cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.88755
title: Data from: On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity

description: A central focus of population genetics has been examining the contribution
 of selective and neutral processes in shaping patterns of intraspecies
 diversity. In terms of selection specifically, surveys of higher organisms
 have shown considerable variation in the relative contributions of
 background selection and genetic hitchhiking in shaping the distribution
 of polymorphisms, though these analyses have rarely been extended to
 bacteria and viruses. Here, we study the evolution of a ubiquitous, viral
 pathogen, human cytomegalovirus (HCMV), by analyzing the relationship
 among intraspecies diversity, interspecies divergence, and rates of
 recombination. We show that there is a strong correlation between
 diversity and divergence, consistent with expectations of neutral
 evolution. However, after correcting for divergence, there remains a
 significant correlation between intraspecies diversity and recombination
 rates, with additional analyses suggesting that this correlation is
 largely due to the effects of background selection. In addition, a small
 number of loci, centered on long non-coding RNAs, also show evidence of
 selective sweeps. These data suggest that HCMV evolution is dominated by
 neutral mechanisms as well as background selection, expanding our
 understanding of linked selection to a novel class of organisms.
description: HCMV-CCMV
 AlignmentAlignment of 41 HCMV and
 1 CCMV whole genome sequences in fasta format. The alignment was used to
 generate figure S7 in the linked publication.HCMV-CCMV-RhCMV
 AlignmentAlignment of 41 HCMV, 1
 CCMV and 2 RhCMV whole genome sequences in fasta format
DOI: 10.5061/dryad.jg613
title: Data from: Modeling spatial expansion of invasive alien species: relative contributions of environmental and anthropogenic factors to the spreading of the harlequin ladybird in France

description: Species distribution models (SDM) have often been used to predict the
 potential ranges of introduced species and prioritize management
 strategies. However, this approach assumes equilibrium between occurrences
 and environmental gradients, an assumption which is violated during the
 invasion process, where many suitable sites are empty because the species
 has not yet reached them. Here we considered the invasive ladybird
 Harmonia axyridis as a case study to show the benefits of using a dynamic
 colonization–extinction model that does not assume equilibrium. We used a
 multi-year occupancy model incorporating environmental, anthropogenic and
 neighborhood effects, to identify factors that explained spreading
 variation of this species in France from 2004, when only a few occupied
 sites were detected, to 2011. We found that anthropogenic factors
 (urbanization, agriculture, vineyards, and presence/absence of highways)
 explained more variation in the diffusion process than environmental
 factors (winter and summer temperatures, wind-speed, and rainfall). The
 surface of urbanization was the major anthropogenic factor increasing the
 probability of colonization. The average summer temperature was the main
 environmental factor affecting colonization, with a negative effect when
 high or low. The neighborhood effect revealed that colonization was mostly
 influenced by contributions coming from a radius of 24 km around the focal
 cell. The contribution of neighborhood decreases over time, suggesting
 that H. axyridis is reaching its equilibrium in France. This is confirmed
 by the small discrepancy observed between the performance of our approach
 and a SDM approach when predicting a single year occupancy pattern at the
 end of the study period. Our approach has the advantage of explicitly
 modelling the state of the biological system during the spatial expansion
 and identifying colonization constraints. This allows managers to explore
 the effect of different actions on the system at key moments of the
 invasion process, hence providing a powerful approach to prioritize
 management strategies.
description: data of
 occupancydata for analysis in
 Presence format. First part : presence-absence. Second part : covariates.
 Third : id/cellsdata.txt
DOI: 10.5061/dryad.g1qr6
title: Data from: Effects of spatial scale of sampling on food web structure

description: This study asks whether the spatial scale of sampling alters structural
 properties of food webs and whether any differences are attributable to
 changes in species richness and connectance with scale. Understanding how
 different aspects of sampling effort affect ecological network structure
 is important for both fundamental ecological knowledge and the application
 of network analysis in conservation and management. Using a highly
 resolved food web for the marine intertidal ecosystem of the Sanak
 Archipelago in the Eastern Aleutian Islands, Alaska, we assess how
 commonly studied properties of network structure differ for 281 versions
 of the food web sampled at five levels of spatial scale representing six
 orders of magnitude in area spread across the archipelago. Species (S) and
 link (L) richness both increased by approximately one order of magnitude
 across the five spatial scales. Links per species (L/S) more than doubled,
 while connectance (C) decreased by approximately two-thirds. Fourteen
 commonly studied properties of network structure varied systematically
 with spatial scale of sampling, some increasing and others decreasing.
 While ecological network properties varied systematically with sampling
 extent, analyses using the niche model and a power-law scaling
 relationship indicate that for many properties, this apparent sensitivity
 is attributable to the increasing S and decreasing C of webs with
 increasing spatial scale. As long as effects of S and C are accounted for,
 areal sampling bias does not have a special impact on our understanding of
 many aspects of network structure. However, attention does need be paid to
 some properties such as the fraction of species in loops, which increases
 more than expected with greater spatial scales of sampling.
description: Food web data for the
 Sanak Islands, AlaskaThe food web data
 compiled for this study, consisting of 339 quadrats, 39 transects, five
 sites, four locales, and one archipelago-wide network. The table provides
 a unique numeric identifier per food web (WebID), the spatial scale
 (WebScale; distinguishing quadrats [Q], transects [T], sites [S], locales
 [L], and the archipelago-scale [A]), a sample number (WebUnit; to identify
 individual transects [quadrat- and transect-scale samples], sites, or
 locales), and the Integrated Taxonomic Information System's (ITIS)
 Taxonomic Serial Number (TSN) and name of each predator and prey (PredTSN,
 PreyTSN, PredName, and PreyName, respectively). Taxa lacking entries in
 ITIS have a unique custom TSN prepended with “san”.WoodEtal_Append1_v2.csv
DOI: 10.5061/dryad.dh3st
title: Data from: Ecosystem productivity is associated to bacterial phylogenetic distance in surface marine waters

description: Understanding the link between community diversity and ecosystem function
 is a fundamental aspect of ecology. Systematic losses in biodiversity are
 widely acknowledged but the impact this may exert on ecosystem functioning
 remains ambiguous. There is growing evidence of a positive relationship
 between species richness and ecosystem productivity for terrestrial
 macroorganisms, but similar links for marine microorganisms, which help
 drive global climate, are unclear. Community manipulation experiments show
 both positive and negative relationships for microbes. These previous
 studies rely, however, on artificial communities and any links between the
 full diversity of active bacterial communities in the environment, their
 phylogenetic relatedness, and ecosystem function remains hitherto
 unexplored. Here we test the hypothesis that productivity is associated to
 diversity in the metabolically active fraction of microbial communities.
 We show in natural assemblages of active bacteria that communities
 containing more distantly related members were associated with higher
 bacterial production. The positive phylogenetic diversity–productivity
 relationship was independent of community diversity calculated as the
 Shannon index. From our long-term (7-year) survey of surface marine
 bacterial communities we also found that similarly productive communities
 had greater phylogenetic similarity to each other, further suggesting that
 the traits of active bacteria are an important predictor of ecosystem
 productivity. Our findings demonstrate that the evolutionary history of
 the active fraction of a microbial community is critical for understanding
 their role in ecosystem functioning.
description: Environmental
 dataThe file contains sample
 date, temperature, salinity, chlorophylla, nitrate concentrations and
 bacterial production data.OTU_tableThe file contains the annotated and resampled OTU table.Phylogenetic_distance_matrixThe file contains the phylogenetic distance matrix calculated with the comdistnt function in the Picante R package.TreeThe file contains the tree used to calculate the phylogenetic diversity.AlignmentThe file contains the alignment used to built the phylogenetic tree.
DOI: 10.5878/002911
title: The Regional Skåne SOM Survey 2015
title: SOM-undersökningen i Skåne 2015
title: Syd-SOM 2015

description: This is the sixth SOM survey conducted in the region of Skåne. The questionnaire was divided into ten subject fields: Local news; Politics and democracy; To live in Skåne; Traffic and communications; Internet and mobile phones; Activities, interests and values; Denmark; Housing; Working life; Background.

Purpose:
Study attitudes and behaviour linked to local and regional issues.
description: Detta är den sjätte SOM-undersökning som genomförts i Skåne. Den första undersökningen genomfördes 2001 i Malmöregionen (A-region 28 samt Eslöv). De senare undersökningarna har genomförts i hela Region Skåne.

Frågeformuläret består av tio sammanhållna frågeområdn: Lokala nyheter; Politik och demokrati; Att leva och bo i Skåne; Trafik och kommunikationer; Internet och mobiltelefoni; Aktiviteter, intressen och värderingar; Danmark; Boende; Arbetsliv; Bakgrund.

Syfte:
Studera attityder och beteenden som är knutna till lokala och regionala frågor och företeelser.
DOI: 10.5878/002907
title: The Regional Skåne SOM Survey 2015
title: SOM-undersökningen i Skåne 2015
title: Syd-SOM 2015

description: This is the sixth SOM survey conducted in the region of Skåne. The questionnaire was divided into ten subject fields: Local news; Politics and democracy; To live in Skåne; Traffic and communications; Internet and mobile phones; Activities, interests and values; Denmark; Housing; Working life; Background.

Purpose:
Study attitudes and behaviour linked to local and regional issues.
description: Detta är den sjätte SOM-undersökning som genomförts i Skåne. Den första undersökningen genomfördes 2001 i Malmöregionen (A-region 28 samt Eslöv). De senare undersökningarna har genomförts i hela Region Skåne.

Frågeformuläret består av tio sammanhållna frågeområdn: Lokala nyheter; Politik och demokrati; Att leva och bo i Skåne; Trafik och kommunikationer; Internet och mobiltelefoni; Aktiviteter, intressen och värderingar; Danmark; Boende; Arbetsliv; Bakgrund.

Syfte:
Studera attityder och beteenden som är knutna till lokala och regionala frågor och företeelser.
DOI: 10.5061/dryad.2bj36
title: Data from: Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and, with the exception of endosymbiotic gene transfers, few ancient transfer events persist

description: While there is compelling evidence for the impact of endosymbiotic gene
 transfer (EGT; transfer from either mitochondrion or chloroplast to the
 nucleus) on genome evolution in eukaryotes, the role of interdomain
 transfer from bacteria and/or archaea (i.e. prokaryotes) is less clear.
 Lateral gene transfers (LGTs) have been argued to be potential sources of
 phylogenetic information, particularly for reconstructing deep nodes that
 are difficult to recover with traditional phylogenetic methods. We sought
 to identify interdomain LGTs by using a phylogenomic pipeline that
 generated 13 465 single gene trees and included up to 487 eukaryotes, 303
 bacteria and 118 archaea. Our goals include searching for LGTs that unite
 major eukaryotic clades, and describing the relative contributions of LGT
 and EGT across the eukaryotic tree of life. Given the difficulties in
 interpreting single gene trees that aim to capture the approximately 1.8
 billion years of eukaryotic evolution, we focus on presence–absence data
 to identify interdomain transfer events. Specifically, we identify 1138
 genes found only in prokaryotes and representatives of three or fewer
 major clades of eukaryotes (e.g. Amoebozoa, Archaeplastida, Excavata,
 Opisthokonta, SAR and orphan lineages). The majority of these genes have
 phylogenetic patterns that are consistent with recent interdomain LGTs
 and, with the notable exception of EGTs involving photosynthetic
 eukaryotes, we detect few ancient interdomain LGTs. These analyses suggest
 that LGTs have probably occurred throughout the history of eukaryotes, but
 that ancient events are not maintained unless they are associated with
 endosymbiotic gene transfer among photosynthetic lineages.
description: Katz alignments for
 dryadAlignments generated by
 Guidance. NOTE: These files are AFTER removal of poor scoring taxa and
 columns.Katz trees for
 dryadGene trees generated
 from alignments that are also uploaded
DOI: 10.5519/qd.w70zjpn2
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (17 records)
DOI: 10.5061/dryad.ds2nj
title: Data from: Quantifying global drivers of zoonotic bat viruses: a process-based perspective

description: Emerging infectious diseases (EIDs), particularly zoonoses, represent a
 significant threat to global health. Emergence is often driven by
 anthropogenic activity (e.g. travel, land use change). Although disease
 emergence frameworks suggest multiple steps from initial zoonotic
 transmission to human-to-human spread, there have been few attempts to
 empirically model specific steps. We create a process-basedframework to
 separate out components of individual emergence steps. We focus on early
 emergence and expand the first step, zoonotic transmission, into processes
 of generation of pathogen richness, transmission opportunity and
 establishment, each with their own hypothesised drivers. Using this
 structure, we build a spatial empirical model of these drivers, taking bat
 viruses shared with humans as a case study. We show that drivers of both
 pathogen richness (host diversity and climatic variability) and
 transmission opportunity (human population density, bushmeat hunting and
 livestock production) are associated with virus sharing between humans and
 bats. We also show spatial heterogeneity between the global patterns of
 these two processes, suggesting high priority locations for pathogen
 discovery and surveillance in wildlife may not necessarily coincide with
 those for public health intervention. Finally, we offer direction for
 future studies of zoonotic EIDs by highlighting the importance of the
 processes underlying their emergence.
description: Global spatial ranges of
 zoonotic bat virusesShapefiles of global
 spatial ranges of 33 zoonotic bat virus species (following ICTV9 Virus
 Taxonomy). Ranges are upper-bound proxies for zoonotic transmission
 created by fusing together entire ranges of all known bat host species
 from systematically mined literature-based records of bat-virus
 associations. Original host distributions sourced from Fritz and Purvis
 2010. Shapefiles follow projection 'long-lat' using WGS-1984
 co-ordinate system. Created using package 'PBSmapping' in R
 version 3.1.1.Brierley_et_al_2015_Zoonotic_bat_virus_shapefiles.rar
DOI: 10.5061/dryad.933
title: Data from: Mixed-model reanalysis of primate data suggests tissue and species biases

description: An emerging issue in evolutionary genetics is whether it is possible to
 use gene expression profiling to identify genes that are associated with
 morphological, physiological, or behavioral divergence between species and
 whether these genes have undergone positive selection. Some of these
 questions were addressed in a recent study (Enard et al. 2002) of the
 difference in gene expression among human, chimp, and orangutan, which
 suggested an accelerated rate of divergence in gene expression in the
 human brain relative to liver. Reanalysis of the Affymetrix data set using
 analysis of variance methods to quantify the contributions of individuals
 and species to variation in expression of 12,600 genes indicates that as
 much as one-quarter of the genome shows divergent expression between
 primate species at the 5% level. The magnitude of fold change ranges from
 1.2-fold up to 8-fold. Similar conclusions apply to reanalysis of Enard et
 al. 2002 parallel murine data set. However, biases inherent to short
 oligonucleotide microarray technology may account for some of the tissue
 and species effects. At high significance levels, more differences were
 observed in the liver than in the brain in each of the pairwise species
 comparisons, so it is not clear that expression divergence is accelerated
 in the human brain. Further, there is an apparent bias toward upregulation
 of gene expression in the brain in both primates and mice, whereas genes
 are equally likely to be up- or downregulated in the liver when these
 species diverge. A small subset of genes that are candidates for adaptive
 divergence may be identified on the basis of a high ratio of interspecific
 to intraspecific divergence.
description: Supplementary Figure
 1HCOscat(Fig1).pdfSupplementary Figure 2FigS2_Hsieh.pdfSupplementary Figure 3PrimateSigGenes(SFig3).xlsSupplementary Figure 4FigS4_Hsieh.pdf
DOI: 10.18167/dvn1/85ekdh
title: Distribution and cover of a recently introduced alien sedge species, Carex pilulifera L., in the subalpine vegetation of Reunion Island
title: Distribution et recouvrement d'une espece vegetale exotique emergeante: Carex pilulifera L. dans la végétation subalpine de l'ile de La Réunion

description: The data comprise presence and cover of alien (including Carex pilulifera L., CYPERACEAE) and native species in subalpine vegetation (Volcano and Maïdo areas) in La Reunion. Additional information on habitat types and presence of burned areas is provided.
DOI: 10.5061/dryad.g73t2
title: Data from: Modeling additive and non-additive effects in a hybrid population using genome-wide genotyping: prediction accuracy implications

description: Hybrids are broadly used in plant breeding and accurate estimation of
 variance components is crucial for optimizing genetic gain. Genome-wide
 information may be used to explore models designed to assess the extent of
 additive and non-additive variance and test their prediction accuracy for
 the genomic selection. Ten linear mixed models, involving pedigree- and
 marker-based relationship matrices among parents, were developed to
 estimate additive (A), dominance (D) and epistatic (AA, AD and DD)
 effects. Five complementary models, involving the gametic phase to
 estimate marker-based relationships among hybrid progenies, were developed
 to assess the same effects. The models were compared using tree height and
 3303 single-nucleotide polymorphism markers from 1130 cloned individuals
 obtained via controlled crosses of 13 Eucalyptus urophylla females with 9
 Eucalyptus grandis males. Akaike information criterion (AIC), variance
 ratios, asymptotic correlation matrices of estimates, goodness-of-fit,
 prediction accuracy and mean square error (MSE) were used for the
 comparisons. The variance components and variance ratios differed
 according to the model. Models with a parent marker-based relationship
 matrix performed better than those that were pedigree-based, that is, an
 absence of singularities, lower AIC, higher goodness-of-fit and accuracy
 and smaller MSE. However, AD and DD variances were estimated with high
 s.es. Using the same criteria, progeny gametic phase-based models
 performed better in fitting the observations and predicting genetic
 values. However, DD variance could not be separated from the dominance
 variance and null estimates were obtained for AA and AD effects. This
 study highlighted the advantages of progeny models using genome-wide
 information.
description: HDY-15-OR0111R_phenotypic_dataexperimental data containing informations related to the variables : FAMILLE FEMALE MALE IC clonealpha BLOC ZONE X Y PLOT IND HT32HDY-15_OR0111R_genotypesmolecular data: tables with row corresponding to male, female and progenies (clones) and columns corresponding to allele dose (0, 1, 2)
DOI: 10.5061/dryad.8f150
title: Data from: High-throughput screening for ligands of the HEPN domain of sacsin

description: Sacsin is a large protein implicated in the neurodevelopmental and
 neurodegenerative disease autosomal recessive spastic ataxia of
 Charlevoix-Saguenay (ARSACS), which features the loss of Purkinje neurons
 in the cerebellum. Although the domain architecture of sacsin suggests
 that it is a neuronal chaperone assisting in protein quality control, the
 precise function of sacsin remains elusive. Using fluorescence
 polarization (FP) assays, we confirmed that the HEPN domain of sacsin
 binds to nucleotides with low micromolar affinities. FP competition assays
 with a variety of nucleotides and nucleotide analogs revealed that the
 binding is primarily mediated by the phosphate groups of nucleotides. A
 high-throughput screen subsequently identified novel small molecule
 ligands of HEPN, providing new chemical probes for cell culture studies
 and drug development. Together, the results are consistent with the HEPN
 domain contributing to the functional activity of sacsin by binding to
 nucleotides or other multiply charged anionic compounds in neurons.
description: FP, NMR and HTS
 dataFluorescence
 polarization, NMR chemical shift perturbations and high-throughput
 screening data for compounds that show binding to the HEPN domain of
 sacsinData
 for archiving.zip