cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.634n8
title: Data from: Exploring the nature of ecological specialization in a coral reef fish community: morphology, diet, and foraging microhabitat use

description: Patterns of ecological specialization offer invaluable information about
 ecosystems. Yet, specialization is rarely quantified across several
 ecological niche axes and variables beyond the link between morphological
 and dietary specialization have received little attention. Here, we
 provide a quantitative evaluation of ecological specialization in a coral
 reef fish assemblage (f. Acanthuridae) along one fundamental and two
 realized niche axes. Specifically, we examined ecological specialization
 in 10 surgeonfish species with regards to morphology and two realized
 niche axes associated with diet and foraging microhabitat utilization
 using a recently developed multidimensional framework. We then
 investigated the potential relationships between morphological and
 behavioural specialization. These relationships differed markedly from the
 traditional ecomorphological paradigm. While morphological specialization
 showed no relationship with dietary specialization, it exhibited a strong
 relationship with foraging microhabitat specialization. However, this
 relationship was inverted: species with specialized morphologies were
 microhabitat generalists, whereas generalized morphotypes were
 microhabitat specialists. Interestingly, this mirrors relationships found
 in plant–pollinator communities and may also be applicable to other
 ecosystems, highlighting the potential importance of including niche axes
 beyond dietary specialization into ecomorphological frameworks. On coral
 reefs, it appears that morphotypes commonly perceived as most generalized
 may, in fact, be specialized in exploiting flat and easily accessible
 microhabitats.
description: BRANDLetal_RAWRaw data containing morphological, dietary, foraging microhabitat utilization and microhabitat abundance data in separate spreadsheets.
DOI: 10.5061/dryad.k4p46
title: Data from: Mixing of porpoise ecotypes in southwestern UK waters revealed by genetic profiling

description: Contact zones between ecotypes are windows for understanding how species
 may react to climate changes. Here, we analysed the fine-scale genetic and
 morphological variation in harbour porpoises (Phocoena phocoena) around
 the UK by genotyping 591 stranded animals at nine microsatellite loci. The
 data were integrated with a prior study to map at high resolution the
 contact zone between two previously identified ecotypes meeting in the
 northern Bay of Biscay. Clustering and spatial analyses revealed that UK
 porpoises are derived from two genetic pools with porpoises from the
 southwestern UK being genetically differentiated, and having larger body
 sizes compared to those of other UK areas. Southwestern UK porpoises
 showed admixed ancestry between southern and northern ecotypes with a
 contact zone extending from the northern Bay of Biscay to the Celtic Sea
 and Channel. Around the UK, ancestry blends from one genetic group to the
 other along a southwest--northeast axis, correlating with body size
 variation, consistent with previously reported morphological differences
 between the two ecotypes. We also detected isolation by distance among
 juveniles but not in adults, suggesting that stranded juveniles display
 reduced intergenerational dispersal. The fine-scale structure of this
 admixture zone raises the question of how it will respond to future
 climate change and provides a reference point for further study.
description: Data UK porpoises
 DRYADData UK porpoises
 including: stranding locations and dates, sex, age and body length of the
 animals (when known), and microsatellite genotyping. Note that EV104 was
 not considered because of null allele issues.Data_UKporpoises_DRYAD.xlsx
DOI: 10.5061/dryad.h0h3t
title: Data from: Multispecies genetic structure and hybridization in the Betula genus across Eurasia

description: Boreal and cool temperate forests are the major land cover of northern
 Eurasia, and information about continental-scale genetic structure and
 past demographic history of forest species is important from an
 evolutionary perspective and has conservation implications. However,
 although many population genetic studies of forest tree species have been
 conducted in Europe or Eastern Asia, continental-scale genetic structure
 and past demographic history remain poorly known. Here, we focus on the
 birch genus Betula, which is commonly distributed in boreal and cool
 temperate forests, and examine 129 populations of two tetraploid and four
 diploid species collected from Iceland to Japan. All individuals were
 genotyped at seven to 18 nuclear simple sequence repeats (nSSRs). Pairwise
 math formula among the six species ranged from 0.285 to 0.903, and genetic
 differentiation among them was clear. structure analysis suggested that
 Betula pubescens is an allotetraploid and one of the parental species was
 Betula pendula. In both species pairs of B. pendula and B. plathyphylla,
 and B. pubescens and B. ermanii, genetic diversity was highest in central
 Siberia. A hybrid zone was detected around Lake Baikal for eastern and
 western species pairs regardless of ploidy level. Approximate Bayesian
 computation suggested that the divergence of B. pendula and B. platyphylla
 occurred around the beginning of the last ice age (36 300 years BP, 95%
 CI: 15 330–92 700) and hybridization between them was inferred to have
 occurred after the last glacial maximum (1614 years BP, 95% CI: 561–4710),
 with B. pendula providing a higher contribution to hybrids.
description: The genotype files of
 multiple birch species in EurasiaTsuda_Betula_sampleInfo:
 This file includes a list of population code, name, country, longitude (E)
 and latitude (N) which are corresponding to
 "Tsuda_Betula1594_7loc_STRUCTURE.txt".
 Tsuda_Betula_TetDip_FSTAT: The genotype data for software FSTAT. To
 analyze diploid-tetraploid combined data keeping allele frequencies,
 tetraploid genotypes were treated as two diploid individuals in FSTAT.
 Tsuda_Betula1594_7loc_STRUCTURE: The input file of STRUCTURE analysis
 based on 7loci of 1594 individuals. Missing data is coded as -9.
 Betula_Betula877_18loc: The input file of STRUCTURE analysis based on
 18loci of 877 diploid individuals. Missing data is coded as -9.
 Tsuda_Betula_4spABC: The input fie of DIYABC based on 18 loci in 4
 species.Tsuda_Betula_Eurasia_MolEcol2016.zip
DOI: 10.5061/dryad.2f5v427
title: Data from: Predation risk for reptiles is highest at remnant edges in agricultural landscapes

description: Preventing biodiversity loss in fragmented agricultural landscapes is a
 global problem. The persistence of biodiversity within remnant vegetation
 can be influenced by an animal's ability to move through the farmland
 matrix between habitat patches. Yet, many of the mechanisms driving
 species occurrence within these landscapes are poorly understood,
 particularly for reptiles. We used scented and unscented plasticine lizard
 models and wildlife cameras to (a) estimate predation risk of reptiles in
 four farmland types (crop field, pasture paddock, restoration tree
 planting and areas with applied woody mulch) relative to the patch edge
 and remnant vegetation, and (b) examine how predation risk was influenced
 by temporal change in the matrix (crop harvesting). Birds (55.1%), mammals
 (41.1%), reptiles (3.4%), and invertebrates (0.5%) attacked models, of
 which 87% were native species. Mammalian predators were 60.2% more likely
 to attack scented models then unscented models. Bird predators were not
 influenced by scent. We found predator attacks on models were highest at
 edges (49%, irrespective of adjacent farmland type, with a reduced risk
 within farmland (29%) and remnant patches (33%) (p &lt; 0.01). Both
 mammal and bird predators contributed to high numbers of predation
 attempts at edges. Removal of crops did not increase predation attempts in
 crop fields or other farmland types, although predation attempts were
 significantly lower along the crop transect after harvesting, compared to
 the woody debris transect. However, numbers of predation attempts were
 higher in edge habitats, particularly prior to harvesting. Synthesis and
 applications. Reptiles are at risk of predation by birds and mammals in
 both remnant patches and the farmland matrix, particularly in edge
 habitat. Our results demonstrate that edge habitats are potentially
 riskier for lizards than the farmland. Vulnerability to predation may be
 increased by a lack of shelter within edge habitats such as by increasing
 visibility of reptiles to predators. Therefore, to benefit reptiles, land
 managers could provide shelter (rocks, logs, and grasses), particularly
 between remnants and linear plantings which could improve landscape
 connectivity.
description: "All predator"
 dataRaw data behind
 "All predator" analysis and provides baseline data for R code
 provided.Predation_experiment_20160909.csvPredation data for bird predators onlyData compiled and collected in the field for bird predators only.Predation_experiment_birds_20160910.csvPredation data for mammals predators onlyData collected in the field and compiled for mammal predators only.Predation_experiment_mammals_20160910.csvR code for predation analysis for all predators, birds and mammal predatorsR script for analysis within the manuscript.Predation analysis_20160909.RPlotting script for graphsR script for producing all figures of significant results within the manuscript.Predation_plottinggraphs_20170327.R
DOI: 10.5061/dryad.432d1
title: Data from: Effects of polyploidy and reproductive mode on life history trait expression

description: Ploidy elevation is increasingly recognized as a common and important
 source of genomic variation. Even so, the consequences and biological
 significance of polyploidy remain unclear, especially in animals. Here,
 our goal was to identify potential life history costs and benefits of
 polyploidy by conducting a large multiyear common garden experiment in
 Potamopyrgus antipodarum, a New Zealand freshwater snail that is a model
 system for the study of ploidy variation, sexual reproduction,
 host–parasite coevolution, and invasion ecology. Sexual diploid and
 asexual triploid and tetraploid P. antipodarum frequently coexist,
 allowing for powerful direct comparisons across ploidy levels and
 reproductive modes. Asexual reproduction and polyploidy are very often
 associated in animals, allowing us to also use these comparisons to
 address the maintenance of sex, itself one of the most important
 unresolved questions in evolutionary biology. Our study revealed that
 sexual diploid P. antipodarum grow and mature substantially more slowly
 than their asexual polyploid counterparts. We detected a strong negative
 correlation between the rate of growth and age at reproductive maturity,
 suggesting that the relatively early maturation of asexual polyploid P.
 antipodarum is driven by relatively rapid growth. The absence of evidence
 for life history differences between triploid and tetraploid asexuals
 indicates that ploidy elevation is unlikely to underlie the differences in
 trait values that we detected between sexual and asexual snails. Finally,
 we found that sexual P. antipodarum did not experience discernable
 phenotypic variance-related benefits of sex and were more likely to die
 before achieving reproductive maturity than the asexuals. Taken together,
 these results suggest that under benign conditions, polyploidy does not
 impose obvious life history costs in P. antipodarum and that sexual P.
 antipodarum persist despite substantial life history disadvantages
 relative to their asexual counterparts.
description: Larkin et al. Ecol and
 Evol data for DryadLife history trait data
 for G1 snails (individual)Family data from Larkin
 et al. 2015 Ecol EvolFamily means and
 variancesFamilyData_Dryad.sav
DOI: 10.5061/dryad.bt7vr
title: Data from: Colonization of the Tibetan Plateau by the homoploid hybrid pine Pinus densata

description: Pinus densata is an intriguingly successful homoploid hybrid species that
 occupies vast areas of the southeastern Tibetan Plateau in which neither
 of its parental species are present, but the colonization processes
 involved are poorly understood. To shed light on how this species
 colonized and became established on the plateau, we surveyed paternally
 inherited chloroplast (cp) and maternally inherited mitochondrial (mt) DNA
 variation within and among 54 populations of P. densata and its putative
 parental species throughout their respective ranges. Strong spatial
 genetic structure of both cp and mtDNA were detected in P. densata
 populations. Mitotypes specific to P. densata were likely generated by
 complex recombination events. A putative ancestral hybrid zone in the
 northeastern periphery of P. densata was identified, and we propose that
 the species then colonized the plateau by migrating westwards. Along the
 colonization route, consecutive bottlenecks and surfing of rare alleles
 caused a significant reduction of genetic diversity and strong population
 differentiation. The direction and intensity of introgression from
 parental species varied among geographic regions. In western parts of its
 range the species seems to have been isolated from seed and pollen flow
 from its parent species for a long time. The observed spatial distribution
 of genetic diversity in P. densata also appears to reflect the persistence
 of this species on the plateau during the last glaciation. Our results
 indicate that both ancient and contemporary population dynamics have
 contributed to the spatial distribution of genetic diversity in P.
 densata, which accordingly reflects its evolutionary history.
description: mtDNA & cpDNA
 frequencies and genotype composition of chlorotypes
DOI: 10.5061/dryad.rp65k
title: Data from: Prospective, observational study comparing automated and visual point-of-care urinalysis in general practice

description: Objective Point-of-care testing (POCT) urinalysis might reduce errors in
 (subjective) reading, registration and communication of test results, and
 might also improve diagnostic outcome and optimise patient management.
 Evidence is lacking. In the present study, we have studied the analytical
 performance of automated urinalysis and visual urinalysis compared with a
 reference standard in routine general practice. Setting The study was
 performed in six general practitioner (GP) group practices in the
 Netherlands. Automated urinalysis was compared with visual urinalysis in
 these practices. Reference testing was performed in a primary care
 laboratory (Saltro, Utrecht, The Netherlands). Primary and secondary
 outcome measures Analytical performance of automated and visual urinalysis
 compared with the reference laboratory method was the primary outcome
 measure, analysed by calculating sensitivity, specificity, positive
 predictive value (PPV) and negative predictive value (NPV) and
 Cohen's κ coefficient for agreement. Secondary outcome measure was
 the user-friendliness of the POCT analyser. Results Automated urinalysis
 by experienced and routinely trained practice assistants in general
 practice performs as good as visual urinalysis for nitrite, leucocytes and
 erythrocytes. Agreement for nitrite is high for automated and visual
 urinalysis. κ's are 0.824 and 0.803 (ranked as very good and good,
 respectively). Agreement with the central laboratory reference standard
 for automated and visual urinalysis for leucocytes is rather poor (0.256
 for POCT and 0.197 for visual, respectively, ranked as fair and poor).
 κ's for erythrocytes are higher: 0.517 (automated) and 0.416
 (visual), both ranked as moderate. The Urisys 1100 analyser was easy to
 use and considered to be not prone to flaws. Conclusions Automated
 urinalysis performed as good as traditional visual urinalysis on reading
 of nitrite, leucocytes and erythrocytes in routine general practice.
 Implementation of automated urinalysis in general practice is justified as
 automation is expected to reduce human errors in patient identification
 and transcribing of results.
description: POCT urine analysers
 Dryad 20JUL2016raw
 dataUserfriendliness POCT
 urine analysers Dryad 20JUL2016raw
 data
DOI: 10.5061/dryad.80dk1
title: Data from: Ancient symbiosis confers desiccation resistance to stored grain pest beetles

description: Microbial symbionts of insects provide a range of ecological traits to
 their hosts that are beneficial in the context of biotic interactions.
 However, little is known about insect symbiont-mediated adaptation to the
 abiotic environment, e.g. temperature and humidity. Here we report on an
 ancient clade of intracellular, bacteriome-located Bacteroidetes symbionts
 that are associated with grain and wood pest beetles of the
 phylogenetically distant families Silvanidae and Bostrichidae. In the
 saw-toothed grain beetle Oryzaephilus surinamensis, we demonstrate that
 the symbionts affect cuticle thickness, melanization and hydrocarbon
 profile, enhancing desiccation resistance and thereby strongly improving
 fitness under dry conditions. Together with earlier observations on
 symbiont contributions to cuticle biosynthesis in weevils, our findings
 indicate that convergent acquisitions of bacterial mutualists represented
 key adaptations enabling diverse pest beetle groups to survive and
 proliferate under the low ambient humidity that characterizes dry grain
 storage facilities.
description: Osur
 CHCscuticular hydrocarbons
 measured by GC/MS of O.surinamensis adults with and without symbionts,
 reared at 30 or 60% relative humidity before and after acute desiccation
 stress (Fig. 4)Osur cuticle
 melanizationMelanization of
 O.surinamensis cuticle with and without symbionts, reared at 30 and 60%
 relative humidity, measured as redness of thorax and cuticle (Fig. 3a and
 S3)Osur cuticle
 thicknessCuticle thicknes of
 O.surinamensis with and without symbionts, reared at 30 and 60% relative
 humidity, larvae and adults.(Fig. 3b and S4)Osur water
 lossweight (water) loss of
 O.surinamensis under acute desiccation stress (&lt;5%relative humidity).
 Beetles were beforehand reared with and without symbionts, at 30 or 60%
 relative humidity (Fig. 5a and S5)Osur
 mortalityMortality of
 O.surinamensis under acute desiccation stress (&lt;5%relative humidity).
 Beetles were beforehand reared with and without symbionts, at 30 or 60%
 relative humidity. (Fig. 5b)Osur population
 growthPopulation growth of
 O.surinamensis, with and without symbionts, reared at 30 and 60% relative
 humidity. (Fig. 6 and S3b)Osur symbiont
 elimination qPCRQuantification of
 symbiont titer after heat and tetracyclin treatments in offspring eggs.
 Abundance measured as DNA amount of 16S / 28S rDNA.
DOI: 10.5061/dryad.3gc6nj6
title: Data from: Local adaptation and ecological differentiation under selection, migration and drift in Arabidopsis lyrata

description: How the balance between selection, migration and drift influences the
 evolution of local adaptation has been under intense theoretical scrutiny.
 Yet, empirical studies that relate estimates of local adaptation to
 quantification of gene flow and effective population sizes have been rare.
 Here, we conducted a reciprocal transplant trial, a common garden trial,
 and a whole-genome based demography analysis to examine these effects
 among Arabidopsis lyrata populations from two altitudinal gradients in
 Norway. Demography simulations indicated that populations within the two
 gradients are connected by gene flow (0.1 &lt; 4Nem &lt; 11) and
 have small effective population sizes (Ne &lt; 6,000), suggesting that
 both migration and drift can counteract local selection. However, the
 three-year field experiments showed evidence of local adaptation at the
 level of hierarchical multi-year fitness, attesting to the strength of
 differential selection. In the lowland habitat, local superiority was
 associated with greater fecundity, while viability accounted for fitness
 differences in the alpine habitat. We also demonstrate that flowering time
 differentiation has contributed to adaptive divergence between these
 locally adapted populations. Our results show that despite the estimated
 potential of gene flow and drift to hinder differentiation, selection
 among these A. lyrata populations has resulted in local adaptation.
description: Low
 phenotypesPhenotype measurements
 from the low-altitude field site. Measurements from the three field
 seasons are marked by years _15, _16 & _17. ID = individual
 identifier. Pop = population. Family = seed family. Block = planting
 block. Surv = survival. Flow = flowering propensity. Fruits = fruit
 production. Fstart = flowering start date.Low_phenotypes.txtHigh phenotypesPhenotype measurements from the high-altitude field site. Measurements from the three field seasons are marked by years _15, _16 & _17. ID = individual identifier. Pop = population. Family = seed family. Block = planting block. Surv = survival. Flow = flowering propensity. Fruits = fruit production. Fstart = flowering start date.High_phenotypes.txtOulu phenotypesPhenotype measurements from the Oulu field site. Measurements from the three field seasons are marked by years _15, _16 & _17. ID = individual identifier. Pop = population. Family = seed family. Block = planting block. Surv = survival. Fruits = fruit production. Fstart = flowering start date. Shootl = flowering shoot length. Inf = inflorescence number. Fmat = fruit maturation date. Fstop = flowering cessation date.Oulu_phenotypes.txtSelection asterExample R scripts for selection gradient analysis with aster models.Selection_aster.rFitness asterExample R scripts for total fitness estimation with aster models.Fitness_aster.rQst_mcmcglmmExample R scripts for Qst estimation with MCMCglmm.
DOI: 10.5061/dryad.74r4q8p
title: Data from: Nighttime intensive care unit discharge and outcomes: a propensity matched retrospective cohort study

description: Background: Nighttime ICU discharge, i.e., discharge from the ICU during
 the night hours, has been associated with increased readmission rates,
 hospital length of stay (LOS) and in-hospital mortality. We sought to
 determine the frequency of nighttime ICU discharge and identify whether
 nighttime ICU discharge is associated with worse outcomes in a private
 adult ICU located in Brazil. Methods: Post hoc analysis of a cohort study
 addressing the effect of ICU readmissions on outcomes. This retrospective,
 single center, propensity matched cohort study was conducted in a
 medical-surgical ICU located in a private tertiary care hospital in São
 Paulo, Brazil. Based on time of transfer, patients were categorized into
 nighttime (7:00 pm to 6:59 am) and daytime (7:00 am to 6:59 pm) ICU
 discharge and were propensity-score matched at a 1:2 ratio. The primary
 outcome of interest was in–hospital mortality. Results: Among 4,313
 eligible patients admitted to the ICU between June 2013 and May 2015,
 1,934 patients were matched at 1:2 ratio [649 (33.6%) nighttime and 1,285
 (66.4%) daytime discharged patients]. The median (IQR) cohort age was 66
 (51-79) years and SAPS III score was 43 (33-55). In-hospital mortality was
 6.5% (42/649) in nighttime compared to 5.6% (72/1,285) in daytime
 discharged patients (OR, 1.17; 95% CI, 0.79 to 1.73; p=0.444). While
 frequency of ICU readmission (OR, 0.95; 95% CI, 0.78 to 1.29; p=0.741) and
 length of hospital stay did not differ between the groups, length of ICU
 stay was lower in nighttime compared to daytime ICU discharged patients [1
 (1-3) days vs. 2 (1-3) days, respectively, p=0.047]. Conclusion: In this
 propensity-matched retrospective cohort study, time of ICU discharge did
 not affect in-hospital mortality.
description: SPSS data
 bankThe de-identified data
 presented here has been used for the analyses reported in the manuscript
 "NIGHTTIME INTENSIVE CARE UNIT DISCHARGE AND OUTCOMES: A PROPENSITY
 MATCHED RETROSPECTIVE COHORT STUDY", including baseline
 characteristics of study participants and the main clinical outcomes
 before propensity score matching.Data_bank.sav