cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fs756
title: Data from: Viruses are a dominant driver of protein adaptation in mammals

description: Viruses interact with hundreds to thousands of proteins in mammals, yet
 adaptation against viruses has only been studied in a few proteins
 specialized in antiviral defense. Whether adaptation to viruses typically
 involves only specialized antiviral proteins or affects a broad array of
 virus-interacting proteins is unknown. Here, we analyze adaptation in
 ~1300 virus-interacting proteins manually curated from a set of 9900
 proteins conserved in all sequenced mammalian genomes. We show that
 viruses (i) use the more evolutionarily constrained proteins within the
 cellular functions they interact with and that (ii) despite this high
 constraint, virus-interacting proteins account for a high proportion of
 all protein adaptation in humans and other mammals. Adaptation is elevated
 in virus-interacting proteins across all functional categories, including
 both immune and non-immune functions. We conservatively estimate that
 viruses have driven close to 30% of all adaptive amino acid changes in the
 part of the human proteome conserved within mammals. Our results suggest
 that viruses are one of the most dominant drivers of evolutionary change
 across mammalian and human proteomes.
description: Coding sequence
 alignments of 9,861 mammalian orthologsThe compressed folder
 contains fasta coding sequence alignments of 9,861 mammalian orthologs.
 Best reciprocal hits of human Ensembl v69 coding sequences were obtained
 with Blat for 23 other mammalian species, and those best reciprocal
 sequences were then aligned with PRANK. Note that best reciprocal hits are
 not sufficient to establish orthology, and we recommend additional
 filtering with synteny information.bestrecip_prank_alignments.tgz
DOI: 10.15468/dl.8dggbf
title: Occurrence Download

description: A dataset containing 4603 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Bassariscus astutus"
 ]
}

 The dataset includes 4603 records from 96 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000476-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1f5r2
title: Data from: Estimates of observer expertise improve species distributions from citizen science data

description: 1. Citizen science data are increasingly making valuable contributions to
 ecological studies. However, many citizen science surveys are also
 designed to encourage wide participation and therefore the participants
 have a range of natural history expertise, leading to variation and
 potentially bias in the data. 2. We assessed a recently proposed measure
 of observer expertise, calculated based on the average numbers of species
 recorded by observers. We investigated if this observer expertise score is
 associated with how often an observer records any individual species.
 Species reporting rates increased monotonically with the observer’s
 expertise score for 197 of 200 species, suggesting that this expertise
 score describes inter-observer variation in the detectability of
 individual species. 3. Expertise scores were incorporated into
 single-species occupancy models as a covariate, to explain inter-observer
 variation in detectability. Including expertise as a detectability
 covariate led to improved model fit and improved predictive performance on
 validation data. The expertise score had a large effect on the estimated
 detectability, comparable in magnitude to the effect of the duration of
 the observation period. 4. Expertise scores were also included into
 single-species occupancy models that estimated seasonal patterns in
 species occupancy and seasonal expertise effects. The addition of a
 seasonal effect of expertise led to improved model fit and increased
 predictive performance on validation data. The seasonal expertise
 variables accounted for bias that may be introduced by seasonal
 differences in the effect of expertise, caused by changes in the
 environment or species behaviour. 5. Measures of observer expertise
 included in models as a covariate can account for heterogeneity and bias
 introduced by variable expertise, although in this example the differences
 in estimated occupancy were small. This method of incorporating observer
 expertise can be used in any regression model of species occurrence,
 occupancy, abundance, or density to produce more reliable ecological
 inference and may be most important where citizen science schemes
 encourage wide participation. Overall, the results highlight the value of
 recording observer identity and other detectability covariates, to control
 for sources of bias associated with the observation process.
description: eBird checklist
 information from BCR23 years 2004-2012This dataset is a
 curated proportion of the eBird dataset ERD5.0 (Munson et al 2013). It
 includes the data necessary to replicate the analysis in the paper. These
 data were collected by citizen scientists participating in the eBird
 survey. The dataset includes checklists from Bird Conservation Region 23
 and years 2004-2012. In addition, there were a number of other filters -
 see the read-me file for further information.eBird_BCR23_2004_2012.txt
DOI: 10.5061/dryad.7q7k1
title: Data from: Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life-cycle in field-grown rice

description: Bacterial communities associated with roots impact the health and
 nutrition of the host plant. The dynamics of these microbial assemblies
 over the plant life cycle is however, not well understood. Here, we use
 dense temporal sampling of 1588 samples from root spatial compartments to
 characterize the bacterial and archaeal components of the root-associated
 microbiota of field grown rice (Oryza sativa) over the course of three
 consecutive growing seasons, as well as two sites in diverse geographic
 regions. The root microbiota was found to be highly dynamic during the
 vegetative phase of plant growth, then stabilized compositionally for the
 remainder of the life cycle. Bacterial and archaeal taxa conserved between
 field sites were defined as predictive features of rice plant age by
 modeling using a random forests approach. The age-prediction models
 revealed that drought stressed plants have developmentally immature
 microbiota compared to unstressed plants. Further, by using genotypes with
 varying developmental rates, we show that shifts in the microbiome are
 correlated with rates of developmental transitions rather than age alone,
 such that different microbiota compositions reflect juvenile and adult
 life stages. These results suggest a model for successional dynamics of
 the root-associated microbiota over the plant life cycle.
description: Arkansas 2016 and
 California 2014-15 R objectR object for Arkansas
 2016 and California 2014-2015 Seasons in "tidy" format. That is,
 each variable is a column and each row corresponds to a single
 observation. This can be used directly with the R scripts in the github
 repo: https://github.com/bulksoil/LifeCycleManuscriptcal_ark_data.rdsCalifornia 2016 R object.R object containing the data for the California 2016 season in "tidy" format.cal_2016.rdsOTU Table Clustered at 97% for all samplesA gzipped tab separated file. The OTU identifiers are in the column 'OTUID'. This is a matrix where each row represents one OTU and each column represents one sample (corresponding to "SampleID" in the mapping file). The data can be unzipped in the UNIX/LINUX terminal using the command 'gunzip lc_study_otu_table.tsv.gz'lc_study_otu_table.tsv.gzSample MetadataA tab separated file with information about the samples in the OTU table.lc_study_mapping_file.tsvR object containing taxonomic information for each OTUThis is an R object (.rds file) containing the taxonomic information for all possible OTUs detected in this dataset. These are the GreenGenes 13_8 97% reference OTUs.gg_otus_tax.rdsOrganellar OTUsR object (.rds file) containing all of the detected mitochondrial and plastid OTUs from the Greengenes 13_8 reference database.organelle.rds
DOI: 10.5061/dryad.dv03078
title: Data from: Clonal evolution and genome stability in a 2,500-year-old fungal individual

description: Individuals of the basidiomycete fungus Armillaria are well-known for
 their ability to spread from woody substrate to substrate on the forest
 floor through the growth of rhizomoprhs. Here we made 248 collections of
 A. gallica in one locality in Michigan’s Upper Peninsula. To identify
 individuals, we genotyped collections with molecular markers and somatic
 compatibility testing. We found several different individuals in proximity
 to one another, but one genetic individual stood out as exceptionally
 large, covering hundreds of tree root systems over approximate 75 hectares
 of forest floor. Based on observed growth rates of the fungus, we estimate
 the minimum age of the large individual as 2,500 years. With whole-genome
 sequencing and variant discovery, we also found that mutation had occurred
 within the somatic cells of the individual, reflecting its historical
 pattern of growth from a single point. The overall rate of mutation over
 the 90 mb genome, however, was extremely low. This same individual was
 first discovered in the late 1980s, but its full spatial extent and
 internal mutation dynamic was unkown at that time. The large individual of
 A. gallica has been remarkably resistant to genomic change as it has
 persisted in place.
description: Genome annotation for A.
 gallica (JGI Armillaria gallica 21-2 v1)Provisional genome
 annotation was done with GeneMarkES under the default settings and SNPs
 were annotated with snpEff.genemark.gff3
DOI: 10.5061/dryad.668tn571
title: Data from: The effect of close relatives on unsupervised Bayesian clustering algorithms in population genetic structure analysis

description: The inference of population genetic structures is essential in many
 research areas in population genetics, conservation biology and
 evolutionary biology. Recently, unsupervised Bayesian clustering
 algorithms have been developed to detect a hidden population structure
 from genotypic data, assuming among others that individuals taken from the
 population are unrelated. Because of this hypothesis, markers in a sample
 taken from a subpopulation can be considered to be in Hardy-Weinberg and
 linkage equilibrium. However, close relatives might be sampled from the
 same subpopulation, and consequently, might cause Hardy-Weinberg and
 linkage disequilibrium and thus bias a population genetic structure
 analysis. In this study, we used simulated and real data to investigate
 the impact of close relatives in a sample on Bayesian population structure
 analysis. We also showed that, when close relatives were identified by a
 pedigree reconstruction approach and removed, the accuracy of a population
 genetic structure analysis can be greatly improved. The results indicate
 that unsupervised Bayesian clustering algorithms cannot be used blindly to
 detect genetic structure in a sample with closely related individuals.
 Rather, when closely related individuals are suspected to be frequent in a
 sample, these individuals should be first identified and removed before
 conducting a population structure analysis.
description: Simulated
 dataData.zip
DOI: 10.15468/dl.y98ee8
title: Occurrence Download

description: A dataset containing 987 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craugastor metriosistus"
 ]
}

 The dataset includes 987 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000473-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0hq44
title: Data from: Resilience of plant-insect interactions in an oak lineage through Quaternary climate change

description: Plant-insect interactions are vital for structuring terrestrial
 ecosystems. It is still unclear how climate change in geological time
 might have shaped plant-insect interactions leading to modern ecosystems.
 We investigated the effect of Quaternary climate change on plant-insect
 interactions by observing insect herbivory on leaves of an evergreen
 sclerophyllous oak lineage (Quercus section Heterobalanus, HET) from a
 late Pliocene flora and eight living forests in southwestern China. Among
 the modern HET populations investigated, the damage diversity tends to be
 higher in warmer and wetter climates. Even though the climate of the
 fossil flora was warmer and wetter than modern sample sites, the damage
 diversity is lower in the fossil flora than in modern HET populations.
 Eleven out of 18 damage types in modern HET populations are observed in
 the fossil flora. All damage types in the fossil flora, except for one
 distinctive gall type, are found in modern HET populations. These results
 indicate that Quaternary climate change did not cause extensive extinction
 of insect herbivores in HET forests. The accumulation of a more diverse
 herbivore fauna over time supports the view of plant species as
 evolutionary “islands” for colonization and turnover of insect species.
description: Supplementary Figure
 1The
 diversity of damage types in the late Pliocene Longmen flora (1-12), and
 eight living HET forests (13-30). The definition of each damage type
 follows Labandeira et al. (2007).Supplementary Table
 1Score sheets of insect
 damage on each sample.Supplementary Table
 2The
 percentage of each damage type on each sample. Abbreviation and detailed
 information on each sample site are listed in Table 1.
DOI: 10.5061/dryad.h0jg4
title: Data from: Development of an ultra-dense genetic map of the sunflower genome

description: The development of ultra-dense genetic maps has the potential to
 facilitate detailed comparative genomic analyses and whole genome sequence
 assemblies. Here we describe the use of a custom Affymetrix GeneChip
 containing nearly 2.4 million features (25 bp sequences) targeting 86,023
 unigenes from sunflower (Helianthus annuus L.) and related species to test
 for single-feature polymorphisms (SFPs) in a recombinant inbred line (RIL)
 mapping population derived from a cross between confectionery and oilseed
 sunflower lines (RHA280 x RHA801). We then employed an existing genetic
 map derived from this same population to rigorously filter out low quality
 data and place 67,486 features corresponding to 22,481 unigenes on the
 sunflower genetic map. The resulting map contains a substantial fraction
 of all sunflower genes and will thus facilitate a number of downstream
 applications, including genome assembly and the identification of
 candidate genes underlying QTL or traits of interest.
description: Helianthus Genespace Est
 AssemblyAll genotyping was
 performed using a custom Affymetrix GeneChip (Affymetrix, CA, USA)
 designed from Helianthus expressed-sequence tags (ESTs). A total of
 283,605 Sanger ESTs from 7 sunflower species (GenBank numbers:
 AJ318230-AJ318330, AJ412174-AJ412667, AJ437699-AJ437975,
 AJ539583-AJ540226, AJ541055-AJ541795, AJ542101-AJ542392,
 AJ827751-AJ829440, BG734514-BG734530, BG874297-BG874313,
 BG891021-BG891022, BQ909263-BQ917261, BQ965129-BQ980049,
 BU015365-BU036497, BU671782-BU672110, CD845604-CD858495,
 CF076145-CF099271, CX943504-CX948070, DY903733-DY959228,
 EE605695-EE627562, EE628472-EE661299, EL412382-EL492411,
 EL511146-EL515442, EL772988) were assembled using TGICL [11]. These
 sequences included 94,017 ESTs from H. annuus; 35,704 from H. argophyllus;
 21,589 from H. ciliaris; 33,959 from H. exilis; 30,504 from H. paradoxus;
 27,479 from H. petiolaris; and 40,353 from H. tuberosus. The final
 assembly included 87,237 “unigenes” corresponding to 27,587 contigs and
 59,650 singletons.Sunflower_EST_assembly.txt
DOI: 10.15468/dl.byyczs
title: Occurrence Download

description: A dataset containing 172097 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((-124.08769 39.86295,-124.01085 37.55487,-121.8978 34.54251,-119.43897 32.52515,-117.13382 29.7302,-114.32922 28.58952,-116.50843 32.80082,-119.31957 35.56506,-120.35321 36.11405,-121.74329 37.59699,-124.08769 39.86295))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bivalvia"
 ]
}

 The dataset includes 172097 records from 85 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000427-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.h8f66
title: Data from: Transcriptomics in the wild: hibernation physiology in free‐ranging dwarf lemurs

description: Hibernation is an adaptive strategy some mammals use to survive highly
 seasonal or unpredictable environments. We present the first investigation
 on the transcriptomics of hibernation in a natural population of primate
 hibernators: Crossley's dwarf lemurs (Cheirogaleus crossleyi). Using
 capture–mark–recapture techniques to track the same animals over a period
 of 7 months in Madagascar, we used RNA‐seq to compare gene expression
 profiles in white adipose tissue (WAT) during three distinct physiological
 states. We focus on pathway analysis to assess the biological significance
 of transcriptional changes in dwarf lemur WAT and, by comparing and
 contrasting what is known in other model hibernating species, contribute
 to a broader understanding of genomic contributions of hibernation across
 Mammalia. The hibernation signature is characterized by a suppression of
 lipid biosynthesis, pyruvate metabolism and mitochondrial‐associated
 functions, and an accumulation of transcripts encoding ribosomal
 components and iron‐storage proteins. The data support a key role of
 pyruvate dehydrogenase kinase isoenzyme 4 (PDK4) in regulating the shift
 in fuel economy during periods of severe food deprivation. This pattern of
 PDK4 holds true across representative hibernating species from disparate
 mammalian groups, suggesting that the genetic underpinnings of hibernation
 may be ancestral to mammals.
description: Cheirogaleus crossleyi
 assembled transcriptsTranscripts were
 assembled from 17 RNA-Seq samples using Trinity. The samples were from
 white adipose tissue from 6 individuals.final_trinity_crossleyi.fastaCheirogaleus crossleyi transcript annotationsList of transcripts with sequence homology hits to human proteins annotated in Ensembl.final_trinity_transcripts_blastx_crossleyi.txtCheirogaleus sibreei assembled transcriptsTranscripts were assembled from 6 RNA-Seq samples using Trinity. The samples were from white adipose tissue from 2 individuals.final_trinity_sibreei.fastaCheirogaleus sibreei transcript annotationsList of transcripts with sequence homology hits to human proteins annotated in Ensembl.final_trinity_transcripts_blastx_sibreei.txt
DOI: 10.5061/dryad.ft6fv
title: Data from: The shepherds' tale: a genome-wide study across 9 dog breeds implicates two loci in the regulation of fructosamine serum concentration in Belgian shepherds

description: Diabetes mellitus is a serious health problem in both dogs and humans.
 Certain dog breeds show high prevalence of the disease, whereas other
 breeds are at low risk. Fructosamine and glycated hemoglobin (HbA1c) are
 two major biomarkers of glycaemia where serum concentrations reflect
 glucose turnover over the past few weeks to months. In this study, we
 searched for genetic factors influencing variation in serum fructosamine
 concentration in healthy dogs using data from nine dog breeds. Considering
 all breeds together, we did not find any genome-wide significant
 associations to fructosamine serum concentration. However, by performing
 breed-specific analyses we revealed an association on CFA 3 (pcorrected ≈
 1.68 × 10−6) in Belgian shepherd dogs. The associated region and its close
 neighborhood harbours interesting candidate genes such as LETM1 and GAPDH
 that are important in glucose metabolism and have previously been
 implicated in the aetiology of diabetes mellitus. To further explore the
 genetics of this breed specificity, we screened the genome for reduced
 heterozygosity stretches private to the Belgian shepherd breed. This
 revealed a region with reduced heterozygosity that shows a statistically
 significant interaction (p = 0.025) with the association region on CFA3.
 This region also harbours some interesting candidate genes and regulatory
 regions but the exact mechanisms underlying the interaction are still
 unknown. Nevertheless, this finding provides a plausible explanation for
 breed-specific genetic effects for complex traits in dogs. Shepherd breeds
 are at low risk of developing diabetes mellitus. The findings in Belgian
 shepherds could be connected to a protective mechanism against the
 disease. Further insight into the regulation of glucose metabolism could
 improve diagnostic and therapeutic methods for diabetes mellitus.
description: Forsberg et al.
 Fructosamine dataForsberg_et_al_fructosamine_data.zip
DOI: 10.5061/dryad.8hm82
title: Data from: A fat-derived metabolite regulates a peptidergic feeding circuit in Drosophila

description: Here, we show that the enzymatic cofactor tetrahydrobiopterin (BH4)
 inhibits feeding in Drosophila. BH4 biosynthesis requires the sequential
 action of the conserved enzymes Punch, Purple, and Sepiapterin Reductase
 (Sptr). Although we observe increased feeding upon loss of Punch and
 Purple in the adult fat body, loss of Sptr must occur in the brain. We
 found Sptr expression is required in four adult neurons that express
 neuropeptide F (NPF), the fly homologue of the vertebrate appetite
 regulator neuropeptide Y (NPY). As expected, feeding flies BH4 rescues the
 loss of Punch and Purple in the fat body and the loss of Sptr in NPF
 neurons. Mechanistically, we found BH4 deficiency reduces NPF staining,
 likely by promoting its release, while excess BH4 increases NPF
 accumulation without altering its expression. We thus show that, because
 of its physically distributed biosynthesis, BH4 acts as a fat-derived
 signal that induces satiety by inhibiting the activity of the NPF neurons.
description: Kim_Shin et al.
 Data-Code-FiguresThis ZIP archive
 includes all the raw data and R code used to generate the figures for our
 paper. We recommend loading and running each Rmarkdown (.Rmd) file in the
 RStudio development environment
 (https://www.rstudio.com).