cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15482/usda.adc/29645888
title: Data and code from: Virome of <i>Solenopsis invicta</i> (Hymenoptera: Formicidae): intercontinental differences in the native and introduced ranges

description: This dataset contains all the raw data and R statistical software code needed to reproduce the maps and statistical analyses presented in the associated manuscript, titled “Virome of <i>Solenopsis invicta</i> (Hymenoptera: Formicidae): intercontinental differences in the native and introduced ranges.” In the manuscript, results are presented from a survey of viruses in 430 red imported fire ant nests at a total of 82 sites in its native range in Argentina and introduced range in the United States. A series of maps and graphs are generated to qualitatively describe the distribution of twenty different viruses, including prevalence of different social forms (monogyne and polygyne colonies) in each continent, and viral abundance by location and by season. In addition, we present a generalized linear mixed model that models the probability of virus presence as a function of viral species, continent, and social form. We investigate spatial patterning in model residuals and we compare the odds of each social form by virus within each continent and the odds of presence of each virus between the two continents. Raw data is provided in CSV form, and code is provided as an RMarkdown notebook along with its rendered HTML output. In addition, a GEOJSON file is included with the spatial coordinates of the study sites.Files<b>Virome survey S_invicta.csv</b>: All raw data, including site-level covariates and coordinates of colony locations within each site. Column "GP9" indicates the social form of the sampled colony (Monogyne or Polygyne) and all following columns indicate presence (1) or absence (0) of 18 different viruses<b>fire_ant_virome_code_supplement.Rmd</b>: RMarkdown notebook with all code needed to import and process the data, generate maps and other figures, fit statistical models, and produce figures and tables with statistical model predictions.<b>fire_ant_virome_code_supplement.html</b>: Rendered output from code notebook<b>fire_ant_sampling_sites.geojson</b>: Spatial coordinates of the 82 sampling sites (unprojected latitude-longitude)
DOI: 10.15482/usda.adc/29645888.v1
title: Data and code from: Virome of <i>Solenopsis invicta</i> (Hymenoptera: Formicidae): intercontinental differences in the native and introduced ranges

description: This dataset contains all the raw data and R statistical software code needed to reproduce the maps and statistical analyses presented in the associated manuscript, titled “Virome of <i>Solenopsis invicta</i> (Hymenoptera: Formicidae): intercontinental differences in the native and introduced ranges.” In the manuscript, results are presented from a survey of viruses in 430 red imported fire ant nests at a total of 82 sites in its native range in Argentina and introduced range in the United States. A series of maps and graphs are generated to qualitatively describe the distribution of twenty different viruses, including prevalence of different social forms (monogyne and polygyne colonies) in each continent, and viral abundance by location and by season. In addition, we present a generalized linear mixed model that models the probability of virus presence as a function of viral species, continent, and social form. We investigate spatial patterning in model residuals and we compare the odds of each social form by virus within each continent and the odds of presence of each virus between the two continents. Raw data is provided in CSV form, and code is provided as an RMarkdown notebook along with its rendered HTML output. In addition, a GEOJSON file is included with the spatial coordinates of the study sites.Files<b>Virome survey S_invicta.csv</b>: All raw data, including site-level covariates and coordinates of colony locations within each site. Column "GP9" indicates the social form of the sampled colony (Monogyne or Polygyne) and all following columns indicate presence (1) or absence (0) of 18 different viruses<b>fire_ant_virome_code_supplement.Rmd</b>: RMarkdown notebook with all code needed to import and process the data, generate maps and other figures, fit statistical models, and produce figures and tables with statistical model predictions.<b>fire_ant_virome_code_supplement.html</b>: Rendered output from code notebook<b>fire_ant_sampling_sites.geojson</b>: Spatial coordinates of the 82 sampling sites (unprojected latitude-longitude)
DOI: 10.5061/dryad.rm090
title: Data from: Population genetic analysis of a parasitic mycovirus to infer the invasion history of its fungal host

description: Hymenoscyphus fraxineus mitovirus 1 (HfMV1) occurs in the fungus
 Hymenoscyphus fraxineus, an introduced plant pathogen responsible for the
 devastating ash dieback epidemic in Europe. Here, we explored the
 prevalence and genetic structure of HfMV1 in order to elucidate the
 invasion history of both the virus and the fungal host. A total of 1298 H.
 fraxineus isolates (181 from Japan and 1117 from Europe) were screened for
 the presence of this RNA virus and 301 virus-positive isolates subjected
 to partial sequence analysis of the viral RNA polymerase gene. Our results
 indicate a high mean prevalence (78.7%) of HfMV1 across European H.
 fraxineus isolates, which is supported by the observed high transmission
 rate (average 83.8%) of the mitovirus into sexual spores of its host. In
 accordance with an expected founder effect in the introduced population in
 Europe, only 1.1% of the Japanese isolates were tested virus positive. In
 Europe, HfMV1 shows low nucleotide diversity but a high number of
 haplotypes, which seem to be subjected to strong purifying selection.
 Phylogenetic and clustering analysis detected two genetically distinct
 HfMV1 groups, both present throughout Europe. This pattern supports the
 hypothesis that only two (mitovirus-carrying) H. fraxineus individuals
 were introduced into Europe as previously suggested from the bi-allelic
 nature of the fungus. Moreover, our data points to reciprocal mating
 events between the two introduced individuals, which presumably initiated
 the ash dieback epidemic in Europe.
description: CH_LT_SSR_HfMV1group_300916_dryadSSR data for the small-scale dataset. 200 fungal isolates were genotyped at 11 microsatellite loci.HfMV1 groups and virulenceHfMV1_groups_and_virulencefor_dryad_111016.xlsxTable S3overall pairwise identities (nuclear sequences)Suplementary tables S3a,b,c.xlsxSupplementary tables S4a,b,coverall pairwise identities (amino acid sequences)Suplementary tables S4a,b,c.xlsx
DOI: 10.5061/dryad.1pr7k
title: Data from: Twenty-four years after the Yellowstone fires: are postfire lodgepole pine stands converging in structure and function?

description: Disturbance and succession have long been of interest in ecology, but how
 landscape patterns of ecosystem structure and function evolve following
 large disturbances is poorly understood. After nearly 25 years, lodgepole
 pine (Pinus contorta var. latifolia) forests that regenerated after the
 1988 Yellowstone Fires (Wyoming, USA) offer a prime opportunity to track
 the fate of disturbance-created heterogeneity in stand structure and
 function in a wilderness setting. In 2012, we resampled 72 permanent plots
 to ask (1) How have postfire stand structure and function changed between
 11 and 24 yr postfire, and what variables explain these patterns and
 changes? (2) How has landscape-level (among-stand) variability in postfire
 stand structure and function changed between 11 and 24 yr postfire? We
 expected to see evidence of convergence beginning to emerge, but also that
 initial postfire stem density would still determine trajectories of
 biomass accumulation. After 24 yr, postfire lodgepole pine density
 remained very high (mean = 21,738 stems ha−1, range = 0 to 344,067 stems
 ha−1). Stem density increased in most plots between 11 and 24 yr postfire,
 but declined sharply where 11-yr-postfire stem density was &gt; 72,000
 stems ha−1. Stems were small in high-density stands, but stand-level
 lodgepole pine leaf area, foliage biomass, and live aboveground biomass
 increased over time and with increasing stem density. After 24 yr, mean
 annual lodgepole pine aboveground net primary production (ANPP) was high
 (mean = 5 Mg ha−1 yr−1, range = 0 to 16.5 Mg ha−1 yr−1). Among stands,
 lodgepole pine ANPP increased with stem density, which explained 69% of
 the variation; another 8% of the variation was explained by environmental
 covariates. Early patterns of postfire lodgepole pine regeneration, which
 were contingent on prefire serotiny and fire severity, remained the
 dominant driver of stand structure and function. We observed mechanisms
 that would lead to convergence in stem density (structure) over time, but
 it was landscape variation in functional variables that declined
 substantially. Stand structure and function have not converged across the
 burned landscape, but our evidence suggests function will converge sooner
 than structure.
description: YNP 2012 Extensive Data
 DryadThese data are for 2012
 in an Excel spreadsheet containing three sheets of data and one of
 metadata.YNP 1999 Extensive Data
 DryadThese data are for 1999
 (originally included in Turner et al. 2004, Ecosystems) and are in an
 Excel spreadsheet with three sheets of data and one with
 metadata.
DOI: 10.5061/dryad.q2t56
title: Data from: Climate change will increase savannas at the expense of forests and treeless vegetation in tropical and subtropical Americas

description: 1. Transition areas between biomes are particularly sensitive to
 environmental changes. Our understanding of the impacts of ongoing climate
 change on terrestrial ecosystems has significantly increased during the
 last years. However, it is largely unknown how climatic change will affect
 transitions among major vegetation types. 2. We modelled the distribution
 of three alternative states (forest, savanna and treeless areas) in the
 tropical and subtropical Americas by means of climate-niche modelling. We
 studied how such distribution will change by the year 2070 by using 17
 downscaled and calibrated global climate models from the Coupled Model
 Intercomparison Project Phase 5 and the latest scenarios provided by the
 5th Assessment Report of the IPCC. 3. Our results support the
 savannization of the tropical and subtropical Americas because of climate
 change, with an increase in savannas mainly at the expense of forests. 4.
 Our models predict an important geographical shift in the current
 distribution of transition areas between forest and savannas, which is
 much less pronounced in the case of those between savannas and treeless
 areas. Largest shifts, up to 600 km northward, are predicted in the
 forest–savanna transitions located in the eastern Amazon. 5. Our findings
 indicate that climate change will promote a shift towards more unstable
 states: the extent of the transition areas will notably increase, and
 largely stable forest areas are predicted to shrink dramatically. 6.
 Synthesis. Our work explores dimensions of the impact of climate change on
 biomes that have received little attention so far. Our results indicate
 that climate change will not only affect the extent of savanna, forest and
 treeless areas in the tropical and subtropical Americas, but also will:
 (i) promote a significant geographical shift and an increase of the extent
 of transition areas between biomes and (ii) decrease the stability of the
 equilibrium between forest, savanna and treeless areas, yielding a more
 unpredictable system.
description: 10Mpoints_database_Anadonetal2014JECOLData used to fit the models. It includes information of 10000 2.5x2.5min cells randomly selected in the Americas. Columns: X coordinate, Y coordinate, Mean Annual Temperature (BIO1), Mean annual precipitation (BIO13), Potential evapotranspiration (PET), Tree cover (MOD44B) and dominant land use (GLC). Models were fitted to only those cells within our study area (35N-35S) and with non-human land uses (i.e. excluding land uses 16-18 and 22). For further details see Materials and Methods section of the article.
DOI: 10.5061/dryad.1rd15
title: Data from: Flower resource and land management drives hoverfly communities and bee abundance in semi-natural and agricultural grasslands

description: 1. Pollination is a key ecosystem service, and appropriate management,
 particularly in agricultural systems, is essential to maintain a diversity
 of pollinator guilds. However, management recommendations frequently focus
 on maintaining plant communities, with the assumption that associated
 invertebrate populations will be sustained. 2. We tested whether plant
 community, flower resources and soil moisture would influence hoverfly
 (Syrphidae) abundance and species richness in floristically-rich
 semi-natural and floristically-impoverished agricultural grassland
 communities in Wales (U.K.), and compared these to two Hymenoptera genera,
 Bombus and Lasioglossum. Interactions between environmental variables were
 tested using generalised linear modelling, and hoverfly community
 composition examined using canonical correspondence analysis. 3. There was
 no difference in hoverfly abundance, species richness, or bee abundance,
 between grassland types. There was a positive association between hoverfly
 abundance, species richness and flower abundance in unimproved grasslands.
 However, this was not evident in agriculturally improved grassland,
 possibly reflecting intrinsically low flower resource in these habitats,
 or the presence of plant species with low or relatively inaccessible
 nectar resources. There was no association between soil moisture content
 and hoverfly abundance or species richness. 4. Hoverfly community
 composition was influenced by agricultural improvement and the amount of
 flower resource. Hoverfly species with semi-aquatic larvae were associated
 with both semi-natural and agricultural wet grasslands, possibly because
 of localised larval habitat. Despite the absence of differences in
 hoverfly abundance and species-richness, distinct hoverfly communities are
 associated with marshy grasslands, agriculturally improved marshy
 grasslands and unimproved dry grasslands, but not with improved dry
 grasslands. 5. Grassland plant community cannot be used as a proxy for
 pollinator community. Management of grasslands should aim to maximise the
 pollinator feeding resource, as well as maintain plant communities.
 Retaining waterlogged ground may enhance the number of hoverflies with
 semi-aquatic larvae.
description: Lucas et al 2017
 DataExcel file of insects
 recorded during study
DOI: 10.5061/dryad.cr5751br
title: Data from: Regional pools and environmental controls of vertebrate richness

description: The species richness of local communities depends on the richness of the
 regional pool and the filtering processes that preclude some regional
 species from occurring locally. These filters may include absolute
 attributes of the local environment and also how representative the local
 environment is of the surrounding region. The latter is consistent with a
 species sorting perspective, in which regional species only occupy the
 local habitats to which they are adapted. Here we evaluate the relative
 effects of local environmental conditions, environmental
 representativeness and environment-independent processes on the
 probability of local species occurrence, given their regional presence, of
 birds, mammals and amphibians worldwide. In multi-predictor models,
 environmental representativeness is a strong independent predictor of
 local species occurrence probability, with a relative contribution greater
 than that of absolute local environmental conditions. Further, we find
 that local occurrence probability diminishes with increased regional
 richness, independent of the local environment. This is consistent with
 reduced local occupancy in richer regions, a pattern which could stem from
 a largely neutral community assembly process. Our results support the
 importance of both environment-independent and species-sorting processes
 and suggest that regional richness and environmental representativeness
 should be jointly used for understanding richness gradients across scales.
description: Bird and mammal species
 inventory locations.This file describes all
 local species inventories of birds and mammals used in this study. The
 name, country, geographic location, and size of each location are
 provided.Dryad.docDryad.pdf
DOI: 10.5061/dryad.217fn
title: Data from: The roles of geography and environment in divergence within and between two closely related plant species inhabiting an island-like habitat

description: Aim: In island-like habitats, geographic isolation facilitates population
 and species divergence by constraining gene flow, while environmental
 isolation can enhance divergence. We tested the relative contribution of
 geographic and environmental isolation in genetic and phenotypic
 divergence within and between two species of the figwort Ameroglossum
 (Scrophulariaceae) inhabiting spatially isolated habitats, known as
 inselbergs. Location: Borborema Plateau, north-eastern Brazil. Methods:
 Multivariate models of redundancy (RDAs) and partial redundancy analyses
 (pRDAs) were used to partition the geographic and climate components of
 genetic variation in 48 microsatellite alleles, and phenotypic variation
 in 11 leaf and flower traits. We also used linear mixed-effect models
 (LMEs) to test independent associations of floral tube length variation
 among inselbergs with local pollinator phenotypes, climate and geography.
 In each approach, we analysed the data for each species separately and in
 pooled models for both species. Results: RDAs revealed that genetic
 variation within and between the species of Ameroglossum was associated
 similarly with geography and climate. Phenotypic variation within A.
 manoel-felixii and between species was also associated similarly with
 geography and climate but, within A. pernambucense, phenotype was more
 strongly associated with climate. Linear mixed-effect models revealed that
 flower divergence in A. manoel-felixii was associated only with the bill
 length of local hummingbirds, whereas floral variation in A. pernambucense
 was associated with geography, bill length and climate. Only climate was
 associated with flower divergence between species. Main conclusions:
 Genetic and phenotypic variation in Ameroglossum are associated with
 geographic and environmental isolation. These findings indicate a
 significant role of ecological factors shaping plant divergence among
 inselbergs, irrespective of their spatial distances.
description: Geographic locations of
 sampling sitesGeographic coordinates
 in decimal degrees of the sampling locations.Genetic
 RDAs-dataData used to test
 associations of genetic variation with geography and climate by means of
 RDA and pRDA.Phenotypic
 RDAs-dataData used to test
 associations of phenotypic variation with geography and climate by means
 of RDA and pRDA.Floral tube length
 variation-dataData used to test
 associations of flower variation with geography, pollinators and climate
 by means of linear mixed-effect models (LMEs)..
DOI: 10.5061/dryad.nt4h3
title: Data from: The effects of familiarity and mating experience on mate choice in mosquitofish, Gambusia holbrooki

description: A preference to mate with novel partners has been shown for both males and
 females in a range of taxa. Preferences for novel mates may result from
 direct recognition of previous sexual partners, or from other cues that
 predict this, such as familiarity. Costs and benefits of mating with
 multiple mates differ for males and females. Despite this, few studies
 have tested whether the sexes differ in their preferences for novel mates.
 Here, we investigated whether males and/or females showed preferences for
 novel mates and whether this differed depending on the type of experience
 with a familiar mate (i.e., previously allowed to mate or allowed visual
 and olfactory exposure only) in the eastern mosquitofish (Gambusia
 holbrooki). We show that mosquitofish prefer to associate with novel fish
 and that there was no significant difference between the sexes in the
 strength of this preference if the choosing fish had previously had an
 opportunity to mate. In contrast, males and females that had not recently
 mated and were familiar due solely to visual and olfactory contact did not
 have a preference for novel mates. Our results suggest that there are
 likely to be benefits of mating with multiple partners for both males and
 females.
description: Vega-Trejo et al. 2014.
 Behav.Ecol. DryadThe file shows the data
 from the manuscript "The effects of familiarity and mating experience
 on mate choice in mosquitofish, Gambusia holbrooki" by Regina
 Vega-Trejo, Rose E. O’Dea, Michael D. Jennions, and Megan L. Head in
 Behavioral Ecology.
DOI: 10.5061/dryad.3780c
title: Data from: Genetic and morphological evidence of a geographically widespread hybrid zone between two crocodile species, Crocodylus acutus and Crocodylus moreletii

description: Hybrid zones represent natural laboratories to study gene flow, divergence
 and the nature of species boundaries between closely related taxa. We
 evaluated the level and extent of hybridization between Crocodylus
 moreletii and C. acutus using genetic and morphological data on 300
 crocodiles from 65 localities. To our knowledge, this is the first genetic
 study that includes the entire historic range and sympatric zone of the
 two species. Contrary to expectations, Bayesian admixture proportions and
 maximum likelihood estimates of hybrid indexes revealed that most sampled
 crocodiles were admixed and that the hybrid zone is geographically
 extensive, extending well beyond their historical region of sympatry. We
 identified a few geographically isolated, non-admixed populations of both
 parental species. Hybrids do not appear to be F1s or recent backcrosses,
 but rather are more likely later-generation hybrids, suggesting that
 hybridization has been going on for several to many generations and is
 mostly the result of natural processes. C. moreletii is not the sister
 species of C. acutus, suggesting that the hybrid zone formed from
 secondary contact rather than primary divergence. Non-admixed individuals
 from the two species were distinguishable based on morphological
 characters, whereas hybrids had a complex mosaic of morphological
 characters that hinders identification in the wild. Very few non-admixed
 C. acutus and C. moreletii populations exist in the wild. Consequently,
 the last non-admixed C. moreletii populations have become critically
 endangered. Indeed, not only the parental species but also the naturally
 occurring hybrids should be considered for their potential conservation
 value.
description: Coord_msat_alleles File contains data for each sample with the locality (name of locality), coordinates (WGS84) and microsatellite genotypes for all individuals msat_Alleles.csv Mantel_Matrix Matrix of individual pairwise geographic distance (kilometers; below diagonal) and genetic distances (above diaginal; Nei´s DA; Nei et al. 1983).