cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q5j65
title: Data from: Energy and the scaling of animal space use

description: Daily animal movements are usually limited to a discrete home range area
 that scales allometrically with body size, suggesting that home-range size
 is shaped by metabolic rates and energy availability across species.
 However, there is little understanding of the relative importance of the
 various mechanisms proposed to influence home-range scaling (e.g.,
 differences in realm productivity, thermoregulation, locomotion strategy,
 dimensionality, trophic guild, and prey size) and whether these extend
 beyond the commonly studied birds and mammals. We derive new home-range
 scaling relationships for fishes and reptiles and use a model-selection
 approach to evaluate the generality of home-range scaling mechanisms
 across 569 vertebrate species. We find no evidence that home-range
 allometry varies consistently between aquatic and terrestrial realms or
 thermoregulation strategies, but we find that locomotion strategy,
 foraging dimension, trophic guild, and prey size together explain 80% of
 the variation in home-range size across vertebrates when controlling for
 phylogeny and tracking method. Within carnivores, smaller relative prey
 size among gape-limited fishes contributes to shallower scaling relative
 to other predators. Our study reveals how simple morphological traits and
 prey-handling ability can profoundly influence individual space use, which
 underpins broader-scale patterns in the spatial ecology of vertebrates.
description: Database of Vertebrate
 Home Range SizesDatabase of mean species
 masses and corresponding empirically measured home range sizes for 569
 vertebrate species from across the globe, including birds, mammals,
 reptiles, and fishes.Tamburelloetal_HomeRangeDatabase.csvMock Data for Prey Mass Model PredictionsMock data used with home range models incorporating prey mass to generate home range size predictions for Figure 2 of "Energy and the scaling of animal space use". Details in manuscript.Tamburelloetal_Fig2_PreymassPredictionData.csvMock Data for Home Range Prediction from Global ModelMock data used with the final global home range model to generate home range size predictions for Online Figure A2 of "Energy and the scaling of animal space use". Details in manuscript.Tamburelloetal_FigA2_MassPredictionDataAllModels.csvR Code Used in Analysis and Plotting (R Markdown)The R code used for data analysis and plotting in "Energy and the scaling of animal space use", provided as an annotated R Markdown file.Tamburelloetal_HomeRangeScaling_RCode.RmdR Code Used in Analysis and Plotting (PDF)The R code used for data analysis and plotting in "Energy and the scaling of animal space use", provided as an annotated PDF.Tamburelloetal_HomeRangeScaling_RCode.pdf
DOI: 10.15468/dl.q9ewtj
title: Occurrence Download

description: A dataset containing 585884 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Meise Botanic Garden Herbarium (BR)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 585884 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001614-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pf093
title: Data from: Properties of different selection signature statistics and a new strategy for combining them

description: Identifying signatures of recent or ongoing selection is of high relevance
 in livestock population genomics. From a statistical perspective,
 determining a proper testing procedure and combining various test
 statistics is challenging. On the basis of extensive simulations in this
 study, we discuss the statistical properties of eight different
 established selection signature statistics. In the considered scenario, we
 show that a reasonable power to detect selection signatures is achieved
 with high marker density (&gt;1 SNP/kb) as obtained from sequencing,
 while rather small sample sizes (~15 diploid individuals) appear to be
 sufficient. Most selection signature statistics such as composite
 likelihood ratio and cross population extended haplotype homozogysity have
 the highest power when fixation of the selected allele is reached, while
 integrated haplotype score has the highest power when selection is
 ongoing. We suggest a novel strategy, called de-correlated composite of
 multiple signals (DCMS) to combine different statistics for detecting
 selection signatures while accounting for the correlation between the
 different selection signature statistics. When examined with simulated
 data, DCMS consistently has a higher power than most of the single
 statistics and shows a reliable positional resolution. We illustrate the
 new statistic to the established selective sweep around the lactase gene
 in human HapMap data providing further evidence of the reliability of this
 new statistic. Then, we apply it to scan selection signatures in two
 chicken samples with diverse skin color. Our analysis suggests that a set
 of well-known genes such as BCO2, MC1R, ASIP and TYR were involved in the
 divergent selection for this trait.
description: chicken
 datachicken.zip
DOI: 10.5878/001480
title: The Regional Skåne SOM Survey 2001
title: SOM-undersökningen i Skåne 2001
title: Syd-SOM 2001

description: The SOM survey in Skåne has been conducted since 2001. The purpose of the regional surveys is to enable SOM researchers to study attitudes and behaviour linked to local and regional issues. They emphasise public services and media, although many of the questions are identical with those used in National SOM in order to make the answers comparable both between the regions and with Sweden at large.

Purpose:
Study attitudes and behaviour linked to local and regional issues.
description: Syd-SOM 2001 omfattar 3 200 slumpmässigt utvalda personer i A-region 28 - Burlöv, Kävlinge, Lomma, Lund, Malmö, Staffanstorp, Svedala, Trelleborg och Vellinge - samt, utanför A-region 28, Eslöv.

Bakom undersökningen står främst forskningsprogrammet Dagspresskollegiet och SOM-institutet vid Göteborgs universitet. Det formulär som användes har samma upplägg och grundläggande struktur som de av SOM-institutet årligen genomförda Riks- och Väst-SOM-undersökningarna för att optimera jämförelse. Följande ämnesområden berördes i Skåneundersökningens formulär: massmedieanvändning; synen på tidningen Arbetets nedläggning; medier, internet och fritid; samhälle och politik; Malmö; tidningen Arbetet; fritid och intressen; samt bakgrundsfrågor.

Syfte:
Studera attityder och beteenden som är knutna till lokala och regionala frågor och företeelser.
DOI: 10.5061/dryad.sd6nj
title: Data from: Mainland size variation informs predictive models of exceptional insular body size change in rodents

description: The tendency for island populations of mammalian taxa to diverge in body
 size from their mainland counterparts consistently in particular
 directions is both impressive for its regularity and, especially among
 rodents, troublesome for its exceptions. However, previous studies have
 largely ignored mainland body size variation, treating size differences of
 any magnitude as equally noteworthy. Here, we use distributions of
 mainland population body sizes to identify island populations as
 ‘extremely’ big or small, and we compare traits of extreme populations and
 their islands with those of island populations more typical in body size.
 We find that although insular rodents vary in the directions of body size
 change, ‘extreme’ populations tend towards gigantism. With classification
 tree methods, we develop a predictive model, which points to resource
 limitations as major drivers in the few cases of insular dwarfism. Highly
 successful in classifying our dataset, our model also successfully
 predicts change in untested cases.
description: CombinedDataCollection of mainland species records from the Natural History Museum of Los Angeles County and the Smithsonian, U.S. Natural History Museum.
DOI: 10.5878/000425
title: The Regional Skåne SOM Survey 2001
title: SOM-undersökningen i Skåne 2001
title: Syd-SOM 2001

description: The SOM survey in Skåne has been conducted since 2001. The purpose of the regional surveys is to enable SOM researchers to study attitudes and behaviour linked to local and regional issues. They emphasise public services and media, although many of the questions are identical with those used in National SOM in order to make the answers comparable both between the regions and with Sweden at large.

Purpose:
Study attitudes and behaviour linked to local and regional issues.
description: Syd-SOM 2001 omfattar 3 200 slumpmässigt utvalda personer i A-region 28 - Burlöv, Kävlinge, Lomma, Lund, Malmö, Staffanstorp, Svedala, Trelleborg och Vellinge - samt, utanför A-region 28, Eslöv.

Bakom undersökningen står främst forskningsprogrammet Dagspresskollegiet och SOM-institutet vid Göteborgs universitet. Det formulär som användes har samma upplägg och grundläggande struktur som de av SOM-institutet årligen genomförda Riks- och Väst-SOM-undersökningarna för att optimera jämförelse. Följande ämnesområden berördes i Skåneundersökningens formulär: massmedieanvändning; synen på tidningen Arbetets nedläggning; medier, internet och fritid; samhälle och politik; Malmö; tidningen Arbetet; fritid och intressen; samt bakgrundsfrågor.

Syfte:
Studera attityder och beteenden som är knutna till lokala och regionala frågor och företeelser.
DOI: 10.5061/dryad.7j55c
title: Data from: Broadband onset inhibition can suppress spectral splatter in the auditory brainstem

description: In vivo intracellular responses to auditory stimuli revealed that, in a
 particular population of cells of the ventral nucleus of the lateral
 lemniscus (VNLL) of rats, fast inhibition occurred before the first action
 potential. These experimental data were used to constrain a leaky
 integrate-and-fire (LIF) model of the neurons in this circuit. The
 post-synaptic potentials of the VNLL cell population were characterized
 using a method of triggered averaging. Analysis suggested that these
 inhibited VNLL cells produce action potentials in response to a particular
 magnitude of the rate of change of their membrane potential. The LIF model
 was modified to incorporate the VNLL cells’ distinctive action potential
 production mechanism. The model was used to explore the response of the
 population of VNLL cells to simple speech-like sounds. These sounds
 consisted of a simple tone modulated by a saw tooth with exponential
 decays, similar to glottal pulses that are the repeated impulses seen in
 vocalizations. It was found that the harmonic component of the sound was
 enhanced in the VNLL cell population when compared to a population of
 auditory nerve fibers. This was because the broadband onset noise, also
 termed spectral splatter, was suppressed by the fast onset inhibition.
 This mechanism has the potential to greatly improve the clarity of the
 representation of the harmonic content of certain kinds of natural sounds.
description: Intracellular data, 8
 cellsThe zip file contains 8
 text files. Each text file is associated with a single intracellular cell
 recording, and contains either 3 or 4 columns. The 3rd column is the cell
 membrane voltage in volts, and the 4th column of numbers is the auditory
 stimulus data. The time step between rows is 50
 microseconds.celldata.zip
DOI: 10.5061/dryad.8487
title: Data from: Sexual selection is positively associated with ecological generalism among agamid lizards

description: Natural and sexual selection shape the evolution of species, but the
 interplay between them is poorly understood. Two phylogenetic studies on
 birds have suggested that species with greater sexual dichromatism use
 more habitats. Here, we show that in Agamid lizards, species with more
 elaborate secondary sexual traits also are ecologically more
 opportunistic. Species with greater dimorphism in head size and
 ornamentation have greater altitudinal range and occupy more habitats,
 respectively, and species with greater sexual dichromatism have a wider
 microhabitat use. Body size was positively associated with sexual and
 ecological traits but associations between ecological and sexual traits
 remained after accounting for body size. The results are consistent with
 the earlier studies and we suggest that sexual and natural selection may
 be linked through sexual selection promotes generalism at the population
 level by favouring ‘good genes’, or higher population densities cause both
 stronger sexual selection and broader resource use.
description: AgamidDataTipExcel file containing the data for each species and the tip names of the Agamid lizard studied. "." denotes a missing value.Variance-covariance matrixVariance-covariance matrix of the phylogeny to the tip names in AgamidDataTip.xls. Branch lengths are set to 1 but polytomies resolved with a branch length of 0.0001.vcv.txt
DOI: 10.5061/dryad.4jj77
title: Data from: Can impacts of climate change and agricultural adaptation strategies be accurately quantified if crop models are annually re-initialized?

description: Estimates of climate change impacts on global food production are
 generally based on statistical or process-based models. Process-based
 models can provide robust predictions of agricultural yield responses to
 changing climate and management. However, applications of these models
 often suffer from bias due to the common practice of re-initializing soil
 conditions to the same state for each year of the forecast period. If
 simulations neglect to include year-to-year changes in initial soil
 conditions and water content related to agronomic management, adaptation
 and mitigation strategies designed to maintain stable yields under climate
 change cannot be properly evaluated. We apply a process-based crop system
 model that avoids re-initialization bias to demonstrate the importance of
 simulating both year-to-year and cumulative changes in pre-season soil
 carbon, nutrient, and water availability. Results are contrasted with
 simulations using annual re-initialization, and differences are striking.
 We then demonstrate the potential for the most likely adaptation strategy
 to offset climate change impacts on yields using continuous simulations
 through the end of the 21st century. Simulations that annually
 re-initialize pre-season soil carbon and water contents introduce an
 inappropriate yield bias that obscures the potential for agricultural
 management to ameliorate the deleterious effects of rising temperatures
 and greater rainfall variability.
description: SALUS
 ProgramPackage to install SALUS
 on a Windows Computer (compressed using WinZip program)SALUS2013-12-21Package.zipCont--08Sep2014CorrectionResulsts from the continuous SALUS model runs.Nebraska_Model_Files.tarNebraska_Model_Files.tar.gz -- files need to run the SALUS Model (using tar and gzip to archive and compress); sep8correction.xdb -- Experiment file for continous runs of the SALUS model; sep8correction_init.xdb -- Experiment file for runs of the SALUS model where soil parameters are reinitialized every year; Nebraska.Sdb -- Soil file; crops_misca.cdb -- Crop pramatersReinit--09Sep2014CorrectionResults from the SALUS model runs where soil parameters were reinitialized at the beginning of each growing season.
DOI: 10.5061/dryad.8492
title: Data from: Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA.

description: Here, we present a new primate phylogeny inferred from molecular
 supermatrix analyses of size 42 kb containing 70% of missing data, and
 representing 75% of primate species diversity. The supermatrix was
 analysed using a gene-partitioned maximum likelihood approach to obtain an
 exhaustive molecular phylogenetic framework. All clades recovered from
 recent molecular works were upheld in our analyses demonstrating that the
 presence of missing data did not bias our supermatrix inference. The
 resulting phylogenetic tree was subsequently dated with a molecular dating
 method to provide a timescale for speciation events. Results obtained from
 our relaxed molecular clock analyses concurred with previous works based
 on the same fossil constraints. The resulting dated tree allowed to infer
 of macroevolutionary processes among the primates. Shifts in
 diversification rate and speciation rates were determined using the
 SymmeTREE method and a birthdeath process. No significant asymmetry was
 detected for the primate clade, but significant shifts in diversification
 rate were identified for seven clades: Anthropoidea, Lemuriformes,
 Lemuridae, Galagidae, Callithrix genus, the Cercopithecinae and Asian
 Macaca. Comparisons with previous primate supertree results reveal that
 (i) there was a diversification event at the root of the Lemuriformes,
 (ii) a higher diversification rate is detected for Cercopithecidae and
 Anthropoidea and (iii) a shift in diversification is always recovered for
 Macaca genus. Macroevolutionary inferences and primate divergence dates
 show that major primate diversification events occurred after the
 Paleogene, suggesting the extinction of ancient primate lineages.
description: Fabre_MolPhylogenetEvol09Nucleotide supermatrix of 27 mitochondrial and nuclear genes for 279 species of extant PrimatesPRIMATES-Chronogram_273_taxaChronogram of the 273-taxon ML tree.PRIMATES-Chronogram_376_taxa_WR05Chronogram with all 376 primate taxa of Wilson & Reeder 2005.
DOI: 10.5061/dryad.rp46p
title: Data from: Hypothesis-driven and field-validated method to prioritize fragmentation mitigation efforts in road projects

description: The active field of connectivity conservation has provided numerous
 methods to identify wildlife corridors with the aim of reducing the
 ecological effect of fragmentation. Nevertheless, these methods often rely
 on untested hypotheses of animal movements, usually fail to generate
 fine-scale predictions of road crossing sites, and do not allow managers
 to prioritize crossing sites for implementing road fragmentation
 mitigation measures. We propose a new method that addresses these
 limitations. We illustrate this method with data from southwestern Gabon
 (central Africa). We used stratified random transect surveys conducted in
 two seasons to model the distribution of African forest elephant
 (Loxodonta cyclotis), forest buffalo (Syncerus caffer nanus), and
 sitatunga (Tragelaphus spekii) in a mosaic landscape along a 38.5 km
 unpaved road scheduled for paving. Using a validation data set of recorded
 crossing locations, we evaluated the performance of three types of models
 (local suitability, local least-cost movement, and regional least-cost
 movement) in predicting actual road crossings for each species, and
 developed a unique and flexible scoring method for prioritizing road
 sections for the implementation of road fragmentation mitigation measures.
 With a data set collected in &lt;10 weeks of fieldwork, the method was
 able to identify seasonal changes in animal movements for buffalo and
 sitatunga that shift from a local exploitation of the site in the wet
 season to movements through the study site in the dry season, whereas
 elephants use the entire study area in both seasons. These three species
 highlighted the need to use species- and season-specific modeling of
 movement. From these movement models, the method ranked road sections for
 their suitability for implementing fragmentation mitigation efforts,
 allowing managers to adjust priority thresholds based on budgets and
 management goals. The method relies on data that can be obtained in a
 period compatible with environmental impact assessment constraints, and is
 flexible enough to incorporate other potential movement models and scoring
 criteria. This approach improves upon available methods and can help
 inform prioritization of road and other linear infrastructure segments
 that require impact mitigation methods to ensure long-term landscape
 connectivity.
description: RoadFragmentationDatasetThis dataset accompanies Vanthomme H., Kolowski J., Nzamba, B.S., Alonso A. 2015. Hypothesis-driven and field-validated method to prioritize fragmentation mitigation efforts in road projects. Ecological Applications (in press). It contains a copy of the main data file exactly as used for this paper.
DOI: 10.5061/dryad.45qj3
title: Data from: Hoverfly locomotor activity is resilient to external influence and intrinsic factors

description: Hoverflies are found across the globe, with approximately 6000 species
 described worldwide. Many hoverflies are being used in agriculture and
 some are emerging as model species for laboratory experiments. As such it
 is valuable to know more about their activity. Like many other dipteran
 flies, Eristalis hoverflies have been suggested to be strongly diurnal,
 but this is based on qualitative visualization by human observers. To
 quantify how hoverfly activity depends on internal and external factors,
 we here utilize a locomotor activity monitoring system. We show that
 Eristalis hoverflies are active during the entire light period when
 exposed to a 12 h light:12 h dark cycle, with a lower activity if exposed
 to light during the night. We show that the hoverflies’ locomotor activity
 is stable over their lifetime and that it does not depend on the diet
 provided. Surprisingly, we find no difference in activity between males
 and females, but the activity is significantly affected by the sex of an
 accompanying conspecific. Finally, we show that female hoverflies are more
 resilient to starvation than males. In summary, Eristalis hoverflies are
 resilient to a range of internal and external factors, supporting their
 use in long-term laboratory experiments.
description: MalinDAMS
DOI: 10.5061/dryad.8499
title: Data from: The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?

description: The use of nucleotide and amino acid sequences allows improved
 understanding of the timing of evolutionary events of life on earth.
 Molecular estimates of divergence times are, however, controversial and
 are generally much more ancient than suggested by the fossil record. The
 limited number of genes and species explored and pervasive variations in
 evolutionary rates are the most likely sources of such discrepancies. Here
 we compared concatenated amino acid sequences of 129 proteins from 36
 eukaryotes to determine the divergence times of several major clades,
 including animals, fungi, plants, and various protists. Due to significant
 variations in their evolutionary rates, and to handle the uncertainty of
 the fossil record, we used a Bayesian relaxed molecular clock
 simultaneously calibrated by six paleontological constraints. We show
 that, according to 95% credibility intervals, the eukaryotic kingdoms
 diversified 950–1,259 million years ago (Mya), animals diverged from
 choanoflagellates 761–957 Mya, and the debated age of the split between
 protostomes and deuterostomes occurred 642–761 Mya. The divergence times
 appeared to be robust with respect to prior assumptions and
 paleontological calibrations. Interestingly, these relaxed clock time
 estimates are much more recent than those obtained under the assumption of
 a global molecular clock, yet bilaterian diversification appears to be
 ≈100 million years more ancient than the Cambrian boundary.
description: Douzery_PNAS_2004Amino acid alignment based on the concatenation of 129 nuclear proteins for 36 eukaryote taxa.Douzery_PNAS_2004Reference tree used in molecular dating analyses.