cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vs76v
title: Data from: Idiosyncratic responses to climate-driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea Islands

description: Organismal traits interact with environmental variation to mediate how
 species respond to shared landscapes. Thus, differences in traits related
 to dispersal ability or physiological tolerance may result in
 phylogeographic discordance among co-distributed taxa, even when they are
 responding to common barriers. We quantified climatic suitability and
 stability, and phylogeographic divergence within three reed frog species
 complexes across the Guineo-Congolian forests and Gulf of Guinea
 archipelago of Central Africa to investigate how they responded to a
 shared climatic and geological history. Our species-specific estimates of
 climatic suitability through time are consistent with temporal and spatial
 heterogeneity in diversification among the species complexes, indicating
 that differences in ecological breadth may partly explain these
 idiosyncratic patterns. Likewise, we demonstrated that fluctuating sea
 levels periodically exposed a land bridge connecting Bioko Island with the
 mainland Guineo-Congolian forest and that habitats across the exposed land
 bridge likely enabled dispersal in some species, but not in others. We did
 not find evidence that rivers are biogeographic barriers across any of the
 species complexes. Despite marked differences in the geographic extent of
 stable climates and temporal estimates of divergence among the species
 complexes, we recovered a shared pattern of intermittent climatic
 suitability with recent population connectivity and demographic expansion
 across the Congo Basin. This pattern supports the hypothesis that genetic
 exchange across the Congo Basin during humid periods, followed by
 vicariance during arid periods, has shaped regional diversity. Finally, we
 identified many distinct lineages among our focal taxa, some of which may
 reflect incipient or unrecognized species.
description: Climate Surface
 LayersClimate surface layers
 in raster ascii format used as predictor variables in modeling exercise.
 Current, Mid Holocene, LGM and LIG refer to contemporary climate
 (1950-2000), Mid Holocene (~6000 years ago), Last Glacial Maximum (~22000
 years ago) and Last Inter Glacial (~120000 years ago). All surfaces were
 generated by Jeremy Vanderwal.ClimateData.zip
DOI: 10.5061/dryad.s618v
title: Data from: Control of signaling alignment during the dynamic courtship display of a jumping spider

description: During communication, alignment between signals and sensors can be
 critical. Signals are often best perceived from specific angles, and
 sensory systems can also exhibit strong directional biases. However, we
 know little about how animals establish and maintain such signaling
 alignment during communication. To investigate this, we characterized the
 spatial dynamics of visual courtship signaling in the jumping spider
 Habronattus pyrrithrix. The male performs forward-facing displays
 involving complex color and movement patterns, with distinct long- and
 short-range phases. The female views displays with 2 distinct eye types
 and can only perceive colors and fine patterns of male displays when they
 are presented in her frontal field of view. Whether and how courtship
 interactions produce such alignment between male display and female field
 of view is unknown. We recorded relative positions and orientations of
 both actors throughout courtship and established the role of each sex in
 maintaining signaling alignment. Males always oriented their displays
 toward the female. However, when females were free to move, male displays
 were consistently aligned with female principal eyes only during
 short-range courtship. When female position was fixed, signaling alignment
 consistently occurred during both phases, suggesting that female movement
 reduces communication efficacy. When female models were experimentally
 rotated to face away during courtship, males rarely repositioned
 themselves to re-align their display. However, males were more likely to
 present certain display elements after females turned to face them. Thus,
 although signaling alignment is a function of both sexes, males appear to
 rely on female behavior for effective communication.
description: Echeverri2017_courtshipAlignmentDataThis dataset describes the geometry of male and female jumping spider during courtship.Echeverri2017_kneeDisplaydataThis dataset describes the timing of males' "knee raise" displays.
DOI: 10.5061/dryad.7g877
title: Data from: Evolutionary analysis of Old World arenaviruses reveals a major adaptive contribution of the viral polymerase

description: The Old World (OW) arenavirus complex includes several species of
 rodent-borne viruses, some of which (i.e., Lassa virus, LASV and
 Lymphocytic choriomeningitis virus, LCMV) cause human diseases. Most LCMV
 and LASV infections are caused by rodent-to-human transmissions. Thus,
 viral evolution is largely determined by events that occur in the wildlife
 reservoirs. We used a set of human- and rodent-derived viral sequences to
 investigate the evolutionary history underlying OW arenavirus speciation,
 as well as the more recent selective events that accompanied LASV spread
 in West Africa. We show that the viral RNA polymerase (L protein) was a
 major positive selection target in OW arenaviruses and during LASV
 out-of-Nigeria migration. No evidence of selection was observed for the
 glycoprotein, whereas positive selection acted on the nucleoprotein (NP)
 during LCMV speciation. Positively selected sites in L and NP are
 surrounded by highly conserved residues, and the bulk of the viral genome
 evolves under purifying selection. Several positively selected sites are
 likely to modulate viral replication/transcription. In both L and NP,
 structural features (solvent exposed surface area) are important
 determinants of site-wise evolutionary rate variation. By incorporating
 several rodent-derived sequences, we also performed an analysis of OW
 arenavirus codon adaptation to the human host. Results do not support a
 previously hypothesized role of codon adaptation in disease severity for
 non-Nigerian strains. In conclusion, L and NP represent the major
 selection targets and possible determinants of disease presentation; these
 results suggest that field surveys and experimental studies should
 primarily focus on these proteins.
description: GPC alignment for
 evolutionary analysesGPCalignNP alignment for evolutionary analyses.NPalignL alignment for evolutionary analyses.LalignGPC, NP and L trees for evolutionary analyses.treesLassa virus Nigerian GPC strains used for gammaMap analyses.GPC_gamma_Nigeria.faLassa virus Non Nigerian GPC strains used for gammaMap analyses.GPC_gamma_OutNigeria.faGPC outgroup used for gammaMap analyses.GPC_outgroup.faLassa virus Nigerian NP strains used for gammaMap analyses.NP_gamma_Nigeria.faLassa virus Non Nigerian NP strains used for gammaMap analyses.NP_gamma_OutNigeria.faNP outgroup used for gammaMap analyses.NP_outgroup.faLassa virus Nigerian L strains used for gammaMap analyses.L_gamma_Nigeria.faLassa virus Non Nigerian L strains used for gammaMap analyses.L_gamma_OutNigeria.faL outgroup used for gammaMap analyses.L_outgroup.faGPC sequences used for CAI analyses.GPCcai.fastaNP sequences used for CAI analyses.NPcai.fastaL sequences used for CAI analyses.Lcai.fastaLassa virus GPC strains isolated from rodents used for gammaMap analyses.GPC_gamma_rodents.faLassa virus L strains isolated from rodents used for gammaMap analyses.L_gamma_rodents.faLassa virus NP strains isolated from rodents used for gammaMap analyses.NP_gamma_rodents.fa
DOI: 10.5061/dryad.421p2
title: Data from: Early photosynthetic eukaryotes inhabited low-salinity habitats

description: The early evolutionary history of the chloroplast lineage remains an open
 question. It is widely accepted that the endosymbiosis that established
 the chloroplast lineage in eukaryotes can be traced back to a single
 event, in which a cyanobacterium was incorporated into a protistan host.
 It is still unclear, however, which Cyanobacteria are most closely related
 to the chloroplast, when the plastid lineage first evolved, and in what
 habitats this endosymbiotic event occurred. We present phylogenomic and
 molecular clock analyses, including data from cyanobacterial and
 chloroplast genomes using a Bayesian approach, with the aim of estimating
 the age for the primary endosymbiotic event, the ages of crown groups for
 photosynthetic eukaryotes, and the independent incorporation of a
 cyanobacterial endosymbiont by Paulinella. Our analyses include both broad
 taxon sampling (119 taxa) and 18 fossil calibrations across all
 Cyanobacteria and photosynthetic eukaryotes. Phylogenomic analyses support
 the hypothesis that the chloroplast lineage diverged from its closet
 relative Gloeomargarita, a basal cyanobacterial lineage, ∼2.1 billion y
 ago (Bya). Our analyses suggest that the Archaeplastida, consisting of
 glaucophytes, red algae, green algae, and land plants, share a common
 ancestor that lived ∼1.9 Bya. Whereas crown group Rhodophyta evolved in
 the Mesoproterozoic Era (1,600–1,000 Mya), crown groups Chlorophyta and
 Streptophyta began to radiate early in the Neoproterozoic (1,000–542 Mya).
 Stochastic mapping analyses indicate that the first endosymbiotic event
 occurred in low-salinity environments. Both red and green algae colonized
 marine environments early in their histories, with prasinophyte green
 phytoplankton diversifying 850–650 Mya.
description: Sanchez-Baracaldo_etal_2017_PNASAlignments for phylogenetic analyses of cyanobacteria and photosynthetic eukaryotes: 26 genes and 119 taxa; 49 cyanobacteria taxa including 136 proteins. Files to perform molecular clock analyses: code, calibration points, alignment including eight genes. Stochastic mapping: files and nexus file with character states for freshwater, marine and brackish.Sanchez-Baracaldo_etal_2017_Data.zip
DOI: 10.5281/zenodo.18267466
title: neural-cyberattacks-temporary-blindness

description: Dataset, input and network files associated to the paper "Simulation of Temporary Blindness Episodes Through Multiple Neural Cyberattacks"
DOI: 10.5281/zenodo.18267467
title: neural-cyberattacks-temporary-blindness

description: Dataset, input and network files associated to the paper "Simulation of Temporary Blindness Episodes Through Multiple Neural Cyberattacks"
DOI: 10.5061/dryad.3k8v9
title: Data from: Whole-genome sequencing approaches for conservation biology: advantages, limitations, and practical recommendations

description: Whole-genome resequencing (WGR) is a powerful method for addressing
 fundamental evolutionary biology questions that have not been fully
 resolved using traditional methods. WGR includes four approaches: the
 sequencing of individuals to a high depth of coverage with either
 unresolved (huWGR) or resolved haplotypes (hrWGR), the sequencing of
 population genomes to a high depth by mixing equimolar amounts of
 unlabelled-individual DNA (Pool-seq), and the sequencing of multiple
 individuals from a population to a low depth (lcWGR). These techniques
 require the availability of a reference genome. This, along with the still
 high cost of shotgun sequencing and the large demand for computing
 resources and storage, has limited their implementation in non-model
 species with scarce genomic resources and in fields such as conservation
 biology. Our goal here is to describe the various WGR methods, their pros
 and cons, and potential applications in conservation biology. WGR offers
 an unprecedented marker density and surveys a wide diversity of genetic
 variations not limited to single nucleotide polymorphisms (e.g. structural
 variants and mutations in regulatory elements), increasing their power for
 the detection of signatures of selection and local adaptation as well as
 for the identification of the genetic basis of phenotypic traits and
 diseases. Currently though, no single WGR approach fulfills all
 requirements of conservation genetics, and each method has its own
 limitations and sources of potential bias. We discuss proposed ways to
 minimize such biases. We envision a not distant future where the analysis
 of whole genomes becomes a routine task in many non-model species and
 fields including conservation biology.
description: data_Genbank_june2017Each file contains the metadata of genomes available in GenBank for a given taxonomic group up to June 2017 (https://www.ncbi.nlm.nih.gov/genome/browse/#). Four levels of assembly were considered: contigs, scaffolds, chromosomes, and complete genome (https://www.ncbi.nlm.nih.gov/assembly/help/#definition).
DOI: 10.5061/dryad.5167d
title: Data from: Morphological and phylogenetic evidences unveil a novel species of Gyroporus (Gyroporaceae, Boletales) from Indian Himalaya

description: Repeated macrofungal forays to East district of Sikkim followed by
 morphological and phylogenetic studies of collected wild mushrooms
 revealed an undescribed species, proposed here as Gyroporus paramjitii.
 This species is featured with hemispheric to plane dark brown to brownish
 orange pileus, concolorous or darker stipe, snow white to pale yellow pore
 surface which is immutable when bruised, 2- to 4-spored basidia, reniform
 to elliptic basidiospores, presence of pleurocystidia and cheilocystidia,
 absence of caulocystidia, trichoderm pattern of pileipellis and
 stipitipellis with encrusted erect hyphal elements and occurrence under
 Castanopsis sp. Macro- and micromorphological details coupled with
 phylogenetic analyses (based on nrITS and nrLSU data) are presented for
 this taxon.
description: Fig. 6-Supplementary
 ITS-treeFig.
 6-Supplementary.jpgFig. 7-Supplementary LSU
 treeFig.
 7-Supplementary.jpg
DOI: 10.5061/dryad.m4h4b
title: Data from: Reduced internalization of TNF-ɑ/TNFR1 down-regulates caspase dependent phagocytosis induced cell death (PICD) in neonatal monocytes

description: Phagocytosis-induced cell death (PICD) is diminished in cord blood
 monocytes (CBMO) as compared to cells from adults (PBMO) due to
 differences in the CD95-pathway. This may support a prolonged
 pro-inflammatory response with sequels of sustained inflammation as seen
 in neonatal sepsis. Here we hypothesized that TNF-α mediated induction of
 apoptosis is impaired in CBMO due to differences in the TNFR1-dependent
 internalization. Monocytes were infected with Escherichia coli-GFP (E.
 coli-GFP). Monocyte phenotype, phagocytic activity, induction of
 apoptosis, and TNF-α/TNF-receptor (TNFR) -expression were analysed. In the
 course of infection TNF-α-secretion of CBMO was reduced to 40% as compared
 to PBMO (p&lt;0.05). Neutralization of TNF-α by an αTNF-α antibody
 reduced apoptotic PICD in PBMO four-fold (p &lt; 0.05 vs. infection
 with E. coli). PICD in CBMO was reduced 5-fold compared to PBMO and showed
 less responsiveness to αTNF-α antibody. CBMO expressed less pro-apoptotic
 TNFR1, which, after administration of TNF-α or infection with E. coli was
 internalized to a lesser extent. With similar phagocytic capacity, reduced
 TNFR1 internalization in CBMO was accompanied by lower activation of
 caspase-8 (p &lt; 0.05 vs. PBMO). Stronger caspase-8 activation in
 PBMO caused more activation of effector caspase-3 and apoptosis (all p
 &lt; 0.05 vs. PBMO). Our results demonstrate that TNFR1
 internalization is critical in mediating PICD in monocytes after infection
 with E.coli and is reduced in CBMO.
description: PONE-D-16-46185_R2
 cumulative dataExcel File containing
 sheets titled with the figures and tables of the given manuscript accepted
 by PLOS ONEPONE-D-16-46185_R2.xls
DOI: 10.5061/dryad.ck2br
title: Data from: Accelerating adaptive inverse distance weighting interpolation algorithm on a graphics processing unit

description: This paper focuses on designing and implementing parallel adaptive inverse
 distance weighting (AIDW) interpolation algorithms by using the graphics
 processing unit (GPU). The AIDW is an improved version of the standard
 IDW, which can adaptively determine the power parameter according to the
 data points’ spatial distribution pattern and achieve more accurate
 predictions than those predicted by IDW. In this paper, we first present
 two versions of the GPU-accelerated AIDW, i.e. the naive version without
 profiting from the shared memory and the tiled version taking advantage of
 the shared memory. We also implement the naive version and the tiled
 version using two data layouts, structure of arrays and array of aligned
 structures, on both single and double precision. We then evaluate the
 performance of parallel AIDW by comparing it with its corresponding serial
 algorithm on three different machines equipped with the GPUs GT730M, M5000
 and K40c. The experimental results indicate that: (i) there is no
 significant difference in the computational efficiency when different data
 layouts are employed; (ii) the tiled version is always slightly faster
 than the naive version; and (iii) on single precision the achieved
 speed-up can be up to 763 (on the GPU M5000), while on double precision
 the obtained highest speed-up is 197 (on the GPU K40c). To benefit the
 community, all source code and testing data related to the presented
 parallel AIDW algorithm are publicly available.
description: GPU_AIDWSupplementary Implementation Details, Source code, and Sample test data of a GPU-accelerated Adaptive Inverse Distance Weighting (AIDW) interpolation algorithm. The original research paper is entitled: Accelerating Adaptive IDW Interpolation Algorithm on a Single GPU URL: http://arxiv.org/abs/1511.02186
DOI: 10.5061/dryad.pc830
title: Data from: Burying beetles regulate the microbiome of carcasses and use it to transmit a core microbiota to their offspring

description: Necrophagous beetles utilize carrion, a highly nutritious resource that is
 susceptible to intense microbial competition, by treating it with
 antimicrobial anal and oral secretions. However, how this regulates the
 carcass microbiota remains unclear. Here, we show that carcasses prepared
 by the burying beetle Nicrophorus vespilloides undergo significant changes
 in their microbial communities subsequent to their burial and
 ‘preparation’. Prepared carcasses hosted a microbial community that was
 more similar to that of beetles’ anal and oral secretions than to the
 native carcass community or the surrounding soil, indicating that the
 beetles regulated the carcass microbiota. A core microbial community
 (Xanthomonadaceae, Enterococcaceae, Enterobacteriaceae, and Yarrowia
 yeasts) was transmitted by the beetles to the larvae via the anal and oral
 secretions and the carcass surface. These core taxa proliferated on the
 carcass, indicating a growth conducive environment for these microbes when
 associated with beetles. However, total bacterial loads were higher on
 decomposing carcasses without beetles than on beetle-prepared carcasses,
 indicating that the beetles and/or their associated symbionts suppress the
 growth of competing microbes. Thus, apart from being a nutritional
 resource, the carcass provides a medium for vertical transmission of a
 tightly regulated symbiotic microbiota, whose activity on the carcass and
 in the larval gut may involve carcass preservation as well as digestion.
description: Nicrophorus_carcassmicrobiome_analysisThis contains files used in the analysis of the Nicrophorus vespilloides microbiome.It contains denoised, quality filtered reads for bacterial (Nvesp_16S_seqs.fna) and fungal (Nvesp_ITS_seqs.fna) datasets, metadata mapping files (16S_metadata.txt and ITS_metadata.txt), representative sequence sets for all OTUs (16S_rep_set.fna and ITS_repset.fasta) and the final OTU tables (16S_otutable.csv and ITS_otutable.csv).
DOI: 10.5061/dryad.d3742
title: Data from: Comparative landscape genetics of pond-breeding amphibians in Mediterranean temporal wetlands: the positive role of structural heterogeneity in promoting gene flow

description: Comparative landscape genetics studies can provide key information to
 implement cost-effective conservation measures favoring a broad set of
 taxa. These studies are scarce, particularly in Mediterranean areas, which
 include diverse but threatened biological communities. Here we focus on
 Mediterranean wetlands in central Iberia and perform a multi-level,
 comparative study of two endemic pond-breeding amphibians, a salamander
 (Pleurodeles waltl) and a toad (Pelobates cultripes). We genotyped 411
 salamanders from 20 populations and 306 toads from 16 populations at 18
 and 16 microsatellite loci, respectively, and identified major factors
 associated with population connectivity through the analysis of three sets
 of variables potentially affecting gene flow at increasingly finer levels
 of spatial resolution. Topographic, land use/cover, and remotely sensed
 vegetation/moisture indices were used to derive optimized resistance
 surfaces for the two species. We found contrasting patterns of genetic
 structure, with stronger, finer-scale genetic differentiation in
 Pleurodeles waltl, and notable differences in the role of fine-scale
 patterns of heterogeneity in vegetation cover and water content in shaping
 patterns of regional genetic structure in the two species. Overall, our
 results suggest a positive role of structural heterogeneity in population
 connectivity in pond-breeding amphibians, with habitat patches of
 Mediterranean scrubland and open oak woodlands (“dehesas”) facilitating
 gene flow. Our study highlights the usefulness of remotely sensed
 continuous variables of land cover, vegetation and water content (e.g.,
 NDVI, NDMI) in conservation-oriented studies aimed at identifying major
 drivers of population connectivity.
description: Microsatellite genotypes
 for Pleurodeles waltlFile contains
 microsatellite genotypes in Genepop format (3-digit)MicrosatelliteData_Pleurodeles
 waltl.txtMicrosatellite genotypes
 for Pelobates cultripesFile contains
 microsatellite genotypes in Genepop format (3-digit)MicrosatelliteData_Pelobates
 cultripes.txtMEC_16-1202_Gutierrez_et_al_SpatialDataThe zip archive contains the spatial data in GeoTIFF format used as input variables for explaining gene flow and to calculate optimized resistance surfaces. Details regarding each file are described in the README section.