cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qh3mm
title: Data from: Aberrant activation of the RANK signaling receptor induces murine salivary gland tumors

description: Unlike cancers of related exocrine tissues such as the mammary and
 prostate gland, diagnosis and treatment of aggressive salivary gland
 malignancies have not markedly advanced in decades. Effective clinical
 management of malignant salivary gland cancers is undercut by our limited
 knowledge concerning the key molecular signals that underpin the
 etiopathogenesis of this rare and heterogeneous head and neck cancer.
 Without knowledge of the critical signals that drive salivary gland
 tumorigenesis, tumor vulnerabilities cannot be exploited that allow for
 targeted molecular therapies. This knowledge insufficiency is further
 exacerbated by a paucity of preclinical mouse models (as compared to other
 cancer fields) with which to both study salivary gland pathobiology and
 test novel intervention strategies. Using a mouse transgenic approach, we
 demonstrate that deregulation of the Receptor Activator of NFkB Ligand
 (RANKL)/RANK signaling axis results in rapid tumor development in all
 three major salivary glands. In line with its established role in other
 exocrine gland cancers (i.e., breast cancer), the RANKL/RANK signaling
 axis elicits an aggressive salivary gland tumor phenotype both at the
 histologic and molecular level. Despite the ability of this cytokine
 signaling axis to drive advanced stage disease within a short latency
 period, early blockade of RANKL/RANK signaling markedly attenuates the
 development of malignant salivary gland neoplasms. Together, our findings
 have uncovered a tumorigenic role for RANKL/RANK in the salivary gland and
 suggest that targeting this pathway may represent a novel therapeutic
 intervention approach in the prevention and/or treatment of this
 understudied head and neck cancer.
description: 10.1371journal.pone.0128467 SUPPORT INFORMATIONZip file contains all raw data files organized by figure
DOI: 10.5061/dryad.7f4p9
title: Data from: Distributed acoustic cues for caller identity in macaque vocalization

description: Individual primates can be identified by the sound of their voice.
 Macaques have demonstrated an ability to discern conspecific identity from
 a harmonically structured ‘coo’ call. Voice recognition presumably
 requires the integrated perception of multiple acoustic features. However,
 it is unclear how this is achieved, given considerable variability across
 utterances. Specifically, the extent to which information about caller
 identity is distributed across multiple features remains elusive. We
 examined these issues by recording and analysing a large sample of calls
 from eight macaques. Single acoustic features, including fundamental
 frequency, duration and Weiner entropy, were informative but unreliable
 for the statistical classification of caller identity. A combination of
 multiple features, however, allowed for highly accurate caller
 identification. A regularized classifier that learned to identify callers
 from the modulation power spectrum of calls found that specific regions of
 spectral–temporal modulation were informative for caller identification.
 These ranges are related to acoustic features such as the call’s
 fundamental frequency and FM sweep direction. We further found that the
 low-frequency spectrotemporal modulation component contained an indexical
 cue of the caller body size. Thus, cues for caller identity are
 distributed across identifiable spectrotemporal components corresponding
 to laryngeal and supralaryngeal components of vocalizations, and the
 integration of those cues can enable highly reliable caller
 identification. Our results demonstrate a clear acoustic basis by which
 individual macaque vocalizations can be recognized.
description: macaque coo
 callsMacaque coo calls
 recorded from eight monkeys. The sub-folders named for each monkey's
 name (AL, BE, IO, MU, QU, SN, TH, TW). Each folder includes 468-1345 WAV
 files, each of which include one utterance of coo call.Fukushima2015.zip
DOI: 10.5061/dryad.t7b1b05
title: Data from: Phylogeny, evidence for a cryptic plastid, and distribution of Chytriodinium parasites (Dinophyceae) infecting copepods

description: Spores of the dinoflagellate Chytriodinium are known to infest copepod
 eggs causing their lethality. Despite the potential to control the
 population of such an ecologically important host, knowledge about
 Chytriodinium parasites is limited: we know little about phylogeny,
 parasitism, abundance, or geographical distribution. We carried out genome
 sequence surveys on four manually isolated sporocytes from the same
 sporangium to analyse the phylogenetic position of Chytriodinium based on
 SSU and concatenated SSU/LSU rRNA gene sequences, and also characterize
 two genes related to the plastidial heme pathway, hemL and hemY. The
 results suggest the presence of a cryptic plastid in Chytriodinium and a
 photosynthetic ancestral state of the parasitic Chytriodinium/Dissodinium
 clade. Finally, by mapping Tara Oceans V9 SSU amplicon data to the
 recovered SSU rRNA gene sequences from the sporocytes, we show that
 globally, Chytriodinium parasites are most abundant within the pico/nano-
 and mesoplankton of the surface ocean and almost absent within
 microplankton, a distribution indicating that they generally exist either
 as free-living spores or host-associated sporangia.
description: Chytriodinium_contigsContigs of Chytriodinium cf. affine in FASTA format. Contigs were generated using Ray assembler; contaminating sequences were removed as described in the publication.
DOI: 10.5061/dryad.23vc1
title: Data from: Long necks enhance and constrain foraging capacity in aquatic vertebrates

description: Highly specialized diving birds display substantial dichotomy in neck
 length with, for example, cormorants and anhingas having extreme necks,
 while penguins and auks have minimized necks. We attached acceleration
 loggers to Imperial cormorants Phalacrocorax atriceps and Magellanic
 penguins Spheniscus magellanicus, both foraging in waters over the
 Patagonian Shelf, to examine the difference in movement between their
 respective heads and bodies in an attempt to explain this dichotomy. The
 penguins had head and body attitudes and movements that broadly concurred
 throughout all phases of their dives. By contrast, although the cormorants
 followed this pattern during the descent and ascent phases of dives,
 during the bottom (foraging) phase of the dive, the head angle differed
 widely from that of the body and its dynamism (measured using vectorial
 dynamic acceleration) was over four times greater. A simple model
 indicated that having the head on an extended neck would allow these
 cormorants to half the energy expenditure that they would expend if their
 body moved in the way their heads did. This apparently energy-saving
 solution is likely to lead to greater heat loss though and would seem
 tenable in slow-swimming species because the loss of streamlining that it
 engenders would make it detrimental for fast-swimming taxa such as
 penguins.
description: Acceleration
 dataDepth, body and head
 acceleration data from 8 Magellanic penguins and 10 Imperial
 cormorantsData.zip
DOI: 10.5061/dryad.4nc28
title: Data from: Genomics of parallel experimental evolution in Drosophila

description: What are the genomic foundations of adaptation in sexual populations? We
 address this question using fitness-character and whole-genome sequence
 data from 30 Drosophila laboratory populations. These 30 populations are
 part of a nearly forty-year laboratory radiation featuring three selection
 regimes, each shared by ten populations for up to 837 generations, with
 moderately large effective population sizes. Each of three sets of ten
 populations that shared a selection regime consist of five populations
 that have long been maintained under that selection regime, paired with
 five populations that had only recently been subjected to that selection
 regime. We find a high degree of evolutionary parallelism in fitness
 phenotypes when most-recent selection regimes are shared, as in previous
 studies from our laboratory. We also find genomic parallelism with respect
 to the frequencies of single-nucleotide polymorphisms, transposable
 elements, insertions, and structural variants, which was expected.
 Entirely unexpected was a high degree of parallelism for linkage
 disequilibrium. The evolutionary genetic changes among these sexual
 populations are rapid and genomically extensive. This pattern may be due
 to segregating functional genetic variation that is abundantly maintained
 genome-wide by selection, variation that responds immediately to changes
 of selection regime.
description: Phenotypic
 dataData on mortality and
 fecundityPhenotypicData.txtSNP data filesData from single nucleotide polymorphism (SNP) analysisGraves-et-al-SNPS.zipTE data filesData from transposable element (TE) insertionGraves-et-al-TEs.zipSV data filesData from structural variant (SV) analysisGraves-et-al-SVs.zip
DOI: 10.5061/dryad.785bn
title: Data from: Constraints on the FST–heterozygosity outlier approach

description: The FST-heterozygosity outlier approach has been a popular method for
 identifying loci under balancing and positive selection since Beaumont and
 Nichols first proposed it in 1996 and recommended its use for studies
 sampling a large number of independent populations (at least 10). Since
 then, their program FDIST2 and a user-friendly program optimized for large
 datasets, LOSITAN, have been used widely in the population genetics
 literature, often without the requisite number of samples. We observed
 empirical datasets whose distributions could not be reconciled with the
 confidence intervals generated by the null coalescent island model. Here,
 we use forward-in-time simulations to investigate circumstances under
 which the FST-heterozygosity outlier approach performs poorly for
 next-generation single-nucleotide polymorphism (SNP) datasets. Our results
 show that samples involving few independent populations, particularly when
 migration rates are low, result in distributions of the FST-heterozygosity
 relationship that are not described by the null model implemented in
 LOSITAN. In addition, even under favorable conditions LOSITAN rarely
 provides confidence intervals that precisely fit SNP data, making the
 associated p-values only roughly valid at best. We present an alternative
 method, implemented in a new R package named fsthet, which uses the raw
 empirical data to generate smoothed outlier plots for the
 FST-heterozygosity relationship.
description: numerical_analysis_figs3-5These are the results from the numerical analysis when run to produce figures 3 through 5 in the manuscript.fdist2_outputThis zipped file contains the output from running fdist2 with a variety of starting parameter combinations. The parameter combinations are listed in the "parameters" file, which has index numbers that match the file names.numerical_analysis_randomsample_lositanThis zipped file contains the genepop output from the numerical analysis along with the loci (.loci) and confidence interval (.ci) files output from LOSITANnumerical_analysis_randomsampleThese are the results of the numerical analysis when run with random sampling to generate the genepop files for LOSITAN.code_availabilityThis document describes where to find the C++ code used in this paper.
DOI: 10.5061/dryad.vq744
title: Data from: Gut microbiota of dung beetles correspond to dietary specializations of adults and larvae

description: Vertebrate dung is central to the dung beetle life cycle, constituting
 food for adults and a protective and nutritive refuge for their offspring.
 Adult dung beetles have soft mandibles and feed primarily on nutritionally
 rich dung particles, while larvae have sclerotized mandibles and consume
 coarser dung particles with a higher C/N ratio. Here, using the dung
 beetles Euoniticellus intermedius and E. triangulatus, we show that these
 morphological adaptations in mandibular structure are also correlated with
 differences in basic gut structure and gut bacterial communities between
 dung beetle life stages. Metagenome functional predictions based on 16S
 rDNA characterization further indicated that larval gut communities are
 enriched in genes involved in cellulose degradation and nitrogen fixation
 compared to adult guts. Larval gut communities are more similar to female
 gut communities than they are to those of males, and bacteria present in
 maternally provisioned brood balls and maternal ‘gifts’ (secretions
 deposited in the brood ball along with the egg) are also more similar to
 larval gut communities than to those of males. Maternal secretions and
 maternally provisioned brood balls, as well as dung, were important
 factors shaping the larval gut community. Differences between gut
 microbiota in the adults and larvae are likely to contribute to
 differences in nutrient assimilation from ingested dung at different life
 history stages.
description: Euoniticellus_microbiome_datasetThis file contains quality trimmed, demultiplexed sequences without barcodes and primers (seqs.fna) produced from using default parameters in split_libraries_fastq.py script in QIIME 1.8.0; and a metadata mapping file (mapping.txt) for all the samples.Euoniticellus_dataset.zipOTU tableOTU table for bacterial communities of samples from Euoniticellus intermedius and Euoniticellus triangulatus, after quality checking and removal of OTUs with abundance less than 0.005%.otu_table.xls
DOI: 10.5061/dryad.37f9t
title: Data from: A map of local adaptation in Arabidopsis thaliana

description: Local adaptation is critical for species persistence in the face of rapid
 environmental change, but its genetic basis is not well understood. We
 identified candidate loci for local adaptation in the plant Arabidopsis
 thaliana from a genome-wide association study of lifetime fitness in
 geographically diverse accessions grown in field experiments in four sites
 across the species’ native range. Fitness-associated loci exhibited both
 geographic and climatic signatures of local adaptation. High-fitness
 alleles were generally distributed closer to the site where they increased
 fitness than genomic controls, occupying specific and distinct climate
 spaces. Independent loci with different molecular functions contributed
 most strongly to fitness variation in each site. Independent local
 adaptation by distinct genetic mechanisms may facilitate flexible
 evolutionary response to changing environment across a species range.
description: Fournier-Leveletal_SupplementaryDataS2SNP markers associated with fitness in multiple field conditionsFournier-Leveletal_SupplementaryDataS1List of accessions and Fitness phenotype in field conditions1209271S8.xlsx
DOI: 10.15468/dl.9ubny3
title: Occurrence Download

description: A dataset containing 1138 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tympanuchus pallidicinctus"
 ]
}

 The dataset includes 1138 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000413-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4n5929c
title: Data from: A quantitative proteomic analysis of cofilin phosphorylation in myeloid cells and its modulation using the LIM kinase inhibitor Pyr1

description: LIM kinases are located at a strategic crossroad, downstream of several
 signaling pathways and upstream of effectors such as microtubules and the
 actin cytoskeleton. Cofilin is the only LIM kinases substrate that is well
 described to date, and its phosphorylation on serine 3 by LIM kinases
 controls cofilin actin-severing activity. Consequently, LIM kinases
 inhibition leads to actin cytoskeleton disorganization and blockade of
 cell motility, which makes this strategy attractive in anticancer
 treatments. LIMK has also been reported to be involved in pathways that
 are deregulated in hematologic malignancies, with little information
 regarding cofilin phosphorylation status. We have used proteomic
 approaches to investigate quantitatively and in detail the phosphorylation
 status of cofilin in myeloid tumor cell lines of murine and human origin.
 Our results show that under standard conditions, only a small fraction (10
 to 30% depending on the cell line) of cofilin is phosphorylated (including
 serine 3 phosphorylation). In addition, after a pharmacological inhibition
 of LIM kinases, a residual cofilin phosphorylation is observed on serine
 3. Interestingly, this 2D gel based proteomic study identified new
 phosphorylation sites on cofilin, such as threonine 63, tyrosine 82 and
 serine 108.
description: MV4_11_Apair of 2D images (control + Pyr1-treated) of MV 4-11 cellsMV4_11_Bpair of 2D images (control + Pyr1-treated) of MV 4-11 cellsMV4_11_CMV4_11_DKasumi_AKasumi_BKasumi_CKasumi_Dpair of 2D images (control + Pyr1-treated) of Kasumi-1 cells32DWT_A32DWT_B32DWT_C32D_D814V_A32D_D814V_B32D_D814V_C
DOI: 10.5061/dryad.4b5n5
title: Data from: Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly

description: Disease epidemiology during ageing shows a transition from cancer to
 degenerative chronic disorders as dominant contributors to mortality in
 the old. Nevertheless, it has remained unclear to what extent molecular
 signatures of ageing reflect this phenomenon. Here we report on the
 identification of a conserved transcriptomic signature of ageing based on
 gene expression data from four vertebrate species across four tissues. We
 find that ageing-associated transcriptomic changes follow trajectories
 similar to the transcriptional alterations observed in degenerative ageing
 diseases but are in opposite direction to the transcriptomic alterations
 observed in cancer. We confirm the existence of a similar antagonism on
 the genomic level, where a majority of shared risk alleles that increase
 the risk of cancer decrease the risk of chronic degenerative disorders and
 vice versa. These results reveal a fundamental trade-off between cancer
 and degenerative ageing diseases that sheds light on the pronounced shift
 in their epidemiology during ageing.
description: Code and data for
 Aramillo Irizar et al. (2017)Source code and data for
 reproducing the analyses reported in the paper.Aramillo_Irizar_2017_Code_and_Data.zip
DOI: 10.5061/dryad.q2q84
title: Data from: Cattle sex-specific recombination and genetic control from a large pedigree analysis

description: Meiotic recombination is an essential biological process that generates
 genetic diversity and ensures proper segregation of chromosomes during
 meiosis. From a large USDA dairy cattle pedigree with over half million
 genotyped animals, we extracted 186,927 three-generation families,
 identified over 8.5 million maternal and paternal recombination events,
 and constructed sex-specific recombination maps for 59,309 autosomal SNPs.
 The recombination map spans for 25.5 Morgans in males and 23.2 Morgans in
 females, for a total studied region of 2,516 Mb (986 kb/cM in males and
 1,085 kb/cM in females). The male map is 10% longer than the female map
 and the sex difference is most pronounced in the subtelomeric regions. We
 identified 1,792 male and 1,885 female putative recombination hotspots,
 with 720 hotspots shared between sexes. These hotspots encompass 3% of the
 genome but account for 25% of the genome-wide recombination events in both
 sexes. Both males and females showed a decreasing trend in recombination
 rate during the past forty years that coincided with the artificial
 selection for milk production, with males exhibiting a more striking
 reduction. Sex-specific GWAS analyses identified PRDM9 and CPLX1 to have
 significant effects on genome-wide recombination rate in both sexes. Two
 novel loci, NEK9 and REC114, were associated with recombination rate in
 both sexes, whereas three loci, MSH4, SMC3 and CEP55, affected
 recombination rate in females only. Among the multiple PRDM9 paralogues on
 the bovine genome, our GWAS of recombination hotspot usage together with
 linkage analysis clearly identified the one on chromosome 1 to be the only
 PRDM9 paralogue affecting cattle recombination. Given the largest sample
 size ever reported for such studies, our results reveal new insights into
 the understanding of cattle and mammalian recombination.
description: Cattle Recombination
 MapMale and female
 recombination mapscattle_rmap.txtMale Crossover DataCrossover information for male meiosiscrossover_male.dataFemale Crossover DataCrossover data for female meiosiscrossover_female.data
DOI: 10.5061/dryad.ms768r4
title: Data from: Use of simulation-based statistical models to complement bioclimatic models in predicting continental scale invasion risks

description: Invasive species represent one of the greatest risks to global
 biodiversity and economic productivity of agroecosystems. The development
 of certain novel crops—e.g., herbaceous perennial biomass crops—may create
 a risk of novel invasions by these crops. Therefore, potential benefits
 and risks need to be weighed in making decisions about their introduction
 and subsequent management. Ideally, such a weighing will be based on good
 estimates of invasion risks in realistic scenarios pertaining to actual
 landscapes of concern regarding invasion. Most previous large-scale
 analyses of invasion risk have used species distribution models and their
 established methods. Unfortunately, these approaches are unable to
 incorporate local scale biotic and spatial factors that influence invasion
 risk. Here we present a case study for how such factors can be efficiently
 incorporated in large-scale analyses of invasion risk, by extending
 simulation models with statistical modeling tools. By these means, we
 predict invasion risk at the scale of the entire United States for a major
 biomass crop, Miscanthus × giganteus. We then combine invasion risk
 predictions for this method with those from bioclimatic methods, producing
 a map of aggregated invasion risk that can offer more nuanced predictions
 of invasion risk than either approach alone. Lastly, we evaluate potential
 risks for invasive crops that differ in invasiveness traits, to examine
 how geographic patterns of invasion risk vary among invaders as a result
 of their particular constellation of traits.
description: Large-scale_prediction_archiveThis compressed archive includes multiple other files including data files (in .rdata format) GIS shapefiles (in folders with the associated .shp, .shx, .dbf, and .prj files for each map) and an R script that will run all analyses and plot all figures. Specific descriptions of each file are supplied in the README.TXT file.