cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.84nj034
title: Data from: Randomized study of the impact of a therapeutic education program on patients suffering from chronic low-back pain who are treated with transcutaneous electrical nerve stimulation

description: Background: Transcutaneous electrical nerve stimulation (TENS) is often
 used for the treatment of low-back pain (LBP). However, its effectiveness
 is controversial. Objective: To determine the efficacy of TENS in the
 treatment LBP when associated to a therapeutic education program (TEP).
 Design: Open randomized monocentric study. Setting: University hospital
 between 2010 and 2014. Patients: A total of 97 patients suffering from
 LBP. Interventions: Routine care (TENS group) or routine care plus a
 therapeutic education program (TENS-TEP group) based on consultation
 support by a pain resource nurse Main outcome measures: EIFEL and Dallas
 Pain Questionnaire scores. Results: Twenty-two patients (44%) were still
 assessable at the end-of-study visit, whereas 33 (70%) were assessable at
 the same time point in the TENS-TEP group (P = 0.013). The EIFEL score and
 the Dallas score had a similar evolution over time between groups (p =
 0.18 and p = 0.50 respectively). Similarly, there were no significant
 differences between the groups with respect to resting pain scores (p =
 0.94 for back pain and p = 0.16 for leg pain) and movement pain scores (p
 = 0.52 for back pain and p = 0.56 for leg pain). At Month 6, there was no
 significant difference between the groups (p = 0.85) with regard to
 analgesics and social impact. Two patients presented a serious adverse
 event during the study (one in each group) but non-attributable to the
 treatment studied. Conclusion: This study does not support the use of TENS
 in the treatment of patients with chronic LBP even though patients
 benefited from a therapeutic education program by a pain resource nurse.
 However, the higher number of premature withdrawals in the TENS group may
 be due to early withdrawal of patients who did not experience improvement
 of their symptoms.
description: Data
 base
DOI: 10.5061/dryad.hj20g
title: Data from: An integrative approach to understanding the evolution and diversity of Copiapoa (Cactaceae), a threatened endemic Chilean genus from the Atacama Desert

description: PREMISE OF THE STUDY: Species of the endemic Chilean cactus genus Copiapoa
 have cylindrical or (sub)globose stems that are solitary or form (large)
 clusters and typically yellow flowers. Many species are threatened with
 extinction. Despite being icons of the Atacama Desert and well loved by
 cactus enthusiasts, the evolution and diversity of Copiapoa has not yet
 been studied using a molecular approach. METHODS: Sequence data of three
 plastid DNA markers (rpl32-trnL, trnH-psbA, ycf1) of 39 Copiapoa taxa were
 analyzed using maximum likelihood and Bayesian inference approaches.
 Species distributions were modeled based on geo-referenced localities and
 climatic data. Evolution of character states of four characters (root
 morphology, stem branching, stem shape, and stem diameter) as well as
 ancestral areas were reconstructed using a Bayesian and maximum likelihood
 framework, respectively. KEY RESULTS: Clades of species are revealed.
 Though 32 morphologically defined species can be recognized, genetic
 diversity between some species and infraspecific taxa is too low to
 delimit their boundaries using plastid DNA markers. Recovered
 relationships are often supported by morphological and biogeographical
 patterns. The origin of Copiapoa likely lies between southern Peru and the
 extreme north of Chile. The Copiapó Valley limited colonization between
 two biogeographical areas. CONCLUSIONS: Copiapoa is here defined to
 include 32 species and five heterotypic subspecies. Thirty species are
 classified into four sections and two subsections, while two species
 remain unplaced. A better understanding of evolution and diversity of
 Copiapoa will allow allocating conservation resources to the most
 threatened lineages and focusing conservation action on real biodiversity.
description: Full sampling alignment
 Copiapoa phylogenyFull sampling alignment
 including 109 sequences of 39 Copiapoa taxa and selected outgroup species.
 Often multiple accessions per Copiapoa taxon are included. Three cpDNA
 markers: ycf1 (coding), trnH-psbA & trnL-rpl32
 (non-coding).ycf1_trnHpsbA_trnLrpl32_full.nexReduced sampling alignment Copiapoa phylogenyReduced sampling alignment including one individual per Copiapoa taxon and a reduced number of outgroup species. Three cpDNA markers: ycf1 (coding), trnH-psbA & trnL-rpl32 (non-coding).ycf1_trnHpsbA_trnLrpl32_reduced.nex
DOI: 10.5061/dryad.gf87q
title: Data from: Soil conditioning affects interactions between native and invasive exotic perennials of semi-natural grasslands

description: 1. Semi–natural perennial grasslands are of increasing importance as
 components of multifunctional agroecosystems, combining biomass production
 with provision of other ecosystem services. Soil legacies from previous
 land use or exotic species can hinder their establishment, but might be
 overcome through a multi–stage successional strategy, whereby certain
 species are used to facilitate native grassland species establishment. We
 tested this strategy via a feedback experiment examining soil conditioning
 effects on interference interactions between native and exotic species. 2.
 Soils in a former maize–soybean production field in Minnesota, USA, were
 conditioned for three years with native or invasive exotic perennials or a
 maize–soybean crop rotation. Nitrogen (N) fertilisation was an additional
 treatment in field plots. In a greenhouse, native and invasive exotic
 perennial grassland seedlings were grown on these soils, in monoculture
 and in native–exotic species pairs, with and without N fertilisation. The
 impact of soil conditioning and field and greenhouse N fertilisation on
 interactions between native and exotic seedlings in mixture was
 determined. 3. Neighbouring plants suppressed biomass production in all
 native and exotic species. The maize–soybean rotation left a soil legacy
 that enhanced suppression of native species when grown with exotic
 species, while exotic species suffered no such disadvantage. 4. The strong
 and specific disadvantage to native species of maize–soybean soils
 decreased with greenhouse N fertilisation, but remained significant, while
 field N addition did not alter this effect. 5. Synthesis and applications.
 We find that the negative soil legacy of the maize–soybean rotation for
 native plant performance in interaction with exotics was greatly
 diminished in soils conditioned by native or exotic perennial species,
 irrespective of nitrogen addition. This highlights the potential value of
 perennial species in conversion from row–crop agriculture to grasslands,
 because all perennial species alleviated the enhanced suppression of
 natives observed on maize–soybean soils. We did not find strong evidence
 that these perennial species were capable of specifically facilitating
 native species over exotics, but a broader range of species should be
 evaluated.
description: Data from Vink SN et al
 Soil conditioning affects interactions between native and invasive exotic
 perennials of semi-natural grasslandsPlant height, biomass
 and calculated relative interaction index (based on biomass data) for each
 treatment combination. Descriptions are provided as comments in the column
 header of the file.
DOI: 10.5061/dryad.rg098gq
title: Data from: Local prey community composition and genetic distance predict venom divergence among populations of the northern Pacific rattlesnake (Crotalus oreganus)

description: Identifying the environmental correlates of divergence in functional
 traits between populations can provide insights into the evolutionary
 mechanisms that generate local adaptation. Here, we assess patterns of
 population differentiation in expressed venom proteins in Northern Pacific
 rattlesnakes (Crotalus oreganus) from 13 locations across California. We
 evaluate the relative importance of major biotic (prey species community
 composition), abiotic (temperature, precipitation, and elevation) and
 genetic factors (genetic distance based on RADseq loci) as correlates of
 population divergence in venom phenotypes. We found that over half of the
 variation in venom composition is associated with among-population
 differentiation for genetic and environmental variables, and that this
 variation occurred along axes defining previously observed functional
 trade-offs between venom proteins that have neurotoxic, myotoxic and
 hemorrhagic effects. Surprisingly, genetic differentiation among
 populations was the best predictor of venom divergence, accounting for 46%
 of overall variation, whereas differences in prey community composition
 and abiotic factors explained smaller amounts of variation (23% and 19%,
 respectively). The association between genetic differentiation and venom
 composition could be due to an isolation by distance effect or, more
 likely it may reflect an isolation-by-environment effect where selection
 against recent migrants is strong, producing a correlation between neutral
 genetic differentiation and venom differentiation. Our findings suggest
 that even coarse estimates of prey community composition can be useful in
 understanding the selection pressures acting on patterns of venom protein
 expression. Additionally, our results suggest that factors other than
 adaptation to spatial variation in prey need to be considered when
 explaining population divergence in venom.
description: Venom HPLC Peak
 AreasThe percent area of each
 of 34 high pressure liquid chromatography (HPLC) peaks for each snake used
 in the study. Peaks locations are identified in figure 1 of the associated
 manuscript.Venom-Peak-Areas.xlsxMammals_Presence_Absence_MatrixPresences (1) and absences (0) for each study locality, as determined by range map overlap for California small mammal species available as prey to Crotalus oreganus.Bioclim-Variables_by-Site19 WorldClim BioClim variables and elevation of each rattlesnake population locality.SnakeDataSize, sex, identification number, and clade/population membership of the rattlesnakes used in the study.StructureInput_popflagSTRUCTURE input file created from loci obtained from Crotalus oreganus used in this study. Loci were obtained using double-digest restriction-site-associated DNA sequencing (RAD-seq). This file was used to run the Bayesian clustering approach of STRUCTURE and for calculation of pairwise population F-statistics.
DOI: 10.5061/dryad.6p1c4
title: Data from: Range-wide phenotypic and genetic differentiation in wild sunflower

description: Background: Divergent phenotypes and genotypes are key signals for
 identifying the targets of natural selection in locally adapted
 populations. Here, we used a combination of common garden phenotyping for
 a variety of growth, plant architecture, and seed traits, along with
 single-nucleotide polymorphism (SNP) genotyping to characterize range-wide
 patterns of diversity in 15 populations of wild sunflower (Helianthus
 annuus L.) sampled along a latitudinal gradient in central North America.
 We analyzed geographic patterns of phenotypic diversity, quantified levels
 of within-population SNP diversity, and also determined the extent of
 population structure across the range of this species. We then used these
 data to identify significantly over-differentiated loci as indicators of
 genomic regions that likely contribute to local adaptation. Results:
 Traits including flowering time, plant height, and seed oil composition
 (i.e., percentage of saturated fatty acids) were significantly correlated
 with latitude, and thus differentiated northern vs. southern populations.
 Average pairwise FST was found to be 0.21, and a STRUCTURE analysis
 identified two significant clusters that largely separated northern and
 southern individuals. The significant FST outliers included a SNP in
 HaFT2, a flowering time gene that has been previously shown to co-localize
 with flowering time QTL, and which exhibits a known cline in gene
 expression. Conclusions: Latitudinal differentiation in both phenotypic
 traits and SNP allele frequencies is observed across wild sunflower
 populations in central North America. Such differentiation may play an
 important adaptive role across the range of this species, and could
 facilitate adaptation to a changing climate.
description: Genotyping data from 246
 lociThe file contains the
 SNP genotyping data for all loci used in McAssey et al., 2016 BMC Plant
 Biology. The first tab contains the data where rows contain individuals
 and every two columns represent the diploid genotype. The second tab
 contains the identity of the polymorphic nucleotides at each locus. The
 third tab contains the marker names as described in Bachlava et al., 2012
 PLoS ONE.10_16_16_Genotype_Data.xlsx
DOI: 10.5061/dryad.gf8m3k8v
title: Data from: Gynodioecy in structured populations: understanding fine-scale sex ratio variation in Beta vulgaris ssp. maritima

description: Natural selection, random processes, and gene flow are known to generate
 sex ratio variations among sexually polymorphic plant populations. In
 gynodioecious species, in which hermaphrodites and females coexist, the
 relative effect of these processes on the maintenance of sex polymorphism
 is still up for debate. The aim of this study was to document sex ratio
 and cytonuclear genetic variation at a very local scale in wind-pollinated
 gynodioecious Beta vulgaris ssp. maritima, and attempt to elucidate which
 processes explained the observed variation. The study sites were
 characterized by geographically distinct patches of individuals and
 appeared to be dynamic entities, with recurrent establishment of distinct
 haplotypes through independent founder events. Along with substantial
 variation in sex ratio and unexpectedly low gene flow within study sites,
 our results showed a high genetic differentiation among a mosaic of
 genetically distinct demes, with isolation by distance or abrupt genetic
 discontinuities taking place within a few tens of meters. Overall, random
 founder events with restricted gene flow could be primary determinants of
 sex structure, by promoting the clumping of sex-determining genes. Such
 high levels of sex structure provide a landscape for differential
 selection acting on sex-determining genes, which could modify the
 conditions of maintenance of gynodioecy in structured populations.
description: Spatial coordinates,
 sexual phenotypes and genotypes for Beta vulgaris ssp. maritima
 individuals collected in two wild populationsData_MEC_11_0787.txt
DOI: 10.5061/dryad.5m2q0
title: Data from: Is there still a French eating model? A taxonomy of eating behaviors in adults living in the Paris metropolitan area in 2010

description: Background: Meal times in France still represent an important moment in
 everyday life. The model of three rigorously synchronized meals is still
 followed by a majority of people, while meal frequencies have flattened in
 other European or North-American countries. We aimed to examine the
 “French model” of eating behavior by identifying and characterizing
 distinct meal patterns. Methods: Analyses were based on data from the SIRS
 cohort, a representative survey of the adult population in the Paris area.
 A clustering algorithm was applied to meal variables (number, time,
 location, with whom the meal is usually shared and activities associated
 with meals). Regression models were used to investigate associations
 between patterns and socio-demographic, social environment and perceived
 food quality variables. Results: Five different patterns were identified
 among 2994 participants. The first three types (prevalence 33%, 17% and
 24%) followed a three-meal pattern, with differences in locations and
 social interactions mainly related to time constraints and age. More
 marked differences were observed in the remaining two types. In the fourth
 type (prevalence 13%), individuals ate one or two meals per day, often
 with an irregular schedule, at home and in front of the television. They
 frequently were unemployed and had lower income. Breakfast skipping,
 increased snacking and a low adherence to dietary guidelines suggested
 that this behavior might have health consequences. In the fifth type
 (12%), people also ate two meals or less per day, possibly with the same
 consequences on food quality. However, meals were often taken outside the
 home, in social settings, and individuals following this pattern were
 typically active, integrated, young people, suggesting that this pattern
 might be an adaptation to a modern urban lifestyle. Conclusions: While a
 majority of the population still follows the three-meal pattern, our
 analysis distinguished two other eating patterns associated with specific
 sociological profiles.
description: Main
 dataThis data file contains
 all variables used for the analyses reported in our article published in
 PLOS One. It is a CSV file that contains 48 variables for 2994 subjects.
 Data originate from from the 2010 wave of the SIRS cohort, a
 representative socio-epidemiological survey of the French-speaking adult
 (≥18) population conducted since 2005 in the Paris metropolitan area
 (population 6.5 million). Further description of the data is available in
 the ReadMe file.data.csv
DOI: 10.5061/dryad.vq4j4
title: Data from: Phylogeographic pattern of range expansion provides evidence for cryptic species lineages in Silene nutans in Western Europe

description: As a result of recent or past evolutionary processes, a single species
 might consist of distinct Evolutionary Significant Units (ESUs), even
 corresponding to cryptic species. Determining the underlying mechanisms of
 range shifts and the processes at work in the build-up of divergent ESUs
 requires elucidating the factors that contribute to population genetic
 divergence across a species’ range. We investigated the large-scale
 patterns of genetic structure in the perennial herbaceous plant species
 Silene nutans (Caryophyllaceae) in Western Europe. We sampled and
 genotyped 111 populations using 13 nuclear microsatellite loci and 6
 plastid single-nucleotide polymorphisms. Broad-scale spatial population
 genetic structure was examined using Bayesian clustering, spatial
 multivariate analyses and measures of hierarchical genetic
 differentiation. The genotypic structure of S. nutans was typical of a
 predominantly allogamous mating system. We also identified plastid
 lineages with no intra-population polymorphism, mirroring two genetically
 differentiated nuclear lineages. No evidence of admixture was found.
 Spatial trends in genetic diversity further suggested independent
 leading-edge expansion associated with founding events and subsequent
 genetic erosion. Overall, our findings suggested speciation processes in
 S. nutans and highlighted striking patterns of distinct stepwise
 recolonisation of Western Europe shaped by Quaternary climate
 oscillations. Two main potential ESUs can be defined in Western Europe,
 corresponding to Eastern and Western nuclear-plastid lineages. In situ
 preservation of populations and genetic rescue implying ex situ
 conservation techniques should take the lineage identity into account.
 This is particularly true in Great Britain, northern France and Belgium,
 where S. nutans is rare and where distinct lineages co-occur in close
 contact.
description: Dryad-MS-HDY-15-OR0093RR-Coordinates/GenotypesCoordinates of sample locations and plastid and nuclear genetic dataDryad-MS-HDY-15-OR0093RR.xlsx
DOI: 10.5061/dryad.41vh5
title: Data from: Burning for biodiversity: highly resilient ant communities respond only to strongly contrasting fire regimes in Australia’s seasonal tropics

description: 1. According to the pyrodiversity paradigm, a wide range of fire regimes
 is required to maintain biodiversity in fire-prone landscapes. However,
 the requisite level of pyrodiversity has seldom been tested and may
 actually be very low. 2. Here, we examine the sensitivity of tropical
 savanna ants to variation in fire regimes using results from a long-term
 fire experiment near Darwin, Australia. Six experimental fire regimes,
 with varying fire frequency and seasonality, have been applied to 18
 one-ha plots in three replicated blocks since 2004, with ants sampled
 prior to experimental burning and then annually after up to 2009. Our
 primary focus is on the extent to which different patterns of ant richness
 and composition are associated with each of the six treatment regimes, or
 whether there is such high overlap that differences only become apparent
 when experimental treatments are grouped to provide strongly contrasting
 fire regimes. 3. When treating each of the six fire treatments separately,
 we were unable to detect a significant influence of fire on any ant
 community response variable. We were only able to detect significant ant
 responses when we grouped the experimental treatments into two contrasting
 fire frequency classes, low (burnt at most once over the 5 years) vs. high
 (burnt every 1 or 2 years). Even then, these responses were only evident
 after 3 years of fire treatment. 4. Our findings demonstrate that ant
 communities have very high resilience in relation to fire, with
 differences evident only between strongly contrasting regimes. Such
 resilience appears to be characteristic of savanna ants throughout the
 world. 5. Synthesis and applications. A large range of finely tuned fire
 regimes is unlikely to promote regional ant diversity. Rather, only very
 limited pyrodiversity (a combination of frequently and infrequently burnt
 areas) would appear to be sufficient for maintaining diversity at a
 landscape scale. It is important that fire management for biodiversity
 conservation focuses on the demonstrated requirements of target species,
 rather than be based on an assumption that ‘pyrodiversity begets
 biodiversity’.
description: Andersen archived
 dataAbundance of each ant
 species at each of the 18 experimental fire plots at the Territory
 Wildlife Park for each sampling period (2003-2009). Data for each sampling
 period are provided on separate pages.