cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k14bq
title: Data from: Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives.

description: • The development of modern crops typically involves both selection and
 hybridization, but to date most studies have focused on the former. In the
 present study we explore how both processes, and their interactions, have
 molded the genome of the cultivated sunflower, a globally important
 oilseed. • To identify genes targeted by selection during the
 domestication and improvement of sunflower, and to detect
 post-domestication hybridization with wild species, we analyzed
 transcriptome sequences of 80 genotypes, including wild, landrace, and
 modern lines of Helianthus annuus, as well as two cross-compatible wild
 relatives, H. argophyllus and H. petiolaris. • Outlier analyses identified
 122 and 15 candidate genes associated with domestication and improvement,
 respectively. As in several previous studies, genes putatively involved in
 oil biosynthesis were the most extreme outliers. Additionally, several
 promising associations were observed with previously mapped QTLs, such as
 branching. Admixture analyses revealed that all of the modern cultivar
 genomes we examined contained one or more introgressions from wild
 populations, with every chromosome having evidence of introgression in at
 least one modern line. • Cumulatively, introgressions cover approximately
 10% of the cultivated sunflower genome. Surprisingly, introgressions do
 not avoid candidate domestication genes likely because of the
 re-introduction of branching.
description: TranscriptomeRef_mar30.TO.HA412.v0.2.cabog.20111122.RHA280xRHA801.gMap2.sortAlignment of manuscript reference transcriptome sequence to reference genome with genetic map positions. bwa mem -t 6 -a -M \ HA412.v0.2.cabog.20111122.RHA280xRHA801.g Map2.fasta \ TranscriptomeRef_mar30.fa \ | samtools view -Sub - \ | samtools sort -@ 2 -m 2G -l 9 - \ TranscriptomeRef_mar30.TO.HA412.v0.2.cabog.20111122. RHA280xRHA801.gMap2.sortTranscriptomeRef_mar30.TO.HA412.v0.2.cabog.20111122.RHA280xRHA801.gMap2.scaffolds.fastaHA412 v0.2 scaffolds matching manuscript reference transcriptome. samtools view \ TranscriptomeRef_mar30.TO.HA412.v0.2.cabog.20111122.RHA280xRHA801.gMap2.sort.bam \ | cut -f 3 \ | sort \ | uniq \ &gt;TranscriptomeRef_mar30.TO.HA412.v0.2.cabog.20111122.RHA280xRHA801.gMap2.scaffolds.list grepFasta \ TranscriptomeRef_mar30.TO.HA412.v0.2.cabog.20111122.RHA280xRHA801.gMap2.scaffolds.list \ &lt; HA412.v0.2.cabog.20111122.RHA280xRHA801.gMap2.fasta \ &gt;TranscriptomeRef_mar30.TO.HA412.v0.2.cabog.20111122.RHA280xRHA801.gMap2.scaffolds.fasta
DOI: 10.5061/dryad.bc1gb
title: Data from: Eco-energetic consequences of evolutionary shifts in body size (after integrating the Corrigendum)

description: Size imposes physiological and ecological constraints upon all organisms.
 Theory abounds on how energy flux covaries with body size, yet causal
 links are often elusive. As a more direct way to assess the role of size,
 we used artificial selection to evolve the phytoplankton species
 Dunaliella tertiolecta towards smaller and larger body sizes. Within 100
 generations (c. 1 year), we generated a fourfold difference in cell volume
 among selected lineages. Large-selected populations produced four times
 the energy than small-selected populations of equivalent total biovolume,
 but at the cost of much higher volume-specific respiration. These
 differences in energy utilisation between large (more productive) and
 small (more energy-efficient) individuals were used to successfully
 predict ecological performance (r and K) across novel resource regimes. We
 show that body size determines the performance of a species by mediating
 its net energy flux, with worrying implications for current trends in size
 reduction and for global carbon cycles.
description: Data and codes in R for
 all figures in Malerba et al. 2017 Ecology LettersInstructions - The main
 file is called "Main script.R". Open it with statistical
 software R. Within the script file: (1) check that all packages are
 installed in the computer (otherwise install before running the script),
 and (2) set the directory where the "Main script.R" file is in
 the computer. After having done that, everything else should work by
 simply running the file in R. The script will read all data, calculate the
 statistics, plot the images, and save the images in the same folder where
 the Main script file is. The file is designed to run in Mac computers.
 Also added in the folder are the final version of all figures after layout
 melioration using Adobe Illustrator and an example of the microscopy
 photos for the lineages (taken in date 11 Sep 2017).Data and codes for Malerba et
 al 2017 Ecology Letters.zip
description: This dataset integrate the Corrigendum published along the
 article.
DOI: 10.5061/dryad.50dc6
title: Data from: A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages

description: Sponges can be dominant organisms in many marine and freshwater habitats
 where they play essential ecological roles. They also represent a key
 group to address important questions in early metazoan evolution. Recent
 approaches for improving knowledge on sponge biological and ecological
 functions as well as on animal evolution have focused on the genetic
 toolkits involved in ecological responses to environmental changes (biotic
 and abiotic), development and reproduction. These approaches are possible
 thanks to newly available, massive sequencing technologies–such as the
 Illumina platform, which facilitate genome and transcriptome sequencing in
 a cost-effective manner. Here we present the first NGS (next-generation
 sequencing) approach to understanding the life cycle of an encrusting
 marine sponge. For this we sequenced libraries of three different life
 cycle stages of the Mediterranean sponge Crella elegans and generated de
 novo transcriptome assemblies. Three assemblies were based on sponge
 tissue of a particular life cycle stage, including non-reproductive
 tissue, tissue with sperm cysts and tissue with larvae. The fourth
 assembly pooled the data from all three stages. By aggregating data from
 all the different life cycle stages we obtained a higher total number of
 contigs, contigs with blast hit and annotated contigs than from one
 stage-based assemblies. In that multi-stage assembly we obtained a larger
 number of the developmental regulatory genes known for metazoans than in
 any other assembly. We also advance the differential expression of
 selected genes in the three life cycle stages to explore the potential of
 RNA-seq for improving knowledge on functional processes along the sponge
 life cycle.
description: Non-reproductive stage
 of Crella elegansIndividual collected by
 SCUBA on March'10 and fixed in RNAlater. Assembled with CLC Genomics
 Workbench 4.6.1 (CLC bio, Aarhus, Denmark).C3_MAR10_non-reproductive.fastaIndividual of Crella elegans with spermatic cystsIndividual collected by SCUBA on April'10 and fixed in RNAlater. Assembled with CLC Genomics Workbench 4.6.1 (CLC bio, Aarhus, Denmark).C4_APR10_spermatic_cysts.fastaIndividual of Crella elegans with larvae in its tissueIndividual collected by SCUBA on October'09 and fixed in RNAlater. Assembled with CLC Genomics Workbench 4.6.1 (CLC bio, Aarhus, Denmark).C1_OCT09_larvae.fastaReference transcriptome obtained by pooling reads from three different life stages of Crella elegans (individual with larvae, individual with spematic cysts and non-reproductive individual)Individuals collected by SCUBA on October'09, March'10 and April'10 and fixed in RNAlater. Each sample was sequenced independently and afterwards reads from all three samples were pooled together and assembled with CLC Genomics Workbench 4.6.1 (CLC bio, Aarhus, Denmark).Reference_transcriptome.fasta
DOI: 10.5061/dryad.2gg2f50
title: Data from: Electrolytic ablation enables cancer cell targeting through pH modulation

description: Minimally invasive ablation strategies enable locoregional treatment of
 tumors. Electrolytic ablation functions through the local delivery of
 direct current, without thermal effects, facilitating enhanced precision.
 However, the clinical application of electrolytic ablation is limited by
 an incompletely characterized mechanism of action. Here we show that acid
 and base production at the electrodes precipitates local pH changes
 causing the rapid cell death that underlies macroscopic tumor necrosis at
 pH &gt; 10.6 or &lt; 4.8. The extent of cell death can be
 modulated by altering the local buffering capacity and antioxidant
 availability. These data demonstrate that electrolytic ablation is
 distinguished from other ablation strategies via its ability to induce
 cellular necrosis by directly altering the tumor microenvironment. These
 findings may enable further development of electrolytic ablation as a
 curative therapy for primary, early stage tumors.
description: All data and code for
 analysis of presented dataThis folder provides all
 data presented and analyzed within the manuscript. This includes R and
 Matlab scripts used to analyze the data and prepare the
 figures.Perkons_NCB_DRYAD.zip
DOI: 10.5061/dryad.11b20
title: Data from: A genome-wide association study identifies a region strongly associated with symmetrical onychomadesis on chromosome 12 in dogs

description: Symmetrical onychomadesis causes periodic loss of claws in otherwise
 healthy dogs. Genome-wide association analysis in 225 Gordon Setters
 identified a single region associated with symmetrical onychomadesis on
 chromosome 12 (spanning about 3.3 mb). A meta-analysis including also
 English Setters indicated that this genomic region predisposes for
 symmetrical onychomadesis in English Setters as well. The associated
 region spans most of the major histocompatibility complex and nearly 1 Mb
 downstream. Like many other autoimmune diseases, associations of
 symmetrical onychomadesis with DLA class II alleles have been reported. In
 this study, no associated markers were revealed within any of the
 DLA-DRB1, -DQA1 or -DQB1 genes, and the odds for symmetrical onychomadesis
 in the Gordon Setters were much higher, carrying significant single
 nucleotide polymorphisms compared to the odds of any of the recorded
 DLA-DRB1/DQA1/DQB1 haplotypes. We noticed that some of the associated DLA
 haplotypes were different between the English Setters and the Gordon
 Setters. Interestingly, associated SNP chip markers showed a more
 consistent pattern of allelic variants related to cases or controls
 regardless of breed. In conclusion, the associated genetic markers
 identified in this study hold the potential to aid in selection of
 breeding animals to reduce the frequency of symmetrical onychomadesis in
 the dog.
description: Dog_PhenotypesFor each Gordon setter and English setter; information on symmetrical onychomadesis disease status, gender, nationality and DLA class II haplotypes is given.Dogs .ped fileThe nucleotide variant is given at each marker on the 170K CanineHD BeadChip (Illumina), for each Gordon setter and English setter.Dogs.pedDogs .map fileSingel nucleotide polymorphism locations are given according to the Canfam 3.1assembly.Dogs.map
DOI: 10.5061/dryad.k2v2006
title: Data from: Studying the microbiota of bats: accuracy of direct and indirect samplings

description: Given the recurrent bat-associated disease outbreaks in humans and recent
 advances in metagenomics sequencing, the microbiota of bats is
 increasingly being studied. However, obtaining biological samples directly
 from wild individuals may represent a challenge and thus, indirect passive
 sampling (without capturing bats) is sometimes used as an alternative.
 Currently, it is not known whether the bacterial community assessed using
 this approach provides an accurate representation of the bat microbiota.
 This study was designed to compare the use of direct sampling (based on
 bat capture and handling) and indirect sampling (collection of bat’s
 excretions under bat colonies) in assessing bacterial communities in bats.
 Using high-throughput 16S rRNA sequencing of urine and faeces samples from
 Rousettus aegyptiacus, a cave-dwelling fruit bat species, we found
 evidence of niche specialization among different excreta samples,
 independent of the sampling approach. However, sampling approach
 influenced both the alpha-and beta-diversity of urinary and faecal
 microbiotas. In particular, increased alpha-diversity and more overlapping
 composition between urine and faeces samples was seen when direct sampling
 was used, suggesting that cross-contamination may occur when collecting
 samples directly from bats in hand. In contrast, results from indirect
 sampling in the cave may be biased by environmental contamination. Our
 methodological comparison suggested some influence of the sampling
 approach on the bat-associated microbiota, but both approaches were able
 to capture differences among excreta samples. Assessment of these
 techniques opens an avenue to use more indirect sampling, in order to
 explore microbial community dynamics in bats.
description: Dietrich_Rousettus_FastqFilesDietrich_Rousettus_Metadata_TableS2Dietrich_Rousettus_Metadata_TableS1_FigureS1
DOI: 10.5061/dryad.r0q02
title: Data from: Squamate Conserved Loci (SqCL): a unified set of conserved loci for phylogenomics and population genetics of squamate reptiles

description: The identification of conserved loci across genomes, along with advances
 in target capture methods and high-throughput sequencing, has helped spur
 a phylogenomics revolution by enabling researchers to gather large numbers
 of homologous loci across clades of interest with minimal upfront
 investment in locus design. Target capture for vertebrate animals is
 currently dominated by two approaches – anchored hybrid enrichment (AHE)
 and ultraconserved elements (UCE) – and both approaches have proven useful
 for addressing questions in phylogenomics, phylogeography, and population
 genomics. However, these two sets of loci have minimal overlap with each
 other; moreover, they do not include many traditional loci that that have
 been used for phylogenetics. Here, we combine across UCE, AHE, and
 traditional phylogenetic gene locus sets to generate the Squamate
 Conserved Loci (SqCL) set, a single integrated probe set that can generate
 high-quality and highly complete data across all three loci types. We use
 these probes to generate data for 44 phylogenetically-disparate taxa that
 collectively span approximately 33% of terrestrial vertebrate diversity.
 Our results generated an average of 4.29 Mb across 4709 loci per
 individual, of which an average of 2.99 Mb was sequenced to high enough
 coverage (≥10×) to use for population genetic analyses. We validate the
 utility of these loci for both phylogenomic and population genomic
 questions, provide a comparison among these locus sets of their relative
 usefulness, and suggest areas for future improvement.
description: pseudo-reference genomes
 for species included in studypseudo-reference genomes
 for the 44 species included in this study and one outgroup; each file is
 annotated with respect to our targetsPRG.zipVCF for Colobosaura modestavariant data for Colobosaura modesta, including variant and invariant sites; filtered for coverage &gt;=10x and quality &gt;=20 and phased using read-backed phasingColobosaura_modesta.qual_filtered.cov_filtered.phased.vcf.gzVCF for Bothrops moojenivariant data for Bothrops moojeni, including variant and invariant sites; filtered for coverage &gt;=10x and quality &gt;=20 and phased using read-backed phasingBothrops_moojeni.qual_filtered.cov_filtered.phased.vcf.gz
DOI: 10.5061/dryad.s5b40
title: Data from: Comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage

description: Characterization and population genetic analysis of multilocus genes, such
 as those found in the major histocompatibility complex (MHC) is
 challenging in nonmodel vertebrates. The traditional method of extensive
 cloning and Sanger sequencing is costly and time-intensive and indirect
 methods of assessment often underestimate total variation. Here, we
 explored the suitability of 454 pyrosequencing for characterizing
 multilocus genes for use in population genetic studies. We compared two
 sample tagging protocols and two bioinformatic procedures for 454
 sequencing through characterization of a 185-bp fragment of MHC DRB exon 2
 in wolverines (Gulo gulo) and further compared the results with those from
 cloning and Sanger sequencing. We found 10 putative DRB alleles in the 88
 individuals screened with between two and four alleles per individual,
 suggesting amplification of a duplicated DRB gene. In addition to the
 putative alleles, all individuals possessed an easily identifiable
 pseudogene. In our system, sequence variants with a frequency below 6% in
 an individual sample were usually artefacts. However, we found that sample
 preparation and data processing procedures can greatly affect variant
 frequencies in addition to the complexity of the multilocus system.
 Therefore, we recommend determining a per-amplicon-variant frequency
 threshold for each unique system. The extremely deep coverage obtained in
 our study (approximately 5000×) coupled with the semi-quantitative nature
 of pyrosequencing enabled us to assign all putative alleles to the two DRB
 loci, which is generally not possible using traditional methods. Our
 method of obtaining locus-specific MHC genotypes will enhance population
 genetic analyses and studies on disease susceptibility in nonmodel
 wildlife species.
description: Reads from run 163 of
 Gulo gulo MHC DRB exon 2 fragmentReads from run 245 of
 Gulo gulo MHC DRB exon 2 fragmentReads from run 329-1 of
 Gulo gulo MHC DRB exon 2 fragmentReads from run 329-2 of
 Gulo gulo MHC DRB exon 2 fragmentReads from run 329-3 of
 Gulo gulo MHC DRB exon 2 fragmentReads from run 329-4 of
 Gulo gulo MHC DRB exon 2 fragmentReads from run Trent-1
 of Gulo gulo MHC DRB exon 2 fragmentList of individuals and
 MID tags for Gulo gulo MHC DRB exon 2 sequencing reads
DOI: 10.5061/dryad.nj16d88
title: Data from: Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex

description: Incomplete or geographically biased sampling poses significant problems
 for research in phylogeography, population genetics, phylogenetics, and
 species delimitation. Despite the power of using genome-wide genetic
 markers in systematics and related fields, approaches such as the
 multispecies coalescent remain unable to easily account for unsampled
 lineages. The Empidonax difficilis / E. occidentalis complex of small
 tyrannid flycatchers (Aves: Tyrannidae) is a classic example of
 widely-distributed species with limited phenotypic geographic variation
 that was broken into two largely cryptic (or “sibling”) lineages following
 extensive study. Though the group is well-characterized north of the U.S.
 Mexico border, the evolutionary distinctiveness and phylogenetic
 relationships of southern populations remain obscure. In this paper, we
 use dense genomic and geographic sampling across the majority of the range
 of the E. difficilis / E . occidentalis complex to assess whether current
 taxonomy and species limits reflect underlying evolutionary patterns, or
 whether they are an artifact of historically biased or incomplete
 sampling. We find that additional samples from Mexico render the widely
 recognized species-level lineage E. occidentalis paraphyletic, though it
 retains support in the best-fit species delimitation model from clustering
 analyses. We further identify a highly divergent unrecognized lineage in a
 previously unsampled portion of the group’s range, which a cline analysis
 suggests is more reproductively isolated than the currently recognized
 species E. difficilis and E. occidentalis. Our phylogeny supports a
 southern origin of these taxa. Our results highlight the pervasive impacts
 of biased geographic sampling, even in well-studied vertebrate groups like
 birds, and illustrate what is a common problem when attempting to define
 species in the face of recent divergence and reticulate evolution.
description: ND2_alignmentNexus file for NADH dehydrogenase subunit 2 (ND2) sequence alignmentrad_loci_50puce_loci_50pS1Table S1: specimen and sampling dataS2Table S2: HZAR confidence intervalssupplemental_figuresSupplemental figures S1-S5
DOI: 10.5061/dryad.k30sg
title: Data from: The Shortlist Method for fast computation of the Earth Mover's Distance and finding optimal solutions to transportation problems

description: Finding solutions to the classical transportation problem is of great
 importance, since this optimization problem arises in many engineering and
 computer science applications. Especially the Earth Mover's Distance
 is used in a plethora of applications ranging from content-based image
 retrieval, shape matching, fingerprint recognition, object tracking and
 phishing web page detection to computing color differences in linguistics
 and biology. Our starting point is the well-known revised simplex
 algorithm, which iteratively improves a feasible solution to optimality.
 The Shortlist Method that we propose substantially reduces the number of
 candidates inspected for improving the solution, while at the same time
 balancing the number of pivots required. Tests on simulated benchmarks
 demonstrate a considerable reduction in computation time for the new
 method as compared to the usual revised simplex algorithm implemented with
 state-of-the-art initialization and pivot strategies. As a consequence,
 the Shortlist Method facilitates the computation of large scale
 transportation problems in viable time. In addition we describe a novel
 method for finding an initial feasible solution which we coin Modified
 Russell's Method.
description: TransportBenchmarkThis benchmark contains 8600 images for comparing methods to solve transportation problems and to compute the Earth Mover's Distance (EMD).