cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dp157
title: Data from: Predicting community structure in snakes on Eastern Nearctic islands using ecological neutral theory and phylogenetic methods

description: Predicting species presence and richness on islands is important for
 understanding the origins of communities and how likely it is that species
 will disperse and resist extinction. The equilibrium theory of island
 biogeography (ETIB) and, as a simple model of sampling abundances, the
 unified neutral theory of biodiversity (UNTB), predict that in situations
 where mainland to island migration is high, species-abundance
 relationships explain the presence of taxa on islands. Thus, more abundant
 mainland species should have a higher probability of occurring on adjacent
 islands. In contrast to UNTB, if certain groups have traits that permit
 them to disperse to islands better than other taxa, then phylogeny may be
 more predictive of which taxa will occur on islands. Taking surveys of 54
 island snake communities in the Eastern Nearctic along with mainland
 communities that have abundance data for each species, we use phylogenetic
 assembly methods and UNTB estimates to predict island communities. Species
 richness is predicted by island area, whereas turnover from the mainland
 to island communities is random with respect to phylogeny. Community
 structure appears to be ecologically neutral and abundance on the mainland
 is the best predictor of presence on islands. With regard to young and
 proximate islands, where allopatric or cladogenetic speciation is not a
 factor, we find that simple neutral models following UNTB and ETIB predict
 the structure of island communities.
description: Code_Burbrink_et_al_2015R code to run statistics in Burbrink et al. 2015.Appendix I.Sites_Presence_AbundancePresence and abundance datafiles for mainland and island communities in csv format.Damocles Island SimulationsThese are the Damocles-generated island simulations in R format, therefore they are read in R using the dget() command (see R code file).DAM_ISL_SIMDamocles-generated mainland simulationsThese are the Damocles-generated mainland simulations in R format, therefore they are read in R using the dget() command (see R code file).DAM_MAIN_SIMIsland Presence Only FileThis shows presence of snakes on each island in the Eastern Nearctic.ISL_PRESMainland presence onlyThis shows presence of snakes in adjacent mainland communities in the Eastern Nearctic.MAIN_PRES.txtIsland Presence and Mainland AbundanceThis is the island presence with mainland abundance file in R format, so read in R using the dget() command. See code for using this.Islands_GLMM_REM_0_FReqPhylogenyThe phylogeny of snakes in the US, to be used for the Eastern Nearctic.Tree.txt
DOI: 10.15468/dl.m3ve48
title: Occurrence Download

description: A dataset containing 600 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Dryopteris championii"
 ]
}

 The dataset includes 600 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001647-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.623wxm
title: Occurrence Download

description: A dataset containing 166 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Dacrycarpus cumingii"
 ]
}

 The dataset includes 166 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001649-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.nv5d2
title: Data from: Forage species in predator diets: synthesis of data from the California Current

description: Characterization of the diets of upper-trophic pelagic predators that
 consume forage species is a key ingredient in the development of
 ecosystem-based fishery management plans, conservation of marine
 predators, and ecological and economic modeling of trophic interactions.
 Here we present the California Current Predator Diet Database (CCPDD) for
 the California Current region of the Pacific Ocean over the past century,
 assimilating over 190 published records of predator food habits for over
 100 predator species and 32 categories of forage taxa (species or groups
 of similar species). Literature searches targeted all predators that
 consumed forage species: seabirds, cetaceans, pinnipeds, bony and
 cartilaginous fishes, and a predatory invertebrate. Diet data were
 compiled into a relational database. Analysis of the CCPDD highlighted
 differences in predator diet data availability based on geography, time
 period and predator taxonomy, as well as prominent prey categories. The
 top 5 forage taxa with the most predators included juvenile rockfish,
 northern anchovy, euphausiid krill, Pacific herring and market squid.
 Predator species with abundant data included Pacific hake, common murre,
 and California sea lion. Most diet data were collected during the summer;
 the lack of winter data will restrict future use of the CCPDD to
 understand seasonal patterns in predator diet unless more such data become
 available. Increased synthesis of historical information can provide new
 resources to understand patterns in the role of forage species in predator
 diet. Increased publication and/or accessibility of long-term datasets and
 data-sharing will further foster the synthesis of information intended to
 inform the management, conservation and understanding of marine food webs.
description: CCPDD Location GIS files
 for polygons and pointsThese files can be used
 to link data from the CCPDD to GIS shape files using the field
 LocatNum.CCPDDlocationdata_v1.zipCCPDD Predator Prey Link DataThis file includes the data from the California Current Predator Diet Database (CCPDD) that was used for the analysis of forage species in predator diet in our publication. Each record (row) includes data for predator and prey taxonomy, citation info, location, date, observation type, sample size and units for measuring amount of prey consumed.CCPDDlinkdata_v1.csv
DOI: 10.5061/dryad.1j6sk
title: Data from: A ground-nesting Galliform’s response to thermal heterogeneity: Implications for ground-dwelling birds

description: The habitat selection choices that individuals make in response to thermal
 environments influence both survival and reproduction. Importantly, the
 way that organisms behaviorally respond to thermal environments depends on
 the availability and juxtaposition of sites affording tolerable or
 preferred microclimates. Although, ground nesting birds are especially
 susceptible to heat extremes across many reproductive stages (i.e.,
 breeding, nesting, brood rearing), the mechanistic drivers of nest site
 selection for these species are not well established from a thermal
 perspective. Our goal was to assess nest site selection relative to the
 configuration of the thermal landscape by quantifying thermal environments
 available to a ground-nesting bird species inhabiting a climatically
 stressful environment. Using northern bobwhite (Colinus virginanus) as a
 model species, we measured black bulb temperature (Tbb) and vegetation
 parameters at 87 nests, 87 paired sites and 205 random landscape sites in
 Western Oklahoma during spring and summer 2013 and 2014. We found that
 thermal space within the study area exhibited differences in Tbb of up to
 40°C during peak diurnal heating, resulting in a diverse thermal landscape
 available to ground-nesting birds. Within this thermally heterogeneous
 landscape, nest sites moderated Tbb by more than 12°C compared to random
 landscape sites. Furthermore, successful nests remained on average 6°C
 cooler than unsuccessful nests on days experiencing ambient temperatures ≥
 39°C. Models of future Tbb associated with 2080 climate change projections
 indicate that nesting bobwhites will face substantially greater Tbb
 throughout the landscape for longer durations, placing an even greater
 importance on thermal choices for nest sites in the future. These results
 highlight the capacity of landscape features to act as moderators of
 thermal extremes and demonstrate how thermal complexity at
 organism-specific scales can dictate habitat selection.
description: Nest_Temperature_2013_2014_PSWMA_Black bulb temperatures recorded at bobwhite nest sites, and 2m paired sites at the Packsaddle WMA, Oklahoma, USA (2013-2014).Landscape_Temperature_2013_2014_PSWMA_Black bulb temperatures recorded at random landscape sites at the Packsaddle WMA, Oklahoma, USA (2013-2014).Nest_Landscape_Temperature_MEANS_Hourly means of black bulb temperatures recorded at nest and random landscape sites at the Packsaddle WMA, Oklahoma, USA (2013-2014).Successful_Unsuccessful_NestsBlack bulb temperatures recorded at successful and unsuccessful nest at the Packsaddle WMA, Oklahoma, USA (2013-2014).VegetationVegetation variables recorded nest and random landscape sites at the Packsaddle WMA, Oklahoma, USA (2013-2014).
DOI: 10.5061/dryad.p2d8k
title: Data from: Extant-only comparative methods fail to recover the disparity preserved in the bird fossil record

description: Most extant species are in clades with poor fossil records, and recent
 studies of comparative methods show have low power to infer even highly
 simplified models of trait evolution without fossil data. Birds are a
 well-studied radiation, yet their early evolutionary patterns are still
 contentious. The fossil record suggests that birds underwent a rapid
 ecological radiation after the end-Cretaceous mass extinction, and several
 smaller, subsequent radiations. This hypothesized series of repeated
 radiations from fossil data is difficult to test using extant data alone.
 By uniting morphological and phylogenetic data on 604 extant genera of
 birds with morphological data on 58 species of extinct birds from 50
 million years ago, the “halfway point” of avian evolution, I have been
 able to test how well extant-only methods predict the diversity of fossil
 forms . All extant-only methods underestimate the disparity, although the
 ratio of within to between clade disparity does suggest high early rates.
 The failure of standard models to predict high early disparity suggests
 that recent radiations are obscuring deep time patterns in the evolution
 of birds. Metrics from different models can be used in conjunction to
 provide more valuable insights than simply finding the model with the
 highest relative fit.
description: Code and analysis
 outputAnalysisCode is the R
 code used to run all analyses and generate all figures in the manuscript.
 FossilAssignments is a Table showing members of the crown clade to which
 each extinct species is stem-ward. The other files are all parameter
 estimates and analysis outputs from the code included.Mitchell_Dryad.zip
DOI: 10.15468/dl.7edq9w
title: Occurrence Download

description: A dataset containing 264134 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Meetnet Agrarische Soorten - Monitoring of birds and mammals in agricultural areas in Flanders, Belgium",
 "Country is Belgium"
 ]
}

 The dataset includes 264134 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001624-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.q1h04
title: Data from: The topology of a discussion: the #occupy case

description: Introduction: We analyse a large sample of the Twitter activity that
 developed around the social movement 'Occupy Wall Street', to
 study the complex interactions between the human communication activity
 and the semantic content of a debate. Methods: We use a network approach
 based on the analysis of the bipartite graph @Users-#Hashtags and of its
 projections: the 'semantic network', whose nodes are hashtags,
 and the 'users interest network', whose nodes are users. In the
 first instance, we find out that discussion topics (#hashtags) present a
 high structural heterogeneity, with a relevant role played by the semantic
 hubs that are responsible to guarantee the continuity of the debate. In
 the users’ case, the self-organisation process of users’ activity, leads
 to the emergence of two classes of communicators: the
 'professionals' and the 'amateurs'. Results: Both the
 networks present a strong community structure, based on the
 differentiation of the semantic topics, and a high level of structural
 robustness when certain sets of topics are censored and/or accounts are
 removed. Conclusions: By analysing the characteristics of the dynamical
 networks we can distinguish three phases of the discussion about the
 movement. Each phase corresponds to a specific moment of the movement:
 from declaration of intent, organisation and development and the final
 phase of political reactions. Each phase is characterised by the presence
 of prototypical #hashtags in the discussion.
description: OccupyWallStreethashuser_Anon (1).csv
DOI: 10.5061/dryad.1b0q8
title: Data from: Phylogenetic divergences of the true bugs (Insecta: Hemiptera: Heteroptera), with emphasis on the aquatic lineages: the last piece of the aquatic insect jigsaw originated in the Late Permian/Early Triassic

description: Heteroptera are among the most diverse hemimetabolous insects. Seven
 infraorders have been recognized within this suborder of Hemiptera. Apart
 from the well-established sister-group relationship between Cimicomorpha
 and Pentatomomorpha (= Terheteroptera), the two terminal lineages, the
 relationships among the other five infraorders are still controversial, of
 which three (Gerromorpha, Nepomorpha and Leptopodomorpha) are intimately
 connected to aquatic environments. However, the various and often
 conflicting available phylogeny hypotheses do not offer a clear background
 for a connection between diversification and palaeoenvironments. In this
 study, a molecular data set representing 79 taxa and 10 149 homologous
 sites is used to infer the phylogenetic relationships within Heteroptera.
 Bayesian inference, maximum-likelihood and maximum parsimony analyses were
 employed. The results of phylogenetic inferences largely confirm the
 widely accepted phylogenetic context. Estimation of the divergence time
 based on the phylogenetic results revealed that Gerromorpha, Nepomorpha
 and Leptopodomorpha originated successively during the period from the
 Late Permian to Early Triassic (269–246 Ma). This timescale is consistent
 with the origin and radiation time of various aquatic holometabolans. Our
 results indicate that the aquatic and semi-aquatic true bugs evolved under
 environmental conditions of high air temperature and humidity in an
 evolutionary scenario similar to that of the aquatic holometabolans.
description: Data matric used for
 phylogenetic reconstruction and divergence time
 estimation
DOI: 10.5061/dryad.hg3j0
title: Data from: The advantage of short paper titles

description: Vast numbers of scientific articles are published each year, some of which
 attract considerable attention, and some of which go almost unnoticed.
 Here, we investigate whether any of this variance can be explained by a
 simple metric of one aspect of the paper's presentation: the length
 of its title. Our analysis provides evidence that journals which publish
 papers with shorter titles receive more citations per paper. These results
 are consistent with the intriguing hypothesis that papers with shorter
 titles may be easier to understand, and hence attract more citations.
description: Paper citation
 countsWe retrieved
 bibliometric data from Scopus (http://www.scopus.com) between 21 October
 2014 and 14 November 2014. We search for any papers that are marked by
 Scopus as an "Article" with the following search query:
 "DOCTYPE(ar) AND PUBYEAR = {year}". Where {year} is replaced by
 each of the years 2007 to 2013. We download the 20,000 most cited papers
 for each year. In total, we retrieve 140,000 records. For each paper, we
 list the year of publication, journal's title, paper's title,
 number of characters in the title and the number of citations that the
 paper has received to date. This is the raw data before cleaning as
 described in the main manuscript.LMP2015.csv
DOI: 10.5061/dryad.2sj8r
title: Data from: Liking the good guys: amplifying local adaptation via the evolution of condition-dependent mate choice

description: Local adaptation can be strengthened through a diversity of mechanisms
 that reduce gene flow between contrasting environments. Recent work
 revealed that mate choice could enhance local adaptation when females
 preferentially mate with locally adapted males and that such female
 preferences readily evolve, but the opposing effects of recombination,
 migration, and costs of female preferences remain relatively unexplored.
 To investigate these effects, we develop a two-patch model with two genes,
 one influencing an ecological trait and one influencing female
 preferences, where both male signals and female preferences are allowed to
 depend on the match between an individual's ecological trait and the
 local environment (condition). Because trait variation is limited when
 migration is rare and the benefits of preferential mating are short-lived
 when migration is frequent, we find that female preferences for males in
 high condition spread most rapidly with intermediate levels of migration.
 Surprisingly, we find that preferences for locally adapted males spread
 fastest with higher recombination rates, which contrasts with earlier
 studies. This is because a stronger preference allele for locally adapted
 males can only get uncoupled from maladapted ecological alleles following
 migration through recombination. The effects of migration and
 recombination depend strongly on the condition of the males being chosen
 by females, but only weakly on the condition of the females doing the
 choosing, except when it comes to the costs of preference. While costs
 always impede the spread of female preferences for locally adapted males,
 the impact is substantially lessened if costs are borne primarily by
 females in poor condition. The abundance of empirical examples of
 condition-dependent mate choice combined with our theoretical results
 suggests that the evolution of mate choice could commonly facilitate local
 adaptation in nature.
description: Veen and Otto
 Mathematica WorkbookMathematica 8.0.4
 workbook titled “Veen and Otto Mathematica Workbook.nb” describing the
 model and analyses.
DOI: 10.15468/dl.tsv8nc
title: Occurrence Download

description: A dataset containing 503 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "Geometry POLYGON((58.68939 5.99390,161.31061 5.99390,161.31061 47.00610,58.68939 47.00610,58.68939 5.99390))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Elaeocarpus chinensis"
 ]
}

 The dataset includes 503 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001650-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.gt410
title: Data from: The association of outdoor activity and age-related cataract in a rural population of Taizhou Eye Study: phase 1 report

description: Purpose: To study the relationship between outdoor activity and risk of
 age-related cataract (ARC) in a rural population of Taizhou Eye Study
 (phrase 1 report). Method: A population-based, cross-sectional study of
 2006 eligible rural adults (≥45 years old) from Taizhou Eye Study was
 conducted from Jul. to Sep. 2012. Participants underwent detailed
 ophthalmologic examinations including uncorrected visual acuity (UCVA),
 best corrected visual acuity (BCVA), intraocular pressure (IOP), slit lamp
 and fundus examinations as well as questionnaires about previous outdoor
 activity and sunlight protection methods. ARC was recorded by LOCSⅢ
 classification system. The prevalence of cortical, nuclear and posterior
 subcapsular cataract were assessed separately for the risk factors and its
 association with outdoor activity. Results: Of all 2006 eligible
 participants, 883 (44.0%) adults were diagnosed with ARC. The prevalence
 rates of cortical, nuclear and posterior subcapsular cataract per person
 were 41.4%, 30.4% and 1.5%, respectively. Women had a higher tendency of
 nuclear and cortical cataract than men (OR = 1.559, 95% CI 1.204–2.019 and
 OR = 1.862, 95% CI 1.456–2.380, respectively). Adults with high myopia had
 a higher prevalence of nuclear cataract than adults without that (OR =
 2.528, 95% CI 1.055–6.062). Multivariable logistic regression revealed
 that age was risk factor of nuclear (OR = 1.190, 95% CI 1.167–1.213) and
 cortical (OR = 1.203, 95% CI 1.181–1.226) cataract; eyes with fundus
 diseases was risk factor of posterior subcapsular cataract (OR = 6.529,
 95% CI 2.512–16.970). Outdoor activity was an independent risk factor of
 cortical cataract (OR = 1.043, 95% CI 1.004–1.083). The risk of cortical
 cataract increased 4.3% (95% CI 0.4%-8.3%) when outdoor activity time
 increased every one hour. Furthermore, the risk of cortical cataract
 increased 1.1% (95% CI 0.1%-2.0%) when cumulative UV-B exposure time
 increased every one year. Conclusion: Outdoor activity was an independent
 risk factor for cortical cataract, but was not risk factor for nuclear and
 posterior subcapsular cataract. The risk of cortical cataract increased
 4.3% when outdoor activity time increased every one hour. In addition, the
 risk of cortical cataract increased 1.1% (95% CI 0.1%-2.0%) when
 cumulative UV-B exposure time increased every one year.
description: Data from: The
 Association of Outdoor Activity and Age-related Cataract in a rural
 population of Taizhou Eye Study: Phase 1 Reportnew PONE-D-15-08786 original
 data set.xls
DOI: 10.5061/dryad.6f75v
title: Data from: Diet evolution and clade richness in Hexapoda: a phylogenetic study of higher taxa

description: Hexapoda, the insects and their relatives, includes over half of all
 described species. Because large proportions of this diversity cluster
 within a small set of phytophagous groups, dietary-substrates have been
 proposed to shape patterns of richness within the clade through
 antagonistic co-evolution and zones of ecological opportunity. Here we
 explore these processes in the context of a recent dated phylogeny of
 Hexapod families. Our results indicate phylogenetic clustering of
 specialized ecologies such as phytophagy and parasitism, but reveal no
 consistent associations between the use of particular dietary substrates
 and clade richness. We also find no evidence that diets expected to
 promote antagonistic co-evolution are consistently associated with
 elevated species richness, nor that sister clades differing in dietary
 state are associated with greater-than-expected differences in richness.
 We do, however, identify variation in the age of, and transition rates
 among, dietary states that are likely to play a role in the observed
 heterogeneity in richness among dietary classes. Based on these findings
 we suggest remaining circumspect about the generality of adaptive zones
 based on broad dietary groupings as an explanation for hexapod richness,
 and suggest that richness heterogeneity may be better explained by
 origination and transitions rates, and variation within dietary
 categories.
description: Definitions of
 ecological states, coding of terminal groups and
 referencesDryadData.docDiet Coding TableIncludes dietary coding and tip names linking to Rainford, J. L., M. Hofreiter, D. B. Nicholson, and P. J. Mayhew. 2014. Phylogenetic Distribution of Extant Richness Suggests Metamorphosis Is a Key Innovation Driving Diversification in Insects. PLoS ONE 9:e109085. [Phylogeny used for analysis]OnlineDietCoding.xls