cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gk1hk
title: Data from: Rapid multiple-level coevolution in experimental populations of yeast killer and non-killer strains

description: Coevolution between different biological entities is considered an
 important evolutionary mechanism at all levels of biological organization.
 Here we provide evidence for coevolution of a yeast killer strain (K)
 carrying cytoplasmic dsRNA viruses coding for anti-competitor toxins and
 an isogenic toxin-sensitive strain (S) during 500 generations of
 laboratory propagation. Signatures of coevolution developed at two levels.
 One of them was coadaptation of K and S. Killing ability of K first
 increased quickly and was followed by the rapid invasion of
 toxin-resistant mutants derived from S, after which killing ability
 declined. High killing ability was shown to be advantageous when sensitive
 cells were present but costly when they were absent. Toxin resistance
 evolved via a two-step process, involving the fitness-enhancing loss of
 one chromosome followed by selection of a recessive resistant mutation on
 the haploid chromosome. The other level of coevolution occurred between
 cell and killer virus. By swapping the killer viruses between ancestral
 and evolved strains, we could demonstrate that changes observed in both
 host and virus were beneficial only when combined, suggesting that they
 involved reciprocal changes. Together, our results show that the yeast
 killer system shows a remarkable potential for rapid multiple-level
 coevolution.
description: Absolute halo size
 measurements of killer strainsExcel spreadsheet of
 measurements of killer patches and absolute halo sizes for estimation of
 the killing ability for 17 killer strains of three different experiments
 .Each measurements' combination listed for each killer and its
 separate replicate.Raw data of changes in
 KA.xlsxMeasurements of absolute
 halo sizes of sensitive/resistant strainsExcel spreadsheet
 representing measurements of killer patches and absolute halo sizes used
 for calculation sensitivity, and fraction of ascendance of toxin-resistant
 clones. Each pair of measurements allocated according to treatment, and
 number of conducted replicates.Raw data of changes in
 sensitivity.xlsxMeasurements of relative
 fitness of killer and sensitive/resistant strainsExcel spreadsheet
 showing colony count of fitness competitions of seven killers, and four
 sensitive/resistant strains from two evolution experiments. Data listing
 measurements from before and after 24hours competitions, and number of
 undertaken replicates.Raw data of
 RF.xlsxMeasurements of changes
 in cell frequencies of coevolving killer and sensitive
 strainsExcel spreadsheet
 showing average frequencies (cell density per ml) of killer and sensitive
 cells in mixed populations during the coevolution experiments. Data
 divided according to three experimental conditions and number of employed
 replicate populations.Raw data of changes in
 frequencies.xlsx
DOI: 10.5061/dryad.85096
title: Data from: Grape moth density in Bordeaux vineyards depends on local habitat management despite effects of landscape heterogeneity on their biological control

description: 1. Biological control of crop pests is a major ecosystem service affected
 by several variables acting at multiple spatial scales. Among these
 variables, heterogeneity at the habitat and landscape scales are known key
 drivers of trophic interactions and pest density in agroecosystems.
 However, studies that try to disentangle their relative effects in
 perennial cropping systems are scarce and nothing is known about their
 impacts on insect pest density and pesticide applications. 2. We examined
 the effect of heterogeneity at these two scales on grape moths, one of the
 most damaging insect pests in European vineyards, and their biological
 control in 20 vineyards during three consecutive years. We used local
 vegetation management and the proportion of semi-natural habitats in the
 surrounding landscape as proxies of heterogeneity at the habitat and
 landscape scales. Grape moth density was measured over time, as well as
 biological control services provided by different groups: birds,
 invertebrate predators, parasitoids and entomopathogenic fungi. 3. Over
 the 3 years, grape moth density was mainly determined by local
 heterogeneity, with significantly fewer larvae of the first generation
 established in vineyards with full compared to partial grass cover. 4.
 Despite these effects, biological control of grape moths was not primarily
 affected by local vegetation management but by landscape heterogeneity,
 and the direction of this effect varied over time. Notably, predation by
 birds increased with landscape heterogeneity in spring, depending on local
 vegetation management, while attacks by pathogenic fungi decreased with
 landscape heterogeneity during winter. 5. Synthesis and applications. Our
 results suggest that bottom-up processes related to habitat heterogeneity
 drive grape moth occurrence much more than top-down processes. These
 results have important implications for the ecological intensification of
 vineyard landscapes. We found that maintaining full grass cover within
 vineyards reduced grape moth density to a level below common intervention
 thresholds. Landscape heterogeneity in the close vicinity of vineyards
 contributed to improved biological pest control by birds, but depended on
 local vegetation management. Moreover, opposing effects of landscape
 management on biological pest control services over time revealed that
 strategies based only on manipulating landscape heterogeneity might not be
 the optimal option to limit grape moth density in vineyards.
description: Data pest and biological
 controlData.xlsx
DOI: 10.5061/dryad.pj0p3
title: Data from: The Caenorhabditis elegans Myc-Mondo/Mad complexes integrate diverse longevity signals

description: The Myc family of transcription factors regulates a variety of biological
 processes, including the cell cycle, growth, proliferation, metabolism,
 and apoptosis. In Caenorhabditis elegans, the “Myc interaction network”
 consists of two opposing heterodimeric complexes with antagonistic
 functions in transcriptional control: the Myc-Mondo:Mlx transcriptional
 activation complex and the Mad:Max transcriptional repression complex. In
 C. elegans, Mondo, Mlx, Mad, and Max are encoded by mml-1, mxl-2, mdl-1,
 and mxl-1, respectively. Here we show a similar antagonistic role for the
 C. elegans Myc-Mondo and Mad complexes in longevity control. Loss of mml-1
 or mxl-2 shortens C. elegans lifespan. In contrast, loss of mdl-1 or mxl-1
 increases longevity, dependent upon MML-1:MXL-2. The MML-1:MXL-2 and
 MDL-1:MXL-1 complexes function in both the insulin signaling and dietary
 restriction pathways. Furthermore, decreased insulin-like/IGF-1 signaling
 (ILS) or conditions of dietary restriction increase the accumulation of
 MML-1, consistent with the notion that the Myc family members function as
 sensors of metabolic status. Additionally, we find that Myc family members
 are regulated by distinct mechanisms, which would allow for integrated
 control of gene expression from diverse signals of metabolic status. We
 compared putative target genes based on ChIP-sequencing data in the
 modENCODE project and found significant overlap in genomic DNA binding
 between the major effectors of ILS (DAF-16/FoxO), DR (PHA-4/FoxA), and Myc
 family (MDL-1/Mad/Mxd) at common target genes, which suggests that diverse
 signals of metabolic status converge on overlapping transcriptional
 programs that influence aging. Consistent with this, there is
 over-enrichment at these common targets for genes that function in
 lifespan, stress response, and carbohydrate metabolism. Additionally, we
 find that Myc family members are also involved in stress response and the
 maintenance of protein homeostasis. Collectively, these findings indicate
 that Myc family members integrate diverse signals of metabolic status, to
 coordinate overlapping metabolic and cytoprotective transcriptional
 programs that determine the progression of aging.
description: Raw Data of Mortality
 Observations of Replica Set ExperimentsDryad
 File.xlsx
DOI: 10.5061/dryad.k3v6h
title: Data from: Immunoglobulin detection in wild birds: effectiveness of three secondary anti-avian IgY antibodies in direct ELISAs in 41 avian species

description: 1.Immunological reagents for wild, non-model species are limited or often
 non-existent for many species. 2. In this study, we compare the reactivity
 of a new anti-passerine IgY secondary antibody with existing secondary
 antibodies developed for use with birds. Samples from 41 species from the
 following six avian orders were analysed: Anseriformes (1 family, 1
 species), Columbiformes (1 family, 2 species), Galliformes (1 family, 1
 species), Passeriformes (16 families, 34 species), Piciformes (1 family, 2
 species) and Suliformes (1 family, 1 species). Direct ELISAs were
 performed to detect total IgY using goat anti-passerine IgY, goat
 anti-chicken IgY or goat anti-bird IgY secondary antibodies. 3.The
 anti-passerine antibody exhibited significantly higher IgY reactivity
 compared to the anti-chicken and/or anti-bird antibodies in 80% of the
 passerine families tested. Birds in the order Piciformes (woodpeckers) and
 order Suliformes (cormorants) were poorly detected by all three secondary
 antibodies. A comparison of serum and plasma IgY levels was made within
 the same individuals for two passerine species (house finch and
 white-crowned sparrow), and serum exhibited significantly more IgY than
 the plasma for all three secondary antibodies. This result indicates that
 serum may be preferred to plasma when measuring total antibody levels in
 blood. 4.This study indicates that the anti-passerine IgY secondary
 antibody can effectively be used in immunological assays to detect
 passerine IgY for species in most passerine families and is preferred over
 anti-chicken and anti-bird secondary antibodies for the majority of
 passerine species. This anti-passerine antibody will allow for more
 accurate detection and quantification of IgY in more wild bird species
 than was possible with previously available secondary antibodies.
description: ELISA data by species
 from: Fassbinder-Orth et al. 2016. Immunoglobulin detection. Methods in
 Ecology and EvolutionThis file contains the
 ELISA data for 41 different avian species and three different IgY
 ELISAsFassbinder-Orth et al. 2016.
 Immunoglobulin detection data for
 Dryad.xlsx
DOI: 10.5061/dryad.3m3k724
title: Data from: Effect of plant root symbionts on performance of native woody species in competition with an invasive grass in multispecies microcosms

description: The majority of terrestrial plants form mutualistic associations with
 arbuscular mycorrhizal fungi (AMF) and rhizobia (i.e. nitrogen fixing
 bacteria). Understanding these associations has important implications for
 ecological theory and for restoration practice. Here we tested whether the
 presence of AMF and rhizobia influence the performance of native woody
 plants invaded by a non-native grass in experimental microcosms. We
 planted eight plant species (i.e. Acacia acuminata, A. microbotrya,
 Eucalyptus loxophleba subsp. loxophleba, E. astringens, Calothamnus
 quadrifidus, Callistemon phoeniceus, Hakea lissocarpha and H. prostrata)
 in microcosms of field-conditioned soil with and without addition of AMF
 and rhizobia in a fully factorial experimental design. After seedling
 establishment, we seeded half the microcosms with an invasive grass Bromus
 diandrus. We measured shoot and root biomass of native plants and Bromus,
 and on roots, the percentage colonization by AMF, number of
 rhizobia-forming nodules and number of proteaceous root clusters. We found
 no effect of plant root symbionts or Bromus addition on performance of
 myrtaceous, and as predicted, proteaceous species as they rely little or
 not at all on AMF and rhiozbia. Soil treatments with AMF and rhiozbia had
 a strong positive effect (i.e. larger biomass) on native legumes (A.
 microbotrya and A. acuminata). However, the beneficial effect of root
 symbionts on legumes became negative (i.e. lower biomass and less nodules)
 if Bromus was present, especially for one legume, i.e. A. acuminata,
 suggesting a disruptive effect of the invader on the mutualism. We also
 found a stimulating effect of Bromus on root nodule production in A.
 microbotrya and AMF colonization in A. acuminata which could be indicative
 of legumes’ increased resource acquisition requirement, i.e. for nitrogen
 and phosphorus, respectively, in response to the Bromus addition. We have
 demonstrated the importance of measuring belowground effects because the
 aboveground effects gave limited indication of the effects occuring
 belowground.
description: birnbaum_et_al_2018_dataraw data file for eight species used in the studybirnbaum_et_al_2018_analysis_Rcodestatistical models used to estimate the effects of soil treatment and invasive Bromus diandrus addition to native species performance in microcosms.
DOI: 10.5061/dryad.4kp7s
title: Data from: Life-history strategy determines constraints on immune function

description: 1) Determining the factors governing investment in immunity is critical
 for understanding host-pathogen ecological and evolutionary dynamics.
 Studies often consider disease resistance in the context of life-history
 theory, with the expectation that investment in immunity will be optimized
 in anticipation of disease risk. Immunity, however, is constrained by
 context-dependent fitness costs. How the costs of immunity vary across
 life-history strategies has yet to be considered. 2) Pea aphids are
 typically unwinged but produce winged offspring in response to high
 population densities and deteriorating conditions. This is an example of
 polyphenism, a strategy used by many organisms to adjust to environmental
 cues. The goal of this study was to examine the relationship between the
 fitness costs of immunity, pathogen resistance, and the strength of an
 immune response across aphid morphs that differ in life-history strategy
 but are genetically identical. 3) We measured fecundity of winged and
 unwinged aphids challenged with a heat-inactivated fungal pathogen, and
 found that immune costs are limited to winged aphids. We hypothesized that
 these costs reflect stronger investment in immunity in anticipation of
 higher disease risk, and that winged aphids would be more resistant due to
 a stronger immune response. However, producing wings is energetically
 expensive. This guided an alternative hypothesis—that investing resources
 into wings could lead to a reduced capacity to resist infection. 4) We
 measured survival and pathogen load after live fungal infection, and we
 characterized the aphid immune response to fungi by measuring immune cell
 concentration and gene expression. We found that winged aphids are less
 resistant and mount a weaker immune response than unwinged aphids,
 demonstrating that winged aphids pay higher costs for a less effective
 immune response. 5) Our results show that polyphenism is an understudied
 factor influencing the expression of immune costs. More generally, our
 work shows that in addition to disease resistance, the costs of immunity
 vary between individuals with different life-history strategies. We
 discuss the implications of these findings for understanding how organisms
 invest optimally in immunity in light of context-dependent constraints.
description: Complete experimental
 and qPCR dataDryad_Data.xlsx
DOI: 10.5061/dryad.qr92p
title: Data from: Sexual conflict and interacting phenotypes: a quantitative genetic analysis of fecundity and copula duration in Drosophila melanogaster

description: Many reproductive traits that have evolved under sexual conflict may be
 influenced by both sexes. Investigation of the genetic architecture of
 such traits can yield important insight into their evolution, but this
 entails that the heritable component of variation is estimated for males
 and females – as an interacting phenotype. We address the lack of research
 in this area through an investigation of egg production and copula
 duration in the fruit fly, Drosophila melanogaster. Despite egg production
 rate being determined by both sexes, which may cause sexual conflict, an
 assessment of this trait as an interacting phenotype is lacking. It is
 currently unclear whether copula duration is determined by males and/or
 females. We found significant female, but not male, genetic variance for
 egg production rate which may indicate reduced potential for ongoing
 sexually antagonistic coevolution. In contrast, copula duration was
 determined by significant genetic variance in both sexes. We also
 identified genetic variation in egg retention among virgin females.
 Although previously identified in wild populations, it is unclear why this
 should be present in a laboratory stock. This study provides a novel
 insight into the shared genetic architecture of reproductive traits that
 are the subject of sexual conflict.
description: Results
 Evolution13-0929Please see comments
 boxes in spreadsheet for a description of data
 contents.ResultsDryadEvolution13-0929.xlsx
DOI: 10.5061/dryad.qk121
title: Data from: Experimental coevolution: rapid local adaptation by parasites depends on host mating system

description: Host-parasite interactions can drive rapid, reciprocal genetic changes
 (coevolution), provided both hosts and parasites have high heritabilities
 for resistance/infectivity. Similarly, the host's mating system
 should also affect the rate of coevolutionary change in host-parasite
 interactions. Using experimental coevolution, we determined the effect of
 obligate outcrossing verses partial self-fertilization (mixed mating) on
 the rate of evolutionary change in a nematode host (Caenorhabditis
 elegans) and its bacterial parasite (Serratia marcescens). Bacterial
 populations were derived from a common ancestor. We measured the effects
 of host mating system on host adaptation to the parasite. We then
 determined the extent of parasite adaptation to their local host
 populations. Obligately outcrossing hosts exhibited more rapid adaptation
 to parasites than did mixed mating hosts. In addition, most of the
 parasites became adapted to infecting their "local" hosts; but
 parasites from obligately outcrossing hosts showed a greater level of
 local adaptation. These results suggest that host populations evolved
 along separate trajectories, and that outcrossing host populations
 diverged further than partially selfing populations. Finally, parasites
 "tracking" outcrossing host populations diverged further than
 parasites tracking the partially selfing host populations. These results
 show that the evolutionary trajectories of both hosts and parasites can be
 shaped by the host's mating system.
description: Outcrossing vs Mixed
 Mating FitnessCompetitive fitness
 assay dataLocal adaptation
 dataMortality rates of host
 x parasite pairings in both obligately outcrossing and mixed mating
 groups
DOI: 10.5061/dryad.482m400
title: Data from: Invasion of Hawaiian rainforests by an introduced amphibian predator and N2-fixing tree increases soil N2O emissions

description: Invasions of introduced species have homogenized ecological communities
 worldwide, leading to losses of native species and the services they
 provide. Some of these invaders substantially alter nutrient cycling,
 which changes conditions for all other organisms, but less is known about
 the potential influence of these species on nitrogen (N) trace gas
 emissions that affect atmospheric processes. We used a natural experiment
 to explore whether the establishment of an introduced nitrogen (N) fixing
 tree (Falcataria moluccana) and recent invasion of an amphibian predator,
 the Caribbean tree frog (Eleutherodactylus coqui), into native Hawaiian
 rainforests has affected soil emissions of nitrous oxide (N2O) and nitric
 oxide (NO), two atmospherically important trace gases produced by soil
 microorganisms. Soil N2O and NO emissions and rates of soil N cycling were
 significantly higher in F. moluccana-dominated stands compared to native
 Metrosideros polymorpha (Ohi’a) stands. Additionally, invasion of E. coqui
 frogs moderately increased soil N2O emissions, primarily in non-native F.
 moluccana forests where soil N availability was already elevated. N2O
 emissions were positively and significantly related to net potential N
 mineralization, and total N2O+NO fluxes increased with soil nitrate (NO3-)
 concentration and rates of nitrification. Previous work in these Hawaiian
 rainforest sites has shown that F. moluccana substantially increases N
 availability by increasing ecosystem N supply compared to uninvaded
 stands, and E. coqui accelerates N availability and litter decomposition,
 although moderately, due to enhanced fluxes of nutrient-rich waste
 products. Here, we show that acceleration of nutrient cycling by
 introduced species can also alter biosphere-atmosphere exchange of
 N-oxides.
description: AlbiziaCoqui_GasesN2O and NO gas data used in Hall, Huber, and Hughes (in press). Invasion of Hawaiian rainforests by an introduced amphibian predator and N2-fixing tree increases soil N2O emissions. EcosphereCoquiAlbizia_SoilsSoils data used in Hall, Huber, and Hughes. Invasion of Hawaiian rainforests by an introduced amphibian predator and N2-fixing tree increases soil N2O emissions. Ecosphere, in press.
DOI: 10.15468/dl.8qaf3b
title: Occurrence Download

description: A dataset containing 120 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Masticophis schotti",
 "Year 1960-2026"
 ]
}

 The dataset includes 120 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000822-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.