cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.74sk3
title: Data from: Host conservatism or host specialization? Patterns of fungal diversification are influenced by host plant specificity in Ophiognomonia (Gnomoniaceae, Diaporthales)

description: In this study evolutionary host plant patterns at ranks from order to
 species were analysed using spatial evolutionary and ecological vicariance
 analysis (SEEVA), based on a multigene phylogeny of 45 ascomycete fungal
 species. The objective was to understand speciation events and host
 associations in Ophiognomonia (Gnomoniaceae). Species of this genus are
 perithecial fungi that occur as endophytes, pathogens, and latent saprobes
 on plants in the families of Betulaceae, Fagaceae, Juglandaceae,
 Lauraceae, Malvaceae, Platanaceae, Rosaceae, Salicaceae, and Sapindaceae.
 A second objective was to determine whether speciation events are
 influenced by host conservatism, host specialization, or host switching at
 different taxonomic host ranks. Host differences between sister clades
 were interpreted using the divergence index (D) from the SEEVA analysis,
 ranging from 0 for no divergence to 1 for maximum possible divergence.
 Several fungal subclades showed clear patterns of host order/family
 conservatism (D = 1.00) for hosts in Betulaceae, Fagaceae, Juglandaceae,
 and Rosaceae. Clear trends of host specialization at host genus and
 species ranks (D = 1.00) were suggested within these host families.
 Independent host jumps were observed for two species at the family rank
 and three at the order rank. As a result of this study, host specificity
 and specialization is hypothesized as a mechanism that can strongly
 contribute to speciation patterns in fungal pathogens.
description: Fig 2_tree
 filePlease see methodology
 in publication for maximum likelihood analyses.Fig 3_tree
 filePlease see methodology
 in publication for maximum likelihood analyses.Fig 4_tree
 filePlease see methodology
 in publication for ML analyses.Clade 1 (Fig 2) GBlocks
 curated alignmentPlease see the
 methodology for alignment curation in GBlocks. THESE ARE NOT FULL LENGTH
 SEQUENCES. Full length sequences can be retrieved from
 GenBank.111114_Clade1Strict_Gblocks.fasClade2 (Fig 3) alignment curation in GblocksPlease see the methodology for alignment curation in GBlocks. THESE ARE NOT FULL LENGTH SEQUENCES. Full length sequences can be retrieved from GenBank.120130_Clade2_Gblocks.fasClade 3 (Fig 4) curation of alignment in GBlocksPlease see the methodology for alignment curation in GBlocks. THESE ARE NOT FULL LENGTH SEQUENCES. Full length sequences can be retrieved from GenBank.111114_Clade3Strict_Gblocks.fasClade 1 (Fig 2) SEEVA fileRaw data from SEEVA analyses.120210_clade1.xlsClade 2 (Fig 3) from SEEVA analysisRaw data from SEEVA analyses.120210_clade2.xlsClade 3 (Fig 4) from SEEVA analysisRaw data from SEEVA analyses.120210_clade3.xls
DOI: 10.5061/dryad.cs3t8
title: Data from: Risk of bias in reports of in vivo research: a focus for improvement

description: The reliability of experimental findings depends on the rigour of
 experimental design. Here we show limited reporting of measures to reduce
 the risk of bias in a random sample of life sciences publications,
 significantly lower reporting of randomisation in work published in
 journals of high impact, and very limited reporting of measures to reduce
 the risk of bias in publications from leading United Kingdom institutions.
 Ascertainment of differences between institutions might serve both as a
 measure of research quality and as a tool for institutional efforts to
 improve research quality.
description: PLoS biology Figure 1
 dataPrevalence of reporting
 of randomisation, blinded assessment of outcome, sample size calculation
 and conflict of interest in 146 publications describing in vivo research
 identified through random sampling from PubMed;PLoS biology Figure 3
 dataReporting of
 randomisation, blinded assessment of outcome, sample size calculations and
 conflict of interest reporting and journal impact factor for 2671
 publications describing the efficacy of interventions in animal models of
 eight different diseases identified in the context of systematic
 reviews,PLoS biology Figure 5
 dataReporting of
 randomisation, blinded assessment of outcome, sample size calculation and
 of inclusion or exclusion criteria in 1173 publications describing in vivo
 research published from 5 leading UK institutions (labelled A through
 E).
DOI: 10.5061/dryad.1kc6c
title: Data from: Biodiversity response to natural gradients of multiple stressors on continental margins

description: Sharp increases in atmospheric CO2 are resulting in ocean warming,
 acidification and deoxygenation that threaten marine organisms on
 continental margins and their ecological functions and resulting ecosystem
 services. The relative influence of these stressors on biodiversity
 remains unclear though, as well as the threshold levels for change and
 when secondary stressors become important. One strategy to interpret
 adaptation potential and predict future faunal change is to examine
 ecological shifts along natural gradients in the modern ocean. Here, we
 assess the explanatory power of temperature, oxygen and the carbonate
 system for macrofaunal diversity and evenness along continental upwelling
 margins using variance partitioning techniques. Oxygen levels have the
 strongest explanatory capacity for variation in species diversity. Sharp
 drops in diversity are seen as O2 levels decline through the 0.5 – 0.15
 ml/l (~22 – 6 μM; ~21 – 5 matm) range, and as temperature increases
 through the 7-10°C range. pCO2 is the best explanatory variable in the
 Arabian Sea but explains little of the variance in diversity in the
 Eastern Pacific Ocean. In contrast, very little variation in evenness is
 explained by these three global change variables. The identification of
 sharp thresholds in ecological response are used here to predict areas of
 the seafloor where diversity is most at risk to future marine global
 change, noting that the existence of clear regional differences cautions
 against applying global thresholds.
description: Supplementary Dataset
 1All
 raw data files used in the paper and all summary statistics used in final
 analyses.Sperling Proc B Supplementary
 Data set 1_revised.xlsx
DOI: 10.5061/dryad.1b1f023
title: Data from: Harvesting changes mating behavior in European lobster

description: Removing individuals from a wild population can affect the availability of
 prospective mates and the outcome of competitive interactions, with
 subsequent effects on mating patterns and sexual selection. Consequently,
 the rate of harvest-induced evolution is predicted to be strongly
 dependent on the strength and dynamics of sexual selection yet, there is
 limited empirical knowledge on the interplay between selective harvesting
 and the mating systems of exploited species. In this study, we used
 genetic parentage assignment to compare mating patterns of the highly
 valued and overexploited European lobster (Homarus gammarus) in a
 designated lobster reserve and nearby fished area in Southern Norway. In
 the area open to fishing, the fishery is regulated by a closed season, a
 minimum legal size and a ban on the harvest of egg-bearing females. Due to
 the differences in size and sex-specific fishing mortality between the two
 areas, males and females are of approximately equal average size in the
 fished area, whereas males tend to be larger in the reserve. Our results
 show that females would mate with males larger than their own body size,
 but the relative size difference was significantly larger in the reserve.
 Sexual selection acted positively on both body size and claw size in males
 in the reserve, while it was non-significant in fished areas. This
 strongly suggests that size truncation of males by fishing reduces the
 variability of traits that sexual selection acts upon. If fisheries
 continue to target large individuals (particularly males) with higher
 relative reproductive success, the weakening of sexual selection will
 likely accelerate fisheries-induced evolution towards smaller body size.
description: Genotype
 dataGenotypes of males,
 females and offspring (eggs) used in the parentage
 assignment.Paternity assesment
 dataAssesment of multiple
 and single paternity in offspring batches.
DOI: 10.5061/dryad.s5700
title: Data from: 28 year temporal sequence of epidemic dynamics in a natural rust – host plant metapopulation

description: A long-term study of disease dynamics caused by the rust Uromyces
 valerianae in 31 discrete populations of Valeriana salina provides a rare
 opportunity to explore extended temporal patterns in the epidemiology of a
 natural host-pathogen metapopulation. Over a 28-year period, pathogen
 population dynamics varied across the metapopulation with disease
 incidence (presence/absence), prevalence (% plants infected) and severity
 (% leaf area covered by lesions) all showing strong population and year
 effects, indicative of heterogeneity among years and host populations in
 the suitability of conditions for the pathogen. Disease incidence within
 individual host populations was significantly affected by host population
 size, disease prevalence the previous year and the proximity of
 neighbouring populations infected in the current year. After accounting
 for these variables there was still a marked temporal component with
 winter sea level having a significant effect; as did summer rainfall in
 the second part of the study period (1997-2011). Disease prevalence was
 also effected by host population size and disease prevalence in the
 previous year. However, it was less affected by spatial aspects of disease
 spread than was disease incidence. Winter sea level and June rainfall
 significantly affected disease prevalence. Assessment of disease impact on
 plant performance found strong variation in disease severity associated
 with the aspect and positioning of host populations. Plants growing in
 lower disease environments produced significantly more seeds than those
 growing in high disease sites. Significant variation in reaction to
 infection by U. valerianae was detected among plants within four
 populations and between these different populations. Synthesis. The
 epidemiology of U. valerianae was highly influenced by host population
 size, previous disease and distance. After accounting for these factors,
 there was a clear temporal signal of change in disease incidence linked to
 winter sea level and summer rainfall. These patterns reinforce the
 importance of considering interactions in multiple populations over long
 periods of time in order to obtain a clear picture of the variability of
 disease-induced selection pressures across time and space. The behaviour
 of the pathogen fitted that predicted for a metapopulation with
 considerable asynchrony in epidemiological patterns among demes.
description: Data for 31
 Valeriana-Uromyces populations over 28 yearsFile contains three work
 sheets giving all epidemiological, spatial and environmental
 dataAll
 Data for 31 populations over 28
 years.xlsx
DOI: 10.5061/dryad.5sc31
title: Data from: The demographic history of populations experiencing asymmetric gene flow: combining simulated and empirical data.

description: Population structure can significantly affect genetic-based demographic
 inferences, generating spurious bottleneck-like signals. Previous studies
 have typically assumed island or stepping-stone models, which are
 characterized by symmetric gene flow. However, many organisms are
 characterized by asymmetric gene flow. Here, we combined simulated and
 empirical data to test whether asymmetric gene flow affects the inference
 of past demographic changes. Through the analysis of simulated genetic
 data with three methods (i.e. bottleneck, M-ratio and msvar), we
 demonstrated that asymmetric gene flow biases past demographic changes.
 Most biases were towards spurious signals of expansion, albeit their
 strength depended on values of effective population size and migration
 rate. It is noteworthy that the spurious signals of demographic changes
 also depended on the statistical approach underlying each of the three
 methods. For one of the three methods, biases induced by asymmetric gene
 flow were confirmed in an empirical multispecific data set involving four
 freshwater fish species (Squalius cephalus, Leuciscus burdigalensis, Gobio
 gobio and Phoxinus phoxinus). However, for the two other methods, strong
 signals of bottlenecks were detected for all species and across two
 rivers. This suggests that, although potentially biased by asymmetric gene
 flow, some of these methods were able to bypass this bias when a
 bottleneck actually occurred. Our results show that population structure
 and dispersal patterns have to be considered for proper inference of
 demographic changes from genetic data.
description: Simulated_Data_per_scenario_GenetixGenetic data simulated under 27 different scenariosEmpirical dataEmpirical data concerning the four species studied in the article and the two rivers.R_ScriptsR scripts used to (i) test msvar MCMC chains convergence (ii) calculate bayes factors for the time of the beginning of demographic changes inferred with msvar (iii) estimate effect sizes and other statistics through posterior parameter distributions for msvar and (iv) to simulate genetic data with ms.
DOI: 10.5061/dryad.94768
title: Data from: Ecological specialization and morphological diversification in Greater Antillean boas

description: Colonization of islands can dramatically influence the evolutionary
 trajectories of organisms, with both deterministic and stochastic
 processes driving adaptation and diversification. Some island colonists
 evolve extremely large or small body sizes, presumably in response to
 unique ecological circumstances present on islands. One example of this
 phenomenon, the Greater Antillean boas, includes both small (&lt;90
 cm) and large (4 m) species occurring on the Greater Antilles and Bahamas,
 with some islands supporting pairs or trios of body-size divergent
 species. These boas have been shown to comprise a monophyletic radiation
 arising from a Miocene dispersal event to the Greater Antilles, though it
 is not known whether co-occurrence of small and large species is a result
 of dispersal or in situ evolution. Here, we provide the first
 comprehensive species phylogeny for this clade combined with morphometric
 and ecological data to show that small body size evolved repeatedly on
 separate islands in association with specialization in substrate use. Our
 results further suggest that microhabitat specialization is linked to
 increased rates of head shape diversification among specialists. Our
 findings show that ecological specialization following island colonization
 promotes morphological diversity through deterministic body size evolution
 and cranial morphological diversification that is contingent on island-
 and species-specific factors.
description: BDNFAlignment of the nuclear
 locus BDNFBMP2Alignment of the nuclear
 locus BMP2CMOSAlignment of the nuclear
 locus CMOSNTF3Alignment of the nuclear
 locus NTF3ODCAlignment of the nuclear
 locus ODCPTGERAlignment of the nuclear
 locus PTGERPTPNAlignment of the nuclear
 locus PTPNRAG1Alignment of the nuclear
 locus RAG1CYTBAlignment of the mtDNA
 locus CYTBND4Alignment of the mtDNA
 locus ND4
DOI: 10.5061/dryad.qf0r2t9
title: Data from: RPASE: individual based allele-specific expression detection without prior knowledge of haplotype phase

description: Variation in gene expression is believed to make a significant
 contribution to phenotypic diversity and divergence. The analysis of
 allele-specific expression (ASE) can reveal important insights into gene
 expression regulation. We developed a novel method called RPASE
 (Read-backed Phasing-based ASE detection) to test for genes that show ASE.
 With mapped RNA-seq data from a single individual and a list of SNPs from
 the same individual as the only input, RPASE is capable of aggregating
 information across multiple dependent SNPs and producing individual-based
 gene-level tests for ASE. RPASE performs well in simulations and
 comparisons. We applied RPASE to multiple bird species and found a
 potentially rich landscape of ASE.
description: Supplementary table
 S2Supplementary table
 S3
DOI: 10.5061/dryad.hh435
title: Data from: The importance of trees for woody pasture bird diversity and effects of the European Union's tree density policy

description: 1. Recent reforms in the Common Agricultural Policy (CAP) aim for a
 greening of the subsidy system with potential improvements for
 biodiversity conservation. As part of that process, the tree density limit
 for pastures to qualify for European Union (EU) subsidies has been
 increased from 50 to 100 trees/ha. However, recent studies show that the
 high biodiversity values of these habitats may be threatened by these
 limits, highlighting the need for policy improvements. Still, little is
 known about the direct effects of tree density limitations on bird
 communities in woody pastures. 2. We investigated how bird diversity and
 species composition are affected by tree density in 49 Swedish woody
 pastures along a gradient of 4 to 214 trees/ha. We recorded bird
 communities, tree density and stand structure estimates in the field and
 estimated forest cover in the surrounding landscape from aerial photos.
 Using generalised additive models (GAM) and redundancy analysis (RDA), we
 analysed how bird territorial species richness, bird abundance and species
 composition are affected by tree density, taking into account other local
 and landscape scale explanatory variables. 3. Tree density had a
 significant positive effect on bird species richness at low tree densities
 and species richness saturated at approximately 50 trees/ha. Shrub density
 had a significant positive linear effect on both bird species richness and
 abundance. Tree and shrub density were also the major drivers of bird
 community composition, with secondary effects of tree species diversity
 and landscape forest cover. 4. Policy implications. These results show
 that tree density is not the limiting factor, but rather a driver of bird
 diversity and species composition in woody pastures and that tree density
 limits may fail to capture the whole range of biological values. To
 improve policy recommendations, we therefore stress the importance of
 considering additional social-ecological drivers associated to management
 quality to preserve biodiversity in woody pastures.12-Jan-2017
description: Bird communities in
 woody pastures, SwedenData on bird communities
 collected in the field from April to June 2014, data on environmental
 variables (incl. tree communities) collected in the field 2013. Landscape
 forest cover was digitized using aerial photos. All data has been compiled
 using Microsoft Excel and R. Please see datasheet "META" for
 details on column headings, and please see publication for more
 information on data collection.Jakobsson & Lindborg
 2017_DATA.xlsx
DOI: 10.5061/dryad.d78c5
title: Data from: Scaling of morphological characters across trait type, sex and environment: a meta-analysis of static allometries

description: Biological diversity is to a large extent a matter of variation in size.
 Proportional (isometric) scaling where large and small individuals are
 magnified versions of each other is often assumed the most common way
 morphological traits scale relative to overall size within species.
 However, the many traits showing non-proportional (allometric) scaling
 have motivated some of the most discussed hypotheses on scaling
 relationships in biology, like the positive allometry hypothesis for
 secondary sexual traits and the negative allometry hypothesis for
 genitals. I evaluate more than 3200 allometric parameters from the
 literature and find that negative allometry, not isometry, is the expected
 scaling relationship of morphological traits within species. Slopes of
 secondary sexual traits are more often steeper compared to other traits,
 but slopes larger than unity is also common for traits not under sexual
 selection. The steepness of the allometric slope is accordingly a weak
 predictor of past and present patterns of selection. Scaling of genitals
 varies across taxonomic groups, but negative allometry of genitals in
 insects and spiders is a consistent pattern. Lastly, I find indications
 that terrestrial organisms have an overall different scaling of
 morphological traits compared to aquatic species.
description: Data on allometric
 slopesallometry_data.xlsx
DOI: 10.5061/dryad.4f1n785
title: Data from: From feces to data: a metabarcoding method for analyzing consumed and available prey in a bird-insect food web

description: Diets play a key role in understanding trophic interactions. Knowing the
 actual structure of food webs contributes greatly to our understanding of
 biodiversity and ecosystem functioning. The research of prey preferences
 of different predators requires knowledge not only of the prey consumed,
 but also of what is available. In this study, we applied DNA metabarcoding
 to analyze the diet of 4 bird species (willow tits Poecile montanus,
 Siberian tits Poecile cinctus, great tits Parus major and blue tits
 Cyanistes caeruleus) by using the feces of nestlings. The availability of
 their assumed prey (Lepidoptera) was determined from feces of larvae
 (frass) collected from the main foraging habitat, birch (Betula spp.)
 canopy. We identified 53 prey species from the nestling feces, of which 11
 (21%) were also detected from the frass samples (8 lepidopterans).
 Approximately 80% of identified prey species in the nestling feces
 represented lepidopterans, which is in line with the earlier studies on
 the parids’ diet. A subsequent laboratory experiment showed a threshold
 for fecal sample size and the barcoding success, suggesting that the
 smallest frass samples do not contain enough larval DNA to be detected by
 high-throughput sequencing. To summarize, we apply metabarcoding for the
 first time in a combined approach to identify available prey (through
 frass) and consumed prey (via nestling feces), expanding the scope and
 precision for future dietary studies on insectivorous birds.
description: OTUSOtus as fasta format
 file. See Otutable.xls to link sample names to data.OTU
 tableReads assigned for each
 OTU in each sample. Contains the metadata information of the
 samples.OTU_table.xlsx