cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gr1c5
title: Data from: Maternal source of variability in the embryo development of an annual killifish

description: Organisms inhabiting unpredictable environments often evolve diversified
 reproductive bet-hedging strategies, expressed as production of multiple
 offspring phenotypes, thereby avoiding complete reproductive failure. To
 cope with unpredictable rainfall, African annual killifish from temporary
 savannah pools lay drought-resistant eggs that vary widely in the duration
 of embryo development. We examined the sources of variability in the
 duration of individual embryo development, egg production and
 fertilization rate in Nothobranchius furzeri. Using a quantitative
 genetics approach (North Carolina Type II design) we found support for
 maternal effects rather than polyandrous mating as the primary source of
 the variability in the duration of embryo development. The number of
 previously laid eggs appeared to serve as an internal physiological cue
 initiating a shift from rapid to slow embryo developmental mode. In annual
 killifish extensive phenotypic variability in progeny traits is adaptive,
 as the conditions experienced by parents have limited relevance to the
 offspring generation. In contrast to genetic control, with high phenotypic
 expression and heritability, maternal control of traits under natural
 selection prevents standing genetic diversity from potentially detrimental
 effects of selection in fluctuating environments.
description: Data_maternal_effectsMaternal_effect_killifish.xlsx
DOI: 10.5061/dryad.401kf
title: Data from: Spatial and temporal components of induced plant responses in the context of herbivore life history and impact on host

description: Plants defend against herbivores and pathogens through integrated
 constitutive and induced defenses. Induced responses may be expressed
 locally or tissue/plant-wide, i.e. systemically, and may also be primed
 for subsequent attack. Although the elicitation and efficacy of induced
 responses are increasingly well-characterized, we have little
 understanding of how timing and within-plant spatial patterns of induced
 defenses relate to different herbivore behaviors and selective pressures.
 We used interactions between pines and their major mortality agents,
 native bark beetle-fungal complexes, to explore this dimension. We
 analyzed concentrations of multiple terpenoid and phenolic classes, and
 lesion formation, to provide a comprehensive profile of specialized
 metabolites and histological responses in red pine (Pinus resinosa)
 phloem. We examined these profiles in constitutive tissue and following
 simulated attack, sampling both at the point of challenge and away from
 the attack site, and following a second simulated attack. Terpenoid
 concentrations increased by &gt; 100-fold at the site of simulated
 attack. In contrast, systemic induction of terpenoids was absent or weak,
 with most exhibiting no change and others increasing only 1.5–2 fold.
 Previous elicitation did not influence terpenoid concentrations, either
 locally or tissue-wide, when trees were challenged a second time.
 Phenolics had mixed responses in localized tissues, with some compounds
 increasing and others decreasing. Like terpenoids, phenolics did not show
 substantial systemic, tissue-wide changes, and likewise showed no evidence
 of priming. Collectively, these results indicate that red pine employs a
 strategy of maximizing its response at each point of attack by bark
 beetles. Pines have been shown to express systemic induced resistance
 against several canker fungi, so the absence of these responses suggests
 agent-specific reactions, rather than inherent incapability. Rapid local
 induction seems to be a better strategy in this instance because when a
 bark beetle succeeds in entering and producing pheromones from a host, the
 resulting mass attack rapidly covers the entire circumference and kills
 the tree. These results highlight how plant defense syndromes can modulate
 the spatial and temporal dynamics of induced responses, in addition to the
 chemical and morphological traits deployed.
description: Red pine phloem
 chemistryMonoterpene,
 sesquiterpene, diterpene acid, and phenolic profiles of red pine (Pinus
 resinosa) phloem. Trees were challenged with simulated bark beetle attack
 and localized and systemic reactions tissues were
 collected.redpine_dryad.xlsxRed pine lesion lengthLesion lengths of simulated bark beetle attacks.redpine_dryad_lesionlength.xlsx
DOI: 10.5061/dryad.b42vd
title: Data from: Connectivity in the cold: the comparative population genetics of vent-endemic fauna in the Scotia Sea, Southern Ocean.

description: We report the first comparative population genetics study for vent fauna
 in the Southern Ocean using cytochrome C oxidase I and microsatellite
 markers. Three species are examined: the kiwaid squat lobster, Kiwa
 tyleri, the peltospirid gastropod Gigantopelta chessoia and a lepetodrilid
 limpet, Lepetodrilus sp. collected from vent fields 440 km apart on the
 East Scotia Ridge (ESR) and from the Kemp Caldera on the South Sandwich
 Island Arc, ~95 km eastwards. We report no differentiation for all species
 across the ESR, consistent with panmixia or recent range expansions. A
 lack of differentiation is notable for Kiwa tyleri, which exhibits
 extremely abbreviated lecithotrophic larval development, suggestive of a
 very limited dispersal range. Larval lifespans may, however, be extended
 by low temperature-induced metabolic rate reduction in the Southern Ocean,
 muting the impact of dispersal strategy on patterns of population
 structure. COI diversity patterns suggest all species experienced
 demographic bottlenecks or selective sweeps in the past million years and
 possibly at different times. ESR and Kemp limpets are divergent, although
 with evidence of very recent ESR-Kemp immigration. Their divergence,
 possibility indicative of incipient speciation, along with the absence of
 the other two species at Kemp, may be the consequence of differing
 dispersal capabilities across a ~1000 m depth range and/or different
 selective regimes between the two areas. Estimates of historic and recent
 limpet gene flow between the ESR and Kemp are consistent with
 predominantly easterly currents in the region and potentially therefore,
 cross-axis currents on the ESR, with biogeographic implications for the
 region.
description: Zip file of input
 filesIncludes fasta sequence
 files, microsatellite genotype files, as well as other input
 filesData_accessibility.zip
DOI: 10.5061/dryad.qg269
title: Data from: Development of a genomic resource and quantitative trait loci mapping of male calling traits in the lesser wax moth, Achroia grisella

description: In the study of sexual selection among insects, the Lesser Waxmoth,
 Achroia grisella (Lepidoptera: Pyralidae), has been one of the more
 intensively studied species over the past 20 years. Studies have focused
 on how the male calling song functions in pair formation and on the
 quantitative genetics of male song characters and female preference for
 the song. Recent QTL studies have attempted to elucidate the genetic
 architecture of male song and female preference traits using AFLP markers.
 We continued these QTL studies using SNP markers derived from an EST
 library that allowed us to measure both DNA sequence variation and map
 loci with respect to the lepidopteran genome. We report that the level of
 sequence variation within A. grisella is typical among other Lepidoptera
 that have been examined, and that comparison with the Bombyx mori genome
 shows that macrosynteny is conserved. Our QTL map shows that a QTL for a
 male song trait, pulse-pair rate, is situated on the Z chromosome, a
 prediction for sexually selected traits in Lepidoptera. Our findings will
 be useful for future studies of genetic architecture of this model species
 and may help identify the genetics associated with the evolution of its
 novel acoustic communication.
description: waxmothF2dataThe file contains the backcross progeny phenotypes and genotypes. The cross was the hybrid male progeny of a Kansas female with a Florida male crossed to a Kansas male. Included are the phenotypic and genotypic values for all individuals.waxmoth_parentals_hybridsThis file contains the phenotypic data for males of the Kansas line, the Florida line, and their hybrid males (Kansas female crossed with a Florida male). The data includes two life history variables and three acoustic calling song variables.
DOI: 10.5061/dryad.ft56mn76
title: Data from: Host-parasite arms races and rapid changes in bird egg appearance

description: Coevolutionary arms races are a powerful force driving evolution,
 adaptation, and diversification. They can generate phenotypic
 polymorphisms which render it harder for a coevolving parasite or predator
 to exploit any one individual of a given species. In birds, egg
 polymorphisms should be an effective defense against mimetic brood
 parasites, and are extreme in the African tawny-flanked prinia (Prinia
 subflava) and its parasite the cuckoo finch (Anomalospiza imberbis). Here
 we use models of avian visual perception to analyze the appearance of
 prinia and cuckoo finch eggs from the same location over forty years. We
 show that the two interacting populations have experienced rapid changes
 in egg traits. Egg colors of both species have diversified over time,
 expanding into avian color space as expected under negative
 frequency-dependent selection. Egg pattern showed signatures of both
 frequency-dependent and directional selection in different traits, which
 appeared to be evolving independently of one another. Host and parasite
 are closely tracking one another's evolution, since parasites showed
 closer color mimicry of contemporaneous hosts. This correlational evidence
 suggests that hosts and parasites are locked in an ongoing arms race in
 egg appearance, driven by constant change in the selective advantage of
 different phenotypes, and that coevolutionary arms races can generate
 remarkably rapid phenotypic change.
description: Blown vs unblown
 colorSpatial data for
 colorSpatial data for
 patternTemporal data for
 colorTemporal data for
 pattern
DOI: 10.5061/dryad.8048
title: Data from: Haploids adapt faster than diploids across a range of environments

description: Despite a great deal of theoretical attention, we have limited empirical
 data about how ploidy influences the rate of adaptation. We evolved
 isogenic haploid and diploid populations of Saccharomyces cerevisiae for
 200 generations in seven different environments. We measured the
 competitive fitness of all ancestral and evolved lines against a common
 competitor and find that in all seven environments haploid lines adapted
 faster than diploids, significantly so in three environments. We apply
 theory that relates the rates of adaptation and measured effective
 population sizes to the properties of beneficial mutations. We obtained
 rough estimates of the average selection coefficients in haploids between
 2-10% for these first selected mutations. Results were consistent with
 semi-dominant to dominant mutations in four environments and recessive to
 additive mutations in two other environments. These results are consistent
 with theory that predicts haploids should evolve faster than diploids at
 large population sizes.
description: Raw data to calculate
 rate of adaptationRaw dataset for rate of
 adaptation calculations (Figure 1) and related
 statistics.dataall.csvR code to analyze raw data for rate of adaptationCompetition Analysis.RRaw data to calculate effective population sizesdatacount.csvR code to analayze effective population sizesR code used to analyze effective population sizes; Figure 2Cell Count Ne.RR code to determine our best estimate of the dominance coefficient in each environmentR code to produce figures 3, S4, S5 -- what is the best estimate of dominance? Note, competition and effective population size R code must be run first in the same session.what is h.R
DOI: 10.5061/dryad.fq988
title: Data from: Effects of landscape configuration and composition on phylogenetic diversity of trees in a highly fragmented tropical forest

description: Fragmentation of tropical forests is a major driver of the global
 extinction crisis. A key question is understanding how fragmentation
 impacts phylogenetic diversity, which summarizes the total evolutionary
 history shared across species within a community. Conserving phylogenetic
 diversity decreases the potential of losing unique ecological and
 phenotypic traits and plays important roles in maintaining ecosystem
 function and stability. Our study was conducted in landscapes within the
 highly fragmented Brazilian Atlantic forest. We sampled living trees with
 d.b.h. ≥ 4.8 cm in 0.1 ha plots within 28 fragment interiors and 12
 fragment edges to evaluate the impacts of landscape configuration,
 composition and patch size, as well as edge effects, on phylogenetic
 diversity indices (PD, a measure of phylogenetic richness; MPD,
 phylogenetic distance between individuals in a community in deep
 evolutionary time; and MNTD, phylogenetic distance between each individual
 and its nearest phylogenetic neighbour). We found that PD and MPD were
 correlated with species richness, while MNTD was not. Best models suggest
 that MPD was positively related to edge density and negatively related to
 the number of forest patches, but that there was no effect of landscape
 configuration and composition metrics on PD or MNTD, or on standardized
 values of phylogenetic structure (sesPD, sesMPD and sesMNTD), which
 control for species richness. Considering all selected models for
 phylogenetic diversity and structure, edge density and number of forest
 patches were most frequently selected. With increasing patch size, we
 found lower PD in interiors but no change at edges and lower sesMNTD
 regardless of habitat type. Additionally, PD and sesMNTD were higher in
 interiors than at edges. Synthesis. Changes in MPD and sesMNTD suggest
 that extirpation of species at edges or in highly fragmented landscapes
 increases the dominance of species within a subset of clades (phylogenetic
 clustering), likely those adapted to disturbance. Smaller patch sizes are
 phylogenetically diverse and overdispersed, probably due to an invasion of
 edge-adapted species. Conservation must enhance patch area and
 connectivity via forest restoration; pivotally, even small forest patches
 are important reservoirs of phylogenetic diversity in the highly
 threatened Brazilian Atlantic forest.
description: Matos.et.al_data_1.1The raw data used to evaluate the effect of landscape metrics on the phylogenetic diversity of the trees.Matos.et.al_data_1.2Worksheet used to run the GLM`s to the effects of landscape metrics on phylogenetic diversity of trees.Matos.et.al_data_2.1The raw data used to evaluate the effect of fragment size and habitat type on the phylogenetic diversity of the trees.Matos.et.al_data_2.2Worksheet used to run the GLMM`s on the effects of fragment size and habitat type on phylogenetic diversity of trees.
DOI: 10.5061/dryad.7kj575k
title: Data from: Roads do not increase carrion use by a vertebrate scavenging community

description: Wildlife-vehicle collisions introduce a considerable amount of carrion
 into the environment, but scavenger use of this resource has not been
 extensively investigated. Scavengers may use roads for reliable foraging
 opportunities, but might also use roads for other purposes and encounter
 carrion opportunistically. We examined scavenging of carrion along linear
 features by placing 52 rabbit carcasses in each of three treatments in
 forested habitat during winter (Dec 2016-Mar 2017) in South Carolina, USA:
 roads, power line clearings (linear feature with fewer carcasses than
 roads due to lack of road kill), and forest interior. We used
 motion-activated cameras to compare arrival times and presence of
 vertebrate scavengers among treatments. There was no difference in
 proportion of carcasses scavenged or scavenger arrival time across
 treatments. No species arrived at roads quicker than other treatments.
 Turkey vultures (Cathartes aura) and coyotes (Canis latrans) scavenged
 equally across treatments, whereas gray foxes (Urocyon cinereoargenteus)
 scavenged along roads and power lines, but not in forests. We suggest that
 scavenger use of carrion near roads at this location during winter relates
 to factors other than carrion availability. Because some scavengers
 readily consumed carrion on roads, this resource has the potential to
 influence the ecology of these species.
description: Image
 analysisAnimal detection data
 generated from camerasHill_et_al_2018.xlsx
DOI: 10.5061/dryad.1cg39
title: Data from: Daphnia invest in sexual reproduction when its relative costs are reduced

description: The timing of sex in facultatively sexual organisms is critical to
 fitness, due to the differing demographic consequences of sexual vs.
 asexual reproduction. In addition to the costs of sex itself, an
 association of sex with the production of dormant life stages also
 influences the optimal use of sex, especially in environments where
 resting eggs are essential to survive unfavourable conditions. Here we
 document population dynamics and the occurrence of sexual reproduction in
 natural populations of Daphnia magna across their growing season. The
 frequency of sexually reproducing females and males increased with
 population density and with decreasing asexual clutch sizes. The frequency
 of sexually reproducing females additionally increased as population
 growth rates decreased. Consistent with population dynamic models showing
 that the opportunity cost of sexual reproduction (foregoing contribution
 to current population growth) diminishes as populations approach carrying
 capacity, we found that investment in sexual reproduction was highest when
 asexual population growth was low or negative. Our results support the
 idea that the timing of sex is linked with periods when the relative cost
 of sex is reduced due to low potential asexual growth at high population
 densities. Thus, a combination of ecological and demographic factors
 select on the optimal timing of sexual reproduction, allowing D. magna to
 balance the necessity of sex against its costs.
description: Data for clutchsize and
 sex ratioThis data contains the
 information of the females carrying asexual eggs from each pond and
 information on the asexual clutch size as well as the sex of the
 offspring. Each sample number contains up to 10 entries for individual
 females from the same sampling event and pond. Additionally, we recorded
 whether the females next clutch contained an ephippium.ClutchsizeData.txtData for Cost of sex lab experimentThis is the data for the analysis of the lab experiment in the Reproductive life-history trade-offs. The data contains the ID, the treatment (light or dark) the birth and death date (where the death date is censored), C1, C2, C3 etc is the date of the first, second, third etc. clutch and the number of males and females or ephippia in the respective clutch.ReproductiveLHTO.txtPopulationSamplingDataThis file contains the data from the population sampling containing the counts of the different categories(females with eggs, females with ephippium, males, etc) for every sampling event and pond. The dataset also contains density information as well as growth rates, birth rates and death rates (calculated for a 3-day interval).
DOI: 10.5061/dryad.p153v
title: Data from: Disentangling the interplay of generative and vegetative propagation among different functional groups during gap colonization in meadows

description: Meadow plant communities are commonly driven by strong competition, and
 the colonization of gaps plays an important role in the maintenance of
 their species diversity. Despite this, species-specific information about
 the dynamics of vegetative and generative propagation, and on the role of
 seed bank and seed rain, is rather scarce. In a 3-year manipulative
 experiment, we aimed to disentangle the effects of seed bank, seed rain
 and vegetative propagation in vegetation and during colonization of
 artificial gaps in a mesotrophic meadow. Vegetative propagation was
 manipulated by felting and the presence of the seed bank by soil
 sterilization using gamma radiation. We focused on the dynamics of four
 main species groups with different regeneration strategies: dicots,
 Cyperaceae, Juncaceae and Poaceae. The shift from seedling dominance in
 early stages towards vegetative resprouts dominating at a later stage in
 the gap colonization process differed considerably among the four species
 groups. Dicots and Juncaceae, regenerating frequently from the seed bank,
 acted as pioneer species, and determined species composition of newly
 disturbed sites. Seed rain became crucial later in the season and resulted
 in shifting dominance to the more competitive Poaceae. Stress-tolerating
 Cyperaceae were colonizing the gaps vegetatively mainly towards the end of
 the experiment. While graminoids showed preference for growing into gaps
 clonally, dicots propagated vegetatively mostly within intact vegetation.
 Although seed rain soon equalized seedling numbers in plots with and
 without a seed bank, the presence of a seed bank proved to be crucial for
 certain species, and its effect on species diversity remained positive in
 all functional groups for the duration of the experiment, demonstrating
 the importance of a seed bank for the maintenance of species diversity.
 Nevertheless, seedling assembly converged to a similar functional
 composition in all gap types after 3 years. We have not detected any
 competitive effect of vegetative resprouts on seedlings or seedlings on
 vegetative resprouts throughout the experiment. Each of the three means of
 regeneration has its unique role in the maintenance of species diversity
 during gap colonization, and the importance of these roles differs in
 different functional groups.
description: Numbers of recruits and
 speciesFE_VitovaMacekLeps.xls
DOI: 10.5061/dryad.f502p
title: Data from: A nutrient mediates intraspecific competition between rodent malaria parasites in vivo

description: Hosts are often infected with multiple strains of a single parasite
 species. Within-host competition between parasite strains can be intense
 and has implications for the evolution of traits that impact patient
 health, such as drug resistance and virulence. Yet the mechanistic basis
 of within-host competition is poorly understood. Here, we demonstrate that
 a parasite nutrient, para-aminobenzoic acid (pABA), mediates competition
 between a drug resistant and drug susceptible strain of the malaria
 parasite, Plasmodium chabaudi. We further show that increasing pABA supply
 to hosts infected with the resistant strain worsens disease and changes
 the relationship between parasite burden and pathology. Our experiments
 demonstrate that, even when there is profound top-down regulation
 (immunity), bottom-up regulation of pathogen populations can occur and
 that its importance may vary during an infection. The identification of
 resources that can be experimentally controlled opens up the opportunity
 to manipulate competitive interactions between parasites and hence their
 evolution.
description: Dataset for Wale et al.
 2017 Proc R Soc BDataset used in the
 paper. Includes daily measurements of red blood cell densities and the
 weight of mouse hosts, as well as the density of each parasite strain.
 Information about units of measurements given in the sheet entitled
 'Notes on Data'.Waleetal_data.xls