cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.st463
title: Data from: Genotypic variation in plant traits shapes herbivorous insect and ant communities on a foundation tree species

description: Community genetics aims to understand the effects of intraspecific genetic
 variation on community composition and diversity, thereby connecting
 community ecology with evolutionary biology. Multiple studies have shown
 that different plant genotypes harbor different communities of associated
 organisms, such as insects. Yet, the mechanistic links that tie insect
 community composition to plant genetics are still not well understood. To
 shed light on these relationships, we explored variation in both plant
 traits (e.g., growth, phenology, defense) and herbivorous insect and ant
 communities on 328 replicated aspen (Populus tremuloides) genets grown in
 a common garden. We measured traits and visually surveyed insect
 communities annually in 2014 and 2015. We found that insect communities
 overall exhibited low heritability and were shaped primarily by
 relationships among key insects (i.e., aphids, ants, and free-feeders).
 Several tree traits affected insect communities and the presence/absence
 of species and functional groups. Of these traits, tree size and foliar
 phenology were the most important. Larger trees had more dense and diverse
 insect communities, while timing of bud break and bud set differentially
 influenced particular species and insect groups, especially leaf modifying
 insects. These findings lay the groundwork for future work that will
 identify plant genes and genetic regions that underlie the structure of
 associated insect communities.
description: WisAsp_CommunityGenetics_TreeTraitInsectCommunityThese data are from the Wisconsin Aspen "WisAsp" (Populus tremuloides) common garden from 2014-5. WisAsp contains a population of 328 replicated aspen genets. Each tree was surveyed for ecologically-relevant tree traits (growth, size, morphology, bud phenology, phytochemistry, extra floral nectaries) and insect communities (herbivorous insects and ants).WisAsp_2014-5_DryadData.xlsx
DOI: 10.5061/dryad.802hc
title: Data from: Poor housing conditions in association with child health in a disadvantaged immigrant population: a cross-sectional study in Rosengård, Malmö, Sweden

description: Objectives: To describe the home environment in terms of housing
 conditions and their association with child health in a disadvantaged
 immigrant population. Design: A cross-sectional observational study.
 Setting: Enrolment took place during 2010–2011 in Rosengård, Malmö,
 Sweden. Participants: Children aged 0–13 years in 2 study neighbourhoods
 were recruited from local health records and from schools. 359 children
 participated, with a participation rate of 40%. Data on health, lifestyle
 and apartment characteristics from questionnaire-led interviews with the
 mothers of the children were obtained together with data from home
 inspections carried out by trained health communicators. Outcome measures:
 Logistic regression analysis was used to estimate ORs for various health
 outcomes, adjusted for demographic information and lifestyle factors.
 Results: The housing conditions were very poor, especially in one of the
 study neighbourhoods where 67% of the apartments had been sanitised of
 cockroaches, 27% were infested with cockroaches and 40% had a visible
 mould. The association between housing conditions and health was mostly
 inconclusive, but there were statistically significant associations
 between current asthma and dampness (OR=4.1, 95% CI 1.7 to 9.9), between
 asthma medication and dampness (OR=2.8, 95% CI 1.2 to 6.4), and between
 mould and headache (OR=4.2, 95% CI 1.2 to 14.8). The presence of
 cockroaches was associated with emergency care visits, with colds, with
 headache and with difficulty falling asleep, and worse general health was
 associated with mould and presence of cockroaches. Conclusions: The
 associations between dampness and asthma, and the association between
 mould and headache, are in line with current knowledge. The presence of
 cockroaches seemed to be associated with various outcomes, including those
 related to mental well-being, which is less described in the literature.
 The results of the present study are hypothesis generating and provide
 strong incentives for future studies in this study population.
description: Raw data from home
 visits and health questionnairesAnonymised data
 generated for a selected group of immigrant families in Malmö, Sweden, who
 were living in a disadvantaged neighbourhood. Home visits were undertaken
 to assess family member's health and apartment characteristics.
 Variable explanations are included in the fileoudin et al. raw data
 dryad.sav
DOI: 10.5061/dryad.3qt42
title: Data from: High gene flow in the American badger overrides habitat preferences and limits broadscale genetic structure

description: Habitat associations are a function of habitat preferences and dispersal
 capabilities, both of which can influence how species responded to
 Quaternary climatic changes and contemporary habitat heterogeneity.
 Predicting resultant genetic structure is not always straightforward,
 especially in species where high dispersal potential and habitat
 preferences yield opposing predictions. The American badger has high
 dispersal capabilities that predict widespread panmixia, but avoids
 closed-canopy forests and clay soils, which could restrict gene flow and
 create ecologically based population genetic structure. We used
 mitochondrial sequence and microsatellite data sets to characterize how
 these opposing forces contribute to genetic structure in badgers at a
 continent-wide scale. Our data revealed an overall lack of ecologically
 based population genetic structure, suggesting that high dispersal
 capabilities were sufficiently realized to overcome most habitat-based
 genetic structure. At a broadscale, badger gene flow is limited only by
 geographic distance (isolation by distance) and large water barriers (Lake
 Michigan and the Mississippi River). The absence of genetic structure in a
 species with strong avoidance of unsuitable habitats advances our
 understanding of when and how genetic structure emerges in widespread,
 highly mobile species.
description: Predictor Variables for
 dbRDA analysisThis file includes all
 the predictor variables for our dbRDA including subspecies, topographic
 barriers, and ecological variables.Inputs.txtMsat Genotypes for all badgersThis file includes all the microsatellite genotypes for 917 individual badgers in Genalex format.BadgerGenotypesGenalex.xlsxFasta file for all mtDNA sequencesThis file contains all d-loop sequences in FASTA format.Rangefas.fas
DOI: 10.5061/dryad.vt55c
title: Data from: Simultaneous pulsed flowering in a temperate legume: causes and consequences of multimodality in the shape of floral display schedules

description: 1. In plants, the temporal pattern of floral displays, or display
 schedules, delimits an individual's mating opportunities. Thus,
 variation in the shape of display schedules can affect the degree of
 population synchrony and the strength of phenological assortative mating
 by flowering onset date. A good understanding of the mechanisms regulating
 the timing of flowering onset has been developed, but we know less about
 factors influencing subsequent patterns of floral display. 2. We observed
 unusual multimodal display schedules in temperate populations of the
 annual legume Chamaecrista fasciculata. Here we ask if ‘flowering pulses’
 are simultaneous among individuals and populations and explore potential
 underlying mechanisms and consequences of pulsed flowering. 3 .We
 monitored daily flower production for individual plants from genetically
 divergent populations during a series of field experiments that
 manipulated three potential influencers of display schedule shape: average
 daily temperature, pollinator availability, and watering schedules. We
 measured floral longevity to isolate the contributions of flower retention
 and flower deployment to display schedules. We assessed relationships
 between flowering and environmental variables and compared estimates of
 population synchrony, individual synchrony, and the strength of
 assortative mating with those of 29 unimodally-flowering species from the
 area. 4. We observed simultaneous flowering pulses in all experiments,
 with peaks aligned among individuals and populations despite variation in
 flowering onset and/or duration. Pulses were not the result of increases
 in average temperature, pollinator availability, or variation in watering
 schedules. Seasonal fluctuations in temperature correlated with floral
 longevity and flower deployment, suggesting that the shape of display
 schedules may be plastic in response to temperature. Average population
 and individual synchrony differed only slightly from those of the species
 with unimodal schedules, while the average strength of assortative mating
 for flowering onset date was strongly reduced (0.21 in C. fasciculata vs.
 0.35 for the 29 other species). 5. Synthesis. Researchers should take
 caution in assuming that components of display schedules are genetically
 or developmentally correlated with flowering onset. Variation in the shape
 of display schedules can influence patterns of gene-flow within or between
 populations, with potential effects on the strength of phenological
 assortative mating and subsequent responses to selection.
description: The display counts for
 all individual plants in all experimentsDisplay_Counts.csvTemperature, precipitation, and humidity data during the course of all experimentsWeather.csvData for marked and recounted flowers used to estimate floral longevityExp3_Longevity.csvThe volumetric water content of soils for watering treatments from experiment 3Exp3_VWC.csv
DOI: 10.5061/dryad.42b68
title: Data from: Intragenomic nuclear RNA variation in a cryptic Amanita taxon

description: Amanita cf. lavendula collections in eastern North America, Mexico, and
 Costa Rica were found to consist of four cryptic taxa, one of which
 exhibited consistently unreadable nuclear rDNA ITS1-5.8S-ITS2 (fungal
 barcode) sequences after ITS1 base 130. This taxon is designated here as
 Amanita cf. lavendula taxon 1. ITS sequences from dikaryotic basidiomata
 were cloned, but sequences recovered from cloning did not segregate into
 distinct haplotypes. Rather, there was a mix of haplotypes that varied
 among themselves predominantly at 28 ITS positions. Analysis of each of
 these 28 variable bases showed predominantly two alternate bases at each
 position. Based on these findings and additional sequence data from the
 nuclear rDNA 28S, RNA polymerase II subunit 2 (RPB2) and mitochondrial
 rDNA small subunit (SSU) and 23S genes, we speculate that taxon 1
 represents an initial hybridization event between two divergent taxa
 followed by failure of the ribosomal repeat to homogenize. Homogenization
 failure may be a result of repeated hybridization between divergent
 internal transcribed spacer (ITS) types with inadequate time for concerted
 evolution of the ribosomal repeat or, alternately, a complete failure of
 the ribosomal homogenization process. To our knowledge, this finding
 represents the first report of a geographically widespread taxon (Canada,
 eastern USA, Costa Rica) with apparent homogenization failure across all
 collections. Findings such as these have implications for fungal barcoding
 efforts and the application of fungal barcodes in identifying
 environmental sequences.
description: Amanita afn lavendula
 taxon 1 cloned ITS sequencesCloned Amanita afn
 lavendula taxon 1 ITS1-5.8S-ITS2 sequencesAmanita afn_lavendua
 Taxon 1 ITS consensus sequenceAmanita afn lavendula
 taxon 1 ITS consensus sequenceAmanita afn_lavendual Taxon 1
 ITS consensus sequence.txtML tree of Amanita afn
 lavendula taxon 1 ML1-2Nexus file. PhyML tree
 based on Mitochondrial rRNA large subunit sequences amplified with primers
 ML1 and ML2ML tree of Amanita afn
 lavendula taxon 1 ML5-6Nexus file: PhyML
 analyses of mitochondrial rRNA large subunit sequences amplified with
 primers ML5 and ML6ML tree of Amanita afn
 lavendula taxon 1 MS1-2Nexus file: PhyML
 analysis of mitochondrial rRNA 16S sequences amplified with primers MS1
 and MS2ML tree of Amanita afn
 lavendula taxon 1 nrLSUNexus file: PhyML
 analysis of nuclear ribosomal LSU sequences of Amanita afn lavendula taxon
 1ML tree of Amanita afn
 lavendula taxon 1 RPB2_trimmedNexus File: PhyML
 analysis of RPB2 (RNA polymerase 2nd largest subunit) amplified with
 primers bRPB2-6F and fRPB2-7cR (Matheny, PB 2005).
DOI: 10.5061/dryad.125g5
title: Data from: Diving behaviour of Cuvier's beaked whales exposed to two types of military sonar

description: Cuvier's beaked whales (Ziphius cavirostris) have stranded in
 association with mid-frequency active sonar (MFAS) use, and though the
 causative mechanism linking these events remains unclear, it is believed
 to be behaviourally mediated. To determine whether MFAS use was associated
 with behavioural changes in this species, satellite tags were used to
 record the diving and movements of 16 Cuvier's beaked whales for up
 to 88 days in a region of frequent MFAS training off the coast of Southern
 California. Tag data were combined with summarized records of concurrent
 bouts of high-power, surface ship and mid-power, helicopter-deployed MFAS
 use, along with other potential covariates, in generalized additive
 mixed-effects models. Deep dives, shallow dives, and surface intervals
 tended to become longer during MFAS use, with some variation associated
 with total amount of overlapping MFAS during the behaviour. These changes
 in dives and surface intervals contributed to a longer interval between
 deep dives, a proxy for foraging disruption in this species. Most
 responses intensified with proximity and were more pronounced during
 mid-power than high-power MFAS use at comparable distances within ~ 50 km,
 despite the significantly lower source level of mid-power MFAS. However,
 distance-mediated responses to high-power MFAS, and increased deep dive
 intervals during mid-power MFAS, were evident up to ~100 km away.
description: Falcone_ZcPaperMetaDataThis folder contains the R code for the GAMM, as well as all the supporting data associated with the manuscript.Zc Tag-Sonar Field DescriptionsDescriptions of fields contained in the associated text files, including their use in each model.
DOI: 10.5061/dryad.1568n
title: Data from: Early postnatal exposure to airborne fine particulate matter induces autism-like phenotypes in male rats

description: Epidemiological studies have revealed that ambient fine particulate matter
 (PM2.5) exposure is closely associated with autism spectrum disorder
 (ASD). However, there is a relative paucity of laboratory data to support
 this epidemic finding. In order to assess the relationship between PM2.5
 exposure and ASD, neonatal male Sprague-Dawley (SD) rats were chosen and
 exposed to PM2.5 (2 or 20 mg/kg body weight, once a day) by intranasal
 instillation from postnatal day (PND) 8 to 22. It was found that when
 exposed to PM2.5 in the early neonatal period for two weeks, both groups
 of the exposure rats manifested typical behavioral features of autism,
 including communication deficits, poor social interaction and novelty
 avoidance. And, we further found, among five ASD candidate genes we chose,
 both the mRNA level and protein expression of SH3 and multiple ankyrin
 repeat domains 3 (Shank3) decreased significantly in the rat hippocampus
 after high dose of PM2.5 exposure. Moreover, results showed that
 PM2.5-exposure significantly increased the levels of pro-inflammatory
 cytokines, IL-1β, IL-6, and TNF-α in the hippocampus and prefrontal
 cortex. The expression of Glial fibrillary acidic protein (GFAP) and
 ionized binding calcium adapter molecule (IBA1), markers of astrocytes and
 microglial cell activation, respectively, also increased in the exposed
 animals. Our work provides new data on the link between postnatal exposure
 to ambient PM2.5 and the onset of ASD-like symptoms in human beings, and
 the increased inflammatory response and abnormalities in Shank3 expression
 in the brain may contribute to the mechanisms of PM2.5 exposure induced
 ASD.
description: Supplementary
 DataSupplementary
 Data
DOI: 10.5061/dryad.p3215
title: Data from: Social effects for locomotion vary between environments in Drosophila melanogaster females

description: Despite strong purifying or directional selection, variation is ubiquitous
 in populations. One mechanism for the maintenance of variation is indirect
 genetic effects, as the fitness of a given genotype will depend somewhat
 on the genes of its social partners. Indirect genetic effects (IGEs)
 describe the effect of genes in social partners on the expression of the
 phenotype of a focal individual. Here we ask what effect IGEs, and
 variation in IGEs between abiotic environments, has on locomotion in
 Drosophila. This trait is known to be subject to intralocus sexually
 antagonistic selection. We estimate the coefficient of interaction, Ψ,
 using six inbred lines of Drosophila. We found that Ψ varied between
 abiotic environments, and that it may vary across among male genotypes in
 an abiotic environment specific manner. We also found evidence that social
 effects of males alter the value of a sexually dimorphic trait in females,
 highlighting an interesting avenue for future research into sexual
 antagonism. We conclude that IGEs are an important component of social and
 sexual interactions and that they vary between individuals and abiotic
 environments in complex ways, with the potential to promote the
 maintenance of phenotypic variation.
description: Full_DatasetFull Dataset of the movement of D. melanogaster flies. This Data contains Information about average movement in pixels per second of each fly in 5 minute intervals of each experiment. Each line contains information about a single fly. There is also information about the percentage of time the fly spends close to the walls. This is calculated by dividing the circular arena into 2 equal area circles and finding the percentage of time the fly is in the outer circle. The columns labels dist1 and dist2 refer to the average distance between the male and female and the two male flies in each arena respectively.Behavior__Analysis_RfileThe R-code for the Analysis performed
DOI: 10.5061/dryad.7f399
title: Data from: Time series data of a broadleaved secondary forest in Japan as affected by deer and mass mortality of oak trees

description: Background: Abandonment of broadleaved secondary forests that have been
 used for various purposes may cause the loss of biodiversity. Some of
 these forests suffer from diseases such as Japanese oak wilt. An
 increasing number of deer also impact some of them. Monitoring and
 recording the status of such forests is important for their proper
 management. New information: This data set provides a concrete example of
 temporal changes in a temperate broadleaved secondary forest. The forest
 has been damaged by mass mortality of oak trees caused by Japanese oak
 wilt disease. In addition, the forest has been under foraging pressure by
 sika deer (Cervus nippon Temminck). The data set can provide information
 on how such a forest has changed in species composition of the canopy and
 sub-canopy layers and in species occurrence in the understory layer.
description: Site
 dataLocation and stand type
 of each quadrat.Site_data.csvElevation dataElevation of grid points (5 m × 5 m) of the study site.Elev_data.csvStem dataList of all stems found from 1993 to 2014.Stem_data.csvStem measurement dataMeasurements of dbh for each stem from 1993 to 2014. Measurement values in 1999 are missing in the most eastern half of the study site because slope collapse prevention works were conducted near the area.Measurement_data.csvUnderstory dataOccurrence of woody species in the understory layer for each quadrat in 1992 and 2014.Understory_data.csv
DOI: 10.5061/dryad.r236r31
title: Data from: Contrasting heterozygosity-fitness correlations across life in a long-lived seabird

description: Selection is a central force underlying evolutionary change and can vary
 in strength and direction, for example across time and space. The fitness
 consequences of individual genetic diversity have often been investigated
 by testing for multi-locus heterozygosity-fitness correlations (HFCs), but
 few studies have been able to assess HFCs across life stages and in both
 sexes. Here, we test for HFCs using a 26-year longitudinal
 individual-based dataset from a large population of a long-lived seabird
 (the common tern, Sterna hirundo), where 7974 chicks and breeders of known
 age were genotyped at 15 microsatellite loci and sampled for life-history
 traits over the complete life cycle. Heterozygosity was not correlated
 with fledging or post-fledging prospecting probabilities, but was
 positively correlated with recruitment probability. For breeders, annual
 survival was not correlated with heterozygosity, but annual fledgling
 production was negatively correlated with heterozygosity in males and
 highest in intermediately heterozygous females. The contrasting HFCs among
 life stages and sexes indicate differential selective processes and
 emphasize the importance of assessing fitness consequences of traits over
 complete life histories.
description: Contrasting
 heterozygosity-fitness correlations across life in a long-lived
 seabirdBichet_et_al_2018_MolEcol_DRYAD.xlsx
DOI: 10.5061/dryad.2856m
title: Data from: Characterizing male-female interactions using natural genetic variation in Drosophila melanogaster

description: Drosophila melanogaster females commonly mate with multiple males
 establishing the opportunity for pre- and postcopulatory sexual selection.
 Traits impacting sexual selection can be affected by a complex interplay
 of the genotypes of the competing males, the genotype of the female, and
 compatibilities between the males and females. We scored males from 96 2nd
 and 94 3rd chromosome substitution lines for traits affecting reproductive
 success when mated with females from 3 different genetic backgrounds. The
 traits included male-induced female refractoriness, male remating ability,
 the proportion of offspring sired under competitive conditions and
 male-induced female fecundity. We observed significant effects of male
 line, female genetic background, and strong male by female interactions.
 Some males appeared to be “generalists” and performed consistently across
 the different females; other males appeared to be “specialists” and
 performed very well with a particular female and poorly with others.
 “Specialist” males did not, however, prefer to court those females with
 whom they had the highest reproductive fitness. Using 143 polymorphisms in
 male reproductive genes, we mapped several genes that had consistent
 effects across the different females including a derived, high fitness
 allele in Acp26Aa that may be the target of adaptive evolution. We also
 identified a polymorphism upstream of PebII that may interact with the
 female genetic background to affect male-induced refractoriness to
 remating. These results suggest that natural variation in PebII might
 contribute to the observed male–female interactions.
description: GENOTYPESExcel file with the genotypes at each Acp marker in the second and third chromosome lines. 1=AA, 2 = CC, 3 = GG, 4 = TT, 5 = INSERTION, 6 = DELETION, NaN = MISSING DATAPHENOTYPESExcel file with the raw phenotype data in different worksheets.PHENOTYPE_DATA.xlsxAcp26Aa alignmentsMEGA formatACP26AA_ALIGNMENT_MEGA