cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1m9q8
title: Data from: Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia

description: Weedy rice is a close relative of domesticated rice (Oryza sativa) that
 competes aggressively with the crop and limits rice productivity
 worldwide. Most genetic studies of weedy rice have focused on populations
 in regions where no reproductively compatible wild Oryza species occur
 (North America, Europe, northern Asia). Here we examined the population
 genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be
 found growing in close proximity to cultivated and weedy rice. Using 375
 accessions and a combined analysis of 24 neutral SSR loci and two rice
 domestication genes (sh4, controlling seed shattering, and Bh4,
 controlling hull color), we addressed the following questions: 1) What is
 the relationship of Malaysian weedy rice to domesticated and wild rice,
 and to weedy rice strains in the US? 2) To what extent does the presence
 of O. rufipogon influence the genetic and phenotypic diversity of
 Malaysian weeds? 3) What do the distributions of sh4 and Bh4 alleles and
 associated phenotypes reveal about the origin and contemporary evolution
 of Malaysian weedy rice? Our results reveal: independent evolutionary
 origins for Malaysian weeds and US strains, despite their very close
 phenotypic resemblance; wild-to-weed gene flow in Malaysian weed
 populations, including apparent adaptive introgression of seed-shattering
 alleles; and a prominent role for modern Malaysian cultivars in the origin
 and recent proliferation of Malaysian weeds. These findings suggest that
 the genetic complexity and adaptability of weedy crop relatives can be
 profoundly influenced by proximity to reproductively compatible wild and
 domesticated populations.
description: @_wrSSR_STRUC_input_140824_@@@Microsatellite genotype data of Malaysian rice##Song12_Suppl_RiceInfo+sh4+Bh4+sample_code_140910This file contains sample naming for sh4 multiple sequence alignment.#_sh4_MSA_140910Multiple sequence alignment for sh4 fragments.
DOI: 10.5061/dryad.7n139
title: Data from: Resistance and resilience to changing climate and fire regime depend on plant functional traits

description: Changing disturbance-climate interactions will drive shifts in plant
 communities: these effects are not adequately quantified by environmental
 niche models used to predict future species distributions. We quantified
 the effects of more frequent fire and lower rainfall - as projected to
 occur under a warming and drying climate - on population responses of
 shrub species in biodiverse Mediterranean-climate type shrublands near
 Eneabba, southwestern Australia. Using experimental fires, we measured the
 density of all shrub species for four dominant plant functional groups
 (resprouter/non-sprouter x serotinous/soil seed bank) before and after
 fire in 33 shrubland sites, covering four post-fire rainfall years and
 fire intervals from 3 – 24 years. Generalized linear mixed effects models
 were used to test our a priori hypotheses of rainfall, fire interval, and
 plant functional type effects on post-fire survival and recruitment. At
 shortened fire intervals, species solely dependent on seedling recruitment
 for persistence were more vulnerable to local extinction than were species
 with both seedling recruitment and vegetative regrowth. Nevertheless,
 seedling recruitment was essential for population maintenance of
 resprouting species. Serotinous species were less resilient than soil seed
 storage species regardless of regeneration mode. Critically, in relation
 to changing climate, a 20% reduction in post-fire winter rainfall
 (essential for seedling recruitment) is predicted to increase the minimum
 inter-fire interval required for self-replacement by 50%, placing many
 species at risk of decline. Synthesis. Our results highlight the
 potentially deleterious biodiversity impacts of climate and fire regime
 change, and underscore weaknesses inherent in studies considering single
 impact factors in isolation. In fire-prone ecosystems characterized by a
 projected warming and drying climate, and increasing fire hazard, adaptive
 approaches to fire management may need to include heightened wildfire
 suppression and lengthened intervals for prescribed fire to best support
 the in situ persistence of perennial plant species and of plant
 biodiversity. This conclusion is at odds with the view that more managed
 fire may be needed to mitigate wildfire risk as climate warms.
description: Enright.etal_PrimaryDataset_PlantResponsesThis file contains plot-by-species response as measured by abundance pre-post fire.PFT_datasetJEcol_1.csvPFT_PlotScaleData_JEcolPlot Locations and details of vegetation, soils, and fire histories.PFT_datasetJEcol_2_ResproutersSeedAdultThis file contains data of resprouting species abundance pre and post fire with post fire data coded by adult or seedling.
DOI: 10.5061/dryad.g7n7g
title: Data from: Two tales of cardiovascular risks-middle-aged women living in Sweden and Scotland: a cross-sectional comparative study

description: Objectives: To compare cardiovascular risk factors as well as rates of
 cardiovascular diseases in middle-aged women from urban areas in Scotland
 and Sweden. Design: Comparative cross-sectional study. Setting: Data from
 the general population in urban areas of Scotland and the general
 population in two major Swedish cities in southeast Sweden, south of
 Stockholm. Participants: Comparable data of middle-aged women (40–65
 years) from the Scottish Health Survey (n=6250) and the Swedish QWIN study
 (n=741) were merged together into a new dataset (n=6991 participants).
 Main outcome measure: We compared middle-aged women in urban areas in
 Sweden and Scotland regarding risk factors for cardiovascular disease
 (CVD), CVD diagnosis, anthropometrics, psychological distress and
 lifestyle. Results: In almost all measurements, there were significant
 differences between the countries, favouring the Swedish women. Scottish
 women demonstrated a higher frequency of alcohol consumption, smoking,
 obesity, low vegetable consumption, a sedentary lifestyle and also more
 psychological distress. For doctor-diagnosed coronary heart disease, there
 were also significant differences, with a higher prevalence among the
 Scottish women. Conclusions: This is one of the first studies that clearly
 shows that Scottish middle-aged women are particularly affected by a worse
 profile of CVD risks. The profound differences in CVD risk and outcome
 frequency in the two populations are likely to have arisen from
 differences in the two groups of women's social, cultural, political
 and economic environments.
description: ScottlandSwededen
 combined datasetThe two datasets, QWIN
 and SHeS, were examined for comparable variables and these data were
 merged into a new dataset entitled QwinSHeS. A group of qualified
 researchers from each site evaluated the questions and defined the
 variables eligible for valid comparisons between the two countries. The
 variables included in the final Swedish – Scottish merged database were:
 sociodemographic characteristics, anthropometrics, lifestyle, classic risk
 factors for CVD, and diagnoses for CVD, general health and psychosocial
 distress (GHQ-questionnaire 12 items).ScotSwedDryad.sav
DOI: 10.5061/dryad.s0n86hq
title: Data from: Body size, developmental instability and climate change

description: Development is often temperature-dependent. We hypothesized smaller size
 and larger asymmetry with increasing temperatures. However, we also
 predicted associations with asymmetry to differ among traits that differ
 in their degree of functional importance (especially the functional wings
 in migratory birds were predicted to be more canalized), timing of
 development (skeletal (femur, tarsus and humerus) vs feather (wing and
 tail traits). We analyzed a large dataset of which we included species
 with at least 20 specimens resulting in 5533 asymmetry values in 1593
 individuals from 66 species. There was a consistent significant decrease
 in size with temperature across all traits. Fluctuating asymmetry for
 wings and femur was on average lower, suggesting higher canalization, and
 it decreased with migration distance, while that was not the case for the
 other traits. Fluctuating asymmetry increased with increasing temperature
 for wings, but not for the other characters, where the different responses
 of different characters to temperature was significant. Since there was no
 significant three-way interaction between temperature, migration distance
 and character, the asymmetry-temperature response was similar in migratory
 and resident species. These findings imply that climate warming reduces
 size of all traits and decreases developmental instability of wings in
 birds.
description: Dongen-Møller-DataAll data in xls format.
DOI: 10.5061/dryad.t2q91
title: Data from: Patterns of relapse in extrapulmonary small cell carcinoma: retrospective analysis of outcomes from two cancer centres

description: Objectives: We conducted a retrospective review of patients with
 extrapulmonary small cell carcinomas (EPSCCs) to explore the distribution,
 treatments, patterns of relapse and outcomes by primary site. Setting: We
 have reviewed the outcomes of one of the largest data sets of consecutive
 patients with EPSCC identified from two major cancer centres.
 Participants: Consecutive patients with a histopathological diagnosis of
 EPSCC from the two institutions were retrospectively identified. Primary
 and secondary outcome measures: Outcomes were evaluated including stage at
 presentation, treatments given, sites of relapse, time to distant relapse,
 progression-free survival and overall survival (OS). Results: From a total
 159 patients, 114 received first-line chemotherapy, 80.5% being
 platinum-based. Response rate was 48%. Commonest primary sites were
 genitourinary and gynaecological. 44% of patients presented with
 metastatic disease. 55.9% relapsed with liver the commonest site, whereas
 only 2.5% developed brain metastases. Median OS was 13.4 months for all
 patients, 7.6 months and 19.5 months for those with metastatic and
 non-metastatic disease, respectively. Gynaecological and head and neck
 patients had significantly better OS compared to gastrointestinal
 patients. Conclusions: EPSCCs demonstrate high response rates to
 chemotherapy and high rates of distant metastases. Primary sites may
 influence prognosis, and survival is optimal with a radical strategy.
 Brain metastases are rare and we therefore do not recommend prophylactic
 cranial irradiation.
description: Table 1: Primary sites
 of extrapulmonary small cell carcinomas identifiedPrimary sites of EPSCC
 were grouped by organ system to aid analysisTable
 1.docxTable 2A: : Univariate
 Cox regression analysis for overall survivalUnivariate Cox
 regression analysis for overall survival for patients with
 EPSCC.Table
 2A.docxTable 2B: Multivariate
 Cox regression model for overall survivalMultivariate Cox
 regression model for overall survival for patients with
 EPSCC.Table
 2B.docxFigure 1: Kaplan–Meier
 plot for progression-free survival (PFS) for all
 patients.Kaplan–Meier plot for
 progression-free survival (PFS) for all patients.Figure
 1.tiffFigure 2a: Kaplan–Meier
 plot for overall survival (OS) for all patients, grouped by disease stage
 at diagnosis.Kaplan–Meier plot for
 overall survival (OS) for all patients, grouped by disease stage at
 diagnosis.Figure
 2a.tiffFigure 2b: Kaplan–Meier
 plot for overall survival (OS) for all patients, grouped by treatment
 intent.Kaplan–Meier plot for
 overall survival (OS) for all patients, grouped by treatment
 intent.Figure
 2b.tiff
DOI: 10.5061/dryad.3m2g1
title: Data from: Morphometric variation of extant platyrrhine molars: taxonomic implications for fossil platyrrhines

description: The phylogenetic position of many fossil platyrrhines with respect to
 extant ones is not yet clear. Two main hypotheses have been proposed: the
 layered or successive radiations hypothesis suggests that Patagonian
 fossils are Middle Miocene stem platyrrhines lacking modern descendants,
 whereas the long lineage hypothesis argues for an evolutionary continuity
 of all fossil platyrrhines with the extant ones. Our geometric
 morphometric analysis of a 15 landmark-based configuration of
 platyrrhines’ first and second lower molars suggest that morphological
 stasis may explain the reduced molar shape variation observed. Platyrrhine
 lower molar shape might be a primitive retention of the ancestral state
 affected by strong ecological constraints throughout the radiation of the
 main platyrrhine families. The Patagonian fossil specimens showed two
 distinct morphological patterns of lower molars, Callicebus—like and
 Saguinus—like, which might be the precursors of the extant forms, whereas
 the Middle Miocene specimens, though showing morphological resemblances
 with the Patagonian fossils, also displayed new, derived molar patterns,
 Alouatta—like and Pitheciinae—like, thereby suggesting that despite the
 overall morphological stasis of molars, phenotypic diversification of
 molar shape was already settled during the Middle Miocene.
description: Raw and Procrustes
 coordinates Nova Delgado etal 2016 PeerJGeometric morphometric
 raw and procrustes coordinates of the landmark configurations for first
 molar (M1) and second molar (M2) of all analyzed
 samples.
DOI: 10.5061/dryad.70917
title: Data from: Relating Ediacaran fronds

description: Ediacaran fronds are key components of terminal-Proterozoic ecosystems.
 They represent one of the most widespread and common body forms ranging
 across all major Ediacaran fossil localities and time slices postdating
 the Gaskiers glaciation, but uncertainty over their phylogenetic
 affinities has led to uncertainty over issues of homology and functional
 morphology between and within organisms displaying this ecomorphology.
 Here we present the first large-scale, multigroup cladistic analysis of
 Ediacaran organisms, sampling 20 ingroup taxa with previously asserted
 affinities to the Arboreomorpha, Erniettomorpha, and Rangeomorpha. Using a
 newly derived morphological character matrix that incorporates multiple
 axes of potential phylogenetically informative data, including
 architectural, developmental, and structural qualities, we seek to
 illuminate the evolutionary history of these organisms. We find strong
 support for existing classification schema and devise apomorphy-based
 definitions for each of the three frondose clades examined here. Through a
 rigorous cladistic framework it is possible to discern the pattern of
 evolution within and between these clades, including the identification of
 homoplasies and functional constraints. This work both validates earlier
 studies of Ediacaran groups and accentuates instances in which previous
 assumptions of their natural history are uninformative.
description: Supplementary Figure
 1Illustration of the
 morphological characters used in this analysis. The first number denotes
 the character followed by the state illustrated, see Supporting Table 1,2
 for details. All characters and states except Character 12 (Growth
 pattern) are figured. Taxa represented are: A) Charniodiscus arboreus; B)
 Avalofractus abalculus; C) Swartpuntia germsi; D) Charnia masoni; E)
 Pectinifrons abyssalis; F) Culmofrons plumosa; G)Ernietta plateauensis; H)
 Rangea schneiderhoehni; I) Beothukis mistakensis; J) Fractofusus misrai
 specimen that is overfolded showing both the dorsal and ventral planes and
 K) Charniodiscus arboreus specimen overfloded showing differences in
 coronal plane. The reconstruction of Rangea is modified from Vickers-Rich
 et al. (2013, Fig. 9).Supplementary Table
 1Character
 listSupplementary Table
 2Character
 matrix
DOI: 10.5061/dryad.qt743
title: Data from: The effect of sitagliptin on carotid artery atherosclerosis in Type 2 Diabetes: the PROLOGUE randomized controlled trial

description: Background: Experimental studies have suggested that dipeptidyl
 peptidase-4 (DPP-4) inhibitors provide cardiovascular protective effects.
 We performed a randomized study to evaluate the effects of sitagliptin
 added on to the conventional therapy compared with conventional therapy
 alone (diet, exercise, and/or drugs, except for incretin-related agents)
 on the intima-media thickness (IMT) of the carotid artery, a surrogate
 marker for the evaluation of atherosclerotic cardiovascular disease, in
 people with type 2 diabetes mellitus (T2DM). Methods and Findings: We used
 a multicenter PROBE (prospective, randomized, open label, blinded
 endpoint) design. Individuals aged ≥30 y with T2DM (6.2% ≤ HbA1c &lt;
 9.4%) were randomly allocated to receive either sitagliptin (25 to 100
 mg/d) or conventional therapy. Carotid ultrasound was performed at
 participating medical centers, and all parameters were measured in a core
 laboratory. Of the 463 enrolled participants with T2DM, 442 were included
 in the primary analysis (sitagliptin group, 222; conventional therapy
 group, 220). Estimated mean (± standard error) common carotid artery IMT
 at 24 mo of follow-up in the sitagliptin and conventional therapy groups
 was 0.827 ± 0.007 mm and 0.837 ± 0.007 mm, respectively, with a mean
 difference of −0.009 mm (97.2% CI −0.028 to 0.011, p = 0.309). HbA1c level
 at 24 mo was significantly lower with sitagliptin than with conventional
 therapy (6.56% ± 0.05% versus 6.72% ± 0.05%, p = 0.008; group mean
 difference −0.159, 95% CI −0.278 to −0.041). Episodes of serious
 hypoglycemia were recorded only in the conventional therapy group, and the
 rate of other adverse events was not different between the two groups. As
 it was not a placebo-controlled trial and carotid IMT was measured as a
 surrogate marker of atherosclerosis, there were some limitations of
 interpretation. Conclusions: In the PROLOGUE study, there was no evidence
 that treatment with sitagliptin had an additional effect on the
 progression of carotid IMT in participants with T2DM beyond that achieved
 with conventional treatment. Trial Registration: University Hospital
 Medical Information Network Clinical Trials Registry UMIN000004490
description: PROLOGUE_raw data for
 submission 20160506
DOI: 10.5061/dryad.kq74g8p7
title: Data from: Contrasting introduction scenarios among continents in the worldwide invasion of the banana fungal pathogen Mycosphaerella fijiensis

description: Reconstructing and characterizing introduction routes is a key step
 towards understanding the ecological and evolutionary factors underlying
 successful invasions and disease emergence. Here, we aimed to decipher
 scenarios of introduction and stochastic demographic events associated
 with the global spread of an emerging disease of bananas caused by the
 destructive fungal pathogen Mycosphaerella fijiensis. We analysed the
 worldwide population structure of this fungus using 21 microsatellites and
 8 sequence-based markers on 735 individuals from 37 countries. Our
 analyses designated South-East Asia as the source of the global invasion,
 and supported the location of the centre of origin of M. Fijiensis within
 this area. We confirmed the occurrence of bottlenecks upon introduction
 into other continents followed by widespread founder events within
 continents. Furthermore, this study suggested contrasting introduction
 scenarios of the pathogen between the African and American continents.
 While potential signatures of admixture resulting from multiple
 introductions were detected in America, all the African samples examined
 seem to descend from a single successful founder event. In combination
 with historical information, our study reveals an original and
 unprecedented global scenario of invasion for this recently emerging
 disease caused by a wind-dispersed pathogen.
description: Microsatellite
 dataMicrosat.txtSequences
DOI: 10.5061/dryad.7kp78
title: Data from: Evolutionary stasis despite selection on a heritable trait in an invasive zooplankton

description: Invasive species are one of the greatest threats to ecosystems and there
 is evidence that evolution plays an important role in the success or
 failure of invasions. Yet, few studies have measured natural selection and
 evolutionary responses to selection in invasive species, particularly
 invasive animals. We quantified the strength of natural selection on the
 defensive morphology (distal spine) of an invasive zooplankton,
 Bythotrephes longimanus, in Lake Michigan across multiple months during
 three growing seasons. We used multiple lines of evidence, including
 historic and contemporary wild-captured individuals and paleoecology of
 retrieved spines, to assess phenotypic change in distal spine length since
 invasion. We found evidence of temporally variable selection, with
 selection for decreased distal spine length early in the growing season
 and selection for increased distal spine length later in the season. This
 trend in natural selection is consistent with seasonal changes in the
 relative strength of non-gape-limited and gape-limited fish predation.
 Yet, despite net selection for increased distal spine length and a known
 genetic basis for distal spine length, we observed little evidence of an
 evolutionary response to selection. Multiple factors likely limit an
 evolutionary response to selection, including genetic correlations,
 trade-offs between components of fitness, and phenotypic plasticity.
description: Bythotrephes
 Morphological Measurements Lake MichiganSee ReadMe
 fileBythotrephes Remnant
 Spines Lake MichiganSee ReadMe
 file.
DOI: 10.5061/dryad.n7fr3
title: Data from: Multilevel and sex-specific selection on competitive traits in North American red squirrels.

description: Individuals often interact more closely with some members of the
 population (e.g. offspring, siblings or group members) than they do with
 other individuals. This structuring of interactions can lead to multilevel
 natural selection, where traits expressed at the group-level influence
 fitness alongside individual-level traits. Such multilevel selection can
 alter evolutionary trajectories, yet is rarely quantified in the wild,
 especially for species that do not interact in clearly demarcated groups.
 We quantified multilevel natural selection on two traits, postnatal growth
 rate and birth date, in a population of North American red squirrels
 (Tamiasciurus hudsonicus). The strongest level of selection was typically
 within-acoustic social neighbourhoods (within 130m of the nest), where
 growing faster and being born earlier than nearby litters was key, while
 selection on growth rate was also apparent both within-litters and
 within-study areas. Higher population densities increased the strength of
 selection for earlier breeding, but did not influence selection on growth
 rates. Females experienced especially strong selection on growth rate at
 the within-litter level, possibly linked to the biased bequeathal of the
 maternal territory to daughters. Our results demonstrate the importance of
 considering multilevel and sex-specific selection in wild species,
 including those that are territorial and sexually monomorphic.
description: FisherMLselectionSQ.dataData file to recreate multilevel selection analysis from "Multilevel and sex-specific selection on competitive traits in North American red squirrels"FisherMLselectionSQ.RcodeR code to recreate multilevel selection analysis from "Multilevel and sex-specific selection on competitive traits in North American red squirrels"