cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.593n8
title: Data from: Evolutionary divergence of adult body size and juvenile growth in sympatric subpopulations of a top predator in aquatic ecosystems

description: Evolutionary theory predicts that different selective regimes may
 contribute to divergent evolution of body size and growth rate among
 populations, but most studies have focused on allopatric populations.
 Here, we studied five sympatric subpopulations of anadromous northern pike
 (Esox lucius) in the Baltic Sea subjected to allopatric habitats for a
 short period of their life cycle due to homing behavior. We report
 differences in adult body size among subpopulations that were in part due
 to variation in growth rate. Body size of emigrating juveniles also
 differed among subpopulations, and differences remained when individuals
 were reared in a common environment, thus indicating evolutionary
 divergence among subpopulations. Furthermore, a QST-FST comparison
 indicated that differences had evolved due to divergent selection rather
 than genetic drift, possibly in response to differences in selective
 mortality among spawning habitats during the allopatric life stage. Adult
 and juvenile size were negatively correlated across subpopulations, and
 reconstruction of growth trajectories of adult fishes suggested that body
 size differences developed gradually and became accentuated throughout the
 first years of life. These results represent rare evidence that sympatric
 subpopulations can evolve differences in key life-history traits despite
 being subjected to allopatric habitats during only a very short fraction
 of their life.
description: Common-garden
 experimentData from 937
 common-garden reared juveniles (35 days old) including offspring from 64
 parental crossings originating from three sympatric subpopulations. The
 following phenotypic traits are included: total length (mm), weight (g)
 and specific growth rate (mm/day).Emigrating juveniles
 body sizeBody size (total length,
 mm) data of 3517 field-sampled emigrating juveniles. Includes data from
 three different years and two subpopulations.Growth
 trajectoriesData of reconstructed
 growth trajectories for 109 adults (≥ 4 years old) by using growth
 increment in cleithra bones. The file includes annual increment in the
 cleithra (mm) for each adult.Size-at-ageBody size (length, cm) data from 95 adults of known age (3-6 years old) originating from three subpopulations.Adult body sizeBody size (total length, cm) data of 4097 adults. Individuals were sampled during spawning migration in five streams (subpopulaitions).
DOI: 10.5061/dryad.n7h53
title: Data from: A new species of horned lizard (genus Phrynosoma) from Guerrero, México, with an updated multilocus phylogeny

description: We describe a new species of Phrynosoma from central northeastern
 Guerrero, México; perform a phylogenetic analysis of mitochondrial and
 nuclear sequence data to estimate its phylogenetic relationships; and
 investigate the monophyly of Phrynosoma asio, P. braconnieri, and P.
 taurus. The new species can be distinguished from all of its congeners by
 the possession of a unique combination of morphological characteristics.
 The molecular genetic data include three fragments of the mitochondrial
 genome and six nuclear genes (2419 and 3909 base pairs in total,
 respectively) for 31 samples belonging to the 16 previously recognized
 species of Phrynosoma and the new species. The new species is strongly
 supported in maximum likelihood analyses of both the concatenated
 mitochondrial and nuclear data as a monophyletic, distinct evolutionary
 lineage sister to, and moderately divergent from, P. taurus, and highly
 divergent from all of the other species of Phrynosoma. A Bayesian species
 tree analysis also strongly supports the monophyly of the Brevicauda
 clade, and a sister relationship between P. taurus and the new species.
description: *BEAST XML
 FileMultilocus nuclear data
 for Phrynosoma *BEAST analysis.nuclear.xmlConcatenated mtDNAConcatenated mtDNA in phylip format for Phrynosoma phylogenymtDNA.phyConcatenated nuclear dataConcatenated nuclear data in phylip format for Phrynosoma phylogenynuclear.phy
DOI: 10.5061/dryad.53b6n5f
title: Data from: Construction and characterization of synthetic bacterial community for experimental ecology and evolution

description: Experimental microbial ecology and evolution have yielded foundational
 insights into ecological and evolutionary processes using simple microcosm
 setups and phenotypic assays with one- or two-species model systems. The
 fields are now increasingly incorporating more complex systems and
 exploration of the molecular basis of observations. For this purpose,
 simplified, manageable and well-defined multispecies model systems are
 required that can be easily investigated using culturing and
 high-throughput sequencing approaches, bridging the gap between simpler
 and more complex synthetic or natural systems. Here we address this need
 by constructing a completely synthetic 33 bacterial strain community that
 can be cultured in simple laboratory conditions. We provide whole-genome
 data for all the strains as well as metadata about genomic features and
 phenotypic traits that allow resolving individual strains by amplicon
 sequencing and facilitate a variety of envisioned mechanistic studies. We
 further show that a large proportion of the strains exhibit coexistence in
 co-culture over serial transfer for 48 days in the absence of any
 experimental manipulation to maintain diversity. The constructed bacterial
 community can be a valuable resource in future experimental work.
description: Antibiotic minimum
 inhibitory concentrationsMinimum inhibitory
 concentrations (µg/ml) for antibiotics from different classes (kanamycin,
 streptomycin, ampicillin, nalidixic acid, erythromycin, and rifampicin)
 for HMC33.1 synthetic bacterial community strains.HMC33_antibiotic_MIC.txtCarbon source utilization phenotypesCarbon source utilization phenotypes (1 able and 0 unable to grow on carbon source as sole carbon source) for HMC33.1 synthetic bacterial community strains (Biolog EcoPlate).HMC33_Biolog_EcoPlate.txtGenomic featuresGenomic feature data collated into a single data frame, displaying strain, contig, locus, and genomic feature information, for HMC33.1 synthetic bacterial community strains. The features include antibiotic resistance genes, virulence factors, plasmid or genomic island associated sequences, prophages, insertion sequences, and CRISPR loci. For each individual feature, the following information is provided: strain, contig, contig_number, length, start, end, type, subtype and tool. Annotated genome files where contig annotations correspond with the annotations in this table are available from the corresponding author upon request.HMC33_genomic_features.txtFunctional modules predicted from genome assembliesGenomic predictions for functional modules (obtained using MAPLE 2.3.0) for HMC33.1 synthetic bacterial community strains. The numbers are module completion ratio (MCR) percentages.HMC33_MAPLE-2.3.0.txt
DOI: 10.5061/dryad.4p24g
title: Data from: The roles of compensatory evolution and constraint in aminoacyl tRNA synthetase evolution

description: Mitochondrial protein translation requires interactions between transfer
 RNAs encoded by the mitochondrial genome (mt-tRNAs) and mitochondrial
 aminoacyl tRNA synthetase proteins (mt-aaRS) encoded by the nuclear
 genome. It has been argued that animal mt-tRNAs have higher deleterious
 substitution rates relative to their nuclear-encoded counterparts, the
 cytoplasmic tRNAs (cyt-tRNAs). This dynamic predicts elevated rates of
 compensatory evolution of mt-aaRS that interact with mt-tRNAs, relative to
 aaRS that interact with cyt-tRNAs (cyt-aaRS). We find that mt-aaRS do
 evolve at significantly higher rates (exemplified by higher dN and dN/dS)
 relative to cyt-aaRS, across mammals, birds, and Drosophila. While this
 pattern supports a model of compensatory evolution, the level at which a
 gene is expressed is a more general predictor of protein evolutionary
 rate. We find that gene expression level explains 10-56% of the variance
 in aaRS dN/dS, and that cyt-aaRS are more highly expressed in addition to
 having have lower dN/dS values relative to mt-aaRS, consistent with more
 highly expressed genes being more evolutionarily constrained. Furthermore,
 we find no evidence of positive selection acting on either class of aaRS
 protein, as would be expected under a model of compensatory evolution.
 Nevertheless, the signature of faster mt-aaRS evolution persists in
 mammalian, but not bird or Drosophila, lineages after controlling for gene
 expression, suggesting some additional effect of compensatory evolution
 for mammalian mt-aaRS. We conclude that gene expression is the strongest
 factor governing differential amino acid substitution rates in proteins
 interacting with mitochondrial versus cytoplasmic factors, with important
 differences in mt-aaRS molecular evolution among taxonomic groups.
description: Accessions, alignments,
 and treesArchive.zip
DOI: 10.5061/dryad.67jg8
title: Data from: Maize leaf epiphytic bacteria diversity patterns are genetically correlated with resistance to fungal pathogen infection

description: Plant leaves host a specific set of microbial epiphytes. Plant genetic and
 solar UV-B radiation effects on the diversity of the phyllosphere were
 examined by measuring epiphytic bacterial ribosomal DNA diversity in a
 maize recombinant inbred (RI) mapping population. Several chromosomal
 quantitative trait loci (QTL) with significant effects on bacterial
 diversity were identified, some of which had effects only in the presence
 of UV-B radiation and others that had effects both with and without UV-B.
 Candidate genes with allele-specific effects were mapped to the bacterial
 diversity chromosomal regions. A glutamate decarboxylase candidate gene
 was located at a UV-B–specific chromosomal locus, and in a comparison
 between two RI lines with contrasting bacterial diversity phenotypes, high
 bacterial diversity was associated with high levels of glutamate
 decarboxylase enzyme activity, a component of the gamma-aminobutyric acid
 (GABA) pathway. The bacterial diversity loci exhibited a significant
 overlap with loci connected with Southern leaf blight (SLB) susceptibility
 in the field. A SLB-resistant inbred genotype had less beta bacterial
 diversity, and antibiotic treatment of inbreds increased this diversity.
 These results suggest that the GABA pathway is genetically associated with
 phyllosphere bacterial diversity. Furthermore, the colocalization of QTL
 between low bacterial diversity and fungal blight–resistance and the
 increase in beta diversity in antibiotic-treated leaves suggest that
 occupation of leaf habitats by a particular set of suppressive bacteria
 may restrict phyllosphere bacterial variability and increase resistance to
 fungal infection.
description: Copy of
 MPMI-23-4-0473E1A detailed report for
 ChromoScan significant regions for significant and suggestive quantitative
 trait loci (QTL) and complete table of QTL Network
 results.Copy of
 MPMI-23-4-0473E2Shows the Simpson
 diversity index, evenness, and number of ribotypes (taxa) for each sample
 in the quantitative trait loci experiment.Copy of
 MPMI-23-4-0473E3Shows examples of
 chromosome region crossover maps for the recombinant inbred line set used
 in this study.MPMI-23-4-0473E4Provides experimental design and quantitative trait loci analysis details.
DOI: 10.5061/dryad.k9f7t
title: Data from: Color discrimination in the tufted capuchin monkey, Sapajus spp.

description: The present study evaluated the efficacy of an adapted version of the
 Mollon-Reffin test for the behavioral investigation of color vision in
 capuchin monkeys. Ten tufted capuchin monkeys (Sapajus spp., formerly
 referred to as Cebus apella) had their DNA analyzed and were characterized
 as the following: one trichromat female, seven deuteranope dichromats (six
 males and one female), and two protanope males, one of which was
 identified as an “ML protanope.” For their behavioral characterization,
 all of the subjects were tested at three regions of the Commission
 International de l'Eclairage (CIE) 1976 u′v′ diagram, with each test
 consisting of 20 chromatic variation vectors that were radially
 distributed around the chromaticity point set as the test background. The
 phenotypes inferred from the behavioral data were in complete agreement
 with those predicted from the genetic analysis, with the threshold
 distribution clearly differentiating between trichromats and dichromats
 and the estimated confusion lines characteristically converging for
 deuteranopes and the “classic” protanope. The discrimination pattern of
 the ML protanope was intermediate between protan and deutan, with
 confusion lines horizontally oriented and parallel to each other. The
 observed phenotypic differentiation confirmed the efficacy of the
 Mollon-Reffin test paradigm as a useful tool for evaluating color
 discrimination in nonhuman primates. Especially noteworthy was the
 demonstration of behavioral segregation between the “classic” and “ML”
 protanopes, suggesting identifiable behavioral consequences of even slight
 variations in the spectral sensitivity of M/L photopigments in dichromats.
description: Goulart et al. (2013) -
 behavioral dataColor discrimination
 data of ten capuchin monkeys (Sapajus spp), two Female, eight Male.
 Discrimination thresholds obtained for each monkey in 20 test vectors
 around three different background coordinates (CIE 1976 u' v'
 chromaticity diagram). Thresholds are presented in terms of distance from
 background point (u' v' units x10^-4) and of u' v'
 coordinates.Goulart et al. (2013) -
 genetic dataAmino acid sequences
 from exons 3 and 5 of the X-linked opsin genes of ten capuchin monkeys
 (Sapajus spp), two Female, eight Male. Sequencing of exons 3 and 5 allowed
 the deduction of the amino acid combinations at positions 180, 277, and
 285 of the resulting opsins, from which the range of potential absorption
 maxima of the corresponding photopigments was inferred.
DOI: 10.5061/dryad.cv45n3b
title: Data from: Circadian periodicity in space use by ungulates of temperate regions: how much, when, and why?

description: 1. When they visit and revisit specific areas, animals may reveal what
 they need from their home range and how they acquire information. The
 temporal dimension of such movement recursions, i.e., periodicity, is
 however rarely studied, yet potentially bears a species, population, or
 individual-specific signature. 2. A recent method allows estimating the
 contribution of periodic patterns to the variance in a movement path. We
 applied it to 709 individuals from 5 ungulate species, looking for species
 signatures in the form of seasonal variation in the intensity of circadian
 patterns. 3. Circadian patterns were commonplace in the movement tracks,
 but the amount of variance they explained was highly variable among
 individuals. It increased in intensity during spring and summer, when key
 resources were spatially segregated, and decreased during winter, when
 food availability was more uniformly low. Other periodicity-inducing
 mechanisms supported by our comparison of species- and sex-specific
 patterns involve young anti-predator behavior, territoriality, and
 behavioral thermoregulation. 4. Model-based continuous-time movement
 metrics represent a new avenue for researchers interested in finding
 individual-, population-, or species-specific signatures in heterogeneous
 movement databases featuring various study designs and sampling
 resolutions. However, we observed large amounts of individual variation,
 so comparative analyses should ideally use both GPS and animal-borne
 loggers to augment the discriminatory power; and be based on large
 samples. We briefly outline potential uses of the intensity of circadian
 patterns as a metric for the study of animal personality and community
 ecology.
description: eta parameter
 valuesThis file contains the
 parameter estimates used to draw Fig. 2Eta for
 Dryad.csv
DOI: 10.5061/dryad.mb552
title: Data from: Phylogeny, traits and biodiversity of a neotropical bat assemblage: close relatives show similar responses to local deforestation

description: If species’ evolutionary pasts predetermine their responses to
 evolutionarily novel stressors, then phylogeny could predict species
 survival in an increasingly human-dominated world. To understand the role
 of phylogenetic relatedness in structuring responses to rapid
 environmental change, we focused on assemblages of Neotropical bats, an
 ecologically diverse and functionally important group. We examined how
 taxonomic and phylogenetic diversity shift between tropical forest and
 farmland. We then explored the importance of evolutionary history by
 ascertaining whether close relatives share similar responses to
 environmental change and which species traits might mediate these trends.
 We analyzed a 5-year data set (5,011 captures) from 18 sites in a
 countryside landscape in southern Costa Rica using statistical models that
 account and correct for imperfect detection of species across sites,
 spatial autocorrelation, and consideration of spatial scale. Taxonomic and
 phylogenetic diversity decreased with deforestation, and assemblages
 became more phylogenetically clustered. Species’ responses to
 deforestation were strongly phylogenetically correlated. Body mass and
 absolute wing loading explained a substantial portion of species variation
 in species’ habitat preferences, likely related to these traits’ influence
 on maneuverability in cluttered forest environments. Our findings
 highlight the role that evolutionary history plays in determining which
 species will survive human impacts and the need to consider diversity
 metrics, evolutionary history, and traits together when making predictions
 about species persistence for conservation or ecosystem functioning.
description: Array of Costa Rican bat
 capture dataCapture data collected
 from the field and arranged in an R data array. Array includes: (1) the
 capture array (X), with the site, year, visit and species information; (2)
 matrix of the number of visits conducted at each site by year combination
 (nrep); (3) the pairwise distance between sites (D); (4) scaled and
 centered proportion of area covered by trees across all spatial scales;
 see full model explanation (Env); (5) relative elevation of site compared
 to surroundings (terrain); (6) whether or not the site was a coffee field
 (coffee.dummy)array.rdataFull occupancy model with traitsR and JAGS code for the full phylogenetic occupancy model with influence of traits includedmodel_with_trait_for_supplement.RFull occupancy model without traitsR and JAGS code for the full occupancy model not including traits as an explanatory variablemodel_notrait_for_supplement.R
DOI: 10.5061/dryad.8h6nf
title: Data from: A three-dimensional analysis of the morphological evolution and locomotor behaviour of the carnivoran hind limb

description: Background: The shape of the appendicular bones in mammals usually
 reflects adaptations towards different locomotor abilities. However, other
 aspects such as body size and phylogeny also play an important role in
 shaping bone design. We used 3D landmark-based geometric morphometrics to
 analyse the shape of the hind limb bones (i.e., femur, tibia, and pelvic
 girdle bones) of living and extinct terrestrial carnivorans (Mammalia,
 Carnivora) to quantitatively investigate the influence of body size,
 phylogeny, and locomotor behaviour in shaping the morphology of these
 bones. We also investigated the main patterns of morphological variation
 within a phylogenetic context. Results: Size and phylogeny strongly
 influence the shape of the hind limb bones. In contrast, adaptations
 towards different modes of locomotion seem to have little influence.
 Principal Components Analysis and the study of phylomorphospaces suggest
 that the main source of variation in bone shape is a gradient of
 slenderness-robustness. Conclusion: The shape of the hind limb bones is
 strongly influenced by body size and phylogeny, but not to a similar
 degree by locomotor behaviour. The slender-robust “morphological
 bipolarity” found in bone shape variability is probably related to a
 trade-off between maintaining energetic efficiency and withstanding
 resistance to stresses. The balance involved in this trade-off impedes the
 evolution of high phenotypic variability. In fact, both morphological
 extremes (slender/robust) are adaptive in different selective contexts and
 lead to a convergence in shape among taxa with extremely different
 ecologies but with similar biomechanical demands. Strikingly, this
 “one-to-many mapping” pattern of evolution between morphology and ecology
 in hind limb bones is in complete contrast to the “many-to-one mapping”
 pattern found in the evolution of carnivoran skull shape. The results
 suggest that there are more constraints in the evolution of the shape of
 the appendicular skeleton than in that of skull shape because of the
 strong biomechanical constraints imposed by terrestrial locomotion.
description: Hind limb morphometric
 dataTable in Excel format
 with morphometric data averaged per species for each hind limb bone
 analysed. Centroid size, log-transformed centroid size and Procrustes
 coordinates are shown for pelvis (1st and 2nd sheets), femur (3rd and 4th
 sheets) and tibia (5th and 6th sheets). 1st, 3rd and 5th sheets show
 values for all the species; 2nd, 4th and 6th sheets include only extant
 species.
DOI: 10.5061/dryad.6sm71
title: Data from: Genetic elimination of field-cage populations of Mediterranean fruit flies

description: The Mediterranean fruit fly (medfly, Ceratitis capitata Wiedemann) is a
 pest of over 300 fruits, vegetables and nuts. The sterile insect technique
 (SIT) is a control measure used to reduce the reproductive potential of
 populations through the mass release of sterilized male insects that mate
 with wild females. However, SIT flies can display poor field performance,
 due to the effects of mass-rearing and of the irradiation process used for
 sterilization. The development of female-lethal RIDL (release of insects
 carrying a dominant lethal) strains for medfly can overcome many of the
 problems of SIT associated with irradiation. Here, we present life-history
 characterizations for two medfly RIDL strains, OX3864A and OX3647Q. Our
 results show (i) full functionality of RIDL, (ii) equivalency of RIDL and
 wild-type strains for life-history characteristics, and (iii) a high level
 of sexual competitiveness against both wild-type and wild-derived males.
 We also present the first proof-of-principle experiment on the use of RIDL
 to eliminate medfly populations. Weekly releases of OX3864A males into
 stable populations of wild-type medfly caused a successive decline in
 numbers, leading to eradication. The results show that genetic control can
 provide an effective alternative to SIT for the control of pest insects.
description: Genetic elimination of
 fieldcage populations of Mediterranean fruit fliesRaw count data for all
 mating and field cage suppression trials detailed in manuscript along with
 life history description dataGenetic elimination of
 fieldcage populations of Mediterranean Fruit Flies
 Dryaddata.xls