment.xlsx
DOI: 10.5061/dryad.585b5k5
title: Data from: Forecasting the response to global warming in a heat-sensitive species

description: Avoiding hyperthermia entails considerable metabolic costs for endotherms.
 Such costs increase in warm conditions, when endotherms may trade food
 intake for cooler areas to avoid heat stress and maximize their energy
 balance. The need to reduce heat stress may involve the adoption of
 tactics affecting space use and foraging behaviour, which are important to
 understand and predict the effects of climate change and inform
 conservation. We used resource selection models to examine the behavioural
 response to heat stress in the Alpine ibex (Capra ibex), a cold-adapted
 endotherm particularly prone to overheating. Ibex avoided heat stress by
 selecting the space based on the maximum daily temperature rather than
 moving hourly to ‘surf the heat wave’, which minimised movement costs but
 prevented optimal foraging. By integrating these findings with new climate
 forecasts, we predict that rising temperatures will force mountain
 ungulates to move upward and overcrowd thermal refugia with reduced
 carrying capacity. Our approach helps in identifying priority areas for
 the conservation of mountain species.
description: Alpine ibex relocation
 data along with environmental predictors used in resource selection
 analysesMale ibex observations
 and environmental data collected from May to October (2010-2011) in the
 Gran Paradiso National Park, Italy.resource_selection_ibex_data.zip
DOI: 10.5061/dryad.952vb31
title: Data from: Forest Giants on Different Evolutionary Branches: Ecomorphological Convergence in Helicopter Damselflies

description: The convergent evolution of analogous features is an evolutionary process
 occurring independently across the tree of life. From the evolution of
 echolocation, prehensile tail, viviparity or winged flight, environmental
 factors often drive this astonishing phenomenon. However, convergent
 evolution is not always conspicuous or easily identified. Giant
 damselflies count among the largest flying insects on Earth, and have
 astonishing ecologies including orb-web spider plucking and oviposition in
 phytotelmata. One species occurs in the Afrotropics and 18 species are
 found in the Neotropics. Convergent evolution was historically
 hypothesized based on the ecological and morphological affinities of these
 two geographically distant lineages, but was not supported by earlier
 phylogenetic inferences supporting their monophyly. Using a molecular
 supermatrix approach and a large selection of outgroups, we revisit and
 reject the monophyly of Afrotropical and Neotropical giant damselflies
 that is otherwise supported by a morphological phylogeny. Molecular
 divergence time estimation suggests an origin of Afrotropical giant
 damselflies in the late Paleogene, and of Neotropical ones at the
 Cretaceous/Paleogene boundary, thereby rejecting a long-standing West
 Gondwana vicariance hypothesis. The strong ecological and morphological
 resemblances between these two independent lineages represents an
 astonishing case of Amphi-Atlantic tropical convergent evolution.
description: File S1 - Matrix of
 morphological charactersMatrix used for the
 morphological phylogeny inferenceFile S2 - MrBayes input
 fileMrBayes input file for
 the phylogenetic inferenceFile S3 - MrBayes input
 file with constraintMrBayes input file for
 the phylogenetic inference with a monophyletic
 constraintMolecular Matrix
 PseudostigmatinaeMolecular matrix used
 for phylogenetic inferenceMatrix18.phyMolecular Matrix Pseudostigmatinae for BEASTMolecular matrix used for dating including partitioning informationMatrix18.nexBEAST XML fileBEAST XML file used for the best analysis based on MLE comparison and including 2 uncorrelated lognormal clocks and a birth death Tree modelPseudo_2UCL_BD_Uni.xmlBEAST tree fileTree obtained in TreeAnnotator after removing the burn-in fraction and based on the best BEAST analysis (2 UCL + BD)Pseudo_2UCL_BD_Uni.tre
DOI: 10.5061/dryad.62940t0
title: Data from: The demographic and life history costs of fear: trait-mediated effects of threat of predation on Aedes triseriatus

description: 1. Predators alter prey populations via direct lethality (density-mediated
 effects), but in many taxa the indirect nonlethal threat of predation may
 be almost as strong an effect, altering phenotypically plastic traits such
 as prey morphology, behaviour, and life history (trait-mediated effects).
 There are costs to anti-predator defences and the strength of prey
 responses to cues of predation likely depends on both the perceived level
 of risk and food availability. 2. The goal of this study was to test the
 hypothesis that the costs of nonlethal trait-mediated interactions
 impacting larvae can have carryover effects that alter life history
 traits, adult characteristics, and ultimately population dynamics. 3. The
 effects of Toxorhynchites rutilus kairomones and chemical alarm cues on
 Aedes triseriatus were assessed in a two-level factorial design
 manipulating nutrient level (low or high) and chemical cues of predation
 (present or absent). 4. Nonlethal chemical cues of predation significantly
 decreased female survivorship, and significantly decreased female size.
 Females emerged as adults significantly earlier when exposed to predation
 cues when there was high nutrient availability. When raised in the low
 nutrient treatment and exposed to predator cues adult females had 2.1
 times the hazard of death compared to high nutrient-no predator cues.
 Females raised in the high nutrient and predator cue treatment blood fed
 sooner than did females from other combinations. 5. Fear of predation can
 substantially alter prey life history traits and behaviour, which can
 cascade into dramatic population, community, and ecosystem effects.
 Exposure to predator cues significantly decreased estimated cohort rate of
 increase, potentially altering the expected population density of the next
 generation.
description: survivorship.txtfecundity_longevity_assays.txtnutrient_reserve_longevity_assays.txtcomposite_index.txt
DOI: 10.5061/dryad.n88kb1m
title: Data from: Conspecific sperm precedence is reinforced, but postcopulatory sexual selection weakened, in sympatric populations of Drosophila

description: Sexual selection can accelerate speciation by driving the evolution of
 reproductive isolation, but forces driving speciation could also
 reciprocally feedback on sexual selection. This might be particularly
 important in the context of ‘reinforcement’, where selection acts directly
 to increase prezygotic barriers to reduce the cost of heterospecific
 matings. Using assays of sperm competition within and between two sister
 species, we show a signature of reinforcement where these species
 interact: populations of Drosophila pseudoobscura that co-occur with
 sister species D. persimilis have an elevated ability to outcompete
 heterospecific sperm, consistent with selection for increased
 postcopulatory isolation. We also find these D. pseudoobscura populations
 have decreased sperm competitive ability against conspecifics, reducing
 the opportunity for sexual selection within these populations. Our
 findings demonstrate that direct selection to increase reproductive
 isolation against other species can compromise the efficacy of sexual
 selection within species, a collateral effect of reproductive traits
 responding to heterospecific interactions.
description: Code to analyze
 population differences in CSPCSP_summary.RCode to analyze premating datapremating analysis.RCode to analyze genotypic effects on CSPCSP genotype effects bootstrap.RCorrelation between mean CSP and ISCaverages taken for each genotype across all replicatescell mean correlation.csvpremating datacode to analyze population differences in ISCISC_summary.Rcode to analyze correlation between ISC and CSPcorrelation between ISC and CSP.RCode to analyze differences in variance in reproductionreproductive variance bootstrap.Rraw CSP dataCSP_total.csvcode to analyze hypothesis test for sexual selection using bootstrapbootstrap hypothesis test sexual selection.Rcode to analyze genotypic effects on ISCISC genotype effects bootstrap.Rdata to analyze association of SNPs with CSP and ISCThese data are for the candidate genes. Each SNP is listed without any identifying information and only variable sites are provided. A code relating each SNP number to the particular gene is contained in the fasta zip file with full alignments for each locus.snp_interaction.csvraw ISC dataISC_total.csvSNP association analysis males genesSNP association analysis female genescontrol_genes_snp_genotypesThese data are for the control genes. Each SNP is listed without any identifying information and only variable sites are provided. A code relating each SNP number to the particular gene is contained in the fasta zip file with full alignments for each locus.Control and Candidate gene fasta filesEach fasta file contains the full CDS aligned for each genotype. Heterozygous sites are marked with ambiguity characters or "-". The two text files relate the SNP numbers used in the analysis with the FBgn numbers for each locusfasta files.zip
DOI: 10.5281/zenodo.18350593
title: KEYS_BRAND7_165F_1_23C_0k_EDLC_module
DOI: 10.5281/zenodo.18350594
title: KEYS_BRAND7_165F_1_23C_0k_EDLC_module