cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kq72k
title: Data from: Perinatal lead (Pb) exposure results in sex-specific effects on food intake, fat, weight, and insulin response across the murine life-course

description: Developmental lead (Pb) exposure has been associated with lower body
 weight in human infants and late onset obesity in mice. We determined the
 association of perinatal Pb exposure in mice with changes in
 obesity-related phenotypes into adulthood. Mice underwent exposure via
 maternal drinking water supplemented with 0 (control), 2.1 (low), 16
 (medium), or 32 (high) ppm Pb-acetate two weeks prior to mating through
 lactation. Offspring were phenotyped at ages 3, 6, and 9 months for energy
 expenditure, spontaneous activity, food intake, body weight, body
 composition, and at age 10 months for glucose tolerance. Data analyses
 were stratified by sex and adjusted for litter effects. Exposed females
 and males exhibited increased energy expenditure as compared to controls
 (p&lt;0.0001 for both). In females, horizontal activity differed
 significantly from controls (p = 0.02) over the life-course. Overall, food
 intake increased in exposed females and males (p&lt;0.0008 and
 p&lt;0.0001, respectively) with significant linear trends at 9 months
 in females (p = 0.01) and 6 months in males (p&lt;0.01). Body weight
 was significantly increased in males at the medium and high exposures (p =
 0.001 and p = 0.006). Total body fat differed among exposed females and
 males (p&lt;0.0001 and p&lt;0.0001, respectively). Insulin
 response was significantly increased in medium exposure males
 (p&lt;0.05). Perinatal Pb exposure at blood lead levels between 4.1
 µg/dL and 32 µg/dL is associated with increased food intake, body weight,
 total body fat, energy expenditure, activity, and insulin response in
 mice. Physiological effects of developmental Pb exposure persist and vary
 according to sex and age.
description: Physiological
 Measurement DataThis file contains
 complete physiological data for fat mass, food intake, VO, VCO, and 9
 month body weight for all mice in the study.LeadMMOC_Complete.xlsxWeekly Weights DataThis file contains weekly weight data (g) for mice used in this study.LeadWeeklyWeights_Complete.xlsxGlucose Tolerance Test DataThis file contains data from the glucose tolerance test, with measures for glucose and insulin at 0, 15, 30, 60, and 120 minutes as well as area under the curve (AUC) measurements for all mice in this study.Glucose_Tolerance_Test_CompleteData.xlsx
DOI: 10.5061/dryad.jf1m0
title: Data from: Ecotypic divergence in Crepis tectorum (Asteraceae): inferring trait lability and correlational constraints from hormonally manipulated phenotypes

description: Despite long-standing interest in the evolutionary role of plant hormones,
 relatively few studies have used hormonally manipulated phenotypes to
 address questions about phenotypic evolution in plants. In the present
 investigation, I subjected plants of Crepis tectorum subsp. pumila to
 simple gibberellin (GA) treatments under both field and greenhouse
 conditions to assess developmental lability and correlational constraints
 of phenotypic traits that distinguish this dwarf ecotype from conspecific
 populations of the much taller weed ecotype (subsp. tectorum). The
 hormonally manipulated plants largely phenocopied the weed ecotype in leaf
 shape, plant stature and branching habit, indicative of both high lability
 and tight integration of traits reflecting gross morphology. Floral size
 traits sometimes declined after GA application, especially under field
 conditions. The latter result conflicts with the positive correlations
 between floral and vegetative size traits seen in previous comparative
 analyses and point to a tradeoff that could act as a constraint on ecotype
 divergence. The response to GA was consistent in direction for most
 traits, as opposed to the magnitude of response, which varied depending on
 the trait, the population, the growing environment, and the timing and
 level of hormone application. Taken together, the results highlight the
 potential for simple hormonal changes to cause large, plastic shifts in
 phenotype, but also illustrate the constrained nature of such influences.
description: Phenotypic data from a
 gibberellin application experiment with Crepis tectorum
 (Asteraceae)The present file
 contains two data sets used in a study of trait lability and constraint in
 Crepis tectorum. See the README file for detailed
 information.Dryad
 All.xls
DOI: 10.5061/dryad.m6k1r
title: Data from: The emotion system promotes diversity and evolvability

description: Studies on the relationship between the optimal phenotype and its
 environment have had limited focus on genotype-to-phenotype pathways and
 their evolutionary consequences. Here, we study how multi-layered trait
 architecture and its associated constraints prescribe diversity. Using an
 idealized model of the emotion system in fish, we find that trait
 architecture yields genetic and phenotypic diversity even in absence of
 frequency-dependent selection or environmental variation. That is, for a
 given environment, phenotype frequency distributions are predictable while
 gene pools are not. The conservation of phenotypic traits among these
 genetically different populations is due to the multi-layered trait
 architecture, in which one adaptation at a higher architectural level can
 be achieved by several different adaptations at a lower level. Our results
 emphasize the role of convergent evolution and the organismal level of
 selection. While trait architecture makes individuals more constrained
 than what has been assumed in optimization theory, the resulting
 populations are genetically more diverse and adaptable. The emotion system
 in animals may thus have evolved by natural selection because it
 simultaneously enhances three important functions, the behavioural
 robustness of individuals, the evolvability of gene pools and the rate of
 evolutionary innovation at several architectural levels.
description: H18 FORTRAN
 codeH18 is the FORTRAN
 program for evolving behaviour based on emotions in a fish
 population.H18.f90Commonfish Common block for FORTRAN programThis file contains a commonblock which will be read by and included in many subroutines of the H18.f90 FORTRAN program.Commonfish.txti101-parameters parameter fileThis file contains the parameter values the researcher may change for the H18.f90 FORTRAN program for fish behaviour by emotion. The file will be read by the FORTRAN program.i101-parameters.txt
DOI: 10.5061/dryad.6tt66
title: Data from: Changes in taste neurons support the emergence of an adaptive behavior in cockroaches

description: In response to the anthropogenic assault of toxic baits, populations of
 the German cockroach have rapidly evolved an adaptive behavioral aversion
 to glucose (a phagostimulant component of baits). We hypothesized that
 changes in the peripheral gustatory system are responsible for glucose
 aversion. In both wild-type and glucose-averse (GA) cockroaches,
 D-fructose and D-glucose stimulated sugar–gustatory receptor neurons
 (GRNs), whereas the deterrent caffeine stimulated bitter-GRNs. In
 contrast, in GA cockroaches, D-glucose also stimulated bitter-GRNs and
 suppressed the responses of sugar-GRNs. Thus, D-glucose is processed as
 both a phagostimulant and deterrent in GA cockroaches, and this newly
 acquired peripheral taste sensitivity underlies glucose aversion in
 multiple GA populations. The rapid emergence of this highly adaptive
 behavior underscores the plasticity of the sensory system to adapt to
 rapid environmental change.
description: DRYAD_Figure1Data for Fig. 1: Sensitivities of the GRNs of WT and GA (T164-BC) cockroaches to various tastants.DRYAD_Figure2Data for Fig. 2: Behavioral and electrophysiological responses to six tastants.DRYAD_Figure3Data for Fig. 3: Glucose-aversion is elicited by stimulation of bitter-GRNs and inhibition of sugar-GRNs.DRYAD_Figure4Data for Fig. 4: Glucose stimulates bitter-GRNs in field-collected cockroaches.
DOI: 10.5061/dryad.nc571
title: Data from: Processing political misinformation: comprehending the Trump phenomenon

description: This study investigated the cognitive processing of true and false
 political information. Specifically, it examined the impact of source
 credibility on the assessment of veracity when information comes from a
 polarizing source (Experiment 1), and effectiveness of explanations when
 they come from one's own political party or an opposition party
 (Experiment 2). These experiments were conducted prior to the 2016
 Presidential election. Participants rated their belief in factual and
 incorrect statements that President Trump made on the campaign trail;
 facts were subsequently affirmed and misinformation retracted.
 Participants then re-rated their belief immediately or after a delay.
 Experiment 1 found that (i) if information was attributed to Trump,
 Republican supporters of Trump believed it more than if it was presented
 without attribution, whereas the opposite was true for Democrats and (ii)
 although Trump supporters reduced their belief in misinformation items
 following a correction, they did not change their voting preferences.
 Experiment 2 revealed that the explanation's source had relatively
 little impact, and belief updating was more influenced by perceived
 credibility of the individual initially purporting the information. These
 findings suggest that people use political figures as a heuristic to guide
 evaluation of what is true or false, yet do not necessarily insist on
 veracity as a prerequisite for supporting political candidates.
description: Processing inaccurate
 information data
DOI: 10.5061/dryad.nk707
title: Data from: Eco-evolutionary feedback promotes Red Queen dynamics and selects for sex in predator populations

description: Although numerous hypotheses exist to explain the overwhelming presence of
 sexual reproduction across the tree of life, we still cannot explain its
 prevalence when considering all inherent costs involved. The Red Queen
 hypothesis states that sex is maintained because it can create novel
 genotypes with a selective advantage. This occurs when the interactions
 between species induce frequent environmental change. Here we investigate
 whether coevolution and eco-evolutionary feedback dynamics in a
 predator-prey system allows for indirect selection and maintenance of
 sexual reproduction in the predator. Combining models and chemostat
 experiments of a rotifer-algae system we show a continuous feedback
 between population and trait change along with recurrent shifts from
 selection by predation and competition for a limited resource. We found
 that a high propensity for sex was indirectly selected and was maintained
 in rotifer populations within environments containing these
 eco-evolutionary dynamics; whereas within environments under constant
 conditions, predators evolved rapidly to lower levels of sex. Thus, our
 results indicate that the influence of eco-evolutionary feedback dynamics
 on the overall evolutionary change has been underestimated.
description: EcoEvoModel_OnePredData for Figure 1EcoEvoModel_TwoPredData for Figure 1IndBasedModel_ExtrinsicData for Figure 2IndBasedModel_EcoEvoData for Figure 2ChemostatDataData used in Figures 3-5 and SIFitnessDataData for Figure 4SexRateDataData for Figure 5
DOI: 10.5061/dryad.456569k
title: Data from: Multifactorial processes underlie parallel opsin loss in neotropical bats

description: The loss of previously adaptive traits is typically linked to relaxation
 in selection, yet the molecular steps leading to such repeated losses are
 rarely known. Molecular studies of loss have tended to focus on gene
 sequences alone, but overlooking other aspects of protein expression might
 underestimate phenotypic diversity. Insights based almost solely on opsin
 gene evolution, for instance, have made mammalian color vision a textbook
 example of phenotypic loss. We address this gap by investigating retention
 and loss of opsin genes, transcripts and proteins across ecologically
 diverse noctilionoid bats. We find multiple, independent losses of
 short-wave sensitive opsins. Mismatches between putatively functional DNA
 sequences, mRNA transcripts, and proteins implicate transcriptional and
 post-transcriptional processes in the ongoing loss of S-opsins in some
 noctilionoid bats. Our results provide a snapshot of evolution in progress
 during phenotypic trait loss, and suggest vertebrate visual phenotypes
 cannot always be predicted from genotypes alone.
description: R code and data files
 for calculating ecological correlates of opsin presence and
 densitySadier_et_al_Opsins.zipRHO_cds_alRHO sequence alignment used for PAML analyses. Sequences were obtained from novel RNA-Seq data, publicly available genomes (GenBank), and unpublished genomes (Rossiter Lab and the Broad Institute). The final alignment included an additional sequence from Phyllostomus discolor available from https://vgp.github.io/genomeark/Phyllostomus_discolor/GenomeArk. The terminal stop codon has been removed.OPN1SW_cds_alOPN1SW sequence alignment used for PAML analyses. Sequences were obtained from novel RNA-Seq data, publicly available genomes (GenBank), and unpublished genomes (Rossiter Lab and the Broad Institute). The final alignment included an additional sequence from Phyllostomus discolor available from https://vgp.github.io/genomeark/Phyllostomus_discolor/GenomeArk. The terminal stop codon has been removed. Sequences were aligned by eye, premature stop codons were masked with ‘Ns’ and columns containing insertions that shifted the translation frame were deleted to keep codons in frame.OPN1LW_cds_alOPN1LW sequence alignment used for PAML analyses. Sequences were obtained from novel RNA-Seq data, publicly available genomes (GenBank), and unpublished genomes (Rossiter Lab and the Broad Institute). The final alignment included an additional sequence from Phyllostomus discolor available from https://vgp.github.io/genomeark/Phyllostomus_discolor/GenomeArk. The terminal stop codon has been removed.
DOI: 10.5061/dryad.6b340
title: Data from: Geographic variation in the Pine Barrens Treefrog (Hyla andersonii): concordance of genetic, morphometric, and acoustic signal data

description: Delimiting species is important to every subfield in biology.
 Templeton's cohesion species concept uses genetic and ecological
 exchangeability to identify sets of populations that ought to be
 considered as the same species, and the lack of exchangeability helps
 determine which populations can be grouped as evolutionarily significant
 units (ESU) in conservation science. However, previous work assessing
 genetic and ecological interchangeability among populations has been
 limited in scope. Here, we provide a method for assessing exchangeability
 that incorporates multiple, independent lines of multivariate evidence in
 genetic, behavioural and morphological data. We use this approach to
 assess exchangeability across three disjunct groups of populations of the
 Pine Barrens Treefrog (Hyla andersonii) from the eastern United States.
 This species is considered threatened by each state in which it occurs and
 conservation management of this taxon requires a clearer understanding of
 how populations in these three regions may differ from one another. We
 find a strikingly concordant pattern in which the first axis of variation
 for each of the three types of data distinguishes populations along a
 latitudinal gradient and the second axis distinguishes the set of
 populations occurring in the Carolinas from those occurring in the New
 Jersey and Florida/Alabama regions. We know of no comparable data set that
 displays such concordance among different types of data across so large a
 geographic range. The overlap in trait values (i.e. exchangeability)
 between neighbouring regions, however, is substantial in all three types
 of data, which supports continued consideration of this taxon as a single
 species.
description: RAxML_COIcytBAligned COI and cytB sequences used as RAxML input file.RAxML_bestTreeResulting best tree with bootstrap values generated using RAxML.Raw acoustic dataJMP raw data file used for acoustic analysesAcoustic_Dryad.jmpRaw morphometric dataJMP raw data file used for morphometric analysesMorpho_Dryad.jmpMicrosatellite genotype dataRaw microsatellite genotype data and input file for Genalex genetic analyses (principal coordinates)Genetic_Genalex_Dryad.xlsxArlequin input fileMicrosatellite data input file for Arlequin (Rst, AMOVA, Mantel Test)Genetic_arlequin_Dryad.arpR script for acoustic calculationsTwo scripts for acoustic signal variable extraction. One calculates mean, sd, cv across calls for a single individual and generates a new data file with all individuals together; the other script calculates these values across waveforms for a single individual.R_script_Acoustic_calc_CC0.rStarting file for R scriptFile required to run R script for acoustic variable calculations. See details within the script document and script ReadMe file.SumStats.csv
DOI: 10.5061/dryad.82201
title: Data from: Disentangling the roles of history and local selection in shaping clinal variation of allele frequencies and gene expression in Norway spruce (Picea abies)

description: Understanding the genetic basis of local adaptation is challenging due to
 the subtle balance among conflicting evolutionary forces that are involved
 in its establishment and maintenance. One system with which to tease apart
 these difficulties are clines in adaptive characters. Here we analyzed
 genetic and phenotypic variation in bud set, a highly heritable and
 adaptive trait, among 18 populations of Norway spruce (Picea abies),
 arrayed along a latitudinal gradient ranging from 47°N to 68°N. We
 confirmed that variation in bud set is strongly clinal using a subset of
 five populations. Genotypes for 137 single nucleotide polymorphisms (SNPs)
 chosen from 18 candidate genes putatively affecting bud set, and 308
 control SNPs chosen from 264 random genes, were analyzed for patterns of
 genetic structure and correlation to environment. Population genetic
 structure was low (FST = 0.05), but latitudinal patterns were apparent
 among Scandinavian populations. Hence, part of the observed clinal
 variation should be attributable to population demography. Conditional on
 patterns of genetic structure, there was enrichment of SNPs within
 candidate genes for correlations with latitude. Twenty-nine SNPs were also
 outliers with respect to FST. The enrichment for clinal variation at SNPs
 within candidate genes (i.e. SNPs in PaGI, PaPhyP, PaPhyN, PaPRR7 and
 PaFTL2) indicated that local selection in the 18 populations, and/or
 selection in the ancestral populations from which they were recently
 derived, shaped the observed cline. Validation of these genes using
 expression studies also revealed that PaFTL2 expression is significantly
 associated with latitude, thereby confirming the central role played by
 this gene in the control of phenology in plants.
description: budsetbudset
 phenotypeExpressionFTL2qPCR results for gene PaFTL2ExpressionCCA1qPCR results for gene PaCCA1ExpressionGIqPCR results for gene PaGIExpressionPRR7qPCR results for gene PaPRR7genotype_pabies445Illumina GoldenGate genotyping results for 18 populations with a latitude range from 47 to 68 N.
DOI: 10.5061/dryad.f0g7v
title: Data from: Evolution of Manduca sexta hornworms and relatives: biogeographical analysis reveals an ancestral diversification in Central America

description: The hawkmoth genus Manduca is a diverse group of very large, conspicuous
 moths that has served as an important model across many biological
 disciplines. Two species in particular, the tobacco hornworm (Manduca
 sexta) and the tomato hornworm (Manduca quinquemaculatus) have been
 researched extensively. Studies across biological fields have referred to
 these two species as being closely related or even sister species, but the
 extent to which these two model organisms are related remains largely
 unknown. We conducted a comprehensive multi-gene phylogenetic analysis of
 Manduca, based on both an ML and Bayesian framework, which resulted in a
 monophyletic Manduca but only when two other genera, Dolba and Euryglottis
 are included. We tentatively conclude that the sister group to Manduca
 sexta comprises the Caribbean M. afflicta and M. johanni, and the sister
 lineage to this clade includes M. quinquemaculatus and the Hawaiian M.
 blackburni. Thus, M. sexta and M. quinquemaculatus are closely related,
 but are not sister species. Biogeographical analyses reveal an ancestral
 center of diversification in Central America, and Manduca appears to have
 subsequently colonized North and South America. Our phylogeny provides an
 important foundation for comparative studies of two model organisms and
 their relatives.
description: Kawahara_et_al_2013_ManducaNexus file for Kawahara et al. (2013) studyManduca_dataset_FINAL.nex
DOI: 10.5061/dryad.5k0s6
title: Data from: Epistatic interactions influence terrestrial-marine functional shifts in cetacean rhodopsin

description: Like many aquatic vertebrates, whales have blue-shifting spectral tuning
 substitutions in the dim-light visual pigment, rhodopsin, that are thought
 to increase photosensitivity in underwater environments. We have
 discovered that known spectral tuning substitutions also have surprising
 epistatic effects on another function of rhodopsin, the kinetic rates
 associated with light-activated intermediates. By using absorbance
 spectroscopy and fluorescence-based retinal release assays on
 heterologously expressed rhodopsin, we assessed both spectral and kinetic
 differences between cetaceans (killer whale) and terrestrial outgroups
 (hippo, bovine). Mutation experiments revealed that killer whale rhodopsin
 is unusually resilient to pleiotropic effects on retinal release from key
 blue-shifting substitutions (D83N and A292S), largely due to a
 surprisingly specific epistatic interaction between D83N and the
 background residue, S299. Ancestral sequence reconstruction indicated that
 S299 is an ancestral residue that predates the evolution of blue-shifting
 substitutions at the origins of Cetacea. Based on these results, we
 hypothesize that intramolecular epistasis helped to conserve
 rhodopsin's kinetic properties while enabling blue-shifting spectral
 tuning substitutions as cetaceans adapted to aquatic environments.
 Trade-offs between different aspects of molecular function are rarely
 considered in protein evolution, but in cetacean and other vertebrate
 rhodopsins, may underlie multiple evolutionary scenarios for the selection
 of specific amino acid substitutions.
description: Data for Dungan &
 Chang 2017, Proceedings BThe .zip archive
 contains two files: 1) A fasta alignment of the rhodopsin coding sequences
 used for ancestral sequence reconstruction and 2) an excel file with
 fluorescence and absorbance data seriesDunganChang2017_ProcB_Data.zip
DOI: 10.5281/zenodo.18381718
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Christopher C. Grinter, https://orcid.org/0000-0002-3769-1664. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.