cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bj83h5d
title: Data from: Convergent evolution of the army ant syndrome and congruence in big-data phylogenetics

description: Army ants are a charismatic group of organisms characterized by a suite of
 morphological and behavioral adaptations that includes obligate collective
 foraging, frequent colony relocation, and highly specialized wingless
 queens. This “army ant syndrome” underlies the ecological success of army
 ants and its evolution has been the subject of considerable debate. It has
 been argued to have arisen once or multiple times within the ant subfamily
 Dorylinae. To address this question in a phylogenetic framework I
 generated data from 2,166 loci and a comprehensive taxon sampling
 representing all 27 genera and 155 or approximately 22% of doryline
 species. Most analyses show strong support for convergent evolution of the
 army ant syndrome in the Old and New World but certain relationships are
 sensitive to analytics. I examine the signal present in this data set and
 find that conflict is diminished when only loci less likely to violate
 common phylogenetic model assumptions are considered. I also provide a
 temporal and spatial context for doryline evolution with time-calibrated,
 biogeographic, and diversification rate shift analyses. This study shows
 that the army ant syndrome is both an example of remarkable convergence of
 a complex set of traits and a case of long-term evolutionary stasis. The
 sensitivity of some of the phylogenetic results underscores the need for
 cautious analysis of phylogenomic data and calls for more efficient
 algorithms employing better-fitting models of molecular evolution.
 Congruence among results obtained using different analytics may be used to
 assess robustness in phylogenomics.
description: Data for project
 entitled "Convergent evolution of the army ant syndrome and
 congruence in big-data phylogenetics" by Marek L.
 BorowiecThis compressed file
 contains sequence files, alignments, configuration files, and output of
 analyses, including phylogenetic trees from the study.dorylinae-phylogenomics.tar.gz
DOI: 10.5061/dryad.d0r79
title: Data from: DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

description: Documenting the diversity of marine life is challenging because many
 species are cryptic, small, and rare, and belong to poorly known groups.
 New sequencing technologies, especially when combined with standardized
 sampling, promise to make comprehensive biodiversity assessments and
 monitoring feasible on a large scale. We used this approach to
 characterize patterns of diversity on oyster reefs across a range of
 geographic scales comprising a temperate location [Virginia (VA)] and a
 subtropical location [Florida (FL)]. Eukaryotic organisms that colonized
 multilayered settlement surfaces (autonomous reef monitoring structures)
 over a 6-mo period were identified by cytochrome c oxidase subunit I
 barcoding (&gt;2-mm mobile organisms) and metabarcoding (sessile and
 smaller mobile organisms). In a total area of ∼15.64 m2 and volume of
 ∼0.09 m3, 2,179 operational taxonomic units (OTUs) were recorded from
 983,056 sequences. However, only 10.9% could be matched to reference
 barcodes in public databases, with only 8.2% matching barcodes with both
 genus and species names. Taxonomic coverage was broad, particularly for
 animals (22 phyla recorded), but 35.6% of OTUs detected via metabarcoding
 could not be confidently assigned to a taxonomic group. The smallest size
 fraction (500 to 106 μm) was the most diverse (more than two-thirds of
 OTUs). There was little taxonomic overlap between VA and FL, and samples
 separated by ∼2 m were significantly more similar than samples separated
 by ∼100 m. Ground-truthing with independent assessments of taxonomic
 composition indicated that both presence–absence information and relative
 abundance information are captured by metabarcoding data, suggesting
 considerable potential for ecological studies and environmental
 monitoring.
description: PGM_RAWDATA_file1This file contains raw PGM (Ion Torrent, Life technology) data for adaptors 7, 8, 10 and 11. See file "PGM_SequencingRun" for corresponding samples.PGM_RAWDATA_file2This file contains raw PGM (Ion Torrent, Life technology) data for adaptors 12, 13, 14 and 15. See file "PGM_SequencingRun" for corresponding samples.Metabarcode_OTU_tableThe column "source ID" presents how each OTU was identified. SAP: Statistical assignment Package; NCBI/BOLD: &gt;97% match to a reference barcode in NCBI and/or BOLD barcode databases; 2mm: match an OTU identified via DNA barcoding in the &gt;2mm fraction; 500μm: match an OTU identified via DNA barcoding in the 2mm-500μm fraction The second sheet lists all OTUs that were discarded because they matched bacterial or non-COI sequences in NCBI.PGM_SequencingRunThe table presents the strategy used for multiplexing samples. Full primer sequences are provided in Table S4Metabarcode_OTUrepresentativesThe file contains one representative sequence per OTUMetabarcode_discardedOTUrepresentativesThe file contains one representative sequence per discarded OTU
DOI: 10.5061/dryad.nk81st2
title: Data from: Slippage of degenerate primers can cause variation in amplicon length

description: It is well understood that homopolymer regions should be avoided for
 primer binding to prevent off-target amplification. However, in
 metabarcoding, it is often difficult to avoid primer degeneracy in order
 to maximize taxa detection. We here investigate primer binding specificity
 using different primer sets from several invertebrate metabarcoding
 studies. Our results indicate that primers frequently bound 1-2 bp
 upstream in taxa where a homopolymer region was present in the
 amplification direction. Primer binding 1 bp downstream was observed less
 frequently. This primer slippage leads to taxon-specific length variation
 in amplicons and subsequent length variation in recovered sequences. Some
 widely used primer sets were severely affected by this bias, while others
 were not. While this variation will only have small impacts on the
 designation of Operational Taxonomic Units (OTUs) by clustering algorithms
 that ignore terminal gaps, primer sets employed in metabarcoding projects
 should be evaluated for their sensitivity to slippage. Moreover, steps
 should be taken to reduce slippage by improving protocols for primer
 design. For example, the flanking region adjacent to the 3′ end of the
 primer is not considered by current primer development software although
 GC clamps in this position could mitigate slippage.
description: Geneious 8
 fileGeneious 8 compatible
 file, containing primer extractions and read mappings for the 10 most
 abundant OTUs for each sample.2018
 slippage.geneiousSlippage_Scripts_raw_dataR scripts and other data files used in this study. Please always use the latest version number of each file (indicated by "_v***.R).sequence_raw_data_demultiplexedSequence data analysed in this study (fastq and fasta file). The full sequencing run is additionally available on SRA.
DOI: 10.5061/dryad.n3bb2
title: Data from: SNP discovery in non-model organisms: strand-bias and base-substitution errors reduce conversion rates

description: Single nucleotide polymorphisms (SNPs) have become the marker of choice
 for genetic studies in organisms of conservation, commercial or biological
 interest. Most SNP discovery projects in nonmodel organisms apply a
 strategy for identifying putative SNPs based on filtering rules that
 account for random sequencing errors. Here, we analyse data used to
 develop 4723 novel SNPs for the commercially important deep-sea fish,
 orange roughy (Hoplostethus atlanticus), to assess the impact of not
 accounting for systematic sequencing errors when filtering identified
 polymorphisms when discovering SNPs. We used SAMtools to identify
 polymorphisms in a velvet assembly of genomic DNA sequence data from seven
 individuals. The resulting set of polymorphisms were filtered to minimize
 ‘bycatch’—polymorphisms caused by sequencing or assembly error. An
 Illumina Infinium SNP chip was used to genotype a final set of 7714
 polymorphisms across 1734 individuals. Five predictors were examined for
 their effect on the probability of obtaining an assayable SNP: depth of
 coverage, number of reads that support a variant, polymorphism type (e.g.
 A/C), strand-bias and Illumina SNP probe design score. Our results
 indicate that filtering out systematic sequencing errors could
 substantially improve the efficiency of SNP discovery. We show that BLASTX
 can be used as an efficient tool to identify single-copy genomic regions
 in the absence of a reference genome. The results have implications for
 research aiming to identify assayable SNPs and build SNP genotyping assays
 for nonmodel organisms.
description: orpg_snpdev_glm_analysisFile contains an R script and set of data in a data folder. The R script contains descriptions of the data files, and reproduces the GLM analysis described in the paperorpg_sevenLibrary_velvetAssemblyAFG formatted output of de novo Velvet assembly of seven orange roughy Illumina libraries. Methods described in the paper.orpg_scaffolds_velvetAssemblyContigs produced by de novo velvet assembly of seven orange roughy Illumina libraries. Contigs are scaffolded, separated by 20 or more Ns. SNP id matches the ContigID-_, where scaffold number increases from 0, and identified the fragment of the contig obtained after splitting it at the Ns. Assembly methods described in the paper.454Contigsperl_scriptsPERL scripts provided in zip file. Instructions for use, and README file included in package.
DOI: 10.5061/dryad.7f1ss
title: Data from: Genome-wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories

description: Once considered a single species, the whitefly, Bemisia tabaci, is a
 complex of numerous morphologically indistinguishable species. Within the
 last three decades, two of its members (MED and MEAM1) have become some of
 the world's most damaging agricultural pests invading countries
 across Europe, Africa, Asia and the Americas and affecting a vast range of
 agriculturally important food and fiber crops through both feeding-related
 damage and the transmission of numerous plant viruses. For some time now,
 researchers have relied on a single mitochondrial gene and/or a handful of
 nuclear markers to study this species complex. Here, we move beyond this
 by using 38,041 genome-wide Single Nucleotide Polymorphisms, and show that
 the two invasive members of the complex are closely related species with
 signatures of introgression with a third species (IO). Gene flow patterns
 were traced between contemporary invasive populations within MED and MEAM1
 species and these were best explained by recent international trade. These
 findings have profound implications for delineating the B. tabaci species
 status and will impact quarantine measures and future management
 strategies of this global pest.
description: B_tabaci SNP calling
 filevcf file of the SNP
 calling from RADseq data (B. tabaci species complex) mapped to the B.
 tabaci MEAM1 reference genomeB_tabaci.vcfB_tabaci_scriptsScripts used to run the STACKS pipeline for SNP callingsam_files_batch_1sam_files_batch_2sam_files_batch_3sam_files_batch_4pyrad_0.85.vcfbatch_1_MED_genome.vcf
DOI: 10.5061/dryad.4kb75
title: Data from: Low-frequency fluctuations of the resting brain: high magnitude does not equal high reliability

description: The amplitude of low-frequency fluctuation (ALFF) measures low-frequency
 oscillations of the blood-oxygen-level-dependent signal, characterizing
 local spontaneous activity during the resting state. ALFF is a commonly
 used measure for resting-state functional magnetic resonance imaging
 (rs-fMRI) in numerous basic and clinical neuroscience studies. Using a
 test-retest rs-fMRI dataset consisting of 21 healthy subjects and three
 repetitive scans, we found that several key brain regions with high ALFF
 intensities (or magnitude) had poor reliability. Such regions included the
 posterior cingulate cortex, the medial prefrontal cortex in the default
 mode network, parts of the right and left thalami, and the primary visual
 and motor cortices. The above finding was robust with regard to different
 sample sizes (number of subjects), different scanning parameters
 (repetition time) and variations of test-retest intervals (i.e.,
 intra-scan, intra-session, and inter-session reliability), as well as with
 different scanners. Moreover, the qualitative, map-wise results were
 validated further with a region-of-interest-based quantitative analysis
 using “canonical” coordinates as reported previously. Therefore, we
 suggest that the reliability assessments be incorporated in future ALFF
 studies, especially for the brain regions with a large ALFF magnitude as
 listed in our paper. Splitting single data into several segments and
 assessing within-scan “test-retest” reliability is an acceptable
 alternative if no “real” test-retest datasets are available. Such
 evaluations might become more necessary if the data are collected with
 clinical scanners whose performance is not as good as those that are used
 for scientific research purposes and are better maintained because the
 lower signal-to-noise ratio may further dampen ALFF reliability.
description: Three-session
 resting-state fMRI dataThis data is
 three-session resting-state fMRI data collected by a 3T Siemens MR scanner
 from 21 healthy adults. The data is not preprocessed. The format of the
 data is NIFTI. More details can be found in data description.txt or
 subject_list.xlsx.data.zip
DOI: 10.5061/dryad.n65k2
title: Data from: SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data

description: SSR_pipeline is a flexible set of programs designed to efficiently
 identify simple sequence repeats (e.g., microsatellites) from paired-end
 high-throughput Illumina DNA sequencing data. The program suite contains 3
 analysis modules along with a fourth control module that can automate
 analyses of large volumes of data. The modules are used to 1) identify the
 subset of paired-end sequences that pass Illumina quality standards, 2)
 align paired-end reads into a single composite DNA sequence, and 3)
 identify sequences that possess microsatellites (both simple and compound)
 conforming to user-specified parameters. The microsatellite search
 algorithm is extremely efficient, and we have used it to identify repeats
 with motifs from 2 to 25bp in length. Each of the 3 analysis modules can
 also be used independently to provide greater flexibility or to work with
 FASTQ or FASTA files generated from other sequencing platforms (Roche 454,
 Ion Torrent, etc.). We demonstrate use of the program with data from the
 brine fly Ephydra packardi (Diptera: Ephydridae) and provide empirical
 timing benchmarks to illustrate program performance on a common desktop
 computer environment. We further show that the Illumina platform is
 capable of identifying large numbers of microsatellites, even when using
 unenriched sample libraries and a very small percentage of the sequencing
 capacity from a single DNA sequencing run. All modules from SSR_pipeline
 are implemented in the Python programming language and can therefore be
 used from nearly any computer operating system (Linux, Macintosh, and
 Windows).
description: Ephydra_packardi_read-pair_set1A gzip file containing one of two fastq files associated with the data set. Each gzip file contains a large FASTQ sequence file. Files contain congruent sequences from the paired-end run. For example, the first entry from file set 1 contains the first half of the read pair, while the first entry from file set 2 contains the second half of the read pair. There are 9015656 sequences in each file, and each sequence uses 4 lines in the file (consistent with the FASTQ format). These data can be used to reproduce the "Benchmarking and Code Performance" section of the manuscript associated with this Dryad submission.Ephydra_packardi_read-pair_set2A gzip file containing one of two fastq files associated with the data set. Each gzip file contains a large FASTQ sequence file. Files contain congruent sequences from the paired-end run. For example, the first entry from file set 1 contains the first half of the read pair, while the first entry from file set 2 contains the second half of the read pair. There are 9015656 sequences in each file, and each sequence uses 4 lines in the file (consistent with the FASTQ format). These data can be used to reproduce the "Benchmarking and Code Performance" section of the manuscript associated with this Dryad submission.
DOI: 10.5061/dryad.pg3888r
title: Data from: Climate change, wildfire, and vegetation shifts in a high-inertia forest landscape: Western Washington, U.S.A.

description: Future vegetation shifts under changing climate are uncertain for forests
 with infrequent stand-replacing disturbance regimes. These high-inertia
 forests may have long persistence even with climate change because
 disturbance-free periods can span centuries, broad-scale regeneration
 opportunities are fewer relative to frequent-fire systems, and mature tree
 species are long-lived with relatively high tolerance for sub-optimal
 growing conditions. Here, we used a combination of empirical and
 process-based modeling approaches to examine vegetation projections across
 high-inertia forests of Washington State, USA, under different climate and
 wildfire futures. We ran our models without forest management (to assess
 inherent system behavior/potential) and also with wildfire suppression.
 Projections suggested relatively stable mid-elevation forests through the
 end of the century despite anticipated increases in wildfire. The largest
 changes were projected at the lowest and uppermost forest boundaries, with
 upward expansion of the driest low-elevation forests and contraction of
 cold, high-elevation subalpine parklands. While forests were overall
 relatively stable in simulations, increases in early-seral conditions and
 decreases in late-seral conditions occurred as wildfire became more
 frequent. With partial fire suppression, projected changes were dampened
 or delayed, suggesting a potential tool to forestall change in some (but
 not all) high-inertia forests, especially since extending fire-free
 periods does little to alter overall fire regimes in these systems. Model
 projections also illustrated the importance of fire regime context and
 projection limitations; the time horizon over which disturbances will
 eventually allow the system to shift are so long that the prevailing
 climatic conditions under which many of those shifts will occur are beyond
 what most climate models can predict with any certainty. This will present
 a fundamental challenge to setting expectations and managing for long-term
 change in these systems.
description: MC2 and STSM models and
 outputThe MC2 folder contains
 NetCDF output generated by the dynamic global vegetation model MC2. The
 STSM folder contains all models and output related to the STSM
 models.Data.zip
DOI: 10.5061/dryad.1qp42
title: Data from: Chromatin is an ancient innovation conserved between Archaea and Eukarya

description: The eukaryotic nucleosome is the fundamental unit of chromatin, comprising
 a protein octamer that wraps ~147bp of DNA and has essential roles in DNA
 compaction, replication and gene expression. Nucleosomes and chromatin
 have long been considered to be unique to eukaryotes, yet studies of
 select archaea have identified homologs of histone proteins that assemble
 into tetrameric nucleosomes. Here we report the first archaeal genome-wide
 nucleosome occupancy map, as observed in the halophile Haloferax volcanii.
 Nucleosome occupancy was compared with gene expression by compiling a
 comprehensive transcriptome of Hfx. volcanii. We found that archaeal
 transcripts possess hallmarks of eukaryotic chromatin structure:
 nucleosome-free regions at transcriptional start sites and conserved 1 and
 +1 promoter nucleosomes. Our observations demonstrate that histones and
 chromatin architecture evolved before the divergence of Archaea and
 Eukarya, suggesting that the fundamental role of chromatin in the
 regulation of gene expression is ancient.
description: Haloferax volcanii
 reference genomeThe Hfx. volcanii genome
 that we used to align readshaloferax_volcanii_merge.faHaloferax nucleosome centre positionsArchaeal browser track with 1-based nucleosome centre positions, bed fileArchaeal_browser_track_2N.bedHaloferax transcriptsManually-curated transcripts based on RNA-seq datatranscripts_DSN_manually_curated.bedExpression data for transcriptsFPKM and expression data for all transcriptstranscripts_expression_FPKM.txtNucleosome MNase-seq data aligned to Haloferax genome (BAM file)Aligned nucleosome readshv-2N-sorted.bamControl undigested data aligned to Haloferax genome (BAM file)Crosslinked undigested DNA controlhv-2G-sorted.bamNucleosome MNase-seq data aligned to Haloferax genome (BAI file)hv-2N-sorted.baiControl undigested data aligned to Haloferax genome (BAI file)hv-2G-sorted.baiControl MNase-seq data aligned to Haloferax genome (BAM file PART1)naked DNA control (MNase-seq)hv-naked-sorted.bam_part1Control MNase-seq data aligned to Haloferax genome (BAM file PART2)naked DNA control (MNase-seq)hv-naked-sorted.bam_part2Control MNase-seq data aligned to Haloferax genome (BAI file)hv-naked-sorted.bai
DOI: 10.5061/dryad.mh206
title: Data from: High mutation rates limit evolutionary adaptation in Escherichia coli

description: Mutation is fundamental to evolution, because it generates the genetic
 variation on which selection can act. In nature, genetic changes often
 increase the mutation rate in systems that range from viruses and bacteria
 to human tumors. Such an increase promotes the accumulation of frequent
 deleterious or neutral alleles, but it can also increase the chances that
 a population acquires rare beneficial alleles. Here, we study how up to
 100-fold increases in Escherichia coli’s genomic mutation rate affect
 adaptive evolution. To do so, we evolved multiple replicate populations of
 asexual E. coli strains engineered to have four different mutation rates
 for 3000 generations in the laboratory. We measured the ability of evolved
 populations to grow in their original environment and in more than 90
 novel chemical environments. In addition, we subjected the populations to
 whole genome population sequencing. Although populations with higher
 mutation rates accumulated greater genetic diversity, this diversity
 conveyed benefits only for modestly increased mutation rates, where
 populations adapted faster and also thrived better than their ancestors in
 some novel environments. In contrast, some populations at the highest
 mutation rates showed reduced adaptation during evolution, and failed to
 thrive in all of the 90 alternative environments. In addition, they
 experienced a dramatic decrease in mutation rate. Our work demonstrates
 that the mutation rate changes the global balance between deleterious and
 beneficial mutational effects on fitness. In contrast to most theoretical
 models, our experiments suggest that this tipping point already occurs at
 the modest mutation rates that are found in the wild.
description: Sequencing
 datawgs_data.tar.gzPhenotype data (mutation rates, growth curves, etc)phenotyping_data.tar.gz