cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1690
title: Data from: The effects of predation risk on mating system expression in a freshwater snail

description: Environmental effects on mating system expression are central to
 understanding mating system evolution in nature. Here I report the results
 from a quantitative-genetic experiment aimed at understanding the role of
 predation risk in the expression and evolution of life-history and
 mating-system traits in a hermaphroditic freshwater snail (Physa acuta). I
 reared 30 full-sib families in four environments that factorially contrast
 predation risk and mate availability and measured age/size at first
 reproduction, growth rate, a morphological defense, and the early survival
 of outcrossed/selfed eggs that were laid under predator/no-predator
 conditions. I evaluated the genetic basis of trade-offs among traits and
 the stability of the G matrix across environments. Mating reduced growth
 while predation risk increased growth, but the effects of mating were
 weaker for predator-induced snails and the effects of predation risk were
 weaker for snails without mates. Predation risk reduced the amount of time
 that individuals waited before self-fertilizing and reduced inbreeding
 depression in the offspring. There was a positive among-family
 relationship between the amount of time that individuals delayed selfing
 under predation risk and the magnitude of inbreeding depression. These
 results highlight several potential roles of enemies in mating-system
 expression and evolution.
description: Aulddata.xlsRaw data from lab experiment. Abbreviations for variables are provided as a separate worksheet.
DOI: 10.5061/dryad.c5m7m
title: Data from: Gene flow in the green mirid, Creontiades dilutus (Hemiptera: Miridae), across arid and agricultural environments with different host plant species

description: Creontiades dilutus (Stål), the green mirid, is a polyphagous herbivorous
 insect endemic to Australia. Although common in the arid interior of
 Australia and found on several native host plants that are spatially and
 temporally ephemeral, green mirids also reach pest levels on several crops
 in eastern Australia. These host-associated dynamics, distributed across a
 large geographic area, raise questions as to whether (1) seasonal
 fluctuations in population size result in genetic bottlenecks and drift,
 (2) arid and agricultural populations are genetically isolated, and (3)
 the use of different host plants results in genetic differentiation. We
 sequenced a mitochondrial COI fragment from individuals collected over 24
 years and screened microsatellite variation from 32 populations across two
 seasons. The predominance of a single COI haplotype and negative Tajima D
 in samples from 2006/2007 fit with a population expansion model. In the
 older collections (1983 and 1993), a different haplotype is most
 prevalent, consistent with successive population contractions and
 expansions. Microsatellite data indicates recent migration between inland
 sites and coastal crops and admixture in several populations. Altogether,
 the data suggest that long-distance dispersal occurs between arid and
 agricultural regions, and this, together with fluctuations in population
 size, leads to temporally dynamic patterns of genetic differentiation.
 Host-associated differentiation is evident between mirids sampled from
 plants in the genus Cullen (Fabaceae), the primary host, and alternative
 host plant species growing nearby in arid regions. Our results highlight
 the importance of jointly assessing natural and agricultural environments
 in understanding the ecology of pest insects.
description: C_dilutus_genotypesGenotypes of 654 green mirid individuals sampled across Australia between 2006 and 2008. These samples were screened using 9 fluorescently labelled microsatellite loci separated by capiliary electrophoresis. Details of the location and host plant of each sample are available in the manuscript.
DOI: 10.5061/dryad.21sf7
title: Data from: Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae)

description: Phylogenetic niche conservatism and convergence are contrasting
 evolutionary patterns that describe phenotypic similarity across
 independent lineages. Assessing whether and how adaptive processes give
 origin to these patterns represent a fundamental step toward understanding
 phenotypic evolution. Phylogenetic model-based approaches offer the
 opportunity not only to distinguish between phylogenetic niche
 conservatism and convergence, but also to determine the extent that
 adaptive processes explain phenotypic similarity. The Myrmotherula complex
 in the Neotropical family Thamnophilidae is a polyphyletic group of
 sexually dimorphic small insectivorous forest birds that are relatively
 homogeneous in size and shape. Here, we integrate a comprehensive
 species-level molecular phylogeny of the Myrmotherula complex with
 morphometric and ecological data within a comparative framework to test
 whether phenotypic similarity is described by a pattern of phylogenetic
 niche conservatism or convergence, and to identify evolutionary mechanisms
 underlying body size and shape evolution. We show that antwrens in the
 Myrmotherula complex represent distantly related clades that exhibit
 adaptive convergent evolution in body size and divergent evolution in body
 shape. Phenotypic similarity in the group is primarily driven by their
 tendency to converge toward smaller body sizes. Differences in body size
 and shape across lineages are associated to ecological and behavioral
 factors.
description: Morphometric data of a
 subset of the ThamnophilidaeTab-delimited file
 containing morphometric data for 362 thamnophilid specimens. Description
 of measured characters is included in the main text.Morphological_Data.txtRelative time-calibrated phylogeny of a subset of the ThamnophilidaeUltrametric phylogeny estimated by Beast v. 1.6.1 (see main text for details) of a subset of the Thamnophilidae, with special focus on the Myrmotherula complex and their close relatives. Phylogeny is given in Newick format and includes only one sample per species.Myrmotherula_Ultrametric.treBayesian phylogeny of a subset of the Thamnohilidae50 % majority-rule Bayesian phylogeny in Newick format of a subset of the Thamnophilidae produced by MrBayes v. 3.1.2 (Figure S.1). Phylogeny contains all individuals sampled per species.Myrmotherula_MrBayes.con.tre
DOI: 10.5061/dryad.1c617
title: Data from: A shift from magnitude to sign epistasis during adaptive evolution of a bacterial social trait

description: While the importance of epistasis in evolution has long been recognized,
 remarkably little is known about the processes by which epistatic
 interactions evolve in real time in specific biological systems. Here, we
 have characterized how the epistatic fitness relationship between a social
 gene and an adapting genome changes radically over a short evolutionary
 time frame in the social bacterium Myxococcus xanthus. We show that a
 highly beneficial effect of this social gene in the ancestral genome is
 gradually reduced – and ultimately reversed into a deleterious effect –
 over the course of an experimental adaptive trajectory in which a
 primitive form of novel cooperation evolved. This reduction and reversal
 of a positive social allelic effect is driven solely by changes in the
 genetic context in which the gene is expressed as new mutations are
 sequentially fixed during adaptive evolution, and explicitly demonstrates
 a significant evolutionary change in the genetic architecture of an
 ecologically important social trait.
description: Zee_etal_Evolution_SwarmingDataThis file contains the Myxococcus swarming data for the pilA-transformed and untransformed strains for all evolutionary timepoints of the E8 lineage.Zee_etal_Evolution_MutationFrequenciesThis is a table showing the presence/absence of mutations the accumulated along the E8 lineage of Myxococcus xanthus for a number of clones at each evolutionary time point.
DOI: 10.5061/dryad.k7c2051
title: Data from: Structural traits dictate abiotic stress amelioration by intertidal oysters

description: 1.Autogenic ecosystem engineers often provide cool microhabitats which are
 used by associated organisms to reduce thermal extremes. The value of such
 habitats is, however, dependant on key structural traits of the ecosystem
 engineer, and the intensity and duration of thermal exposure. 2.Using an
 experimental mesocosm that mimicked the rocky intertidal environment, we
 assessed how the spatial configuration of the habitat formed by an
 autogenic ecosystem engineer, the oyster, influences its capacity to
 mitigate heat stress experienced by invertebrates during simulated
 emersion periods on tropical, Hong Kong rocky shores. 3.At the average
 temperature experienced during summer low tides, oyster habitat
 ameliorated environmental and organismal temperatures, irrespective of the
 structural configuration of the oyster bed. As temperatures increased,
 however, vertically orientated oysters provided microclimates that
 facilitated cooler invertebrate body temperatures than horizontal beds,
 which no longer conferred any associational benefit as compared to bare
 rock surfaces. 4.In the absence of oysters, physiological indicators of
 stress to associated organisms (i.e. heart rate and osmolality) increased
 with the intensity and duration of exposure to high temperatures. Such
 effects were, however, mitigated by association with vertical but not
 horizontal oyster configurations. In contrast, the osmolality of the
 oysters was not related to temperature, suggesting they remained in a
 state of metabolic quiescence throughout emersion. 5.Structural traits
 such as the spatial configuration of ecosystem engineers are, therefore,
 critical to their effectiveness in environmental amelioration. As such,
 variations in the morphological traits of ecosystem engineers, which have
 important implications for their ecological role, need to be incorporated
 into conservation and restoration projects aimed at climate change
 adaptation.
description: Intertidal mesocosm
 data_ McAfee et al.Raw data for temperature
 changes and biological responses in an intertidal mesocosm
 setting.McAfee et al.
 FE-2018-00027_Dryad data storage.xlsx
DOI: 10.5061/dryad.5c1g6
title: Data from: Out-of-sample predictions from plant–insect food webs: robustness to missing and erroneous trophic interaction records

description: With increasing biotic introductions, there is a great need for predictive
 tools to anticipate which new trophic interactions will develop and which
 will not. Phylogenetic constraint of interactions in both native and novel
 food webs can make some novel interactions predictable. However, many food
 webs are sparsely sampled, or may include inaccurate interactions. In such
 cases, it is unclear whether modeling methods are still useful to
 anticipate novel interactions. We ran bootstrap simulations of host-use
 models on a Lepidoptera–plant data set to remove native trophic records or
 add erroneous records in order to observe the effect of missing or
 erroneous data on the prediction of interactions with novel plants. We
 found that the model was robust to a large amount of missing interaction
 records, but lost predictive power with the addition of relatively few
 erroneous interaction records. The loss of predictive power with missing
 records was due to inaccuracy in estimating phylogenetic distance between
 native and novel hosts. Removal of interaction records proportionally to
 their encounter frequency in the field had little effect on the loss of
 predictive power. Host-use models may have immediate value for predicting
 novel interactions from large, but sparsely sampled databases of trophic
 interactions.
description: phyloeny matching
 datasetBased on the published
 DaPhNe plant phylogeny (Durka & Michalski 2012 Ecology), trimmed to
 plants within present food web dataset (2587 taxa). Missing taxa added
 (113) as described in manuscript. Phylogeny is in newick
 format.German Phyl trimmed to AltPea
 dataset.trePearse_Altermatt2015-R
 code for DryadR code with general
 functions for host use models and predictions. Appended at the end of the
 file is specific code for the manuscript.
DOI: 10.5061/dryad.t0hd4
title: Data from: Facultative pupal mating in Heliconius erato: implications for mate choice, female preference, and speciation

description: Mating systems have broad impacts on how sexual selection and mate choice
 operate within a species, but studies of mating behavior in the laboratory
 may not reflect how these processes occur in the wild. Here, we examined
 the mating behavior of the neotropical butterfly Heliconius erato in the
 field by releasing larvae and virgin females and observing how they mated.
 H. erato is considered a pupal-mating species (i.e., males mate with
 females as they emerge from the pupal case). However, we observed only two
 teneral mating events, and experimentally released virgins were almost all
 mated upon recapture. Our study confirms the presence of some pupal-mating
 behavior in H. erato, but suggests that adult mating is likely the
 prevalent mating strategy in this species. These findings have important
 implications for the role of color pattern and female mate choice in the
 generation of reproductive isolation in this diverse genus.
description: pupal_mating_dataThis file contains raw data from the pupal mating experiments describe din the paper. Sheet 1 contains behavior observations from experiment 1. Sheet 2 contains butterfly capture/recapture data from experiments 1 and 2. Sheet 3 contains the information of the virgin females released as part of experiment 2. Sheet 4 contains the measures of forewing length from experiments 1 and 2. Sheet 5 contains information on the number of butterflies observed at each site. Sheet 6 contains the data on the experimental larvae placed out at each site. Sheet 7 gives the data on male discovery of experimental pupae.data_archive.xlsxR_density_analysisR script used to compare density of adults across sites. This uses the data from sheet 5 of the Excel file.density_comparison.RR_wing_length_analysisR script to perform our wing length analysis and create figure 2. This uses the data from sheet 4 of the Excel file.wing_length_analysis.RSupplemental_rmarkdownThe Rmarkdown file used to generate the supplemental material document. Some file paths may need to be changed to recreate this document on your own computer.supplemental.Rmd
DOI: 10.5061/dryad.7g401
title: Data from: Metabolic erosion primarily through mutation accumulation, and not tradeoffs, drives limited evolution of substrate specificity in Escherichia coli

description: Evolutionary adaptation to a constant environment is often accompanied by
 specialization and a reduction of fitness in other environments. We
 assayed the ability of the Lenski Escherichia coli populations to grow on
 a range of carbon sources after 50,000 generations of adaptation on
 glucose. Using direct measurements of growth rates, we demonstrated that
 declines in performance were much less widespread than suggested by
 previous results from Biolog assays of cellular respiration. Surprisingly,
 there were many performance increases on a variety of substrates. In
 addition to the now famous example of citrate, we observed several other
 novel gains of function for organic acids that the ancestral strain only
 marginally utilized. Quantitative growth data also showed that strains
 with higher mutation rate exhibited significantly more declines,
 suggesting that most metabolic erosion was driven by mutation accumulation
 and not by physiological tradeoffs. These reductions in growth by mutator
 strains were ameliorated by growth at lower temperature, consistent with
 the hypothesis that this metabolic erosion is largely caused by
 destabilizing mutations to the associated enzymes. We further hypothesized
 that reductions in growth rate would be greatest for substrates used most
 differently from glucose, and we used flux balance analysis to formulate
 this question quantitatively. To our surprise, we found no significant
 relationship between decreases in growth and dissimilarity to glucose
 metabolism. Taken as a whole, these data suggest that in a single resource
 environment, specialization does not mainly result as an inevitable
 consequence of adaptive tradeoffs, but rather due to the gradual
 accumulation of disabling mutations in unused portions of the genome.
description: growthRateDataGrowth rate data for evolved and ancestral strainsbiologData
DOI: 10.5061/dryad.mb49d60
title: Data from: Standing genetic diversity and selection at functional gene loci are associated with differential invasion success in two non-native fish species

description: Invasive species are expected to experience a unique combination of high
 genetic drift due to demographic factors while also experiencing strong
 selective pressures. The paradigm that reduced genetic diversity should
 limit the evolutionary potential of invasive species and thus their
 potential for range expansion has received little empirical support,
 possibly due to the choice of genetic markers. Our goal was to test for
 effects of genetic drift and selection at functional genetic markers as
 they relate to the invasion success of two paired invasive goby species,
 one widespread (successful) and one with limited range expansion (less
 successful). We genotyped fish using two marker types: single nucleotide
 polymorphisms (SNPs) in known-function, protein-coding genes and
 microsatellites to contrast the effects of neutral genetic processes. We
 identified reduced allelic variation in the invaded range for the
 less-successful tubenose goby. SNPs putatively under selection were
 responsible for the observed differences in population structure between
 marker types for round goby (successful) but not tubenose goby (less
 successful). A higher proportion of functional loci experienced divergent
 selection for round goby, suggesting increased evolutionary potential in
 invaded ranges may be associated with round goby's greater invasion
 success. Genes involved in thermal tolerance were divergent for round goby
 populations but not tubenose goby, consistent with the hypothesis that
 invasion success for fish in temperate regions is influenced by capacity
 for thermal tolerance. Our results highlight the need to incorporate
 functional genetic markers in studies to better assess evolutionary
 potential for the improved conservation and management of species.
description: Goby_SNP_GTseq_genotypingScript to map short reads to transcriptomic reference and call SNPs using GATK best practices workflowRG_usat_dataRound goby microsatellite data in genepop formatRG_usat.genTNG_usat_dataTubenose goby microsatellite data in genepop formatTNG_usat.genRG_SNP_dataRound goby SNP genotype data in genepop formatRG_SNP_genepop.genTNG_SNP_dataTubenose goby SNP genotypes in genepop formatTNG_SNP_genepop.genGobySNP_main_analysis_scriptR code for conducting all but the outlier analyses as described in the paperGobySNP_main_analysis.RGobySNP_outliers_scriptR code for conducting FLK outlier analysis as described in the paperGobySNP_outliers.R
DOI: 10.5061/dryad.7n94f
title: Data from: Integrating morphology and kinematics in the scaling of hummingbird hovering metabolic rate and efficiency

description: Wing kinematics and morphology are influential upon the aerodynamics of
 flight. However, there is a lack of studies linking these variables to
 metabolic costs, particularly in the context of morphological adaptation
 to body size. Furthermore, the conversion efficiency from chemical energy
 into movement by the muscles (mechanochemical efficiency) scales with mass
 in terrestrial quadrupeds, but this scaling relationship has not been
 demonstrated within flying vertebrates. Positive scaling of efficiency
 with body size may reduce the metabolic costs of flight for relatively
 larger species. Here, we assembled a dataset of morphological, kinematic,
 and metabolic data on hovering hummingbirds to explore the influence of
 wing morphology, efficiency, and mass on hovering metabolic rate (HMR). We
 hypothesize that HMR would decline with increasing wing size, after
 accounting for mass. Furthermore, we hypothesize that efficiency will
 increase with mass, similarly to other forms of locomotion. We do not find
 a relationship between relative wing size and HMR, and instead find that
 the cost of each wingbeat increases hyperallometrically while wingbeat
 frequency declines with increasing mass. This suggests that increasing
 wing size is metabolically favourable over cycle frequency with increasing
 mass. Further benefits are offered to larger hummingbirds due to the
 positive scaling of efficiency.
description: Groom_etal_Supplemental_Raw_Data_Brazil_RSPBMorphological, metabolic, and kinematic data of hummingbirds in Sao Paulo, Brazil. The location of each individual is also included within the file.Groom_etal_Arizona_supplemental.xlsxWing morphology from free living hummingbirds in Arizona.Groom_etal_wingmorph_Arizona_supplemental.xlsxGroom_etal_Arizona_MR_RSPBMetabolic rates of free-living hummingbirds in Arizona.
DOI: 10.5061/dryad.gq08c
title: Data from: Mechanistic insights into landscape genetic structure of two tropical amphibians using field-derived resistance surfaces

description: Conversion of forests to agriculture often fragments distributions of
 forest species and can disrupt gene flow. We examined effects of prevalent
 land uses on genetic connectivity of two amphibian species in northeastern
 Costa Rica. We incorporated data from field surveys and experiments to
 develop resistance surfaces that represent local mechanisms hypothesized
 to modify dispersal success of amphibians, such as habitat-specific
 predation and desiccation risk. Because time lags can exist between forest
 conversion and genetic responses, we evaluated landscape effects using
 land-cover data from different time periods. Populations of both species
 were structured at similar spatial scales but exhibited differing
 responses to landscape features. Litter frog population differentiation
 was significantly related to landscape resistances estimated from
 abundance and experiment data. Model support was highest for
 experiment-derived surfaces that represented responses to microclimate
 variation. Litter frog genetic variation was best explained by
 contemporary landscape configuration, indicating rapid population response
 to land-use change. Poison frog genetic structure was strongly associated
 with geographic isolation, which explained up to 45% of genetic variation,
 and long-standing barriers, such as rivers and mountains. However, there
 was also partial support for abundance and microclimate response derived
 resistances. Differences in species responses to landscape features may be
 explained by overriding effects of population size on patterns of
 differentiation for poison frogs, but not litter frogs. In addition,
 pastures are likely semi-permeable to poison frog gene flow because the
 species is known to use pastures when remnant vegetation is present, but
 litter frogs do not. Ongoing reforestation efforts will likely increase
 connectivity in the region by increasing tree cover and reducing area of
 pastures.
description: O. pumilio MRDM
 inputGenetic, geographic, and
 resistance distances used in multiple regression on distance
 matrices.OopDistances.txtC. bransfordii MRDM infileGenetic, geographic, and resistance distances used in multiple regression on distance matrices analyses.CraDistances.txtO. pumilio RDA x_variablesExplanatory variables used in redundancy analysesOop_Xvars.txtC. bransfordii RDA x_variablesExplanatory variables used in redundancy analyses.Cra_Xvars.txtO. pumilio STRUCTURE infileSTRUCTURE infileOpum_STRUCTUREinfile.strC. bransfordii STRUCTURE infileSTRUCTURE infileCbra_STRUCTUREinfile.str