cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jd5716f
title: Data from: Genome-wide association and genomic prediction models of tocochromanols in fresh sweet corn kernels

description: Sweet corn (Zea mays L.), a highly consumed fresh vegetable in the United
 States, varies for tocochromanol (tocopherol and tocotrienol) levels, but
 makes limited contribution to daily intake of vitamin E and antioxidants.
 We performed a genome-wide association study of six tocochromanol
 compounds and 14 derivative traits across a sweet corn inbred line
 association panel to identify genes associated with natural variation for
 tocochromanols and vitamin E in fresh kernels. Concordant with prior
 studies in mature maize kernels, an association was detected between vte4
 (γ-tocopherol methyltransferase) and α-tocopherol content, along with vte1
 (tocopherol cyclase) and hggt1 (homogentisate geranylgeranyltransferase)
 for tocotrienol variation. Additionally, two kernel starch synthesis
 genes, shrunken2 (sh2) and sugary1 (su1), were associated with
 tocotrienols, with the strongest evidence for sh2, in combination with
 fixed, strong vte1 and hggt1 alleles, accounting for the greater amount of
 tocotrienols in su1sh2 and sh2 lines. In prediction models with
 genome-wide markers, predictive abilities were higher for tocotrienols
 than tocopherols, and these models were superior to those that used marker
 sets targeting a priori genes involved in the biosynthesis and/or genetic
 control of tocochromanols. Through this quantitative genetic analysis, we
 have established a key step for increasing tocochromanols in fresh kernels
 of sweet corn for human health and nutrition.
description: Raw_GBS_SweetCorn_384indiv_955K_RefGen_v2.hmpRaw genotypes from 384 sweet corn inbred lines using genotyping-by-sequencing (GBS) with 955,690 high confidence single-nucleotide polymorphism markers (SNPs) that were called using default parameters in the TASSEL 5 GBSv1 production pipeline with the ZeaGBSv2.7 Production TagsOnPhysicalMapfile in B73 RefGen_v2 coordinates. File in Hapmap format.sweet_raw_clean_toco384.hmp.txt
DOI: 10.5061/dryad.9fs7n
title: Data from: Nest etiquette - where ants go when nature calls

description: Sanitary behaviour is an important, but seldom studied, aspect of social
 living. Social insects have developed several strategies for dealing with
 waste and faecal matter, including dumping waste outside the nest and
 forming specialised waste-storage chambers. In some cases waste material
 and faeces are put to use, either as a construction material or as a
 long-lasting signal, suggesting that faeces and waste may not always be
 dangerous. Here we examine a previously undescribed behaviour in ants –
 the formation of well-defined faecal patches. Lasius niger ants were
 housed in plaster nests and provided with coloured sucrose solution. After
 two months, 1–4 well defined dark patches, the colour of the sucrose
 solution, formed within each of the plaster nests. These patches never
 contained other waste material such as uneaten food items, or nestmate
 corpses. Such waste was collected in waste piles outside the nest. The
 coloured patches were thus distinct from previously described ‘kitchen
 middens’ in ants, and are best described as ‘toilets’. Why faeces is not
 removed with other waste materials is unclear. The presence of the toilets
 inside the nest suggests that they may not be an important source of
 pathogens, and may have a beneficial role.
description: Ant nest and foraging
 box imagesThis series of images
 show 21 small nests of Lasius niger ants, which have been provided with
 coloured sugar solution and coloured protein gel. One picture is taken of
 the entire foraging box every week for two months. To take the picture, an
 opaque covering is briefly removed from the nest (c. 3 seconds) and then
 replaced.Weekly ant nest
 pictures.zip
DOI: 10.5061/dryad.4368h
title: Data from: A sequel to Sanger: amplicon sequencing that scales

description: Although high-throughput sequencers (HTS) have largely displaced their
 Sanger counterparts, the short read lengths and high error rates of most
 platforms constrain their utility for amplicon sequencing. The present
 study tests the capacity of single molecule, real-time (SMRT) sequencing
 implemented on the SEQUEL platform to overcome these limitations,
 employing 658 bp amplicons of the mitochondrial cytochrome c oxidase I
 gene as a model system. By examining templates from more than 5,000
 species and 20,000 specimens, the performance of SMRT sequencing was
 tested with amplicons showing wide variation in GC composition and varied
 sequence attributes. SMRT and Sanger sequences were very similar, but SMRT
 sequencing provided more complete coverage, especially for amplicons with
 homopolymer tracts. Because it can characterize amplicon pools from 10,000
 DNA extracts in a single run, the SEQUEL reduces costs 40-fold from Sanger
 analysis. Reflecting the capacity of each instrument to recover sequences
 from more than five million DNA extracts a year, this platform facilitates
 massive amplicon characterization.
description: CCSReads_DS-PBBC1Sequel CCS reads for 99%, 99.9%, and 99.99% partitions of data set DS-PBBC1.CCSReads_DS-PBBC2Sequel CCS reads for 99%, 99.9%, and 99.99% partitions of data set DS-PBBC2.CCSReads_DS-PBBC3Sequel CCS reads for 99%, 99.9%, and 99.99% partitions of data set DS-PBBC3.CCSReads_DS-PBBC4Sequel CCS reads for 99%, 99.9%, and 99.99% partitions of data set DS-PBBC4.mBRAVE_DS-PBBC1mBRAVE output for data set DS-PBBC1.mBRAVE_DS-PBBC2mBRAVE output for data set DS-PBBC2.mBRAVE_DS-PBBC3mBRAVE output for data set DS-PBBC3.mBRAVE_DS-PBBC4mBRAVE output for data set DS-PBBC4.
DOI: 10.5061/dryad.j631f
title: Data from: Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation

description: Differential gene flow, reductions in diversity following linked selection
 and/or features of the genome can structure patterns of genomic
 differentiation during the process of speciation. Possible sources of
 reproductive isolation are well studied between coastal and inland
 subspecies groups of Swainson's thrushes, with differences in
 seasonal migratory behaviour likely playing a key role in reducing hybrid
 fitness. We assembled and annotated a draft reference genome for this
 species and generated whole-genome shotgun sequence data for populations
 adjacent to the hybrid zone between these groups. We documented
 substantial genomewide heterogeneity in relative estimates of genetic
 differentiation between the groups. Within population diversity was lower
 in areas of high relative differentiation, supporting a role for selective
 sweeps in generating this pattern. Absolute genetic differentiation was
 reduced in these areas, further suggesting that recurrent selective sweeps
 in the ancestral population and/or between divergent populations following
 secondary contact likely occurred. Relative genetic differentiation was
 also higher near centromeres and on the Z chromosome, suggesting that
 features of the genome also contribute to genomewide heterogeneity. Genes
 linked to migratory traits were concentrated in islands of
 differentiation, supporting previous suggestions that seasonal migration
 is under divergent selection between Swainson's thrushes. Differences
 in migratory behaviour likely play a central role in the speciation of
 many taxa; we developed the infrastructure here to permit future
 investigations into the role several candidate genes play in reducing gene
 flow between not only Swainson's thrushes but other species as well.
description: Catharus_ustulatus_draft_assembly_annotation_Feb13_2015.tarFolder containing draft genome assembly and annotation. Assembly generated using a reference-based approach and three paired-end 100bp Illumina libraries (one fragment, two mate pair). Annotation generated using the MAKER pipeline.SNP tableSNP table generated using snp-frequency-diff.pl in Popoolation2. Includes statistics on the major and minor alleles for all SNPs in coastal (_1) and inland (_2) populations of Swainson's thrushes.snp_table_coastal_inland.txt
DOI: 10.5061/dryad.69g60
title: Data from: A bioacoustic record of a conservancy in the Mount Kenya ecosystem

description: Environmental degradation is a major threat facing ecosystems around the
 world. In order to determine ecosystems in need of conservation
 interventions, we must monitor the biodiversity of these ecosystems
 effectively. Bioacoustic approaches offer a means to monitor ecosystems of
 interest in a sustainable manner. In this work we show how a bioacoustic
 record from the Dedan Kimathi University wildlife conservancy, a
 conservancy in the Mount Kenya ecosystem, was obtained in a cost effective
 manner. A subset of the dataset was annotated with the identities of bird
 species present since they serve as useful indicator species. These data
 reveal the spatial distribution of species within the conservancy and also
 point to the effects of major highways on bird populations. This dataset
 will provide data to train automatic species recognition systems for birds
 found within the Mount Kenya ecosystem. Such systems are necessary if
 bioacoustic approaches are to be employed at the large scales necessary to
 influence wildlife conservation measures.
description: DeKUWC Audio Recordings
 2016We provide acoustic
 recordings from the Dedan Kimathi University Wildlife Conservancy (DeKUWC)
 in the Mt. Kenya ecosystem obtained using a low cost acoustic recorder. A
 total of 2701 minute long recordings are provided including both daytime
 and nighttime recordings. We present an annotation of a subset of the
 daytime recordings indicating the bird species present in the recordings.
 The dataset contains recordings of at least 36 bird species. In addition,
 the presence of a few nocturnal species within the conservancy is also
 confirmed.DeKUWC-Recordings-DataPackage-2016.zip
DOI: 10.5061/dryad.qb7r0d3
title: Data from: Is it possible to reconstruct an accurate cell lineage using CRISPR recorders?

description: Cell lineages provide the framework for understanding how multicellular
 organisms are built and how cell fates are decided during development.
 Describing cell lineages in most organisms is challenging, given the
 number of cells involved; even a fruit fly larva has ~50,000 cells and a
 small mammal has more than 1 billion cells. Recently, the idea of using
 CRISPR to induce mutations during development as heritable markers for
 lineage reconstruction has been proposed and trialled by several groups.
 While an attractive idea, its practical value depends on the accuracy of
 the cell lineages that can be generated by this method. Here, we use
 computer simulations to estimate the performance of this approach under
 different conditions. Our simulations incorporate empirical data on
 CRISPR-induced mutation frequencies in Drosophila. We show significant
 impacts from multiple biological and technical parameters - variable cell
 division rates, skewed mutational outcomes, target dropouts and different
 mutation sequencing strategies. Our approach reveals the limitations of
 recently published CRISPR recorders, and indicates how future
 implementations can be optimised to produce accurate cell lineages.
description: Sequencing data to
 analyse the targeting efficiencies of different sgRNA:target
 pairsThe zip file contains:
 1) a README spreadsheet in standard GEO format, with further informations
 about the data. 2) RAW DATA folder, containing the raw FASTQ output of the
 sequencing run, as well as a run report in PDF. 1) Six folders containing
 demultiplexed read for each experimental condition (indicated by the
 folder name). Each folder contains 11 files, corresponding to the 11
 amplicons sequenced per condition.Salvador-Martinez et al.
 2018.zip
DOI: 10.5061/dryad.ft94b
title: Data from: Nonparallelism in MHC IIβ diversity accompanies nonparallelism in pathogen infection of lake whitefish (Coregonus clupeaformis) species pairs as revealed by next generation sequencing

description: Major histocompatibility (MHC) immune system genes may evolve in response
 to pathogens in the environment. Because they also may affect mate choice,
 they are candidates for having great importance in ecological speciation.
 Here, we use next-generation sequencing to test the general hypothesis of
 parallelism in patterns of MHCIIβ diversity and bacterial infections among
 five dwarf and normal whitefish sympatric pairs. A second objective was to
 assess the functional relationships between specific MHCIIβ alleles and
 pathogens in natural conditions. Each individual had between one and four
 alleles, indicating two paralogous loci. In Cliff Lake, the dwarf ecotype
 was monomorphic for the most common allele. In Webster Lake, the skew in
 the allelic distribution was towards the same allele but in the normal
 ecotype, underscoring the nonparallel divergence among lakes. Our signal
 of balancing selection matched putative peptide binding region residues in
 some cases, but not in others, supporting other recent findings of
 substantial functional differences in fish MHCIIβ compared with mammals.
 Individuals with fewer alleles were less likely to be infected; thus, we
 found no evidence for the heterozygote advantage hypothesis. MHCIIβ
 alleles and pathogenic bacteria formed distinct clusters in multivariate
 analyses, and clusters of certain alleles were associated with clusters of
 pathogens, or sometimes the absence of pathogens, indicating functional
 relationships at the individual level. Given that patterns of MHCIIβ and
 bacteria were nonparallel among dwarf and normal whitefish pairs, we
 conclude that pathogens driving MHCIIβ evolution did not play a direct
 role in their parallel phenotypic evolution.
description: R_scripts_inputs_outputs.tarHere are the R scripts as well as input and output files for the statistical analyses for this paper.SplitsTree.tarThis folder contains the fasta input files and nexus files for each of the two splitstree networks in the paper.Pathogen_data.tarSequence data from Lake whitefish kidney tissue for both dwarf and normal forms from all five lakesMHC_454This compressed file contains two folders with all of the raw 454 files for MHCIIb for this project. Each file name includes on of three libraries (02, 03, or 04) and a MID number 1-153. These numbers correspond to various spreadsheets in the R scripts folder.MHC_full_dataset.tar.gz
DOI: 10.5061/dryad.c5805
title: Data from: Primary productivity explains size variation across the Pallid bat’s (Antrozous pallidus) western geographic range

description: 1. Body size is associated with many aspects of the life history, ecology,
 and physiology of animals. Within a species, body size can vary
 substantially across space and time, and the mechanisms generating these
 patterns have been the focus of evolutionary and ecology research. 2.
 Bergmann’s Rule predicts a negative relationship between body size and
 temperature across the geographic range of endothermic animals; larger
 animals have a lower surface to volume ratio, which would allow for
 greater heat conservation. Despite the broad support for this pattern, its
 underlying mechanisms are heavily debated. Numerous alternative
 explanations have been proposed to explain why larger animals are found in
 colder climates, and vice versa, including heat dissipation, environmental
 seasonality, and resource availability. 3. We used the Pallid bat,
 Antrozous pallidus, as a model to evaluate Bergmannian size patterns and
 the relative support for major explanatory hypotheses of geographic body
 size variation. We tested the hypothesis that geographic size variation is
 predicted by productivity, as opposed to seasonality, heat conservation or
 dissipation, or some combination of these processes. Additionally, we
 investigated the potential ecomorphological consequences of size variation
 in Pallid bats by determining if skull shape (an indicator of bite
 performance) varies with size. 4. Whereas we did find that Pallid bat
 populations in northern latitudes are composed of larger individuals, our
 results suggest that net primary productivity and, to a lesser extent heat
 conservation, best explains size variation throughout the western range of
 this species. We also found that skull shape in Pallid bats changes in
 tandem with skull size, with larger bats having cranial traits associated
 with greater bite force production. 5. The results of our study indicate
 that variation in resource availability may be a key factor underlying
 spatial patterns in size, morphology and, possibly, feeding performance
 within wide-ranging bat species.
description: Antrozous pallidus
 dataThis folder contains
 photographs and landmark coordinates for the lateral and ventral cranium
 as well as raster files for each of the environmental variables used in
 the study. (See manuscript methods for details).data.zip
DOI: 10.15468/dl.h4etc5
title: Occurrence Download

description: A dataset containing 452239 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 PRINTF('%04d-%02d-%02d', "year", "month", "day") yearmonthday,
 countrycode countrycode,
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, countrycode, PRINTF('%04d-%02d-%02d', "year", "month", "day"))) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, countrycode, PRINTF('%04d-%02d-%02d', "year", "month", "day"))) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, countrycode, PRINTF('%04d-%02d-%02d', "year", "month", "day"))) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, countrycode, PRINTF('%04d-%02d-%02d', "year", "month", "day"))) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, countrycode, PRINTF('%04d-%02d-%02d', "year", "month", "day"))) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, countrycode, PRINTF('%04d-%02d-%02d', "year", "month", "day"))) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.basisofrecord IN ('HUMAN_OBSERVATION', 'MACHINE_OBSERVATION', 'OCCURRENCE')
 AND occurrence.countrycode = 'US'
 AND GBIF_STRINGARRAYCONTAINS(occurrence.classifications['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c'], '1457', TRUE)
 AND (occurrence.classificationdetails['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c']['specieskey'] &lt;&gt; '' AND occurrence."year" IS NOT NULL AND occurrence."month" IS NOT NULL AND occurrence."day" IS NOT NULL AND occurrence.hascoordinate = TRUE)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 PRINTF('%04d-%02d-%02d', "year", "month", "day"),
 occurrence.countrycode

 The dataset's 452239 records were derived from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000310-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1kp0s
title: Data from: The potential influence of morphology on the evolutionary divergence of an acoustic signal.

description: The evolution of acoustic behaviour and that of the morphological traits
 mediating its production are often coupled. Lack of variation in the
 underlying morphology of signalling traits has the potential to constrain
 signal evolution. This relationship is particularly likely in field
 crickets, where males produce acoustic advertisement signals to attract
 females by stridulating with specialized structures on their forewings. In
 this study, we characterize the size and geometric shape of the forewings
 of males from six allopatric populations of the black field cricket
 (Teleogryllus commodus) known to have divergent advertisement calls. We
 sample from each of these populations using both wild-caught and
 common-garden-reared cohorts, allowing us to test for multivariate
 relationships between wing morphology and call structure. We show that the
 allometry of shape has diverged across populations. However, there was a
 surprisingly small amount of covariation between wing shape and call
 structure within populations. Given the importance of male size for sexual
 selection in crickets, the divergence we observe among populations has the
 potential to influence the evolution of advertisement calls in this
 species
description: Cricket_wings_DryadDryad repo. for Pitchers et al. 2014 "The potential influence of morphology on the evolutionary divergence of an acoustic signal" JEB list of included files: CGwing_analyses_final_2014.Rmd - Rmarkdown file for the analyses CGwing_analyses_final_2014.html - Html document produced by 'Knitting' the Rmd file Cricket_Wing_LMs.csv - datasheet of landmark coordinates from wing images CGCricketCallMeasures.csv - datasheet of call structure measures Cricket_Wing_Photos.zip - archive containing the original, unprocessed wing images
DOI: 10.5061/dryad.5rk06
title: Data from: Home-made cost effective preservation buffer is a better alternative to commercial preservation methods for microbiome research

description: The investigation of wildlife gastrointestinal microbiomes by
 next-generation sequencing approaches is a growing field in microbial
 ecology and conservation. Such studies often face difficulties in sample
 preservation if neither freezing facilities nor liquid nitrogen (LQN) are
 readily available. Thus, in order to prevent microbial community changes
 because of bacterial growth after sampling, preservation buffers need to
 be applied to samples. However, the amount of microbial community
 variation attributable to the different preservation treatments and
 potentially affecting biological interpretation is hardly known. Here, we
 sampled feces of 11 sheep (Ovis aries sp.) by using swabs and analyzed the
 effect of air-drying, an inexpensive self-made nucleic acid preservation
 buffer (NAP), DNA/RNA Shield™, and RNAlater®, each together with freezing
 (for 10 days) or storing at room temperature (for 10 days) prior to 16S
 rRNA gene high-throughput sequencing to determine bacterial communities.
 Results revealed that the proportions of operational taxonomic units
 (OTUs) belonging to a bacterial phylum were affected by the preservation
 treatments, and that alpha diversities (observed OTUs, Shannon index, and
 phylogenetic diversity (PD)) were lower in all preservation treatments
 than in samples taken by forensic swabs and immediately frozen which is
 considered as the favored preservation treatment in the absence of any
 logistic constraints. Overall, NAP had better preservation qualities than
 RNAlater® and DNA/RNA Shield™ making this self-made buffer a valuable
 solution in wildlife microbiome studies.
description: Sequence reads of sheep
 fecal bacterial communitiesThe compressed folder
 "Sheep_fecal_microbiome" contains forward and reverse sequence
 reads in fastq-format of sheep fecal bacterial communities and blank
 samples sequenced in the respective study.Sheep_fecal_microbiome.tar.gz