cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48597/zqfr-vsqb
title: Measurement of PAHs (polycyclic aromatic hydrocarbons) at Zeppelin mountain (Ny-Ålesund)

description: Measurement of PAHs (polycyclic aromatic hydrocarbons) at Zeppelin mountain (Ny-Ålesund)
DOI: 10.15468/dl.pxekyj
title: Occurrence Download

description: A dataset containing 417 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is New Zealand",
 "TaxonKey is Sciadocladus menziesii"
 ]
}

 The dataset includes 417 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001472-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0h2g0
title: Data from: SNPs across time and space: population genomic signatures of founder events and epizootics in the House Finch (Haemorhous mexicanus)

description: Identifying genomic signatures of natural selection can be challenging
 against a background of demographic changes such as bottlenecks and
 population expansions. Here, we disentangle the effects of demography from
 selection in the House Finch (Haemorhous mexicanus) using samples
 collected before and after a pathogen-induced selection event. Using
 ddRADseq, we genotyped over 18,000 SNPs across the genome in native
 pre-epizootic western US birds, introduced birds from Hawaii and the
 eastern United States, post-epizootic eastern birds, and western birds
 sampled across a similar time span. We found 14% and 7% reductions in
 nucleotide diversity, respectively, in Hawaiian and pre-epizootic eastern
 birds relative to pre-epizootic western birds, as well as elevated levels
 of linkage disequilibrium and other signatures of founder events. Despite
 finding numerous significant frequency shifts (outlier loci) between
 pre-epizootic native and introduced populations, we found no signal of
 reduced genetic diversity, elevated linkage disequilibrium, or outlier
 loci as a result of the epizootic. Simulations demonstrate that the
 proportion of outliers associated with founder events could be explained
 by genetic drift. This rare view of genetic evolution across time in an
 invasive species provides direct evidence that demographic shifts like
 founder events have genetic consequences more widespread across the genome
 than natural selection.
description: VCF files of 3 datasets
 used in analysesVCF files for all 3
 datasets used for analysis, along with an xlsx file of individual ID #s
 and corresponding metadata, and a README file with a description of each
 dataset.HF_RadSeqDatasets_Dryad.zip
DOI: 10.5061/dryad.jh6h1
title: Data from: Asymmetric geographic range expansion explains the latitudinal diversity gradients of four major taxa of marine plankton

description: Extensive investigation of the close association between biological
 diversity and environmental temperature has not yet yielded a generally
 accepted, empirically validated mechanism to explain latitudinal gradients
 of species diversity, which occur in most taxa. Using the highly resolved
 late Cenozoic fossil records of four major taxa of marine plankton, we
 show that their gradients arise as a consequence of asymmetric geographic
 range expansion rather than latitudinal variation in diversification rate,
 as commonly believed. Neither per capita speciation nor extinction rates
 trend significantly with temperature or latitude for these marine
 plankton. Species of planktonic foraminifera and calcareous nannoplankton
 that originate in the temperate zone preferentially spread toward and
 arrive earlier in the tropics to produce a normal gradient with tropical
 diversity peaks; by contrast, temperate-zone originating species of
 diatoms and radiolarians preferentially spread toward and arrive earlier
 in polar regions to produce reversed gradients with high-latitude
 diversity peaks. Our results suggest that temperature affects latitudinal
 diversity gradients chiefly by its effect on species’ range limits rather
 than on probabilities of speciation and extinction. We show that this
 mechanism also appears to operate in various multicellular taxa, thus
 providing a widely applicable explanation for the origin of latitudinal
 diversity gradients.
description: raw
 dataMicrofossil occurrence
 data from Neptune Sandbox Berlinfinal-neptune-data.csv
DOI: 10.5061/dryad.67f9c
title: Data from: Meiotic recombination shapes precision of pedigree- and marker-based estimates of inbreeding

description: The proportion of an individual’s genome that is identical-by-descent
 (GWIBD) can be estimated from pedigrees (inbreeding coefficient “Pedigree
 F”) or molecular markers (“Marker F”), but both estimators come with
 error. Assuming unrelated pedigree founders, Pedigree F is the expected
 proportion of GWIBD given a specific inbreeding constellation. Meiotic
 recombination introduces variation around that expectation (Mendelian
 noise) and related pedigree founders systematically bias Pedigree F
 downwards. Marker F is an estimate of the actual proportion of GWIBD but
 it suffers from the sampling error of markers plus the error that occurs
 when a marker is homozygous without reflecting common ancestry
 (identical-by-state). We here show via simulation of a zebra finch and a
 human linkage map that three aspects of meiotic recombination (independent
 assortment of chromosomes, number of cross-overs and their distribution
 along chromosomes) contribute to variation in GWIBD and thus the precision
 of Pedigree and Marker F. In zebra finches, where the genome contains
 large blocks which are rarely broken up by recombination, the Mendelian
 noise was large (nearly twofold larger standard deviations compared to
 humans) and Pedigree F thus less precise than in humans, where cross-overs
 are distributed more uniformly along chromosomes. Effects of meiotic
 recombination on Marker F were reversed, such that the same number of
 molecular markers yielded more precise estimates of GWIBD in zebra finches
 than in humans. As a consequence, in species inheriting large blocks that
 rarely recombine, even small numbers of microsatellite markers will often
 be more informative about inbreeding and fitness than large pedigrees.
description: Data & simulation
 codeThe Data.zip file
 contains all data sets (seven-generations pedigrees and microsatellite
 genotypes) and the annotated source codes (R scripts) for linkage map
 construction and smoothing, finding the optimal interference distance and
 for the gene-dropping simulations. The attached README provides further
 information on each of the files.Data.zip
DOI: 10.5061/dryad.m7ph3
title: Data from: How much do we know about the breeding biology of bird species in the world?

description: Knowledge on species’ breeding biology is the building blocks of avian
 life history theory. A review for the current status of the knowledge at a
 global scale is needed to highlight the priority for future research. We
 collected all available information on three critical nesting parameters
 (clutch size, incubation period and nestling period) for the close to 10
 000 bird species in the world and identified taxonomic, geographic and
 habitat gaps in the distribution of knowledge on avian breeding biology.
 The results show that only one third of all extant species are well known
 regarding the three nesting parameters analyzed, while the rest are partly
 or poorly known. Most data deficient taxonomic groups are tropical forest
 nesters, particularly from the Amazon basin, southeast Asia, Equatorial
 Africa and Madagascar – the places that harbor the world's highest
 bird diversity. These knowledge gaps could be hampering our understanding
 of avian life histories. Ornithologists are encouraged to pay more efforts
 to explore the breeding biology of those poorly-known species.
description: The current status of
 the knowledge on avian breeding biologyTables A1-3. The current
 status of the knowledge on avian breeding biology by different levels of
 taxonomy.Appendix
 1.pdf
DOI: 10.5061/dryad.dd56c
title: Data from: Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface

description: Classical empirical potentials/force-fields (FF) provide atomistic
 insights into material phenomena through molecular dynamics and Monte
 Carlo simulations. Despite their wide applicability, a systematic
 evaluation of materials properties using such potentials and, especially,
 an easy-to-use user-interface for their comparison is still lacking. To
 address this deficiency, we computed energetics and elastic properties of
 variety of materials such as metals and ceramics using a wide range of
 empirical potentials and compared them to density functional theory (DFT)
 as well as to experimental data, where available. The database currently
 consists of 3248 entries including energetics and elastic property
 calculations, and it is still increasing. We also include computational
 tools for convex-hull plots for DFT and FF calculations. The data covers
 1471 materials and 116 force-fields. A major feature of this database is
 that the web interface offers easy look up tables to compare at a glance
 the results from different potentials (for the same system). In addition,
 both the complete database and the software coding used in the process
 have been released for public use online (presently at
 http://www.ctcms.nist.gov/~knc6/periodic.html) in a user-friendly way
 designed to enable further material design and discovery.
description: dataJARVIS-FF contains the
 scripts used in making repository for evaluating classical force field
 available at http://www.ctcms.nist.gov/~knc6/periodic.html. 1)
 from_ctcms.py is the script to get force-fields from ctcms interatomic
 potential repository website (http://www.ctcms.nist.gov/potentials/) 2)
 ctcms_alloy.py is the scripts for setting up MPinterface
 (https://github.com/JARVIS-Unifies/MPInterfaces) and running LAMMPS
 calculation. Similar scripts have been used for other force-fields such as
 AIREBO,COMB, ReaxFF and so on. 3) postprocess.py is the post-procesing
 script after running ctcms_alloy.py 4) data.json is the classical
 force-field data for matrerial properties such as elastic constnats,
 energies. 5) get_entries_from_json.py and get_entries_from_ecjson.py is
 the script to compare materials project (MP) and JARVIS-FF data such as
 energetics, convex hull plot. Note lammps.py in MPinterfaces has been
 changed to MP_lammps.py. The ec.json for DFT elastic constatnt is obtained
 from
 http://datadryad.org/resource/doi:10.5061/dryad.h505v.
DOI: 10.5061/dryad.p811t
title: Data from: Community assembly and drivers of phytoplankton functional structure

description: We analysed the functional composition of coastal phytoplankton
 communities (n = 7941) along the gradient from marine to brackish waters
 of the Baltic Sea, using species-specific morphological and ecological
 functional traits (ability to fix atmospheric nitrogen, mixotrophy, use of
 silica in cell walls, formation of chains or colonies, motility, accessory
 pigment composition, and size), to describe and measure the functional
 differences between species. Mean pairwise functional distance of
 phytoplankton communities increased from spring to mid- and late summer in
 all regions, due to higher pigment diversity, increased share of
 mixotrophic and nitrogen-fixing species, more diverse size distribution
 and reduced dominance of silica users. A null model that simulated the
 expected community composition from empirical spatial distribution and
 environmental preferences of individual taxa was used to partition the
 effects of habitat filtering and biotic interactions on the community
 assembly. About every fourth community departed significantly from random
 expectations, signalling the notable effect of biotic interactions in the
 assembly of natural phytoplankton communities.
description: Baltic Sea phytoplankton
 monitoring data from 1981-2008Phytoplankton species
 composition and metadata of 7941 monitoring samples, and functional trait
 table of phytoplankton. For more details, see the ReadMe
 file.Klais_et_al.RData
DOI: 10.5061/dryad.19gp1
title: Data from: Evidence for concerted movement of nuclear and mitochondrial clines in a lizard hybrid zone

description: Moving hybrid zones provide compelling examples of evolution in action,
 yet long-term studies that test the assumptions of hybrid zone stability
 are rare. Using replicated transect samples collected over a 10 year
 interval from 2002 to 2012, we find evidence for concerted movement of
 genetic clines in a plateau fence lizard hybrid zone (Sceloporus
 tristichus) in Arizona. Cline-fitting analyses of SNP and mtDNA data both
 provide evidence that the hybrid zone shifted northward by approximately
 two kilometres during the 10 year interval. For each sampling period, the
 mtDNA cline centre is displaced from the SNP cline centre and maintaining
 an introgression distance of approximately 3 km. The northward expansion
 of juniper trees into the Little Colorado River Basin in the early 1900s
 provides a plausible mechanism for hybrid zone formation and movement, and
 a broad-scale quantification of recent land cover change provides support
 for increased woody species encroachment at the southern end of the hybrid
 zone. However, population processes can also contribute to hybrid zone
 movement, and the current stability of the ecotone habitats in the centre
 of the hybrid zone suggests that movement could decelerate in the future.
description: Mitochondrial DNA
 alignmentMitochondrial DNA
 alignment (ND1 gene) in phylip format.mitochondrialDNA.phyUnlinked SNP, phylipUnlinked SNPs in phylip format.unlinked_snps.phyUnlinked SNPs, allelesUnlinked SNPs, alleles, for Structure and Adegenet analyses.unlinked_snps.str
DOI: 10.5061/dryad.c3n62
title: Data from: The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates

description: Illumina reads of the SSU-rDNA-V9 region obtained from the circumglobal
 Tara Oceans expedition allow the investigation of protistan plankton
 diversity patterns on a global scale. We analyzed 6,137,350 V9-amplicons
 from ocean surface waters and the deep chlorophyll maximum, which were
 taxonomically assigned to the phylum Ciliophora. For open ocean samples
 global planktonic ciliate diversity is relatively low (ca. 1,300 observed
 and predicted ciliate OTUs). We found that 17% of all detected ciliate
 OTUs occurred in all oceanic regions under study. On average, local
 ciliate OTU richness represented 27% of the global ciliate OTU richness,
 indicating that a large proportion of ciliates is widely distributed. Yet,
 more than half of these OTUs shared &lt;90% sequence similarity with
 reference sequences of described ciliates. While alpha-diversity measures
 (richness and exp(Shannon H)) are hardly affected by contemporary
 environmental conditions, species (OTU) turnover and community similarity
 (β-diversity) across taxonomic groups showed strong correlation to
 environmental parameters. Logistic regression models predicted significant
 correlations between the occurrence of specific ciliate genera and
 individual nutrients, the oceanic carbonate system and temperature.
 Planktonic ciliates displayed distinct vertical distributions relative to
 chlorophyll a. In contrast, the Tara Oceans dataset did not reveal any
 evidence that latitude is structuring ciliate communities.
description: Tara V9 ciliate
 dataThis file contains
 ciliate sequences (V9 SSU rDNA) from ocean surface waters (SRF) and the
 deep chlorophyll maximum (DCM) of 47 sampling stations in the world's
 oceans. The data has been collected during the Tara Oceans expedition
 (2009 - 2012). For details on sampling procedure and sequence handling
 please refer to 'De Vargas et al. (2015). Eukaryotic plankton
 diversity in the sunlit ocean. Science, 348:1261605'. The complete
 Tara Oceans sequence data is available at the European Nucleotide Archive
 under project PRJEB6610.Tara_V9_ciliate_data.zip
DOI: 10.34810/data2161
title: Partitura i enregistrament del Pianto della Madonna a cinc veus de Giacomo Garibbi (1586)

description: Es tracta d'una obra musical a cinc veus impresa a Venècia el 1586 atribuïda, l'autoria
del text i la música, al franciscà Giacomo Garibbi (actiu a la segona meitat del segle
XVI). Es conserva al fons musical del CRAI-Biblioteca de Fons Antic de la Universitat
de Barcelona, E-Bu, B-45/6/25-3. Constitueix l'única edició (un unicum), fins a dia
d'avui, completa coneguda a nivell internacional, que ha restat oculta fins a la seva
descoberta el juny de 2024. No obstant això, convé assenyalar que hi ha un altre exemplar, encara que incomplet (només queda la part textual i no pas la musical), que es troba a la Biblioteca Ambrosiana de Milà. Transcripció del manuscrit original a càrrec d'Antonio Ezquerro Esteban. Adaptació musical de la transcripció per a l'enregistrament sonor i visual a càrrec de Carles Prat Vives.
&lt;br&gt; Enregistrament de la peça interpretada pel Cor Francesc Valls de la Catedral de
Barcelona. Director: Carles Prat. Membres del cor: Maria Casado, Belen Barnaus, Brenda Sara, Anabel Pérez, Mariona Llobera, Assumpta Cumí, Aniol Botines, Oriol Guimerà, Tomàs
Maxé, Pablo Acosta.
DOI: 10.5061/dryad.f3bd1
title: Data from: Positive selection of the TRIM family regulatory region in primate genomes

description: Viral selection pressure has acted on restriction factors that play an
 important role in the innate immune system by inhibiting the replication
 of viruses during primate evolution. Tripartite motif-containing (TRIM)
 family members are some of these restriction factors. It is becoming
 increasingly clear that gene expression differences, rather than
 protein-coding regions changes, could play a vital role in the
 anti-retroviral immune mechanism. Increasingly, recent studies have
 created genome-scale catalogues of DNase I hypersensitive sites (DHSs),
 which demark potentially functional regulatory DNA. To improve our
 understanding of the molecular evolution mechanism of antiviral
 differences between species, we leveraged 14 130 DHSs derived from 145
 cell types to characterize the regulatory landscape of the TRIM region.
 Subsequently, we compared the alignments of the DHSs across six primates
 and found 375 DHSs that are conserved in non-human primates but exhibit
 significantly accelerated rates of evolution in the human lineage
 (haDHSs). Furthermore, we discovered 31 human-specific potential
 transcription factor motifs within haDHSs, including the KROX and SP1,
 that both interact with HIV-1. Importantly, the corresponding haDHS was
 correlated with antiviral factor TRIM23. Thus, our results suggested that
 some viruses may contribute, through regulatory DNA differences, to
 organismal evolution by mediating TRIM gene expression to escape immune
 surveillance.
description: The motifs identified in
 TRIM haDHSsUsing the FIMO software
 to identified the putative transcription binding site motifs in TRIM
 haDHSs. And the corresponding six-primates sequences of these motifs were
 downloaed from Ensembl.The motif identified in TRIM
 haDHSs.rarSelection analysis of
 TRIM DHSThe TRIM DHS data was
 generated from 145 cell types DHS data in ENCODE. And the methodology of
 DHS selection analysis was based on our previous DHS
 research(Comprehensive identification and analysis of human accelerated
 regulatory DNA, Rachel et al.Genome Research).Transposable elements
 within TRIM DHSThis files showed the
 transposable elements that overlapped with TRIM haDHSs and conversed DHSs
 and their detailed information. The first three columns represented the
 position of DHS, the fourth to sixth columns represented the position of
 transposable elements. The annotation file of transposable elements came
 from ReapeatsMasker output file in UCSC.SNP_in_haDHS(from 1000
 human genome project)This file showed all the
 SNPs(data from 1000 human genome project) that located in TRIM haDHSs,
 with their information such as the positions of SNPs and allele
 frequencies.
DOI: 10.5061/dryad.32mq0
title: Data from: A model to identify urban traffic congestion hotspots in complex networks

description: The rapid growth of population in urban areas is jeopardizing the mobility
 and air quality worldwide. One of the most notable problems arising is
 that of traffic congestion. With the advent of technologies able to sense
 real-time data about cities, and its public distribution for analysis, we
 are in place to forecast scenarios valuable for improvement and control.
 Here, we propose an idealized model, based on the critical phenomena
 arising in complex networks, that allows to analytically predict
 congestion hotspots in urban environments. Results on real cities’ road
 networks, considering, in some experiments, real- traffic data, show that
 the proposed model is capable of identifying susceptible junctions that
 might becomes hotspots if mobility demand increases.
description: DataNetworks and traffic
 data used in the manuscript.
DOI: 10.5061/dryad.6bm2c
title: Data from: Analysis of animal accelerometer data using hidden Markov models

description: Use of accelerometers is now widespread within animal biologging as they
 provide a means of measuring an animal's activity in a meaningful and
 quantitative way where direct observation is not possible. In sequential
 acceleration data, there is a natural dependence between observations of
 behaviour, a fact that has been largely ignored in most analyses. Analyses
 of acceleration data where serial dependence has been explicitly modelled
 have largely relied on hidden Markov models (HMMs). Depending on the aim
 of an analysis, an HMM can be used for state prediction or to make
 inferences about drivers of behaviour. For state prediction, a supervised
 learning approach can be applied. That is, an HMM is trained to classify
 unlabelled acceleration data into a finite set of pre-specified
 categories. An unsupervised learning approach can be used to infer new
 aspects of animal behaviour when biologically meaningful response
 variables are used, with the caveat that the states may not map to
 specific behaviours. We provide the details necessary to implement and
 assess an HMM in both the supervised and unsupervised learning context and
 discuss the data requirements of each case. We outline two applications to
 marine and aerial systems (shark and eagle) taking the unsupervised
 learning approach, which is more readily applicable to animal activity
 measured in the field. HMMs were used to infer the effects of temporal,
 atmospheric and tidal inputs on animal behaviour. Animal accelerometer
 data allow ecologists to identify important correlates and drivers of
 animal activity (and hence behaviour). The HMM framework is well suited to
 deal with the main features commonly observed in accelerometer data and
 can easily be extended to suit a wide range of types of animal activity
 data. The ability to combine direct observations of animal activity with
 statistical models, which account for the features of accelerometer data,
 offers a new way to quantify animal behaviour and energetic expenditure
 and to deepen our insights into individual behaviour as a constituent of
 populations and ecosystems.
description: Acceleration data from a
 Verreaux's eagleThis file contains the
 dataset analysed in the associated publication under section "Real
 data examples", subsection "Modelling activity data in a soaring
 raptor".Verreauxs.accel.txtAcceleration data from a blacktip reef sharkThis file contains the dataset analysed in the associated publication under section "Real data examples", subsection "Diel activity changes in a reef-associated shark".BlacktipB.txt