cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gf4qj
title: Data from: When virulence originates from nonagricultural hosts: evolutionary and epidemiological consequences of introgressions following secondary contacts in Venturia inaequalis

description: In pathogens, introgressions through secondary contacts between divergent
 populations from agricultural and nonagricultural disease reservoirs are
 expected to have crucial evolutionary and epidemiological implications.
 Despite the importance of this question for disease management,
 experimental demonstrations of these implications remain scarce. Recently,
 we identified a virulent population of the apple scab pathogen Venturia
 inaequalis that migrated from nonagricultural hosts to European domestic
 apple orchards. Here, we investigated the occurrence of gene flow between
 agricultural and nonagricultural populations sampled in two orchards, and
 thereafter its consequences on the pathogenicity of hybrids. Population
 genetic structure and demographic inferences based on the genotypes of 104
 strains revealed a high amount of gene flow between the two populations in
 one orchard. In this site, mating between populations was made possible by
 the presence of a common host. Our results revealed an invasion of the
 virulent trait in the agricultural population; a main direction of
 introgression in hybrids from the agricultural to nonagricultural genetic
 backgrounds; and a population of hybrids with transgressive traits. We
 demonstrate a secondary contact with gene flow between divergent
 populations of pathogens. Our findings highlight evolutionary and
 epidemiological changes in pathogens and have concrete implications for
 sustainable disease management.
description: Leroy_2015_newphytologist_dataset_969AFLPour dataset: 104 strains genotyped at 969 AFLP loci (binary 0/1 character matrix, missing data = -9)
DOI: 10.15468/dl.f9autc
title: Occurrence Download

description: A dataset containing 32647 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-86.791 34.448,-75.904 34.448,-75.904 38.67,-86.791 38.67,-86.791 34.448))",
 "OccurrenceStatus is Present",
 "TaxonKey is Decapoda"
 ]
}

 The dataset includes 32647 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000606-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7hn84
title: Data from: Higher seed number compensates for lower fruit set in deceptive orchids

description: 1. Floral deception is widespread in orchids, with more than one third of
 the species being pollinated this way. The evolutionary success of
 deceptive orchids is puzzling, as species employing this strategy are
 thought to have low reproductive success (less flowers yielding fruits)
 because of low pollination rates. However, direct measurements of total
 seed production in orchids – which is a better measure of reproductive
 success – are scarce due to the extremely small size of their seeds. 2.
 Here, we quantified seed numbers in 1,015 fruits belonging to 48 orchid
 species from the Pannonian ecoregion (central Europe) and obtained
 fruit-set and thousand-seed weight data for these species from the
 literature. We used phylogenetic comparative methods to test the
 hypothesis that deceptive species should compensate for their lower
 fruit-set by having either more flowers, larger seeds or more seeds in a
 fruit. 3. Similarly to previous studies, we found that deceptive orchids
 have substantially lower fruits-set than nectar-rewarding ones. Also, we
 found that deceptive species have more seeds in a fruit but not more
 flowers or larger seeds compared to nectar-rewarding ones. Based on our
 results, deceptive species compensate for their lower fruit-set by having
 higher seed numbers per fruit. As a consequence, their seed numbers per
 shoot do not differ from that of nectar-rewarding ones. 4. Together with
 other benefits of deceptive pollination (e.g. lower energy expenditure due
 to the lack of nectar production and higher genetic variability due to
 decreased probability of geitonogamous pollination), our results can
 explain why deceptive strategies are so widespread in the orchid family.
 5. Synthesis. Our results indicate that deceptive orchids can compensate
 for their lower fruit-set by having more (but not larger) seeds in a fruit
 than rewarding species. These findings highlight possible ways in which
 plants can increase their reproductive success in face of pollinator
 limitation. We emphasize that fruit-set in itself is an inappropriate
 measure of the reproductive success of orchids – the total number of seeds
 per shoot is a much better approximation.
description: Seed number
 dataAll capsular seed number
 data measured by the authors and used in the analyses. The file also
 contains the locality and time of collection and the name of the
 collector.Orchids-seed-nr-data_Sonkoly-et-al_JEcol_2015.csvITS alignmentnrITS alignment underpinning the analysesOrchids-ITS-alignment_Sonkoly-et-al_JEcol_2015.fasPaup*Logfile created while searching for a phylogenetic hypothesis underpinning the analyses.Orchids-ITS-MPrunPaup_Sonkoly-et-al_JEcol_2015.logr8sLogfile created while transforming one of the MP trees to an ultrametric tree in r8s.Orchids-ITS-NPRS-r8s_Sonkoly-et-al_JEcol_2015.logUltrametric treeThe ultrametric tree underpinning the analyses in newick formatOrchids-ITS-UltrametricTree_Sonkoly-et-al_JEcol_2015.nwkReadMe fileReadMe file describing the files, variables and abbreviations
DOI: 10.5061/dryad.c9j53
title: Data from: Genetic differentiation in the boreal dragonfly Leucorrhinia dubia in the Palearctic region

description: The last glacial period had a strong influence on the population genetic
 structure of boreal species in southern and central Europe. In addition,
 recent and current human impact on the boreal environment has led to
 habitat loss, which also has a large influence on population genetic
 structure of species. Here we present the spatial genetic structure of the
 boreal dragonfly Leucorrhinia dubia using ddRAD sequencing. We sampled
 individuals from nine locations in Europe, three in Asia (Russia and
 Japan) and one location of L. intermedia in Japan. Results showed three
 distinct genetic clusters in Europe. One genetic cluster consisted of
 individuals sampled from the locations in the Swiss Alps, a second
 consisted of individuals sampled in the United Kingdom, and a third
 cluster consisted of individuals from the rest of the seven sampled
 locations in Europe covering a latitudinal gradient from the French
 Pyrenees to the north of Finland. There was also a week support that the
 French Pyrenees and Austrian Alps samples differentiated from the cluster
 of the five samples from central and north Europe. We suggest that these
 clusters reflect historical recolonization patterns since the last
 glaciation. The L. dubia individuals sampled from locations in Asia formed
 one cluster referring to L. dubia orientalis separated from the
 individuals sampled in European and from the L. intermedia locality
 sampled. Our result suggests that aquatic insects in the fragmented boreal
 landscape in south central Europe and United Kingdom need conservation
 consideration.
description: SNP data
 LeucorrhiniaThis excel file contain
 four sets of partitioned SNP data for the dragonflies in the study. The
 data in this excel file is formated in genpop format and each tab starting
 with "SNPs…" can be exported to a text file. The last tab
 contain population information for each individual.
DOI: 10.5061/dryad.j82n2
title: Data from: Postoperative changes in fecal bacterial communities and fermentation products in obese patients undergoing bilio-intestinal bypass

description: We assessed the gut microbial ecology of 11 severely obese patients before
 and after bilio-intestinal bypass (BIB). Fecal samples were evaluated for
 microbial communities using 16S rDNA Illumina sequencing, real-time PCR
 targeting functional genes, and gas chromatography of short chain fatty
 acids (SCFAs). At 6 months after surgery, subjects exhibited significant
 improvements in metabolic markers (body weight, glucose, and lipid
 metabolism) compared with baseline. The fecal microbiota of post-surgery
 individuals was characterized by an overall decrease of bacterial
 diversity, with a significant reduction in Lachnospiraceae,
 Clostridiaceae, Ruminococcaceae, Eubacteriaceae, and Coriobacteriaceae. On
 the contrary, there were significant increases of genera Lactobacillus,
 Megasphaera, and Acidaminococcus and the family Enterobacteriaceae. The pH
 was decreased in fecal samples from patients after BIB and SCFA profiles
 were altered, with lower percentages of acetate and propionate and higher
 levels of valerate and hexanoate. Some changes in the bacterial
 populations were associated with variations in the patients’ metabolic
 health parameters, namely Gemmiger and glucose, Lactobacillus and glucose,
 and Faecalibacterium and triglycerides. The results from this study of BIB
 patients furthers our understanding of the composition of gut microbiota
 and the functional changes that may be involved in improving
 obesity-related conditions following weight-loss surgery.
description: OTU_tableAbundances and taxonomic assignment (98% identity threshold) of bacterial OTUs in the fecal samples of obese subjects undergoing bilio-intestinal bypass surgery. The sample ID indicates the status (pre-surgery, before bilio–intestinal bypass; post-surgery, after bilio–intestinal bypass) followed by patient number.OTU_alignmentConsensus sequences representative for each bacterial OTU in the fecal samples of obese subjects undergoing bilio-intestinal bypass surgery.OTU_sequences.fasta
DOI: 10.5061/dryad.mk21p72
title: Data from: Arrival date and microorganisms in barn swallows

description: Migration between breeding sites and winter quarters constitute a major
 life history strategy in birds. The benefits of such migrations must at
 least equal the costs for such behavior to evolve and be maintained. We
 tested whether there was a relationship between abundance and diversity of
 microorganisms on nest lining feathers and timing of arrival by barn
 swallows Hirundo rustica. Nest lining feathers are chosen and transported
 by adult barn swallows to their nests just before and during egg laying,
 at a time when barn swallows have arrived weeks earlier, implying that any
 heterogeneity in abundance and diversity of microorganisms on feathers in
 nests must arise from feather preferences. There was a negative
 relationship between arrival date and the total number of fledglings
 showing that early arrival is advantageous. The arrival date of adult barn
 swallows was significantly positively correlated with the abundance of
 specific bacteria (Bacillus licheniformis) and positively correlated with
 the abundance of the fungus Trichoderma reesei and negatively correlated
 with the abundance of the fungus Mucor circinelloides. Moreover, we found
 a significant positive relationship between arrival date and mean total
 number of bacterial colonies in TSA medium. There was a significant
 negative relationship between arrival date and mean total number of
 bacterial colonies in FMA medium, and Simpson’s diversity index of the
 abundance of bacteria in FMA medium. Such heterogeneity may arise from
 some microorganisms being beneficial, others detrimental and yet others
 benign and of no significant importance. In contrast, there was no
 significant relationship between arrival date and age of individuals.
 These findings are consistent with the hypothesis that early arriving barn
 swallows differ in abundance and diversity of microorganisms from late
 arriving conspecifics, and that they choose feathers for their nests that
 differ in terms of microorganisms from those chosen by late arrival
 individuals.
description: Supplementary Material
 (SM)Data
DOI: 10.5061/dryad.n76v191
title: Data from: Prevalence of sleep-disordered breathing after stroke and TIA: a meta-analysis

description: Objective: To perform a systematic review and meta-analysis on the
 prevalence of sleep-disordered breathing (SDB) after stroke. Methods: We
 searched PubMed, Embase (Ovid), the Cochrane Library, and CINAHL (from
 their commencements to 7th of April 2017) for clinical studies reporting
 prevalence and/or severity of SDB after stroke or transitory ischemic
 attack (TIA). Only sleep apnea tests performed with full polysomnography
 and diagnostic devices of the AASM categories I-IV were included. We
 conducted random-effects meta-analysis. PROSPERO registration number:
 CRD42017072339. Results: The initial search identified 5211 publications.
 89 studies (including 7096 patients) met inclusion criteria. 54 studies
 were performed in the acute phase after stroke (after less than 1 month),
 23 studies in the subacute phase (after 1-3 months) and 12 studies in the
 chronic phase (after more than 3 months). Mean apnea-hypopnea index (AHI)
 was 26.0/h (SD 21.7-31.2). Prevalence of SDB with AHI greater than 5/h and
 greater than 30/h was found in 71% (95% CI 66.6-74.8) and 30% (95% CI
 24.4-35.5) of patients, respectively. Severity and prevalence of SDB were
 similar in all examined phases after stroke, irrespective of the type of
 sleep apnea test performed. Heterogeneity between studies (I2) was mostly
 high. Conclusion: The high prevalence of SDB after stroke and TIA, which
 persists over time, is important in light of recent studies reporting the
 a) feasibility and b) efficacy of SDB treatment in this clinical setting.
description: Appendix
 e-1Search
 strategyAppendix
 e-2Study
 characteristicsAppendix
 e-3Quality
 assessmentAppendix
 e-4Funnel
 plotsAppendix
 e-5Reference list of all
 studies included in the meta-analysis
DOI: 10.5061/dryad.cp6gg
title: Data from: Multilocus phylogeny reveals unexpected diversification patterns in Asian Wolf Snakes (genus Lycodon)

description: The diverse group of Asian Wolf Snakes of the genus Lycodon represents one
 of many poorly understood radiations of advanced snakes in the superfamily
 Colubroidea. Outside of three species having previously been represented
 in higher-level phylogenetic analyses, nothing is known of the
 relationships among species in this unique, moderately diverse, group. The
 genus occurs widely from central to southeast Asia, with a variety of
 range sizes from widespread forms to those that are endmic to small
 islands. One-third of the diversity is found in the Philippine
 archipelago. Both morphological similarity and highly variable diagnostic
 characters have contributed to confusion over species-level diversity.
 Additionally, the placement of the genus among genera in the subfamily
 Colubrinae remains uncertain, although previous studies have supported a
 close relationship with the genus Dinodon. In this study we provide the
 first estimate of phylogenetic relationships within the genus Lycodon
 using a multi-locus dataset. We provide statistical tests of monophyly
 based on biogeographic, morphological, and taxonomic hypotheses. With few
 exceptions, we are able to reject many of these hypotheses, indicating a
 need for taxonomic revisions. Mapping of color patterns on our preferred
 phylogenetic tree suggests that banded and blotched morphotypes have
 evolved on multiple occasions in the history of the genus, whereas the
 solid-color (and possibly speckled) morphotype evolved only once. Our
 results reveal that the colubrid genus Dinodon is nested within Lycodon—a
 clear finding that necessitates the placing of the former genus in
 synonymy with the latter.
description: Lycodon Alignment
 FileThis is the nexus
 alignment file used for phylogenetic analyses. The character set for each
 of the three genes is at the bottom of the file.Lycodon_AllData.nexBayesian ConsensusThis is the consensus topology resulting from Bayesian analyses.Bayesian_Consensus.treBeast resultsThis is the consensus topology resulting from relative time analyses in BeastBeastMCCT.treMaximum Likelihood ResultsThis topology shows results from partitioned ML analyses in RAxMLHPC v7.0ML_Bootstrap.treKey to Identification NumbersThis pdf file contains the list of individuals used in phylogenetic analyses. Museum catalog numbers and field collection numbers are provided for each sample, when available. In a few instances, voucher numbers for sequences downloaded from GenBank were unavailable.KEY_FieldCatNumbers.pdf
DOI: 10.5061/dryad.8dm60
title: Data from: Thermal plasticity in postembryonic life history traits of a widely distributed Collembola: Effects of macroclimate and microhabitat on genotypic differences

description: Life history traits in many ectotherms show complex patterns of variation
 among conspecific populations sampled along wide latitudinal or climatic
 gradients. However, few studies have assessed whether these patterns can
 be explained better by thermal reaction norms of multiple life history
 traits, covering major aspects of the life cycle. In this study, we
 compared five populations of a Holarctic, numerically dominant soil
 microarthropod species, Folsomia quadrioculata, sampled from a wide
 latitudinal gradient (56–81°N), for growth, development, fecundity, and
 survival across four temperatures (10, 15, 20, and 25°C) in common garden
 experiments. We evaluated the extent to which macroclimate could explain
 differences in thermal adaptation and life history strategies among
 populations. The common garden experiments revealed large genotypic
 differences among populations in all the traits, which were little
 explained by latitude and macroclimate. In addition, the life history
 strategies (traits combined) hardly revealed any systematic difference
 related to latitude and macroclimate. The overall performance of the
 northernmost population from the most stochastic microclimate and the
 southernmost population, which remains active throughout the year, was
 least sensitive to the temperature treatments. In contrast, performance of
 the population from the most predictable microclimate peaked within a
 narrow temperature range (around 15°C). Our findings revealed limited
 support for macroclimate-based predictions, and indicated that local soil
 habitat conditions related to predictability and seasonality might have
 considerable influence on the evolution of life history strategies of F.
 quadrioculata. This study highlights the need to combine knowledge on
 microhabitat characteristics, and demography, with findings from common
 garden experiments, for identifying the key drivers of life history
 evolution across large spatial scales, and wide climate gradients. We
 believe that similar approaches may substantially improve the
 understanding of adaptation in many terrestrial ectotherms with low
 dispersal ability.
description: Life history
 traitsData
 file.xlsx
DOI: 10.5061/dryad.b911r
title: Data from: Inferring contemporary dispersal processes in plant metapopulations: comparison of direct and indirect estimates of dispersal for the annual species Crepis sancta

description: Analyzing population dynamics in changing habitats is a prerequisite for
 population dynamics forecasting. The recent development of metapopulation
 modeling allows the estimation of dispersal kernels based on the
 colonization pattern but the accuracy of these estimates compared with
 direct estimates of the seed dispersal kernel has rarely been assessed. In
 this study, we used recent genetic methods based on parentage analysis
 (spatially explicit mating models) to estimate seed and pollen dispersal
 kernels as well as seed and pollen immigration in fragmented urban
 populations of the plant species Crepis sancta with contrasting patch
 dynamics. Using two independent networks, we documented substantial seed
 immigration and a highly restricted dispersal kernel. Moreover,
 immigration heterogeneity among networks was consistent with previously
 reported metapopulation dynamics, showing that colonization was mainly due
 to external colonization in the first network (propagule rain) and local
 colonization in the second network. We concluded that the differences in
 urban patch dynamics are mainly due to seed immigration heterogeneity,
 highlighting the importance of external population source in the
 spatio-temporal dynamics of plants in a fragmented landscape. The results
 show that indirect and direct methods were qualitatively consistent,
 providing a proper interpretation of indirect estimates. This study
 provides attempts to link genetic and demographic methods and show that
 patch occupancy models may provide simple methods for analyzing population
 dynamics in heterogeneous landscapes in the context of global change.
description: individual
 microsatellite markers and spatial coordinates HM 2006Individual genotypes and
 spatial coordinates for all individuals sampled in the patch network HM in
 2006.popHM2006.xlsindividual microsatellite markers and spatial coordinates HM 2007Individual genotypes and spatial coordinates for all individuals sampled in the patch network HM in 2007.popHM2007.xlsindividual microsatellite markers and spatial coordinates JC2006Individual genotypes and spatial coordinates for all individuals sampled in the patch network JC in 2006.popJC2006.xlsindividual microsatellite markers and spatial coordinates JC2007Individual genotypes and spatial coordinates for all individuals sampled in the patch network JC in 2007.popJC2007.xls
DOI: 10.5061/dryad.8qf25s3
title: Data from: Attracting Common Carp to a bait site with food reveals strong positive relationships between fish density, feeding activity, environmental DNA, and sex pheromone release that could be used in invasive fish management

description: Measurement of environmental DNA (eDNA) is becoming a common technique to
 survey for rare and invasive fish due to its sensitivity and specificity.
 However, its utility is limited by an incomplete understanding of factors
 governing its sources and fates. Failure to detect eDNA is especially
 difficult to interpret so surveillance techniques often collect large
 numbers of samples across broad regions. If, however, fish could be
 reliably attracted to a single location where their eDNA could be easily
 measured that would be useful. We conducted a proof‐of‐concept study of
 this idea using invasive Common Carp. We monitored the distribution of
 radio‐tagged Carp and their eDNA across a 67 ha lake focusing at the bait
 site while a pheromone (Prostaglandin F2α; PGF2α) was also measured to
 determine their reproductive condition. Prior to baiting, Carp were
 patchily distributed and while eDNA was occasionally detectable, it was
 patchy and only loosely associated with moderately dense groups of fish.
 Further, neither Carp, nor their eDNA were consistently measurable at the
 bait site and surrounding region, and the pheromone was not measurable at
 all. However, once baiting commenced, Carp started visiting the bait site
 and feeding, especially at night, where eDNA levels increased 500‐fold as
 fish densities doubled and PGF2α became detectable. Fish presence, eDNA
 and pheromone concentrations peaked at night after 6 days, strongly
 suggesting feeding activity was the main driver. While the presence of
 eDNA precisely coincided with this aggregation, levels had dropped
 dramatically within 5 m. PGF2α levels dropped less rapidly and
 demonstrated the presence of live mature fish. We suggest that food could
 be used to train fish to come to locations where they otherwise are too
 scarce to be reliably measured, increasing their eDNA release, making them
 measurable, and their reproductive condition also discernable by measuring
 pheromones.
description: eDNA
 DataeDNA readouts for water
 samplesFor
 DRYAD eDNA Data.xlsFor Dryad_pheromone
 dataProstaglandin F2alpha
 readouts for water samplesFor Dryad_radio tracking
 bait dayFor Dryad_radio tracking
 bait nightFor Dryad_radio tracking
 control dayFor Dryad_radio tracking
 control nightFor Dryad_stationary
 receiver raw data