cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5878/000477
title: The Regional Skåne SOM Survey 2008
title: SOM-undersökningen i Skåne 2008
title: Syd-SOM 2008

description: This is the fourth SOM survey conducted in the region of Skåne. The questionnaire was divided into seven subject fields: news and newspapers; politics, society and democracy; society and service; media technology and media use; activities and interests; working life; and background information.

Purpose:
Study attitudes and behaviour linked to local and regional issues.
description: Detta är den fjärde SOM-undersökning som genomförts i Skåne. Den första undersökningen genomfördes 2001 i Malmöregionen (A-region 28 samt Eslöv). De senare undersökningarna har genomförts i hela Region Skåne.

Det formulär som användes har samma upplägg och grundläggande struktur som motsvarande regionala undersökningar som årligen genomförs i Västsverige, detta för att optimera möjligheterna till jämförelse av resultaten för Region Skåne och Västra Götalandsregionen. Många av frågorna är dessutom utformade likadant som i de tidigare undersökningarna i Skåne (2001, 2004 och 2006) för att på det sättet möjliggöra jämförelser bakåt i tiden. Det ska i sammanhanget beaktas att urvalet och frågorna i formuläret skiljer sig betydligt åt mellan 2001 års undersökning och övriga undersökningar genomförda i Skåne.

Frågeformuläret består av sju sammanhållna frågeområden: nyheter och tidningar; politik, samhälle och demokrati; samhälle och service; medieteknik och medieanvändning; aktiviteter och intressen; arbetsliv; samt bakgrundsfrågor.

Syfte:
Studera attityder och beteenden som är knutna till lokala och regionala frågor och företeelser.
DOI: 10.5061/dryad.4nd2j
title: Data from: Testing for Depéret’s rule (body size increase) in mammals using combined extinct and extant data

description: Whether or not evolutionary lineages in general show a tendency to
 increase in body size has often been discussed. This tendency has been
 dubbed “Cope's rule” but because Cope never hypothesized it, we
 suggest renaming it after Depéret, who formulated it clearly in 1907.
 Depéret's rule has traditionally been studied using fossil data, but
 more recently a number of studies have used present-day species. While
 several paleontological studies of Cenozoic placental mammals have found
 support for increasing body size, most studies of extant placentals have
 failed to detect such a trend. Here, we present a method to combine
 information from present-day species with fossil data in a Bayesian
 phylogenetic framework. We apply the method to body mass estimates of a
 large number of extant and extinct mammal species, and find strong support
 for Depéret's rule. The tendency for size increase appears to be
 driven not by evolution toward larger size in established species, but by
 processes related to the emergence of new species. Our analysis shows that
 complementary data from extant and extinct species can greatly improve
 inference of macroevolutionary processes.
description: Body size estimates of
 fossil mammalsEstimates of body size
 for fossil mammals, with geological age and taxonomic position, as well as
 information on the methods and source publications used to obtain each
 estimate.OSM1.xlsOSM2Phylogenetic tree of mammals with fossil species for which body size estimates were available added.
DOI: 10.12751/g-node.2hgfq9
title: In vivo 2P-calcium imaging dataset of auditory cortical populations for pulsed sound stimuli

description: This repository is a dataset of imaged neuronal populations in the auditory cortex of mice being exposed to a set of short sound stimuli in a single session.
Two experimental cohorts according to the type of pulsed sound set. In the data directory, we provide 2-dimensional GCaMP6-based signal data, consisting of neuronal ROIs and imaging frames across multiple days 
for each FOV and mouse. This data is obtained after extracting and preprocessing the time series from two-channel images 
(channel one is histone-fused mCherry, H2B::mCherry, red fluorescent protein, channel two is GCaMP6m, green fluorescent genetically encoded calcium indicator).
Additionally, we provide the information about auditory sensory stimulations. Further information about analysis of this dataset can be found in the corresponding published article.
DOI: 10.5061/dryad.hb37q
title: Data from: Estimating sampling error of evolutionary statistics based on genetic covariance matrices using maximum likelihood

description: We explore the estimation of uncertainty in evolutionary parameters using
 a recently devised approach for resampling entire additive genetic
 variance–covariance matrices (G). Large-sample theory shows that
 maximum-likelihood estimates (including restricted maximum likelihood,
 REML) asymptotically have a multivariate normal distribution, with
 covariance matrix derived from the inverse of the information matrix, and
 mean equal to the estimated G. This suggests that sampling estimates of G
 from this distribution can be used to assess the variability of estimates
 of G, and of functions of G. We refer to this as the REML-MVN method. This
 has been implemented in the mixed-model program WOMBAT. Estimates of
 sampling variances from REML-MVN were compared to those from the
 parametric bootstrap and from a Bayesian Markov chain Monte Carlo (MCMC)
 approach (implemented in the R package MCMCglmm). We apply each approach
 to evolvability statistics previously estimated for a large,
 20-dimensional data set for Drosophila wings. REML-MVN and MCMC sampling
 variances are close to those estimated with the parametric bootstrap. Both
 slightly underestimate the error in the best-estimated aspects of the G
 matrix. REML analysis supports the previous conclusion that the G matrix
 for this population is full rank. REML-MVN is computationally very
 efficient, making it an attractive alternative to both data resampling and
 MCMC approaches to assessing confidence in parameters of evolutionary
 interest.
description: REMLMVN
 dataThis zip archive has the
 data formatted for use in Wombat and R, species means, and the
 eigenvectors used to project the data into 20 dimensions. Details are in
 the README file.REMLMVN.zip
DOI: 10.5061/dryad.g830h
title: Data from: Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks

description: The idea that species boundaries can be semipermeable to gene flow is now
 widely accepted but the evolutionary importance of introgressive
 hybridization remains unclear. Here we examine the genomic contribution of
 gene flow between two hybridizing chipmunk species, Tamias ruficaudus and
 Tamias amoenus. Previous studies have shown that ancient hybridization has
 resulted in complete fixation of introgressed T. ruficaudus mitochondrial
 DNA (mtDNA) in some populations of T. amoenus, but the extent of nuclear
 introgression is not known. We used targeted capture to sequence over
 10500 gene regions from multiple individuals of both species. We found
 that most of the nuclear genome is sorted between these species and that
 overall genealogical patterns do not show evidence for introgression. Our
 analysis rules out all but very minor levels of interspecific gene flow,
 indicating that introgressive hybridization has had little impact on the
 overall genetic composition of these species outside of the mitochondrial
 genome. Given that much of the evidence for introgression in animals has
 come from mtDNA, our results underscore that unraveling the importance
 introgressive hybridization during animal speciation will require a
 genome-wide perspective that is still absent for many species.
description: 8,759 multi-sequence
 alignmentsGood_etal_DRYAD.tar.gz
DOI: 10.5061/dryad.9028
title: Data from: Extremely long-distance seed dispersal by an overfished Amazonian frugivore

description: Throughout Amazonia, overfishing has decimated populations of fruit-eating
 fishes, especially the largebodied characid, Colossoma macropomum. During
 lengthy annual floods, frugivorous fishes enter vast Amazonian
 floodplains, consume massive quantities of fallen fruits and egest viable
 seeds. Many tree and liana species are clearly specialized for
 icthyochory, and seed dispersal by fish may be crucial for the maintenance
 of Amazonian wetland forests. Unlike frugivorous mammals and birds, little
 is known about seed dispersal effectiveness of fishes. Extensive mobility
 of frugivorous fish could result in extremely effective,
 multi-directional, long-distance seed dispersal. Over three annual flood
 seasons, we tracked fine-scale movement patterns and habitat use of wild
 Colossoma, and seed retention in the digestive tracts of captive
 individuals. Our mechanistic model predicts that Colossoma disperses seeds
 extremely long distances to favourable habitats. Modelled mean dispersal
 distances of 337–552 m and maximum of 5495 m are among the longest ever
 reported. At least 5 per cent of seeds are predicted to disperse 1700–2110
 m, farther than dispersal by almost all other frugivores reported in the
 literature. Additionally, seed dispersal distances increased with fish
 size, but overfishing has biased Colossoma populations to smaller
 individuals. Thus, overexploitation probably disrupts an ancient
 coevolutionary relationship between Colossoma and Amazonian plants.
description: Anderson et al telemetry
 dataThis Excel file contains
 radiotelemetry data from 24 Colossoma macropomum individuals included in
 our field study (2004-2006)Anderson et al gut
 retentionretainThis text file contains
 individual level gut retention time data for captive fish from 2005 and
 2006. Each line of data represents an individual seed, and indicates the
 time (hour) at which the seed was defecated by a given fish. Multiple
 seeds were fed to captive fish in each gut retention trial. Status codes
 seeds as 1 when defecated. Censored seeds (undefecated) are coded with
 0.Simulation model
 resultsThis Excel file contains
 5 sheets: one for each of the seed species included in the study. Each
 sheet has the results of the simulation models, needed to produce the
 dispersal kernel figures (Figure 1 and Appendix Figure S2). Each
 simulation model was run for 100,000 iterations. Included in each sheet
 are columns for : Seed dispersal distance bins, frequency of dispersal to
 suitable habitats, proportion of seeds dispersed to suitable habitats,
 frequency of dispersal to permanent bodies of water, and proportion of
 seeds dispersed to permanent bodies of water.
DOI: 10.5061/dryad.f8j12
title: Data from: Biogeography of the Phalaenopsis amabilis species complex inferred from nuclear and plastid DNAs

description: Background: Phalaenopsis is one of the important commercial orchids in the
 world. Members of the P. amabilis species complex represent invaluable
 germplasm for the breeding program. However, the phylogeny of the P.
 amabilis species complex is still uncertain. The Phalaenopsis amabilis
 species complex (Orchidaceae) consists of subspecies amabilis, moluccana,
 and rosenstromii of P. amabilis, as well as P. aphrodite ssp. aphrodite,
 P. ap. ssp. formosana, and P. sanderiana. The aims of this study were to
 reconstruct the phylogeny and biogeographcial patterns of the species
 complex using Neighbor Joining (NJ), Maxinum Parsimony (MP), Bayesian
 Evolutionary Analysis Sampling Trees (BEAST) and Reconstruct Ancestral
 State in Phylogenies (RASP) analyses based on sequences of internal
 transcribed spacers 1 and 2 from the nuclear ribosomal DNA and the
 trnH-psbA spacer from the plastid DNA. Results: A pattern of vicariance,
 dispersal, and vicariance + dispersal among disjunctly distributed taxa
 was uncovered based on RASP analysis. Although two subspecies of P.
 aphrodite could not be differentiated from each other in dispersal state,
 they were distinct from P. amabilis and P. sanderiana. Within P. amabilis,
 three subspecies were separated phylogenetically, in agreement with the
 vicariance or vicariance + dispersal scenario, with geographic subdivision
 along Huxley’s, Wallace’s and Lydekker’s Lines. Molecular dating revealed
 such subdivisions among taxa of P. amabilis complex dating back to the
 late Pleistocene. Population-dynamic analyses using a Bayesian skyline
 plot suggested that the species complex experienced an in situ range
 expansion and population concentration during the late Last Glacial
 Maximum (LGM). Conclusions: Taxa of the P. amabilis complex with disjunct
 distributions were differentiated due to vicariance or
 vicariance + dispersal, with events likely occurring in the late
 Pleistocene. Demographic growth associated with the climatic oscillations
 in the Würm glacial period followed the species splits. Nevertheless, a
 subsequent population slowdown occurred in the late LGM due to extinction
 of regional populations. The reduction of suitable habitats resulted in
 geographic fragmenttation of the remaining taxa.
description: Additional file Table
 S1Alignment data for
 Phalaenopsis amabilis species complex rDNA ITSAdditional file Table
 S2Alignment data for
 Phalaenopsis amabilis species complex trnH-psbA spacer
DOI: 10.5061/dryad.038q8
title: Worldwide evidence of a unimodal relationship between productivity and plant species richness

description: The search for predictions of species diversity across environmental
 gradients has challenged ecologists for decades. The humped-back model
 (HBM) suggests that plant diversity peaks at intermediate productivity; at
 low productivity few species can tolerate the environmental stresses, and
 at high productivity a few highly competitive species dominate. Over time
 the HBM has become increasingly controversial, and recent studies claim to
 have refuted it. Here, by using data from coordinated surveys conducted
 throughout grasslands worldwide and comprising a wide range of site
 productivities, we provide evidence in support of the HBM pattern at both
 global and regional extents. The relationships described here provide a
 foundation for further research into the local, landscape, and historical
 factors that maintain biodiversity.
description: raw plot data from
 globally distributed sitesfraser_plotdata.csvR script for within_site_GLMs_Fig2A_TableS2within_site_GLMs_Fig2A_TableS2.RR script for Table_1_analyses_FigS1Table_1_analyses_FigS1.RR script for varied_grain_analyses_FigS2varied_grain_analyses_FigS2.RR script for HBmodels_FigS3HBmodels_FigS3.RR script for max_richness_FigS4max_richness_FigS4.RR script for within_site_GLMs_reduced_data_Figs_S5_2B_S6within_site_GLMs_reduced_data_Figs_S5_2B_S6.R
DOI: 10.5061/dryad.0sn23
title: Data from: A nonstationary Markov model detects directional evolution in hymenopteran morphology

description: Directional evolution has played an important role in shaping the
 morphological, ecological, and molecular diversity of life. However,
 standard substitution models assume stationarity of the evolutionary
 process over the time scale examined, thus impeding the study of
 directionality. Here we explore a simple, nonstationary model of evolution
 for discrete data, which assumes that the state frequencies at the root
 differ from the equilibrium frequencies of the homogeneous evolutionary
 process along the rest of the tree (i.e., the process is nonstationary,
 nonreversible, but homogeneous). Within this framework, we develop a
 Bayesian approach for testing directional versus stationary evolution
 using a reversible-jump algorithm. Simulations show that when only data
 from extant taxa are available, the success in inferring directionality is
 strongly dependent on the evolutionary rate, the shape of the tree, the
 relative branch lengths, and the number of taxa. Given suitable
 evolutionary rates (0.1–0.5 expected substitutions between root and tips),
 accounting for directionality improves tree inference and often allows
 correct rooting of the tree without the use of an outgroup. As an
 empirical test, we apply our method to study directional evolution in
 hymenopteran morphology. We focus on three character systems: wing veins,
 muscles, and sclerites. We find strong support for a trend toward loss of
 wing veins and muscles, while stationarity cannot be ruled out for
 sclerites. Adding fossil and time information in a total-evidence dating
 approach, we show that accounting for directionality results in more
 precise estimates not only of the ancestral state at the root of the tree,
 but also of the divergence times. Our model relaxes the assumption of
 stationarity and reversibility by adding a minimum of additional
 parameters, and is thus well suited to studying the nature of the
 evolutionary process in data sets of limited size, such as morphology and
 ecology.
description: Supplementary Table S1:
 Characters PartitionsMorphological character
 matrix with numbers from this and the previous publication (Ronquist et
 al. 2012), partition assignment, and descriptions of character
 states.Supplementary_Table_S1_Characters_Partitions.xlsxSupplementary Files S2: Scripts SimulationsArchive containing a bash script and several R scripts used for simulating and analyzing the data from the simulation study.Supplementary_Files_S2_Scripts_Simulations.rarSupplementary Files S3: Results SimulationsPdf files containing all graphs produced in the simulation study (see ReadMe.txt for details).Supplementary_Files_S3_Results_Simulations.rarSupplementary File S4: Tracing the High-Rates ArtefactDetailed explanation of the occurrence of false positives when analyzing random or highly saturated data, and of the impact of the branch length prior.Supplementary_File_S4_Tracing_the_High-Rates_Artefact.pdf
DOI: 10.5061/dryad.r4553
title: Data from: Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment

description: Background: The past decade has witnessed remarkable progress towards
 resolution of the Tree of Life. However, despite the increased use of
 genomic scale datasets, some phylogenetic relationships remain difficult
 to resolve. Here we employ anchored phylogenomics to capture 107 nuclear
 loci in 29 species of acanthomorph teleost fishes, with 25 of these
 species sampled from the recently delimited clade Ovalentaria. Previous
 studies employing multilocus nuclear exon datasets have not been able to
 resolve the nodes at the base of the Ovalentaria tree with confidence.
 Here we test whether a phylogenomic approach will provide better support
 for these nodes, and if not, why this may be. Results: After using a novel
 method to account for paralogous loci, we estimated phylogenies with
 maximum likelihood and species tree methods using DNA sequence alignments
 of over 80,000 base pairs. Several key relationships within Ovalentaria
 are well resolved, including 1) the sister taxon relationship between
 Cichlidae and Pholidichthys, 2) a clade containing blennies, grammas,
 clingfishes, and jawfishes, and 3) monophyly of Atherinomorpha
 (topminnows, flyingfishes, and silversides). However, many nodes in the
 phylogeny associated with the early diversification of Ovalentaria are
 poorly resolved in several analyses. Through the use of rarefaction curves
 we show that limited phylogenetic resolution among the earliest nodes in
 the Ovalentaria phylogeny does not appear to be due to a deficiency of
 data, as average global node support ceases to increase when only 1/3rd of
 the sampled loci are used in analyses. Instead this lack of resolution may
 be driven by model misspecification as a Bayesian mixed model analysis of
 the amino acid dataset provided good support for parts of the base of the
 Ovalentaria tree.Conclusions: Although it does not appear that the limited
 phylogenetic resolution among the earliest nodes in the Ovalentaria
 phylogeny is due to a deficiency of data, it may be that both stochastic
 and systematic error resulting from model misspecification play a role in
 the poor resolution at the base of the Ovalentaria tree as a Bayesian
 approach was able to resolve some of the deeper nodes, where the other
 methods failed.
description: Eytan-etal2015_AssemblyCodeJava code used for processing sequencing runs before phylogenetic analyses.Ovalentaria_AlignmentsAlignments used for phylogenetic analysesrandom_sample_raxmlPython script for generating randomized nucleotide datasets of different lengths for analysis in RAxML. These were used to generate the rarefaction curves shown in the study. Requires docopt.py, which is not included.
DOI: 10.15468/dl.nhh3jb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bathytroctes microlepis Günther, 1878",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((45.5755 -13.3048,45.7911 -12.8231,45.6061 -12.3752,45.0241 -12.1382,44.9648 -12.0572,44.9648 -13.45,45.02 -13.4845,45.5755 -13.3048))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010693-250525065834625/datasets/export for details.
DOI: 10.5281/zenodo.17710656
title: Catalan Surveillance Network of SARS-CoV-2 in Sewage

description: The Catalan Surveillance Network of SARS-CoV-2 in Sewage started in July 2020 to monitor 56 wastewater treatment plants (WWTPs) all over the country representing the sewage from the 80% of the total population.  The sampling plan consist in a weekly collection of 24 hours-composed-flow proportional water sample from the entrance of each WWTPs. The raw sewage samples are send to references laboratories for analysis within 24h after collection. Samples are concentrated, the RNA extracted and finally amplyfied using two target genes (N1/N2 or N1/IP4).


Here, we periodically release the dataset of the results obtained for each WWTP analysed with sampling date, gene copies per litre for each viral target, the daily flow from the WWTP, rain events registered and extra comments.


Moreover, since November 2021, the network analyses periodically the presence of Variants of Concern (VOCs) in the studied WWTPs. Raw data generated from sequencing is available upon request at coordinaciosars@icra.cat.
description: This program is funded by the Catalan Government. The coordination team is composed by membres from the Catalan Agency of Water, the Catalan Public Health Agency and the Catalan Institute for Water Research.
DOI: 10.15468/dl.xkckuf
title: Occurrence Download

description: A dataset containing 19742 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Syncerus caffer"
 ]
}

 The dataset includes 19742 records from 131 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007533-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.