cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f8d4r
title: Data from: Methylation of avpr1a in the cortex of wild prairie voles: effects of CpG position and polymorphism

description: DNA methylation can cause stable changes in neuronal gene expression, but
 we know little about its role in individual differences in the wild. In
 this study, we focus on the vasopressin 1a receptor (avpr1a), a gene
 extensively implicated in vertebrate social behaviour, and explore natural
 variation in DNA methylation, genetic polymorphism and neuronal gene
 expression among 30 wild prairie voles (Microtus ochrogaster). Examination
 of CpG density across 8 kb of the locus revealed two distinct CpG islands
 overlapping promoter and first exon, characterized by few CpG
 polymorphisms. We used a targeted bisulfite sequencing approach to measure
 DNA methylation across approximately 3 kb of avpr1a in the retrosplenial
 cortex, a brain region implicated in male space use and sexual fidelity.
 We find dramatic variation in methylation across the avrp1a locus, with
 pronounced diversity near the exon–intron boundary and in a genetically
 variable putative enhancer within the intron. Among our wild voles,
 differences in cortical avpr1a expression correlate with DNA methylation
 in this putative enhancer, but not with the methylation status of the
 promoter. We also find an unusually high number of polymorphic CpG sites
 (polyCpGs) in this focal enhancer. One polyCpG within this enhancer
 (polyCpG 2170) may drive variation in expression either by disrupting
 transcription factor binding motifs or by changing local DNA methylation
 and chromatin silencing. Our results contradict some assumptions made
 within behavioural epigenetics, but are remarkably concordant with
 genome-wide studies of gene regulation.
description: Bisulfite sequencing raw
 readsPaired end reads from
 targeted bisulfite sequencing of avpr1a in 30 wild-caught prairie
 volesbis-seq-reads.tar.gz
DOI: 10.5061/dryad.06bp2
title: Data from: Tissue-specific transcriptome characterization for developing tadpoles of the northern leopard frog (Lithobates pipiens)

description: A potential cause of amphibian population declines are the impacts of
 environmental degradation on tadpole development. We conducted RNA
 sequencing on developing northern leopard frog tadpoles and through de
 novo transcriptome assembly we annotated a large number of open reading
 frames comparable in number and extent to genes identified in Xenopus.
 Using our transcriptome, we found transcript level changes between early
 (Gosner 26–31) and late (Gosner 36–41) stage tadpoles were the greatest in
 the tail, which is reabsorbed throughout development. There was an
 up-regulation of immunity genes in both the head and tail of the late
 tadpoles and a down-regulation of genes associated with the energy
 pathways of the mitochondria and the production of myosin. Overall,
 transcript level changes across development were consistent with studies
 on Xenopus and our findings highlight the broader utility of using RNA-seq
 to identify genes differentially expressed throughout development and in
 response to environmental pressures.
description: Lithobates pipiens
 transcriptomeSQLite database of
 northern leopard frog transcriptome produced using Trinity and annotated
 using Trinotate. Can be accessed in R using the RSQLite
 package.Lpipiens_transcriptome.sqlite
DOI: 10.5061/dryad.93kc5cb
title: Data from: Energy exchanges at contact events guide sensorimotor integration across intermodal delays

description: The brain must consider the arm's inertia to predict the arm's
 movements elicited by commands impressed upon the muscles. Here, we
 present evidence suggesting that the integration of sensory information
 leading to the representation of the arm's inertia does not take
 place continuously in time but only at discrete transient events, in which
 kinetic energy is exchanged between the arm and the environment. We used a
 visuomotor delay to induce cross-modal variations in state feedback and
 uncovered that the difference between visual and proprioceptive velocity
 estimations at isolated collision events was compensated by a change in
 the representation of arm inertia. The compensation maintained an
 invariant estimate across modalities of the expected energy exchange with
 the environment. This invariance captures different types of dysmetria
 observed across individuals following prolonged exposure to a fixed
 intermodal temporal perturbation and provides a new interpretation for
 cerebellar ataxia.
description: Pong_DataThe file contains pong and reaching data for all the four groups.
DOI: 10.5061/dryad.nv1f0
title: Data from: Genomic atolls of differentiation in coral reef fishes (Hypoplectrus spp, Serranidae)

description: Because the vast majority of species are well-diverged, relatively little
 is known about the genomic architecture of speciation during the early
 stages of divergence. Species within recent evolutionary radiations are
 often minimally diverged from a genomic perspective, and therefore provide
 rare opportunities to address this question. Here, we leverage the hamlet
 radiation (Hypoplectrus spp, brightly colored reef fishes from the
 tropical western Atlantic) to characterize genomic divergence during the
 early stages of speciation. Transect surveys and spawning observations in
 Belize, Honduras, and Panama confirm that sympatric barred (H. puella),
 black (H. nigricans) and butter (H. unicolor) hamlets are phenotypically
 distinct and reproductively isolated, although hybrid spawnings and
 individuals with intermediate phenotypes are seen on rare occasions. A
 survey of approximately 100,000 restriction-site associated SNPs in 126
 samples from the three species across the three replicate populations
 reveals extremely slight genome-wide divergence among species
 (Fst=0.0038), indicating that ecomorphological differences and functional
 reproductive isolation are maintained in sympatry in a backdrop of
 extraordinary genomic similarity. Nonetheless, a very small proportion of
 SNPs (0.05% on average) are identified as Fst outliers among sympatric
 species. Remarkably, a single SNP is identified as an outlier in repeated
 populations for the same species pair. A mini-contig assembled de novo
 around this SNP falls into the genomic region containing the HoxCa10 and
 HoxCa11 genes in 10 teleost species, suggesting an important role for Hox
 gene evolution in this radiation. This finding, if confirmed, would
 provide a better understanding of the links between micro- and
 macroevolutionary processes.
description: contig_sequencesSequences of the mini-contigs assembled around SNPs of interest. Blast hits indicated between parentheses.genepop_input_filesequence_datasnp_callsStacks catalogStacks catalog for the main assembly (m=3 M=2)stacks_catalog.tsvStructure input file (60th-70th percentiles)Structure input file (60th-70th percentiles)structure_input_file_60.txtStructure input file (70th-80th percentiles)Structure input file (70th-80th percentiles)structure_input_file_70.txtStructure input file (80th-90th percentiles)Structure input file (80th-90th percentiles)structure_input_file_80.txtStructure input file (above 90th percentiles)Structure input file (above 90th percentiles)structure_input_file_90.txtStructure input file (all data)Structure input file (all data)structure_input_file_all.txtTree file (above 90th percentile)Tree file (above 90th percentile)tree_file_90.txtTree file (all data)Tree file (all data)tree_file_all.txtMicrosatellite data (Genepop format, 3-digit)Microsatellite data (Genepop format, 3-digit)usats_raw_data.txt
DOI: 10.5061/dryad.65sd4
title: Data from: Dispensing pollen via catapult: explosive pollen release in mountain laurel (Kalmia latifolia)

description: The astonishing amount of floral diversity has inspired countless
 assumptions about the function of diverse forms and their adaptive
 significance; yet many of these hypothesized functions are untested. We
 investigated an often-repeated adaptive hypothesis about how an extreme
 floral form functions. In this study, we conducted four investigations to
 understand the adaptive function of explosive pollination in Kalmia
 latifolia, the mountain laurel. We first performed a kinematic analysis of
 anther movement. Second, we constructed a heat map of pollen trajectories
 in three-dimensional space. Third, we conducted field observations of
 pollinators and their behaviors while visiting K. latifolia. Finally, we
 conducted a pollination experiment to investigate the importance of
 pollinators for fertilization success. Our results suggest that insect
 visitation dramatically improves fertilization success and that bees are
 the primary pollinators that trigger explosive pollen release.
description: Supplemental Code and
 Data for Kalmia catapultThis file is a zipped
 folder that contains all the code and data used for statistical analysis
 for the paper, "Dispensing pollen via catapult: Explosive pollen
 release in mountain laurel (Kalmia latifolia)". There is code written
 in MATLAB, R, and Python.SupplementalCode_Kalmia.zip
DOI: 10.5061/dryad.5n01h
title: Data from: Modelling dynamics in protein crystal structures by ensemble refinement

description: Single-structure models derived from X-ray data do not adequately account
 for the inherent, functionally important dynamics of protein molecules. We
 generated ensembles of structures by time-averaged refinement, where local
 molecular vibrations were sampled by molecular-dynamics (MD) simulation
 whilst global disorder was partitioned into an underlying overall
 translation–libration–screw (TLS) model. Modeling of 20 protein datasets
 at 1.1–3.1 Å resolution reduced cross-validated R_free values by 0.3–4.9%,
 indicating that ensemble models fit the X-ray data better than single
 structures. The ensembles revealed that, while most proteins display a
 well-ordered core, some proteins exhibit a ‘molten core’ likely supporting
 functionally important dynamics in ligand binding, enzyme activity and
 protomer assembly. Order–disorder changes in HIV protease indicate a
 mechanism of entropy compensation for ordering the catalytic residues upon
 ligand binding by disordering specific core residues. Thus, ensemble
 refinement extracts dynamical details from the X-ray data that allow a
 more comprehensive understanding of structure–dynamics–function
 relationships.
description: Ensemble refinement 20
 datasetsensemble_refinement_elife_20_datasets.tar
DOI: 10.5061/dryad.q82kn
title: Data from: Distinctive fungal communities in an obligate African ant-plant mutualism

description: Three ant species nest obligately in the swollen-thorn domatia of the
 African ant-plant Vachellia (Acacia) drepanolobium, a model system for the
 study of ant-defence mutualisms and species coexistence. Here we report on
 the characteristic fungal communities generated by these ant species in
 their domatia. First, we describe behavioural differences between the ant
 species when presented with a cultured fungal isolate in the laboratory.
 Second, we use DNA metabarcoding to show that each ant species has a
 distinctive fungal community in its domatia, and that these communities
 remain characteristic of the ant species over two Kenyan sampling
 locations separated by 190 km. Third, we find that DNA extracted from
 female alates of Tetraponera penzigi and Crematogaster nigriceps contained
 matches for most of the fungal metabarcodes from those ant species'
 domatia, respectively. Fungal hyphae and other debris are also visible in
 sections of these alates' infrabuccal pockets. Collectively, our
 results indicate that domatium fungal communities are associated with the
 ant species occupying the tree. To the best of our knowledge, this is the
 first record of such ant-specific fungal community-level differences on
 the same myrmecophytic host species. These differences may be shaped by
 ant behaviour in the domatia, and by ants vectoring fungi when they
 disperse to establish new colonies. The roles of the fungi with respect to
 the ants and their host plant remain to be determined.
description: denoised
 sequencesFASTA file of sequences
 following processing of .sff files with Ampliconnoise in QIIME. Each
 sequence is labelled as &gt;sample.no_sequence.no, where sample.no
 corresponds to the original .sff file names, and sequence.no is sequential
 within each sample.amplnoiseout.fna.tar.gzmetadata fileMetadata file describing samples in this study.kenya_mapfile.txtmetadata file keyKey to metadata file describing samples in this study.kenya_mapfile_key.txtraw data filesRaw 454 data files (.sff format). Data are already demultiplexed, with one file for each sample in study, as described in the accompanying metadata file.Baker_2016_rawdata.tar.gz
DOI: 10.5061/dryad.vj2s888
title: Data from: Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

description: Hybridization, incomplete lineage sorting, and phylogenetic error produce
 similar incongruence patterns, representing a great challenge for
 phylogenetic reconstruction. Here, we use sequence capture data and
 multiple species tree and species network approaches to resolve the
 backbone phylogeny of the Neotropical genus Lachemilla, while
 distinguishing among sources of incongruence. We used 396 nuclear loci and
 nearly complete plastome sequences from 27 species to clarify the
 relationships among the major groups of Lachemilla, and explored multiple
 sources of conflict between gene trees and species trees inferred with a
 plurality of approaches. All phylogenetic methods recovered the four major
 groups previously proposed for Lachemilla, but species tree methods
 recovered different topologies for relationships between these four
 clades. Species network analyses revealed that one major clade,
 Orbiculate, is likely of ancient hybrid origin, representing one of the
 main sources of incongruence among the species trees. Additionally, we
 found evidence for a potential whole genome duplication event shared by
 Lachemilla and allied genera. Lachemilla shows clear evidence of ancient
 and recent hybridization throughout the evolutionary history of the group.
 Also, we show the necessity to use phylogenetic network approaches that
 can simultaneously accommodate incomplete lineage sorting and gene flow
 when studying groups that show patterns of reticulation.
description: Data from
 Morales-Briones et al New Phylogenomics of Lachemilla New
 PhythologistData_from_Morales-Briones_et_al_New_Phytologist_Phylogenomics_Lachemilla.zip
DOI: 10.5061/dryad.5r10j
title: Data from: A new model for ancient DNA decay based on paleogenomic meta-analysis

description: The persistence of DNA over archaeological and paleontological timescales
 in diverse environments has led to a revolutionary body of paleogenomic
 research, yet the dynamics of DNA degradation are still poorly understood.
 We analyzed 185 paleogenomic datasets and compared DNA survival with
 environmental variables and sample ages. We find cytosine deamination
 follows a conventional thermal age model, but we find no correlation
 between DNA fragmentation and sample age over the timespans analyzed, even
 when controlling for environmental variables. We propose a model for
 ancient DNA decay wherein fragmentation rapidly reaches a threshold, then
 subsequently slows. The observed loss of DNA over time may be due to a
 bulk diffusion process in many cases, highlighting the importance of
 tissues and environments creating effectively closed systems for DNA
 preservation. This model of DNA degradation is largely based on mammal
 bone samples due to published genomic dataset availability. Continued
 refinement to the model to reflect diverse biological systems and tissue
 types will further improve our understanding of ancient DNA breakdown
 dynamics.
description: Fragment length
 tablesFragment length
 frequency tables from genomic read alignments, n=185.lenTables.tar.gzmapDamage resultsResults (all output files) of mapDamage analyses, n=185 samples.mapDamage.tar.gzLambda estimationResults and plots of fragment length distribution (lambda) estimation, n=185 datasets.lambdaEstimates.tar.gzKmer summary statistics tablesKmer base-stacking energy, Shannon entropy, and genomic enrichment for all datasets (n=185)kmerEnrichment.tar.gzHistone periodicity estimationPlots and results of histone periodicity estimation in datasets yielding significant estimates, n=112.histoneEstimates.tar.gzScripts and expedient codeCustom scripts and expedient code used in analyses.scripts.tar.gzREADMESummary of repository contents.
DOI: 10.5061/dryad.g6q07
title: Data from: Projected polar bear sea ice habitat in the Canadian Arctic Archipelago

description: Background: Sea ice across the Arctic is declining and altering physical
 characteristics of marine ecosystems. Polar bears (Ursus maritimus) have
 been identified as vulnerable to changes in sea ice conditions. We use sea
 ice projections for the Canadian Arctic Archipelago from 2006 – 2100 to
 gain insight into the conservation challenges for polar bears with respect
 to habitat loss using metrics developed from polar bear energetics
 modeling. Principal Findings: Shifts away from multiyear ice to annual ice
 cover throughout the region, as well as lengthening ice-free periods, may
 become critical for polar bears before the end of the 21st century with
 projected warming. Each polar bear population in the Archipelago may
 undergo 2–5 months of ice-free conditions, where no such conditions exist
 presently. We identify spatially and temporally explicit ice-free periods
 that extend beyond what polar bears require for nutritional and
 reproductive demands. Conclusions/Significance: Under business-as-usual
 climate projections, polar bears may face starvation and reproductive
 failure across the entire Archipelago by the year 2100.
description: Depth-bathymetry
 fileUse as land mask file
 when depth=0depth.ncMITgcm_SeaIce_GFDL_CM3_RCP85_2006-2100Monthly average sea ice and snow conditions in the Canadian Arctic Archipelago 2006-2100 under climate warming scenario RCP85. Model output in netcdf files, time steps of 1 month starting on January 2006.MITgcm_SeaIce_GFDL_CM3_RCP85_2006_2100.zip
DOI: 10.5061/dryad.f81sj
title: Data from: Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants

description: Maize is well known for its exceptional structural diversity, including
 copy number variants (CNVs) and presence/absence variants (PAVs), and
 there is growing evidence for the role of structural variation in maize
 adaptation. While PAVs have been described in this important crop species,
 the extent of presence/absence variation and the relative position of
 inbred-specific regions remain to be elucidated. De novo genome sequencing
 of the F2 maize inbred line which played a key role in European breeding
 programs over the past 50 years revealed thousands of novel genomic
 regions, making up 88Mb of DNA, that are present in the F2 but not in B73.
 Comparison of B73 and F2 PAV localization revealed contrasted chromosomal
 distributions between the two inbreds and specific evolutionary dynamics
 of PAVs as compared to SNPs. Detailed sequence and functional annotation
 of F2 PAV sequences revealed hundreds of new genes with transcriptional
 support, but also a large fraction of repetitive sequences. Detailed
 analysis of sequence breakpoint highlights the role of double strand break
 repair, but also transposon insertion in PAV generation. Typing of the B73
 and F2 PAVs in maize temperate inbreds revealed that some PAVs are found
 only in European Flint material, thus pinpointing structural features that
 may be at the origin of adaptive traits involved in the success of this
 material. Linkage disequilibrium (LD) analysis revealed that LD is strong
 within PAVs, as expected by the absence of recombination in crosses where
 PAV is missing in one of the parents.
description: Draft pan-genome
 sequence of american B73 and european F2 maize linesThe archive file
 contains the draft sequence of the american B73 and the european F2 maize
 lines pan-genome (fast format), the gene prediction for F2-specific
 regions (gtf format) and the location of F2- and B73-specific regions (gff
 format). More details are available from README files included in the
 archive.Zea.B73.F2.pan-genome.INRA.tgzZeaMaysF2 draft assemblyZea mays F2 assembly draft release 1.0 02/2014 Aude Darracq, Johann Joets Contact: joets@moulon.inra.fr UMR GGE, 91190 Gif-sur-Yvette, France Assembly was conducted from a set of several illumina sequencing libraries paired-end and mate-pair as well as w mseq library for a total depth of 90X. Reads have been cleaned and error corrected before beeing assembled with ABySS software (K=81). Contigs were further assembled into scaffolds using SSPACE and gap were filled using Gapfiller. # scaffolds (&gt;200 bp) 590,011 largest scaffold 130 kb scaffold N50 14 kb assembly length 1.6 Gb % of covered genome 65ZeaMaysF2_draft_assembly.INRA.tgz
DOI: 10.5061/dryad.9480j
title: Data from: Fungal communities in Scandinavian lakes along a longitudinal gradient

description: This study investigates the diversity and distribution of fungal
 communities in 77 oligotrophic lakes in southern Norway and Sweden using
 454-sequencing with fungal-specific primers targeting ITS2 region of the
 rRNA gene. A total of 232 operational taxonomic units (OTUs) belonging to
 four recognized phyla were detected. A large proportion (70.69%) of the
 detected OTUs were Dikarya (Ascomycota and Basidiomycota), while
 Chytridiomycota dominated quantitatively (63.37% reads). The most abundant
 aquatic fungi were taxonomically assigned to Chytridiomycota, whose
 members are known to be saprobes on a large variety of substrates and
 parasites of phytoplankton, zooplankton, fungi and invertebrates,
 suggesting that resident fungi strictly depend on surfaces and, therefore,
 are closely associated with other types of aquatic organisms. Our results
 indicate that surface waters of oligotrophic lakes harbour a diverse pool
 of fungi, both with tentative terrestrial and true aquatic origin.
 Longitude and environmental factors were important in structuring the
 fungal community composition.
description: Raw 454 reads and
 mapping files for aquatic fungal communities in Scandinavian
 lakesThis zip-file contains:
 1) raw reads from 454 Roche sequencing machine (.sff) 2) qual file (.qual)
 3) raw reads (.fna) 4) flowgram file (.flow) 5) mapping file for forward
 reads (.txt) and 6) mapping file for reverse reads (.txt). In forward
 mapping file forward primer is the linker primer and in reverse mapping
 file reverse primer is the linker primer to recover all reads from the
 mixed orientation raw data.Khomich_et_al_2017_FUNECO.zip