cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.28kd1
title: Data from: Comparative analyses of sex-ratio variation in dioecious flowering plants

description: Dioecious plant species commonly exhibit deviations from the equilibrium
 expectation of 1:1 sex ratio, but the mechanisms governing this variation
 are poorly understood. Here, we use comparative analyses of 243 species,
 representing 123 genera and 61 families to investigate ecological and
 genetic correlates of variation in the operational (flowering) sex ratio.
 After controlling for phylogenetic non-independence, we examined the
 influence of growth form, clonality, fleshy fruits, pollen and seed
 dispersal vector, and the possession of sex chromosomes on sex-ratio
 variation. Male-biased flowering sex ratios were twice as common as
 female-biased ratios. Male bias was associated with long-lived growth
 forms (e.g. trees) and biotic seed dispersal and fleshy fruits, whereas
 female bias was associated with clonality, especially for herbaceous
 species, and abiotic pollen dispersal. Female bias occurred in species
 with sex chromosomes and there was some evidence for a greater degree of
 bias in those with heteromorphic sex chromosomes. Although the role of
 interactions among these correlates require further study, our results
 indicate that sex-based differences in costs of reproduction, pollen and
 seed dispersal mechanisms and sex chromosomes can each play important
 roles in affecting flowering sex ratios in dioecious plants.
description: SexRatioFINAL_GLMApril2012Life history traits and sex ratio data used in the GEE phylogenetic comparative analysis and GLM.Phylo6_247_April2012Original nexus file containing the phylogenetic data. This is not the final data analysed as it contains an additional 4 species removed prior to analysis due to failing quality criteria (see manuscript). Moreover, this is the base tree from which 200 further trees were created (see next file).200treesNoiseBL&PolyResolvActually phylogenies used in the final GEE analyses. 200 tree were generated using Mesquite to randomly resolve polytomies and to add noise to branch lengths.
DOI: 10.5061/dryad.q1cb1
title: Data from: Karyotype analysis of Panax ginseng C.A. Meyer, 1843 (Araliaceae) based on rDNA loci and DAPI band distribution

description: Ginseng has long been considered a valuable plant owing to its medicinal
 properties; however, genomic information based on chromosome
 characterization and physical mapping of cytogenetic markers has been very
 limited. Dual-color FISH karyotype and DAPI banding analyses of Panax
 ginseng C. A. Meyer, 1843 were conducted using 5S and 45S rDNA probes. The
 somatic chromosome complement was 2n=48 with lengths from 3.3 µm to 6.3
 µm. The karyotype was composed of 12 metacentric, 9 submetacentric, and 3
 subtelocentric pairs. The 5S rDNA probe localized to the intercalary
 region of the short arm of pair 11, while the 45S rDNA was located at the
 secondary constriction of the subtelocentric satellited chromosome 14.
 DAPI bands were clearly observed for most chromosomes, with various signal
 intensities and chromosomal distributions that consequently improved
 chromosome identification. As a result, all 24 chromosomes could be
 distinguished and numbers were assigned to each chromosome for the first
 time. The results presented here will be useful for the on-going ginseng
 genome sequencing and further molecular-cytogenetic studies and breeding
 programs of ginseng.
description: Chromosome analyses of
 P. ginseng C. A. Meyer based on chromosome length and centromeric
 position.This shows the
 measurements of each chromosome arm, arm ratio, and the type of each
 chromosome of P. ginseng C.A.MeyerTable
 1.xlsxSummary of the rDNA and
 DAPI band distribution patternsDescription of each P.
 ginseng chromosome based on the presence or absence of rDNA signals and
 DAPI bands.Table
 2.xlsxChromosome complement
 and rDNA distributionImages showing the 45S
 and 5S rDNA loci among three P. ginseng cultivars, ‘Sunun’, ‘Gopoong’,
 ‘Chunpoong’, and one local landrace, ‘Hwangsook’.Fig1.jpgKaryotype idiogram of ginsengMetaphase spread and the karyotype idiogram of P. ginsengFig2.jpgDiagrammatic idiogram of the P. ginseng karyotypeDiagram of P. ginseng karyotype showing the rDNA signals, the DAPI bands, chromosome groups, and the relative DNA content in each chromosome.Figure 3.jpg
DOI: 10.5061/dryad.8m30f
title: Data from: Is local selection so widespread in river organisms? Fractal geometry of river networks leads to high bias in outlier detection

description: Identifying local adaptation is crucial in conservation biology in order
 to define ecotypes and establish management guidelines. Local adaptation
 is often inferred from the detection of loci showing a high
 differentiation between populations, the so-called FST outliers. Methods
 of detection of loci under selection are reputed to be robust in most
 spatial population models. However, using simulations we showed that FST
 outlier tests provided a high rate of false positives (up to 60%) in
 fractal environments such as river networks. Surprisingly, the number of
 sampled demes was correlated with parameters of population genetic
 structure, such as the variance of FSTs, and hence strongly influenced the
 rate of outliers. This unappreciated property of river networks therefore
 needs to be accounted for in genetic studies on adaptation and
 conservation of river organisms.
description: Aquasplatche network
 simulation settingsTen folders
 corresponding to the ten networks described in Fourcade et al. Simulations
 can be performed using Aquasplatche.
DOI: 10.5061/dryad.2gd84
title: Data from: A semantic model for species description applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia

description: Taxonomic descriptions are unparalleled sources of knowledge of
 life's phenotypic diversity. As natural language prose, these data
 sets are largely refractory to computation and integration with other
 sources of phenotypic data. By formalizing taxonomic descriptions using
 ontology-based semantic representation, we aim to increase the reusability
 and computability of taxonomists' primary data. Here, we present a
 revision of the ensign wasp (Hymenoptera: Evaniidae) fauna of New
 Caledonia using this new model for species description. Descriptive
 matrices, specimen data, and taxonomic nomenclature are gathered in a
 unified Web-based application, mx, then exported as both traditional
 taxonomic treatments and semantic statements using the OWL Web Ontology
 Language. Character:character-state combinations are then annotated
 following the entity–quality phenotype model, originally developed to
 represent mutant model organism phenotype data; concepts of anatomy are
 drawn from the Hymenoptera Anatomy Ontology and linked to phenotype
 descriptors from the Phenotypic Quality Ontology. The resulting set of
 semantic statements is provided in Resource Description Framework format.
 Applying the model to real data, that is, specimens, taxonomic names,
 diagnoses, descriptions, and redescriptions, provides us with a foundation
 to discuss limitations and potential benefits such as automated data
 integration and reasoner-driven queries. Four species of ensign wasp are
 now known to occur in New Caledonia: Szepligetella levipetiolata,
 Szepligetella deercreeki Deans and Mikó sp. nov., Szepligetella irwini
 Deans and Mikó sp. nov., and the nearly cosmopolitan Evania appendigaster.
 A fifth species, Szepligetella sericea, including Szepligetella impressa,
 syn. nov., has not yet been collected in New Caledonia but can be found on
 islands throughout the Pacific and so is included in the diagnostic key.
description: Appendix
 1Characters and character
 states used in the descriptions, with semantic phenotype
 annotation.new_caledonia_appendix_1.docxAppendix 2Verbatim locality label information of specimens examined, and museum repository codens used in this manuscript.new_caledonia_appendix_2.docxData matrix and semantic annotation for the Evaniidae of New Caledonia.Web Ontology Language (OWL) representation of data matrix and semantic annotation for the Evaniidae of New Caledonia.new_caledonia_merged.owl
DOI: 10.5061/dryad.fg868
title: Data from: Evolution of transcription networks in response to temporal fluctuations

description: Organisms respond to changes in their environment over a wide range of
 biological and temporal scales. Such phenotypic plasticity can involve
 developmental, behavioral, physiological, and genetic shifts. The adaptive
 value of a plastic response is known to depend on the nature of the
 information that is available to the organism as well as the direct and
 indirect costs of the plastic response. We modeled the dynamic process of
 simple gene regulatory networks as they responded to temporal fluctuations
 in environmental conditions. We simulated the evolution of networks to
 determine when genes that function solely as transcription factors, with
 no direct function of their own, are beneficial to the function of the
 network. When there is perfect information about the environment and there
 is no timing information to be extracted then there is no advantage to
 adding pure transcription factor genes to the network. In contrast, when
 there is either timing information that can be extracted or only indirect
 information about the current state of the environment then additional
 transcription factor genes improve the evolved network fitness.
description: Evolution_dataAll simulation data: Fitness and parameters and matlab source code.
DOI: 10.5061/dryad.f3050
title: Data from: Fossil embryos from the Middle and Late Cambrian period of Hunan, south China

description: Comparative embryology is integral to uncovering the pattern and process
 of metazoan phylogeny, but it relies on the assumption that life histories
 of living taxa are representative of their antecedents. Fossil embryos
 provide a crucial test of this assumption and, potentially, insight into
 the evolution of development, but because discoveries so far lack
 phylogenetic constraint, their significance is moot. Here we describe a
 collection of embryos from the Middle and Late Cambrian period (500
 million years ago) of Hunan, south China, that preserves stages of
 development from cleavage to the pre-hatching embryo of a
 direct-developing animal comparable to living Scalidophora (phyla
 Priapulida, Kinorhyncha, Loricifera). The latest-stage embryos show
 affinity to the Lower Cambrian embryo Markuelia, whose life-history
 strategy contrasts both with the primitive condition inferred for metazoan
 phyla and with many proposed hypotheses of affinity, all of which
 prescribe indirect development. Phylogenetic tests based on these
 embryological data suggest a stem Scalidophora affinity. These discoveries
 corroborate, rather than contradict, the predictions of comparative
 embryology, providing direct historical support for the view that the
 life-history strategies of living taxa are representative of their stem
 lineages.
description: Dong_et_al_2004_datamatrixCladistic data matrix
DOI: 10.5061/dryad.9ct2f
title: Data from: Finite element modelling vs. classic beam theory: comparing methods for stress estimation in a morphologically diverse sample of vertebrate long bones

description: Classic beam theory is frequently employed in biomechanics to model the
 stress behaviour of vertebrate long bones, particularly when creating
 intraspecific scaling models. Although methodologically straightforward,
 classic beam theory requires complex irregular bones to be approximated as
 slender beams, and the errors associated with simplifying complex organic
 structures to such an extent are unknown. Alternative approaches, such as
 Finite Element Analysis (FEA), whilst much more time-consuming to perform,
 require no such assumptions. This paper compares the results obtained
 using classic beam theory with those from FEA to quantify the beam theory
 errors and to provide recommendations about when a full FEA analysis is
 essential for reasonable biomechanical predictions. High-resolution
 computed tomographic (CT) scans of eight vertebrate long bones were used
 to calculate diaphyseal stress due to various loading regimes. Under
 compression, FEA values of minimum principal stress (σ_min) were on
 average 142%(±28% SE) larger than those predicted by beam theory, with
 deviation between the two models correlated to shaft curvature (2-tailed
 p=0.03, r^2=0.56). Under bending, FEA values of maximum principal stress
 (σ_max) and beam theory values differed on average by 12% (±4% SE), with
 deviation between the models significantly correlated to cross-sectional
 asymmetry at midshaft (2-tailed p=0.02, r^2=0.62). In torsion, assuming
 maximum stress values occurred at the location of minimum cortical
 thickness brought beam theory and FEA values closest in line, and in this
 case FEA values of τ_torsion were on average 14% (±5% SE) higher than beam
 theory. Therefore, FEA is the preferred modelling solution when estimates
 of absolute diaphyseal stress are required, although values calculated by
 beam theory for bending may be acceptable in some situations.
description: Bush Baby Femur 3D
 GeometryGalago senegalensis
 (NMS.Z.2002.94.2). Body mass = 0.22kg. Created in GeoMagic Studio
 v12.bushbaby.objEagle Femur 3D GeometryHaliaeetus albicilla (NMS.Z.2000.23). Body mass = 4.79kg. Created in GeoMagic Studio v12.eagle.objFlamingo Femur 3D GeometryPhoenicopterus ruber (NMS.Z.2000.193.1). Body mass = 2.60kg. Created in GeoMagic Studio v12.flamingo.objGiraffe Tibia 3D GeometryGiraffa camelopardalis (NMS.Z.2001.148.3). Body mass = 1192kg. Created in GeoMagic Studio v12.giraffe.objGuillemot Tibia 3D GeometryUria aalge (MM BB.9009.5.1). Body mass = 0.99kg. Created in GeoMagic Studio v12.guillemot.objHedgehog Femur 3D GeometryErinaceus europaeus (WML 1988.226). Body mass = 0.68kg. Created in GeoMagic Studio v12.hedgehog.objHyrax Femur 3D GeometryProcavia capensis (NMS.Z.2009.76). Body mass = 3.14kg. Created in GeoMagic Studio v12.hyrax.objPolecat Tibia 3D GeometryMustela putorius (NMS.Z.2000.307.40). Body mass = 1.11kg. Created in GeoMagic Studio v12.polecat.obj
DOI: 10.5061/dryad.39sc7
title: Data from: Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing

description: Caviar-producing sturgeons belonging to the genus Acipenser are considered
 to be one of the most endangered species groups in the world. Continued
 overfishing in spite of increasing legislation, zero catch quotas and
 extensive aquaculture production have led to the collapse of wild stocks
 across Europe and Asia. The evolutionary relationships among Adriatic,
 Russian, Persian and Siberian sturgeons are complex because of past
 introgression events and remain poorly understood. Conservation
 management, traceability and enforcement suffer a lack of appropriate DNA
 markers for the genetic identification of sturgeon at the species,
 population and individual level. This study employed RAD sequencing to
 discover and characterize single nucleotide polymorphism (SNP) DNA markers
 for use in sturgeon conservation in these four tetraploid species over
 three biological levels, using a single sequencing lane. Four population
 meta-samples and eight individual samples from one family were barcoded
 separately before sequencing. Analysis of 14.4 Gb of paired-end RAD data
 focused on the identification of SNPs in the paired-end contig, with
 subsequent in silico and empirical validation of candidate markers.
 Thousands of putatively informative markers were identified including, for
 the first time, SNPs that show population-wide differentiation between
 Russian and Persian sturgeons, representing an important advance in our
 ability to manage these cryptic species. The results highlight the
 challenges of genotyping-by-sequencing in polyploid taxa, while
 establishing the potential genetic resources for developing a new range of
 caviar traceability and enforcement tools.
description: mec12-0761_DRYAD
 entry
DOI: 10.5061/dryad.1v8j7
title: Data from: Recurrent and recent selective sweeps in the piRNA pathway

description: Uncontrolled transposable element (TE) insertions and excisions can cause
 chromosome breaks and mutations with dramatic deleterious effects. The
 PIWI interacting RNA (piRNA) pathway functions as an adaptive TE silencing
 system during germline development. Several essential piRNA pathway
 proteins appear to be rapidly evolving, suggesting that TEs and the
 silencing machinery may be engaged in a classical “evolutionary arms
 race.” Using a variety of molecular evolutionary and population genetic
 approaches, we find that the piRNA pathway genes rhino, krimper, and
 aubergine show patterns suggestive of extensive recurrent positive
 selection across Drosophila species. We speculate that selection on these
 proteins reflects crucial roles in silencing unfamiliar elements during
 vertical and horizontal transmission of TEs into naïve populations and
 species, respectively.
description: branch dS
 valuesgenomic branch dN-dS and dS
 values.xlsgenomic results
 summariesm0 clean mlc
 filespolymorphism_fasta_files_5-25-12empirical_ms_filesempirical_clsw_inpempirical_clsw_outssw_inp_neutralssw_out_neutralneutral_ssw_analyzed_clswssw_inp_selectivessw_out_selectiveselective_ssw_analyzed_clswtreescodeml.ctl filesmost PAML piRNA resultsPAML piRNA divergence alignmentsbranch-sites results finalclsw_inp_simulations
DOI: 10.5061/dryad.mn71g
title: Data from: The genetic architecture of biofilm formation in a clinical isolate of Saccharomyces cerevisiae

description: Biofilms are microbial communities that form on surfaces. They are the
 primary form of microbial growth in nature and can have detrimental
 impacts on human health. Some strains of the budding yeast Saccharomyces
 cerevisiae form colony biofilms, and there is substantial variation in
 colony architecture between biofilm-forming strains. To identify the
 genetic basis of biofilm variation, we developed a novel version of
 quantitative trait locus mapping, which leverages cryptic variation in a
 clinical isolate of S. cerevisiae. We mapped 13 loci linked to
 heterogeneity in biofilm architecture and identified the gene most closely
 associated with each locus. Of these candidate genes, six are members of
 the cyclic AMP-protein kinase A pathway, an evolutionarily conserved cell
 signaling network. Principal among these is CYR1, which encodes the enzyme
 that catalyzes production of cAMP. Through a combination of gene
 expression measurements, cell signaling assays, and gene overexpression,
 we determined the functional effects of allelic variation at CYR1. We
 found that increased pathway activity resulting from protein coding and
 expression variation of CYR1 enhances the formation of colony biofilms.
 Four other candidate genes encode kinases and transcription factors that
 are targets of this pathway. The protein products of several of these
 genes together regulate expression of the sixth candidate, FLO11, which
 encodes a cell adhesion protein. Our results indicate that epistatic
 interactions between alleles with both positive and negative effects on
 cyclic AMP-protein kinase A signaling underlie much of the architectural
 variation we observe in colony biofilms. They are also among the first to
 demonstrate genetic variation acting at multiple levels of an integrated
 signaling and regulatory network. Based on these results, we propose a
 mechanistic model that relates genetic variation to gene network function
 and phenotypic outcomes.
description: Bulk Genotype
 TableThis file contains the
 allele counts (number of occurrences of an allele in a sequencing read)
 for each heterozygous site found in YJM311 from the YJM311 (parental),
 simple, intermediate, and complex se- quencing runs, and the G-statistic
 values at each of these sites for the pairwise comparisons between the
 simple, intermediate, and complex pools. Note that heterozygous sites
 where neither allele matched the reference sequence are very rare, so were
 excluded from these results. Each row in the file contains data on a
 single heterozygous site identified in YJM311. The coordinates are based
 on Saccharomyces Genome Database (SGD) release r62, (release date:
 February 18, 2009).bsa_geno_table.csvIndividual Segregant Phenotype and Genotype TableThis file compiles phenotype and genotype data collected on individual segregants from the Bulk Segregant Analysis. Each row in the file contains data on a single segregant.seg_strain_table.csv
DOI: 10.5281/zenodo.18232599
title: Supplementary Tables

description: These are the supplementary tables of this preprint:
DOI: 10.5061/dryad.dn822
title: Data from: The evolution of locomotor rhythmicity in tetrapods

description: Differences in rhythmicity (relative variance in cycle period) between
 mammal, fish, and lizard feeding systems have been hypothesized to be
 associated with differences in their sensorimotor control systems. We
 tested this hypothesis by examining whether the locomotion of
 tachymetabolic tetrapods (birds and mammals) is more rhythmic than that of
 bradymetabolic tetrapods (lizards, alligators, turtles, salamanders).
 Species averages of intra-individual coefficients of variation in cycle
 period were compared while controlling for gait and substrate. Variance in
 locomotor cycle periods is significantly lower in tachymetabolic than in
 bradymetabolic animals for data sets that include treadmill locomotion,
 non-treadmill locomotion, or both. When phylogenetic relationships are
 taken into account, the non-treadmill analysis and the pooled analyses
 remain significant, the treadmill analysis becomes nonsignificant (but
 only marginally). The co-occurrence of relatively high rhythmicity in both
 feeding and locomotor systems of tachymetabolic tetrapods suggests that
 the anatomical substrate of rhythmicity is in the motor control system,
 not in the musculoskeletal components.
description: finallocomotiondata
DOI: 10.5061/dryad.5253n
title: Data from: How the online social networks are used: dialogs-based structure of MySpace

description: Quantitative study of collective dynamics in online social networks is a
 new challenge based on the abundance of empirical data. Conclusions,
 however, may depend on factors such as user's psychology profiles and
 their reasons to use the online contacts. In this study, we have compiled
 and analysed two datasets from MySpace. The data contain networked
 dialogues occurring within a specified time depth, high temporal
 resolution and texts of messages, in which the emotion valence is assessed
 by using the SentiStrength classifier. Performing a comprehensive
 analysis, we obtain three groups of results: dynamic topology of the
 dialogues-based networks have a characteristic structure with Zipf's
 distribution of communities, low link reciprocity and disassortative
 correlations. Overlaps supporting ‘weak-ties’ hypothesis are found to
 follow the laws recently conjectured for online games. Long-range temporal
 correlations and persistent fluctuations occur in the time series of
 messages carrying positive (negative) emotion; patterns of user
 communications have dominant positive emotion (attractiveness) and strong
 impact of circadian cycles and interactivity times longer than 1 day.
 Taken together, these results give a new insight into the functioning of
 online social networks and unveil the importance of the amount of
 information and emotion that is communicated along the social links. All
 data used in this study are fully anonymized.
description: MySpace_2months_2bin_randomizedOriginal data collected in networked dialogs from MySpace within specified time depth. Texts of messages annotated using emotion classifier with graded estimate of positive and negative emotion valence.