cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.73675
title: Data from: Is dispersal guided by the environment? A comparison of interspecific gene flow estimates among differentiated regions of a newt hybrid zone.

description: How frequently genes pass through a hybrid zone may be influenced by the
 environment. Accordingly, in long hybrid zones that span more than one
 environmental setting, different patterns may emerge. We reconstruct the
 amount and direction of gene flow across such a heterogeneous hybrid zone
 in two species of marbled newts (Triturus marmoratus and T. pygmaeus), in
 four widely separated areas of the Iberian Peninsula from one
 mitochondrial and three nuclear genes. The main environmental conditions
 associated with the position of the contact zone are determined as
 precipitation, rivers, altitude and relief. Elsewhere its position is not
 correlated with any environmental factor and is instead determined by the
 shortest geographical distance between fixed positions at either side
 (mountains in the East and river in the West). In areas where the position
 of the zone is stable, gene flow was bidirectional. Where T. pygmaeus has
 superseded Triturus marmoratus over a large area gene flow was
 unidirectional. The prediction that a major river would reduce gene flow
 was not confirmed.
description: DNA sequences in IMa2
 format of marbled newts from the Iberian PeninsulaIMa2 input files for
 four different areas of the T. marmoratus / T. pygmaeus hybrid zone
 (Coastal Portugal, Tejo river, Idanha-a-Nova and Sierra da Gata). BF =
 beta-Fibrinogen intron 7 ; CALC = Calreticulin intron 3 ; PDGFRA =
 Platelet-derived growth factor receptor alpha intron 11 and ND4 =
 mitochondrial NADH dehydrogenase subunit 4.IM.zipLocality data of sampling location of Triturus marmoratus and T. pygmaeusLocality data of sampled populations of T. marmoratus and T. pygmaeus, including Locality name and order number, country, hybrid zone area as described in the paper, and GPS coordinates.Locality data for Dryad.xlsx
DOI: 10.5061/dryad.57s62
title: Data from: Comparing forest structure and biodiversity on private and public land: secondary tropical dry forests in Costa Rica

description: Secondary forests constitute a substantial proportion of tropical
 forestlands. These forests occur on both public and private lands and
 different underlying environmental variables and management regimes may
 affect post‐abandonment successional processes and resultant forest
 structure and biodiversity. We examined whether differences in ownership
 led to differences in forest structure, tree diversity, and tree species
 composition across a gradient of soil fertility and forest age. We
 collected soil samples and surveyed all trees in 82 public and 66 private
 0.1‐ha forest plots arrayed across forest age and soil gradients in
 Guanacaste, Costa Rica. We found that soil fertility appeared to drive the
 spatial structure of public vs. private ownership; public conservation
 lands appeared to be non‐randomly located on areas of lower soil
 fertility. On private lands, areas of crops/pasture appeared to be
 non‐randomly located on higher soil fertility areas while forests occupied
 areas of lower soil fertility. We found that forest structure and tree
 species diversity did not differ significantly between public and private
 ownership. However, public and private forests differed in tree species
 composition: 11 percent were more prevalent in public forest and 7 percent
 were more prevalent in private forest. Swietenia macrophylla, Cedrela
 odorata, and Astronium graveolens were more prevalent in public forests
 likely because public forests provide stronger protection for these highly
 prized timber species. Guazuma ulmifolia was the most abundant tree in
 private forests likely because this species is widely consumed and
 dispersed by cattle. Furthermore, some compositional differences appear to
 result from soil fertility differences due to non‐random placement of
 public and private land holdings with respect to soil fertility. Land
 ownership creates a distinctive species composition signature that is
 likely the result of differences in soil fertility and management between
 the ownership types. Both biophysical and social variables should be
 considered to advance understanding of tropical secondary forest structure
 and biodiversity.
description: Tree species composition
 data for private tropical dry forest plotsTree species composition
 data for 66 0.1-ha private tropical dry forest plots in Guanacaste, Costa
 RicaPrivate
 Species Abundance Dryad.csvPrivate Plots Data for
 DryadPlot level data for 66
 0.1-ha plots in tropical dry forests in Guanacaste Costa Rica includes:
 forest stand age, community weighted mean wood density, aboveground
 biomass, basal area, stem density for trees &gt;10 cm DBH, stem density
 for trees &lt;10 cm DBH but 1.3m or higher, Shannon Diversity Index, soil
 chemical variables, and Principal Component Axes for soil chemical
 variables.
DOI: 10.5061/dryad.dc394
title: Data from: Complementary plant nutrient-acquisition strategies promote growth of neighbour species

description: 1. Greater understanding of positive interspecific interactions in
 nutrient-poor soils is a priority, particularly in phosphorus- (P) limited
 ecosystems where plants with contrasting nutrient-acquiring strategies
 co-occur. It is also relevant to agro-ecosystems, since global P stocks
 are being depleted. In this study, we assess positive interactions between
 sympatric plants with contrasting nutrient-acquiring strategies from
 highly P-impoverished soils from the biodiversity hotspot of south-western
 Australia. 2. Four plant species (Banksia menziesii, Eucalyptus marginata,
 Verticordia nitens, and Melaleuca preissiana) that are non-mycorrhizal
 (cluster rooted), ectomycorrhizal (EM), arbuscular (AM), or dual AM/EM,
 respectively, were grown together in a specially-designed ‘common garden’
 microcosm with nutrient-poor or fertilised soil, with or without root
 intermingling and fungal hyphae contact. We measured growth, mycorrhizal
 colonisation, root intermingling, and nutrient uptake to determine
 positive or negative growth patterns among the various plant assemblies.
 3. Growth of the AM/EM host was best when interacting with both the EM
 host and a non-mycorrhizal nutrient-mining plant with cluster roots
 (Banksia) in microcosms where root intermingling was not possible. Growth
 promotion was only seen in pots with nutrient-poor soils, where the better
 growth of Melaleuca coincided with higher shoot P, manganese, calcium,
 iron and boron content, whereas an increase in soil nutrient status
 through fertiliser addition resulted in a decrease in nutrient sharing
 between co-occurring species. Furthermore, the dual AM/EM Melaleuca
 exhibited enhanced EM colonisation and favoured EM over AM fungi when
 grown beside Eucalyptus and Banksia. We surmise that mycorrhizal networks
 were instrumental in the variation in both mycorrhizal type and
 colonisation levels. 4. We conclude that complementarity of plant
 nutrient-acquisition strategies can promote growth of neighbour species.
 The results show a synergistic effect between EM hyphal scavenging and
 mobilisation of limiting nutrients by cluster roots. The positive and
 negative interactions enable coexistence to go far beyond the traditional
 view that plants interact mainly through resource depletion. This study
 improves our understanding of how root interactions could shape plant
 communities and promote species diversity and packing in
 nutrient-impoverished habitats.
description: Teste FunctionalEcology
 RawData FE-2013-00901_R1Raw data from
 FE-2013-00901.R1 includes: plant growth, colonisation by mycorrhizal
 fungi, root intermingling in pots, and foliar nutrient
 levels.Teste FE-2013-00901.R1 RAWDATA
 .xlsx
DOI: 10.5061/dryad.2j0ks
title: Data from: Change in sex pheromone expression by nutritional shift in male cockroaches

description: Environmental conditions during sexual maturation impact sexual signal
 expression, but little is known about how individual histories of changing
 environmental conditions affect the intensity of male sexual
 advertisement. We investigated the effects of shifting dietary nutrient
 composition (protein vs. carbohydrates) in male Nauphoeta cinerea
 cockroaches on consumption, final lipid reserves, and sex pheromone levels
 subsequent to completing sexual maturation on a specific diet, at high and
 low concentration of dietary nutrients. Consumption, lipid reserves, and
 sex pheromone levels were highly affected by dietary nutrient composition
 with higher values on carbohydrate-biased diet, and males had
 significantly higher and lower levels of consumption, lipid reserves, and
 sex pheromones when shifted to a carbohydrate-biased and a protein-biased
 diet, respectively, compared with males maintained on either initial diet
 throughout the experiment. Males shifted to a carbohydrate-biased diet at
 high nutrient concentration fully recouped their sex pheromone levels,
 attaining levels that were not significantly lower than those in males
 maintained on carbohydrate-biased diet at high nutrient concentration
 throughout the experiment. Our study shows that male sexual display in N.
 cinerea is plastic and highly affected by present as well as previous
 dietary conditions. Signaling of adaptive quality through male sex
 pheromones can therefore vary dynamically within the early adult life of a
 male in response to the nutritional composition of food that is available
 to ingest. This contrasts morphological sexual traits in arthropods that
 are affected during development and are fixed at adulthood.
description: Nutritional history and
 sex pheromone expressionConsumption and
 pheromone data for Nauphoeta cinerea males with different nutritional
 histories
DOI: 10.5061/dryad.m5n98
title: Data from: Predicting classifier performance with limited training data: applications to computer-aided diagnosis in breast and prostate cancer

description: Clinical trials increasingly employ medical imaging data in conjunction
 with supervised classifiers, where the latter require large amounts of
 training data to accurately model the system. Yet, a classifier selected
 at the start of the trial based on smaller and more accessible datasets
 may yield inaccurate and unstable classification performance. In this
 paper, we aim to address two common concerns in classifier selection for
 clinical trials: (1) predicting expected classifier performance for large
 datasets based on error rates calculated from smaller datasets and (2) the
 selection of appropriate classifiers based on expected performance for
 larger datasets. We present a framework for comparative evaluation of
 classifiers using only limited amounts of training data by using random
 repeated sampling (RRS) in conjunction with a cross-validation sampling
 strategy. Extrapolated error rates are subsequently validated via
 comparison with leave-one-out cross-validation performed on a larger
 dataset. The ability to predict error rates as dataset size increases is
 demonstrated on both synthetic data as well as three different
 computational imaging tasks: detecting cancerous image regions in prostate
 histopathology, differentiating high and low grade cancer in breast
 histopathology, and detecting cancerous metavoxels in prostate magnetic
 resonance spectroscopy. For each task, the relationships between 3
 distinct classifiers (k-nearest neighbor, naive Bayes, Support Vector
 Machine) are explored. Further quantitative evaluation in terms of
 interquartile range (IQR) suggests that our approach consistently yields
 error rates with lower variability (mean IQRs of 0.0070, 0.0127, and
 0.0140) than a traditional RRS approach (mean IQRs of 0.0297, 0.0779, and
 0.305) that does not employ cross-validation sampling for all three
 datasets.
description: Dataset
 D1D1.zipDataset D2D2.zipDataset D3D3.zip
DOI: 10.5061/dryad.9gd17
title: Data from: Laparoscopic assistance for primary transanal pull-through in Hirschsprung’s disease: a systematic review and meta-analysis.

description: Objective: To compare outcomes following totally transanal endorectal
 pull-through (TTERPT) versus pull-through with any form of laparoscopic
 assistance (LAPT) for infants with uncomplicated Hirschsprung's
 disease. Design: Systematic review and meta-analysis. Setting: Five
 hospitals with a paediatric surgical service. Participants: 405 infants
 with uncomplicated Hirschsprung's disease. Interventions: TTERPT
 versus LAPT. Primary and secondary outcome measures: Primary outcomes:
 mortality, postoperative enterocolitis, faecal incontinence, constipation,
 unplanned laparotomy or stoma formation, and injury to abdominal viscera.
 Secondary outcomes: Haemorrhage requiring transfusion of blood products,
 abscess formation, intestinal obstruction, intestinal ischaemia, enteric
 fistula formation, urinary incontinence or retention, impotency and
 duration of procedure. Results: Five eligible studies comprising 405
 patients were identified from 2107 studies. All studies were retrospective
 case series, with variability in outcome assessment quality and length of
 follow-up. Operative duration was 50.29 min shorter with TTERPT (95% CI
 39.83 to 60.74, p&lt;0.00001). There were no significant differences
 identified between TTERPT and LAPT for incidence of postoperative
 enterocolitis (OR=0.78, 95% CI 0.44 to 1.38, p=0.39), faecal incontinence
 (OR=0.44, 95% CI 0.09 to 2.20, p=0.32) or constipation (OR=0.84, 95% CI
 0.32 to 2.17, p=0.71). Conclusions: This meta-analysis did not find any
 evidence to suggest a higher rate of enterocolitis, incontinence or
 constipation following TTERPT compared with LAPT. Further long-term
 comparative studies and multicentre data pooling are needed to determine
 whether a purely transanal approach offers any advantages over a
 laparoscopically assisted approach to rectosigmoid Hirschsprung's
 disease.
description: lap vs transanal for
 Hirschsprung'sOriginal data in RevMan
 5.3 format used to generate meta-analysis statistics.
DOI: 10.5061/dryad.91b7m
title: Data from: Contrasting genetic diversity and population structure among three sympatric Madagascan shorebirds: parallels with rarity, endemism, and dispersal

description: Understanding the relative contributions of intrinsic and extrinsic
 factors to population structure and genetic diversity is a central goal of
 conservation and evolutionary genetics. One way to achieve this is through
 comparative population genetic analysis of sympatric sister taxa, which
 allows evaluation of intrinsic factors such as population demography and
 life history while controlling for phylogenetic relatedness and geography.
 We used ten conserved microsatellites to explore the population structure
 and genetic diversity of three sympatric and closely related plover
 species in southwestern Madagascar: Kittlitz's plover (Charadrius
 pecuarius), white-fronted plover (C. marginatus), and Madagascar plover
 (C. thoracicus). Bayesian clustering revealed strong population structure
 in the rare and endemic Madagascar plover, intermediate population
 structure in the white-fronted plover, and no detectable population
 structure in the geographically widespread Kittlitz's plover. In
 contrast, allelic richness and heterozygosity were highest for the
 Kittlitz's plover, intermediate for the white-fronted plover and
 lowest for the Madagascar plover. No evidence was found in support of the
 “watershed mechanism” proposed to facilitate vicariant divergence of
 Madagascan lemurs and reptiles, which we attribute to the vagility of
 birds. However, we found a significant pattern of genetic isolation by
 distance among populations of the Madagascar plover, but not for the other
 two species. These findings suggest that interspecific variation in
 rarity, endemism, and dispersal propensity may influence genetic structure
 and diversity, even in highly vagile species.
description: Madagascar Plover
 GenotypesMP_Genotypes.txtWhite-fronted Plover GenotypesWfP_Genotypes.txtKittlitz's Plover GenotypesKiP_Genotypes.txt
DOI: 10.5061/dryad.r3320
title: Data from: Costs and benefits of admixture between foreign genotypes and local populations in the field

description: Admixture is the hybridization between populations within one species. It
 can increase plant fitness and population viability by alleviating
 inbreeding depression and increasing genetic diversity. However,
 populations are often adapted to their local environments and admixture
 with distant populations could break down local adaptation by diluting the
 locally adapted genomes. Thus, admixed genotypes might be selected against
 and be outcompeted by locally adapted genotypes in the local environments.
 To investigate the costs and benefits of admixture, we compared the
 performance of admixed and within-population F1 and F2 generations of the
 European plant Lythrum salicaria in a reciprocal transplant experiment at
 three European field sites over a two-year period. Despite strong
 differences between site and plant populations for most of the measured
 traits, including herbivory, we found limited evidence for local
 adaptation. The effects of admixture depended on experimental site and
 plant population, and were positive for some traits. Plant growth and
 fruit production of some populations increased in admixed offspring and
 this was strongest with larger parental distances. These effects were only
 detected in two of our three sites. Our results show that, in the absence
 of local adaptation, admixture may boost plant performance, and that this
 is particularly apparent in stressful environments. We suggest that
 admixture between foreign and local genotypes can potentially be
 considered in nature conservation to restore populations and/or increase
 population viability, especially in small inbred or maladapted
 populations.
description: Lythrum salicaria
 transplant dataExcel file of growth,
 reproduction and herbivory measurements of Lythrum salicaria grown at
 three transplant field sites in Europe during a two year experiment.
 Column headings are explained in the file.Lythrum_transplant_core_DRYAD.xlsx
DOI: 10.5061/dryad.846mh
title: Data from: Escherichia coli populations in unpredictably fluctuating environments evolve to face novel stresses through enhanced efflux activity

description: There is considerable understanding about how laboratory populations
 respond to predictable (constant or deteriorating environment) selection
 for single environmental variables such as temperature or pH. However,
 such insights may not apply when selection environments comprise multiple
 variables that fluctuate unpredictably, as is common in nature. To address
 this issue, we grew replicate laboratory populations of Escherichia coli
 in nutrient broth whose pH and concentrations of salt (NaCl) and hydrogen
 peroxide (H2O2) were randomly changed daily. After ~170 generations, the
 fitness of the selected populations had not increased in any of the three
 selection environments. However, these selected populations had
 significantly greater fitness in four novel environments which have no
 known fitness-correlation with tolerance to pH, NaCl or H2O2.
 Interestingly, contrary to expectations, hypermutators did not evolve.
 Instead, the selected populations evolved an increased ability for
 energy-dependent efflux activity that might enable them to throw out
 toxins, including antibiotics, from the cell at a faster rate. This
 provides an alternate mechanism for how evolvability can evolve in
 bacteria and potentially lead to broad-spectrum antibiotic resistance,
 even in the absence of prior antibiotic exposure. Given that environmental
 variability is increasing in nature, this might have serious consequences
 for public health.
description: Karve+_JEvolBiol_2015_Dryad_DataPlease refer to the Materials and Methods section of the associated paper for details.
DOI: 10.5061/dryad.89627
title: Data from: Size doesn't matter, sex does: a test for boldness in sister species of Brachyrhaphis fishes

description: The effect of divergent natural selection on the evolution of behavioral
 traits has long been a focus of behavioral ecologists. Predation, due to
 its ubiquity in nature and strength as a selective agent, has been
 considered an important environmental driver of behavior. Predation is
 often confounded with other environmental factors that could also play a
 role in behavioral evolution. For example, environments that contain
 predators are often more ecologically complex and “risky” (i.e., exposed
 and dangerous). Previous work shows that individuals from risky
 environments are often more bold, active, and explorative than those from
 low-risk environments. To date, most comparative studies of
 environmentally driven behavioral divergence are limited to comparisons
 among populations within species that occur in divergent selective
 environments but neglect comparisons between species following speciation.
 This limits our understanding of how behavior evolves post-speciation. The
 Central American live-bearing fish genus Brachyrhaphis provides an ideal
 system for examining the relationship between selective environments and
 behavior, within and between species. Here, we test for differences in
 boldness between sister species B. roseni and B. terrabensis that occur in
 streams with and without piscivorous predators, respectively. We found
 that species do differ in boldness, with species that occur with predators
 being bolder than those that do not. Within each species, we found that
 sexes differed in boldness, with males being bolder than females. We also
 tested for a relationship between size (a surrogate for metabolic rate)
 and boldness, but found no size effects. Therefore, sex, not size, affects
 boldness. These results are consistent with the hypothesis that complex
 and risky environments favor individuals with more bold behavioral traits,
 but they are not consistent with the hypothesis that size (and therefore
 metabolic rate) drives divergence in boldness. Finally, our results
 provide evidence that behavioral trait divergence continues even after
 speciation is complete.
description: Ingley_et_al_E&E_FINAL__Broseni_Bterrabensis_SL_M_BoldnessData file consists of an Excel spread sheet. The spread sheet contains the identification number associated with each individual tested, species, sex, mass (g), standard length (mm), and time to emerge from a shelter into a novel environment (seconds).