cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m98pt3k
title: Data from: A metatranscriptomic analysis of diseased social wasps (Vespula vulgaris) for pathogens, with an experimental infection of larvae and nests

description: Social wasps are a major pest in many countries around the world.
 Pathogens may influence wasp populations and could provide an option for
 population management via biological control. We investigated the
 pathology of nests of apparently healthy common wasps, Vespula vulgaris,
 with nests apparently suffering disease. First, next-generation sequencing
 and metatranscriptomic analysis were used to examine pathogen presence.
 The transcriptome of healthy and diseased V. vulgaris showed 27 known
 microbial phylotypes. Four of these were observed in diseased larvae alone
 (Aspergillus fumigatus, Moellerella wisconsensis, Moku virus, and the
 microsporidian Vavraia culicis). Kashmir Bee Virus (KBV) was found to be
 present in both healthy and diseased larvae. Moellerella wisconsensis is a
 human pathogen that was potentially misidentified in our wasps by the
 MEGAN analysis: it is more likely to be the related bacteria Hafnia alvei
 that is known to infect social insects. The closest identification to the
 putative pathogen identified as Vavraia culicis was likely to be another
 microsporidian Nosema vulgaris. PCR and subsequent Sanger sequencing using
 published or our own designed primers, confirmed the identity of
 Moellerella sp. (which may be Hafnia alvei), Aspergillus sp., KBV, Moku
 virus and Nosema. Secondly, we used an infection study by homogenising
 diseased wasp larvae and feeding them to entire nests of larvae in the
 laboratory. Three nests transinfected with diseased larvae all died within
 19 days. No pathogen that we monitored, however, had a significantly
 higher prevalence in diseased than in healthy larvae. RT-qPCR analysis
 indicated that pathogen infections were significantly correlated, such as
 between KBV and Aspergillus sp. Social wasps clearly suffer from an array
 of pathogens, which may lead to the collapse of nests and larval death.
description: Trinity FASTA assemblies
 and RNAseq FASTQ raw data for Vespula vulgarisRNAseq data from Vespula
 vulgaris nests sampled in the field in Lincoln, Canterbury, New Zealand in
 2016. The FASTQ data include 12 Illumina Hiseq files*: 6 samples from
 nests symptomatic of an unknown disease (labelled as
 'Diseased'), and 6 samples from nests not symptomatic (labelled
 as 'Healthy'). Two Trinity FASTA assemblies (labelled as
 'assemblies'): one of the RNAseq data from symptomatic nest
 samples and one of the RNAseq data from asymptomatic nest samples. *FASTQ
 data uploaded as separate zip filesassemblies.zipRNAseq FASTQ Diseased data for Vespula vulgarisRNAseq FASTQ data from 6 Vespula vulgaris samples symptomatic of an unknown disease.Diseased.zipRNAseq FASTQ Healthy data for Vespula vulgarisRNAseq FASTQ data from 6 Vespula vulgaris samples asymptomatic of an unknown disease.Healthy.zip
DOI: 10.5061/dryad.1r89hq8
title: Data from: Rapid divergence of mussel populations despite incomplete barriers to dispersal

description: Striking genetic structure among marine populations at small spatial
 scales is becoming evident with extensive molecular studies. Such
 observations suggest isolation at small scales may play an important role
 in forming patterns of genetic diversity within species.
 Isolation-by-distance, isolation-by-environment, and historical priority
 effects are umbrella terms for a suite of processes that underlie genetic
 structure, but their relative importance at different spatial and temporal
 scales remains elusive. Here, we use marine lakes in Indonesia to assess
 genetic structure and test relative roles of the processes in shaping
 genetic differentiation in populations of a bivalve mussel (Brachidontes
 sp.). Marine lakes are landlocked water bodies of similar age (6,000 –
 10,000 years), but with heterogeneous environments and varying degrees of
 connection to the sea. Using a population genomic approach (double-digest
 Restriction-site Associated DNA sequencing), we show strong genetic
 structuring across populations (range FST: 0.07 – 0.24), and find limited
 gene flow through admixture plots. At large spatial scales
 (&gt;1400km), a clear isolation-by-distance pattern was detected. At
 smaller spatial scales (&lt;200km), this pattern is maintained, but
 accompanied by an association of genetic divergence with degree of
 connection. No signatures of isolation-by-environment were found. We
 hypothesize that (incomplete) dispersal barriers can cause initial
 isolation, allowing priority effects to give the numerical advantage
 necessary to initiate strong genetic structure. Priority effects may be
 strengthened by local adaptation, which our data potentially corroborates
 by showing a high correlation between mussel genotypes and temperature.
 Our study indicates an often-neglected role of evolution-mediated priority
 effects in shaping divergence.
description: Brachidontes_rawreadsLarge file (~16Gb) containing raw reads in fastq format from all 125 individuals analysed in this study, sampled from seven marine lakes in Indonesia. Allocations of individuals to marine lakes can be found in the text file Populations.txt. In Brachidontes_Reference.fasta the obtained reference file can be found to which individuals were aligned.PopulationsSimple text file allocating individual reads to marine lakes from which they were sampled.Brachidontes_ReferenceReference file in fasta format to which individual reads were aligned.
DOI: 10.5061/dryad.nt722
title: Data from: Population genomics of local adaptation versus speciation in coral reef fishes (Hypoplectrus spp, Serranidae)

description: Are the population genomic patterns underlying local adaptation and the
 early stages of speciation similar? Addressing this question requires a
 system in which i. local adaptation and the early stages of speciation can
 be clearly identified and distinguished, ii. the amount of genetic
 divergence driven by the two processes is similar, and iii. comparisons
 can be repeated both taxonomically (for local adaptation) and
 geographically (for speciation). Here, we report just such a situation in
 the hamlets (Hypoplectrus spp), brightly colored reef fishes from the
 wider Caribbean. Close to 100,000 SNPs genotyped in 126 individuals from
 three sympatric species sampled in three repeated populations provide
 genome-wide levels of divergence that are comparable among allopatric
 populations (Fst estimate = 0.0042) and sympatric species (Fst estimate =
 0.0038). Population genetic, clustering and phylogenetic analyses reveal
 very similar patterns for local adaptation and speciation, with a large
 fraction of the genome undifferentiated (Fst estimate ≈ 0), a very small
 proportion of Fst outlier loci (0.05-0.07%), and remarkably few repeated
 outliers (1-3). Nevertheless, different loci appear to be involved in the
 two processes in Hypoplectrus, with only 7% of the most differentiated
 SNPs and outliers shared between populations and species comparisons. In
 particular, a tropomyosin (Tpm4) and a previously identified hox (HoxCa)
 locus emerge as candidate loci (repeated outliers) for local adaptation
 and speciation, respectively. We conclude that marine populations may be
 locally adapted notwithstanding shallow levels of genetic divergence, and
 that from a population genomic perspective this process does not appear to
 differ fundamentally from the early stages of speciation.
description: SNP calls for RAD data
 grouped by location, vcf formatSNP calls for filtered
 and assembled RAD data grouped by location (Belize, Honduras, Panama), vcf
 format.batch_12_locations.vcfSNP calls for RAD data grouped by samples, vcf formatSNP calls for filtered and assembled RAD data grouped by samples (species/location, 9 samples), vcf format.batch_12_samples.vcfConsensus sequences of the three repeated outliersConsensus sequences of the three mini-contigs assembled around the repeated outlier SNPs.Mini_contigs.txtFiletered and assembled RAD dataFiltered and assembled RAD data for the assembly with m=3 and M=2RAD_data.zip
DOI: 10.5061/dryad.8m3t6
title: Data from: Plasmid and clonal interference during post-horizontal gene transfer evolution

description: Plasmids are nucleic acid molecules that can drive their own replication
 in a living cell. They can be transmitted horizontally and can thrive in
 the host cell to high copy numbers. Plasmid replication and gene
 expression consume cellular resources and cells carrying plasmids incur
 fitness costs. But many plasmids carry genes that can be beneficial under
 certain conditions, allowing the cell to endure in the presence of
 antibiotics, toxins, competitors or parasites. Horizontal transfer of
 plasmid-encoded genes can thus instantaneously confer differential
 adaptation to local or transient selection conditions. This conflict
 between cellular fitness and plasmid spread sets the scene for multilevel
 selection processes. We have engineered a system to study the short term
 evolutionary impact of different synonymous versions of a plasmid-encoded
 antibiotic resistance gene. Applying experimental evolution under
 different selection conditions and deep sequencing allowed us to show
 rapid local adaptation to the presence of antibiotic and to the specific
 version of the resistance gene transferred. We describe the presence of
 clonal interference at two different levels: at the within-cell level,
 because a single cell can carry several plasmids, and at the between-cell
 level, because a bacterial population may contain several clones carrying
 different plasmids and displaying different fitness in the
 presence|absence of antibiotic. Understanding the within-cell and
 between-cell dynamics of plasmids after horizontal gene transfer is
 essential to unravel the dense network of mobile elements underlying the
 worldwide threat to public health of antibiotic resistance.
description: Raw_Illumina_Data_1Raw_Illumina_Data_1130821_SND104_A_L001_A.tarRaw_Illumina_Data_2Raw_Illumina_Data_2130821_SND104_A_L001_B1-B6.tarRaw_Illumina_Data_3Raw_Illumina_Data_3130821_SND104_A_L001_B7-B12.tarRaw_Illumina_Data_4Raw_Illumina_Data_4130821_SND104_A_L001_C1-C6.tarRaw_Illumina_Data_5Raw_Illumina_Data_5130821_SND104_A_L001_C7-C12.tarRaw_Illumina_Data_6Raw_Illumina_Data_6130821_SND104_A_L001_D1-D8.tarRaw_Illumina_Data_7Raw_Illumina_Data_7130821_SND104_A_L001_D9-D12.tarRaw_Illumina_Data_8Raw_Illumina_Data_8130821_SND104_A_L001_E1-E5.tarRaw_Illumina_Data_9Raw_Illumina_Data_9130821_SND104_A_L001_E6-E11.tarRaw_Illumina_Data_10Raw_Illumina_Data_10130821_SND104_A_L001_F1-F4.tarRaw_Illumina_Data_11Raw_Illumina_Data_11130821_SND104_A_L001_F5-F8.tarRaw_Illumina_Data_12Raw_Illumina_Data_12130821_SND104_A_L001_F9-F11.tarRaw_Illumina_Data_13Raw_Illumina_Data_13130821_SND104_A_L001_G1-G7.tarRaw_Illumina_Data_14Raw_Illumina_Data_14130821_SND104_A_L001_G8-G11.tarRaw_Illumina_Data_15Raw_Illumina_Data_15130821_SND104_A_L001_H1-H5.tarRaw_Illumina_Data_16Raw_Illumina_Data_16130821_SND104_A_L001_H6-H11.tarReference_plasmid_sequencesReference_plasmid_sequencesreference_sequences.txtSample_listList_of_raw_illumina_data
DOI: 10.5061/dryad.8m3kv
title: Data from: Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring

description: Current biodiversity assessment and biomonitoring are largely based on the
 morphological identification of selected bioindicator taxa. Recently,
 several attempts have been made to use eDNA metabarcoding as an
 alternative tool. However, until now, most applied metabarcoding studies
 have been based on the taxonomic assignment of sequences that provides
 reference to morphospecies ecology. Usually, only a small portion of
 metabarcoding data can be used due to a limited reference database and a
 lack of phylogenetic resolution. Here, we investigate the possibility to
 overcome these limitations using a taxonomy-free approach that allows the
 computing of a molecular index directly from eDNA data without any
 reference to morphotaxonomy. As a case study, we use the benthic diatoms
 index, commonly used for monitoring the biological quality of rivers and
 streams. We analysed 87 epilithic samples from Swiss rivers, the
 ecological status of which was established based on the microscopic
 identification of diatom species. We compared the diatom index derived
 from eDNA data obtained with or without taxonomic assignment. Our
 taxonomy-free approach yields promising results by providing a correct
 assessment for 77% of examined sites. The main advantage of this method is
 that almost 95% of OTUs could be used for index calculation, compared to
 35% in the case of the taxonomic assignment approach. Its main limitations
 are under-sampling and the need to calibrate the index based on the
 microscopic assessment of diatoms communities. However, once calibrated,
 the taxonomy-free molecular index can be easily standardized and applied
 in routine biomonitoring, as a complementary tool allowing fast and
 cost-effective assessment of the biological quality of watercourses.
description: Diatom3_S1_L001_R1_001Illumina fastqDiatom3_S1_L001_R2_001Illumina fastqDIATOM5_S1_L001_R1_001Illumina fastqDIATOM5_S1_L001_R2_001Illumina fastq
DOI: 10.5061/dryad.2686c
title: Data from: DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities

description: Morphology-based profiling of benthic communities has been extensively
 applied to aquatic ecosystems' health assessment. However, it remains
 a low-throughput, and sometimes ambiguous, procedure. Despite DNA
 metabarcoding has been applied to marine benthos, a comprehensive approach
 providing species-level identifications for estuarine macrobenthos is
 still lacking. Here we report a combination of experimental and field
 studies to assess the aptitude of COI metabarcoding to provide robust
 species-level identifications for high-throughput monitoring of estuarine
 macrobenthos. To investigate the ability of metabarcoding to detect all
 species present in bulk DNA extracts, we contrived three phylogenetically
 diverse communities, and applied four different primer pairs to generate
 PCR products within the COI barcode region. Between 78-83% of the species
 in the contrived communities were recovered through HTS. Subsequently, we
 compared morphology and metabarcoding-based approaches to determine the
 species composition from four distinct estuarine sites. Our results
 indicate that species richness would be considerably underestimated if
 only morphological methods were used: globally 27 species identified
 through morphology versus 61 detected by metabarcoding. Although further
 refinement is required to improve efficiency and output of this approach,
 here we show the great aptitude of COI metabarcoding to provide high
 quality and auditable species identifications in estuarine macrobenthos
 monitoring.
description: fastq data of the
 assembled communitiesMix 1, 2 and 3 indicate
 the three different assembled communities. Primer pairs A, B, C and D are
 LoboF1/LoboR1, LoboF1/250R, ArF2/ArR5 and ArF2/LoboR1,
 respectively.fastq assembled
 communities.zipfastq data of the
 natural communities part1B indicates primer pair
 LoboF1/250R. 1, 2, 3 and 4 (after primers) indicate the four different
 natural communities. 1, 2, 3, 4 and 5 (after hyphen) indicate the five
 samples of each natural community.fastq natural communities
 primerB.zipfastq data of the
 natural communities part2D indicates the primer
 pair ArF2/LoboR1. 1, 2, 3 and 4 (after primers) indicate the four
 different natural communities. 1, 2, 3, 4 and 5 (after hyphen) indicate
 the five samples of each natural community.fastq natural communities
 primersD.zip
DOI: 10.5061/dryad.js7q8b3
title: Data from: Temporal activity patterns of predators and prey across broad geographic scales

description: Predators and prey are locked in an evolutionary arms race that shapes
 their behaviour and life history. Predators target prey vulnerabilities to
 maximise hunting success, while prey trade-off foraging against predation
 avoidance. Though studies have demonstrated how predation risk can alter
 how prey allocate daily foraging effort, little work has considered the
 implications of this temporal component of behaviour from a predator’s
 perspective, or assessed its influence on broad-scale predator-prey
 interactions. We develop a method to compare daily activity patterns of
 avian predators and prey using data from two large citizen science
 datasets collected on different continents. Our analyses reveal evidence
 for convergent daily hunting strategies across avian predators, with
 distinct differences according to prey type. By comparing predator data
 with correspondent data from songbirds, our study suggests that predators
 (Accipiters) specialised to hunt songbirds match the activity patterns of
 their prey species. These results indicate predators have evolved common
 temporal hunting strategies to exploit temporal patterns in prey
 behaviour.
description: READMEThis file explains how
 to use the provided R scripts and data to produce the figures that
 accompany: Lang SDJ, Mann RP & Farine DR 2018. Temporal activity
 patterns of predators and prey across broad geographic scales
 .eBird scripts
 0-6Zip file containing the
 full pipeline of R script files for analysing the provided eBird data (see
 Readme for details)eBird_collatedSource files for analyses of eBird data from scratch (see Readme for details).eBird_obstimes_3hrsFull eBird dataset that has been processed using 'obstimes' code of eBird script #1, but not subsetted per species (see Readme for details).All_eBird_spp_3hrsZipped folder of multiple eBird files subsetted by species using eBird script #2 (see Readme for details).All_eBird_spp_modeldataZipped folder of multiple eBird files containing model data for each species, produced using eBird script #3 (see Readme for details).Full_model_dataset_eBirdRdata file of eBird model data for all species, produced using eBird script #4 (see Readme for details).BirdTrack scripts 1-6Zip file containing the full pipeline of R script files for analysing the provided BirdTrack data (see Readme for details).BirdTrack_SourceZipped folder of cleaned BirdTrack source csv files (see Readme for details).All_BirdTrack_spp_3hrsZipped folder of multiple BirdTrack files subsetted by species, obstimed using BirdTrack script #1 (see Readme for details).All_BirdTrack_spp_modeldataZipped folder of multiple BirdTrack files containing model data for each species, produced using BirdTrack script #3 (see Readme for details).Full_model_dataset_BirdTrackRdata file of BirdTrack model data for all species, produced using BirdTrack script #4 (see Readme for details).
DOI: 10.5061/dryad.7s2dq
title: Data from: Influence of full-length dystrophin on brain volumes in mouse models of Duchenne muscular dystrophy

description: Duchenne muscular dystrophy (DMD) affects besides muscle also the brain,
 resulting in memory and behavioral problems. The consequences of
 dystrophinopathy on gross macroscopic alterations are unclear. To
 elucidate the effect of dystrophin expression on brain morphology, we used
 high-resolution post-mortem MRI in mouse models that either express 0%
 (mdx), 100% (BL10) or a low amount of full-length dystrophin
 (mdx-Xist∆hs). While absence or low amounts of dystrophin did not result
 in significantly different whole brain volume and skull morphology, we
 found differences in volume of individual brain structures. The found
 results are in line with observations in humans, where whole brain volume
 was found to be reduced only in patients lacking both full-length
 dystrophin and the shorter isoform Dp140.
description: Template and brain
 volumesThis zip file contains
 the following information: mouse brain template, brain ROIs, registration
 settings and the processed data. Each mouse brain was registered to a
 template mouse brain and volumes (whole brain + 22 structures) were
 extracted using the ROIs. Volumes are stored [per structure per mouse] and
 volumes are stored [per structure per strain].MRI data part
 1Contains Bruker scan
 data (including localizer scans) as 2dseq files and can be easily read
 with Bruker ParaVision software. On request, data can be converted to
 Nifti/Dicom.MRI data part
 2Contains Bruker scan
 data (including localizer scans) as 2dseq files and can be easily read
 with Bruker ParaVision software. On request, data can be converted to
 Nifti/Dicom.
DOI: 10.5061/dryad.9642b
title: Data from: Genomic associations with bill length and disease reveal drift and selection across island bird populations

description: Island species provide excellent models for investigating how selection
 and drift operate in wild populations, and for determining how these
 processes act to influence local adaptation and speciation. Here, we
 examine the role of selection and drift in shaping genomic and phenotypic
 variation across recently separated populations of Berthelot's pipit
 (Anthus berthelotii), a passerine bird endemic to three archipelagos in
 the Atlantic. We first characterised genetic diversity and population
 structuring, which supported previous inferences of a history of recent
 colonisations and bottlenecks. We then tested for regions of the genome
 associated with the ecologically important traits of bill length and
 malaria infection, both of which vary substantially across populations in
 this species. We identified a SNP associated with variation in bill length
 among individuals, islands and archipelagos; patterns of variation at this
 SNP suggest that both phenotypic and genotypic variation in bill length is
 largely shaped by founder effects. Malaria was associated with SNPs
 near/within genes involved in the immune response, but this relationship
 was not consistent among archipelagos, supporting the view that disease
 resistance is complex and rapidly evolving. Although we found little
 evidence for divergent selection at candidate loci for bill length and
 malaria resistance, genome scan analyses pointed to several genes related
 to immunity and metabolism as having important roles in divergence and
 adaptation. Our findings highlight the utility and challenges involved
 with combining association mapping and population genetic analysis in
 non-equilibrium populations, to disentangle the effects of drift and
 selection on shaping genotypes and phenotypes.
description: Pipit dataset .bed
 files.bed and associated .bim
 and .fam files for each pipit dataset.pipit_datasets_bed_files.zipPipit sample informationPhenotypic and population information for each samplepipit_sample_information.csvChromosome codesChromosome name and associated numeric code used in .bim fileschromosome_codes.txtPipit .qseq filesThis zip file contains a separate .qseq file of raw RAD reads for each individual sample.pipit_qseq_files.zipAnthus berthelotii draft genomeDraft genome of Anthus berthelotii, from sample 816 in Porto SantoAnthus_berthelotii_PS_816_genome.zip