cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rm857
title: Data from: Weekend admission as an independent predictor of mortality: an analysis of Scottish hospital admissions

description: OBJECTIVES: Weekend admissions have been shown to be associated with an
 increased risk of mortality compared with weekday admissions for many
 diagnoses. We analysed emergency department admissions within the Scottish
 National Health Service to investigate whether mortality is increased in
 case of weekend emergency department admissions. DESIGN: A cohort study.
 SETTING: Scotland National Health Service (NHS) emergency departments.
 PARTICIPANTS: 5 271 327 emergency department admissions between 1999 and
 2009. We included all patients admitted via emergency departments recorded
 in the Scottish Morbidity Records (SMR01) in NHS, Scotland for whom
 complete demographic data were available. PRIMARY OUTCOME MEASURES: Death
 as recorded by the General Register Office (GRO). RESULTS: There was a
 significantly increased probability of death associated with a weekend
 emergency admission compared with admission on a weekday (unadjusted OR
 1.27, 95% CI 1.26 to 1.28, p&lt;0.0001; adjusted for year of
 admission, gender, age, deprivation quintile and number of comorbidities
 OR 1.42, 95% CI 1.40 to 1.43, p&lt;0.0001). CONCLUSIONS: Despite a
 general reduction in mortality over the last 11 years, there is still a
 significant excess mortality associated with weekend emergency admissions.
 Further research should be undertaken to identify the precise mechanisms
 underlying this effect so that measures can be put in place to reduce
 patient mortality.
description: Scottish weekend
 admissions for DryadSee notes tab for
 description of data and source.
DOI: 10.5061/dryad.nd853
title: Data from: Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species

description: Unlike most anadromous fishes that have evolved strict homing behaviour,
 Pacific lamprey (Entosphenus tridentatus) seem to lack philopatry as
 evidenced by minimal population structure across the species range. Yet
 unexplained findings of within-region population genetic heterogeneity
 coupled with the morphological and behavioural diversity described for the
 species suggest that adaptive genetic variation underlying fitness traits
 may be responsible. We employed restriction site–associated DNA sequencing
 to genotype 4439 quality filtered single nucleotide polymorphism (SNP)
 loci for 518 individuals collected across a broad geographical area
 including British Columbia, Washington, Oregon and California. A subset of
 putatively neutral markers (N = 4068) identified a significant amount of
 variation among three broad populations: northern British Columbia,
 Columbia River/southern coast and ‘dwarf’ adults (FCT = 0.02, P ≪ 0.001).
 Additionally, 162 SNPs were identified as adaptive through outlier tests,
 and inclusion of these markers revealed a signal of adaptive variation
 related to geography and life history. The majority of the 162 adaptive
 SNPs were not independent and formed four groups of linked loci. Analyses
 with matsam software found that 42 of these outlier SNPs were
 significantly associated with geography, run timing and dwarf life
 history, and 27 of these 42 SNPs aligned with known genes or highly
 conserved genomic regions using the genome browser available for sea
 lamprey. This study provides both neutral and adaptive context for
 observed genetic divergence among collections and thus reconciles previous
 findings of population genetic heterogeneity within a species that
 displays extensive gene flow.
description: Quality filtered
 genotypes of Pacific lamprey in GENEPOP formatGENEPOP file: 518
 Pacific lamprey individuals from 21 collections, genotyped with a set of
 4,439 quality filtered SNPs from a larger dataset of 8,772 unique SNP loci
 identified using methods described by Hess et al. 2013. "POP"
 headings delineate collections of individuals and include collections
 names listed in Table 1, Hess et al. 2013.Lamprey_4439Loci518IndGP_DRYAD.txt
DOI: 10.5061/dryad.7d2g2
title: Data from: Relaxed phylogenetics and the Palaeoptera problem: resolving deep ancestral splits in the insect phylogeny

description: The order in which the three groups of winged insects diverged from their
 common ancestor has important implications for understanding the origin of
 insect flight. But despite this importance, the split between the Odonata
 (dragonflies and damselflies), Ephemeroptera (mayflies) and Neoptera (the
 other winged orders) remains very much unresolved. Indeed, previous
 studies have obtained strong apparent support for each of the three
 possible branching patterns. Here, we present a systematic reinvestigation
 of the basal pterygote split. Our results suggest that outgroup choice and
 limited taxon sampling have been major sources of systematic error, even
 for datasets with a large number of characters (e.g., in phylogenomic
 datasets). In particular, a dataset of 113 taxa provides consistent
 support for the Palaeoptera hypothesis (the grouping of Odonata with
 Ephemeroptera), while results from datasets with fewer taxa give
 inconsistent results, and are highly sensitive to minor changes in data
 and methods. We also focus on recent methods that exploit temporal
 information, combined with additional assumptions about the evolutionary
 process, and so reduce the influence of outgroup choice. These methods are
 shown to provide more consistent results, for example, supporting
 Palaeoptera, even for datasets that previously supported other hypotheses.
 Together, these results have implications for understanding insect origins
 and for resolving other problematic splits in the tree of life.
description: Dataset1Nexus file for Dataset 1, 113-taxon datasetDataset2Nexus file for Dataset 2, 38-taxon dataset.Supplementary Table 1Supplementary Table 1Thomas_et_al_10-10-12.SuppTable1.pdfSupplementary Table 2Supplementary Table 2Thomas_et_al_10-10-12.SuppTable2.pdfSupplementary Table 3Supplementary Table 3Thomas_et_al_10-10-12.SuppTable3.pdfSupplementary Table 4Supplementary Table 4Thomas_et_al_10-10-12.SuppTable4.pdfSupplementary Table 5Supplementary Table 5Thomas_et_al_10-10-12.SuppTable5.pdfSupplementary Table 6Supplementary Table 6Thomas_et_al_10-10-12.SuppTable6.pdf
DOI: 10.5061/dryad.k37m7
title: Data from: ITS1 versus ITS2 as DNA metabarcodes for fungi

description: The nuclear ribosomal Internal Transcribed Spacer ITS region is widely
 used as a DNA metabarcoding marker to characterize the diversity and
 composition of fungal communities. In amplicon pyrosequencing studies of
 fungal diversity, one of the spacers ITS1 or ITS2 of the ITS region is
 normally used. In this methodological study we evaluate the usability of
 ITS1 vs. ITS2 as a DNA metabarcoding marker for fungi. We analyse three
 data sets: two comprising ITS1 and ITS2 sequences of known taxonomic
 affiliations and a third comprising ITS1 and ITS2 environmental amplicon
 pyrosequencing data. Clustering analyses of sequences with known taxonomy
 using the bioinformatics pipeline ClustEx revealed that a 97% similarity
 cut-off represent a reasonable threshold for estimating the number of
 known species in the data sets for both ITS1 and ITS2. However, no single
 threshold value worked well for all fungi at the same time within the
 curated UNITE database, and we found that the Operational Taxonomic Unit
 (OTU) concept is not easily translated into the level of species because
 many species are distributed over several clusters. Clustering analyses of
 the 134 692 ITS1 and ITS2 pyrosequences using a 97% similarity cut-off
 revealed a high similarity between the two data sets when it comes to
 taxonomic coverage. Although some groups are under- or unrepresented in
 the two data sets due to, e.g. primer mismatches, our results indicate
 that ITS1 and ITS2 to a large extent yield similar results when used as
 DNA metabarcodes for fungi.
description: ITS1_UNITEIts1 sequences of UNITE accessioned fungi.ITS2_UNITEITS2 sequences of UNITE accessioned fungiITS1_ascoITS1 sequences of ascomycetous fungi in INSD databases.ITS1_basiITS1 sequences of basidiomycetous fungi from INSD databases.ITS2_ascoITS2 sequences of ascomycetous fungi from INSD databasesITS2_basiITS2 sequences of basidiomycetous fungi from INSD databases
DOI: 10.5061/dryad.53f4b
title: Data from: Not just passengers: Pigeons, Columba livia, can learn homing routes while flying with a more experienced conspecific

description: For animals that travel in groups, the directional choices of conspecifics
 are potentially a rich source of information for spatial learning. In this
 study, we investigate how the opportunity to follow a locally experienced
 demonstrator affects route learning by pigeons over repeated homing
 flights. This test of social influences on navigation takes advantage of
 the individually distinctive routes that pigeons establish when trained
 alone. We found that pigeons learn routes just as effectively while flying
 with a partner as control pigeons do while flying alone. However, rather
 than learning the exact route of the demonstrator, the paired routes
 shifted over repeated flights, which suggests that the birds with less
 local experience also took an active role in the navigational task. The
 efficiency of the original routes was a key factor in how far they
 shifted, with less efficient routes undergoing the greatest changes. In
 this context, inefficient routes are unlikely to be maintained through
 repeated rounds of social transmission, and instead more efficient routes
 are achieved because of the interaction between social learning and
 information pooling.
description: GPS_tracksCompressed folder (.zip) containing GPS tracks of homing pigeons, in csv format.
DOI: 10.5061/dryad.bn43b
title: Data from: Parallel and nonparallel ecological, morphological and genetic divergence in lake-stream stickleback from a single catchment

description: Parallel phenotypic evolution in similar environments has been well
 studied in evolutionary biology, however comparatively little is known
 about influence of determinism and historical contingency on the nature,
 extent and generality of this divergence. Taking advantage of a novel
 system containing multiple lake-stream stickleback populations, we
 examined the extent of ecological, morphological and genetic divergence
 between three-spined stickleback present in parapatric environments.
 Consistent with other lake-stream studies we found a shift towards a
 deeper body and shorter gill rakers in stream fish. Morphological shifts
 were concurrent with changes in diet, indicated by both stable isotope and
 stomach contents analysis. Performing a multivariate test for shared and
 unique components of evolutionary response to the distance gradient from
 the lake, we found a strong signature of parallel adaptation. Non-parallel
 divergence was also present, attributable mainly to differences between
 river locations. We additionally found evidence of genetic sub-structuring
 across five lake-stream transitions, indicating that some level of
 reproductive isolation occurs between populations in these habitats.
 Strong correlations between pairwise measures of morphological, ecological
 and genetic distance between lake and stream populations supports the
 hypothesis that divergent natural selection between habitats drives
 adaptive divergence and reproductive isolation. Lake-stream stickleback
 divergence in Lough Neagh provides evidence for the deterministic role of
 selection and supports the hypothesis that parallel selection in similar
 environments may initiate parallel speciation.
description: Stable isotope and
 stomach contents from Lough Neagh sticklebacksStable isotopes values
 for sticklebacks and macroinvetebrates from the Lough Neagh catchment,
 Northern Ireland. Additionally includes stomach contents
 data.ecological.xlsxMorphological data for Lough Neagh sticklebacksShape and measured trait data from sticklebacks collected across the Lough Neagh catchment.morphological.xlsxMicrosatellite data for Lough Neagh sticklebacksMicrosatellite data for nine loci in sticklebacks from the Lough Neagh catchment in Northern Ireland, UK.microsatellites.xlsx
DOI: 10.5061/dryad.f81sf
title: Data from: Stretched to the limit; can a short pelagic larval duration connect adult populations of an Indo-Pacific diadromous fish (Kuhlia rupestris)?

description: Freshwater species on tropical islands face localized extinction and the
 loss of genetic diversity. Their habitats can be ephemeral due to
 variability in freshwater run-off and erosion. Even worse, anthropogenic
 effects on these ecosystems are intense. Most of these species are
 amphidromous or catadromous (i.e. their life cycle includes a marine
 larval phase), which buffers them against many of these effects. A long
 pelagic larval duration (PLD) was thought to be critical to ensure the
 colonization and persistence in tropical islands, but recent findings
 indicated that several species with short PLDs are successful in those
 ecosystems. To test the potential of a short PLD in maintaining genetic
 connectivity and forestalling extirpation, we studied Kuhlia rupestris, a
 catadromous fish species with an extensive distribution in the western
 Pacific and Indian Oceans. Using a combination of molecular genetic
 markers (13 microsatellite loci and two gene regions from mtDNA) and
 modelling of larval dispersal, we show that a short PLD constrains genetic
 connectivity over a wide geographical range. Molecular markers showed that
 the short PLD did not prevent genetic divergence through evolutionary time
 and speciation has occurred or is occurring. Modelling of larvae dispersal
 suggested limited recent connectivity between genetically homogeneous
 populations across the Coral Sea. However, a short PLD can maintain
 connectivity on a subocean basin scale. Conservation and management of
 tropical diadromous species needs to take into account that population
 connectivity may be more limited than previously suspected in those
 species.
description: Microsatellite_GenotypesSequence_Alignment_ATPSequence_Alignment_ND4Sampling_location_dateLarval_dispersal_modeling_raw results
DOI: 10.5061/dryad.215jd
title: Data from: Progressive genome-wide introgression in agricultural Campylobacter coli

description: Hybridization between distantly related organisms can facilitate rapid
 adaptation to novel environments, but is potentially constrained by
 epistatic fitness interactions among cell components. The zoonotic
 pathogens Campylobacter coli and C. jejuni differ from each other by
 around 15% at the nucleotide level, corresponding to an average of nearly
 40 amino acids per protein-coding gene. Using whole genome sequencing, we
 show that a single C. coli lineage, which has successfully colonized an
 agricultural niche, has been progressively accumulating C. jejuni DNA.
 Members of this lineage belong to two groups, the ST-828 and ST-1150
 clonal complexes. The ST-1150 complex is less frequently isolated and has
 undergone a substantially greater amount of introgression leading to
 replacement of up to 23% of the C. coli core genome as well as import of
 novel DNA. By contrast, the more commonly isolated ST-828 complex bacteria
 have 10–11% introgressed DNA, and C. jejuni and nonagricultural C. coli
 lineages each have &lt;2%. Thus, the C. coli that colonize
 agriculture, and consequently cause most human disease, have hybrid
 origin, but this cross-species exchange has so far not had a substantial
 impact on the gene pools of either C. jejuni or nonagricultural C. coli.
 These findings also indicate remarkable interchangeability of basic
 cellular machinery after a prolonged period of independent evolution.
description: BIGS_sequencesWhole genome sequencing reads for BIGSdb isolates 1-30 (isolates 26,27,28,29 are already published with accession numbers: NC_009839; NC_008787; NC_003912; NC_002163). For isolates 1-3 de novo 454 sequencing was assembled using Newbler (April 2009). For isolates 4-25 and 30 de novo illumnia sequencing was assembled using Velvet 1.0.
DOI: 10.5061/dryad.5g4r0
title: Data from: The role of selection in driving landscape genomic structure of the waterflea Daphnia magna

description: The combined analysis of neutral and adaptive genetic variation is crucial
 to reconstruct the processes driving population genetic structure of
 natural populations. However, such combined analysis is challenging
 because of the complex interaction among neutral and selective processes
 in the landscape. Overcoming this level of complexity requires an unbiased
 search for the evidence of selection in the genomes of populations sampled
 from their natural habitats and the identification of demographic
 processes that lead to present-day populations genetic structure.
 Ecological model species with a suite of genomic tools and well-understood
 ecologies are best suited to resolve this complexity and elucidate the
 role of selective and demographic processes in the landscape genomic
 structure of natural populations. Here we investigate the water flea
 Daphnia magna, an emerging model system in genomics and a renowned
 ecological model system. We infer past and recent demographic processes by
 contrasting patterns of local and regional neutral genetic diversity at
 markers with different mutation rates. We assess the role of the
 environment in driving genetic variation in our study system by
 identifying correlates between biotic and abiotic variables naturally
 occurring in the landscape and patterns of neutral and adaptive genetic
 variation. Our results indicate that selection plays a major role in
 determining the population genomic structure of D. magna. First,
 environmental selection directly impacts genetic variation at loci
 hitchhiking with genes under selection. Secondly, priority effects
 enhanced by local genetic adaptation (cf. monopolization) affect neutral
 genetic variation by reducing gene flow among populations and genetic
 diversity within populations.
description: Orsinietal_micros_genotypingMicrosatellite genotyping results. Nineteen populations distributed at regional scale in Belgium were used for this analysis. Individual ID and sample location are shownOrsinietal_SNP_genotypingSNP genotyping results. Nineteen populations distributed at regional scale in Belgium were used for this analysis. Individual ID and sample location are shownOrsinietal_mtDNA_alignmentfasta file showing the alignment of the partial sequence of the COI mtDNA gene. Individual ID and correspondent NCBI accession number are shown
DOI: 10.5061/dryad.m1063
title: Data from: Transcriptomics and in vivo tests reveal novel mechanisms underlying endocrine disruption in an ecological sentinel, Nucella lapillus

description: Anthropogenic endocrine disruptors now contaminate all environments
 globally, with concomitant deleterious effects across diverse taxa. While
 most studies on endocrine disruption (ED) have focused on vertebrates, the
 superimposition of male sexual characteristics in the female dogwhelk,
 Nucella lapillus (imposex), caused by organotins, provides one of the most
 clearcut ecological examples of anthropogenically induced ED in aquatic
 ecosystems. To identify the underpinning mechanisms of imposex for this
 ‘nonmodel’ species, we combined Roche 454 pyrosequencing with custom
 oligoarray fabrication inexpensively to both generate gene models and
 identify those responding to chronic tributyltin (TBT) treatment. The
 results supported the involvement of steroid, neuroendocrine peptide
 hormone dysfunction and retinoid mechanisms, but suggested additionally
 the involvement of putative peroxisome proliferator–activated receptor
 (PPAR) pathways. Application of rosiglitazone, a well-known vertebrate
 PPARγ ligand, to dogwhelks induced imposex in the absence of TBT. Thus,
 while TBT-induced imposex is linked to the induction of many genes and has
 a complex phenotype, it is likely also to be driven by PPAR-responsive
 pathways, hitherto not described in invertebrates. Our findings provide
 further evidence for a common signalling pathway between invertebrate and
 vertebrate species that has previously been overlooked in the study of
 endocrine disruption.
description: Nucella_CoAssemblyCo-assembly data: list of contigs and singletonsSRA021021Control and TBT-exposed libraries: sequencing results
DOI: 10.5061/dryad.4pd30
title: Data from: Joint allelic effects on fitness and metric traits

description: Theoretical explanations of empirically observed standing genetic
 variation, mutation, and selection suggest that many alleles must jointly
 affect fitness and metric traits. However, there are few direct
 demonstrations of the nature and extent of these pleiotropic associations.
 We implemented a mutation accumulation (MA) divergence experimental design
 in Drosophila serrata to segregate genetic variants for fitness and metric
 traits. By exploiting naturally occurring MA line extinctions as a measure
 of line-level total fitness, manipulating sexual selection, and measuring
 productivity we were able to demonstrate genetic covariance between
 fitness and standard metric traits, wing size and shape. Larger size was
 associated with lower total fitness and male sexual fitness, but higher
 productivity. Multivariate wing shape traits, capturing major axes of wing
 shape variation among MA lines, evolved only in the absence of sexual
 selection, and to the greatest extent in lines that went extinct,
 indicating that mutations contributing wing shape variation also typically
 had deleterious effects on both total fitness and male sexual fitness.
 This pleiotropic covariance of metric traits with fitness will drive their
 evolution, and generate the appearance of selection on the metric traits
 even in the absence of a direct contribution to fitness.
description: MA_wingsData file of wing shape and size traits from two sexual selection treatments collected in three generations of a mutation accumulation experimentForster_wingsWing shape and size data from a half-sib breeding design conducted in a population of Drosophila serrata sharing a common ancestor with the mutation accumulation linesProductivityLine mean productivity data from MA lines extant in generation 27Viab_Prod.txt