cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8b35s
title: Data from: Fascicles from energy-storing tendons show an age-specific response to cyclic fatigue loading

description: Some tendons, such as the human Achilles and equine superficial digital
 flexor tendon (SDFT), act as energy stores, stretching and recoiling to
 increase efficiency during locomotion. Our previous observations of
 rotation in response to applied strain in SDFT fascicles suggest a helical
 structure, which may provide energy-storing tendons with a greater ability
 to extend and recoil efficiently. Despite this specialization,
 energy-storing tendons are prone to age-related tendinopathy. The aim of
 this study was to assess the effect of cyclic fatigue loading (FL) on the
 microstructural strain response of SDFT fascicles from young and old
 horses. The data demonstrate two independent age-related mechanisms of
 fatigue failure; in young horses, FL caused low levels of matrix damage
 and decreased rotation. This suggests that loading causes alterations to
 the helix substructure, which may reduce their ability to recoil and
 recover. By contrast, fascicles from old horses, in which the helix is
 already compromised, showed greater evidence of matrix damage and suffer
 increased fibre sliding after FL, which may partially explain the
 age-related increase in tendinopathy. Elucidation of helix structure and
 the precise alterations occurring owing to both ageing and FL will help to
 develop appropriate preventative and repair strategies for tendinopathy.
description: Confocal
 ImagesConfocal images of grids
 at 0 to 10 % strain increments. Each sample is identified by a number.
 Please see the ReadMe file for a description of the
 abbreviationsFatigue test raw
 dataRaw data from fatigue
 loading experiments. Samples are denoted by horse number followed by
 fascicle number. See ReadMe file for details of horse ages and naming
 conventions.
DOI: 10.5061/dryad.qv633
title: Data from: A pragmatic approach to the analysis of diets of generalist predators: the use of next-generation sequencing with no blocking probes

description: Predicting whether a predator is capable of affecting the dynamics of a
 prey species in the field implies the analysis of the complete diet of the
 predator, not simply rates of predation on a target taxon. Here, we
 employed the Ion Torrent next-generation sequencing technology to
 investigate the diet of a generalist arthropod predator. A complete
 dietary analysis requires the use of general primers, but these will also
 amplify the predator unless suppressed using a blocking probe. However,
 blocking probes can potentially block other species, particularly if they
 are phylogenetically close. Here, we aimed to demonstrate that enough prey
 sequence could be obtained without blocking probes. In communities with
 many predators, this approach obviates the need to design and test
 numerous blocking primers, thus making analysis of complex community food
 webs a viable proposition. We applied this approach to the analysis of
 predation by the linyphiid spider Oedothorax fuscus in an arable field. We
 obtained over two million raw reads. After discarding the low-quality and
 predator reads, the libraries still contained over 61 000 prey reads (3%
 of the raw reads; 6% of reads passing quality control). The libraries were
 rich in Collembola, Lepidoptera, Diptera and Nematoda. They also contained
 sequences derived from several spider species and from horticultural pests
 (aphids). Oedothorax fuscus is common in UK cereal fields, and the results
 showed that it is exploiting a wide range of prey. Next-generation
 sequencing using general primers but without blocking probes provided
 ample sequences for analysis of the prey range of this spider and proved
 to be a simple and inexpensive approach.
description: splitA perl script that takes
 a fastq file obtained by bidirectional sequencing and separates the
 forward and reverse reads in two different files.reduceA perl script that
 divides a group of sequences from a fasta file in two sets. One set
 contains the sequences that match the variable $lbl_dom, and the other set
 contains the rest of sequencesrun_314Raw data in fastq format from the sequencing of the Oedothorax fuscus sample using a 314 Ion Torrent chiprun_318
DOI: 10.5061/dryad.mv66s
title: Data from: Microbiome investigation in the ecological speciation context of lake whitefish (Coregonus clupeaformis) using next-generation sequencing

description: Few studies have applied NGS methods to investigate the microbiome of
 vertebrates in their natural environment and in freshwater fishes in
 particularly. Here, we used pyrosequencing of the 16S gene rRNA to (i)
 test for differences in kidney bacterial communities (i.e. microbiota) of
 dwarf and normal whitefish found as sympatric pairs, (ii) test the
 hypothesis of higher bacterial diversity in normal compared with dwarf
 whitefish and (iii) test for the occurrence of parallelism with the
 presence and composition of bacterial communities across species pairs
 inhabiting different lakes. The kidney microbiota of 253 dwarf and normal
 whitefish from five lakes was analysed combining a double-nested PCR
 approach with 454 pyrosequencing. Bacteria were detected in 52.6% of the
 analysed whitefish. There was no overall significant difference among
 lakes and forms, although the lake × form interaction was found
 significant. We identified 579 bacterial genera, which is substantially
 more than previous descriptions using less sensitive techniques of fish
 bacterial diversity in kidney, pathogenic or not. Ten of these genera
 contained eighteen pathogenic species. Differences in bacteria composition
 between whitefish forms were not parallel among lakes. In accordance with
 the higher diversity of prey types, normal whitefish kidney tissue
 consistently had a more diverse bacterial community and this pattern was
 parallel among lakes. These results add to building evidence from previous
 studies on this system that the adaptive divergence of dwarf, and normal
 whitefish has been driven by both parallel and nonparallel ecological
 conditions across lakes.
description: raw-dataMID-tagsIndividual-distribution-libraries
DOI: 10.5061/dryad.1kn38
title: Data from: Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides) from different thermal environments

description: Recent evidence suggests that corals can acclimatize or adapt to local
 stress factors through differential regulation of their gene expression.
 Profiling gene expression in corals from diverse environments can
 elucidate the physiological processes that may be responsible for
 maximizing coral fitness in their natural habitat and lead to a better
 understanding of the coral's capacity to survive the effects of
 global climate change. In an accompanying paper, we show that Porites
 astreoides from thermally different reef habitats exhibit distinct
 physiological responses when exposed to 6 weeks of chronic temperature
 stress in a common garden experiment. Here, we describe expression
 profiles obtained from the same corals for a panel of 9 previously
 reported and 10 novel candidate stress response genes identified in a
 pilot RNA-Seq experiment. The strongest expression change was observed in
 a novel candidate gene potentially involved in calcification, SLC26, a
 member of the solute carrier family 26 anion exchangers, which was
 down-regulated by 92-fold in bleached corals relative to controls. The
 most notable signature of divergence between coral populations was
 constitutive up-regulation of metabolic genes in corals from the warmer
 inshore location, including the gluconeogenesis enzymes pyruvate
 carboxylase and phosphoenolpyruvate carboxykinase and the lipid
 beta-oxidation enzyme acyl-CoA dehydrogenase. Our observations highlight
 several molecular pathways that were not previously implicated in the
 coral stress response and suggest that host management of energy budgets
 might play an adaptive role in holobiont thermotolerance.
description: Porites astreoides
 transcriptomeThis file contains the
 transcriptome as a .fasta file and associated annotation tables for
 isogroups and gene ontology terms.P_astreoides_db_annot_april2013.zipRaw qPCR dataThis file contains raw qPCR data, split by short term candidates and long-term candidates. Technical replicates have been averaged to yield a single Cp value per sample per gene.RawCp_TechRepsAvg.zipqPCR Statistical AnalysesThis file contains normalized qPCR data for both the short-term and long-term gene candidates, as described in the paper, in addition to an R script for analyzing and plotting data.qPCRstats.zipPilot RNAseq DataThis file contains cleaned SOLiD reads (in colorspace) and a table of read counts mapping to the Porites astreoides transcriptome as described in the paper.RNAseqData.zip
DOI: 10.5061/dryad.68n87
title: Data from: The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish

description: Atlantic killifish populations have rapidly adapted to normally lethal
 levels of pollution in four urban estuaries. Through analysis of 384 whole
 killifish genome sequences and comparative transcriptomics in four pairs
 of sensitive and tolerant populations, we identify the aryl hydrocarbon
 receptor–based signaling pathway as a shared target of selection. This
 suggests evolutionary constraint on adaptive solutions to complex toxicant
 mixtures at each site. However, distinct molecular variants apparently
 contribute to adaptive pathway modification among tolerant populations.
 Selection also targets other toxicity-mediating genes and genes of
 connected signaling pathways; this indicates complex tolerance phenotypes
 and potentially compensatory adaptations. Molecular changes are consistent
 with selection on standing genetic variation. In killifish, high
 nucleotide diversity has likely been a crucial substrate for selective
 sweeps to propel rapid adaptation.
description: killifish population
 tree dataThis archive contains
 data used to estimate a population tree in the associated manuscript. It
 contains a VCF file and associated population allele frequencies for ~800k
 SNPs sampled from across the fundulus heteroclitus autosomes. It also
 contains an R script used to estimate and plot the
 tree.kfish_science_treedata.zip
DOI: 10.5061/dryad.s58qh
title: Data from: Internal states drive nutrient homeostasis by modulating exploration-exploitation trade-off

description: Internal states can profoundly alter the behavior of animals. A
 quantitative understanding of the behavioral changes upon metabolic
 challenges is key to a mechanistic dissection of how animals maintain
 nutritional homeostasis. We used an automated video tracking setup to
 characterize how amino acid and reproductive states interact to shape
 exploitation and exploration decisions taken by adult Drosophila
 melanogaster. We find that these two states have specific effects on the
 decisions to stop at and leave proteinaceous food patches. Furthermore,
 the internal nutrient state defines the exploration-exploitation
 trade-off: nutrient-deprived flies focus on specific patches while
 satiated flies explore more globally. Finally, we show that olfaction
 mediates the efficient recognition of yeast as an appropriate protein
 source in mated females and that octopamine is specifically required to
 mediate homeostatic postmating responses without affecting internal
 nutrient sensing. Internal states therefore modulate specific aspects of
 exploitation and exploration to change nutrient selection.
description: Fly tracking data from
 Corrales-Carvajal et al 2016This package contains
 tracking data (head and body centroids) of single walking fruit flies
 (Drosophila melanogaster) in an arena (height = 2 mm, radius = 33 mm)
 containing 18 food patches: 9 patches of sucrose 180 g/L and 9 patches of
 yeast 180 g/L. This arena was designed based on the fly-bowl (Simon &
 Dickinson, 2010). The detailed information for the experimental condition
 of each fly is given (e.g. Genotype, mating status, metabolic state, etc).
 We provide all the tracking data that was used to generate all the results
 shown in Corrales-Carvajal et al 2016. More details about the tracking
 setup, foraging arena and experimental protocol can be found in the
 materials and methods of the associated publication.Fly tracking data from
 Corrales-Carvajal 2016.zip
DOI: 10.5061/dryad.nh6v4
title: Data from: Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle

description: [No abstract entered]
description: WGS Variants from 556 NZ
 Dairy Animals Chr23:30627379-40627379rtg_3.3.1_556_animal_Chr23:30627379-40627379_for_dryad.vcf.gzExome Variants in Multiple Breeds Chr20:34783594-42331973GATK-10MB-Window-Exomes.vcf.gzHairy syndrome genotypes and phenotypesGenotypes and phenotype used for genome-wide analysis of the hairy syndrome, Plink binary format (.bim .bed .fam)gen_phen_data_for_paper.zipHairy bull progeny TaqMan resultsHairy_bull_progeny_TaqMan_results.txtphysiological phenotypesphysiological_phenos.zipDFAM association results for 628,279 SNPDFAM_assoc_results.zipPhased genotypes and phenotypes for 82 Senepol crossbreedsphased_gen_phen_data_slick.zip
DOI: 10.5061/dryad.q70q40m
title: Data from: Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes

description: The number of de novo genome sequence assemblies is increasing
 exponentially; however, relatively few contain one scaffold/contig per
 chromosome. Such assemblies are essential for studies of
 genotype-to-phenotype association, gross genomic evolution, and
 speciation. Inter-species differences can arise from chromosomal changes
 fixed during evolution, and we previously hypothesized that a higher
 fraction of elements under negative selection contributed to
 avian-specific phenotypes and avian genome organization stability. The
 objective of this study is to generate chromosome-level assemblies of
 three avian species (saker falcon, budgerigar, and ostrich) previously
 reported as karyotypically rearranged compared to most birds. We also test
 the hypothesis that the density of conserved non-coding elements is
 associated with the positions of evolutionary breakpoint regions.
description: genomesThis file contains the fasta files of the three genomes assembled at chromosome level.
DOI: 10.5061/dryad.1hc35
title: Data from: Experimental swap of Anopheles gambiae's assortative mating preferences demonstrates key role of X-chromosome divergence island in incipient sympatric speciation.

description: Although many theoretical models of sympatric speciation propose that
 genes responsible for assortative mating amongst incipient species should
 be associated with genomic regions protected from recombination, there are
 few data to support this theory. The malaria mosquito, Anopheles gambiae,
 is known for its sympatric cryptic species maintained by pre-mating
 reproductive isolation and its putative genomic islands of speciation, and
 is therefore an ideal model system for studying the genomic signature
 associated with incipient sympatric speciation. Here we selectively
 introgressed the island of divergence located in the pericentric region of
 the X chromosome of An. gambiae s.s. into its sister taxon An. coluzzii
 through 5 generations of backcrossing followed by two generations of
 crosses within the introgressed strains that resulted in An. coluzzii-like
 recombinant strains fixed for the M and S marker in the X chromosome
 island. The mating preference of recombinant strains was then tested by
 giving virgin recombinant individuals a choice of mates with X-islands
 matching and non-matching their own island type. We show through genetic
 analyses of transferred sperm that recombinant females consistently mated
 with matching island-type males thereby associating assortative mating
 genes with the X-island of divergence. Furthermore, full-genome sequencing
 confirmed that protein-coding differences between recombinant strains were
 limited to the experimentally swapped pericentromeric region. Finally,
 targeted-genome comparisons showed that a number of these unique
 differences were conserved in sympatric field populations, thereby
 revealing candidate speciation genes. The functional demonstration of a
 close association between speciation genes and the X-island of
 differentiation lends unprecedented support to island-of-speciation models
 of sympatric speciation facilitated by pericentric recombination
 suppression.
description: SNP Data Mopti, RbMM,
 RbSS strains and 2 field populationsSNPs identified by
 full-genome sequencing for Mopti, RbMM, RbSS strains and targeted
 sequencing of X-island for 2 An. coluzzii and gambiae s.s. populations
 from Ghana. The files were generated by GATK (VCF
 format).SNP
 Data Resequencing.zip
DOI: 10.5061/dryad.6p2h0
title: Data from: Protocols for dry DNA storage and shipment at room temperature

description: The globalization of DNA barcoding will require core analytical facilities
 to develop cost-effective, efficient protocols for the shipment and
 archival storage of DNA extracts and PCR products. We evaluated three
 dry-state DNA stabilization systems: commercial Biomatrica® DNAstable®
 plates, home-made trehalose and polyvinyl alcohol (PVA) plates on 96-well
 panels of insect DNA stored at 56 °C and at room temperature. Controls
 included unprotected samples that were stored dry at room temperature and
 at 56 °C, and diluted samples held at 4 °C and at −20 °C. PCR and
 selective sequencing were performed over a 4-year interval to test the
 condition of DNA extracts. Biomatrica® provided better protection of DNA
 at 56 °C and at room temperature than trehalose and PVA, especially for
 diluted samples. PVA was the second best protectant after Biomatrica® at
 room temperature, whereas trehalose was the second best protectant at 56
 °C. In spite of lower PCR success, the DNA stored at −20 °C yielded longer
 sequence reads and stronger signal, indicating that temperature is a
 crucial factor for DNA quality which has to be considered especially for
 long-term storage. Although it is premature to advocate a transition to
 DNA storage at room temperature, dry storage provides an additional layer
 of security for frozen samples, protecting them from degradation in the
 event of freezer failure. All three forms of DNA preservation enable
 shipment of dry DNA and PCR products between barcoding facilities.
description: MER-13-0064_E-gelsThis file contains original E-gel images for the manuscript MER-13-0064 1) PVA is labeled as ‘NVI’ 2) Fridge storage is labeled as ‘fresh’ in some E-gels 3) E-gels were reused twice 4) Please refer to Table 2 in the manuscript for detailed experiment setup decriptionMER-13-0064_Sequence_dataThis file contains original sequence trace files for the manuscript MER-13-0064 1) PVA is labeled as ‘NVI’ 2) Fridge and Freezer storage is labeled as ‘fresh’ in some trace file names and was changed later in Excel for data parsing 3) Please refer to Table 2 in the manuscript for experiment setup descriptionMER-13-0064_calculationsCalculations in MS Excel used for generation of graphs in Tableau.
DOI: 10.5061/dryad.dm540
title: Data from: Genomic signals of selection predict climate-driven population declines in a migratory bird

description: The ongoing loss of biodiversity caused by rapid climatic shifts requires
 accurate models for predicting species’ responses. Despite evidence that
 evolutionary adaptation could mitigate climate change impacts, evolution
 is rarely integrated into predictive models. Integrating population
 genomics and environmental data, we identified genomic variation
 associated with climate across the breeding range of the migratory
 songbird, yellow warbler (Setophaga petechia). Populations requiring the
 greatest shifts in allele frequencies to keep pace with future climate
 change have experienced the largest population declines, suggesting that
 failure to adapt may have already negatively affected populations.
 Broadly, our study suggests that the integration of genomic adaptation can
 increase the accuracy of future species distribution models and ultimately
 guide more effective mitigation efforts.
description: Yellow warbler
 assemblyYellow warbler assembly
 including: 1) fasta file with 18,414 scaffolds and 2) .gff file with
 annotations generated with the MAKER pipeline.YWAR_assembly.tar.gz
DOI: 10.5061/dryad.tg0mt
title: Data from: Standing chromosomal variation in Lake Whitefish species pairs: the role of historical contingency and relevance for speciation

description: The role of chromosome changes in speciation remains a debated topic,
 although demographic conditions associated with divergence should promote
 their appearance. We tested a potential relationship between chromosome
 changes and speciation by studying two Lake Whitefish (Coregonus
 clupeaformis) lineages that recently colonized postglacial lakes following
 allopatry. A dwarf limnetic species evolved repeatedly from the normal
 benthic species, becoming reproductively isolated. Lake Whitefish hybrids
 experience mitotic and meiotic instability, which may result from
 structurally divergent chromosomes. Motivated by this observation, we test
 the hypothesis that chromosome organization differs between Lake Whitefish
 species pairs using cytogenetics. While chromosome and fundamental numbers
 are conserved between the species (2n = 80, NF = 98), we observe extensive
 polymorphism of subtle karyotype traits. We describe intrachromosomal
 differences associated with heterochromatin and repetitive DNA, and test
 for parallelism among three sympatric species pairs. Multivariate analyses
 support the hypothesis that differentiation at the level of subchromosomal
 markers mostly appeared during allopatry. Yet we find no evidence for
 parallelism between species pairs among lakes, consistent with
 colonization effect or postcolonization differentiation. The reported
 intrachromosomal polymorphisms do not appear to play a central role in
 driving adaptive divergence between normal and dwarf Lake Whitefish. We
 discuss how chromosomal differentiation in the Lake Whitefish system may
 contribute to the destabilization of mitotic and meiotic chromosome
 segregation in hybrids, as documented previously. The chromosome
 structures detected here are still difficult to sequence and assemble,
 demonstrating the value of cytogenetics as a complementary approach to
 understand the genomic bases of speciation.
description: Macrogen_sequence_filesFile produced during the sequencing of the PCR products used for FISH of 5S and 28S rDNA. File names contain "5S" or "28S" depending on what product they refer to.C-BandCMA3GiemsaFISH_rDNAFISH_rDNA