cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2s07s
title: Data from: Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity

description: Individuals harbor diverse communities of symbiotic bacteria, which differ
 dramatically among host individuals. This heterogeneity poses an
 immunological challenge of distinguishing between mutualistic and
 pathogenic members of diverse and host-specific microbial communities. We
 propose that Major Histocompatibility class II (MHC) genotypes contribute
 to recognition and regulation of gut microbes, and thus MHC polymorphism
 contributes to microbial variation among hosts. Here, we confirm that,
 within a single wild vertebrate population of threespine stickleback,
 different MHC II amino acid sequence motifs are associated with
 among-individual variation in gut microbiota. The presence of certain MHC
 motifs is associated with altered relative abundance (increase or
 decrease) of some microbial Families. Furthermore, hosts with more diverse
 MHC motifs had less diverse gut microbiota. Our results show that MHC
 affects host regulation of gut microbiota in natural populations,
 consistent with limited experimental evidence that MHC controls gut
 microbes in laboratory mice. One implication is that MHC might influence
 the efficacy of therapeutic strategies to treat dysbiosis-associated
 disease. For example, we hypothesize that microbial transplants to treat
 dysbiosis might be constrained by MHC match between donor and recipient.
 Another implication is that macroparasite-driven selection on MHC has the
 potential to indirectly alter the host gut microbiota, and vice versa. Our
 findings therefore open up a variety of avenues for further investigation
 into MHC-microbiota interactions.
description: Bolnick MolecEcol Dryad
 SubmissionA zip file containing 14
 .csv or .txt data files including fish metadata (morphology, sex, diet),
 gut microbiota composition, and MHC genotype.
DOI: 10.5061/dryad.31j20
title: Data from: Drosophila wing modularity revisited through a quantitative genetic approach

description: To predict the response of complex morphological structures to selection
 it is necessary to know how the covariation among its different parts is
 organized. Two key features of covariation are modularity and integration.
 The Drosophila wing is currently considered a fully integrated structure.
 Here, we study the patterns of integration of the Drosophila wing and test
 the hypothesis of the wing being divided into two modules along the
 proximo-distal axis, as suggested by developmental, biomechanical, and
 evolutionary evidence. To achieve these goals we perform a multilevel
 analysis of covariation combining the techniques of geometric
 morphometrics and quantitative genetics. Our results indicate that the
 Drosophila wing is indeed organized into two main modules, the wing base
 and the wing blade. The patterns of integration and modularity were highly
 concordant at the phenotypic, genetic, environmental, and developmental
 levels. Besides, we found that modularity at the developmental level was
 considerably higher than modularity at other levels, suggesting that in
 the Drosophila wing direct developmental interactions are major
 contributors to total phenotypic shape variation. We propose that the
 precise time at which covariance-generating developmental processes occur
 and/or the magnitude of variation that they produce favor proximo-distal,
 rather than anterior-posterior, modularity in the Drosophila wing.
description: CovMatrix Symmetric
 componentCovariance matrix for
 the symmetric component of shape obtained by conducting the Procrustes
 ANOVA procedure implemented in MorphoJCovMatrix Asymmetry
 componentCovariance matrix for
 the asymmetric component of shape obtained by conducting the Procrustes
 ANOVA procedure implemented in MorphoJPC scores Symmetric
 componentPC scores obtained from
 the PC analysis carried out for the symmetric component of
 shape.PC scores Asymmetry
 componentPC scores obtained from
 the PC analysis carried out for the asymmetric component of
 shape.CSValues of the symmetric
 centroid size and the logarithm of the symmetric centroid
 size.
DOI: 10.5061/dryad.3127rs3
title: Data from: Species and genetic diversity are not congruent in fragmented dry grasslands

description: Biological diversity comprises both species diversity (SD) and genetic
 diversity (GD) and it has been postulated that both levels of diversity
 depend on similar mechanisms. Species-genetic diversity correlations
 (SGDC) are, therefore, supposed to be generally positive. However, in
 contrast to theory, empirical data are contradictory. Furthermore, there
 is a pronounced lack of multispecies studies including also the ecological
 factors potentially driving species and genetic diversity. We analysed the
 relationship between the species diversity of dry grasslands and the
 genetic diversity of several dry grassland plant species, therefore, in
 the context of habitat fragmentation and habitat conditions. Our study
 revealed a lack of correlation between species and genetic diversity. We
 demonstrated previously that SD mainly depends on habitat conditions
 (vegetation height and cover of litter), whereas GD is significantly
 affected by habitat fragmentation (distance to the nearest dry grassland
 in 1830 and connectivity in 2013). This seems to be the main reason why SD
 and GD are not congruent in fragmented grasslands. Our results support,
 hence, the observation that positive SGDCs can mainly be found in natural,
 island like study systems in equilibrium and at similar levels of
 heterogeneity. In fragmented dry grassland ecosystems, which differ in
 heterogeneity, this state of equilibrium may not have been reached
 mitigating the positive relationship between SD and GD. From our study it
 can be concluded that in fragmented dry grasslands the protection of SD
 does not necessarily ensure the conservation of GD.
description: Aflp_dataThe data set contains the 01-matrices from AFLP analysis for the five analysed dry grassland plant species.Vegetation surveys all speciesThe data set contains all plant species, which occurred in the plots from the vegetation survey.Vegetation surveys grassland specialistsThe data set contains all grassland specialists which occurred in the plots from the vegetation survey.
DOI: 10.5061/dryad.053m3
title: Data from: Assessing species boundaries and the phylogenetic position of the rare Szechwan Ratsnake, Euprepiophis perlacea (Serpentes: Colubridae), using coalescent-based methods

description: Delimiting species and clarifying phylogenetic relationships are the main
 goals of systematics. For species with questionable taxonomic status,
 species delimitation approaches using multi-species coalescent models with
 multiple loci are recommended if morphological data are unavailable or
 unhelpful. Moreover, these methods will also reduce subjectivity based on
 genetic distance or requirement of monophyletic genetic lineages. We
 determine the validity and phylogenetic position of a rare and long
 controversial species of Chinese reptile, the Szechwan ratsnake
 (Euprepiophis perlacea), using multi-locus data from multiple individuals
 and coalescent-based approaches. Species were first delimited using
 Bayesian Phylogenetics & Phylogeography (BP&P), Brownie
 and Bayes Factor model comparison approaches, while relationships among
 species were estimated using species tree inference in *BEAST. Results
 indicate that Euprepiophis perlacea is a distinct species sister to
 Euprepiophis mandarinus. Despite gene tree discrepancy, the coalescent
 model-based approaches used here demonstrate the taxonomic validity and
 the phylogenetic position of Euprepiophis perlacea. These approaches
 objectively test the validity of questionable species diagnoses based on
 morphological characters and determine their phylogenetic position.
description: Perlaceaspeciestreexml for inferring specie tree in *BEAST using one mitochondria gene and three nuclear genesperlspeciestree_nuclearonlyxml for inferring specie tree in *BEAST using three nuclear genesmodel1_1xml file for running species tree in *BEAST based on model 1 (assuming Euprepiophis perlacea and Euprepiophis manderinus are two independent species)model2_1xml file for running species tree in *BEAST based on model 2 (assuming Euprepiophis perlacea and Euprepiophis manderinus are one species)m1_1pathSamplingxml file for calculating marginal likelihood of model 1 (Euprepiophis perlacea and Eupreophis manderinus are two species) using path-sampling estimatorm1_1stepstonexml file for calculating marginal likelihood of model 1 (Euprepiophis perlacea and Eupreophis manderinus are two species) using stepstone estimatorm2_1pathSamplingxml file for calculating marginal likelihood of model 2 (Euprepiophis perlacea and Eupreophis manderinus are one species) using path-sampling estimatorm2_1stepstonexml file for calculating marginal likelihood of model 2 (Euprepiophis perlacea and Eupreophis manderinus are one species) using stepstone estimator
DOI: 10.5061/dryad.0s87v
title: Data from: Lineage divergence, local adaptation across a biogeographic break, and artificial transport, shape the genetic structure in the ascidian Pyura chilensis

description: Marine benthic organisms inhabit a heterogeneous environment in which
 connectivity between populations occurs mainly through dispersive larval
 stages, while local selective pressures acting on early life history
 stages lead to non-random mortality, shaping adaptive genetic structure.
 In order to test the influence of local adaptation and neutral processes
 in a marine benthic species with low dispersal, in this study we used
 Genotyping by Sequencing technology to compare the neutral and putatively
 selected signals (neutral and outlier loci, respectively) in SNPs
 scattered throughout the genome in six local populations of the
 commercially exploited ascidian Pyura chilensis along the southeast
 Pacific coast (24°–42°S). This species is sessile as an adult, has a
 short-lived larval stage, and may also be dispersed by artificial
 transport as biofouling. We found that the main signal in neutral loci was
 a highly divergent lineage present at 39°S, and a subjacent signal that
 indicated a separation at 30°S (north/south), widely reported in the area.
 North/south separation was the main signal in outlier loci, and the linage
 divergence at 39°S was subjacent. We conclude that the geographic
 structure of the genetic diversity of outlier and neutral loci was
 established by different strengths of environmental, historical and
 anthropogenic factors.
description: 2332SNPsY14PCVCF file containing genotypes for 2332 SNPs scattered throughout the genome detected using Genotyping by Sequencing in the ascidia Pyura chilensis. This is the original data which is the base for all performed analyses.
DOI: 10.5061/dryad.81tr1
title: Data from: Perioperative medication management: expanding the role of the preadmission clinic pharmacist in a single centre, randomised controlled trial of collaborative prescribing

description: Objectives: Current evidence to support non-medical prescribing is
 predominantly qualitative, with little evaluation of accuracy, safety and
 appropriateness. Our aim was to evaluate a new model of service for the
 Australia healthcare system, of inpatient medication prescribing by a
 pharmacist in an elective surgery pre admission clinic (PAC) against usual
 care, using an endorsed performance framework. Design: Single centre,
 randomised controlled, two arm trial Setting: Elective surgery pre
 admission clinic in Brisbane based tertiary hospital Participants: Four
 hundred adults scheduled for elective surgery were randomised to
 intervention or control. Intervention: A pharmacist generated the
 inpatient medication chart to reflect the patient’s regular medication,
 made a plan for medication perioperatively and prescribed VTE prophylaxis.
 In the control arm, the medication chart was generated by the Resident
 Medical Officers (RMO). Outcome Measures: Primary outcome was frequency of
 omissions and prescribing errors when compared against the medication
 history. The clinical significance of omissions was also analysed.
 Secondary outcome was appropriateness of VTE prophylaxis prescribing.
 Results: There were significantly less unintended omissions of
 medications: 11 of 887 (1.2%) intervention orders compared with 383 of
 1217 (31.5%) control (p&lt;0.001). There were significantly less
 prescribing errors involving selection of drug, dose or frequency: 2 in
 857 (0.2%) intervention orders compared with 51 in 807 (6.3%) control
 (p&lt;0.001). Orders with at least one component of the prescription
 missing, incorrect or unclear occurred in 20826 of 904 (235%) intervention
 orders and 445667 of 1034 (4364.5%) control (p&lt;0.001). VTE
 prophylaxis on admission to the ward was appropriate in 93% of
 intervention patients and 90% control (p=0.29). Conclusion: Medication
 charts in the intervention arm contained fewer clinically significant
 omissions, and prescribing errors, when compared to control. There was no
 difference in appropriateness of VTE prophylaxis on admission between the
 two groups. Trial Registration: Registered with ANZCTR – ACTR Number
 ACTRN12609000426280
description: PAC
 datasetData collected in pre
 admission clinic, analysed using SPSS and access databases, amalgamated in
 to Excel spreadsheet
DOI: 10.5061/dryad.n1k111m
title: Data from: Flightless birds are not neuroanatomical analogs of non-avian dinosaurs

description: Background: In comparative neurobiology, major transitions in behavior are
 thought to be associated with proportional size changes in brain regions.
 Bird-line theropod dinosaurs underwent a drastic locomotory shift from
 terrestrial to volant forms, accompanied by a suite of well-documented
 postcranial adaptations. To elucidate the potential impact of this
 locomotor shift on neuroanatomy, we first tested for a correlation between
 loss of flight in extant birds and whether the brain morphology of these
 birds resembles that of their flightless, non-avian dinosaurian ancestors.
 We constructed virtual endocasts of the braincase for 80 individuals of
 non-avian and avian theropods, including 25 flying and 19 flightless
 species of crown group birds. The endocasts were analyzed using a
 three-dimensional (3-D) geometric morphometric approach to assess changes
 in brain shape along the dinosaur-bird transition and secondary losses of
 flight in crown-group birds (Aves). Results: While non-avian dinosaurs and
 crown-group birds are clearly distinct in endocranial shape, volant and
 flightless birds overlap considerably in brain morphology.
 Phylogenetically informed analyses show that locomotory mode does not
 significantly account for neuroanatomical variation in crown-group birds.
 Linear discriminant analysis (LDA) also indicates poor predictive power of
 neuroanatomical shape for inferring locomotory mode. Given current
 sampling, Archaeopteryx, the oldest known bird, is inferred to be
 terrestrial based on its endocranial morphology. Conclusion: The results
 demonstrate that loss of flight does not correlate with appreciable amount
 of neuroanatomical changes across Aves, but rather is partially
 constrained due to phylogenetic inertia, evident from sister taxa having
 similarly shaped endocasts. Although the present study does not explicitly
 test whether endocranial changes along the dinosaur-bird transition are
 due to acquisition of powered flight, the prominent relative expansion of
 the cerebrum, in areas associated with flight-related cognitive capacity,
 suggests that the acquisition of flight may have been an important initial
 driver of brain shape evolution in theropods.
description: Coelurosaur
 TreeThe tree file for the
 Coelurosaur dataset, including branch lengths. This file can be trimmed to
 only include the Aves dataset.Coelurosaur
 LandmarksComplete set of
 unaligned landmarks for the Coelurosaur dataset in NTS
 format.Avian
 LandmarksComplete set of
 unaligned landmarks for the Aves dataset in NTS format.
DOI: 10.5061/dryad.540k5
title: Data from: Independent axes of genetic variation and parallel evolutionary divergence of opercle bone shape in threespine stickleback

description: Evolution of similar phenotypes in independent populations is often taken
 as evidence of adaptation to the same fitness optimum. However, the
 genetic architecture of traits might cause evolution to proceed more often
 toward particular phenotypes, and less often toward others, independently
 of the adaptive value of the traits. Freshwater populations of Alaskan
 threespine stickleback have repeatedly evolved the same distinctive
 opercle shape after divergence from an oceanic ancestor. Here we
 demonstrate that this pattern of parallel evolution is widespread,
 distinguishing oceanic and freshwater populations across the Pacific Coast
 of North America and Iceland. We test whether this parallel evolution
 reflects genetic bias by estimating the additive genetic
 variance-covariance matrix (G) of opercle shape in an Alaskan oceanic
 (putative ancestral) population. We find significant additive genetic
 variance for opercle shape and that G has the potential to be biasing,
 because of the existence of regions of phenotypic space with low additive
 genetic variation. However, evolution did not occur along major
 eigenvectors of G, rather occurred repeatedly in the same directions of
 high evolvability. We conclude that the parallel opercle evolution is most
 likely due to selection during adaptation to freshwater habitats, rather
 than due to biasing effects of opercle genetic architecture.
description: Kimmel et al
 ARCHIVE
DOI: 10.5061/dryad.bm46p
title: Data from: Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples

description: Gene flow is an essential component of population adaptation and species
 evolution. Understanding of the natural and anthropogenic factors
 affecting gene flow is also critical for the development of appropriate
 management, breeding and conservation programs. Here, we explored the
 natural and anthropogenic factors impacting crop-to-wild and within wild
 gene flow in apples in Europe using an unprecedented dense sampling of
 1,889 wild apple (Malus sylvestris) from European forests and 339 apple
 cultivars (Malus domestica). We made use of genetic, environmental and
 ecological data (microsatellite markers, apple production across
 landscapes and records of apple flower visitors respectively). We provide
 the first evidence that both human activities, through apple production,
 and human disturbance, through modifications of apple flower visitor
 diversity, have had a significant impact on crop-to-wild interspecific
 introgression rates. Our analysis also revealed the impact of previous
 natural climate change on historical gene flow in the non-introgressed
 wild apple M. sylvestris, by identifying five distinct genetic groups in
 Europe and a north-south gradient of genetic diversity. These findings
 identify human activities and climate as key drivers of gene flow in a
 wild temperate fruit tree, and provide a practical basis for conservation,
 agroforestry and breeding programs for apples in Europe.
description: Production apple, number
 of orchards and area of orchardsdryad_appleProd_France.xlsxGenetic SSR datadryad_dom_syl_26SSR.xlsxFlower visitors in applesdryad_flower_visitors_SPIPOLL.xlsx
DOI: 10.5061/dryad.4pg37
title: Data from: Integrating genetic analysis of mixed populations with a spatially-explicit population dynamics model

description: Inferring the dynamics of populations in time and space is a central
 challenge in ecology. Intra-specific structure (for example genetically
 distinct sub-populations or meta-populations) may require methods that can
 jointly infer the dynamics of multiple populations. This is of particular
 importance for harvested species, for which management must balance
 utilization of productive populations with protection of weak ones. Here
 we present a novel method for simultaneous learning about the
 spatio-temporal dynamics of multiple populations that combines genetic
 data with prior information about abundance and movement in an integrated
 population modelling approach. We apply the Bayesian genetic mixed stock
 analysis to 17 wild and 10 hatchery-reared Baltic salmon (S. salar)
 stocks, quantifying uncertainty in stock composition in time and space,
 and in population dynamics parameters such as migration timing and speed.
 Our results indicate that the commonly used “equal prior probabilities”
 assumption may not be appropriate for all mixed stock analyses.
 Incorporation of prior information about stock abundance and movement
 resulted in more precise and plausible estimates of mixture compositions
 in time and space. Inclusion of a population dynamics model also allowed
 robust interpolation of expected catch composition at areas and times with
 no genetic observations. The genetic data were informative about
 stock-specific movement patterns, updating priors for migration path,
 timing and speed. The model we present here forms the basis for optimizing
 the spatial and temporal allocation of harvest to support the management
 of mixed populations of migratory species.
description: Baltic_salmon_baseline_dataBaseline genotypes (17 microsatellite loci) for Baltic salmon from 27 stocks (3593 individuals of known stock of origin).Baltic_salmon_mixture_dataBaltic salmon mixture data: Genotypes (17 microsatellite loci) for 2058 Baltic salmon individuals sampled from Swedish and Finnish coastal trap net fisheries in 2014.
DOI: 10.5061/dryad.7np24
title: Data from: Wheat alleles introgress into selfing wild relatives: empirical estimates from Approximate Bayesian Computation in Aegilops triuncialis.

description: Extensive gene flow between wheat (Triticum sp.) and several wild
 relatives of the genus Aegilops has recently been detected despite
 notoriously high levels of selfing in these species. Here, we assess and
 model the spread of wheat alleles into natural populations of the barbed
 goatgrass (Aegilops triuncialis), a wild wheat relative prevailing in the
 Mediterranean flora. Our sampling, based on an extensive survey of 31 Ae.
 triuncialis populations collected along a 60 km x 20 km area in Southern
 Spain (Grazalema Mountain chain, Andalousia, totaling 458 specimens) is
 completed with 33 wheat cultivars representative of the European
 domesticated pool. All specimens were genotyped with amplified fragment
 length polymorphism with the aim of estimating wheat admixture levels in
 Ae. triuncialis populations. This survey first confirmed extensive
 hybridization and backcrossing of wheat into the wild species. We then
 used explicit modeling of populations and Approximate Bayesian Computation
 to estimate the selfing rate of Ae. triuncialis along with the magnitude,
 the tempo and the geographic distance over which wheat alleles introgress
 into Ae. triuncialis populations. These simulations confirmed that
 extensive introgression of wheat alleles (2.7 x 10-4 wheat immigrants for
 each Ae. triuncialis resident, at each generation) into Ae. triuncialis
 occurs despite a high selfing rate (Fis ≈ 1 and selfing rate = 97%). These
 results are discussed in light of risks associated with the release of
 genetically-modified wheat cultivars in Mediterranean agrosystems.
description: QnemoPajkovic2014