cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.066mr
title: Data from: Frog tongue acts as muscle-powered adhesive tape

description: Frogs are well known to capture fast-moving prey by flicking their sticky
 tongues out of the mouth. This tongue projection behaviour happens
 extremely fast which makes frog tongues a biological high-speed adhesive
 system. The processes at the interface between tongue and prey, and thus
 the mechanism of adhesion, however, are completely unknown. Here, we
 captured the contact mechanics of frog tongues by filming tongue adhesion
 at 2000 frames per second through an illuminated glass. We found that the
 tongue rolls over the target during attachment. However, during the
 pulling phase, the tongue retractor muscle acts perpendicular to the
 target surface and thus prevents peeling during tongue retraction. When
 the tongue detaches, mucus fibrils form between the tongue and the target.
 Fibrils commonly occur in pressure- sensitive adhesives, and thus frog
 tongues might be a biological analogue to these engineered materials. The
 fibrils in frog tongues are related to the presence of microscopic
 papillae on the surface. Together with a layer of nanoscale fibres
 underneath the tongue epithelium, these surface papillae will make the
 tongue adaptable to asperities. For the first time, to the best of our
 knowledge, we are able to integrate anatomy and function to explain the
 processes during adhesion in frog tongues.
description: Micro-CT scan of an
 isolated tongue of Ceratophrys ornataThis file contains the
 raw micro-CT data of the tongue in a female ornate horned frog Ceratophrys
 ornata. The specimen had a snout-vent-length of 70mm. To be able to
 identify soft tissue structures in the specimen, the animal was treated
 with Lugol's iodine potassium iodide solution.Ceratophrys_ornata_tongueCT.zipMicro-CT scan of Ceratophrys ornata tongue tissueMicro-CT scan of a piece of tongue tissue of the ornate horned frog Ceratophrys ornata. This piece was cut out from the tongue of the specimen after the animal was treated with Lugol's solution to allow for soft tissue visualization.Ceratophrys_ornata_tongueTissueCT.zipMicro-CT scan of the head of Ceratophrys ornataThis is a micro-CT scan of the head of a 70mm female Ceratophrys ornata. The specimen was submerged in Lugol's iodine potassium iodide solution so that cranial muscles and other soft tissue structures are visible.Ceratophrys_ornata_frogCT.zip
DOI: 10.5061/dryad.qp4kb
title: Data from: Chromosome arm specific patterns of polymorphism associated with chromosomal inversions in the major African malaria vector, Anopheles funestus

description: Chromosomal inversions facilitate local adaptation of beneficial mutations
 and modulate genetic polymorphism, but the extent of their effects within
 the genome is still insufficiently understood. The genome of Anopheles
 funestus, a malaria mosquito endemic to sub-Saharan Africa, contains an
 impressive number of paracentric polymorphic inversions, which are
 unevenly distributed among chromosomes and provide an excellent framework
 for investigating the genomic impacts of chromosomal rearrangements. Here
 we present results of a fine-scale analysis of genetic variation within
 the genome of two weakly differentiated populations of Anopheles funestus
 inhabiting contrasting moisture conditions in Cameroon. Using population
 genomic analyses, we found that genetic divergence between the two
 populations is centered on regions of the genome corresponding to three
 inversions, which are characterized by high values of FST, absolute
 sequence divergence and fixed differences. Importantly, in contrast to the
 2L chromosome arm, which is collinear, nucleotide diversity is
 significantly reduced along the entire length of three autosome arms
 bearing multiple overlapping chromosomal rearrangements. These findings
 support the idea that interactions between reduced recombination and
 natural selection within inversions contribute to sculpt nucleotide
 polymorphism across chromosomes in An. funestus.
description: Individual fastq files
 for Anopheles funestus from CameroonAnopheles_funetus_fastq.tar.gz
DOI: 10.5061/dryad.6d006j3
title: Data from: Parallel plumage color evolution and introgressive hybridization in wheatears

description: Genetic and phenotypic mosaics, in which various phenotypes and different
 genomic regions show discordant patterns of species or population
 divergence, offer unique opportunities to study the role of ancestral and
 introgressed genetic variation in phenotypic evolution. Here, we
 investigated the evolution of discordant phenotypic and genetic divergence
 in a monophyletic clade of four songbird taxa – pied wheatear (O.
 pleschanka), Cyprus wheatear (O. cypriaca), and western and eastern
 subspecies of black-eared wheatear (O. h. hispanica and O. h.
 melanoleuca). Phenotypically, black back and neck-sides distinguish pied
 and Cyprus wheatears from the white-backed/necked black-eared wheatears.
 Meanwhile, mitochondrial variation only distinguishes western black-eared
 wheatear. In the absence of nuclear genetic data, and given frequent
 hybridization among eastern black-eared and pied wheatear, it remains
 unclear whether introgression is responsible for discordance between
 mitochondrial divergence patterns and phenotypic similarities, or whether
 plumage coloration evolved in parallel. Multispecies coalescent analyses
 of about 20’000 SNPs obtained from RAD data mapped to a draft genome
 assembly resolve the species tree, provide evidence for the parallel
 evolution of color phenotypes, and establish western and eastern
 black-eared wheatears as independent taxa that should be recognized as
 full species. The presence of the entire admixture spectrum in the Iranian
 hybrid zone and the detection of footprints of introgression from pied
 into eastern black-eared wheatear beyond the hybrid zone despite strong
 geographic structure of ancestry proportions furthermore suggest a
 potential role for introgression in parallel plumage color evolution. Our
 results support the importance of standing heterospecific and/or ancestral
 variation in phenotypic evolution.
description: RAD-sequencing read
 dataThis file contains
 individual files with forward (*.1.fq.gz) and reverse (*.2.fq.gz)
 RAD-sequencing read data for each individual. The gzip.tar archive was
 generated using tar.Oenanthe_RAD-reads_fastq.gz.tarOenanthe melanoleuca reference genome assemblyThis file contains the Oenanthe melanoleuca reference genome assembly. This reference genome was sequenced from a male Oenanthe melanoleuca from, Crete (Greece) collected by the Peabody Museum of Natural History of Yale University (collection number YPM 101348). Scaffolds are sorted by decreasing lengths.Oenmel_Supernova1_2017.fasta
DOI: 10.5061/dryad.14sr463
title: Data from: Morphology of the core fibrous layer of the cetacean tail fluke

description: The cetacean tail fluke blades are not supported by any vertebral
 elements. Instead, the majority of the blades are composed of a densely
 packed collagenous fiber matrix known as the core layer. Fluke blades from
 six species of odontocete cetaceans were examined to compare the
 morphology and orientation of fibers at different locations along the
 spanwise and chordwise fluke blade axes. The general fiber morphology was
 consistent with a three‐dimensional structure comprised of two‐dimensional
 sheets of fibers aligned tightly in a laminated configuration along the
 spanwise axis. The laminated configuration of the fluke blades helps to
 maintain spanwise rigidity while allowing partial flexibility during
 swimming. When viewing the chordwise sectional face at the leading edge
 and mid‐chord regions, fibers displayed a crossing pattern. This
 configuration relates to bending and structural support of the fluke
 blade. The trailing edge core was found to have parallel fibers arranged
 more dorso‐ventrally. The fiber morphology of the fluke blades was
 dorso‐ventrally symmetrical and similar in all species except the pygmy
 sperm whale (Kogia breviceps), which was found to have additional core
 layer fiber bundles running along the span of the fluke blade. These
 additional fibers may increase stiffness of the structure by resisting
 tension along their long spanwise axis.
description: Delphinus delphis
 Mid-Span SlicesDelphinus delphis Tail
 Base SlicesDelphinus delphis Tail
 Tip SlicesGrampus griseus Mid-Span
 SlicesGrampus griseus Tail
 Base SlicesGrampus griseus Tail Tip
 SlicesKogia breviceps Mid-Span
 SlicesKogia breviceps Tail
 Base SlicesKogia breviceps Tail Tip
 SlicesLagenorhynchus
 albirostris Mid-Span SlicesLagenorhynchus
 albirostris Tail Base SlicesLagenorhynchus
 albirostris Tail Tip SlicesPhocoena phocoena
 Mid-Span SlicesPhocoena phocoena Tail
 Base SlicesPhocoena phocoena Tail
 Tip SlicesTursiops truncatus
 Mid-Span SlicesTursiops truncatus Tail
 Base SlicesTursiops truncatus Tail
 Tip Slices
DOI: 10.5061/dryad.2tv2s
title: Data from: Widespread cumulative influence of small effect size mutations on yeast quantitative traits

description: Quantitative traits are influenced by pathways that have traditionally
 been defined through genes that have a large loss- or gain-of-function
 effect. However, in theory, a large number of small effect-size genes
 could cumulatively play a substantial role in pathway function. Here, we
 determined the number, strength and identity of all non-essential test
 genes that affect two quantitative galactose-responsive traits, in
 addition to re-analyzing two previously screened quantitative traits. We
 find that over a quarter of assayed genes have a detectable, quantitative
 effect on phenotype. Despite their ubiquity, these genes are enriched in
 core cellular processes in a trait-specific manner. In a simulated
 population with 50% frequency of all-or-none alleles, we show that small
 effect-size alleles are capable of contributing more to trait variation
 than alleles in a canonical, large-effect size pathway. In total, by
 demonstrating that the genes effecting quantitative traits can be highly
 distributed and interconnected, this work challenges the concept of
 pathways as modular and independent.
description: Data and analysis script
 for GAL screenGAL_screen.zipData and analysis script for PHO screenPHO_screen.zipData and analysis script to measure cycloheximide effectChx_effect.zip
DOI: 10.5061/dryad.37hc1
title: Data from: The consequences of not accounting for background selection in demographic inference

description: Recently, there has been increased awareness of the role of background
 selection (BGS) in both data analysis and modelling advances. However, BGS
 is still difficult to take into account because of tractability issues
 with simulations and difficulty with nonequilibrium demographic models.
 Often, simple rescaling adjustments of effective population size are used.
 However, there has been neither a proper characterization of how BGS could
 bias or shift inference when not properly taken into account, nor a
 thorough analysis of whether rescaling is a sufficient solution. Here, we
 carry out extensive simulations with BGS to determine biases and behaviour
 of demographic inference using an approximate Bayesian approach. We find
 that results can be positively misleading with significant bias, and
 describe the parameter space in which BGS models replicate observed
 neutral nonequilibrium expectations.
description: scriptsAndCodeAll the scripts and code used. Outside things like ABC toolbox or R of course.allExpBin.gzgzip Binary format abc simulation data for the growth model.
DOI: 10.5061/dryad.18tg7
title: Data from: High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA

description: Microsatellite markers have played a major role in ecological,
 evolutionary and conservation research during the past 20 years. However,
 technical constrains related to the use of capillary electrophoresis and a
 recent technological revolution that has impacted other marker types have
 brought to question the continued use of microsatellites for certain
 applications. We present a study for improving microsatellite genotyping
 in ecology using high-throughput sequencing (HTS). This approach entails
 selection of short markers suitable for HTS, sequencing PCR-amplified
 microsatellites on an Illumina platform and bioinformatic treatment of the
 sequence data to obtain multilocus genotypes. It takes advantage of the
 fact that HTS gives direct access to microsatellite sequences, allowing
 unambiguous allele identification and enabling automation of the
 genotyping process through bioinformatics. In addition, the massive
 parallel sequencing abilities expand the information content of single
 experimental runs far beyond capillary electrophoresis. We illustrated the
 method by genotyping brown bear samples amplified with a multiplex PCR of
 13 new microsatellite markers and a sex marker. HTS of microsatellites
 provided accurate individual identification and parentage assignment and
 resulted in a significant improvement of genotyping success (84%) of
 faecal degraded DNA and costs reduction compared to capillary
 electrophoresis. The HTS approach holds vast potential for improving
 success, accuracy, efficiency and standardization of microsatellite
 genotyping in ecological and conservation applications, especially those
 that rely on profiling of low-quantity/quality DNA and on the construction
 of genetic databases. We discuss and give perspectives for the
 implementation of the method in the light of the challenges encountered in
 wildlife studies.
description: Readmeobitools_scriptScripts to filter raw sequence data and perform conversion to tableR_python_scriptsR and python scripts to extract genotypes from tabular data filerawdata_scandinavia.ngsfilterngsfilter file for scandinavian rawdata analysisfiltereddata_referencesassembled and filtered fastq sequences from reference samplesrawdata_pyrenees_R1Raw fastq paired-end 1 sequences from pyrenean bear samplesrawdata_pyrenees_R2Raw fastq paired-end 2 sequences from pyrenean bear samplesrawdata_scandinavia_R1Raw fastq paired-end 1 sequences from scandinavian bear samplesrawdata_scandinavia_R2Raw fastq paired-end 2 sequences from scandinavian bear samples
DOI: 10.5061/dryad.vn607
title: Data from: Museum samples reveal rapid evolution by wild honey bees exposed to a novel parasite

description: Understanding genetic changes caused by novel pathogens and parasites can
 reveal mechanisms of adaptation and genetic robustness. Using whole-genome
 sequencing of museum and modern specimens, we describe the genomic changes
 in a wild population of honey bees in North America following the
 introduction of the ectoparasitic mite, Varroa destructor. Even though
 colony density in the study population is the same today as in the past, a
 major loss of haplotypic diversity occurred, indicative of a drastic
 mitochondrial bottleneck, caused by massive colony mortality. In contrast,
 nuclear genetic diversity did not change, though hundreds of genes show
 signs of selection. The genetic diversity within each bee colony,
 particularly as a consequence of polyandry by queens, may enable
 preservation of genetic diversity even during population bottlenecks.
 These findings suggest that genetically diverse honey bee populations can
 recover from introduced diseases by evolving rapid tolerance, while
 maintaining much of the standing genetic variation.
description: Compressed archive with
 intermediate analysis files and bioinformatic scriptsSee readme for package
 contents.ithaca_bees.tar.gz
DOI: 10.5061/dryad.rg58m
title: Data from: Automated segmentation of skin strata in reflectance confocal microscopy depth stacks

description: Reflectance confocal microscopy (RCM) is a powerful tool for in-vivo
 examination of a variety of skin diseases. However, current use of RCM
 depends on qualitative examination by a human expert to look for specific
 features in the different strata of the skin. Developing approaches to
 quantify features in RCM imagery requires an automated understanding of
 what anatomical strata is present in a given en-face section. This work
 presents an automated approach using a bag of features approach to
 represent en-face sections and a logistic regression classifier to
 classify sections into one of four classes (stratum corneum, viable
 epidermis, dermal-epidermal junction and papillary dermis). This approach
 was developed and tested using a dataset of 308 depth stacks from 54
 volunteers in two age groups (20–30 and 50–70 years of age). The
 classification accuracy on the test set was 85.6%. The mean absolute error
 in determining the interface depth for each of the stratum corneum/viable
 epidermis, viable epidermis/dermal-epidermal junction and dermal-epidermal
 junction/papillary dermis interfaces were 3.1 μm, 6.0 μm and 5.5 μm
 respectively. The probabilities predicted by the classifier in the test
 set showed that the classifier learned an effective model of the anatomy
 of human skin.
description: Metadata for all
 sections in datasetIdentifies the
 characteristics of each RCM en-face section in the dataset. A detailed
 description is included in the README.txt file.metadata.csvsections_500This file contains the complete dataset of en-face sections at a resolution of 500x500 pixels. This file contains one dataset called 'sections' - this is a three dimensional array of uint8 values. The first axis is individual sections in the dataset. The second and third axes are the rows and columns of intensity values of that section.sections_250This file contains the complete dataset of en-face sections at a resolution of 250x250 pixels. This file contains one dataset called 'sections' - this is a three dimensional array of uint8 values. The first axis is individual sections in the dataset. The second and third axes are the rows and columns of intensity values of that section.
DOI: 10.5061/dryad.5nv17
title: Data from: Automated identification of social interaction criteria in Drosophila melanogaster

description: The study of social behaviour within groups has relied on fixed
 definitions of an ‘interaction’. Criteria used in these definitions often
 involve a subjectively defined cut-off value for proximity, orientation
 and time (e.g. courtship, aggression and social interaction networks) and
 the same numerical values for these criteria are applied to all of the
 treatment groups within an experiment. One universal definition of an
 interaction could misidentify interactions within groups that differ in
 life histories, study treatments and/or genetic mutations. Here, we
 present an automated method for determining the values of interaction
 criteria using a pre-defined rule set rather than pre-defined values. We
 use this approach and show changing social behaviours in different
 manipulations of Drosophila melanogaster. We also show that chemosensory
 cues are an important modality of social spacing and interaction. This
 method will allow a more robust analysis of the properties of interacting
 groups, while helping us understand how specific groups regulate their
 social interaction space.
description: SchneiderLevine Part
 1The
 trajectories are in matlab files named X_movie_#.mat (where X is the
 strain/treament). They contain the xy coordinates and angle of each fly
 within the arena, as well as major and minor axes estimates. A file named
 "normalization.mat" contains the arenas xy coordinate centers
 and radius (in pixels) of each arena. There are file parts to the tar.gz
 datafile. In linux go to the download folder and run: cat
 SchneiderLevine.parta? &gt; SchneiderLevine2014.tar.gzSchneiderLevine.partaaSchneiderLevine Part 2SchneiderLevine.partabSchneiderLevine Part 3SchneiderLevine.partacSchneiderLevine Part 4SchneiderLevine.partadSchneiderLevine Part 5SchneiderLevine.partaeSchneiderLevine Part 6SchneiderLevine.partaf
DOI: 10.5061/dryad.tj48997
title: Data from: A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements

description: Molecular phylogenetics has transitioned into the phylogenomic era, with
 data derived from next-generation sequencing technologies allowing
 unprecedented phylogenetic resolution in all animal groups, including
 understudied invertebrate taxa. Within the most diverse harvestmen
 suborder, Laniatores, most relationships at all taxonomic levels have yet
 to be explored from a phylogenomics perspective. Travunioidea is an
 early-diverging lineage of laniatorean harvestmen with a Laurasian
 distribution, with species distributed in eastern Asia, eastern and
 western North America, and south-central Europe. This clade has had a
 challenging taxonomic history, but the current classification consists of
 ~77 species in three families, the Travuniidae, Paranonychidae, and
 Nippononychidae. Travunioidea classification has traditionally been based
 on structure of the tarsal claws of the hind legs. However, it is now
 clear that tarsal claw structure is a poor taxonomic character due to
 homoplasy at all taxonomic levels. Here, we utilize DNA sequences derived
 from capture of ultraconserved elements (UCEs) to reconstruct travunioid
 relationships. Data matrices consisting of 317–677 loci were used in
 maximum likelihood, Bayesian, and species tree analyses. Resulting
 phylogenies recover four consistent and highly supported clades; the
 phylogenetic position and taxonomic status of the enigmatic genus Yuria is
 less certain. Based on the resulting phylogenies, a revision of
 Travunioidea is proposed, now consisting of the Travuniidae,
 Cladonychiidae, Paranonychidae (Nippononychidae is synonymized), and the
 new family Cryptomastridae Derkarabetian & Hedin, fam. n.,
 diagnosed here. The phylogenetic utility and diagnostic features of the
 intestinal complex and male genitalia are discussed in light of
 phylogenomic results, and the inappropriateness of the tarsal claw in
 diagnosing higher-level taxa is further corroborated.
description: 50_percent_taxon_coverage50% taxon coverage concatenated matrix used in phylogenomic analyses (phylip format).70_percent_taxon_coverage70% taxon coverage concatenated matrix used in phylogenomic analyses (phylip format).Individual_loci_pre_manual_editingZip archive containing multiple sequence alignments for all loci produced from phyluce analyses, before manual editing of individual loci.Individual_loci_post_manual_editingZip archive containing multiple sequence alignments for all loci produced from phyluce analyses, after manual editing of individual loci.Raw_assembliesZip archive containing raw contig assemblies (fasta format) for all samples used in this study.