cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4m24c
title: Data from: Mosaic heterochrony and evolutionary modularity: the trilobite genus Zacanthopsis as a case study

description: Logical connections exist between evolutionary modularity and
 heterochrony, two unifying and structuring themes in the expanding field
 of evolutionary developmental biology. The former sees complex phenotypes
 as being made up of semi-independent units of evolutionary transformation;
 the latter requires such a modular organization of phenotypes to occur in
 a localized or mosaic fashion. This conceptual relationship is illustrated
 here by analyzing the evolutionary changes in the cranidial ontogeny of
 two related species of Cambrian trilobites. With arguments from
 comparative developmental genetics and functional morphology, we delineate
 putative evolutionary modules within the cranidium and examine patterns of
 evolutionary changes in ontogeny at both global and local scales. Results
 support a case of mosaic heterochrony, i.e. a combination of local
 heterochronies affecting the different parts individuated in the
 cranidium, leading to the complex pattern of allometric repatterning
 observed at the global scale. Through this example, we show that recasting
 morphological analyses of complex phenotypes with a priori knowledge or
 hypotheses about their organizational and variational properties can
 significantly improve our interpretation and understanding of evolutionary
 changes among related taxa, fossil and extant. Such considerations open
 avenues to investigate the large-scale dynamics of modularity and its role
 in phenotypic evolution.
description: GerberHopkinsTrilobiteDataThe following table provides the morphological data for the 203 specimens used in the study. The first column corresponds to the designation name of specimens in the Institute for Cambrian Studies at the University of Chicago (ICS) or at the University of California Riverside (UCR), where the material is housed. The second column corresponds to the affiliation of specimens to the two species considered, Zacanthopsis levis (1) and Zacanthopsis palmeri (2). The remaining columns correspond to the raw coordinates of the set of 25 2D-landmarks used to capture the shape of the trilobite cranidia. Questions regarding collection localities or identification and preparation of material should be directed to the second author (Melanie Hopkins).
DOI: 10.5061/dryad.nk885
title: Data from: What drives selection on flowering time? An experimental manipulation of the inherent correlation between genotype and environment

description: The optimal timing of the seasonal switch from somatic growth to
 reproduction can depend on an individual's condition at reproduction,
 the quality of the environment in which it will reproduce, or both. In
 annual plants, vegetative size (a function of age at flowering) affects
 resources available for seed production, while exposure to mutualists,
 antagonists, and abiotic stresses in the environment (functions of Julian
 date of flowering), influences success in converting resources into
 offspring. The inherent tight correlation between age, size, and
 environment obscures their independent fitness contributions. We isolated
 the fitness effects of these factors by experimentally manipulating the
 correlation between age at flowering and date of flowering in Brassica
 rapa. We staggered the planting dates of families with differing ages at
 flowering to produce experimental populations in which age at flowering
 and date of flowering were positively-, negatively-, or uncorrelated. In
 all populations, plants with an early date of flowering produced more seed
 than those flowering late, regardless of age or size at flowering onset.
 The temporal environment was thus the principal driver of selection on
 flowering time, but its importance relative to that of age and size varied
 with the presence/absence of herbivores and seed predators.
description: Austen&Weis_DataForSelectionFLtimeData (several files in zip folder) collected from 2009 and 2010 experimental field populations.Austen&Weis_Archive_SelectionOnFlwTime.zip
DOI: 10.5061/dryad.g6c5q
title: Data from: Acoustic telemetry reveals cryptic residency of whale sharks

description: Although whale sharks (Rhincodon typus) have been documented to move
 thousands of kilometres, they are most frequently observed at a few
 predictable seasonal aggregation sites. The absence of sharks at the
 surface during visual surveys has led to the assumption that sharks
 disperse to places unknown during the long ‘off-seasons’ at most of these
 locations. Here we compare 2 years of R. typus visual sighting records
 from Mafia Island in Tanzania to concurrent acoustic telemetry of tagged
 individuals. Sightings revealed a clear seasonal pattern with a peak
 between October and February and no sharks observed at other times. By
 contrast, acoustic telemetry demonstrated year-round residency of R.
 typus. The sharks use a different habitat in the off-season, swimming
 deeper and further away from shore, presumably in response to prey
 distributions. This behavioural change reduces the sharks'
 visibility, giving the false impression that they have left the area. We
 demonstrate, for the first time to our knowledge, year-round residency of
 unprovisioned, individual R. typus at an aggregation site, and highlight
 the importance of using multiple techniques to study the movement ecology
 of marine megafauna.
description: Acoustic
 detectionsDate (in two weeks
 intervals) and shark ID's of acoustically detected
 individualsacoustic-detections.csvTagged sharksDetails of tagged sharks: Date of tagging, ecocean ID number, gender and size (m)tagged-sharks.csvNumber of stationsAcoustic effort. Number of working acoustic receiver stations per 2-week periodnumber-stations.csvVisual / Photographic identificationsSharks identified on visual surveysvisual-sightings.csvSearching hoursVisual effort. Number of searching hours per 2-week periodsearching-hours.csvIndividuals' swimming depth and distance from shoreMean swimming depth and distance from shore per individual per 2-week periodmean-depth-distance.csvR script - presence/absence functionpresence-absence.R
DOI: 10.15468/dl.2weus8
title: Occurrence Download

description: A dataset containing 85 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Pantherophis bairdi",
 "Year 1960-2026"
 ]
}

 The dataset includes 85 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000831-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p2yn26
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Browallia abbreviata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000830-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.s584c
title: Data from: Can novel genetic analyses help to identify low-dispersal marine invasive species?

description: Genetic methods can be a powerful tool to resolve the native versus
 introduced status of populations whose taxonomy and biogeography are
 poorly understood. The genetic study of introduced species is presently
 dominated by analyses that identify signatures of recent colonization by
 means of summary statistics. Unfortunately, such approaches cannot be used
 in low-dispersal species, in which recently established populations
 originating from elsewhere in the species' native range also
 experience periods of low population size because they are founded by few
 individuals. We tested whether coalescent-based molecular analyses that
 provide detailed information about demographic history supported the
 hypothesis that a sea squirt whose distribution is centered on Tasmania
 was recently introduced to mainland Australia and New Zealand through
 human activities. Methods comparing trends in population size (Bayesian
 Skyline Plots and Approximate Bayesian Computation) were no more
 informative than summary statistics, likely because of recent
 intra-Tasmanian dispersal. However, IMa2 estimates of divergence between
 putatively native and introduced populations provided information at a
 temporal scale suitable to differentiate between recent (potentially
 anthropogenic) introductions and ancient divergence, and indicated that
 all three non-Tasmanian populations were founded during the period of
 European settlement. While this approach can be affected by inaccurate
 molecular dating, it has considerable (albeit largely unexplored)
 potential to corroborate nongenetic information in species with limited
 dispersal capabilities.
description: Pyura_doppelgangera_COI_sequencesAligned mitochondrial dna cytochrome c oxidase subunit I (COI) sequences for the ascidian Pyura doppelgangeraPyura_doppelgangera_ANT_sequencesAligned nuclear DNA Adenine Nucleotide Transporter (ANT, also known as ADP/ATP translocase) sequences for the ascidian Pyura doppelgangeraPyura_doppelgangera_Microsats_10populationsComplete microsatellite data set in Genepop format.Pyura_doppelgangera_Microsats_10populations_Reduced
DOI: 10.6084/m9.figshare.31152202
title: Surface currents measured by HF radars in the Taiwan Strait during the winter monsoon in 2013

description: This dataset was originally published on borealisdata.ca in 2021, under the repository https://borealisdata.ca/dataverse/odl, with the access link https://doi.org/10.5683/SP2/QK4LGH. However, due to frequent inaccessibility of the website in some countries and regions, the authors have decided to create a replica on Zenodo for interested readers of the paper to access.
DOI: 10.6084/m9.figshare.31152202.v2
title: Surface currents measured by HF radars in the Taiwan Strait during the winter monsoon in 2013

description: This dataset was originally published on borealisdata.ca in 2021, under the repository https://borealisdata.ca/dataverse/odl, with the access link https://doi.org/10.5683/SP2/QK4LGH. However, due to frequent inaccessibility of the website in some countries and regions, the authors have decided to create a replica on Zenodo for interested readers of the paper to access.
DOI: 10.5061/dryad.3h9f5
title: Data from: Macrophage adaptation leads to parallel evolution of genetically diverse Escherichia coli small-colony variants with increased fitness in vivo and antibiotic collateral sensitivity

description: Small-colony variants (SCVs) are commonly observed in evolution
 experiments and clinical isolates, being associated with antibiotic
 resistance and persistent infections. We recently observed the repeated
 emergence of Escherichia coli SCVs during adaptation to the interaction
 with macrophages. To identify the genetic targets underlying the emergence
 of this clinically relevant morphotype, we performed whole-genome
 sequencing of independently evolved SCV clones. We uncovered novel
 mutational targets, not previously associated with SCVs (e.g. cydA, pepP),
 and observed widespread functional parallelism. All SCV clones had
 mutations in genes related to the electron-transport chain. As SCVs
 emerged during adaptation to macrophages, and often show increased
 antibiotic resistance, we measured SCV fitness inside macrophages and
 measured their antibiotic resistance profiles. SCVs had a fitness
 advantage inside macrophages and show increased aminoglycoside resistance
 in vitro, but had collateral sensitivity to other antibiotics (e.g.
 tetracycline). Importantly, we observed similar results in vivo. SCVs had
 a fitness advantage upon colonization of the mouse gut, which could be
 tuned by antibiotic treatment: kanamycin (aminoglycoside) increased SCV
 fitness, but tetracycline strongly reduced it. Our results highlight the
 power of using experimental evolution as the basis for identifying the
 causes and consequences of adaptation during host-microbe interactions.
description: Data for Figures 1 and
 S2Data was obtained from
 competitions between different bacterial strains in the presence of
 macrophages.Data_Figures1andS2.csvData for Figures 2 and S7Data was obtained from measuring inhibition halos for different antibiotic-strain combinations.Data_Figures2andS7.csvData for Figures 3 and S3Data was obtained from competing a mixture of SCV clones against the Ancestral in vivo, inside the mouse gutData_Figures3andS3.csvData for Figure S5Data was obtained from measuring growth curves for each clone in a Bioscreen C.Data_FigureS5.csvData for Figure S6A-CData was obtained from measuring growth curves for each clone in a Bioscreen C.Data_FigureS6A-C.csvData for Figure S6D-FData was obtained from measuring growth curves for each clone in a Bioscreen C.Data_FigureS6D-F.csv
DOI: 10.6084/m9.figshare.31152202.v1
title: a) Readme.txt

description: This dataset was originally published on borealisdata.ca in 2021, under the repository https://borealisdata.ca/dataverse/odl, with the access link https://doi.org/10.5683/SP2/QK4LGH. However, due to frequent inaccessibility of the website in some countries and regions, the authors have decided to create a replica on Zenodo for interested readers of the paper to access.
DOI: 10.5061/dryad.f5vn5
title: Data from: Neuroendocrine correlates of sex-role reversal in barred buttonquails

description: Sex differences in brain structure and behaviour are well documented among
 vertebrates. An excellent model exploring the neural mechanisms of sex
 differences in behaviour is represented by sex-role-reversed species. In
 the majority of bird species, males compete over access to mates and
 resources more strongly than do females. It is thought that the
 responsible brain regions are therefore more developed in males than in
 females. Because these behaviours and brain regions are activated by
 androgens, males usually have increased testosterone levels during
 breeding. Therefore, in species with sex-role reversal, certain areas of
 the female brain should be more developed or steroid hormone profiles
 should be sexually reversed. Here, I studied circulating hormone levels
 and gene expression of steroid hormone receptors and aromatase in a
 captive population of barred buttonquails (Turnix suscitator). While
 females performed courtship and agonistic behaviours, there was no
 evidence for sexually reversed hormone profiles. However, I found
 female-biased sex differences in gene expression of androgen receptors in
 several hypothalamic and limbic brain regions that were already in place
 at hatching. Such sex differences are not known from non-sex-role-reversed
 species. These data suggest that increased neural sensitivity to androgens
 could be involved in the mechanisms mediating sex-role-reversed
 behaviours.
description: Data_adultsData on body weight, behaviour and gene expression of adult buttonquailsData_hatchlingsData on body weight and gene expression of hatchling buttonquails
DOI: 10.5061/dryad.rf02203
title: Data from: Lecanora caperatica (Lecanoraceae, lichenized ascomycetes) a new sorediate species widespread in eastern North America

description: Lecanora caperatica is described based on collections from throughout
 temperate eastern North America. It is a crustose sorediate species in the
 L. subfusca group which has pulcaris-type apothecia, and produces
 atranorin and caperatic acid often with accessory roccellic/angardianic
 acid. The species is chemically similar to the European L. mugosphagneti
 which differs in ecology, thallus morphology and in having albella-type
 apothecia. The generic placement of L. caperatica, and its affinity to the
 L. subfusca group, are confirmed by molecular phylogenetic analysis.
description: data_packetThis is a zipped folder that contains the following. 1) A concatenated alignment of ITS and mtSSU sequences from sorediate Lecanora species from the Malicek et al (2017) paper with four new sequences added. File can be found in in both NEXUS (.nex) and PHYLIP (.phy) formats. 2) A concatenated alignment of the six-gene data set of lecanoroid lichens from Zhao et al (2015) with four new sequences added. File can be found in in both NEXUS (.nex) and PHYLIP (.phy) formats. 3) PDFs of results of the maximum liklihood analyses of single loci from the Malicek et al.(2017) dataset to confirm absence of conflict between loci. Full citations: MalÌcek, J., Berger, F., Palice, Z., & Vondr·k, J. 2017. Corticolous sorediate Lecanora species (Lecanoraceae, Ascomycota) containing atranorin in Europe. The Lichenologist 49: 431-455. Zhao, X., Leavitt, S. D., Zhao Z. T., Zhang, L. L., Arup U., Grube, M., PÈrez-Ortega S., Printzen C., Sliwa, L., Kraichak, E., Divakar, P. K., A. Crespo & H. T. Lumbsch. 2015. Towards a revised generic classification of lecanoroid lichens (Lecanoraceae, Ascomycota) based on molecular, morphological and chemical evidence. Fungal Diversity 78: 293-304.
DOI: 10.5061/dryad.0g98k
title: Data from: Evolution of sexual dimorphism in phenotypic covariance structure in Phymata

description: Sexual dimorphism is a consequence of both sex-specific selection and
 potential constraints imposed by a shared genetic architecture underlying
 sexually homologous traits. However, genetic architecture is expected to
 evolve to mitigate these constraints, allowing the sexes to approach their
 respective optimal mean phenotype. In additon, sex-specific selection is
 expected to generate sexual dimorphism of trait covariance structure (e.g.
 the phenotypic covariance matrix, P) but previous empirical work has not
 fully addressed this prediction. We compared patterns of phenotypic
 divergence, for three traits in 7 taxa in the insect genus Phymata
 (Reduviidae), to ask whether sexual dimorphism in P is common and whether
 its magnitude relates to the extent of sexual dimorphism in trait means.
 We found that sexual dimorphism in both mean and covariance structure was
 pervasive but also that the multivariate distance between sex-specific
 means was correlated with sex differences in the leading eigenvector of P,
 while accounting for uncertainty in phylogenetic relationships.
 Collectively, our findings suggest that sexual dimorphism in covariance
 structure may be a common but underappreciated feature of dioecious
 populations.
description: Dryad data(Punzalan and
 Rowe 2015 Evolution)Phenotypic (3 traits)
 and locality data for 7 species/subspecies of Phymata from museum
 specimens. Additional museum/collection data associated with each
 individual (distinguished by the column 'ID') is available upon
 request. Key to column headers is provided on separate worksheet in the
 same file.
DOI: 10.5061/dryad.t8g60
title: Data from: Determinants and co-expression of anti-predator responses in amphibian tadpoles: a meta-analysis

description: A wide range of taxa respond to perceived predation risk (PPR) through
 inducible defenses, and many prey are capable of responding both
 behaviorally and morphologically to the same risk event. In cases where
 multiple defenses confer protection by independent means (i.e., they are
 mechanistically independent) responses will either be co-expressed, or the
 expression of one defense will limit the capacity (or need) to respond
 along another axis. Our ability to generate a broad understanding of these
 patters has been limited, in part, by difficulties in comparing results
 across studies that employ distinct experimental protocols. Using the
 extensive literature on tadpole responses to PPR, we conducted a
 meta-analysis to identify the ecological and experimental determinants of
 inducible defence expression. We then assessed whether the magnitude of
 response to PPR along behavioural versus morphological response axes was
 positively, or negatively, correlated. The most commonly quantified
 responses to perceived risk in tadpoles included reductions in movement
 and swimming behaviour, and altered tail morphology. Our analyses reveal
 that tadpole behavioural responses are strongly influenced by prey family,
 predator taxon, evolutionary history with the predator (native vs.
 non-native), amount of prey consumed by the predator, and how perceived
 risk was manipulated (e.g., presence vs. absence of alarm cues). Tail
 morphology was similarly influenced by these factors, but also whether the
 target prey was palatable to predators. Thus, our results identify
 ecological and experimental features that critically influence the
 observed effect size in tadpole responses to PPR. A positive correlation
 between behavioural and morphological responses in studies where both were
 measured indicates that trait co-specialization is the predominant pattern
 of defense deployment in larval amphibians. This positive relationship
 suggests that survival tends to be maximized in tadpoles through
 equivalent coactivation of multiple independent axes of protection,
 opposed to maximal expression along any single axis.
description: Data for meta-analyses
 and regressionsHossie et al 2016 OIKOS -
 Dataset.xlsx
DOI: 10.5061/dryad.cn0d6h5
title: Data from: Bayesian phylogenetic analysis of combined data

description: The recent development of Bayesian phylogenetic inference using Markov
 chain Monte Carlo (MCMC) techniques has facilitated the exploration of
 parameter-rich evolutionary models. At the same time, stochastic models
 have become more realistic (and complex) and have been extended to new
 types of data, such as morphology. Based on this foundation, we developed
 a Bayesian MCMC approach to the analysis of combined data sets and
 explored its utility in inferring relationships among gall wasps based on
 data from morphology and four genes (nuclear and mitochondrial, ribosomal
 and protein coding). Examined models range in complexity from those
 recognizing only a morphological and a molecular partition to those having
 complex substitution models with independent parameters for each gene.
 Bayesian MCMC analysis deals efficiently with complex models: convergence
 occurs faster and more predictably for complex models, mixing is adequate
 for all parameters even under very complex models, and the parameter
 update cycle is virtually unaffected by model partitioning across sites.
 Morphology contributed only 5% of the characters in the data set but
 nevertheless influenced the combined-data tree, supporting the utility of
 morphological data in multigene analyses. We used Bayesian criteria (Bayes
 factors) to show that process heterogeneity across data partitions is a
 significant model component, although not as important as among-site rate
 variation. More complex evolutionary models are associated with more
 topological uncertainty and less conflict between morphology and
 molecules. Bayes factors sometimes favor simpler models over considerably
 more parameter-rich models, but the best model overall is also the most
 complex and Bayes factors do not support exclusion of apparently weak
 parameters from this model. Thus, Bayes factors appear to be useful for
 selecting among complex models, but it is still unclear whether their use
 strikes a reasonable balance between model complexity and error in
 parameter estimates.
description: DataNylander_et_al_30Apr03.nex