cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4t8h5
title: Data from: Patterns of migrating soaring migrants indicate attraction to marine wind farms

description: Monitoring of bird migration at marine wind farms has a short history, and
 unsurprisingly most studies have focused on the potential for collisions.
 Risk for population impacts may exist to soaring migrants such as raptors
 with K-strategic life-history characteristics. Soaring migrants display
 strong dependence on thermals and updrafts and an affinity to land areas
 and islands during their migration, a behaviour that creates corridors
 where raptors move across narrow straits and sounds and are attracted to
 islands. Several migration corridors for soaring birds overlap with the
 development regions for marine wind farms in NW Europe. However, no
 empirical data have yet been available on avoidance or attraction rates
 and behavioural reactions of soaring migrants to marine wind farms. Based
 on a post-construction monitoring study, we show that all raptor species
 displayed a significant attraction behaviour towards a wind farm. The
 modified migratory behaviour was also significantly different from the
 behaviour at nearby reference sites. The attraction was inversely related
 to distance to the wind farm and was primarily recorded during periods of
 adverse wind conditions. The attraction behaviour suggests that migrating
 raptor species are far more at risk of colliding with wind turbines at sea
 than hitherto assessed.
description: Skov_SoaringMigrants_MarineWindFarms_RealTimeTrackingRadar and laser rangefinder track data on migrating raptors from study site and two reference sites. Each record represents a track node.
DOI: 10.5061/dryad.d8691c1
title: Data from: Aging infrastructure creates opportunities for cost-efficient restoration of aquatic ecosystem connectivity

description: A hallmark of industrialization is the construction of dams for water
 management and roads for transportation, leading to fragmentation of
 aquatic ecosystems. Many nations are striving to address both maintenance
 backlogs and mitigation of environmental impacts as their infrastructure
 ages. Here, we test whether accounting for road repair needs could offer
 opportunities to boost conservation efficiency by piggybacking
 connectivity restoration projects on infrastructure maintenance. Using
 optimization models to align fish passage restoration sites with likely
 road repair priorities, we find potential increases in conservation
 return-on-investment ranging from 17% to 25%. Importantly, these gains
 occur without compromising infrastructure or conservation priorities;
 simply communicating openly about objectives and candidate sites enables
 greater accomplishment at current funding levels. Society embraces both
 reliable roads and thriving fisheries, so overcoming this coordination
 challenge should be feasible. Given deferred maintenance crises for many
 types of infrastructure, there could be widespread opportunities to
 enhance the cost-effectiveness of conservation investments by coordinating
 with infrastructure renewal efforts.
description: Neeson_2018_barrier_dataThis data set describes barrier attributes and project costs for all dams and road-crossings in the Saginaw River, Michigan, USA.
DOI: 10.5061/dryad.8pt2c
title: Data from: Prevalence of vancomycin-variable Enterococcus faecium (VVE) among vanA-positive sterile site isolates and patient factors associated with VVE bacteremia

description: Vancomycin-variable enterococci (VVE) are vanA-positive,
 vancomycin-susceptible enterococci with the ability to revert to a
 vancomycin-resistant phenotype on exposure to vancomycin. We sought to
 assess the prevalence of VVE and to determine clinical characteristics of
 patients infected with VVE. We prospectively collected Enterococcus
 faecium sterile site isolates from Toronto Invasive Bacterial Diseases
 Network hospitals from January 2015 to June 2016 and calculated VVE
 (defined as vanA-positive, vancomycin-susceptible isolates) prevalence
 among vanA-containing isolates. We performed chart reviews of VVE and
 vancomycin-resistant E. faecium (VRE) bacteremias identified from January
 2012 to June 2016, and on a random sample of patients with bacteremia due
 to vanA/vanB-negative, vancomycin-susceptible enterococci (VSE) from
 January 2015 to June 2016. Clinical characteristics were compared and
 factors associated with mortality assessed. Because of the potential
 reversion from VVE to VRE, pulsed-field gel electrophoresis (PFGE) was
 performed for strains causing breakthrough bacteremia in order to identify
 relatedness among strains with different phenotypic resistance within the
 same patient. VVE comprised 47% (18/38) of vanA-positive isolates. The
 charts of 36 VRE, 25 VVE, and 79 VSE patients were reviewed. Central
 venous catheter associated bacteremia was more common in VVE (44%) and VRE
 patients (57%) than in VSE patients (28%) (P=0.01). The Pitt bacteremia
 (OR 1.3, P=0.002) and the Charlson score (OR 1.2, P=0.008) were the only
 independent mortality predictors. PFGE of strains causing breakthrough
 bacteremia showed high within-patient clonality, irrespective of
 vanA-positivity or vancomycin-susceptibility. A substantial proportion of
 vanA-positive isolates are VVE and are therefore not detected with
 conventional selective culture methods. Bacteremia sources of patients
 with VVE are similar to those infected with VRE. We detected no
 association between VVE and 30-day mortality or breakthrough bacteremia.
description: EF_SASCode_Tbl2:3SAS code for analysis of data from chart review and for analysis of mortality risk factorsEF_DataDictionary_ChartReview_Tbl2and3Data dictionary for CRFEF_TotalData_Tbl1Shows data on all E. faecium sterile site isolates including susceptibility results and PCR resultsEF_Data_ChartReview_Tbl2and3Data for Tables 2 and 3PFGE_Table4Pulsed-field gel electrophoresis of E. faecium blood isolates of patients with breakthrough bacteremia with VSE, VVE or VRE (see Table 4 in manuscript).
DOI: 10.5061/dryad.c8jg8
title: Data from: Evolution of smooth tubercle bacilli PE and PE_PGRS genes: evidence for a prominent role of recombination and imprint of positive selection

description: Background: PE and PE_PGRS are two mycobateria-restricted multigene
 families encoding membrane associated and secreted proteins that have
 expanded mainly in the pathogenic species, notably the Mycobacterium
 tuberculosis complex (MTBC). Several lines of evidence attribute to PE and
 PE_PGRS genes critical roles in mycobacterial pathogenicity. To get more
 insight into the nature of these genes, we sought to address their
 evolutionary trajectories in the group of smooth tubercle bacilli (STB),
 the putative ancestor of the clonal MTBC. Methodology/Principal Findings:
 By focussing on six polymorphic STB PE/PE_PGRS genes, we demonstrate
 significant incongruence among single gene genealogies and detect strong
 signals of recombination using various approaches. Coalescent-based
 estimation of population recombination and mutation rates (ρ and θ,
 respectively) indicates that the two mechanisms are of roughly equal
 importance in generating diversity (ρ/θ = 1.457), a finding in a marked
 contrast to house keeping genes (HKG) whose evolution is chiefly brought
 about by mutation (ρ/θ = 0.012). In comparison to HKG, we found 15 times
 higher mean rate of nonsynonymous substitutions, with strong evidence of
 positive selection acting on PE_PGRS62 (dN/dS = 1.42), a gene that has
 previously been shown to be essential for mycobacterial survival in
 macrophages and granulomas. Imprint of positive selection operating on
 specific amino acid residues or along branches of PE_PGRS62 phylogenetic
 tree was further demonstrated using maximum likelihood- and covarion-based
 approaches, respectively. Strikingly, PE_PGR62 proved highly conserved in
 present-day MTBC strains. Conclusions/Significance: Overall the data
 indicate that, in STB, PE/PE_PGRS genes have undergone a strong
 diversification process that is speeded up by recombination, with evidence
 of positive selection. The finding that positive selection involved an
 essential PE_PGRS gene whose sequence appears to be driven to fixation in
 present-day MTBC strains lends further support to the critical role of
 PE/PE_PGRS genes in the evolution of mycobacterial pathogenicity.
description: PE3PE4PE_PGRS26PE_PGRS35PE_PGRS51PE_PGRS62concatenated_PE3-PE4-PE_PGRS26-PE_PGRS35-PE_PGRS51-PE_PGRS62concatenated_gyrA-gyrB-hsp65-katG-rpoBTOPALi_Model_Selection_resultTo determine the best substitution model of each alignment, we used the TOPALi v2 package.
DOI: 10.5061/dryad.0hc2m
title: Data from: Long-term dynamics of adaptation in asexual populations

description: Experimental studies of evolution have increased greatly in recent years,
 stimulated by the growing power of genomic tools. However, organismal
 fitness remains the ultimate metric for interpreting these experiments,
 and the dynamics of fitness remain poorly understood over long timescales.
 Here, we examine fitness trajectories for 12 Escherichia coli populations
 during 50,000 generations. Mean fitness appears to increase without bound,
 consistent with a power law. We also derive this power-law relation
 theoretically by incorporating clonal interference and diminishing-returns
 epistasis into a dynamical model of changes in mean fitness over time.
description: Concatenated.LTEE.data.all.csvThis is the primary data file for the fitness competitions of each individual population against the oppositely-marked ancestor for as many of the 50,000 generations as could be measured in our standard competitions.Concatenated.40k.v.50kThis is the data file of the competitions against a 40,000 generation clone, from evolved populations at both 40,000 and 50,000 generations.Final.Dryad.ScriptThis is the analysis script for the empirical data, written to be copy and pasted into an R terminal.adaptation model_diminishing returns_continuous_notatedThis is the Mathematica Notebook file for the theoretical and simulation portion of the paper.adaptation model_diminishing returns_continuous_notatedThis is a pdf of the Mathematica Notebook file.
DOI: 10.5061/dryad.mf41g
title: Data from: Edaphic factors determining the occurrence of herbaceous legumes in Amazonian savannas

description: Edaphic factors have been indicated as a determinant of the distribution
 of plant communities in Amazonia. The aim of this study was to detect
 which edaphic factors determine the occurrence of herbaceous legumes in
 Amazonian savannas. Therefore, an inventory of herbaceous flora of the
 family Leguminosae was conducted in 34 permanent plots established in two
 savanna areas of Roraima, northern Brazilian Amazon. The importance value
 index was higher for Chamaecrista desvauxii (24.9%), Aeschynomene hystrix
 (15.7%) and Galactia jussiaeana (10.8%), all having high abundance and
 wide distribution. The results indicated low density or absence of
 individuals and species in plots established on poorly drained soils
 (hydromorphic). Diversity and species richness tended to be higher in
 habitats formed on well drained soils, greater fertility and lower
 concentrations of exchangeable aluminum. It is suggested that poor and
 seasonally flooded soils tend to reduce the chances of occurrence of
 herbaceous legumes in savanna areas of Roraima, adversely affecting its
 richness/diversity.
description: Edaphic factors
 determining the occurrence of herbaceous legumes in Amazonian
 savannasData collected in two
 savanna areas of the northern Brazilian Amazon.legumin_savanna_RR.xlsx
DOI: 10.5061/dryad.39309
title: Data from: Adaptive functional divergence of the warm temperature acclimation-related protein (WAP65) in fishes and the ortholog Hemopexin (HPX) in mammals

description: Gene duplication is an important mechanism that leads to genetic novelty.
 Different, nonexclusive processes are likely involved, and many adaptive
 and nonadaptive events may contribute to the maintenance of duplicated
 genes. In some teleosts, a duplicate copy of the mammalian ortholog
 Hemopexin (HPX) is present, known as the warm temperature
 acclimation-related protein (WAP65). Both WAP65 and HPX have been
 associated with iron homeostasis due to the affinity to bind the
 toxic-free heme circulating in the blood stream. We have assessed the
 evolutionary dynamics of WAP65 and HPX genes to understand the adaptive
 role of positive selection at both nucleotide and amino acid level. Our
 results showed an asymmetrical evolution between the paralogs WAP65-1 and
 WAP65-2 after duplication with a slight acceleration of the evolutionary
 rate in WAP65-1, but not in WAP65-2, and few sites contributing to the
 functional distinction between the paralogs, whereas the majority of the
 protein remained under negative selection or relaxed negative selection.
 WAP65-1 is functionally more distinct from the ancestral protein function
 than WAP65-2. HPX is phylogenetically closer to WAP65-2 but even so
 functional divergence was detected between both proteins. In addition, HPX
 showed a fast rate of evolution when compared with both WAP65-1 and
 WAP65-2 genes. The assessed 3-dimensional (3-D) structure of WAP65-1 and
 WAP65-2 suggests that the functional differences detected are not causing
 noticeable structural changes in these proteins. However, such subtle
 changes between WAP65 paralogs may be important to understand the
 differential gene retention of both copies in 20 out of 30 teleosts
 species studied.
description: 1.AlignmentsMultiple sequence alignments.2.PhylogeneticTreesPhylogenetic Trees: BAY, ML and NJ, for the 66 sequences used in this study. File format (.xtg) readable in TreeGraph.2.PhylogeneticTree.zip3.DIVERGEFunctional divergence results. Alignment and tree used to produce the results.4.SelectionPositive Selection results from PAML and TreeSAAP. Control files used for Branch, Branch-Site and Site models.5.Protein3DModelsProtein 3D model obtained for WAP65-1 and WAP65-2 in the European seabass (Dicentrarchus labrax) from I-Tasser server.
DOI: 10.5061/dryad.2k5rf
title: Data from: Habitat-associated phylogenetic community patterns of microbial ammonia oxidizers

description: Microorganisms mediating ammonia oxidation play a fundamental role in the
 connection between biological nitrogen fixation and anaerobic nitrogen
 losses. Bacteria and Archaea ammonia oxidizers (AOB and AOA, respectively)
 have colonized similar habitats worldwide. Ammonia oxidation is the
 rate-limiting step in nitrification, and the ammonia monooxygenase (Amo)
 is the key enzyme involved. The molecular ecology of this process has been
 extensively explored by surveying the gene of the subunit A of the Amo
 (amoA gene). In the present study, we explored the phylogenetic community
 ecology of AOB and AOA, analyzing 5776 amoA gene sequences from
 &gt;300 isolation sources, and clustering habitats by environmental
 ontologies. As a whole, phylogenetic richness was larger in AOA than in
 AOB, and sediments contained the highest phylogenetic richness whereas
 marine plankton the lowest. We also observed that freshwater ammonia
 oxidizers were phylogenetically richer than their marine counterparts. AOA
 communities were more dissimilar to each other than those of AOB, and
 consistent monophyletic lineages were observed for sediments, soils, and
 marine plankton in AOA but not in AOB. The diversification patterns showed
 a more constant cladogenesis through time for AOB whereas AOA apparently
 experienced two fast diversification events separated by a long
 steady-state episode. The diversification rate (γ statistic) for most of
 the habitats indicated γ_AOA &gt; γ_AOB. Soil and sediment experienced
 earlier bursts of diversification whereas habitats usually eutrophic and
 rich in ammonium such as wastewater and sludge showed accelerated
 diversification rates towards the present. Overall, this work shows for
 the first time a global picture of the phylogenetic community structure of
 both AOB and AOA assemblages following the strictest analytical standards,
 and provides an ecological view on the differential evolutionary paths
 experienced by widespread ammonia-oxidizing microorganisms. The emerged
 picture of AOB and AOA distribution in different habitats provides a new
 view to understand the ecophysiology of ammonia oxidizers on Earth.
description: Alignment files and
 treesThe file contains all
 bacterial and archaeal amoA aligned sequences, gblocks trimmed alignments
 and resulting tree files from
 doi:10.1371/journal.pone.0047330dryad_fernandez-guerra_2012_pone.tar.gz
DOI: 10.5061/dryad.540bt
title: Data from: Adaptive and neutral markers both show continent-wide population structure of mountain pine beetle (Dendroctonus ponderosae)

description: Assessments of population genetic structure and demographic history have
 traditionally been based on neutral markers while explicitly excluding
 adaptive markers. In this study, we compared the utility of putatively
 adaptive and neutral single-nucleotide polymorphisms (SNPs) for inferring
 mountain pine beetle population structure across its geographic range.
 Both adaptive and neutral SNPs, and their combination, allowed range-wide
 structure to be distinguished and delimited a population that has recently
 undergone range expansion across northern British Columbia and Alberta.
 Using an equal number of both adaptive and neutral SNPs revealed that
 adaptive SNPs resulted in a stronger correlation between sampled
 populations and inferred clustering. Our results suggest that adaptive
 SNPs should not be excluded prior to analysis from neutral SNPs as a
 combination of both marker sets resulted in better resolution of genetic
 differentiation between populations than either marker set alone. These
 results demonstrate the utility of adaptive loci for resolving population
 genetic structure in a nonmodel organism.
description: Mountain pine beetle
 genotype informationThis file contains
 genotype information for mountain pine beetle individuals samples from 62
 different sites across Canada and the USA.Sequenom_Ecology_Evolution_Dyrad_submission_2016.xlsx
DOI: 10.5061/dryad.t39g3
title: Data from: Nonadditive effects of consumption in an intertidal macroinvertebrate community are independent of food availability but driven by complementarity effects

description: Suboptimal environmental conditions are ubiquitous in nature and commonly
 drive the outcome of biological interactions in community processes.
 Despite the importance of biological interactions for community processes,
 knowledge on how species interactions are affected by a limiting resource,
 e.g. low food availability, remains limited. Here, we tested whether
 variation in food supply causes non-additive consumption patterns, using
 the macroinvertebrate community of intertidal sandy beaches as a model
 system. We quantified isotopically labelled diatom consumption by three
 macroinvertebrate species (Bathyporeia pilosa, Haustorius arenarius and
 Scolelepis squamata) kept in mesocosms in either monoculture or a
 3-species community at a range of diatom densities. Our results show that
 B. pilosa was the most successful competitor in terms of consumption at
 both high and low diatom density, while H. arenarius and especially S.
 squamata consumed less in a community than in their respective
 monocultures. Non-additive effects on consumption in this
 macroinvertebrate community were present and larger than mere additive
 effects, and similar across diatom densities. The underlying species
 interactions, however, did change with diatom density. Complementarity
 effects related to niche-partitioning were the main driver of the net
 diversity effect on consumption, with a slightly increasing contribution
 of selection effects related to competition) with decreasing diatom
 density. For the first time we showed that non-additive effects of
 consumption are independent of food availability in a macroinvertebrate
 community. This suggests that in communities with functionally different,
 and thus complementary, species, non-additive effects can arise even when
 food availability is low. Hence, at a range of environmental conditions,
 species interactions hold important potential to alter ecosystem
 functioning.
description: exp_2a_13C_15N_harvest_and_t0_macroinvertebratesSee first tab for informationexp_2a_biomass_t0_macroinvertebratesSee first tab for informationexp_2a_survival_and_biomass_harvest_macroinvertebratesSee first tab for informationexp_2b_13C_15N_part1_harvest_and_t0_macroinvertebratesSee first tab for informationexp_2b_13C_15N_part2_harvest_macroinvertebratesexp_2b_survival_and_biomass_harvest_macroinvertebratesSee first tab for informationexp_2b_biomass_t0_macroinvertebratesSee first tab for information
DOI: 10.5061/dryad.f9f75
title: Data from: Spatiotemporal relationship between adult census size and genetic population size across a wide population size gradient

description: Adult census population size (N) and effective number of breeders (Nb) are
 highly relevant for designing effective conservation strategies. Both
 parameters are often challenging to quantify, however, making it of
 interest to determine whether one parameter can be generalized from the
 other. Yet, the spatiotemporal relationship between N and Nb has not been
 well characterized empirically in many taxa. We analysed this relationship
 for 5–7 consecutive years in twelve brook trout populations varying
 greatly in N (49-10032) and Nb (3-567) and identified major environmental
 variables affecting the two parameters. N or habitat size alone explained
 47–57% of the variance in Nb, and Nb was strongly correlated with
 effective population size. The ratio Nb/N ranged from 0.01 to 0.45 and
 increased at small N or following an annual decrease in N, suggesting
 density-dependent constraints on Nb. We found no evidence for a
 consistent, directional difference between variability in Nb and/or Nb/N
 among small and large populations; however, small populations had more
 varying temporal variability in Nb/N ratios than large populations.
 Finally, Nb and Nb/N were 2.5- and 2.3-fold more variable among
 populations than temporally within populations. Our results demonstrate a
 clear linkage between demographic and evolutionary parameters, suggesting
 that Nb could be used to approximate N (or vice versa) in natural
 populations. Nevertheless, using one variable to infer the other to
 monitor trends within populations is less recommended, perhaps even less
 so in small populations given their less predictable Nb vs. N dynamics.
description: Velocity data for 12
 Cape Race streamsVelocity (m/s)
 measurements measured in the field on cross-sections in 12 streams between
 2010 and 2016. Pop; genetically distinct brook trout
 populations.Cape
 Race_Velocity.csvIndividual genotypes for
 12 brook trout populationsIndividual genotype data
 from 12 microsatellites in 12 brook trout populations sampled from
 2009-2015.Cape
 Race_Genotypes.csv