cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.83dc2
title: Data from: Assessing the utility of whole genome amplified DNA for next-generation molecular ecology

description: DNA quantity can be a hindrance in ecological and evolutionary research
 programmes due to a range of factors including endangered status of target
 organisms, available tissue type, and the impact of field conditions on
 preservation methods. A potential solution to low-quantity DNA lies in
 whole genome amplification (WGA) techniques that can substantially
 increase DNA yield. To date, few studies have rigorously examined sequence
 bias that might result from WGA and next-generation sequencing of nonmodel
 taxa. To address this knowledge deficit, we use multiple displacement
 amplification (MDA) and double-digest RAD sequencing on the grey mouse
 lemur (Microcebus murinus) to quantify bias in genome coverage and SNP
 calls when compared to raw genomic DNA (gDNA). We focus our efforts in
 providing baseline estimates of potential bias by following
 manufacturer's recommendations for starting DNA quantities
 (&gt;100 ng). Our results are strongly suggestive that MDA enrichment
 does not introduce systematic bias to genome characterization. SNP calling
 between samples when genotyping both de-novo and with a reference genome
 are highly congruent (&gt;98%) when specifying a minimum threshold of
 20X stack depth to call genotypes. Relative genome coverage is also
 similar between MDA and gDNA, and allelic dropout is not observed. SNP
 concordance varies based on coverage threshold, with 95% concordance
 reached at ~12X coverage genotyping de-novo and ~7X coverage genotyping
 with the reference genome. These results suggest that MDA may be a
 suitable solution for next-generation molecular ecological studies when
 DNA quantity would otherwise be a limiting factor.
description: Blair-MER-StacksfilesAll output files from Stacks analyses testing for bias in whole genome amplified DNA (using multiple displacement amplification; MDA) as compared to genomic DNA. Data include both sequencing runs and assemblies with and without the Microcebus murinus reference genome. Analyses are partitioned by tissue sample (e.g. MM1812). Within a single tissue sample, MDA and gDNA sequences are represented by different barcode sequences (see paper). Comparisons between treatments (gDNA vs. MDA) were performed at the SNP level.
DOI: 10.5061/dryad.470pd
title: Data from: From cacti to carnivores: improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

description: Premise of the Study— The Caryophyllales contains ~12,500 species and is
 known for its cosmopolitan distribution, convergence of trait evolution,
 and extreme adaptations. Some relationships within the Caryophyllales,
 like those of many large plant clades, remain unclear and phylogenetic
 studies often recover alternative hypotheses. We explore the utility of
 broad and dense transcriptome sampling across the order for resolving
 evolutionary relationships in Caryophyllales. Methods— We generated 84
 transcriptomes and combined these with 224 publicly available
 transcriptomes to perform a phylogenomic analysis of Caryophyllales. To
 overcome the computational challenge of ortholog detection in such a large
 data set, we developed an approach for clustering gene families that
 allowed us to analyze &gt;300 transcriptomes and genomes. We then
 inferred the species relationships using multiple methods and performed
 gene tree conflict analyses. Key Results— Our phylogenetic analyses
 resolved many clades with strong support, but also showed significant
 gene-tree discordance. This discordance is a common feature of
 phylogenomic studies but also represents an opportunity to understand
 processes that have structured phylogenies. We also found taxon sampling
 influences species-tree inference, highlighting the importance of more
 focused studies with additional taxon sampling. Conclusions—
 Transcriptomes are useful both for species tree inference and for
 uncovering evolutionary complexity within lineages. Through analyses of
 gene-tree conflict and multiple methods of species tree inference, we
 demonstrate that phylogenomic data can provide unparalleled insight into
 the evolutionary history of Caryophyllales. We also discuss a method for
 overcoming computational challenges associated with homolog clustering in
 large datasets.
description: Dryad.tgzYou can untar and unzip with tar -xzvf Dryad.tgz. This will create one folder called Dryad. In that folder there are four separate folders. The first contains the 305 species tree and orthologs used to create the tree, seen in figure 3 of the publication. The Next is the Assemblies, these are in both PEP and CDS, they are associated with their keys but those can be changed using the NameKey.txt file. The next folder is FamilyAnalyses, this contains the orthologs, conflict analysis and species tree analyses for the five major families analyzed. The final folder is programs which contains a set of scripts used for the analysis.
DOI: 10.5061/dryad.4f0bh
title: Data from: Comparison of photo-matching algorithms commonly used for photographic capture-recapture studies

description: Photographic capture–recapture is a valuable tool for obtaining
 demographic information on wildlife populations due to its noninvasive
 nature and cost-effectiveness. Recently, several computer-aided
 photo-matching algorithms have been developed to more efficiently match
 images of unique individuals in databases with thousands of images.
 However, the identification accuracy of these algorithms can severely bias
 estimates of vital rates and population size. Therefore, it is important
 to understand the performance and limitations of state-of-the-art
 photo-matching algorithms prior to implementation in capture–recapture
 studies involving possibly thousands of images. Here, we compared the
 performance of four photo-matching algorithms; Wild-ID, I3S Pattern+,
 APHIS, and AmphIdent using multiple amphibian databases of varying image
 quality. We measured the performance of each algorithm and evaluated the
 performance in relation to database size and the number of matching images
 in the database. We found that algorithm performance differed greatly by
 algorithm and image database, with recognition rates ranging from 100% to
 22.6% when limiting the review to the 10 highest ranking images. We found
 that recognition rate degraded marginally with increased database size and
 could be improved considerably with a higher number of matching images in
 the database. In our study, the pixel-based algorithm of AmphIdent
 exhibited superior recognition rates compared to the other approaches. We
 recommend carefully evaluating algorithm performance prior to using it to
 match a complete database. By choosing a suitable matching algorithm,
 databases of sizes that are unfeasible to match “by eye” can be easily
 translated to accurate individual capture histories necessary for robust
 demographic estimates.
description: Images and source code
 for the publication.The archive contains all
 the images and the source code used for the analysis in the referenced
 publication. It also contains the obtained equality tables, such that the
 whole comparison does not need to be run again. Moreover, code for
 analyzing the results is provided. Refer to the contained readme.html file
 for more detailed information.comparisonOfPhotoMatchingAlgorithms.tar.gz
DOI: 10.5061/dryad.kj2pb
title: Data from: Genetic evidence for species cohesion, substructure, and hybrids in spruce

description: The origin and history of species are shaped by various evolutionary
 dynamics, including their persistence in the face of potential gene flow
 from related taxa. In this study we use broad geographic and taxonomic
 sampling (2,219 individuals) to establish the distribution of species,
 hybrids, and cryptic genetic variation within the conifer genus Picea
 (spruce) across western North America. We demonstrate that the six species
 of spruce in this region are distinguishable based on their genetic
 composition, and that the more closely related Engelmann spruce (P.
 engelmannii) and white spruce (P. glauca) have generated numerous and
 widespread hybrids. These hybrids occur in the central Rocky Mountains,
 well to the south of the well-established region of admixture in Canada.
 Additionally, we provide evidence for subdivision within Engelmann spruce,
 manifested as a southern Rocky Mountains form, and a northern Rocky
 Mountain and Cascade mountains (western) form. In the intervening central
 Rocky Mountains region (forests in Wyoming and adjacent states) we found
 primarily individuals with admixed ancestry. Following their origin, these
 species of spruce have interacted repeatedly and in different geographic
 contexts. Multiple pairs of species have been shown to hybridize, yet the
 species persist and retain distinguishable compositions. At the same time,
 large geographic areas exist where hybrids are pervasive. Consequently,
 spruce provide a case study for the maintenance of species boundaries,
 particularly for how widespread hybridization need not lead to the
 collapse and loss of species.
description: De novo reference
 genomeconsen_contigs_picea_denovo_12mil_92minmatch_6taxa.fastavariants_6taxa_fileA.vcfThe complete .vcf file need to be concatenated including the files: variants_6taxa_fileA.vcf.gz, variants_6taxa_fileB.vcf.gz, and variants_6taxa_fileC.vcf.gz. Concatenate the files and extract as follows: $ cat variants_6taxa_file*.vcf.gz &gt; variants_6taxa_file.vcf.gz $ gunzip variants_6taxa_file.vcf.gzvariants_6taxa_fileB.vcfvariants_6taxa_fileC.vcfvariants_EngWhiHyb_fileA.vcfThe complete .vcf file need to be concatenated including the files: variants_EngWhiHyb_fileA.vcf.gz and variants_EngWhiHyb_fileB.vcf.gz. Concatenate the files and extract as follows: $ cat variants_EngWhiHyb_file*.vcf.gz &gt; variants_EngWhiHyb_file.vcf.gz $ gunzip variants_EngWhiHyb_file.vcf.gzvariants_EngWhiHyb_fileB.vcfR script used for Bayesian Linear Mixed ModelsThis R script is used together with the source code bayesLMM.R.commands.RbayesLMMSource code for the Bayesian Linear Mixed Models.Individual fastq filesIndividual fastq files to accompany “Genetic evidence for species cohesion, substructure, and hybrids in spruce" are available through the University of Wyoming DataCorral repository at doi:10.15786/faym-nh07
DOI: 10.5061/dryad.jc68d
title: Data from: Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon

description: In eukaryotes, alternative splicing (AS) promotes transcriptome and
 proteome diversity. The extent of genome-wide AS changes occurring during
 a plant-microbe interaction is largely unknown. Here, using
 high-throughput, paired-end RNA sequencing, we generated an isoform-level
 spliceome map of Brachypodium distachyon infected with Panicum mosaic
 virus and its satellite virus. Overall, we detected ∼44,443 transcripts in
 B. distachyon, ∼30% more than those annotated in the reference genome.
 Expression of ∼28,900 transcripts was ≥2 fragments per kilobase of
 transcript per million mapped fragments, and ∼42% of multi-exonic genes
 were alternatively spliced. Comparative analysis of AS patterns in B.
 distachyon, rice (Oryza sativa), maize (Zea mays), sorghum (Sorghum
 bicolor), Arabidopsis thaliana, potato (Solanum tuberosum), Medicago
 truncatula, and poplar (Populus trichocarpa) revealed conserved ratios of
 the AS types between monocots and dicots. Virus infection quantitatively
 altered AS events in Brachypodium with little effect on the AS ratios. We
 discovered AS events for &gt;100 immune-related genes encoding
 receptor-like kinases, NB-LRR resistance proteins, transcription factors,
 RNA silencing, and splicing-associated proteins. Cloning and molecular
 characterization of SCL33, a serine/arginine-rich splicing factor,
 identified multiple novel intron-retaining splice variants that are
 developmentally regulated and modulated during virus infection. B.
 distachyon SCL33 splicing patterns are also strikingly conserved compared
 with a distant Arabidopsis SCL33 ortholog. This analysis provides new
 insights into AS landscapes conserved among monocots and dicots and
 uncovered AS events in plant defense-related genes.
description: Supplemental Data Set
 2_TopHat outputSupplemental_Data_Set_2_TopHat_output.rarSupplemental Data Set 3_Cufflinks outputSupplemental Data Set 4_Cuffmerge outputSupplemental Data Set 5_ASTALAVISTA output
DOI: 10.5061/dryad.bv376
title: Data from: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies

description: Based on an extensive simulation study, McGregor and colleagues recently
 recommended the use of surrogate variable analysis (SVA) to control for
 the confounding effects of cell-type heterogeneity in DNA methylation
 association studies in scenarios where no cell-type proportions are
 available. As their recommendation was mainly based on simulated data, we
 sought to replicate findings in two large-scale empirical studies. In our
 empirical data, SVA did not fully correct for cell-type effects, its
 performance was somewhat unstable, and it carried a risk of missing true
 signals caused by removing variation that might be linked to actual
 disease processes. By contrast, a reference-based correction method
 performed well and did not show these limitations. A disadvantage of this
 approach is that if reference methylomes are not (publicly) available,
 they will need to be generated once for a small set of samples. However,
 given the notable risk we observed for cell-type confounding, we argue
 that, to avoid introducing false-positive findings into the literature, it
 could be well worth making this investment.
description: CellType_Means.csvsee readMe file for details.Sample1.tarSample2.tarSample3.tarSample4.tarSample5.tarSample6.tar
DOI: 10.5061/dryad.db005
title: Data from: Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status

description: Macroevolutionary rates of diversification and anthropogenic extinction
 risk differ vastly throughout the Tree of Life. This results in a highly
 heterogeneous distribution of Evolutionary distinctiveness (ED) and threat
 status among species. We examine the phylogenetic distribution of ED and
 threat status for squamates (amphisbaenians, lizards, and snakes) using
 fully-sampled phylogenies containing 9574 species and expert-based
 estimates of threat status for ~ 4000 species. We ask whether threatened
 species are more closely related than would be expected by chance and
 whether high-risk species represent a disproportionate amount of total
 evolutionary history. We found currently-assessed threat status to be
 phylogenetically clustered at broad level in Squamata, suggesting it is
 critical to assess extinction risks for close relatives of threatened
 lineages. Our findings show no association between threat status and ED,
 suggesting that future extinctions may not result in a disproportionate
 loss of evolutionary history. Lizards in degraded tropical regions (e.g.,
 Madagascar, India, Australia, and the West Indies) seem to be at
 particular risk. A low number of threatened high-ED species in areas like
 the Amazon, Borneo, and Papua New Guinea may be due to a dearth of
 adequate risk assessments. It seems we have not yet reached a tipping
 point of extinction risk affecting a majority of species; 63% of the
 assessed species are not threatened and 56% are Least Concern.
 Nonetheless, our results show that immediate efforts should focus on
 geckos, iguanas, and chameleons, representing 67% of high-ED threatened
 species and 57% of Unassessed high-ED lineages.
description: Squamata Tree, Methods,
 and DataThe tree, methods, and
 data used to create the fully-sampled PASTIS phylogenies and the estimates
 of ED for all species.Squamata_Tree_Methods_Data.zipsquam_shl_new_Posterior_9755.1000First 1000 fully-sampled squamate trees.squam_shl_new_Posterior_9755.2000Second 1000 fully-sampled squamate trees.squam_shl_new_Posterior_9755.3000Third 1000 fully-sampled squamate trees.squam_shl_new_Posterior_9755.4000Fourth 1000 fully-sampled squamate trees.squam_shl_new_Posterior_9755.5000Fifth 1000 fully-sampled squamate trees.squam_shl_new_Posterior_9755.6000Sixth 1000 fully-sampled squamate trees.squam_shl_new_Posterior_9755.7000Seventh 1000 fully-sampled squamate trees.squam_shl_new_Posterior_9755.8000Eighth 1000 fully-sampled squamate trees.squam_shl_new_Posterior_9755.9000Ninth 1000 fully-sampled squamate trees.squam_shl_new_Posterior_9755.10000Tenth 1000 fully-sampled squamate trees.
DOI: 10.5061/dryad.372c76c
title: Data from: A whole methylome study of ethanol exposure in brain and blood: an exploration of the utility of peripheral blood as proxy tissue for brain in alcohol methylation studies

description: Background: Recent reviews have highlighted the potential use of
 blood‐based methylation biomarkers as diagnostic and prognostic tools of
 current and future alcohol use and addiction. Due to the substantial
 overlap that often exists between methylation patterns across different
 tissues, including blood and brain, blood‐based methylation may track
 methylation changes in brain; however, little work has explored the
 overlap in alcohol‐related methylation in these tissues. Methods: To study
 the effects of alcohol on the brain methylome and identify possible
 biomarkers of these changes in blood, we performed a methylome‐wide
 association study in brain and blood from 40 male DBA/2J mice that
 received either an acute ethanol (EtOH) or saline intraperitoneal
 injection. To investigate all 22 million CpGs in the mouse genome, we
 enriched for the methylated genomic fraction using methyl‐CpG binding
 domain (MBD) protein capture followed by next‐generation sequencing
 (MBD‐seq). We performed association tests in blood and brain separately
 followed by enrichment testing to determine whether there was overlapping
 alcohol‐related methylation in the 2 tissues. Results: The top result for
 brain was a CpG located in an intron of Ttc39b (p = 5.65 × 10−08), and for
 blood, the top result was located in Espnl (p = 5.11 × 10−08). Analyses
 implicated pathways involved in inflammation and neuronal differentiation,
 such as CXCR4, IL‐7, and Wnt signaling. Enrichment tests indicated
 significant overlap among the top results in brain and blood. Pathway
 analyses of the overlapping genes converge on MAPKinase signaling (p = 5.6
 × 10−05) which plays a central role in acute and chronic responses to
 alcohol and glutamate receptor pathways, which can regulate neuroplastic
 changes underlying addictive behavior. Conclusions: Overall, we have shown
 some methylation changes in brain and blood after acute EtOH
 administration and that the changes in blood partly mirror the changes in
 brain suggesting the potential for DNA methylation in blood to be
 biomarkers of alcohol use.
description: READMECpG
 LocationsContains RaMWAS
 formatted files of CpG locationsCpG_locations.zipPhenotype FileContains phenotype data used in association analyses. Please see README file for data packets for description of variables.phenotype_file.txtCoverageContains RaMWAS formatted coverage (i.e., CpG score) files for each CpGcoverage.tar.gz
DOI: 10.5061/dryad.1vm20t6
title: Data from: Modeling spatiotemporal abundance of mobile wildlife in highly variable environments using boosted GAMLSS hurdle models

description: 1. Modeling organism distributions from survey data involves numerous
 statistical challenges, including zero-inflation, overdispersion, and
 selection and incorporation of environmental covariates. In environments
 with high spatial and temporal variability, addressing these challenges
 often requires numerous assumptions regarding organism distributions and
 their relationships to biophysical features. These assumptions may limit
 the resolution or accuracy of predictions resulting from survey-based
 distribution models. 2. We propose an iterative modeling approach that
 incorporates a negative binomial hurdle, followed by modeling the
 relationship of organism distribution and abundance to environmental
 covariates using generalized additive models (GAM) and generalized
 additive models for location, scale, and shape (GAMLSS). Our approach
 accounts for key features of survey data by separating binary
 (presence-absence) from count (abundance) data, separately modeling the
 mean and dispersion of count data, and incorporating selection of
 appropriate covariates and response functions from a suite of potential
 covariates while avoiding overfitting. 3. We apply our modeling approach
 to surveys of sea duck abundance and distribution in Nantucket Sound
 (Massachusetts, USA), which has been proposed as a location for offshore
 wind energy development. Our model results highlight the importance of
 spatiotemporal variation in this system, as well as identifying key
 habitat features including distance to shore, sediment grain size, and
 seafloor topographic variation. 4. Our work provides a powerful, flexible,
 and highly repeatable modeling framework with minimal assumptions that can
 be broadly applied to the modeling of survey data with high spatiotemporal
 variability. Applying GAMLSS models to the count portion of survey data
 allows us to incorporate potential overdispersion, which can dramatically
 affect model results in highly dynamic systems. Our approach is
 particularly relevant to systems in which little a priori knowledge is
 available regarding relationships between organism distributions and
 biophysical features, since it incorporates simultaneous selection of
 covariates and their functional relationships with organism responses.
description: NanSound_Ecol&EvolResults_ltduModel output for Long-tailed DuckResults_scotModel results for scoter species
DOI: 10.5061/dryad.35ks2
title: Data from: A public database of memory and naive B-cell receptor sequences

description: The vast diversity of B-cell receptors (BCR) and secreted antibodies
 enables the recognition of, and response to, a wide range of epitopes, but
 this diversity has also limited our understanding of humoral immunity. We
 present a public database of more than 37 million unique BCR sequences
 from three healthy adult donors that is many fold deeper than any existing
 resource, together with a set of online tools designed to facilitate the
 visualization and analysis of the annotated data. We estimate the clonal
 diversity of the naive and memory B-cell repertoires of healthy
 individuals, and provide a set of examples that illustrate the utility of
 the database, including several views of the basic properties of
 immunoglobulin heavy chain sequences, such as rearrangement length,
 subunit usage, and somatic hypermutation positions and dynamics.
description: Public B-cell
 datasetpublic-bcell-dataset.tgz