cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.84r5q
title: Data from: Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote

description: Some microbial eukaryotes, such as the extremophilic red alga Galdieria
 sulphuraria, can live in hot, toxic metal-rich, acidic environments. To
 elucidate the underlying molecular mechanisms of adaptation, we sequenced
 the 13.7 Mb genome of G. sulphuraria. This alga shows an enormous
 metabolic flexibility, growing either photoautotrophically or
 heterotrophically on more than 50 carbon sources. Environmental adaptation
 seems to have been facilitated by horizontal gene transfer from various
 bacteria and archaea, often followed by gene family expansion. At least 5%
 of protein-coding genes of G. sulphuraria were probably acquired
 horizontally. These proteins are involved in ecologically important
 processes ranging from heavy metal detoxification to glycerol uptake and
 metabolism. Thus, our findings show that a pan-domain gene pool has
 facilitated environmental adaptation in this unicellular eukaryote.
description: 208_GenomesList of 208 sequenced genomes used to generate protein families and phylogenetic treesGaldieria_in_Richmond_Mine_FISHMicrographs of two G. sulphuraria cells detected using Cya1208 rRNA probe in an A-drift biofilm from the Richmond Mine
DOI: 10.5061/dryad.bj23c
title: Data from: Habitat diversity and connectivity govern the conservation value of restored aquatic floodplain habitats

description: Floodplains have been strongly altered by human activities such as
 channelization and other river regulations. Globally, there is a growing
 interest in their restoration because of an increasing understanding of
 the ecological importance of these habitats for feeding, spawning, nursery
 or overwintering of aquatic species. In this study, a large floodplain
 restoration project of the upper Danube River was used to investigate
 colonization and succession patterns of fish, macroinvertebrates,
 macrophytes and periphyton in relation to abiotic habitat variables that
 can be restored through ecosystem management. Highest species diversity
 was detected near the contact zones of the floodplain channel to the main
 stem of the Danube, and in the transition zones of river sections (RS) and
 oxbow lakes (OS). The highest proportions of all taxa (82%) and of
 distinctive species (22%) were detected in RS, followed by OS (66% of all
 taxa, 8% distinctive species) and floodplain ponds (FP, 47% of all taxa,
 5% distinctive species). The habitat types RS, OS and FP significantly
 differed in overall community composition and their colonization processes
 comprising fast colonization of current-adapted specialists in RS, and
 mostly generalist species in OS and FP. Our results indicate that
 restoration of floodplain habitats should not only consider the
 re-establishment of maximum connectivity, but also provide a mosaic of
 distinct habitat types with different degrees of connectivity and
 disturbance. Each habitat type in the floodplain supported a unique
 assemblage of species, which suggests that such habitat mosaics can
 facilitate exceptionally diverse ecosystems.
description: Pander et al 2017
 Biological Conservation Data Dryad
DOI: 10.5061/dryad.pc6tp4q
title: Data from: Hotspot mutations and ColE1 plasmids contribute to the fitness of Salmonella Heidelberg in poultry litter

description: Salmonella enterica subsp. enterica serovar Heidelberg (S. Heidelberg) is
 a clinically-important serovar linked to food-borne illness, and commonly
 isolated from poultry. Investigations of a large, multistate outbreak in
 the USA in 2013 identified poultry litter (PL) as an important
 extra-intestinal environment that may have selected for specific S.
 Heidelberg strains. Poultry litter is a mixture of bedding materials and
 chicken excreta that contains chicken gastrointestinal (GI) bacteria,
 undigested feed, feathers, and other materials of chicken origin. In this
 study, we performed a series of controlled laboratory experiments which
 assessed the microevolution of two S. Heidelberg strains (SH-2813 and
 SH-116) in PL previously used to raise 3 flocks of broiler chickens. The
 strains are closely related at the chromosome level, differing from the
 reference genome by 109 and 89 single nucleotide polymorphisms/InDels,
 respectively. Whole genome sequencing was performed on 86 isolates
 recovered after 0, 1, 7 and 14 days of microevolution in PL. Only strains
 carrying an IncX1 (37kb), 2 ColE1 (4 and 6kb) and 1 ColpVC (2kb) plasmids
 survived more than 7 days in PL. Competition experiments showed that
 carriage of these plasmids was associated with increased fitness. This
 increased fitness was associated with an increased copy number of IncX1
 and ColE1 plasmids. Further, all Col plasmid-bearing strains had hotspot
 mutations in 37 loci on the chromosome and in 3 loci on the IncX1 plasmid.
 Additionally, we observed a decrease in susceptibility to tobramycin,
 kanamycin, gentamicin, neomycin and fosfomycin for Col plasmid-bearing
 strains. Our study demonstrates how positive selection from poultry litter
 can change the evolutionary path of S. Heidelberg.
description: Chromosomal_SNPs-InDelsVariant Call Format files for chromosome encoded SNPs/InDels identified for each isolate from this study.Command/scripts used for SNPs/InDels identificationUnix command line scripts used for SNP/InDel identitcationCommand scripts used for SNPs:InDel identification.docx
DOI: 10.5061/dryad.575
title: Data from: Hidden morphological support for the phylogenetic placement of Pseudoryx nghetinhensis with bovine bovids: a combined analysis of gross anatomical evidence and DNA sequences from five genes

description: The saola, Pseudoryx nghetinhensis, was unknown to science until its
 formal description in 1993. This endangered species is a member of the
 ruminant artiodactyl family Bovidae (cattle, sheep, goats, and antelopes).
 However, given its puzzling combination of morphological traits, the
 specific affinities of Pseudoryx within Bovidae are controversial. A
 preliminary genetic investigation suggested that Pseudoryx should be
 placed in the subfamily Bovinae (cattle, buffaloes, spiral-horned
 antelopes, and nilgai), but a recent cladistic analysis of skeletal and
 dental characters allied Pseudoryx with caprine bovids (sheep, goats, musk
 oxen, goat antelopes, and Pantholops). The morphological and molecular
 hypotheses differ in assigning the saola to either of the two most
 divergent clades of Bovidae. In this report, phylogenetic analyses of DNA
 sequences from five genes are used to test these alternatives. Protein
 coding regions, introns, and ribosomal DNAs from the nuclear and
 mitochondrial genomes discount the hypothesis that Pseudoryx is a close
 relative of Caprinae. Instead, combined analyses of the DNA data and
 published morphological evidence place Pseudoryx with Bovini (cattle and
 buffaloes), a subclade of Bovinae. In separate analysis, the matrix of
 morphological characters links Pseudoryx with caprine bovids, but in the
 context of the molecular data, the gross anatomical evidence strongly
 supports a grouping of Pseudoryx with Bovinae. Surprisingly, the
 morphological partition provides the most character support in the
 combined analysis. This striking result is obscured by separate analyses
 of the individual data sets and the taxonomic congruence approach.
description: 1216 Vuquang Data
 Set1216Vuquang.dataLac1 Vuquang Data SetaLac1Vuquang.datAll Data Vuquang Data SetalldataVuquang.datbCas XI Vuquang Data SetbCasXIVuquang.datCore Vuquang Data SetcoreVuquang.datMorph Vuquang Data SetMorphVuquang.datkCas XI Vuquang Data SetkCasXIVuquang.dat
DOI: 10.5061/dryad.p1qq2r1
title: Data from: Comparison of the efficacy and safety of drug therapies for macular edema secondary to central retinal vein occlusion

description: Objectives: To evaluate the efficacy and safety of anti-vascular
 endothelial growth factor (VEGF) agents and corticosteroids for the
 treatment of macular edema (ME) secondary to central retinal vein
 occlusion (CRVO). Design: Systematic review and network meta-analysis.
 Participants: Patients from previously reported randomized controlled
 trials (RCTs) comparing anti-VEGF and corticosteroids for the treatment of
 ME secondary to CRVO. Methods: Literature searches were conducted using
 PubMed, Medline, Embase, Cochrane Library, and clinicaltrials.gov until
 March 2017. Therapeutic effects were estimated using the proportions of
 patients gaining/losing ≥15 letters, best-corrected visual acuity (BCVA),
 and central retinal thickness (CRT). Treatment safety was estimated using
 the proportions of adverse events, namely increased intraocular pressure
 (IOP), cataracts, vitreous hemorrhage (VH), and retinal tear. The software
 ADDIS (version 1.16.8) was used for analysis. Treatment effect and safety
 of different drugs could be ranked based on simulation. Results: Eleven
 RCTs comprising 2060 patients were identified. Regarding patients gaining
 ≥15 letters, aflibercept and ranibizumab were significantly more effective
 than sham/placebo at 6 months. Regarding patients losing ≥15 letters at 6
 months, ranibizumab showed significant improvement compared to
 dexamethasone. Aflibercept, bevacizumab, or ranibizumab showed greater
 improvements in BCVA than sham/placebo at 6 months. Intravitreal
 ranibizumab injection demonstrated greater CRT reduction than both sham
 and dexamethasone did. Dexamethasone had a higher risk of increased IOP
 than aflibercept and ranibizumab. Ranibizumab demonstrated a greater risk
 of cataracts than dexamethasone. Aflibercept and ranibizumab demonstrated
 low incidence of VH and retinal tear, respectively. Aflibercept had a
 slight advantage over ranibizumab as assessed by benefit-risk analysis.
 Conclusions: Anti-VEGF agents have advantages in the treatment of ME
 secondary to CRVO. Aflibercept and ranibizumab showed marked BCVA
 improvement and CRT reduction. Aflibercept may have a slight advantage
 over ranibizumab. The results of this study can serve as a reference for
 clinicians to provide patient-tailored treatment.
description: original data of CRVO
 with MEthe original data of
 this network meta-analysisCRVO with
 ME.addisSpecific literatures of
 included and excluded studiesCharacteristics of
 included studies
DOI: 10.5061/dryad.fs4k13k
title: Data from: Do migratory and resident birds differ in their responses to interacting effects of climate, weather and vegetation?

description: Aim: Knowledge of the individual and collective effects of habitat,
 weather variability, and climate on bird populations is limited, with the
 result that species vulnerability to the collective impacts of global
 change is poorly understood. We quantified the effects of interactions
 between these potential drivers on the occurrence of resident, migratory,
 and nomadic birds in Australian temperate woodlands. Location: A 1.8
 million hectare temperate woodland belt in south-eastern Australia. Time
 period: 2002-2015. Major taxa studied: Temperate woodland birds. Methods:
 We used logistic mixed models to quantify the factors affecting the
 occurrence of three groups of birds (residents, partial migrants, nomads)
 at 203 long-term field sites located in three vegetation types
 (restoration plantings, natural regrowth woodland, old growth woodland)
 surveyed repeatedly between 2002 and 2015. Potential explanatory variables
 included vegetation type, three long-term climate variables (mean annual
 rainfall, maximum temperature, minimum temperature), and the three
 corresponding weather variables for 12 months preceding each survey.
 Results: We found four-way interactions between bird movement category,
 type of vegetation cover, and rainfall (both as a long-term climate
 variable and a short-term weather variable). Increased occurrence of
 nomads and partial migrants, but not resident species, was associated with
 high short-term rainfall. The effects were more marked in long-term
 climatically-wet areas, and also differed between vegetation types. Models
 for maximum and minimum temperature were simpler than those for rainfall,
 but showed evidence of partial migrants and nomadic species avoiding low
 minimum or high maximum temperatures in some vegetation types. Main
 conclusions: Our analyses revealed that birds with different movement
 patterns exhibit different responses to weather and long-term climate.
 Nomadic species in particular respond to rainfall strongly in
 climatically-wet locations (presumably because of large pulses in
 resources). Drying conditions resulting from climate change may therefore
 create problems for the future persistence of nomadic bird species.
description: Woodland bird responses
 to climate, weather and vegetationData used to inform the
 paper 'Do migratory and resident birds differ in their responses to
 interacting effects of climate, weather and
 vegetation?'.SWS migration paper
 data.csv
DOI: 10.5061/dryad.j1h3cs3p
title: Data from: Influence of salinity on bacterioplankton communities from the Brazilian rain forest to the coastal Atlantic Ocean

description: BACKGROUND: Planktonic bacteria are recognized as important drivers of
 biogeochemical processes in all aquatic ecosystems, however, the taxa that
 make up these communities are poorly known. The aim of this study was to
 investigate bacterial communities in aquatic ecosystems at Ilha Grande,
 Rio de Janeiro, Brazil, a preserved insular environment of the Atlantic
 rain forest and how they correlate with a salinity gradient going from
 terrestrial aquatic habitats to the coastal Atlantic Ocean.
 METHODOLOGY/PRINCIPAL FINDINGS: We analyzed chemical and microbiological
 parameters of water samples and constructed 16S rRNA gene libraries of
 free living bacteria obtained at three marine (two coastal and one
 offshore) and three freshwater (water spring, river, and mangrove)
 environments. A total of 836 sequences were analyzed by MOTHUR, yielding
 269 freshwater and 219 marine operational taxonomic units (OTUs) grouped
 at 97% stringency. Richness and diversity indexes indicated that
 freshwater environments were the most diverse, especially the water
 spring. The main bacterial group in freshwater environments was
 Betaproteobacteria (43.5%), whereas Cyanobacteria (30.5%),
 Alphaproteobacteria (25.5%), and Gammaproteobacteria (26.3%) dominated the
 marine ones. Venn diagram showed no overlap between marine and freshwater
 OTUs at 97% stringency. LIBSHUFF statistics and PCA analysis revealed
 marked differences between the freshwater and marine libraries suggesting
 the importance of salinity as a driver of community composition in this
 habitat. The phylogenetic analysis of marine and freshwater libraries
 showed that the differences in community composition are consistent.
 CONCLUSIONS/SIGNIFICANCE: Our data supports the notion that a divergent
 evolutionary scenario is driving community composition in the studied
 habitats. This work also improves the comprehension of microbial community
 dynamics in tropical waters and how they are structured in relation to
 physicochemical parameters. Furthermore, this paper reveals for the first
 time the pristine bacterioplankton communities in a tropical island at the
 South Atlantic Ocean.
description: Silveira2011
DOI: 10.5061/dryad.7q10s
title: Data from: What's the meaning of local? Using molecular markers to define seed transfer zones for ecological restoration in Norway

description: According to the Norwegian Diversity Act, practitioners of restoration in
 Norway are instructed to use seed mixtures of local provenance. However,
 there are no guidelines for how local seed should be selected. In this
 study, we use genetic variation in a set of alpine species (Agrostis
 mertensii, Avenella flexuosa, Carex bigelowii, Festuca ovina, Poa alpina
 and Scorzoneroides autumnalis) to define seed transfer zones to reduce
 confusion about the definition of ‘local seeds’. The species selected for
 the study are common in all parts of Norway and suitable for commercial
 seed production. The sampling covered the entire alpine region (7–20
 populations per species, 3–15 individuals per population). We
 characterised genetic diversity using amplified fragment length
 polymorphisms. We identified different spatial genetic diversity
 structures in the species, most likely related to differences in
 reproductive strategies, phylogeographic factors and geographic
 distribution. Based on results from all species, we suggest four general
 seed transfer zones for alpine Norway. This is likely more conservative
 than needed for all species, given that no species show more than two
 genetic groups. Even so, the approach is practical as four seed mixtures
 will serve the need for restoration of vegetation in alpine regions in
 Norway.
description: AFLP
 dataAFLP
 data
DOI: 10.5061/dryad.g4d30
title: Data from: Environmental versus anthropogenic effects on population adaptive divergence in the freshwater snail Lymnaea stagnalis

description: Repeated pesticide contaminations of lentic freshwater systems located
 within agricultural landscapes may affect population evolution in
 non-target organisms, especially in species with a fully aquatic life
 cycle and low dispersal ability. The issue of evolutionary impact of
 pollutants is therefore conceptually important for ecotoxicologists. The
 impact of historical exposure to pesticides on genetic divergence was
 investigated in the freshwater gastropod Lymnaea stagnalis, using a set of
 14 populations from contrasted environments in terms of pesticide and
 other anthropogenic pressures. The hypothesis of population adaptive
 divergence was tested on 11 life-history traits, using QST -FST
 comparisons. Despite strong neutral differentiation (mean FST = 0.291),
 five adult traits or parameters were found to be under divergent
 selection. Conversely, two early expressed traits showed a pattern
 consistent with uniform selection or trait canalization, and four adult
 traits appeared to evolve neutrally. Divergent selection patterns were
 mostly consistent with a habitat effect, opposing pond to ditch and
 channel populations. Comparatively, pesticide and other human pressures
 had little correspondence with evolutionary patterns, despite hatching
 rate impairment associated with global anthropogenic pressure. Globally,
 analyses revealed high genetic variation both at neutral markers and
 fitness-related traits in a species used as model in ecotoxicology,
 providing empirical support for the need to account for genetic and
 evolutionary components of population response in ecological risk
 assessment.
description: Life history and
 genotypic data used in this studyLife history traits were
 measured under common-garden conditions on a set of families stemming from
 14 populations of the freshwater snail Lymnaea stagnalis. Each family is
 identified in the file as G0 (wild-caught parent). A subset of
 laboratory-born G1s were followed from birth to adulthood. Shell size data
 were used to estimate growth parameters of the Gompertz model.Trait
 variance, within and among populations, was used to infer quantitative
 genetic differentiation (QST). Genotypic data were obtained from 12
 microsatellite markers and used to infer population neutral
 differentiation (FST).online_rawdatabase.xlsx
DOI: 10.15139/s3/whi4oc
title: Data Management and Sharing Plan for: p16INK4a Expression, Chemotherapy Toxicity, and Aging in Women with Breast Cancer

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5061/dryad.45g3s
title: Data from: Body temperature distributions of active diurnal lizards in three deserts: skewed up or skewed down?

description: 1. The performance of ectotherms integrated over time depends in part on
 the position and shape of the distribution of body temperatures (Tb)
 experienced during activity. For several complementary reasons,
 physiological ecologists have long expected that Tb distributions during
 activity should have a long left tail (left-skewed); but only infrequently
 have they quantified the magnitude and direction of Tb skewness in nature.
 2. To evaluate whether left-skewed Tb distributions are general for
 diurnal desert lizards, we compiled and analyzed Tb (∑ = 9,023
 temperatures) from our own prior studies of active desert lizards on three
 continents (25 species in Western Australia, 10 in the Kalahari Desert of
 Africa, and 10 species in western North America). We gathered these data
 over several decades, using standardized techniques. 3. Many species
 showed significantly left-skewed Tb distributions, even when records were
 restricted to summer months. However, magnitudes of skewness were always
 small, such that mean Tb were never more than 1°C lower than median Tb.
 The significance of Tb skewness was sensitive to sample size, and power
 tests reinforced this sensitivity. 4. The magnitude of skewness was not
 obviously related to phylogeny, desert, body size, or median body
 temperature. Moreover, formal phylogenetic analysis is inappropriate
 because geography and phylogeny are confounded (that is, are highly
 collinear). 5. Skewness might be limited if lizards pre-warm inside
 retreats before emerging in the morning, emerge only when operative
 temperatures are high enough to speed warming to activity Tb, or if cold
 lizards are especially wary and difficult to spot or catch. Telemetry
 studies may help evaluate these possibilities.
description: AustraliaTbDataBody temperature data for lizards from Western Australia. area = site name, number = field tag number, species name, BT = body temperature (°C), time and date, microhabitat, and family. for general methods, see E. R. Pianka, Ecology and Natural History of Desert Lizards. (Princeton University Press, Princeton, N.J., 1986).KalahariTbDataBody temperature data for lizards from Western Australia. area = site name, number = field tag number, species name, BT = body temperature (°C), time and date, microhabitat, and family. for general methods, see E. R. Pianka, Ecology and Natural History of Desert Lizards. (Princeton University Press, Princeton, N.J., 1986) and R. B. Huey, E. R. Pianka, J. Hoffmann, Seasonal variation in thermoregulatory behavior and body temperatures of diurnal Kalahari lizards. Ecology 58, 1066-1075 (1977).NorthAmericanTbDataBody temperature data for lizards from Western Australia. area = site name, number = field tag number, species name, BT = body temperature (°C), time and date, microhabitat, and family. for general methods, see E. R. Pianka, Ecology and Natural History of Desert Lizards. (Princeton University Press, Princeton, N.J., 1986).