cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.620cq
title: Data from: Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits

description: Genome-wide association studies (GWAS) are a powerful method to dissect
 the genetic basis of traits, though in practice the effects of complex
 genetic architecture and population structure remain poorly understood. To
 compare mapping strategies we dissect the genetic control of flavonoid
 pigmentation traits in the cereal grass sorghum using high-resolution
 genotyping-by-sequencing (GBS) SNP markers. Studying the grain tannin
 trait, we find that General Linear Models (GLM) are not able to precisely
 map tan1-a, a known loss-of-function allele of the Tannin1 gene, with
 either a small panel (n = 142) or large association panel (n = 336), and
 that indirect associations limit the mapping of the Tannin1 locus to
 Mb-resolution. A GLM that accounts for population structure (Q) or
 standard Mixed Linear Model (MLM) that accounts for kinship (K) can
 identify tan1-a, while compressed MLMs performs worse than the naive GLM.
 Interestingly, a simple loss-of-function genome scan, for
 genotype-phenotype covariation only in the putative loss-of-function
 allele, is able to precisely identify the Tannin1 gene without considering
 relatedness. We also find that the tan1-a allele can be mapped with gene
 resolution in a biparental recombinant inbred line (RIL) family (n = 263)
 using GBS markers, but lower precision in the mapping of vegetative
 pigmentation traits suggest that consistent gene-level resolution will
 likely require larger families or multiple RILs. These findings highlight
 that complex association signals can emerge from even the simplest traits
 given epistasis and structured alleles, but that gene-resolution mapping
 of these traits is possible with high marker density and appropriate
 models.
description: stemBorer_data_nofilterSAP.filteredSNP.imp.all.hmpGenotyping-by-sequencing genotypes for the Sorghum Association Panel, imputed using TASSEL
DOI: 10.5061/dryad.7n10n
title: Data from: A genes eye view of ontogeny: De novo assembly and profiling of the Gryllus rubens transcriptome

description: Crickets (Orthoptera:Gryllidae) are widely used model organisms for
 developmental, evolutionary, neurobiological, and behavioral research.
 Here we developed a de novo transcriptome from pooled RNA-seq Illumina
 data spanning 7 stages in the life cycle of Gryllus rubens. Approximately
 705 Mbp of data was assembled and filtered to form 27,312 transcripts. We
 were able to annotate 52% of our transcripts using BLAST and assign at
 least one gene ontology term to 41%. Pooled samples from three different
 ontogenetic stages were used for transcriptomic profiling of the annotated
 transcriptome revealing patterns of differential gene expression that
 highlight processes in the different life stages. Embryonic and early
 instar development was enriched for ecdysteriod metabolism, cytochrome
 P450s, and glutathione production. Late instar development was enriched
 for regulation of gene expression and many of the genes highly expressed
 during this stage were involved in conserved developmental signaling
 pathways suggesting that these developmental pathways are active beyond
 embryonic development. Adults were enriched for fat transport (mostly
 relating to egg production) and production of octopamine, an important
 neurohormone. We also identified genes involved in conserved developmental
 pathways (Hedgehog, Hippo, Wnt, JAK/STAT, TGF-beta, Notch, and MEK/ERK).
 This is the first transcriptome spanning ontogeny in Gryllus rubens and a
 valuable resource for future work on development and evolution in
 Orthoptera.
description: Rubens_transcriptome_annotatedOutput of transcriptome annotation from Blast2Gofilter_transcriptspython script for filtering initial transcriptome assemblyFiltered transcriptomeThis transcriptome has been filtered to contain only contigs with FPKM value of 0.5 or greater and a minimum contig length of 600 bp. Additionly we retained only isoforms that accounted for 51% or more of the expression of a gene.tr2.fpkm0.5_l600_uniq.faUnfiltered transcriptomeraw trinity output without filtering.tr2.fastaRubens_RSEM_outputRSEM output for all pools.
DOI: 10.5061/dryad.ts3t7
title: Data from: On the occurrence of false positives in tests of migration under an isolation with migration model

description: The population genetic study of divergence is often carried out using a
 Bayesian genealogy sampler, like those implemented in ima2 and related
 programs, and these analyses frequently include a likelihood ratio test of
 the null hypothesis of no migration between populations. Cruickshank and
 Hahn (2014, Molecular Ecology, 23, 3133–3157) recently reported a high
 rate of false-positive test results with ima2 for data simulated with
 small numbers of loci under models with no migration and recent splitting
 times. We confirm these findings and discover that they are caused by a
 failure of the assumptions underlying likelihood ratio tests that arises
 when using marginal likelihoods for a subset of model parameters. We also
 show that for small data sets, with little divergence between samples from
 two populations, an excellent fit can often be found by a model with a low
 migration rate and recent splitting time and a model with a high migration
 rate and a deep splitting time.
description: Hey_etal_MolEcol_dryad
DOI: 10.5061/dryad.sm12c
title: Data from: Genetic basis for red coloration in birds

description: The yellow and red feather pigmentation of many bird species [1] plays
 pivotal roles in social signaling and mate choice [2, 3]. To produce red
 pigments, birds ingest yellow carotenoids and endogenously convert them
 into red ketocarotenoids via an oxidation reaction catalyzed by a
 previously unknown ketolase [4–6]. We investigated the genetic basis for
 red coloration in birds using whole-genome sequencing of red siskins
 (Spinus cucullata), common canaries (Serinus canaria), and ‘‘red factor’’
 canaries, which are the hybrid product of crossing red siskins with common
 canaries [7]. We identified two genomic regions introgressed from red
 siskins into red factor canaries that are required for red coloration. One
 of these regions contains a gene encoding a cytochrome P450 enzyme,
 CYP2J19. Transcriptome analysis demonstrates that CYP2J19 is significantly
 upregulated in the skin and liver of red factor canaries, strongly
 implicating CYP2J19 as the ketolase that mediates red coloration in birds.
 Interestingly, a second introgressed region required for red feathers
 resides within the epidermal differentiation complex, a cluster of genes
 involved in development of the integument. Lastly, we present evidence
 that CYP2J19 is involved in ketocarotenoid formation in the retina. The
 discovery of the carotenoid ketolase has important implications for
 understanding sensory function and signaling mediated by carotenoid
 pigmentation.
description: Individual SNP
 genotypesIndividual genotypes
 from 49 individuals from four breeds carrying the red factor (Lipochrome
 red, n = 35; Black red, n = 3; Portuguese Harlequin, n = 7; Agata red, n =
 4), and 15 individuals from three breeds of yellow canary (Lipochrome
 yellow, n = 4; Harz roller, n = 4; Gibber italicus, n = 3) and one wild
 population (n = 4). We used 114 SNPs located in three independent genomic
 regions identified as outliers using differentiation and introgression
 statistics.SNP Canary
 Genotypes.xlsxDe novo transcriptome
 assembly for (color) canariesDe novo assembly for
 each color phenotype transcriptome was performed. Here we provide a
 summary of assembly parameters and the two transcriptomes generated for
 the “Red” and “Yellow” individuals.De_novo_transcriptome_assembly.zip
DOI: 10.5061/dryad.d9v38
title: Data from: The functional diversity of retinal ganglion cells in the mouse

description: In the vertebrate visual system, all output of the retina is carried by
 retinal ganglion cells. Each type encodes distinct visual features in
 parallel for transmission to the brain. How many such ‘output channels’
 exist and what each encodes are areas of intense debate. In the mouse,
 anatomical estimates range from 15 to 20 channels, and only a handful are
 functionally understood. By combining two-photon calcium imaging to obtain
 dense retinal recordings and unsupervised clustering of the resulting
 sample of more than 11,000 cells, here we show that the mouse retina
 harbours substantially more than 30 functional output channels. These
 include all known and several new ganglion cell types, as verified by
 genetic and anatomical criteria. Therefore, information channels from the
 mouse eye to the mouse brain are considerably more diverse than shown thus
 far by anatomical studies, suggesting an encoding strategy resembling that
 used in state-of-the-art artificial vision systems.
description: Optical recordings of
 &gt;11,000 RGCsThe dataset contains
 recordings of 11,210 retinal ganglion cells from the mouse retina obtained
 by two-photon calcium imaging with the synthetic calcium indicator OGB-1
 to a standardized set of stimuli (see Baden et al. 2016 for details). In
 addition, the dataset contains morphological, genetic and
 immunohistochemical metadata, where available.BadenEtAl_RGCs_2016_v1.mat
DOI: 10.5061/dryad.0318j
title: Data from: Repurposed transcriptomic data facilitate discovery of innate immunity Toll-Like Receptor (TLR) genes across Lophotrochozoa

description: The growing volume of genomic data from across life represents
 opportunities for deriving valuable biological information from data that
 were initially collected for another purpose. Here, we use transcriptomes
 collected for phylogenomic studies to search for toll-like receptor (TLR)
 genes in poorly sampled lophotrochozoan clades (Annelida, Mollusca,
 Brachiopoda, Phoronida, and Entoprocta) and one ecdysozoan clade
 (Priapulida). TLR genes are involved in innate immunity across animals by
 recognizing potential microbial infection. They have an extracellular
 leucine-rich repeat (LRR) domain connected to a transmembrane domain and
 an intracellular toll/interleukin-1 receptor (TIR) domain. Consequently,
 these genes are important in initiating a signaling pathway to trigger
 defense. We found at least one TLR ortholog in all but two taxa examined,
 suggesting that a broad array of lophotrochozoans may have innate immune
 systems similar to those observed in vertebrates and arthropods.
 Comparison to the SMART database confirmed the presence of both the LRR
 and the TIR protein motifs characteristic of TLR genes. Because we looked
 at only one transcriptome per species, discovery of TLR genes was limited
 for most taxa. However, several TRL-like genes that vary in the number and
 placement of LRR domains were found in phoronids. Additionally, several
 contigs contained LRR domains but lacked TIR domains, suggesting they were
 not TLRs. Many of these LRR-containing contigs had other domains (e.g.,
 immunoglobin) and are likely involved in innate immunity.
description: Transcriptome
 assemblies, TLR/LRR nucleotide sequences, and TLR/LRR amino acid
 sequencesData files for:
 Halanych, K.M. and Kocot, K.M. 2014. Data from: Repurposed Transcriptomic
 Data Facilitate Discovery of Innate Immunity Toll-Like Receptor (TLR)
 Genes Across Lophotrochozoa. See README file for detailed
 description.TLR_files.zip
DOI: 10.5061/dryad.3hk99
title: Data from: Is telomere length a molecular marker of past thermal stress in wild fish?

description: Telomeres protect eukaryotic chromosomes; variation in telomere length has
 been linked (primarily in homoeothermic animals) to variation in stress,
 cellular ageing and disease risk. Moreover, telomeres have been suggested
 to function as biomarker for quantifying past environmental stress, but
 studies in wild animals remain rare. Environmental stress, such as extreme
 environmental temperatures in poikilothermic animals, may result in
 oxidative stress that accelerates telomere attrition. However, growth,
 which may depend on temperature, can also contribute to telomere
 attrition. To test for associations between multitissue telomere length
 and past water temperature while accounting for the previous individual
 growth, we used quantitative PCR to analyse samples from 112
 young-of-the-year brown trout from 10 natural rivers with average water
 temperature differences of up to 6°C (and an absolute maximum of 23°C). We
 found negative associations between relative telomere length (RTL) and
 both average river temperature and individual body size. We found no
 indication of RTL–temperature association differences among six tissues,
 but we did find indications for differences among the tissues for
 associations between RTL and body size; size trends, albeit nonsignificant
 in their differences, were strongest in muscle and weakest in fin.
 Although causal relationships among temperature, growth, oxidative stress,
 and cross-sectional telomere length remain largely unknown, our results
 indicate that telomere-length variation in a poikilothermic wild animal is
 associated with both past temperature and growth.
description: Dye-normalised
 fluorescence qPCR dataDye-normalised
 fluorescence qPCR dataDye.Norm.Fluorescence.Data.txtWater.Temperature.DataAverage daily water temperature between 2014-05-31 and 2014-09-22 for 10 Estonian RiversqPCR.Cq.Tm.DataAnalysed qPCR data (yielding Cq and Tm) with sample informationSample.Info.DataLength data for 112 brown trout individuals from 10 Estonian rivers
DOI: 10.5061/dryad.sp70n
title: Data from: Octopaminergic modulation of the visual flight speed regulator of Drosophila

description: Recent evidence suggests that flies' sensitivity to large-field optic
 flow is increased by the release of octopamine during flight. This
 increase in gain presumably enhances visually mediated behaviors such as
 the active regulation of forward speed, a process that involves the
 comparison of a vision-based estimate of velocity with an internal set
 point. To determine where in the neural circuit this comparison is made,
 we selectively silenced the octopamine neurons in the fruit fly
 Drosophila, and examined the effect on vision-based velocity regulation in
 free-flying flies. We found that flies with inactivated octopamine neurons
 accelerated more slowly in response to visual motion than control flies,
 but maintained nearly the same baseline flight speed. Our results are
 parsimonious with a circuit architecture in which the internal control
 signal is injected into the visual motion pathway upstream of the
 interneuron network that estimates groundspeed.
description: vanBreugel_Suver_Dickinson_JEB_2014_Octopamine_AccelerationThis dataset, a text file, contains all of the trajectories used in the following paper: van Breugel, F; Suver, M; and Dickinson, M (2014). Octopaminergic modulation of the visual flight speed regulator of Drosophila. J Exp Biol 217, 1-8. Each row describes one frame of data, trajectories can be parsed by selecting rows with the same object id number (the first column). The column values are described in the second line of the data file. The data was collected using an automated 10-camera 3D tracking system, and smoothed with a constant velocity kalman smoother. See the Methods section of the paper for more details.
DOI: 10.5061/dryad.8n8v3
title: Data from: A three-dimensional computer simulation of feeding behaviour in red and giant pandas relates skull biomechanics with dietary niche partitioning

description: The red (Ailurus fulgens) and giant (Ailuropoda melanoleuca) pandas are
 mammalian carnivores convergently adapted to a bamboo feeding diet.
 However, whereas Ailurus forage almost entirely on younger leaves, fruits
 and tender trunks, Ailuropoda rely more on trunks and stems. Such a
 difference in foraging mode is considered as strategy for resource
 partitioning where they are sympatric. Here we use FEA to test for
 mechanical differences and similarities in skull performance between
 Ailurus and Ailuropoda related to diet. Feeding simulations suggest that
 the two panda species have similar ranges of mechanical advantage and
 strain energy profiles across the dentition, which reflects their
 durophagous diet. However, the stress distributions and peaks in the
 skulls of Ailurus and Ailuropoda are remarkably different for biting at
 all tooth locations. Although the skull of Ailuropoda is capable of
 resisting higher stresses than the skull of Ailurus, the latter is able to
 distribute stresses more evenly through the skull. These differences in
 skull biomechanics reflect their distinct bamboo feeding preference as
 Ailurus use repetitive chewing in an extended mastication to feed on soft
 leaves and Ailuropoda exhibit more punctual periods of chomp-and-swallow
 feeding to break the hard bamboo trunks.
description: Panda_FEA_models_BioLettThree-dimensional models for FE analysis of the Ailurus and Ailuropoda skulls. Open .st7 files with Strand7 software.
DOI: 10.5061/dryad.7cp50
title: Data from: Ecology of sleeping: the microbial and arthropod associates of chimpanzee beds

description: The indoor environment created by the construction of homes and other
 buildings is often considered to be uniquely different from other
 environments. It is composed of organisms that are less diverse than those
 of the outdoors and strongly sourced by, or dependent upon, human bodies.
 Yet, no one has ever compared the composition of species found in
 contemporary human homes to that of other structures built by mammals,
 including those of non-human primates. Here we consider the microbes and
 arthropods found in chimpanzee beds, relative to the surrounding
 environment (n = 41 and 15 beds, respectively). Based on the study of
 human homes, we hypothesized that the microbes found in chimpanzee beds
 would be less diverse than those on nearby branches and leaves and that
 their beds would be primarily composed of body-associated organisms.
 However, we found that differences between wet and dry seasons and
 elevation above sea level explained nearly all of the observed variation
 in microbial diversity and community structure. While we can identify the
 presence of a chimpanzee based on the assemblage of bacteria, the dominant
 signal is that of environmental microbes. We found just four ectoparasitic
 arthropod specimens, none of which appears to be specialized on
 chimpanzees or their structures. These results suggest that the life to
 which chimpanzees are exposed while in their beds is predominately the
 same as that of the surrounding environment.
description: SleepEcology_MappingFileData mapping file.SleepEcology_seqs.fastqRaw data file. Microbes were collected in relation to 41 chimpanzee beds located in the Issa Valley, western Tanzania, between August 2013 and April 2014. All samples were collected with dual-tipped sterile BBL Culture Swabs, and DNA was subsequently extracted with a MO BIO PowerSoil DNA Isolation Kit. Extracted DNA was sequenced on the Illumina MiSeq platform, targeting the V1-V2 region of the 16S rRNA gene.SleepEcology_OTU_rar_V2Rarefied dataset used in analyses. Sequences were rarefied to 5600 reads per sample.SleepEcology_CodeWorkflow used to process raw data files in the UPARSE pipeline and analyze sequencing output within the R environment.
DOI: 10.5061/dryad.8qp4n
title: Data from: Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas

description: For the last 500 years, the Americas have been a melting pot both for
 genetically diverse humans and for the pathogenic and commensal organisms
 associated with them. One such organism is the stomach-dwelling bacterium
 Helicobacter pylori, which is highly prevalent in Latin America where it
 is a major current public health challenge because of its strong
 association with gastric cancer. By analyzing the genome sequence of H.
 pylori isolated in North, Central and South America, we found evidence for
 admixture between H. pylori of European and African origin throughout the
 Americas, without substantial input from pre-Columbian (hspAmerind)
 bacteria. In the US, strains of African and European origin have remained
 genetically distinct, while in Colombia and Nicaragua, bottlenecks and
 rampant genetic exchange amongst isolates have led to the formation of
 national gene pools. We found three outer membrane proteins with atypical
 levels of Asian ancestry in American strains, as well as alleles that were
 nearly fixed specifically in South American isolates, suggesting a role
 for the ethnic makeup of hosts in the colonization of incoming strains.
 Our results show that new H. pylori subpopulations can rapidly arise,
 spread and adapt during times of demographic flux, and suggest that
 differences in transmission ecology between high and low prevalence areas
 may substantially affect the composition of bacterial populations.
description: BIGSdb gene-by-gene
 alignment, fasta formatThis is a fasta format
 gene-by-gene alignment of all the genomes included in the study to all
 loci in the H. pylori reference genome 26695. The loci are subsequently
 concatenated into one entry per genome.BIGSdb_gene-by-gene_alignment.fasta.gzBIGSdb gene-by-gene alignment, xmfa formatThis is an extended fasta (xmfa) format gene-by-gene alignment of all the genomes included in the study to all loci in the H. pylori reference genome 26695.BIGSdb_gene-by-gene_alignment.xmfa.gzGzipped tar archive of contig filesThis tarball contains all 402 draft- and complete genomes compared within this study.contigs.tar.gz
DOI: 10.5061/dryad.1642b
title: Data from: Online spatial normalization for real-time fMRI

description: Real-time functional magnetic resonance imaging (rtfMRI) is a recently
 emerged technique that demands fast data processing within a single
 repetition time (TR), such as a TR of 2 seconds. Data preprocessing in
 rtfMRI has rarely involved spatial normalization, which can not be
 accomplished in a short time period. However, spatial normalization may be
 critical for accurate functional localization in a stereotactic space and
 is an essential procedure for some emerging applications of rtfMRI. In
 this study, we introduced an online spatial normalization method that
 adopts a novel affine registration (AFR) procedure based on principal axes
 registration (PA) and Gauss-Newton optimization (GN) using the
 self-adaptive β parameter, termed PA-GN(β) AFR and nonlinear registration
 (NLR) based on discrete cosine transform (DCT). In AFR, PA provides an
 appropriate initial estimate of GN to induce the rapid convergence of GN.
 In addition, the β parameter, which relies on the change rate of cost
 function, is employed to self-adaptively adjust the iteration step of GN.
 The accuracy and performance of PA-GN(β) AFR were confirmed using both
 simulation and real data and compared with the traditional AFR. The
 appropriate cutoff frequency of the DCT basis function in NLR was
 determined to balance the accuracy and calculation load of the online
 spatial normalization. Finally, the validity of the online spatial
 normalization method was further demonstrated by brain activation in the
 rtfMRI data.
description: fMRI_Data_From_A_Finger_Tapping_Run_Subject_01-20The data were acquired from a finger tapping run in an rtfMRI experiment, which consisted of eight on-going runs. Twenty volunteers (age 22.3 ± 1.6, 8 females) participated in the experiment, which was approved by the Institutional Review Board (IRB) of the State Key Laboratory of Cognitive Neuroscience and Learning in Beijing Normal University; all of the subjects signed informed consent prior to scanning. The run, which lasted 4.5 min, consisted of five rest blocks and four task blocks, of which each block lasted 30 s. During the rest blocks, a text cue “REST” was shown in the center of the screen and the subjects were instructed to take a rest. In the task blocks, a text cue “PUSH” was shown, and the subjects were instructed to tap their right-hand fingers.
DOI: 10.5281/zenodo.18380363
title: Characterization, ultrafiltration, depolymerization and gel formulation of ulvans extracted via a novel ultrasound-enzyme assisted method