cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3m0rf
title: Data from: Long-term data suggest jarrah-forest establishment at restored mine sites is resistant to climate variability

description: 1. Global climate change is projected to increase the frequency and
 intensity of drought in dry regions due to warming temperatures and
 declining rainfall. Severe drought can trigger tree mortality and drive
 persistent vegetation change. 2. To date, most empirical studies have
 focused on drought-induced mortality of adult trees, but this needs to be
 matched by similar efforts to understand drought impacts on seedling
 establishment if we are to understand the resilience of the world's
 forests to projected climate change. 3. The Eucalyptus marginata
 (jarrah)-forest ecoregion of south-western Australia has experienced a 17%
 reduction in mean annual rainfall from 1975 to 2011 compared with mean
 rainfall from 1900 to 1974. Drought-induced mortality of adult trees has
 been documented for jarrah forest, but there is limited understanding of
 its capacity to recover, making it difficult to predict the likelihood of
 persistent effects. 4. Long-term records of jarrah-forest restoration
 following bauxite mining are available for the 19-year period between 1992
 and 2010. Records include annual data on seedling establishment in
 restored mine sites for 587 species in 1938 plots during a period of
 climatic variability. 5. We built a structural equation model to
 discriminate the relative effects of climate, restoration practice, and
 their interactive effects on three response variables including species
 richness of the restored plant assemblages. Climate variability had a
 significant negative effect on richness, but the effect size was
 relatively small, being less than half that of varying restoration
 practice. We suggest this is due, in part, to the reliability of rainfall
 (i.e. no change in the coefficient of variation, seasonality or evenness,
 between recent and historical climates) despite a threefold difference in
 the absolute amount of wet-season rainfall. Importantly, there was no
 evidence that restoration practices were compromised by interacting
 effects of increased climate variability. 6. Synthesis. Jarrah-forest
 establishment in a restoration context appears resistant to recent changes
 in climate. Our research highlights the importance of deriving multiple
 metrics of climate change to understand community responses. In
 particular, rainfall reliability should be a focus of future research to
 determine its broader significance to seedling establishment in forests
 subject to a drying climate.
description: Standish et al.
 JEcol-2014-0252R1
DOI: 10.5061/dryad.b649s
title: Data from: Genetic architecture of nonadditive inheritance in Arabidopsis thaliana hybrids

description: The ubiquity of nonparental hybrid phenotypes, such as hybrid vigor and
 hybrid inferiority, has interested biologists for over a century and is of
 considerable agricultural importance. Although examples of both phenomena
 have been subject to intense investigation, no general model for the
 molecular basis of nonadditive genetic variance has emerged, and
 prediction of hybrid phenotypes from parental information continues to be
 a challenge. Here we explore the genetics of hybrid phenotype in 435
 Arabidopsis thaliana individuals derived from intercrosses of 30 parents
 in a half diallel mating scheme. We find that nonadditive genetic effects
 are a major component of genetic variation in this population and that the
 genetic basis of hybrid phenotype can be mapped using genome-wide
 association (GWA) techniques. Significant loci together can explain as
 much as 20% of phenotypic variation in the surveyed population and include
 examples that have both classical dominant and overdominant effects. One
 candidate region inherited dominantly in the half diallel contains the
 gene for the MADS-box transcription factor AGAMOUS-LIKE 50 (AGL50), which
 we show directly to alter flowering time in the predicted manner. Our
 study not only illustrates the promise of GWA approaches to dissect the
 genetic architecture underpinning hybrid performance but also demonstrates
 the contribution of classical dominance to genetic variance.
description: Table S1. Germplasm
 information.The parental genotypes
 of each hybrid are listed along with whether the line was included in the
 final data set (yes=1, no=0). Lines were not included if their
 manually-fertilized parent did not germinate.TableS1.xlsxTable S2. GCA, SCA, and heritability estimates.Values for plots in Fig 1.TableS2.xlsxTable S3. Summary of significant SNPs detected in GWA analyses.Number of significant SNPs detected for each trait for both within-study and across-study Bonferroni correction.TableS3.xlsxTable S4. Summary of significant SNPs per trait.IDs (chr_position) of all significant SNPs and their significance status in each GWA study.TableS4.xlsxTable S5. Summary of SConES SNPs.Number of associated SNPs detected for each trait.TableS5.xlsxTable S6. Summary of associated SConES SNPs per trait.IDs (chr_position) of all associated SNPs and their significance status in each GWA study.TableS6.xlsxTable S7. Summary of candidate genes.IDs and location of all significant regions, their associated traits, genetic behavior, and candidate causal genes.TableS7.xlsxTable S8. Gene Ontology (GO) enrichment.GO terms significantly associated with the top 1,000 associated SNPs of each trait are listed. Significance was established using a 5% FDR threshold within each trait.TableS8.xlsxTable S9. Genomic control (GC) values.Genomic control values for all GWA analyses. Q-Q plots for GWAs with significant SNPs are shown in SI Appendix, Fig S20.TableS9.xlsx
DOI: 10.5061/dryad.d1n31
title: Data from: Ecological speciation in anemone-associated snapping shrimps (Alpheus armatus species complex)

description: Divergent natural selection driven by competition for limited resources
 can promote speciation, even in the presence of gene flow. Reproductive
 isolation is more likely to result from divergent selection when the
 partitioned resource is closely linked to mating. Obligate symbiosis and
 host fidelity (mating on or near the host) can provide this link, creating
 ideal conditions for speciation in the absence of physical barriers to
 dispersal. Symbiotic organisms often experience competition for hosts, and
 host fidelity ensures that divergent selection for a specific host or host
 habitat can lead to speciation and strengthen pre-existing reproductive
 barriers. Here, we present evidence that diversification of a sympatric
 species complex occurred despite the potential for gene flow and that
 partitioning of host resources (both by species and by host habitat) has
 contributed to this diversification. Four species of snapping shrimps
 (Alpheus armatus, A. immaculatus, A. polystictus and A. roquensis) are
 distributed mainly sympatrically in the Caribbean, while the fifth species
 (A. rudolphi) is restricted to Brazil. All five species are obligate
 commensals of sea anemones with a high degree of fidelity and ecological
 specificity for host species and habitat. We analysed sequence data from
 10 nuclear genes and the mitochondrial COI gene in 11–16 individuals from
 each of the Caribbean taxa and from the only available specimen of the
 Brazilian taxon. Phylogenetic analyses support morphology-based species
 assignments and a well-supported Caribbean clade. The Brazilian A.
 rudolphi is recovered as an outgroup to the Caribbean taxa.
 Isolation–migration coalescent analysis provides evidence for historical
 gene flow among sympatric sister species. Our data suggest that both
 selection for a novel host and selection for host microhabitat may have
 promoted diversification of this complex despite gene flow.
description: anemone_IMA2_inputInput files for IMa2 analysis
DOI: 10.5061/dryad.8t2g6
title: Data from: Genetic relationships and ecological divergence in Salix species and populations in Taiwan

description: Linking ecology with evolutionary biology is important to understand how
 environments drive population and species divergence. Phenotypically
 diverse Salix species, such as lowland riparian willow trees and middle-
 to high-elevation multistemmed shrubs and alpine dwarf shrubs, provide
 opportunities for studying genetic divergence driven by ecological
 factors. We used amplified fragment length polymorphism (AFLP) to quantify
 the genetic variation of 185 individuals from nine populations of four
 Salix species in Taiwan. Our phylogenetic analyses distinguished two
 riparian species and the separation of riparian species from multistemmed
 and dwarf shrub species. Variance partitioning for the total data found
 that environment explained a substantially larger proportion of genetic
 variation than geography. However, no genetic variation was explained by
 geography alone when only compared within and between species. Spatially
 structured regional environmental effects explained more variation than
 pure environments in most comparisons within and between species,
 suggesting that unmeasured environmental variables and/or past demographic
 histories played important roles in shaping population and species
 divergence. Based on forward selection analysis, annual mean temperature,
 aspect, and fraction of absorbed photosynthetically active radiation were
 the most influential ecological factors in shaping genetic variation
 within and between species. Nevertheless, different combinations of
 environmental variables correlated significantly with genetic variation
 within and between species. We identified eight AFLP loci that potentially
 evolved under selection intraspecifically using different outlier
 detection methods. These loci correlated with more than one environmental
 variable, suggesting local adaptation along environmental gradients at the
 population level.
description: SalixaflpAmplified fragment length polymorphism (AFLP) genotyping data of 185 samples from nine populations of four Taiwanese Salix species and eight samples from six Chinese Salix species .
DOI: 10.5061/dryad.7fd7p
title: Data from: Edge influence on vegetation at natural and anthropogenic edges of boreal forests in Canada and Fennoscandia

description: 1. Although anthropogenic edges are an important consequence of timber
 harvesting, edges due to natural disturbances or landscape heterogeneity
 are also common. Forest edges have been well-studied in temperate and
 tropical forests, but less so in less productive, disturbance-adapted
 boreal forests. 2. We synthesized data on forest vegetation at edges of
 boreal forests and compared edge influence among edge types (fire, cut,
 lake/wetland; old vs. young), forest types (broadleaf vs. coniferous) and
 geographic regions. Our objectives were to quantify vegetation responses
 at edges of all types and to compare the strength and extent of edge
 influence among different types of edges and forests. 3. Research was
 conducted using the same general sampling design in Alberta, Ontario and
 Quebec in Canada, and in Sweden and Finland. We conducted a meta-analysis
 for a variety of response variables including forest structure, deadwood
 abundance, regeneration, understorey abundance and diversity, and
 nonvascular plant cover. We also determined the magnitude and distance of
 edge influence using randomization tests. 4. Some edge responses (lower
 tree basal area, tree canopy and bryophyte cover; more logs; higher
 regeneration) were significant overall across studies. Edge influence on
 ground vegetation in boreal forests was generally weak, not very extensive
 (distance of edge influence usually &lt; 20 m) and decreased with
 time. We found more extensive edge influence at natural edges, at younger
 edges and in broadleaf forests. The comparison among regions revealed
 weaker edge influence in Fennoscandian forests. 5. Synthesis. Edges
 created by forest harvesting do not appear to have as strong, extensive or
 persistent influence on vegetation in boreal as in tropical or temperate
 forested ecosystems. We attribute this apparent resistance to shorter
 canopy heights, inherent heterogeneity in boreal forests and their
 adaptation to frequent natural disturbance. Nevertheless, notable
 differences between forest structure responses to natural (fire) and
 anthropogenic (cut) edges raise concerns about biodiversity implications
 of extensive creation of anthropogenic edges. By highlighting universal
 responses to edge influence in boreal forests that are significant
 irrespective of edge or forest type, and those which vary by edge type, we
 provide a context for the conservation of boreal forests.
description: Data for meta-analysis
 and synthesis of boreal edgesData from each study is
 on a separate page, labelled with the study area and study number. Please
 see the article Table 2. On each page, data are at different distances
 from the edge along transects for different response variables. Please see
 the article Table S1 for details on sampling and data
 collection.Boreal edges data for
 Dryad.xls
DOI: 10.15468/dl.69ydz8
title: Occurrence Download

description: A dataset containing 1040544 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "TaxonKey is Tracheophyta",
 {
 "or" : [
 "GadmGid is CAN.11_1",
 "StateProvince is one of (Quebec, Québec, Québec (Prov.), Quebec Province, Que, Que., Quebec / Québec, Nunavit, Quebec Prov., Qu#bec, Quebec/Labrador, Montreal, Qu√©bec, Ontario/Quebec, Ontario - Quebec, Quebec prov, Québec - Nunavik, Quebec prov., Qubec, Quebec, The Quebec sector of the Ottawa District, Quebeck, Qu�#bec, Qu_bec, Quebec/Québec, Quebéc, [Quebec], Ungava and Labrador, Labrador Prov., Province de Québec, QuÃ©bec, Newfoundland, Labrador, Nunavik, Pq, Quebec ?, Quebec province, Quebec-Labrador, Quebec?, Prov. Quebec, quebec, Ontario,Quebec, Quinbec, Ontario, Quebec, Nouveau-Quebec, Province of Quebec, Quebeq, Québec/Quebec, Ontario / Quebec, Quabec, Montreal?, Newfoundland and Labrador / Quebec, Province/Subdivision: Quebec/Nunavik, Nearest town/village: Kuujjuaq, Quebec County, Québec Nordique, Montreal, Canada., Newfoundland and Labrador/Quebec, QUEBEC PROV., Québec, Nunavik, Montréal, Prov. Québec, Province Quebec, Província Quebec, Qebec, Qubec/Ontario, Quebe, Quebec (魁北克), Quebec, Blue Sea Lake, Quebec, Ontario, Québec - Labrador, queb, Canada: Quebec, Foret Montmorency, Res. faunique des Laurentides., Gaspe Peninsula, Gaspe Pininsula, Gaspe-est, Gulf of St. Lawrence, Labr, Labr., Labrador 59°NB, Labrador Peninsula, Labrador, 59°NB, Labrador, Hudson Bay, Labrador, coastal region, Motreal, New Quebec Territory, Newfoundland / Quebec, Newfoundland and Labrador, Québec, Newfoundland, Quebec, Northern Québec, Nova Scotia and Quebec, Nova Scotia,Ontario,Quebec, Nova Scotia, Quebec & Ontario, Oka, Deux-Montagnes County., Ontario-Quebec, Ontario.Quebec, Kamouraska, Ouebec, Plantes du Quebec, Province de Quebec, Province de quebec, Province of Quebec., Province/Subdivision: Quebec/Nunavik, Nearest town/village: Kuujjuarapik, Province/Subdivision: Quebec/Nunavik, Nearest town/village: Kangiqsujuaq, QUebec, Qeubec, QubÃ©ec, Quebc, QuebeC Province, Quebec (魁北克省), Quebec, Brompton, Quebec, S, Quebec, S., Quebed/Labrador, QuebÃ©c, Québe)"
 ]
 }
 ]
}

 The dataset includes 1040544 records from 350 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000522-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3640g
title: Data from: Learning to speciate: the biased learning of mate preferences promotes adaptive radiation

description: Bursts of rapid repeated speciation called adaptive radiations have
 generated much of Earth’s biodiversity and fascinated biologists since
 Darwin, but we still do not know why some lineages radiate and others do
 not. Understanding what causes assortative mating to evolve rapidly and
 repeatedly in the same lineage is key to understanding adaptive radiation.
 Many species that have undergone adaptive radiations exhibit mate
 preference learning, where individuals acquire mate preferences by
 observing the phenotypes of other members of their populations. Mate
 preference learning can be biased if individuals also learn phenotypes to
 avoid in mates, and shift their preferences away from these avoided
 phenotypes. We used individual-based computational simulations to study
 whether biased and unbiased mate preference learning promote ecological
 speciation and adaptive radiation. We found that ecological speciation can
 be rapid and repeated when mate preferences are biased, but is inhibited
 when mate preferences are learned without bias. Our results suggest that
 biased mate preference learning may play an important role in generating
 animal biodiversity through adaptive radiation.
description: Gilman and Kozak
 codesCodes used to generate
 simulated data.
DOI: 10.5061/dryad.1p3kn
title: Data from: Individual correlates of infectivity of influenza A virus infections in households

description: Background: Identifying individual correlates of infectivity of influenza
 virus is important for disease control and prevention. Viral shedding is
 used as a proxy measure of infectivity in many studies. However, the
 evidence for this is limited. Methods: In a detailed study of influenza
 virus transmission within households in 2008–12, we recruited index cases
 with confirmed influenza infection from outpatient clinics, and followed
 up their household contacts for 7–10 days to identify secondary
 infections. We used individual-based hazard models to characterize the
 relationship between individual viral shedding and individual infectivity.
 Results: We analyzed 386 households with 1147 household contacts. Index
 cases were separated into 3 groups according to their estimated level of
 viral shedding at symptom onset. We did not find a statistically
 significant association of virus shedding with transmission. Index cases
 in medium and higher viral shedding groups were estimated to have 21% (95%
 CI: -29%, 113%) and 44% (CI: -16%, 167%) higher infectivity, compared with
 those in the lower viral shedding group. Conclusions: Individual viral
 load measured by RT-PCR in the nose and throat was at most weakly
 correlated with individual infectivity in households. Other correlates of
 infectivity should be examined in future studies.
description: Read me (data file
 explanations)Household
 dataThis data file contains
 information on the information recrutied from the household transmission
 study in Hong Kong, from 2008-2012.data.csvInfluenza proxy dataThe influenza proxy used in the analysis. ( 1/1/2008 is set as Day 1)ILILAB.csvScripts of log-linear random effects modelR syntax to use log-linear random effects censored regression model to fix the observed viral shedding data and divide index cases into three viral shedding groups. This will create a data file [grouped_data.csv] for further analysis.lmec regression.rRegression model resultsThe results generated from the above log-linear random effects censored regression model.grouped_data.csvMatlab function 1Contain the matlab function to generate results on the model in the main analysis.Model_1.mMatlab function 2Contain the matlab function to generate results on the additional analysis of exploring the effect of presence of symptom. (a to i respents fever, sore throat, cough, runny nose, phlegm, muscle pain, headache, any three or more of above symptoms and ILI (fever + cough or sough) ).Model_2.mFigure 1 scriptsFigure_1.rTable 1 scriptsTable_1.rTable 2 scriptsTable_2.rTable 3 scriptsTable_3.r
DOI: 10.5061/dryad.mt685
title: Data from: Socioeconomic determinants of antibiotic consumption in the state of São Paulo, Brazil: the effect of restricting over-the-counter sales

description: Background: Improper antibiotic use is one of the main drivers of
 bacterial resistance to antibiotics, increasing infectious diseases
 morbidity and mortality and raising costs of healthcare. The level of
 antibiotic consumption has been shown to vary according to socioeconomic
 determinants (SED) such as income and access to education. In many Latin
 American countries, antibiotics could be easily purchased without a
 medical prescription in private pharmacies before enforcement of
 restrictions on over-the-counter (OTC) sales in recent years. Brazil
 issued a law abolishing OTC sales in October 2010. This study seeks to
 find SED of antibiotic consumption in the Brazilian state of São Paulo
 (SSP) and to estimate the impact of the 2010 law. Methods: Data on all
 oral antibiotic sales having occurred in the private sector in SSP from
 2008 to 2012 were pooled into the 645 municipalities of SSP. Linear
 regression was performed to estimate consumption levels that would have
 occurred in 2011 and 2012 if no law regulating OTC sales had been issued
 in 2010. These values were compared to actual observed levels, estimating
 the effect of this law. Linear regression was performed to find
 association of antibiotic consumption levels and of a greater effect of
 the law with municipality level data on SED obtained from a nationwide
 census. Results: Oral antibiotic consumption in SSP rose from 8.44 defined
 daily doses per 1,000 inhabitants per day (DID) in 2008 to 9.95 in 2010,
 and fell to 8.06 DID in 2012. Determinants of a higher consumption were
 higher human development index, percentage of urban population, density of
 private health establishments, life expectancy and percentage of females;
 lower illiteracy levels and lower percentage of population between 5 and
 15 years old. A higher percentage of females was associated with a
 stronger effect of the law. Conclusions: SSP had similar antibiotic
 consumption levels as the whole country of Brazil, and they were
 effectively reduced by the policy.
description: Oral antibiotic
 consumption in the state of São Paulo, 2008-2012Data about retail
 antibiotic sales by pharmacy in the state of São Paulo for the years of
 2008 to 2012, measured in defined daily doses, were provided by
 Intercontinental Medical Health Statistics Brazil. These data were
 organised calculating annual oral antibiotic consumption for each
 municipality, and merged with socioeconomic variables, available from a
 national census, to create this data file, using the statistical software
 STATA 13.0. Predicted consumption was calculated using linear regression,
 and the policy effect variables was calculated as follows: (100*(Observed
 consumption in 2011 and 2012-predicted consumption in 2011 and
 2012))/(predicted consumption in 2011 and 2012). Sheet 2 contains data on
 monthly oral antibiotic consumption in the state of São Paulo during the
 same period.SPoralatbconsumption.xlsx