cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n2606
title: Data from: Bayesian inference of reticulate phylogenies under the multispecies network coalescent

description: The multispecies coalescent (MSC) is a statistical framework that models
 how gene genealogies grow within the branches of a species tree. The field
 of computational phylogenetics has witnessed an explosion in the
 development of methods for species tree inference under MSC, owing mainly
 to the accumulating evidence of incomplete lineage sorting in phylogenomic
 analyses. However, the evolutionary history of a set of genomes, or
 species, could be reticulate due to the occurrence of evolutionary
 processes such as hybridization or horizontal gene transfer. We report on
 a novel method for Bayesian inference of genome and species phylogenies
 under the multispecies network coalescent (MSNC). This framework models
 gene evolution within the branches of a phylogenetic network, thus
 incorporating reticulate evolutionary processes, such as hybridization, in
 addition to incomplete lineage sorting. As phylogenetic networks with
 different numbers of reticulation events correspond to points of different
 dimensions in the space of models, we devise a reversible-jump Markov
 chain Monte Carlo (RJMCMC) technique for sampling the posterior
 distribution of phylogenetic networks under MSNC. We implemented the
 methods in the publicly available, open-source software package PhyloNet
 and studied their performance on simulated and biological data. The work
 extends the reach of Bayesian inference to phylogenetic networks and
 enables new evolutionary analyses that account for reticulation.
description: PGENETICS-D-15-02479R1-DATAThis directory contains four input files on which PhyloNet can be run to conduct the Bayesian analyses reported in the paper for the four data sets (the wheat data set, the mouse data set, the mosquito autosome data set, and the mosquito X chromosome data set).
DOI: 10.5061/dryad.m550m
title: Data from: Origins of the 2009 H1N1 influenza pandemic in swine in Mexico

description: Asia is considered an important source of influenza A virus (IAV)
 pandemics, owing to large, diverse viral reservoirs in poultry and swine.
 However, the zoonotic origins of the 2009 A/H1N1 influenza pandemic virus
 (pdmH1N1) remain unclear, due to conflicting evidence from swine and
 humans. There is strong evidence that the first human outbreak of pdmH1N1
 occurred in Mexico in early 2009. However, no related swine viruses have
 been detected in Mexico or any part of the Americas, and to date the most
 closely related ancestor viruses were identified in Asian swine. Here, we
 use 58 new whole-genome sequences from IAVs collected in Mexican swine to
 establish that the swine virus responsible for the 2009 pandemic evolved
 in central Mexico. This finding highlights how the 2009 pandemic arose
 from a region not considered a pandemic risk, owing to an expansion of IAV
 diversity in swine resulting from long-distance live swine trade.
description: XML files. Datasets for
 swine influenza phylogenetic analysisDatasets containing sets
 of sequences used for the phylogenetic analysis of the different genomic
 segments of swine influenzaXML
 files.zipSupplementary Data file
 1acknowledgement of the
 authors and research laboratories that contributed sequence
 dataData
 set 1.csvSupplementary Data file
 2acknowledgement of the
 authors and research laboratories that contributed sequence
 dataData
 set 2.csvSupplementary data file
 32009
 pandemic H1N1 genome sequences used in the analysisData set
 3.csvgenebank acc
 numbersaccession numbers of the
 58 new genomes of swine influenza from Mexico analyzed in this
 studyFigure 1 - source data
 1source data used in
 figure 1 of the manuscriptFigure 2 - figure
 supplement 1Characteristics of the
 58 swIAVs collected in Mexico for this study.Figure 6 - source data
 1Pairwise information on
 imports of live swine from specific countries is available from 1996-2012.
 Data available from the United Nations' Commodity Trade Statistics
 Database, http://comtrade.un.org.Figure 7- source data
 1Times to the most recent
 common ancestor (tMRCA) and posterior probabilities (&gt;0.01) used in
 figure 7Figure 7--source data
 1.csv
DOI: 10.5061/dryad.6p2v0
title: Data from: Evidence for low-level hybridization between two allochronic populations of the pine processionary moth, Thaumetopoea pityocampa (Lepidoptera: Notodontidae)

description: Divergence between populations sharing the same habitat can be initiated
 by different reproductive times, leading to allochronic differentiation. A
 spatially localized allochronic summer population (SP) of the pine
 processionary moth Thaumetopoea pityocampa, recently discovered in
 Portugal, occurs in sympatry with the local winter population (WP). We
 examined the level of genetic differentiation between the two populations
 and estimated the current gene flow within the spatial framework of their
 co-occurrence. Mitochondrial data indicated that the two sympatric
 populations were genetically closer than other WP populations. Conversely,
 microsatellite genotyping uncovered greater differentiation between the
 two sympatric populations than between allopatric ones. While male
 trapping confirmed that reproduction of SP and WP occurred at distinct
 times, clustering approaches demonstrated the presence of a few LateSP
 individuals emerging within the WP flight period, although genetically
 identified as SP. We also identified rare recent hybridization events
 apparently occurring mainly in the margins of the current SP range. The
 ongoing gene flow detected between the ancestral and the emerging
 allochronic populations revealed an incomplete reproductive isolation,
 which must therefore be taken into account and integrated with studies
 focussed on ecological drivers, so that a complete understanding of the
 ongoing speciation process might be achieved.
description: Microsatellite genotypes
 of Thaumeatopoea pityocampa (parental populations and hybrids) simulated
 from alleles frequencies estimated in STRUCTURE clusters SP and
 WPThe
 file is organized according to NEWHYBRID format. Individuals codes (first
 column) describe the genetic class of these simulated genotypes: parental
 SP (pSPsim), parental WP (pWPsim), F1sim, F2sim, back-cross SP (bcSPsim),
 back-cross WP (bcWPsim). 1000 genotypes were simulated for each genetic
 class.simul
 mat SPWPF1F2bcSPbcWP genepop pour
 DRIAD.xlsxMicrosatellite genotypes
 of Thaumeatopoea pityocampa (parental populations and hybrids) simulated
 from parental populationstaking into account only SP and WP individuals
 assigned with STRUCTURE with a q-value &gt;0.9 in their respective
 clusterThe file is organized
 according to NEWHYBRID format. Individuals codes (first column) describe
 the genetic class of these simulated genotypes: parental SP (pSPsim),
 parental WP (pWPsim), F1sim, F2sim, back-cross SP (bcSPsim), back-cross WP
 (bcWPsim). 1000 genotypes were simulated for each genetic
 class305A1000SPWPF1F2bcSPbcWPréordonné pour dryad.xlsxMicrosatellite genotypes of Thaumeatopoea pityocampa individuals from 5 portuguese populationsThe file is organized according to NEWHYBRID format. Individuals codes (first column) are the ones used in the paper. Complete information on the sampling is available in Table S1.données microsat NH pour DRYAD.xlsx
DOI: 10.6084/m9.figshare.30091288
title: Dynamic response of the ring-stiffened underwater vehicle under far-field underwater explosion

description: Figs of Dynamic response of the ring-stiffened underwater vehicle under far-field underwater explosion
DOI: 10.5061/dryad.t6j72
title: Data from: The oldest actinopterygian highlights the cryptic early history of the hyperdiverse ray-finned fishes

description: Osteichthyans comprise two divisions, each containing over 32,000 living
 species: Sarcopterygii (lobe-finned fishes and tetrapods) and
 Actinopterygii (ray-finned fishes). Recent discoveries from China
 highlight the morphological disparity of early sarcopterygians and extend
 their origin into the late Silurian. By contrast, the oldest unambiguous
 actinopterygians are roughly 30 million years younger, leaving a long
 temporal gap populated by fragments and rare body fossils of controversial
 phylogenetic placement. Here we reinvestigate the enigmatic osteichthyan
 Meemannia from the Early Devonian (∼415 million years ago) of China,
 previously identified as an exceptionally primitive lobe-finned fish.
 Meemannia combines “cosmine”-like tissues taken as evidence of
 sarcopterygian affinity with actinopterygian-like skull roof and braincase
 geometry, including endoskeletal enclosure of the spiracle and a lateral
 cranial canal. We report comparable histological structures in undoubted
 ray-finned fishes and conclude that they are general osteichthyan
 features. Phylogenetic analysis places Meemannia as an early-diverging
 ray-finned fish, resolving it as the sister lineage of Cheirolepis plus
 all younger actinopterygians. This brings the first appearance of ray-fins
 more in line with that of lobe-fins and fills a conspicuous faunal gap in
 the otherwise diverse late Silurian-earliest Devonian vertebrate faunas of
 the South China Block.
description: Dryad Figures_Lu et
 alAdditional figures for
 MeemanniaDRYAD Figures_Lu et
 al_CB.pdfSupplemental Data
 1A
 large-format PDF for a phylogenetic tree depicting all character state
 transformations on internal nodes.Data Matrix_Lu et
 alThe
 Nexus format file of the data matrix of MeemanniaData Matrix Lu et
 al.nex
DOI: 10.6084/m9.figshare.30091288.v2
title: Dynamic response of the ring-stiffened underwater vehicle under far-field underwater explosion

description: Figs of Dynamic response of the ring-stiffened underwater vehicle under far-field underwater explosion
DOI: 10.6084/m9.figshare.30091288.v1
title: Dynamic response of the ring-stiffened underwater vehicle under far-field underwater explosion

description: Figs of Dynamic response of the ring-stiffened underwater vehicle under far-field underwater explosion
DOI: 10.6084/m9.figshare.31157527.v1
title: <b>Dynamics of Carbonaceous Aerosols at Yulong Snow Mountain: Resolving Temporal Variability and </b><b>Light </b><b>Absorption with High-Resolution Measurements</b>

description: This dataset presents the black carbon (BC) and organic carbon (OC) content of carbonaceous aerosols, along with associated parameters.
DOI: 10.6084/m9.figshare.31157527
title: <b>Dynamics of Carbonaceous Aerosols at Yulong Snow Mountain: Resolving Temporal Variability and </b><b>Light </b><b>Absorption with High-Resolution Measurements</b>

description: This dataset presents the black carbon (BC) and organic carbon (OC) content of carbonaceous aerosols, along with associated parameters.
DOI: 10.5061/dryad.31r0d
title: Data from: Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing

description: Accurate and robust detection of mRNA molecules in thick tissue samples
 can reveal gene expression patterns in single cells within their native
 environment. Preserving spatial relationships while accessing the
 transcriptome of selected cells is a crucial feature for advancing many
 biological areas – from developmental biology to neuroscience. However,
 because of the high autofluorescence background of many tissue samples, it
 is difficult to detect single-molecule fluorescence in situ hybridization
 (smFISH) signals robustly in opaque thick samples. Here, we draw on
 principles from the emerging discipline of dynamic nucleic acid
 nanotechnology to develop a robust method for multi-color, multi-RNA
 imaging in deep tissues using single-molecule hybridization chain reaction
 (smHCR). Using this approach, single transcripts can be imaged using
 epifluorescence, confocal or selective plane illumination microscopy
 (SPIM) depending on the imaging depth required. We show that smHCR has
 high sensitivity in detecting mRNAs in cell culture and whole-mount
 zebrafish embryos, and that combined with SPIM and PACT (passive CLARITY
 technique) tissue hydrogel embedding and clearing, smHCR can detect single
 mRNAs deep within thick (0.5 mm) brain slices. By simultaneously achieving
 ∼20-fold signal amplification and diffraction-limited spatial resolution,
 smHCR offers a robust and versatile approach for detecting single mRNAs in
 situ, including in thick tissues where high background undermines the
 performance of unamplified smFISH.
description: ctgf-mousebrainscg10-mousebrainyfp-mousebrain
DOI: 10.15468/dl.enj8nx
title: Occurrence Download

description: A dataset containing 402 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hyalesthes obsoletus"
 ]
}

 The dataset includes 402 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001455-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cf860
title: Data from: miR-17-3p exacerbates oxidative damage in human retinal pigment epithelial cells

description: Oxidative stress has been shown to contribute to the development of
 age-related macular degeneration (AMD). MicroRNAs (miRNA) are small
 non-coding RNA molecules that function in RNA silencing and
 post-transcriptional regulation of gene expression. We showed miR-17-3p to
 be elevated in macular RPE cells from AMD patients and in ARPE-19 cells
 under oxidative stress. Transfection of miR-17-3p mimic in ARPE-19 induced
 cell death and exacerbated oxidative lethality that was alleviated by
 miR-17-3p inhibitor. The expression of antioxidant enzymes manganese
 superoxide dismutase (MnSOD) and thioredoxin reductase-2 (TrxR2) were
 suppressed by miR-17-3p mimic and reversed by miR-17-3p inhibitor. These
 results suggest miR-17-3p aggravates oxidative damage-induced cell death
 in human RPE cells, while miR-17-3p inhibitor acts as a potential
 protector against oxidative stress by regulating the expression of
 antioxidant enzymes.
description: statistic-update
DOI: 10.5061/dryad.n3mj3
title: Data from: Context dependence in complex adaptive landscapes: frequency and trait-dependent selection surfaces within an adaptive radiation of Caribbean pupfishes

description: The adaptive landscape provides the foundational bridge between micro- and
 macroevolution. One well-known caveat to this perspective is that fitness
 surfaces depend on ecological context, including competitor frequency,
 traits measured, and resource abundance. However, this view is based
 largely on intraspecific studies. It is still unknown how
 context-dependence affects the larger features of peaks and valleys on the
 landscape which ultimately drive speciation and adaptive radiation. Here I
 explore this question using one of the most complex fitness landscapes
 measured in the wild in a sympatric pupfish radiation endemic to San
 Salvador Island, Bahamas by tracking survival and growth of
 laboratory-reared F2 hybrids. I present new analyses of the effects of
 competitor frequency, dietary isotopes, and trait subsets on this fitness
 landscape. Contrary to expectations, decreasing competitor frequency
 increased survival only among very common phenotypes, whereas less common
 phenotypes rarely survived despite few competitors, suggesting that
 performance, not competitor frequency, shapes large-scale features of the
 fitness landscape. Dietary isotopes were weakly correlated with phenotype
 and growth, but did not explain additional survival variation. Nonlinear
 fitness surfaces varied substantially among trait subsets, revealing one-,
 two-, and three-peak landscapes, demonstrating the complexity of selection
 in the wild, even among similar functional traits.
description: raw trait and fitness
 dataTrait measurements for
 F2 hybrids and F1 parentals, survival and growth rate in field enclosures,
 and isotopes (d13C and d15N) of survivors. Data for high and low-density
 treatments in Crescent Pond (CP) and Little Lake (LL).rawdata.csvstable isotope dataStable isotope data (d13C and d15N) for wild-caught pupfishes and resources in Crescent Pond and Little Lake.isotopes.csvCrescent Pond - size-corrected trait data + survival + growth + d13C + d15NSize-corrected trait residuals plus survival, growth, and isotope data used for analyses of Crescent Pond high and low-density field enclosures.Little Lake - size-corrected trait data + survival + growth + d13C + d15NSize-corrected trait residuals plus survival, growth, and isotope data used for analyses of Little Lake high and low-density field enclosures.size-correction and fitness landscape plotting scriptR code for size-correction of raw trait data and fitness landscape plotting using the Fields package in R.isotope plotsR code for plotting wild-caught isotope data.
DOI: 10.5061/dryad.81k11
title: Data from: Using network analysis to study behavioural phenotypes: an example using domestic dogs

description: Phenotypic integration describes the complex interrelationships between
 organismal traits, traditionally focusing on morphology. Recently,
 research has sought to represent behavioural phenotypes as composed of
 quasi-independent latent traits. Concurrently, psychologists have opposed
 latent variable interpretations of human behaviour, proposing instead a
 network perspective envisaging interrelationships between behaviours as
 emerging from causal dependencies. Network analysis could also be applied
 to understand integrated behavioural phenotypes in animals. Here, we
 assimilate this cross-disciplinary progression of ideas by demonstrating
 the use of network analysis on survey data collected on behavioural and
 motivational characteristics of police patrol and detection dogs (Canis
 lupus familiaris). Networks of conditional independence relationships
 illustrated a number of functional connections between descriptors, which
 varied between dog types. The most central descriptors denoted desirable
 characteristics in both patrol and detection dog networks, with ‘Playful’
 being widely correlated and possessing mediating relationships between
 descriptors. Bootstrap analyses revealed the stability of network results.
 We discuss the results in relation to previous research on dog
 personality, and benefits of using network analysis to study behavioural
 phenotypes. We conclude that a network perspective offers widespread
 opportunities for advancing the understanding of phenotypic integration in
 animal behaviour.
description: rawDataRaw data before any statistical analysesPatrolDog_GGM_AssociationMatrixAssociation matrix of raw correlations for patrol dogs shown in the network figureDetectionDog_GGM_AssociationMatrixAssociation matrix of raw correlations for detection dogs shown in the network figurefinalMIdata_averaged_roundedFinal set of multiply imputed data (averaged over 15 multiply imputed data sets and rounded to be integers)R script fileR script to run the analyses and reproduce the figures in the article.Rscript.RSupplementary_MaterialSupplementary Material for the article, including further details and results of the statistical analyses not included in the manuscript.
DOI: 10.5061/dryad.72591
title: Data from: Allometry in Anisian (Middle Triassic) segminiplanate conodonts and its implications for conodont taxonomy

description: Conodonts are a clade of chordates and are valuable indicator fossils for
 biostratigraphy. The segminiplanate (neogondolelliform) conodonts
 represent a major morphological group ranging from upper Carboniferous to
 Upper Triassic marine sediments. However, the morphological similarity of
 segminiplanate P1 elements generates problems for taxonomy, especially in
 the Permian and Triassic clades. This paper represents the first study of
 morphological variation in Triassic segminiplanate conodonts using a
 geometric morphometric approach. The laminar microstructures observed in
 conodont cross-sections indicate that, within our analysed specimens,
 smaller conodonts with fewer laminae are generally from an earlier
 ontogenetic stage while larger conodonts with more laminae are from a
 later stage of ontogeny. Using linear regressions between relative warp
 scores from both upper and lateral views and conodont length, we
 demonstrate strongly allometric growth patterns for the species
 Paragondolella bifurcata Budurov & Stefanov. Our results indicate
 that the species-group taxon Pg. praeszaboi bystrickyi (Kovacs et al.) is
 an early growth stage of Pg. bifurcata and thus synonymous. We suggest
 that the allometry of conodonts should be considered seriously, especially
 when there are numerous transitional morphologies between large- and
 small-sized conodonts. Reconstructing the ontogenetic series and using
 larger-sized conodonts within the numerous transitional morphologies in
 the population of a rock sample for the definition of new species are
 suggested for future studies.
description: File 1Relative warp scores of
 upper viewS1-Relative warp scores of
 upper view.xlsxFile 2Results of the MANOVA
 with pairwise comparisons between samples based on the first twelve
 relative warpsS2- Results of the
 MANOVA.xlsxFile 3Relative Warp scores of
 lateral viewS3-Relative Warp scores of
 lateral view.xlsx
DOI: 10.5061/dryad.79s67
title: Data from: Evolution of the leucine-rich repeat receptor-like protein kinase gene family: Ancestral copy number and functional divergence of BAM1 and BAM2 in Brassicaceae

description: Gene duplication allows for functional divergence and innovation that
 provide selective advantages. However, in flowering plants genetic studies
 have revealed that single-gene mutations affecting one of two or more
 closely related paralogs often fail to cause detectable morphological
 defects, suggesting functional redundancy. Flowering plants have hundreds
 of genes encoding leucine-rich repeat receptor-like protein kinases
 (LRR-RLKs), several of which play important roles in anther development
 but little is known about their evolutionary history and possible
 functional divergence. We investigated the evolutionary relationship of
 the LRR-RLK gene family by phylogenetic analysis and found that these
 closely related paralogs resulted from multiple duplication events, such
 as the one resulting in BAM1 and BAM2. We further used qRT-PCR to verify
 gene expression changes in immature anthers from the bam1/bam2 single and
 double mutants compared with wild type providing strong evidence that the
 BAM1 and BAM2 genes have evolved different functions, with differential
 effects on anther gene expression. Moreover, careful examination of anther
 development in bam1 and bam2 single mutants revealed previously
 unrecognized extra cell division in tapetum cell layers. Thus our results
 from phylogenetic, molecular and morphological analyses uncover sequence
 and functional differences between paralogs whose single mutants lack
 obvious fertility defects, effectively revealing functional divergence of
 duplicate genes.
description: Data
 S1Sequences and their
 alignments used for phylogenetic analyses