cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dh7kh
title: Data from: Genome-level homology and phylogeny of Vibrionaceae (Gammaproteobacteria: Vibrionales) with three new complete genome sequences

description: Background: Phylogenetic hypotheses based on complete genome data are
 presented for the Gammaproteobacteria family Vibrionaceae. Two taxon
 samplings are presented: one including all those taxa for which the genome
 sequences are complete in terms of arrangement (chromosomal location of
 fragments; 19 taxa) and one for which the genome sequences contain
 multiple contigs (44 taxa). Analyses are presented under the Maximum
 Parsimony and Maximum Likelihood optimality criteria for total evidence
 datasets, the two chromosomes separately, and individual analyses of
 locally collinear blocks. Three of the genomes included in the 44 taxon
 dataset, those of Vibrio gazogenes, Salinivibrio costicola, and Aliivibrio
 logei have been newly sequenced and their genome sequences are documented
 here. Results: Phylogenetic results for the 19-taxon datasets show similar
 levels of collinear subset of dataset incongruence as a previous study of
 22 taxa from the sister family Shewanellaceae, while also echoing the
 strong phylogenetic performance of random subsets of data also shown in
 this study. Phylogenetic results for both the 19-taxon and 44-taxon
 datasets corroborate previous hypotheses about the placement of
 Photobacterium and Aliivibrio within Vibrionaceae and also highlight
 problems with how Photobacterium is delimited and indicate that it likely
 should be dissolved into Vibrio to produce a phylogenetic taxonomy. The
 19-taxon and 44-taxon trees based on the large chromosome are congruent
 for the majority of taxa that are present in both datasets. Analyses of
 the 44-taxon sampling based on the second, small chromosome are quite
 different from those based on the large chromosome, which is not
 surprising given the dramatically divergent nature of the small chromosome
 and the difficulty in postulating primary homologies. Conclusions: The
 phylogenetic analyses presented here represent the most comprehensive
 genome-level phylogenetic analyses in terms of taxa and data. Based on the
 availability of genome data for many bacterial species on GenBank, many
 other bacterial groups would also be amenable to similar genome-scale
 phylogenetic analyses even when present in multiple contigs. The result
 that collinear subsets of data are incongruent with the concatenated
 dataset and with each other while random data subsets show very little
 incongruence echoes the result of previous work on Shewanellaceae. The
 44-taxon phylogenetic analysis presented here thus represents the future
 of phylogenomic analyses in scope and complexity.
description: 44_taxon_dataset_large_chromosomeAlignment of large chromosome LCB for 44-taxon dataset43_taxon_dataset_small_chromosomeAlignment of small chromosome 43-taxon dataset (LCBs concatenated)19_taxon_dataset_small_chromosomeAlignment of small chromosome 19-taxon dataset (LCBs concatenated)19_taxon_dataset_large_chromosomeAlignment of large chromosome for 19-taxon dataset (LCBs concatenated)
DOI: 10.5061/dryad.6t442
title: Data from: Diversity and stability of egg-bacterial assemblages: the role of paternal care in the glassfrog Hyalinobatrachium colymbiphyllum

description: Embryos of oviparous organisms must cope with harsh environments and are
 especially susceptible to disease, considering that many immune mechanisms
 do not develop until later in life. Parents may transmit symbiotic
 microflora to eggs, which can contribute to embryo immune defense. Despite
 the importance of symbiotic microbes for immune function and survival of
 adult amphibians, vertical transfer of symbionts in amphibians has
 received less attention than in other taxa. Here, we test the role of
 male-only parental care in establishing and maintaining the diversity of
 egg-bacterial assemblages in a Neotropical glassfrog (Centrolenidae).
 Previous research suggests that father Hyalinobatrachium colymbiphyllum
 may transfer bacterial symbionts to their eggs. We combined a male-removal
 experiment in situ with 16S rRNA gene amplicon sequencing to determine
 whether egg attendance by father H. colymbiphyllum influences the
 bacterial community and survival of eggs. We found that eggs harbor a
 diverse and stable bacterial assemblage. Despite different host
 environments, we found that adult skin and eggs supported very similar
 bacterial assemblages—even after removing fathers. While we found overlap
 in the bacteria present on eggs and their fathers, our experiment reveals
 that extended male care does not contribute to the maintenance of
 egg-bacterial communities, so there may be other potential routes of
 transfer. This study contributes to our understanding of the diversity and
 maintenance of egg microbiomes, and motivates further research on how
 initial bacteria are acquired and the ontogenetic development of
 host–symbiont communities.
description: Clutch monitoring
 dataSummary of fates of
 embryos from male removal experiment.Hyacol_clutch_monitoring_data.csvSequence metadataMetadata for all sequences contained in adjoining sequence (.fastq) file.Hyacol_sequence_metadata.csvSequencesRaw, demultiplexed sequence reads collected from swabs of eggs and adults during male removal experiment.Hyacol_sequences.tar.gz
DOI: 10.5061/dryad.b2p3j
title: Data from: Adaptation to random and systematic errors: Comparison of amputee and non-amputee control interfaces with varying levels of process noise

description: The objective of this study was to understand how people adapt to errors
 when using a myoelectric control interface. We compared adaptation across
 1) non-amputee subjects using joint angle, joint torque, and myoelectric
 control interfaces, and 2) amputee subjects using myoelectric control
 interfaces with residual and intact limbs (five total control interface
 conditions). We measured trial-by-trial adaptation to self-generated
 errors and random perturbations during a virtual, single degree-of-freedom
 task with two levels of feedback uncertainty, and evaluated adaptation by
 fitting a hierarchical Kalman filter model. We have two main results.
 First, adaptation to random perturbations was similar across all control
 interfaces, whereas adaptation to self-generated errors differed. These
 patterns matched predictions of our model, which was fit to each control
 interface by changing the process noise parameter that represented system
 variability. Second, in amputee subjects, we found similar adaptation
 rates and error levels between residual and intact limbs. These results
 link prosthesis control to broader areas of motor learning and adaptation
 and provide a useful model of adaptation with myoelectric control. The
 model of adaptation will help us understand and solve prosthesis control
 challenges, such as providing additional sensory feedback.
description: sharedTbTdataThe file 'sharedTbTdata' contains the processed data for all subjects. There are three matrices with able-bodied subject data, denoted by AB. (n x c x b), where n is subject number, a is control signal (1=angle, 2=torque, 3=EMG), and b is trial number. There are three matrices with transhumeral amputee subject data, denoted by TH. (n x d x b), where n is subject number, d is limb used (1=residual limb, 2=amputated limb), and b is trial number. endpoint_actualAB endpoint_actualTH and contain movement endpoint data. fb_sdAB and fb_sdTH contain the standard deviation of feedback for each trial. 40 degrees is the high feedback uncertainty condition, and 0 degrees is the low feedback uncertainty condition. visperturbAB and visperturbTH contain visual perturbation data for each trial. Perturbations were either -40, 0, or 40 degrees.Raw Data and Processing Files
DOI: 10.5061/dryad.sq85v00
title: Data from: Urban hubs of connectivity: contrasting patterns of gene flow within and among cities in the Western black widow spider

description: As urbanization drastically alters the natural landscape and generates
 novel habitats within cities, the potential for changes to gene flow for
 urban-dwelling species increases. The Western black widow spider
 (Latrodectus hesperus) is a medically-relevant urban adapter pest species,
 for which we have previously identified population genetic signatures
 consistent with urbanization facilitating gene flow, likely due to
 human-mediated transport. Here, in an analysis of 1.9 million genomewide
 SNPs, we contrast broad-scale geographic analyses of 10 urban and 11
 non-urban locales with fine-scale within-city analyses including 30 urban
 locales across the Western U.S. These hierarchical datasets enable us to
 test hypotheses of how urbanization impacts multiple urban cities and
 their genetic connectivity at different spatial scales. Coupled fine-scale
 and broad-scale analyses reveal contrasting patterns of high and low
 genetic differentiation among locales within cities as a result of low and
 high genetic connectivity, respectively, of these cities to the overall
 population network. We discuss these results as they challenge the use of
 cities as replicates of urban eco-evolution, and have implications for
 conservation and human health in a rapidly growing urban habitat.
description: Raw
 SNPsVCF format for all SNPs
 for all individualsTotalRawSNPs.vcf.gz
DOI: 10.5061/dryad.5c1tj
title: Data from: Genome-wide selection components analysis in a fish with male pregnancy

description: A major goal of evolutionary biology is to identify the genome-level
 targets of natural and sexual selection. With the advent of
 next-generation sequencing, whole-genome selection components analysis
 provides a promising avenue in the search for loci affected by selection
 in nature. Here, we implement a genome-wide selection components analysis
 in the sex-role-reversed Gulf pipefish, Syngnathus scovelli. Our approach
 involves a double-digest restriction-site associated DNA sequencing
 (ddRAD-seq) technique, applied to adult females, non-pregnant males,
 pregnant males and their offspring. An FST comparison of allele
 frequencies among these groups reveals 47 genomic regions putatively
 experiencing sexual selection, as well as 468 regions showing a signature
 of differential viability selection between males and females. A
 complementary likelihood ratio test identifies similar patterns in the
 data as the FST analysis. Sexual selection and viability selection both
 tend to favor the rare alleles in the population. Ultimately, we conclude
 that genome-wide selection components analysis can be a useful tool to
 complement other approaches in the effort to pinpoint genome-level targets
 of selection in the wild.
description: Archive of
 codeThis is the archived
 GitHub repository containing the code used to analyze the data in this
 paper.Variant Call
 FileIn this file are the SNP
 data for all loci and all individuals, output by Stacks' populations
 module. The README file contains the population map that assigns each
 individual to a group (FEM = females, OFF = offspring, NPM = non pregnant
 males, PRM = pregnant males)batch_1.vcfInput file for likelihood ratio testsThis file was used as input for the likelihood ratio tests. The columns are: Chromosome, Position, Individual ID, Genotype (Format: Allele 1, Allele 2), Likelihood of AA, Likelihood of Aa, Likelihood of aa. Genotypes were generated by Stacks and the Stacks hard calls were given a likelihood of 1. The other two genotype likelihoods were set to 0.000001.pipefish_input_full.LLm.txtSupplemental simulation outputThe output from the various runs of the simulation model described in the supplement are in this compressed folder.sca_simulation_output.tar.gzVariant Call File with inferred maternal allelesThis is a file containing the original genotypes and the inferred maternal alleles. The maternal alleles were generated from the Stacks Variant Call File output (archived here as Variant Call File) using the program infer_mat_vcf. This file was generated by merge_vcfs.R.biallelic_merge.vcf
DOI: 10.5061/dryad.11n64
title: Data from: "Development of the draft genome sequence of the marbled flounder Pseudopleuronectes yokohamae as a reference of population genomic analysis" in Genomic Resources Notes accepted 1 February 2015 – 31 March 2015

description: This article documents the public availability of the draft genome
 sequence data (raw reads, assembled contigs and unassembled reads) and
 RAD-tag read data of the marbled flounder Pseudopleuronectes yokohamae
 (Pleuronectiformes; Pleuronectidae).
description: Assembly.zip.bz2This file contains two assembly files; contig_sequences.fa is a fasta formatted file of contig sequences from de novo assembly. un-assembled_reads.fastq is a fastq formatted file of un-assembled reads from de novo assembly.
DOI: 10.5061/dryad.c2j90
title: Data from: Nanoscopic imaging of thick heterogeneous soft-matter structures in aqueous solution

description: Precise nanometre-scale imaging of soft structures at room temperature
 poses a major challenge to any type of microscopy because fast thermal
 fluctuations lead to significant motion blur if the position of the
 structure is measured with insufficient bandwidth. Moreover, precise
 localization is also affected by optical heterogeneities, which lead to
 deformations in the imaged local geometry, the severity depending on the
 sample and its thickness. Here we introduce quantitative thermal noise
 imaging, a three-dimensional scanning probe technique, as a method for
 imaging soft, optically heterogeneous and porous matter with
 submicroscopic spatial resolution in aqueous solution. By imaging both
 individual microtubules and collagen fibrils in a network, we demonstrate
 that structures can be localized with a precision of ~10 nm and that their
 local dynamics can be quantified with 50 kHz bandwidth and subnanometre
 amplitudes. Furthermore, we show how image distortions caused by optically
 dense structures can be corrected for.
description: Data for Fig 1-4, S4 and
 S7Raw
 and processed data used to generate Fig 1-4, S4 and S7. Please see the
 ReadMe file for additional guidance.Supporting
 Data.zip
DOI: 10.5061/dryad.1nc50
title: Data from: Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato

description: Hybrid zones can be valuable tools for studying evolution and identifying
 genomic regions responsible for adaptive divergence and underlying
 phenotypic variation. Hybrid zones between subspecies of Heliconius
 butterflies can be very narrow and are maintained by strong selection
 acting on colour pattern. The co-mimetic species H. erato and H. melpomene
 have parallel hybrid zones where both species undergo a change from one
 colour pattern form to another. We use restriction associated DNA
 sequencing to obtain several thousand genome wide sequence markers and use
 these to analyse patterns of population divergence across two pairs of
 parallel hybrid zones in Peru and Ecuador. We compare two approaches for
 analysis of this type of data; alignment to a reference genome and de novo
 assembly, and find that alignment gives the best results for species both
 closely (H. melpomene) and distantly (H. erato, ~15% divergent) related to
 the reference sequence. Our results confirm that the colour pattern
 controlling loci account for the majority of divergent regions across the
 genome, but we also detect other divergent regions apparently unlinked to
 colour pattern differences. We also use association mapping to identify
 previously unmapped colour pattern loci, in particular the Ro locus.
 Finally, we identify a new cryptic population of H. timareta in Ecuador,
 which occurs at relatively low altitude and is mimetic with H. melpomene
 malleti.
description: Heliconius erato emma
 (Peru) imagesPeru_Hera_emma.tifHeliconius erato favorinus (Peru) imagesPeru_Hera_favorinus.tifHeliconius erato hybrids (Peru) imagesPeru_Hera_hybrids.tifHeliconius melpomene aglaope (Peru) imagesPeru_Hmel_aglaope.tifHeliconius melpomene amaryllis (Peru) imagesPeru_Hmel_amaryllis.tifHeliconius melpomene hybrids (Peru) imagesPeru_Hmel_hybrids.tifNadeau_GR_2014_scriptsZipped archive of scripts
DOI: 10.5061/dryad.rg54h
title: Data from: Structural design of the minute clypeasteroid echinoid Echinocyamus pusillus

description: The clypeasteroid echinoid skeleton is a multi-plated, light-weight shell
 construction produced by biomineralization processes. In shell
 constructions, joints between individual elements are considered as weak
 points, yet, these echinoid skeleton shows an extensive preservation
 potential in both Recent and fossil environments. The remarkable strength
 of the test is achieved by skeletal reinforcement structures and their
 constructional layouts. Micro-computed tomography and scanning electron
 microscopy are used for micro-structural and volumetric analyses of the
 echinoid’s skeleton. It is shown, that strengthening mechanisms act on
 different hierarchical levels from the overall shape of the skeleton to
 micro-skeletal interlocking. The tight-fitting and interlocking plate
 joints lead to a shell considered to behave as a monolithic structure. The
 plate’s architecture features distinct regions interpreted as a
 significant load transferring system. The internal support system follows
 the segmentation of the remaining skeleton, where sutural layout and
 stereom distribution are designed for effective load transfer. The
 structural analysis of the multi-plated, yet monolithic skeleton of
 Echinocyamus pusillus reveals new aspects of the micro-morphology and its
 structural relevance for the load-bearing behaviour. The analysed
 structural principles allow E. pusillus to be considered as a role model
 for the development of multi-element, light-weight shell constructions.
description: gg-al-1_73
DOI: 10.5061/dryad.6880rf1
title: Data from: Table for five, please: dietary partitioning in boreal bats

description: Differences in diet can explain resource partitioning in apparently
 similar, sympatric species. Here, we analyzed 1,252 fecal droppings from
 five species (Eptesicus nilssonii, Myotis brandtii, M. daubentonii, M.
 mystacinus, and Plecotus auritus) to reveal their dietary niches using
 fecal DNA metabarcoding. We identified nearly 550 prey species in 13
 arthropod orders. Two main orders (Diptera and Lepidoptera) formed the
 majority of the diet for all species, constituting roughly 80%–90% of the
 diet. All five species had different dietary assemblages. We also found
 significant differences in the size of prey species between the bat
 species. Our results on diet composition remain mostly unchanged when
 using either read counts as a proxy for quantitative diet or
 presence–absence data, indicating a strong biological pattern. We conclude
 that although bats share major components in their ecology (nocturnal life
 style, insectivory, and echolocation), species differ in feeding behavior,
 suggesting bats may have distinctive evolutionary strategies. Diet
 analysis helps illuminate life history traits of various species, adding
 to sparse ecological knowledge, which can be utilized in conservation
 planning.
description: Raw FASTQ prey
 readsRaw FASTQ prey reads
 with sample names in the header. See README.txt for sample
 metadata.ZBJ.tgzRaw FASTQ bat readsRaw FASTQ bat reads with sample names in the header. Please see README.TXT for sample metadata.SFF.tgzPrey ZOTUSDenoised, chimera-filtered prey ZOTUS.Prey_ZBJ_denoised_zotus.faBat ZOTUSDenoised, chimera-filtered bat ZOTUS.Bat_SFF_denoised_zotus.fa
DOI: 10.5281/zenodo.18386057
title: IMS Monitoring & Evaluation (M&E) Pre-Coded Excel Calculator

description: A modifiable excel sheet containing a page for each of the measurement tools recommended within the compendium of tools in the IMS M&E Framework. Each tool has a five excel sheets: four sheets for four different data collection timpoints and one sheet that will conduct a simple analysis of the collected data for that tool. Please contact zempc@tcd.ie if you have any questions.
DOI: 10.5281/zenodo.18386058
title: IMS Monitoring & Evaluation (M&E) Pre-Coded Excel Calculator

description: A modifiable excel sheet containing a page for each of the measurement tools recommended within the compendium of tools in the IMS M&E Framework. Each tool has a five excel sheets: four sheets for four different data collection timpoints and one sheet that will conduct a simple analysis of the collected data for that tool. Please contact zempc@tcd.ie if you have any questions.
DOI: 10.5061/dryad.117tn
title: Data from: DNA metabarcoding of Amazonian ichthyoplankton swarms

description: Tropical rainforests harbor extraordinary biodiversity. The Amazon basin
 is thought to hold 30% of all river fish species in the world. Information
 about the ecology, reproduction, and recruitment of most species is still
 lacking, thus hampering fisheries management and successful conservation
 strategies. One of the key understudied issues in the study of population
 dynamics is recruitment. Fish larval ecology in tropical biomes is still
 in its infancy owing to identification difficulties. Molecular techniques
 are very promising tools for the identification of larvae at the species
 level. However, one of their limits is obtaining individual sequences with
 large samples of larvae. To facilitate this task, we developed a new
 method based on the massive parallel sequencing capability of next
 generation sequencing (NGS) coupled with hybridization capture. We focused
 on the mitochondrial marker cytochrome oxidase I (COI). The results
 obtained using the new method were compared with individual larval
 sequencing. We validated the ability of the method to identify Amazonian
 catfish larvae at the species level and to estimate the relative abundance
 of species in batches of larvae. Finally, we applied the method and
 provided evidence for strong temporal variation in reproductive activity
 of catfish species in the Ucayalí River in the Peruvian Amazon. This new
 time and cost effective method enables the acquisition of large datasets,
 paving the way for a finer understanding of reproductive dynamics and
 recruitment patterns of tropical fish species, with major implications for
 fisheries management and conservation.
description: Fasta-filesSequence fasta file format as listed in S1 Table.Bam-filesFastq-files1Sequence in .fastq file format as listed in S1 Table.Fastq-files2Sequence in .fastq file format as listed in S1 Table.
DOI: 10.5061/dryad.tf04g6v
title: Data from: Genome-wide exon-capture approach identifies genetic variants of Norway spruce genes associated with susceptibility to Heterobasidion parviporum infection

description: Root and butt rot caused by members of the Heterobasidion annosum species
 complex is the most economically important disease of conifer trees in
 boreal forests. Wood decay in the infected trees dramatically decreases
 their value and causes considerable losses to forest owners. Trees vary in
 their susceptibility to Heterobasidion infection, but the genetic
 determinants underlying the variation in the susceptibility are not
 well-understood. We performed the identification of Norway spruce genes
 associated with the resistance to Heterobasidion parviporum infection
 using genome-wide exon-capture approach. Sixty-four clonal Norway spruce
 lines were phenotyped, and their responses to H. parviporum inoculation
 were determined by lesion length measurements. Afterwards, the spruce
 lines were genotyped by targeted resequencing and identification of
 genetic variants (SNPs). Genome-wide association analysis identified 10
 SNPs located within 8 genes as significantly associated with the larger
 necrotic lesions in response to H. parviporum inoculation. The genetic
 variants identified in our analysis are potential marker candidates for
 future screening programs aiming at the differentiation of
 disease-susceptible and resistant trees.
description: VCF file containing
 information on the identified SNPsThe VCF file sontains
 information on the genetic variants (SNPs) identified by exome
 resequencing genotyping of 64 clonal Norway spruce
 lines.FAS_101201_64samples_for_GWAS.vcf