cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9b495
title: Data from: Novel molecular approach demonstrates turbid river plumes reduce predation mortality on larval fish

description: Turbidity associated with river plumes is known to affect the search
 ability of visual predators and thus can drive “top-down” impacts on prey
 populations in complex ecosystems; however, traditional quantification of
 predator-prey relationships (i.e., stomach content analysis) often fail
 with larval fish due to rapid digestion rates. Herein, we use novel
 molecular genetic methods to quantify larval Yellow Perch (YP) in predator
 stomachs in western Lake Erie to test the hypothesis that turbidity drives
 variation in larval predation. We characterize predator stomach content
 DNA to first identify YP DNA (single nucleotide polymorphism) then
 quantify larval YP predation (microsatellite allele counting) in two river
 plumes differing in turbidity. Our results showed elevated larval YP
 predation in the less turbid river plume, consistent with a top-down
 impact of turbidity on larval survival. Our analyses highlight novel
 ecological hypothesis testing using the power of innovative molecular
 genetic approaches.
description: Yellow Perch predation
 dataPresence/absence and
 number of Yellow Perch (YP) detected in predator fish stomachs from the
 western basin of Lake Erie. Data generated using SNP and microsatellite
 analyses respectively. Site: D = Detroit River plume, M = Maumee River
 plume; pred: Predator species, WA = walleye, WB = White Bass, WP = White
 Perch; yp: presence (1) or absence (0) of YP in predator stomachs as
 detected with SNP assay; YP##bands: the number of YP sized microsatellite
 bands detected in stomach content DNA for locus ##; YP##fish: the number
 of larval YP inferred from the number of microsatellite bands for
 microsatellite ## and the allele accumulation curve (see Supplemental
 Figure 1); Avefish: the average number of larval YP detected in stomach
 content DNA based on all 5 microsatellite loci.Carreon-MartinezYPpredationData.csvYP_SNP_Validation_Non-target_Ct_valuesData generated during qPCR validation of Yellow Perch SNP assay. Column headings: DNA concentration (ng/uL): final concentration of DNA in ng/uL added to validation assays; WA Ct: Cycle number at which Walleye DNA reached the amplification threshold when amplified with the Yellow Perch specific SNP assay; WB Ct: Cycle number at which White Bass DNA reached the amplification threshold when amplified with the Yellow Perch specific SNP assay; WP Ct: Cycle number at which White Perch DNA reached the amplification threshold when amplified with the Yellow Perch specific SNP assay; mean Ct: Average of all non-target predator Ct values when amplified with the Yellow Perch specific SNP assay; SD Ct: Standard Deviation of all non-target predator Ct values when amplified with the Yellow Perch specific SNP assay; SE Ct: Standard Error of all non-target predator Ct values when amplified with the Yellow Perch specific SNP assayBasinwidePredationEstimatesDescription of calculations of basin wide Yellow Perch predation mortality estimates.
DOI: 10.5061/dryad.4j8pq
title: Data from: Chemical communication, sexual selection, and introgression in wall lizards

description: Divergence in communication systems should influence the likelihood that
 individuals from different lineages interbreed, and consequently shape the
 direction and rate of hybridization. Here, we studied the role of chemical
 communication in hybridization, and its contribution to asymmetric and
 sexually selected introgression, between two lineages of the common wall
 lizard (Podarcis muralis). Males of the two lineages differed in the
 chemical composition of their femoral secretions. Chemical profiles
 provided information regarding male secondary sexual characters, but the
 associations were variable and inconsistent between lineages. In
 experimental contact zones, chemical composition was weakly associated
 with male reproductive success, and did not predict the likelihood of
 hybridization. Consistent with these results, introgression of chemical
 profiles in a natural hybrid zone resembled that of neutral nuclear
 genetic markers overall, but one compound in particular (tocopherol methyl
 ether) matched closely the introgression of visual sexual characters.
 These results imply that associations between male chemical profiles,
 sexual characters and reproductive success largely reflect transient and
 environmentally driven effects, and that genetic divergence in chemical
 composition is largely neutral. We therefore suggest that femoral
 secretions in wall lizards primarily provide information about residency
 and individual identity rather than function as sexual signals.
description: MacGregoretal_ChemicalsDataRaw abundance and relative abundance data for 21 lipophilic compounds in the femoral secretions of male wall lizards. For data on the morphology and reproductive success of the enclosure males see MacGregor et al. 2017. Functional Ecology.
DOI: 10.5061/dryad.bg3g3
title: Data from: Functional divergence of the nuclear receptor NR2C1 as a modulator of pluripotentiality during hominid evolution

description: Genes encoding nuclear receptors (NRs) are attractive as candidates for
 investigating the evolution of gene regulation because they (1) have a
 direct effect on gene expression and (2) modulate many cellular processes
 that underlie development. We employed a three-phase investigation linking
 NR molecular evolution among primates with direct experimental assessment
 of NR function. Phase 1 was an analysis of NR domain evolution and the
 results were used to guide the design of phase 2, a codon-model-based
 survey for alterations of natural selection within the hominids. By using
 a series of reliability and robustness analyses we selected a single gene,
 NR2C1, as the best candidate for experimental assessment. We carried out
 assays to determine whether changes between the ancestral and extant
 NR2C1s could have impacted stem cell pluripotency (phase 3). We evaluated
 human, chimpanzee, and ancestral NR2C1 for transcriptional modulation of
 Oct4 and Nanog (key regulators of pluripotency and cell lineage
 commitment), promoter activity for Pepck (a proxy for differentiation in
 numerous cell types), and average size of embryological stem cell colonies
 (a proxy for the self-renewal capacity of pluripotent cells). Results
 supported the signal for alteration of natural selection identified in
 phase 2. We suggest that adaptive evolution of gene regulation has
 impacted several aspects of pluripotentiality within primates. Our study
 illustrates that the combination of targeted evolutionary surveys and
 experimental analysis is an effective strategy for investigating the
 evolution of gene regulation with respect to developmental phenotypes.
description: NR
 alignmentsNR
 alignmentspaml_files_for_dryad.zipStructural_partitionsStructural_partitions4cat_structural_partitions.zip
DOI: 10.5061/dryad.gq264
title: Data from: Lean-season primary productivity and heat dissipation as key drivers of geographic body-size variation in a widespread marsupial

description: Geographic body-size variation characterises many mammal species.
 Hypotheses centring around heat conservation, heat dissipation, primary
 productivity and seasonality have been advanced to explain geographic
 body-size patterns. However, identification of the primary body-size
 drivers has often been hampered by a paucity of data for broadly
 distributed species and the application of regression models that have not
 explicitly accounted for the spatial clustering inherent in such datasets.
 We used Australia's most widespread marsupial, the common brushtail
 possum Trichosurus vulpecula, as a model species with which to test five
 proposed drivers of geographic body-size variation. Using geo-referenced
 skull measurements from 588 specimens and a suite of putative
 environmental covariates, we employed spatial simultaneous autoregressive
 models, together with information criteria, to evaluate these different
 hypotheses. Our analysis identified a strong, positive relationship
 between possum body size and primary productivity during the least
 productive season, whereas the relationship with mean annual productivity
 received less support. Consistent with the heat-dissipation hypothesis, T.
 vulpecula body size also decreased with increasing mean summer maximum
 temperature. Spatial autoregression coefficients estimated from the
 simultaneous autoregressive models were always high, suggesting that
 additional abiotic or biotic factors might contribute to the spatial
 patterns observed. We argue that the analysis of geographic body-size
 variation should consider multi-causal possibilities rather than treating
 the numerous hypotheses as competing, mutually exclusive alternatives.
description: Trichosurus_vulpecula_variables_dataOrigin (i.e., wildlife collection) and registration numbers of all specimens used in the analyses, together with all extracted environmental covariates
DOI: 10.5061/dryad.7v387
title: Data from: Oral microflora in preschool children attending a fluoride varnish program: a cross-sectional study

description: Background: To compare the oral microflora in preschool children attending
 a fluoride varnish program with a reference group receiving a standard
 oral health program without fluoride varnish applications. A second aim
 was to relate the microbial composition to the caries prevalence. Methods:
 Five hundred seven 3-year-old children were enrolled from a cohort of 3403
 preschool children taking part in a community based oral health project.
 Two hundred sixty-three of them had attended caries-preventive program
 with semi-annual applications of a fluoride varnish since the age of 1
 year (test group) while 237 had received standard preventive care
 (reference group). Oral samples were collected with a sterile swab and
 analysed with checkerboard DNA-DNA hybridization using 12 pre-determined
 bacterial probes. Caries and background data were collected from clinical
 examinations and questionnaires. Results: Gram-positive streptococci (S.
 intermedius, S. salivarius, S. oralis) were most frequently detected and
 displayed the highest counts in both groups. There were no significant
 differences between the groups concerning prevalence of any of the
 selected bacterial strains except for S. oralis that occurred less
 frequently in the reference group. In children with caries, V. parvula
 were significantly more common (p &lt; 0.05) while strains of
 Lactobacillus, Bifidobacterium and Neisseria were more prevalent among the
 caries-free children (p &lt; 0.05). Conclusions: A 2-year community
 program with semi-annual fluoride varnish applications did not seem to
 significantly influence the oral microflora in preschool children. Trial
 registration: www.controlled-trials.com (ISRCTN35086887) 20131216
 ‘retrospectively registered’.
description: ReadMefileThis read me file describes the data file and supplementary file accompanying the above publication and contact for correspondence1) 2016-11-26 Data set of the trialThe submitted file include data from the Stop Caries Stockholm study. The database contains data on data caries, oral microorganisms and patient background factors2) 2016-11-26 List of the variables in the supplementary dataset used in the trial and explanation of the codingList of the variables in the supplementary dataset used in the trial and explanation of the coding
DOI: 10.5061/dryad.ft5jj
title: Data from: Temperature niche shift observed in a Lepidoptera population under allochronic divergence

description: A process of adaptive divergence for tolerance to high temperatures was
 identified by using a rare model-system, consisting of two sympatric
 populations of a Lepidoptera (Thaumetopoea pityocampa) with different
 life-cycle timings, a "mutant" population with summer larval
 development, Leiria SP, and the founder natural population, having winter
 larval development, Leiria WP. A third, allopatric population (Bordeaux
 WP) was also studied. First and second instar larvae were experimentally
 exposed to daily-cycles of heat treatment reaching maximum values of 36,
 38, 40 and 42ºC; control groups placed at 25ºC. A lethal temperature
 effect was only significant at 42ºC, for Leiria SP, whereas all
 temperatures tested had a significant negative effect upon Leiria WP, thus
 indicating an upper threshold of survival c.a. 6ºC above that of the WP.
 Cox regression model, for pooled heat treatments, predicted mortality
 hazard to increase for Leiria WP (+108%) and Bordeaux WP (+78%) in
 contrast with Leiria SP; to increase by 24% for each additional ºC; and to
 decrease by 53% from first to second instar larvae. High variability among
 individuals was observed, a population characteristic that may favour
 selection and consequent adaptation. Present findings provide an example
 of ecological differentiation, following a process of allochronic
 divergence. Results further contribute to a better understanding of the
 implications of climate change for ecological genetics.
description: Temperature-trials-dataData collected in the laboratory, organized for survival analysis. Columns specify population, larval instar, year of the trial, trial code, days since beginning of the trial (days 1-3 refer to heat treatment period; following days refer to post-treatment), state of each individual (1=dead, 0=censored), temperature and treatment/control groups.
DOI: 10.5061/dryad.rr460
title: Data from: A context-dependent induction of natal habitat preference in a generalist herbivorous insect

description: In many species adults exploit sensory information experienced in their
 natal habitat when searching for resources. This behavioral plasticity may
 help animals to establish themselves in new habitats by quickly locating
 suitable resources and avoiding unsuitable resources in complex
 environments. However the processes guiding positive or negative natal
 habitat preference induction (NHPI) remain poorly understood. In the
 polyphagous moth Spodoptera littoralis, earlier studies have shown that
 female innate host-plant preference is modulated by larval feeding
 experience. In this context, the aim of this study was to investigate how
 variability in food quality associated with habitat olfactory cues can
 modulate NHPI in this species. We found that larvae showed appetitive or
 aversive responses to the experienced plant olfactory cues based on their
 values as predictors of food quality. Furthermore, larval exposure to
 host-plant olfactory cues alone induced oviposition preference for these
 plants in adult females, but only when the females had been feeding on
 high-quality food as larvae. Females reared on poor quality food retained
 their innate plant oviposition preference as adults. These results show
 that NHPI in S. littoralis is context-dependent and based on food quality
 with which olfactory cues are associated. They also suggest that larval
 experience to plant olfactory cues alone is sufficient to modulate the
 adult host plant preference. Finally, this study suggests that polyphagous
 insects with particular innate plant preferences may only show phenotypic
 plasticity in this trait when the fitness benefits are high.
description: data_lhomme_et_al_behavioralecologyRaw data used in the Figures 2, 3 and 4
DOI: 10.5061/dryad.9sn26
title: Data from: Do invasive plants structure microbial communities to accelerate decomposition in intermountain grasslands?

description: Invasive plants are often associated with greater productivity and soil
 nutrient availabilities, but whether invasive plants with dissimilar
 traits change decomposer communities and decomposition rates in consistent
 ways is little known. We compared decomposition rates and the fungal and
 bacterial communities associated with the litter of three problematic
 invaders in intermountain grasslands; cheatgrass (Bromus tectorum),
 spotted knapweed (Centaurea stoebe) and leafy spurge (Euphorbia esula), as
 well as the native bluebunch wheatgrass (Pseudoroegneria spicata). Shoot
 and root litter from each plant was placed in cheatgrass, spotted
 knapweed, and leafy spurge invasions as well as remnant native communities
 in a fully reciprocal design for 6 months to see whether decomposer
 communities were species-specific, and whether litter decomposed fastest
 when placed in a community composed of its own species (referred to
 hereafter as home-field advantage–HFA). Overall, litter from the two
 invasive forbs, spotted knapweed and leafy spurge, decomposed faster than
 the native and invasive grasses, regardless of the plant community of
 incubation. Thus, we found no evidence of HFA. T-RFLP profiles indicated
 that both fungal and bacterial communities differed between roots and
 shoots and among plant species, and that fungal communities also differed
 among plant community types. Synthesis. These results show that litter
 from three common invaders to intermountain grasslands decomposes at
 different rates and cultures microbial communities that are
 species-specific, widespread, and persistent through the dramatic shifts
 in plant communities associated with invasions.
description: Decomposition_chemistry_microbial_McTeeThese data include soil temperature, pH, and decomposition rates of root and shoot litter placed in the field. It also includes Terminal restriction fragment length polymorphism (T-RFLP) of fungi and bacteria that inhabited the litter. The file includes seven sheets. The TRFLP data that is suffixed with "fun" in the sheet name means that plant species were grouped based on whether they were a forb or grass. We provide a supplement in the manuscript that includes code for different analyses using R Software.McTee_Data.xlsx
DOI: 10.5061/dryad.3hq2c
title: Data from: Stochastic environmental fluctuations drive epidemiology in experimental host–parasite metapopulations

description: Environmental fluctuations are important for parasite spread and
 persistence. However, the effects of the spatial and temporal structure of
 environmental fluctuations on host–parasite dynamics are not well
 understood. Temporal fluctuations can be random but positively
 autocorrelated, such that the environment is similar to the recent past
 (red noise), or random and uncorrelated with the past (white noise). We
 imposed red or white temporal temperature fluctuations on experimental
 metapopulations of Paramecium caudatum, experiencing an epidemic of the
 bacterial parasite Holospora undulata. Metapopulations (two subpopulations
 linked by migration) experienced fluctuations between stressful (5°C) and
 permissive (23°C) conditions following red or white temporal sequences.
 Spatial variation in temperature fluctuations was implemented by exposing
 subpopulations to the same (synchronous temperatures) or different
 (asynchronous temperatures) temporal sequences. Red noise, compared with
 white noise, enhanced parasite persistence. Despite this, red noise
 coupled with asynchronous temperatures allowed infected host populations
 to maintain sizes equivalent to uninfected populations. It is likely that
 this occurs because subpopulations in permissive conditions rescue
 declining subpopulations in stressful conditions. We show how patterns of
 temporal and spatial environmental fluctuations can impact parasite spread
 and host population abundance. We conclude that accurate prediction of
 parasite epidemics may require realistic models of environmental noise.
description: Duncan_Paramecium_data_7_13Data describing Paramecium dynamicsDuncan_Paramecium_7_13.xlsDuncan_Paramecium_Time_7_13Data for Paramecium temporal analysesDuncan_parasite_7_13File describing parasite population parametersDuncan_Parasite_time_07_13Data for analysis of parasite temporal analyses
DOI: 10.5061/dryad.rn583
title: Data from: Genetic diversity among INERA maize inbred lines with single nucleotide polymorphism (SNP) markers and their relationship with CIMMYT, IITA, and temperate lines

description: Background: Genetic diversity provides the capacity for plants to meet
 changing environments. It is fundamentally important in crop improvement.
 Fifty-nine local maize lines developed at INERA and 41 exotic (temperate
 and tropical) inbred lines were characterized using 1057 SNP markers to
 (1) analyse the genetic diversity in a diverse set of maize inbred lines;
 (2) determine the level of genetic diversity in INERA inbred lines and
 patterns of relationships of these inbred lines developed from two
 sources; and (3) examine the genetic differences between local and exotic
 germplasms. Results: Roger’s genetic distance for about 64% of the pairs
 of lines fell between 0.300 and 0.400. Sixty one per cent of the pairs of
 lines also showed relative kinship values of zero. Model-based population
 structure analysis and principal component analysis revealed the presence
 of 5 groups that agree, to some extent, with the origin of the germplasm.
 There was genetic diversity among INERA inbred lines, which were
 genetically less closely related and showed a low level of heterozygosity.
 These lines could be divided into 3 major distinct groups and a mixed
 group consistent with the source population of the lines. Pairwise
 comparisons between local and exotic germplasms showed that the temperate
 and some IITA lines were differentiated from INERA lines. There appeared
 to be substantial levels of genetic variation between local and exotic
 germplasms as revealed by missing and unique alleles. Conclusions: Allelic
 frequency differences observed between the germplasms, together with
 unique alleles identified within each germplasm, shows the potential for a
 mutual improvement between the sets of germplasm. The results from this
 study will be useful to breeders in designing inbred-hybrid breeding
 programs, association mapping population studies and marker assisted
 breeding.
description: Table S1 Summary of the
 100 maize inbred linesTable S2 Summary
 statistics for the 1057 informative SNP markers identified from the
 1151-SNPsTable S3 Inbred lines
 with their proportional memberships in the model-based subgroups
 determined by structureTable S4 Markers with
 missing alleles identified in INERA collection compared with CIMMYT, IITA
 and Temperate germplasm collections
DOI: 10.15468/dl.hzmfbx
title: Occurrence Download

description: A dataset containing 1770540 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OrderKey is Anura",
 "Country is Australia",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 {
 "not" : {
 "TaxonKey" : [
 "is Rhinella marina"
 ]
 }
 }
 ]
}

 The dataset includes 1770540 records from 120 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000660-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.