cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kd0k4
title: Data from: Origin and genetic diversity of diploid parthenogenetic Artemia in Eurasia

description: There is wide interest in understanding how genetic diversity is generated
 and maintained in parthenogenetic lineages, as it will help clarify the
 debate of the evolution and maintenance of sexual reproduction. There are
 three mechanisms that can be responsible for the generation of genetic
 diversity of parthenogenetic lineages: contagious parthenogenesis,
 repeated hybridization and microorganism infections (e.g. Wolbachia).
 Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca)
 are a good model system to investigate evolutionary transitions between
 reproductive systems as they include sexual species and lineages of
 obligate parthenogenetic populations of different ploidy level, which
 often co-occur. Diploid parthenogenetic lineages produce occasional fully
 functional rare males, interspecific hybridization is known to occur, but
 the mechanisms of origin of asexual lineages are not completely
 understood. Here we sequenced and analysed fragments of one mitochondrial
 and two nuclear genes from an extensive set of populations of diploid
 parthenogenetic Artemia and sexual species from Central and East Asia to
 investigate the evolutionary origin of diploid parthenogenetic Artemia,
 and geographic origin of the parental taxa. Our results indicate that
 there are at least two, possibly three independent and recent maternal
 origins of parthenogenetic lineages, related to A. urmiana and Artemia sp.
 from Kazakhstan, but that the nuclear genes are very closely related in
 all the sexual species and parthenogegetic lineages except for A. sinica,
 who presumable took no part on the origin of diploid parthenogenetic
 strains. Our data cannot rule out either hybridization between any of the
 very closely related Asiatic sexual species or rare events of contagious
 parthenogenesis via rare males as the contributing mechanisms to the
 generation of genetic diversity in diploid parthenogenetic Artemia
 lineages.
description: ATPman
 datasetAlignment of ATPase
 sequences in fasta formatITS
 datasetITS1 sequence alignment
 in fasta formatCOI
 datasetCytochrome c oxidase I
 sequence alignment in fasta format
DOI: 10.5061/dryad.1k01d
title: Data from: Characteristics of pneumonia deaths after earthquake and tsunami: an ecological study of 5.7 million subjects in 131 municipalities, Japan

description: Objective: On 11 March 2011, the Great East Japan Earthquake struck off
 Japan. Although some studies showed that the earthquake increased the risk
 of pneumonia death, no study reported whether and how much tsunami
 increased the risk. We examined the risk for pneumonia death after the
 earthquake/tsunami. Design: This is an ecological study. Setting: Data on
 population and pneumonia deaths obtained from the Vital Statistics 2010
 and 2012, National Census 2010 and Basic Resident Register 2010 and 2012
 in Japan. Participants: About 5.7 million subjects residing in Miyagi,
 Iwate and Fukushima Prefectures during 1 year after the disaster were
 targeted. All municipalities (n=131) were categorized into inland (n=93),
 that is, the earthquake-impacted area, and coastal types (n=38), that is,
 the earthquake- and tsunami-impacted area. Outcome measures: The number of
 pneumonia deaths per week was totaled from 12 March 2010 to 9 March 2012.
 The number of observed pneumonia deaths (O) and the sum of the sex- and
 age-classes in the observed population multiplied by the sex- and
 age-classes of expected pneumonia mortality (E) were calculated. Expected
 pneumonia mortality was the pneumonia mortality during the year before.
 Standardized mortality ratios (SMRs) were calculated for pneumonia deaths
 (O/E), adjusting for sex and age using the indirect method. SMRs were then
 calculated by coastal and inland municipalities. Results: Six thousand six
 hundred three subjects died of pneumonia during 1 year after the
 earthquake. SMRs significantly increased during the 1st to 12th week. In
 the 2nd week, SMRs in coastal and inland municipalities were 2.49 (95% CI
 2.02 to 7.64) and 1.48 (95% CI 1.24 to 2.61), respectively. SMRs of
 coastal municipalities were higher than those of inland municipalities.
 Conclusions: Earthquake increased the risk of pneumonia death and tsunamis
 additionally increased the risk.
description: SMRs for pneumonia
 deathDataset containing area,
 week from earthquake, observed number of pneumonia deaths, expected number
 of pneumonia deaths, standardized mortality ratios and p
 valueSMRs.xlsx
DOI: 10.5061/dryad.3tj44
title: Data from: Geographic determinants of gene flow in two sister species of tropical Andean frogs

description: Complex interactions between topographic heterogeneity, climatic and
 environmental gradients, and thermal niche conservatism are commonly
 assumed to indicate the degree of biotic diversification in montane
 regions. Our aim was to investigate factors that disrupt gene flow between
 populations and to determine if there is evidence of downslope asymmetric
 migration in highland frogs with wide elevational ranges and thermal
 niches. We determined the role of putative impediments to gene flow (as
 measured by least-cost path (LCP) distances, topographic complexity, and
 elevational range) in promoting genetic divergence between populations of
 2 tropical Andean frog sister species (Dendropsophus luddeckei, N = 114;
 Dendropsophus labialis, N = 74) using causal modeling and multiple matrix
 regression. Although the effect of geographic features was species
 specific, elevational range and LCP distances had the strongest effect on
 gene flow, with mean effect sizes (Mantel r and regression coefficients
 β), between 5 and 10 times greater than topographic complexity. Even
 though causal modeling and multiple matrix regression produced congruent
 results, the latter provided more information on the contribution of each
 geographic variable. We found moderate support for downslope migration. We
 conclude that the climatic heterogeneity of the landscape, the elevational
 distance between populations, and the inability to colonize suboptimal
 habitats due to thermal niche conservatism influence the magnitude of gene
 flow. Asymmetric migration, however, seems to be influenced by life
 history traits.
description: Data Guarnizo and
 Cannatella 2013All aligned DNA
 sequences used in the study in FASTA format.
DOI: 10.5061/dryad.232k9q5
title: Data from: Causes of seasonal decline in reproduction of the cooperatively-breeding acorn woodpecker

description: Clutch size and reproductive success decline seasonally in a wide range of
 temperate avian taxa. Two competing hypotheses have been proposed to
 explain such declines: the “timing” hypothesis, which states that
 conditions affecting reproduction decline intrinsically with date, and the
 “quality” hypothesis, which proposes that high-quality individuals or
 individuals in high-quality situations breed earlier. We contrasted the
 relative importance of these two hypotheses using a long-term dataset of
 the cooperatively-breeding acorn woodpecker (Melanerpes formicivorus) in
 central coastal California (USA). This population exhibits an 11% seasonal
 decline in clutch size, a 60% seasonal decline in fledging success, and a
 77% seasonal decline in fledgling overwinter survival. Clutch size tracks
 seasonal availability of flying insects, which are a likely ecological
 driver of the seasonal decline in reproduction and, because of the
 nonlinear relationship of flying insects with date, constitute a likely
 factor constraining even earlier nesting. By parsing lay date data into
 within-female and between-female components, we found that only the
 within-female component had a statistically significant direct effect on
 clutch size, supporting the timing hypothesis. For both fledging success
 and overwinter survival, however, both within- and between-female effects
 were highly significant, with between-female effects (differences in
 female quality) being stronger than within-female effects. These results
 suggest that timing per se is a key factor affecting the seasonal decline
 in clutch size, but that both differences in female quality and an
 intrinsic seasonal decline in conditions drive the even more dramatic
 seasonal declines in fledging success and overwinter survivorship of
 fledglings.
description: Acorn woodpecker clutch
 size and reproductive success dataThe file includes data
 used in the paper on group composition, group history, and annual
 conditions (weather; acorn crop) along with clutch size, young fledged,
 and young surviving to February. Metadata are listed in the second
 sheet.SeasonalDeclineData.xls
DOI: 10.5061/dryad.cs78t
title: Data from: LobeFinder: a convex hull-based method for quantitative boundary analyses of lobed plant cells

description: Dicot leaves are comprised of a heterogeneous mosaic of jig-saw-puzzle
 piece shaped pavement cells that vary greatly in size and the complexity
 of their shape. Given the importance of the epidermis and this particular
 cell type for leaf expansion, there is a strong need to understand how
 pavement cells morph from a simple polyhedral shape into highly lobed and
 interdigitated cells. At present, it is still unclear how and when the
 patterns of lobing are initiated in pavement cells, and one major
 technological bottleneck to address the problem is the lack of a robust
 and objective methodology to identify and track lobing events during the
 transition from simple cell geometry to lobed cells. We developed a
 convex-hull based algorithm termed LobeFinder to identify lobes, quantify
 geometric properties, and create a useful graphical output for further
 analysis. The algorithm was validated against manually curated cell images
 of pavement cells of widely varying sizes and shapes. The ability to
 objectively count and detect new lobe initiation events provides an
 improved quantitative framework to analyze mutant phenotypes, detect
 symmetry-breaking events in time-lapse image data, and quantify the
 time-dependent correlation between cell shape change and intracellular
 factors that may play a role in the morphogenesis process.
description: Lobefinder_v1.0
DOI: 10.5061/dryad.18ph4
title: Data from: Species-specific plant-soil feedback effects on above-ground plant-insect interactions

description: 1. Plant–soil feedback (PSF) effects on plant performance strongly depend
 on the plant species that conditioned the soil. Recent studies have shown
 that PSF can change above-ground plant–insect interactions via
 soil-mediated changes in plant quality, but whether these effects depend
 on species-specific soil conditioning is unknown. We examined how PSF
 effects of several plant species influence above-ground plant–aphid
 interactions. 2. We grew ragwort (Jacobaea vulgaris) in field soil
 conditioned specifically by 10 plant species, belonging to three
 functional groups (grasses, forbs and legumes), in a multispecies mixture
 of the conditioned soils and in control (unconditioned) field soil. We
 measured plant biomass, concentrations of primary (amino acids) and
 secondary (pyrrolizidine alkaloids) metabolites in phloem exudates, and
 performance of the generalist aphid Brachycaudus cardui and the specialist
 Aphis jacobaeae. 3. We observed that plant species, via species-specific
 effects on soil fungal communities, exerted unique plant–soil effects on
 J. vulgaris biomass, amino acid concentrations in phloem exudates and
 aphid performance. The direction and magnitude of the species-specific PSF
 effects on aphid performance differed between both aphid species. PSF
 effects on soil fungal communities, plant biomass and A. jacobaeae
 performance also differed between grasses, forbs and legumes, with soil
 conditioning by forbs resulting in lowest plant biomass and aphid
 performance. 4. Synthesis. Our study provides novel evidence that PSF
 effects on above-ground plant–insect interactions are highly species
 specific. Our results add a new dimension to the rapidly developing
 research fields of PSF and above-below-ground interactions, and highlights
 that these fields are tightly linked.
description: Data_Kos et al_Journal
 of Ecology 2015.xlsxIn a greenhouse
 experiment, we grew Jacobaea vulgaris plants in soil conditioned by 10
 plant species, in a multispecies mixture, or in unconditioned (mixed
 field) soil. For all soils, we measured fungal community composition For
 each plant, we recorded biomass, chemistry (amino acids and pyrrolizidine
 alkaloids (PA) in phloem exudates), performance of a specialist and a
 generalist aphid Biomass and chemistry were measured at 2 sampling times:
 6 and 13 weeks after transplanting in the conditioned
 soils
DOI: 10.5061/dryad.5j3p272
title: Data from: An unfavorable body composition is common in early arthritis patients: a case control study

description: Background. An unfavorable body composition is often present in chronic
 arthritis patients. This unfavorable composition is a loss of muscle mass,
 with a stable or increased (abdominal) fat mass. Since it is unknown when
 this unfavorable composition develops, we compared body composition in
 disease-modifying antirheumatic drugs (DMARD)-naive early arthritis
 patients with non-arthritis controls and explored the association, in
 early arthritis patients, with disease activity and traditional
 cardiovascular risk factors. Methods. 317 consecutive early arthritis
 patients (84% rheumatoid arthritis according to 2010 ACR/EULAR criteria)
 and 1268 age-/gender-/ethnicity-matched non-arthritis controls underwent a
 Dual-energy X-ray absorptiometry scan to assess fat percentage, fat mass
 index, fat mass distribution and appendicular lean (muscle) mass index.
 Additionally, disease activity, health assessment questionnaire (HAQ),
 acute phase proteins, lipid profile and blood pressure were evaluated.
 Results. Loss of muscle mass (corrected for age suspected muscle mass) was
 4-5 times more common in early arthritis patients, with a significantly
 lower mean appendicular lean mass index (females 6% and males 7% lower,
 p&lt;0.01). Patients had more fat distributed to the trunk (females
 p&lt;0.01, males p=0.07) and females had a 4% higher mean fat mass
 index (p&lt;0.01). An unfavorable body composition was associated with
 a higher blood pressure and an atherogenic lipid profile. There was no
 relationship with disease activity, HAQ or acute phase proteins.
 Conclusion. Loss of muscle mass is 4-5 times more common in early
 arthritis patients, and is in early arthritis patients associated with a
 higher blood pressure and an atherogenic lipid profile. Therefore,
 cardiovascular risk is already increased at the clinical onset of
 arthritis making cardiovascular risk management necessary in early
 arthritis patients.
description: Early arthritis
 patients, DEXA data for publishing 2018
DOI: 10.5061/dryad.7pr554s8
title: Data from: Did pollination shifts drive diversification in southern African Gladiolus? Evaluating the model of pollinator-driven speciation

description: The pollinator-driven ecological speciation model has frequently been
 invoked to explain plant richness in biodiversity hotspots. Here, we test
 the hypothesis that high species diversity in southern Africa, one of the
 world's most floristically rich regions, has primarily been driven by
 ecological shifts in pollination systems, by focusing on Gladiolus (260
 species), a flagship example of a clade with diverse pollination biology.
 We use phylogenetic methods to estimate rates of transitions between the
 seven highly specialized pollination strategies in Gladiolus. We find that
 pollination systems have evolved multiple times and that some pollination
 strategies arose by a variety of evolutionary pathways. Pollination shifts
 account for up to a third of all lineage splitting events in the genus,
 providing partial support for the pollinator-driven speciation model.
 Transitions from the ancestral pollination mode to derived systems have
 also resulted in increased rates of diversification, suggesting that
 certain pollination systems may speed up speciation processes,
 independently of pollination shifts per se. This study confirms that
 frequent pollination shifts have played a role in driving high phenotypic
 and species diversity, but suggests that additional factors need to be
 invoked in order to account for the spectacular diversification in
 southern African Gladiolus.
description: Gladiolus_treeMaximum-likelihood estimate of phylogeny obtained in RaxML v.7.2.1 (Stamatakis 2006), based on the re-analysis of the Gladiolus matrix of Valente et al. 2011 (matK, psbA-trnH, trnS-trnG, rpl32-trnL, trnQ-rps16) with indel character information added.TablePollination systems of the 148 species of Gladiolus sampled.
DOI: 10.15468/dl.fvygaq
title: Occurrence Download

description: A dataset containing 9394 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Otoliths Reference Collection. CBMR-AFORO (ICM-CSIC)"
 ]
}

 The dataset includes 9394 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000677-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.nf4bm
title: Data from: Heterogeneous patterns of abundance of epigeic arthropod taxa along a major elevation gradient

description: Species diversity is the variable most commonly studied in recent
 ecological research. Ecological processes, however, are driven by
 individuals and affected by their abundances. Understanding the variation
 in animal abundances along climatic gradients is important for predicting
 changes in ecosystem processes under global warming. High abundances make
 arthropods, despite their small body sizes, important actors in food webs,
 yet abundance distributions of major arthropod taxa along climatic
 gradients remain poorly documented. We sampled arthropod assemblages in
 disturbed and undisturbed vegetation types along an elevational gradient
 of 860–4550 m asl on the southern slopes of Mt. Kilimanjaro, Tanzania. In
 our analysis, we focused on 13 taxa of arthropods that represented three
 major functional groups: predators, herbivores, and decomposers. Abundance
 patterns were unimodal for most of the taxa and functional groups,
 including decomposer arthropods, and most of them peaked at low elevations
 in lower montane forest. When we assigned beetles to functional groups,
 however, decomposer beetle abundances declined almost linearly, and
 abundances of predator beetles (ca. 2400 m asl) and herbivore beetles (ca.
 3000 m asl, undisturbed vegetation) peaked at higher elevations and
 exhibited unimodal patterns. Temperature, not primary productivity, was
 the best predictor of abundance for most of the taxa and groups.
 Disturbance was only of minor importance. Our results revealed different
 trends in the response of arthropod abundance along the elevational
 gradient that depended on the level of taxonomic and functional
 resolution. This highlights the need for more comparisons of different
 taxa along the same climatic gradients.
description: Roeder_et_al_Biotropica_Kilimanjaro_arthropod_abundances_data_and_meta-dataRaw data of arthropod abundances per trap for pitfall traps. Taxonomical resolution: order to family (depending on taxon).Roeder_et_al_arthropod_abundances_data_and_meta-data.xlsx
DOI: 10.5061/dryad.2sq12
title: Data from: Simultaneous determination of underivatized vitamin B1 and B6 in whole blood by Reversed Phase Ultra High Performance Liquid Chromatography Tandem Mass spectrometry

description: Background: Vitamin B1 (thiamine-diphosphate) and B6
 (pyridoxal-5’phosphate) are micronutrients. Analysis of these
 micronutrients is important to diagnose potential deficiency which often
 occurs in elderly people due to malnutrition, in severe alcoholism and in
 gastrointestinal compromise due to bypass surgery or disease. Existing
 High Performance Liquid Chromatography (HPLC) based methods include the
 need for derivatization and long analysis time. We developed an Ultra High
 Performance Liquid Chromatography Tandem Mass spectrometry (UHPLC-MS/MS)
 assay with internal standards for simultaneous measurement of
 underivatized thiamine-diphosphate and pyridoxal-5’phosphate without use
 of ion pairing reagent. Methods: Whole blood, deproteinized with
 perchloric acid, containing deuterium labelled internal standards
 thiamine-diphosphate(thiazole-methyl-D3) and
 pyridoxal-5’phosphate(methyl-D3), was analyzed by UHPLC-MS/MS. The method
 was validated for imprecision, linearity, recovery and limit of
 quantification. Alternate (quantitative) method comparisons of the new
 versus currently used routine HPLC methods were established with Deming
 regression. Results: Thiamine-diphosphate and pyridoxal-5’phosphate were
 measured within 2.5 minutes instrumental run time. Limits of detection
 were 2.8 nmol/L and 7.8 nmol/L for thiamine-diphosphate and
 pyridoxal-5’phosphate respectively. Limit of quantification was 9.4 nmol/L
 for thiamine-diphosphate and 25.9 nmol/L for pyridoxal-5’phosphate. The
 total imprecision ranged from 3.5-7.7 % for thiamine-diphosphate (44-157
 nmol/L) and 6.0-10.4 % for pyridoxal-5’phosphate (30-130 nmol/L).
 Extraction recoveries were 101-102% ± 2.5 % (thiamine-diphosphate) and
 98-100 % ± 5 % (pyridoxal-5’phosphate). Deming regression yielded slopes
 of 0.926 and 0.990 in patient samples (n=282) and national proficiency
 testing samples (n=12) respectively, intercepts of +3.5 and +3 for
 thiamine-diphosphate (n=282 and n=12) and slopes of 1.04 and 0.84,
 intercepts of -2.9 and +20 for pyridoxal-5’phosphate (n=376 and n=12).
 Conclusion: The described UHPLC-MS/MS method allows simultaneous
 determination of underivatized thiamine-diphosphate and
 pyridoxal-5’phosphate in whole blood without intensive sample preparation.
description: rawdata
 excel
DOI: 10.5061/dryad.15264
title: Data from: Chronic neonicotinoid pesticide exposure and parasite stress differentially affects learning in honeybees and bumblebees

description: Learning and memory are crucial functions which enable insect pollinators
 to efficiently locate and extract floral rewards. Exposure to pesticides
 or infection by parasites may cause subtle but ecologically important
 changes in cognitive functions of pollinators. The potential interactive
 effects of these stressors on learning and memory have not yet been
 explored. Furthermore, sensitivity to stressors may differ between
 species, but few studies have compared responses in different species.
 Here, we show that chronic exposure to field-realistic levels of the
 neonicotinoid clothianidin impaired olfactory learning acquisition in
 honeybees, leading to potential impacts on colony fitness, but not in
 bumblebees. Infection by the microsporidian parasite Nosema ceranae
 slightly impaired learning in honeybees, but no interactive effects were
 observed. Nosema did not infect bumblebees (3% infection success).
 Nevertheless, Nosema treated bumblebees had a slightly lower rate of
 learning than controls, but faster learning in combination with
 neonicotinoid exposure. This highlights the potential for complex
 interactive effects of stressors on learning. Our results underline that
 one cannot readily extrapolate findings from one bee species to others.
 This has important implications for regulatory risk assessments which
 generally use honeybees as a model for all bees.
description: Data_PER_LearningAcquisitionProboscis extension response (PER) data of 10 CS-US trials for honeybees and bumblebees.Data_PER_Responsiveness_UnrewardedAndMemoryTestResponsiveness to sugar stimulus test, unrewarded test and memory test data for honeybees and bumblebees.Data_SugarConsumptionCollectionSugar water consumption/collection data for honeybees and bumblebees.