cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4tp56
title: Data from: Experimental reduction of intromittent organ length reduces male reproductive success in a bug

description: It is now clear in many species that male and female genital evolution has
 been shaped by sexual selection. However, it has historically been
 difficult to confirm correlations between morphology and fitness, as
 genital traits are complex and manipulation tends to impair function
 significantly. In this study, we investigate the functional morphology of
 the elongate male intromittent organ (or processus) of the seed bug
 Lygaeus simulans, in two ways. We first use micro-computed tomography
 (micro-CT) and flash-freezing to reconstruct in high resolution the
 interaction between the male intromittent organ and the female internal
 reproductive anatomy during mating. We successfully trace the path of the
 male processus inside the female reproductive tract. We then confirm that
 male processus length influences sperm transfer by experimental ablation
 and show that males with shortened processi have significantly reduced
 post-copulatory reproductive success. Importantly, male insemination
 function is not affected by this manipulation per se. We thus present
 rare, direct experimental evidence that an internal genital trait
 functions to increase reproductive success and show that, with appropriate
 staining, micro-CT is an excellent tool for investigating the functional
 morphology of insect genitalia during copulation.
description: Data
 allAll data from processus
 manipulation experiments 1-3CT scan
 filesRaw slice images from CT
 scans, and VAXML files and 3D pdfs of 3D
 reconstructions.
DOI: 10.5061/dryad.jk17vk0
title: Data from: Control of entropy in neural models of environmental state

description: Humans and animals construct internal models of their environment in order
 to select appropriate courses of action. The representation of uncertainty
 about the current state of the environment is a key feature of these
 models that controls the rate of learning as well as directly affecting
 choice behaviour. To maintain flexibility, given that uncertainty
 naturally decreases over time, most theoretical inference models include a
 dedicated mechanism to drive up model uncertainty. Here we probe the
 long-standing hypothesis that noradrenaline is involved in determining the
 entropy, and thus flexibility, of neural models. Pupil diameter, which
 indexes neuromodulatory state including noradrenaline release, predicted
 increases (but not decreases) in entropy in a neural state model encoded
 in human medial orbitofrontal cortex, as measured using multivariate
 functional MRI. Activity in anterior cingulate cortex predicted pupil
 diameter. These results provide evidence for top-down, neuromodulatory
 control of entropy in neural state models.
description: Epoched Pupil
 DataThis is epoched pupil
 data from the fMRI session, as detailed in the paper, and can be used to
 reproduce the pupil results.epoched_pupil.mat
DOI: 10.34740/kaggle/dsv/14630389
title: Balochi Language to English Translation Dataset
DOI: 10.5061/dryad.463n4v7
title: Data from: Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, and immune defence‐related genes

description: Elucidating the genetic basis of adaptation to the local environment can
 improve our understanding of how the diversity of life has evolved. In
 this study we used a dense SNP array to identify candidate loci
 potentially underlying fine-scale local adaptation within a large Atlantic
 salmon (Salmo salar) population. By combining outlier, gene–environment
 association, and haplotype homozygosity analyses, we identified multiple
 regions of the genome with strong evidence for diversifying selection.
 Several of these candidate regions had previously been identified in other
 studies, demonstrating that the same loci could be adaptively important in
 Atlantic salmon at sub-drainage, regional and continental scales. Notably,
 we identified signals consistent with local selection around genes
 associated with variation in sexual maturation, energy homeostasis, and
 immune defence. These included the large-effect age-at-maturity gene
 vgll3, the known obesity gene mc4r, and major histocompatibility complex
 II. Most strikingly, we confirmed a genomic region on Ssa09 that was
 extremely differentiated among subpopulations, and that is also a
 candidate for local selection over the global range of Atlantic salmon.
 This region co-localized with a haplotype strongly associated with
 spawning ecotype in sockeye salmon (Oncorhynchus nerka), with
 circumstantial evidence that the same gene (six6) may be the selective
 target in both cases. The phenotypic effect of this region in Atlantic
 salmon remains cryptic, although allelic variation is related to upstream
 catchment area and co-varies with timing of the return spawning migration.
 Our results further inform management of Atlantic salmon and open multiple
 avenues for future research.
description: SsalLocSeln_genotypes.tarTar.gz archive containing genotype data in Plink PED format.SsalLocSeln_code.tarTar.gz archive containing code and necessary files for running analyses.SsalLocSeln_results.tarTar.gz archive containing final results for all analyses and all SNPs, including package-specific significance tests.SsalLocSeln_raw_results.tarTar.gz archive containing raw output files from analyses.SsalLocSeln_ggplot.tarTar.gz archive containing ggplot2 code and data files for making the figures in the manuscript.
DOI: 10.5061/dryad.s3tc6
title: Data from: A new mesophotic goby, Palatogobius incendius (Teleostei: Gobiidae), and the first record of invasive lionfish preying on undescribed biodiversity

description: A new species of deep-reef fish in the goby genus Palatogobius is
 described from recent submersible collections off Curaçao and Dominica.
 Video footage of schools of this species reveal predation by the invasive
 Indo-Pacific lionfish (Pterois spp.), the first record of undescribed
 fauna potentially being eaten by lionfish outside of its native range. We
 present molecular phylogenetic data for all valid species of Palatogobius
 and related genera, as well as a taxonomic key to the species of
 Palatogobius and a generic key to Palatogobius and related genera in the
 western Atlantic. Lastly, we discuss ecological and behavioral aspects of
 some deep-reef fishes in light of potential threats from invasive
 lionfish.
description: Lionfish preying upon
 undescribed speciesDuring a submersible
 dive off the coast of Curacao in 2015, researchers from the Smithsonian
 Deep Reef Observation Project (DROP) observed an invasive lionfish preying
 on an undescribed species of deep-reef fish. The species is a member of
 the family Gobiidae (gobies), and the genus Palatogobius. It occurs in
 large schools on deep reefs at depths of 88-200 m. It is currently being
 formally described in a scientific journal by the Smithsonian team. This
 species is one of many new species recently discovered through exploratory
 submersible diving in the Caribbean.Lionfish_preying_upon_undescribed_species_full_I.mp4
DOI: 10.5061/dryad.v1ff0
title: Data from: Lambda interferon restructures the nasal microbiome and increases susceptibility to Staphylococcus aureus superinfection

description: Much of the morbidity and mortality associated with influenza virus
 respiratory infection is due to bacterial coinfection with pathogens that
 colonize the upper respiratory tract such as methicillin-resistant
 Staphylococcus aureus (MRSA) and Streptococcus pneumoniae. A major
 component of the immune response to influenza virus is the production of
 type I and III interferons. Here we show that the immune response to
 infection with influenza virus causes an increase and restructuring of the
 upper respiratory microbiota in wild-type (WT) mice but not in Il28r−/−
 mutant mice lacking the receptor for type III interferon. Mice lacking the
 IL-28 receptor fail to induce STAT1 phosphorylation and expression of its
 regulator, SOCS1. Il28r−/− mutant mice have increased expression of
 interleukin-22 (IL-22), as well as Ngal and RegIIIγ, in the nasal cavity,
 the source of organisms that would be aspirated to cause pneumonia.
 Proteomic analysis reveals changes in several cytoskeletal proteins that
 contribute to barrier function in the nasal epithelium that may contribute
 to the effects of IL-28 signaling on the microbiota. The importance of the
 effects of IL-28 signaling in the pathogenesis of MRSA pneumonia after
 influenza virus infection was confirmed by showing that WT mice nasally
 colonized before or after influenza virus infection had significantly
 higher levels of infection in the upper airways, as well as significantly
 greater susceptibility to MRSA pneumonia than Il28r−/− mutant mice did.
 Our results suggest that activation of the type III interferon in response
 to influenza virus infection has a major effect in expanding the upper
 airway microbiome and increasing susceptibility to lower respiratory tract
 infection.
description: Demultiplexed sequence
 reads16S rRNA sequences in
 fastq format. The paired-end reads have been merged and assigned to sample
 IDs using sample-specific barcodes.demultiplexed_seqs_merged_alldata.fq.gzMetadata for sequenced samplesIndicates flu (+/ -) and group (wt versus IL28R) for sequenced samples included in the study.Metadata_Mouse_IL28R_WT_Flu.xlsx
DOI: 10.5061/dryad.vv82q
title: Data from: Microsatellite markers from the Ion Torrent: a multi-species contrast to 454 shotgun sequencing

description: The development and screening of microsatellite markers have been
 accelerated by next-generation sequencing (NGS) technology and in
 particular GS-FLX pyro-sequencing (454). More recent platforms such as the
 PGM semiconductor sequencer (Ion Torrent) offer potential benefits such as
 dramatic reductions in cost, but to date have not been well utilized.
 Here, we critically compare the advantages and disadvantages of
 microsatellite development using PGM semiconductor sequencing and GS-FLX
 pyro-sequencing for two gymnosperm (a conifer and a cycad) and one
 angiosperm species. We show that these NGS platforms differ in the
 quantity of returned sequence data, unique microsatellite data and primer
 design opportunities, mostly consistent with the differences in read
 length. The strength of the PGM lies in the large amount of data generated
 at a comparatively lower cost and time. The strength of GS-FLX lies in the
 return of longer average length sequences and therefore greater
 flexibility in producing markers with variable product length, due to
 longer flanking regions, which is ideal for capillary multiplexing. These
 differences need to be considered when choosing a NGS method for
 microsatellite discovery. However, the ongoing improvement in read lengths
 of the NGS platforms will reduce the disadvantage of the current short
 read lengths, particularly for the PGM platform, allowing greater
 flexibility in primer design coupled with the power of a larger number of
 sequences.
description: IonXpress_001_Macrozamia
 riedleiIonXpress_001_Macrozamia.fastaIonXpress_015_Podocarpus drouynianusIonXpress_015_Podocarpus.fastaIonXpress_016_Ricinocarpos
DOI: 10.5061/dryad.d7pr6
title: Data from: Dry habitats were crucibles of domestication in the evolution of agriculture in ants

description: The evolution of ant agriculture, as practiced by the fungus-farming
 “attine” ants, is thought to have arisen in the wet rainforests of South
 America about 55-65 Ma. Most subsequent attine agricultural evolution,
 including the domestication event that produced the ancestor of higher
 attine cultivars, is likewise hypothesized to have occurred in South
 American rainforests. The “out-of-the-rainforest” hypothesis, while
 generally accepted, has never been tested in a phylogenetic context. It
 also presents a problem for explaining how fungal domestication might have
 occurred, given that isolation from free-living populations is required.
 Here, we use phylogenomic data from ultra-conserved element (UCE) loci to
 reconstruct the evolutionary history of fungus-farming ants, reduce
 topological uncertainty, and identify the closest non-fungus-growing ant
 relative. Using the phylogeny we infer the history of attine agricultural
 systems, habitat preference, and biogeography. Our results show that the
 out-of-the-rainforest hypothesis is correct with regard to the origin of
 attine ant agriculture; however, contrary to expectation, we find that the
 transition from lower to higher agriculture very likely occurred in a
 seasonally dry habitat, inhospitable to the growth of free-living
 populations of attine fungal cultivars. We suggest that dry habitats
 favored the isolation of attine cultivars over the evolutionary time spans
 necessary for domestication to occur.
description: Raw illumina reads (SRA
 BioProject PRJNA379607).Raw illumina reads for
 all newly sequenced specimens in this
 study.Alignment supermatrices
 - filtered, trimmedSeveral of the
 concatenated supermatrices analyzed in this study. Includes the
 attine-118t-f75 matrix, attine-119t-f75 matrix, and the
 attine-118t-f75-base-comp matrix.alignment-supermatrices.zipData partitioning schemesData partitioning schemes for the attine-118t-f75 supermatrix. Includes by-locus, rculster, and kmeans schemes. In RAxML format.attine-118t-f75-partitioning-schames.zipBEAST XML data files.All BEAST XML files used in divergence dating analyses. Five separate DNA matrices were created using 20 randomly selected UCE loci.beast-xml-files.zipBigeography, trait, and diversification rate analysis filesData files and scripts for all biogeography, trait, and diversification rate analyses.biogeo-trait-diversification-files.zipAll phylogenetic treesAll resulting phylogenetic trees generated in this study.phylogenetic-trees.zipSupplementary tablesAll supplementary tables (same as Appendix 1 in paper).supplementary-tables.xlsUCE alignments - unfiltered, untrimmedUCE alignments for the 118t and 119t datasets. Data were aligned using MAFFT, but were not trimmed or filtered. Data from the 119t alignment set were uploaded to GenBank.uce-alignments-untrimmed.zipTrinity assembliesBulk trinity assemblies. Includes newly sequenced samples and samples from previous studies.all-trinity-contigs.zip
DOI: 10.5061/dryad.mm81p
title: Data from: Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts

description: The phylogenetic relationships for rapid species radiations are difficult
 to disentangle. Here we study one such case, namely the genus Triturus,
 which is composed of the marbled and crested newts. We analyze data for 38
 genetic markers, positioned in 3-prime untranslated regions of
 protein-coding genes, obtained with 454 sequencing. Our dataset includes
 twenty Triturus newts and represents all nine species. Bayesian analysis
 of population structure allocates all individuals to their respective
 species. The branching patterns obtained by data concatenation, Bayesian
 concordance analysis and coalescent-based estimations of the species tree
 differ from one another. The data concatenation based species tree shows
 high branch support but branching order is considerably affected by allele
 choice in the case of heterozygotes in the concatenation process. Bayesian
 concordance analysis expresses the conflict between individual gene trees
 for part of the Triturus species tree as low concordance factors. The
 coalescent-based species tree is relatively similar to a previously
 published species tree based upon morphology and full mtDNA and any
 conflicting internal branches are not highly supported. Our findings
 reflect high gene tree discordance due to incomplete lineage sorting
 (possibly aggravated by hybridization) in combination with low information
 content of the markers employed (as can be expected for relatively recent
 species radiations). This case study highlights the complexity of
 resolving rapid radiations and we acknowledge that to convincingly resolve
 the Triturus species tree even more genes will have to be consulted.
description: Sanger
 sequencingThe additional sequences
 obtained with Sanger sequencing (in ABI format).Sanger_sequencing.zipSNP reportThe SNP report produced with GS Amplicon Variant Analyzer 2.8.AlignmentsThe alignments (raw, with indels removed, and collapsed into haplotypes).Input filesThe input files for BAPS, MrBayes, BUCKy and *BEAST.Input_files_BAPS_MrBayes_Bucky_StarBEAST.zipIndividual gene treesThe individual gene trees resulting from MrBayes used in BUCKy.Gene_trees_MrBayes_BUCKy.zip*BEAST species treesThe species tree resulting from the eight *BEAST runs.Species_trees_StarBeast.zip454 sequencingThe raw 454 reads (in SFF format).454sequencing_RAW_data.sff
DOI: 10.5061/dryad.65th7
title: Data from: Deep sequencing of a candidate region harboring the SOX9 gene for the canine XX disorder of sex development

description: A disorder of sex development (DSD) in dogs with female sex chromosomes
 (78, XX), a lack of the SRY gene and the presence of testes or ovotestes
 is commonly diagnosed in numerous breeds. The molecular background of DSD
 is not fully recognized but has been linked to the copy number variation
 in the region harboring the SOX9 gene. We applied a genome-wide
 association study and targeted next-generation sequencing techniques to
 compare DSD and normal female dogs. The genome-wide association study did
 not indicate a significant chromosome region. Targeted next-generation
 sequencing of a 1.5-Mb region on canine chromosome 9 harboring the SOX9
 gene revealed two putatively DSD-associated copy number variations 355 kb
 upstream and 691 kb downstream of SOX9, four blocks of low polymorphism
 and two blocks of an elevated heterozygosity. An initial next-generation
 sequencing analysis showed an association with two SNPs, but validation in
 larger cohorts did not confirm this result. We identified a large
 homologous fragment (over 243.8 kb), named hfMAGI2, located upstream of
 SOX9, that overlaps a known copy number variation region. It shows a high
 sequence similarity with the 5′ flanking region of the MAGI2 gene located
 on canine chromosome 18 that encodes a protein involved in ovary formation
 during early embryonic development. Our study showed that the identified
 copy number variation region located upstream of the SOX9 gene contains
 potential regulatory sequences (long non-coding RNA and hfMAGI2) and led
 to the assumption that a multiplication of this element may alter
 expression of the SOX9 gene, triggering the DSD phenotype.
description: DSD27analysis_FinalReport.txt
DOI: 10.5061/dryad.5bc8vd7
title: Data from: Zebrafish differentially process colour across visual space to match natural scenes

description: Animal eyes have evolved to process behaviorally important visual
 information, but how retinas deal with statistical asymmetries in visual
 space remains poorly understood. Using hyperspectral imaging in the field,
 in vivo 2-photon imaging of retinal neurons, and anatomy, here we show
 that larval zebrafish use a highly anisotropic retina to asymmetrically
 survey their natural visual world. First, different neurons dominate
 different parts of the eye and are linked to a systematic shift in inner
 retinal function: above the animal, there is little color in nature, and
 retinal circuits are largely achromatic. Conversely, the lower visual
 field and horizon are color rich and are predominately surveyed by
 chromatic and color-opponent circuits that are spectrally matched to the
 dominant chromatic axes in nature. Second, in the horizontal and lower
 visual field, bipolar cell terminals encoding achromatic and
 color-opponent visual features are systematically arranged into distinct
 layers of the inner retina. Third, above the frontal horizon, a high-gain
 UV system piggybacks onto retinal circuits, likely to support prey
 capture.
description: Data
 StructureList of all uploaded
 data and explanationsSelected Figure panel
 dataSelected Figure panel
 dataFigure
 Arrangement.zipProcessed
 dataPreprocessed
 dataPreprocessed traces
 (z-normalised) with timing and stimulus arrays for tetrachromatic noise
 stimulus
DOI: 10.5061/dryad.687q0
title: Data from: A new Givetian Athyridid species from NW Africa discovered by 3D reconstruction of shell morphology of internal molds

description: A new method of analyzing the internal shell morphology (including the
 complete brachidium of internal molds) of articulated brachiopod shells
 through the use of serial sections and digital three-dimensional
 reconstruction is presented. The method introduced is essential for the
 study of internal shell structures such as brachidia, or cardinalia, if
 computed tomography (CT) is not suitable or if a CT scanner is not
 available. A new species of Athyris from Givetian beds of Northwest Africa
 was selected to exemplify this method. To compare this species with
 figured serial sections in the literature, two-dimensional drawings of
 grinding surfaces are provided. Athyris africana n. sp. is only preserved
 as internal molds of articulated specimens. The new species is included in
 the evolutionary lineage of the group around Athyris concentrica. The
 faunal assemblage of A. africana n. sp. shows affinities to Western
 European and North American brachiopod faunas.
description: Supplemental Data
 1Data
 set of images of grinding surfaces of Athyris africana n. sp. SMF 94007.2
 (right), SMF 94007.3 (center), SMF 94007.4 (left and used for
 reconstruction).Schemm-Gregory_2014_Supplemental_Data_1.zipSupplemental Data 23-D reconstruction of Athyris africana n. sp. created in SPIERSedit based on Supplemental Data 1. The reconstruction provided is weakly smoothed.Schemm-Gregory_2014_Supplemental_Data_2.spvSupplemental Data 3Measurements of material studied. Abbreviations: *=holotype; ●=figured; ∆=drawn; +=sectioned; ◊=SEM.Schemm-Gregory_2014_Supplemental_Data_3.doc
DOI: 10.5061/dryad.305s0
title: Data from: A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales

description: Comparisons of flowering plant genomes reveal multiple rounds of ancient
 polyploidy characterized by large intra-genomic syntenic blocks. Three
 such whole genome duplication (WGD) events, designated as rho (ρ), sigma
 (σ), and tau (τ), have been identified in the genomes of cereal grasses.
 Precise dating of these WGD events is necessary to investigate how they
 have influenced diversification rates, evolutionary innovations, and
 genomic characteristics such as the GC profile of protein coding
 sequences. The timing of these events has remained uncertain due to the
 paucity of monocot genome sequence data outside the grass family
 (Poaceae). Phylogenomic analysis of protein coding genes from sequenced
 genomes and transcriptome assemblies from 35 species, including
 representatives of all families within the Poales, has resolved the timing
 ofrho and sigma relative to speciation events and placed tau prior to
 divergence of Asparagales and the commelinids but after divergence with
 eudicots. Examination of gene family phylogenies indicates that
 rhooccurred just prior to the diversification of Poaceae and sigma
 occurred before early diversification of Poales lineages but after the
 Poales-commelinid split. Additional lineage specific WGD events were
 identified on the basis of the transcriptome data. Gene families
 exhibiting high GC content are underrepresented among those with duplicate
 genes that persisted following these genome duplications. However, genome
 duplications had little overall influence on lineage-specific changes in
 the GC content of coding genes. Improved resolution of the timing of WGD
 events in monocot history provides evidence for the influence of
 polyploidization on functional evolution and species diversification.
description: McKain_etal_2016_Poales_WGD_GC.tar.gzAll data for project. See ReadMe.