cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pv805
title: Data from: Risk factors for ectopic pregnancy in Germany: a retrospective study of 100,197 patients

description: Aim: The goal of this study was to identify potential risk factors for
 ectopic pregnancy in women followed in German gynecological practices.
 Methods: The present study included pregnant women diagnosed with ectopic
 pregnancy and pregnant women without ectopic pregnancy followed in 262
 gynecological practices between January 2012 and December 2016. The
 effects of demographic and clinical variables on the risk of developing
 ectopic pregnancy were estimated using a multivariate logistic regression
 model. Results: This study included 3,003 women with ectopic pregnancy and
 97,194 women without ectopic pregnancy. The mean age was 31.4 years
 (SD=5.9 years) in ectopic pregnancy patients and 31.1 years (SD=5.6 years)
 in non-ectopic pregnancy patients. Women aged 36–40 (OR=1.12) and 41–45
 years (OR=1.46) were at a higher risk of ectopic pregnancy than women aged
 31–35 years. Prior ectopic pregnancy was strongly associated with a risk
 of recurring ectopic pregnancy (OR=8.17). Prior genital surgery (OR=2.67),
 endometriosis (OR=1.51), and eight other gynecological diseases were also
 positively associated with ectopic pregnancy (ORs ranging from 1.19 to
 2.06). Finally, there was a 1.80-fold increase in women previously
 diagnosed with psychiatric disorders. Conclusions: Prior ectopic pregnancy
 and prior genital surgery were strongly associated with ectopic pregnancy
 in women followed in German gynecological practices. Psychiatric diseases
 had an additional impact on the risk of ectopic pregnancy.
description: ectopic
DOI: 10.5061/dryad.vh36n
title: Data from: Para-aminosalicylic acid acts as an alternative substrate of folate metabolism in Mycobacterium tuberculosis

description: Folate biosynthesis is an established anti-infective target, and the
 antifolate para-aminosalicylic acid (PAS) was one of the first
 anti-infectives introduced into clinical practice on the basis of
 target-based drug discovery. Fifty years later, PAS continues to be used
 to treat tuberculosis. PAS is assumed to inhibit dihydropteroate synthase
 (DHPS) in Mycobacterium tuberculosis by mimicking the substrate
 p-aminobenzoate (PABA). However, we found that sulfonamide inhibitors of
 DHPS inhibited growth of M. tuberculosis only weakly because of their
 intracellular metabolism. In contrast, PAS served as a replacement
 substrate for DHPS. Products of PAS metabolism at this and subsequent
 steps in folate metabolism inhibited those enzymes, competing with their
 substrates. PAS is thus a prodrug that blocks growth of M. tuberculosis
 when its active forms are generated by enzymes in the pathway they poison.
description: Fig1AMicrosoft excel file
 containing raw data for Fig1a.Fig1BMicrosoft excel file
 containing raw data for Fig1B.Fig3AMicrosoft excel file
 containing raw data for Fig3A.Fig3B_AICARMicrosoft excel file containing raw data for Fig3B AICAR.Fig3B_MethionineMicrosoft excel file containing raw data for Fig3B Methionine.Fig3B_HomocysteineMicrosoft excel file containing raw data for Fig3B Homocysteine.Fig3B_GlycineMicrosoft excel file containing raw data for Fig3B Glycine.Fig3B_SerineMicrosoft excel file containing raw data for Fig3B Serine.Fig3B_dUMPFig3B_dUMP.xls: Microsoft excel file containing raw data for Fig3B dUMP.Fig3CMicrosoft excel file containing raw data for Fig 3C.FigS2Microsoft excel file containing raw data for Fig S2.
DOI: 10.5061/dryad.8606
title: Data from: Evidence of neutral and adaptive genetic divergence between European trout populations sampled along altitudinal gradients

description: Species with a wide geographical distribution are often composed of
 distinct subgroups which may be adapted to their local environment.
 European trout (Salmo trutta species complex) provide an example of such a
 complex consisting of several genetically and ecologically distinct forms.
 However, trout populations are strongly influenced by human activities,
 and it is unclear to what extent neutral and adaptive genetic differences
 have persisted. We sampled 30 Swiss trout populations from heterogeneous
 environments along replicated altitudinal gradients in three major
 European drainages. More than 850 individuals were genotyped at 18
 microsatellite loci which included loci diagnostic for evolutionary
 lineages and candidate markers associated with temperature tolerance,
 reproductive timing and immune defence. We find that the phylogeographic
 structure of Swiss trout populations has not been completely erased by
 stocking. Distinct genetic clusters corresponding to the different
 drainages could be identified, although nonindigenous alleles were clearly
 present, especially in the two Mediterranean drainages. We also still
 detected neutral genetic differentiation within rivers which was often
 associated with the geographical distance between populations. Five loci
 showed evidence of divergent selection between populations with several
 drainage-specific patterns. Lineage-diagnostic markers, a marker linked to
 a quantitative trait locus for upper temperature tolerance in other
 salmonids and a marker linked to the major histocompatibility class I gene
 were implicated in local adaptation and some patterns were associated with
 altitude. In contrast, tentative evidence suggests a signal of balancing
 selection at a second immune relevant gene (TAP2). Our results confirm the
 persistence of both neutral and potentially adaptive genetic differences
 between trout populations in the face of massive human-mediated dispersal.
description: KellerEtAl_MicrosatelliteGenotypes
DOI: 10.5061/dryad.sm819
title: Data from: Plumage color manipulation has no effect on social dominance or fitness in zebra finches

description: Colourful plumage ornaments may evolve because they play a role in mate
 choice or in intrasexual competition, acting as signals of species
 identity or of individual quality. The zebra finch (Taeniopygia guttata)
 is a model organism for the study of mate choice and its colourful plumage
 ornaments are thought to be used in both of these contexts. Numerous
 genetic colour variants have been described for this species, but they are
 rare in the wild. This raises the question whether discrimination against
 deviant phenotypes maintains the species’ uniform plumage colour (rare
 mate disadvantage). Further, comparison to closely related species
 suggests that the lack of colourful ornaments in female zebra finches is a
 derived condition. Male preferences for less ornamented females may have
 led to sexual dichromatism in the zebra finch. Here, we test the role of
 plumage ornaments experimentally by altering male and female colouration
 to mimic two types of naturally occurring genetic colour variants. We
 estimated effects on social dominance and reproductive success in large
 breeding aviaries in one domesticated and two recently wild-derived
 populations. Hypotheses, methods and analyses were preregistered to ensure
 maximal objectivity of the results presented. Despite a fairly drastic
 manipulation and a powerful experimental design, we found no effect of the
 treatment on social dominance or on reproductive success. Our results
 suggest that mate choice is not the mechanism that maintains homogeneity
 of zebra finch plumage colouration, or that can explain the loss of
 ornaments in females.
description: Agression
 observationsIndividual
 data
DOI: 10.5061/dryad.m6k89833
title: Data from: Natural selection in the water: freshwater invasion and adaptation by water color in the Amazonian pufferfish

description: Natural selection and ecological adaptation are ultimately responsible for
 much of the origin of biodiversity. Yet the identification of divergent
 natural selection has been hindered by the spatial complexity of natural
 systems, the difficulty in identifying genes under selection and their
 relationship to environment, and the confounding genomic effects of time.
 Here we employed genome scans, population genetics and sequence-based
 phylogeographic methods to identify divergent natural selection on
 population boundaries in a freshwater invader, the Amazonian pufferfish,
 Colomesus asellus. We sampled extensively across markedly different
 hydrochemical settings in the Amazon Basin and use ‘water color’ to test
 for ecological isolation. We distinguish the relative contribution of
 natural selection across hydrochemical gradients from biogeographic
 history in the origin and maintenance of population boundaries within a
 single species and across a complex ecosystem. We show that spatially
 distinct population structure generated by multiple forces (i.e. water
 color and vicariant biogeographic history) can be identified if the
 confounding effects of genetic drift have not accumulated between
 selective populations. Our findings have repercussions for studies aimed
 at identifying engines of biodiversity and assessing their temporal
 progression in understudied and ecologically complex tropical ecosystems.
description: AFLP_PufferAFLP profiles for 290 Colomesus asellus individuals collected in the Amazon Basin, Brazil. File includes: individual ID, site label, latitude, longitude and presence absence data for 460 AFLP loci. Missing data is denoted by a space.
DOI: 10.5061/dryad.sv181
title: Data from: Radial changes in wood specific gravity of tropical trees: inter- and intra-specific variation during secondary succession

description: Variation in wood specific gravity (WSG) within and across species of
 tropical trees is poorly studied in relation to vegetation change during
 tropical forest succession. We investigated WSG of 91 species in eight
 long-term plots along a successional chronosequence in northeastern Costa
 Rica. Radial changes in WSG were described by the rate of change (slope)
 along the stem radius. Significant radial changes were found in 42 of 74
 species, with 37 species exhibiting increases from inner to outer wood,
 and 5 exhibiting decreases. Radial increases were commonly observed in
 species with inner WSG below 0.5, whereas radial decreases were observed
 in species with inner WSG above 0.7. Wood specific gravity weighted by
 cross-sectional area (wWSG) varied four-fold among species. Species
 classified as second-growth specialists had lower wWSG, lower inner and
 outer WSG, and higher slopes than old-growth specialists; successional
 generalists showed intermediate trait values. Among 18 species sampled in
 both second- and old-growth forests, 4 species (22%) showed significant
 variation in wWSG between forest types. Of 33 widely sampled species,
 seven species (21%) showed a significant effect of stem diameter on wWSG.
 Second-growth plots had lower stand-level wWSG and more pronounced radial
 increases than old-growth plots. Individual tree biomass for species with
 radial increases and low WSG was substantially underestimated when based
 on unweighted WSG compared to wWSG. Wood specific gravity varied with
 successional stage at multiple levels: within species, among successional
 specialist groups, and across plots of varying ages. Radial increases in
 WSG are common among trees in early and intermediate stages of tropical
 forest succession. This trait may confer growth advantages early in
 succession and increased resistance to physical or biotic damage during
 later successional stages.
description: Individual Stem
 DataIncludes records of each
 stem cored for the study including basic measurements of mass and volume.
 Calculations of wood specific gravity and slope included for each
 stem.complete.individual.data.txt
DOI: 10.5061/dryad.nq816
title: Data from: Water stress strengthens mutualism among ants, trees, and scale insects

description: Abiotic environmental variables strongly affect the outcomes of species
 interactions. For example, mutualistic interactions between species are
 often stronger when resources are limited. The effect might be indirect:
 water stress on plants can lead to carbon stress, which could alter
 carbon-mediated plant mutualisms. In mutualistic ant–plant symbioses,
 plants host ant colonies that defend them against herbivores. Here we show
 that the partners' investments in a widespread ant–plant symbiosis
 increase with water stress across 26 sites along a Mesoamerican
 precipitation gradient. At lower precipitation levels, Cordia alliodora
 trees invest more carbon in Azteca ants via phloem-feeding scale insects
 that provide the ants with sugars, and the ants provide better defense of
 the carbon-producing leaves. Under water stress, the trees have smaller
 carbon pools. A model of the carbon trade-offs for the mutualistic
 partners shows that the observed strategies can arise from the carbon
 costs of rare but extreme events of herbivory in the rainy season. Thus,
 water limitation, together with the risk of herbivory, increases the
 strength of a carbon-based mutualism.
description: Pringle.etal.PlosBiologyRaw data files and ReadMe file.
DOI: 10.5061/dryad.1nh877d
title: Data from: Supplementary stocking selects for domesticated genotypes

description: Stocking of hatchery produced fish is common practise to mitigate declines
 in natural populations and may have unwanted genetic consequences. Here we
 describe a novel phenomenon arising where broodstock used for stocking may
 be introgressed with farmed individuals. We test how stocking affects
 introgression in a wild population of Atlantic salmon (Salmo salar) by
 quantifying how the number of adult offspring recaptured in a stocked
 river depend on parental introgression. We found that hatchery conditions
 favour farmed genotypes such that introgressed broodstock produce up to
 four times the number of adult offspring compared to non-introgressed
 broodstock, leading to increased introgression in the recipient spawning
 population. Our results provide the first empirical evidence that stocking
 can unintentionally favour introgressed individuals and through selection
 for domesticated genotypes compromise the fitness of stocked wild
 populations.
description: SupplementarySoftwareR code.seaAge_analysisThis is a c++ file required to run the sea age analysis. The user does not need to open the cpp file, but the cpp file must be in the same working directory as the R code.SourceDataThis file contains source data to reproduce all tables and figures. The file contains 3 data sets. Readme information is included in the xlsx file. Save the respective work sheets as txt files to use as Source data for the accompanying R code.
DOI: 10.5061/dryad.d875g
title: Data from: A keystone mutualism underpins resilience of a coastal ecosystem to drought

description: Droughts are increasing in severity and frequency, yet the mechanisms that
 strengthen ecosystem resilience to this stress remain poorly understood.
 Here, we test whether positive interactions in the form of a mutualism
 between mussels and dominant cordgrass in salt marshes enhance ecosystem
 resistance to and recovery from drought. Surveys spanning 250 km of
 southeastern US coastline reveal spatially dispersed mussel mounds
 increased cordgrass survival during severe drought by 5- to 25-times.
 Surveys and mussel addition experiments indicate this positive effect of
 mussels on cordgrass was due to mounds enhancing water storage and
 reducing soil salinity stress. Observations and models then demonstrate
 that surviving cordgrass patches associated with mussels function as
 nuclei for vegetative re-growth and, despite covering only 0.1–12% of
 die-offs, markedly shorten marsh recovery periods. These results indicate
 that mutualisms, in supporting stress-resistant patches, can play a
 disproportionately large, keystone role in enhancing ecosystem resilience
 to climatic extremes.
description: FL-SC Coastal Die off
 SurveyData on the size of
 die-offs and patch distribution within those dieoffs observed at marsh
 sites located along the southeastern US coastlineCoastal
 Survey.xlsxDieOff Recovery
 2012-15Data on the area of
 marsh die offs on Sapelo Island Georgia in 2012 and in 2015, after 3 years
 of recovery. Data on the patch density within each die off is also
 includedMussel Addition
 Experiment: Ammonium Salinity Expansion DataData from a 2012 mussel
 addition experiment showing the concentration of ammonia and porewater
 salinity in cordgrass transplants either with mussels added or not added.
 In addition, data on the expansion (number of new tillers) observed after
 8 months.Oakdale Ammonium Salinity
 Expansion Data.xlsxSalinity Well
 PairsSalinity data from pairs
 of wells either location inside mussel mounds or in the adjacent marsh
 without mussels; data were collected nearly weekly from May - August
 2013Sapelo natural patch
 expansionData on the rate of
 expansion of 79 patches remaining wishing Sapelo Island marsh die offs
 after 6, 12 and 19 months.Soil water
 storageData on the grams of
 water stored per gram of soil from cores collected from inside and outside
 mussel mounds in a Sapelo Island, GA marsh
DOI: 10.5061/dryad.16n63
title: Data from: Rhesus monkeys show human-like changes in gaze following across the lifespan

description: Gaze following, or co-orienting with others, is a foundational skill for
 human social behavior. The emergence of this capacity scaffolds critical
 human-specific abilities such as theory of mind and language. Nonhuman
 primates also follow others’ gaze, but less is known about how the
 cognitive mechanisms supporting this behavior develop over the lifespan.
 Here we experimentally tested gaze following in 481 semi-free-ranging
 rhesus macaques (Macaca mulatta) ranging from infancy to old age. We found
 that monkeys began to follow gaze in infancy and this response peaked in
 the juvenile period—suggesting that younger monkeys were especially
 attuned to gaze information, like humans. After sexual maturity, monkeys
 exhibited human-like sex-differences in gaze following, with adult females
 showing more gaze following than males. Finally, older monkeys showed
 reduced propensity to follow gaze, just as older humans do. In a second
 study (n=80), we confirmed that macaques exhibit similar baseline rates of
 looking upwards in a control condition, regardless of age. Our findings
 indicate that—despite important differences in human and nonhuman primate
 life history characteristics and typical social experiences—monkeys
 undergo robust ontogenetic shifts in gaze following across early
 development, adulthood, and aging that are strikingly similar to those of
 humans.
description: Rosati et al Gaze
 Development (Study 1)Trial data for gaze
 development study (variable key in file).Rosati_etal_Gaze_Study1.xlsRosati et al Gaze Control (Study 2)Trial data for gaze directional control (variable key in file).Rosati_etal_Gaze_Study2.xls
DOI: 10.5061/dryad.r885q
title: Data from: Temporal dynamics of encrusting communities during the Late Devonian: a case study from the Central Devonian Field, Russia

description: In this study we focused on the dynamics of encrusting assemblages
 preserved on brachiopod hosts collected from upper Frasnian and lower
 Famennian deposits of the Central Devonian Field, Russia. Because the
 encrusted brachiopods come from deposits bracketing the Frasnian/Famennian
 (F/F) boundary, the results also shed some light on ecological differences
 in encrusting communities before and after the Frasnian–Famennian (F-F)
 event. To explore the diversity dynamics of encrusting assemblages, we
 analyzed more than 1300 brachiopod valves (substrates) from two
 localities. Taxon accumulation plots and shareholder quorum subsampling
 (SQS) routines indicated that a reasonably small sample of brachiopod host
 valves (n=50) is sufficient to capture the majority of the encrusting
 genera recorded at a given site. The richness of encrusters per substrate
 declined simultaneously with the number of encrusting taxa in the lower
 Famennian, accompanied by a decrease in epibiont abundance, with a
 comparable decrease in mean encrustation intensity (percentage of
 bioclasts encrusted by one or more epibionts). Epibiont abundance and
 occupancy roughly mirror each other. Strikingly, few ecological
 characteristics are correlated with substrate size, possibly reflecting
 random settlement of larvae. Evenness, which is negatively correlated with
 substrate size, shows greater within-stage variability among samples than
 between Frasnian and Famennian intervals and may indicate the instability
 of early Famennian biocenoses following the faunal turnover. The
 occurrence distribution of encrusters points to nonrandom associations and
 exclusions among several encrusting taxa. However, abundance and occupancy
 of microconchids remained relatively stable throughout the sampled time
 interval. The notable decline in abundance (~60%) and relatively minor
 decline in diversity (~30%) suggest jointly that encrusting communities
 experienced ecological collapse rather than a major mass extinction event.
 The differences between the upper Frasnian and lower Famennian encrusting
 assemblages may thus record a turnover associated with the F-F event.
description: Appendix
 1
DOI: 10.5061/dryad.5h5q4
title: Data from: Combining chloroplast and nuclear microsatellites to investigate origin and dispersal of New World sweet potato landraces

description: We analyzed a representative collection of New World sweet potato
 landraces (329 accessions from Mexico to Peru) with both chloroplast and
 nuclear microsatellite markers. Both kinds of markers supported the
 existence of two geographically restricted genepools, corresponding to
 accessions from the north-western part of South America and accessions
 from the Caribbean and Central America super-region. Our conservative
 cpSSRs markers revealed that the divergence between the two haplotype
 groups is associated with numerous mutation events concerning various
 markers, supporting the idea that this divergence may be ancient,
 predating domestication. For both kind of markers, we found no significant
 difference in diversity between the two genepools and detected
 region-specific alleles in both groups. Previous studies have favoured the
 hypothesis of a single domestication of this crop. Our analysis suggests
 at least two independent domestications, in Meso-America and in the
 north-western part of South America. Sweet potato was then dispersed from
 these centres throughout tropical America. Comparison of nuclear and
 chloroplast data suggests that exchanges of clones and sexual reproduction
 were both important processes in landrace diversification in this clonally
 propagated crop. Our analysis provides useful tools for rationalizing the
 conservation and use of germplasm collections.
description: DRYAD Sample
 LocationPasseport data of the
 334 accessions used in the present manuscript. Accession CIP number,
 accession name, Collection number, Accession country of origin, Elevation
 of collecting site, Latitude and Longitude of collecting site, are
 provided. All accessions are issued from CIP genebank (International
 potato center). Complete passeport data are also available on the CIP web
 site
 (http://germplasmdb.cip.cgiar.org/biomart/martview/acc7fbd28f3343fa2c81be86a979e5a3).cpSSRs dataCholoroplast microsatellites data. Each accession number is presented with its allelic composition for the seven loci used in our study (ccmp2, ntcp18, ntcp28, ntcp26, ibcp5, ibcp8 and ibcp10).nuclear SSRs dataNuclear microsatellites data of the 130 New World sweet potato landraces. For hexaploids, we can obtain from 1 to 6 peaks or bands (6 alleles) per locus. Allelic composition (from allele 1 to allele 6) is provided for each accession, for the 13 microsatellites used in our study.