cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mw6m905zg
title: Data from: Parasite-driven cascades or hydra effects: susceptibility and foraging depression shape parasite-host-resource interactions

description: This contains data for the manuscript listed in the title.We measured the
 foraging rates of individual zooplankton hosts, Daphnia
 dentifera, on phytoplankton resources, Ankistrodesmus falcatus,
 in the presence of fungal parasites of zooplankton, Metschnikowia
 bicuspidata. Some of these data are previously published
 (Genotypes12_foraging.csv by Strauss, Alexander T., et al. "Genotypic
 variation in parasite avoidance behaviour and other mechanistic, nonlinear
 components of transmission." Proceedings of the Royal
 Society B 286.1915 (2019): 20192164.) and some are published now
 for the first time (Genotype3_foraging.csv).In addition, we present novel
 evidence from a mesocosm experiment
 (Mesocosm_data1.csv-Mesocosm_data20.csv) of populations of each genotype
 or each pair of genotypes with phytoplankton resources and fungal
 parasites present or absent; our last treatment was low or high nutrient
 supply for the phytoplankton. With data on infection prevalence, host
 density, and phytoplankton density, we show how host traits and nutrients
 control outcomes for prevalence, host density, and phytoplankton
 density.These data may be reused with appropriate citation.
description: Mesocosm data is in Mesocosm_data.RDS The data
 object is organized such that each row (first dimension) is a
 tank.  Each column is a treatment, descriptor, or
 measure. Disease, Phosphorus, and Genotype are treatments
 Tank is a unique Tank ID Juveniles is the
 number of juveniles in a 1 L sample, thus equating to density in units of
 per liter Swith0eggs is the number of susceptible
 adults with 0 eggs Columns X1-X15 are susceptible
 adults with 1-15 eggs, respectively. Males is the
 number of adult males. InfJuveniles is the number of
 juveniles in a 1 L sample, thus equating to density in units of per
 liter Iwith0eggs is the number of infected adults with
 0 eggs Columns X1.1-X15.1 are infected adults with 1-15
 eggs, respectively. Each layer (3rd dimension) is a
 different time point corresponding to experimental days
 which can be accessed as individual .csv files if desired. For example,
 Mesocosm_data1.csv corresponds to the data for day 14.
 Data collected at days:
 14,20,27,30,34,36,41,44,48,51,55,58,62,64,69,72,76,79,83,86
DOI: 10.5061/dryad.4xgxd25bw
title: Global patterns and drivers of beta diversity facets of reef fish faunas

description: Aim: Exploring the relationships between the different facets of beta
 diversity and both past and current environmental conditions can unveil
 the processes that have shaped spatial patterns of biodiversity. In the
 marine realm, large-scale patterns and processes of beta diversity have
 been less investigated. Our study aimed to investigate the patterns and
 drivers of multiple facets of beta diversity and its components,
 contrasting pairs of reef fish assemblages among marine realms. Location:
 Tropical reefs. Taxon: Reef fishes. Methods: Based on trait data and
 phylogenetic relationships for 5,182 tropical reef fish species, we
 calculated compositional differences between pairs of reef fish
 assemblages across the Atlantic, Tropical Eastern Pacific (TEP), and
 Indo-Pacific realms. We also applied a partitioning approach to
 distinguish between the turnover and nestedness components. We then
 evaluated the relative importance of several variables related to
 historical and contemporary environmental conditions in shaping spatial
 patterns of beta diversity using Constrained Analysis of Principal
 Coordinates (CAP) models. Results: Both the turnover and nestedness
 components contributed to total phylogenetic and taxonomic beta diversity
 in the TEP and Indo-Pacific realms, while the turnover component was found
 to be more important in the Atlantic realm. In contrast, total trait beta
 diversity displayed very low values and was primarily explained by the
 nestedness component. Taxonomic and phylogenetic differences in the
 composition of tropical reef fish assemblages were influenced by both
 historical and contemporary factors or solely by historical variables.
 Main conclusions: Our results suggest that past climate changes
 and historical contingency left an imprint in the present-day composition
 of tropical reef fish assemblages. The very low levels of trait beta
 diversity indicate that reef fish assemblages display similar trait
 composition even among geographically distant assemblages with contrasting
 evolutionary histories, which may result from environmental filtering or
 evolutionary convergence, or the combination of both processes.
DOI: 10.5061/dryad.mpg4f4r25
title: Nest architecture is linked with ecological success in songbirds

description: Nests are essential constructions that directly determine fitness, yet
 their structure can vary substantially across bird species. While there is
 evidence supporting a link between nest architecture and the habitat a
 species occupies, we still ignore what ecological and evolutionary
 processes are linked to different nest types. Using information on 3175
 species of songbirds, we show that – after controlling for latitude and
 body size – species that build domed nests (i.e., nests with a roof) have
 smaller ranges, are less likely to colonise urban environments and have
 potentially higher extinction rates compared to species with open and
 cavity nests. Domed nests could be a costly specialisation, and we show
 these nests take more time to be built, which could restrict breeding
 opportunities. These diverse strands of evidence suggest that transition
 from domed to open nests in passerines could represent an important
 evolutionary innovation behind the success of the largest bird radiation.
description: The dataset presented was collated from various online resouces
 and comprises data on nest information and other variables for 3175
 species of passerine birds. This data has been cleaned and is the ones
 employed in all analyses. We also attach code and files that are needed to
 reproduce analyses and main graphs.
description: Description of files:
 <strong>Nests_Dryad_Jan2022.rmd: </strong>R Markdown
 file containing all PGLS regressions and code for main figures in the
 text. 
 <strong>env_nest_size_total_2022.csv:</strong> Dataset with all information needed to run the analyses in PGLS models <strong>function_pgls_dryad.R:</strong> Function needed for code above, runs a PGLS <strong>mcc_tree10.rds:</strong> MCC tree used for main analyses, obtained from distribution of 10000 from birdtree.org <strong>nest_building.csv:</strong> Data file with information for nest building analysis, 277 species <strong>Model_nest_building_reduced.rds:</strong> Model results used for graph of nest building <strong>MCC_Range_nest.logsize.lat.cont.q2.oct.cat2.R:</strong> Model results used for predictions in Figure on range size <strong>Model_nest_building100_2021.rds: </strong>Model results for 100 trees from building analysis <strong>Additional dataset: </strong>File with information on additional comments and sources of nest information
DOI: 10.5061/dryad.j6q573ngc
title: Intrinsic excitability mechanisms of neuronal ensemble formation

description: Neuronal ensembles are coactive groups of cortical neurons, found in
 spontaneous and evoked activity, that can mediate perception and behavior.
 To understand the mechanisms that lead to the formation of ensembles, we
 co-activated optogenetically and electrically layer 2/3 pyramidal neurons
 in brain slices from mouse visual cortex, in animals from both sexes,
 replicating in vitro an optogenetic protocol to generate ensembles in
 vivo. Using whole-cell and perforated patch-clamp pair recordings we find
 that, after optogenetic or electrical stimulation, coactivated neurons
 increase their correlation in spontaneous activity, a hallmark of ensemble
 formation. Coactivated neurons showed small biphasic changes in
 presynaptic plasticity, with an initial depression followed by a
 potentiation after a recovery period. Unexpectedly, optogenetic and
 electrical stimulation-induced significant increases in frequency and
 amplitude of spontaneous EPSPs, even after single-cell stimulation. In
 addition, we observed strong and persistent increases in neuronal
 excitability after stimulation, with increases in membrane resistance and
 reduction in spike threshold. A pharmacological agent that blocks changes
 in membrane resistance can revert this effect. These significant increases
 in excitability may partly explain the observed biphasic synaptic
 plasticity. We propose that cell-intrinsic changes in excitability are
 involved in the formation of neuronal ensembles. We propose an “iceberg”
 model, by which increased neuronal excitability makes subthreshold
 connections suprathreshold, enhancing the effect of already existing
 synapses, and generating a new neuronal ensemble.
description: See README.txt for details
DOI: 10.15468/dl.a9anw3
title: Occurrence Download

description: A dataset containing 440 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aeromachus pygmaeus"
 ]
}

 The dataset includes 440 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003064-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.h44j0zpn5
title: Dataset: Elisa cohort study on SARS-CoV-2 transmission

description: The Elisa study is a population-based cohort study in Lübeck and the
 surrounding area (northern Germany) with the aim to determine the
 prevalence and influencing factors of infections with the Sars-CoV2 over a
 one-year period. The study collected data from April 2020 to February
 2021. A cohort of 3000 randomly selected individuals were screened by swab
 (PCR) for active corona infection and blood draws were performed to
 determine antibodies at seven time points. In addition, continuous
 app-based questionnaires were administered to study participants regarding
 symptoms, behavior, and social factors. The data set consists of a file
 with baseline variables and examination results for the 3000 participants
 and another file with the continuous survey data (90,000 interviews).
description: For details note the ReadMe file. Please also
 refer to publication: Klein C. et al. One-year surveillance of SARS-CoV-2
 transmission of the ELISA Cohort: A model for population-based monitoring
 of infection risk. AAAS. 2022. accepted for publication.
description: Refer to the provided codebooks
DOI: 10.5061/dryad.h44j0zpn6
title: Datasets for manuscript: The nature, representation and measure of genetic information

description: Current studies in genetics very often refer to notions from information
 science. The concept of genetic information is still disputed because it
 attributes semantic traits to what seem to be regular biochemical
 entities. Some researchers maintain that the use of information in biology
 is just metaphorical and maybe even misleading. In this paper, we offer an
 analysis of the nature and characteristics of the use of information in
 proteins, protein families, and their sequences. It is argued that the
 foundation of the metaphorical view is relatively weak given the current
 findings in bioinformatics, and it is shown that the present understanding
 of genetics fits well into the context of the modern philosophy of
 information. Here, we propose an extension of Floridi’s conceptual model
 of information to include genetic information better. In addition, we
 discuss how to understand the qualitative aspects of genetic information
 and how to measure its quantitative aspects and present a joint
 statistical model including qualitative genetics, where the nominal
 genetic function is represented jointly with its metric self-information.
 The functional information of protein families in the Cath and Pfam
 databases are analysed. The paper concludes that scientific work may place
 information firmly as one of the fundamental components of molecular
 biology. The protein alignment files from the
 Cath and Pfam databases are in FASTA format.
description: Searched for protein alignments in the
 <strong><em>Cath</em></strong> and <strong><em>Pfam</em></strong> databases, and converted the files to FASTA format. Alignments are obtained from http://www.cathdb.info/browse/  (version 4.3), and from: https://pfam.xfam.org/browse  (version 34.0).
description: The dataset consist of standard FASTA files, and the data may be
 read and analysed by the Matlab toolbox<em>
 DeltaProt</em>. Ref:<br>Thorvaldsen, S., Flå, T. and Willassen, N.P.
 (2010). DeltaProt: A software toolbox for comparative genomics.
 <em>BMC Bioinformatics</em> 11, 573. https://doi.org/10.1186/1471-2105-11-573
DOI: 10.5061/dryad.gqnk98spz
title: Population structure, patterns of natal dispersal, and demographic history in a declining aerial insectivore, the purple martin Progne subis

description: Genetic variation is a fundamental component of biodiversity, and studying
 population structure, gene flow, and demographic history can help guide
 conservation strategies for many species. Like other aerial insectivores,
 the purple martin (Progne subis) is in decline, and yet their genetic
 background remains largely unknown. To address this knowledge gap, we
 assessed population structure in the nominate eastern subspecies (P. s.
 subis) with relation to natal dispersal and examined historical genetic
 patterns in all three subspecies (P. s. subis, P. s. arboricola, P. s.
 hesperia) across their North American breeding range by estimating
 effective population sizes over time. We used next-generation sequencing
 strategies for genomic analyses, integrating whole-genome resequencing
 data with continent-wide band encounter records to examine natal
 dispersal. We documented population structure across P. s. subis, with the
 highest differentiation between the northern (Alberta) and more southern
 colonies and following patterns of isolation-by-distance. Consistent with
 spatial patterns of genetic differentiation, we also found greater
 longitudinal than latitudinal natal dispersal distances, signifying
 potential latitudinal constraints on gene flow. Earlier contractions in
 effective population sizes in the western P. s. arboricola and P. s.
 hesperia compared to the eastern P. s. subis subspecies suggest these
 subspecies originated from two different glacial refugia. Together, these
 findings support latitudinal distinction in P. s. subis, and elucidate the
 origin of subspecies differentiation, highlighting the importance to
 conserve populations across the range to maximize genetic diversity and
 adaptive potential in the purple martin.
description: This dataset contains the unfiltered and
 filtered single-nucleotide-polymorphisms (SNPs) for 71 purple martins and
 corresponding code for the filtering process and population analyses. DNA
 was sequenced through skimSeq low-coverage whole-genome sequencing. The
 processed dataset has been filtered for quality (QUAL &gt; 20, MQ
 &gt; 20, MAF &gt; 0.05, missingness &lt; 20%), HWE,
 bi-allelic, autosomes, and LD-pruned with r<sup>2</sup>=0.2.
 Raw sequence reads are available on the Sequence Read Archive
 (SRA). Additionally included is code for analyzing bird
 band encounter records (data was obtained from North American Bird Banding
 Program in May 2019).
description: The filtered dataset includes four outliers that
 were removed from downstream population analyses. See the metadata file
 for details on sample information. This study also looked at 4 additional samples
 for demographic history, and raw sequence data for these samples are
 available in the same SRA BioProject. See README.txt for more
 details.
DOI: 10.5281/zenodo.17771215
title: MLVA31 database of Bacillus anthracis strains

description: Bacillus anthracis MLVA database contains MLVA31 profiles of 559 strains isolated woldwide with known geographic origin
DOI: 10.5281/zenodo.18399383
title: MLVA31 database of Bacillus anthracis strains

description: Bacillus anthracis MLVA database contains MLVA31 profiles of 559 strains isolated woldwide with known geographic origin
DOI: 10.5061/dryad.zcrjdfnf5
title: Data from: Phenotypic selection on an ornamental trait is not modulated by breeding density in a pied flycatcher population

description: Most studies of phenotypic selection in the wild have focused on
 morphological and life-history traits and looked at abiotic (climatic)
 variation as the main driver of selection. Consequently, our knowledge of
 the effects of biotic environmental variation on phenotypic selection on
 sexual traits is scarce. Population density can be considered a proxy for
 the intensity of intra- and inter-sexual competition and could therefore
 be a key factor influencing the covariation between individual fitness and
 the expression of sexual traits. Here, we used an individual-based data
 set from a population of pied flycatchers (Ficedula hypoleuca) monitored
 over 24 years to analyse the effect of breeding density on phenotypic
 selection on dorsal plumage colouration, a heritable and sexually selected
 ornament in males of this species. Using the number of recruits as a
 fitness proxy, our results show overall stabilizing selection on male
 dorsal colouration, with intermediate phenotypes being favoured over
 extremely dark and dull individuals. However, our results did not support
 the hypothesis that breeding density mediates phenotypic selection on this
 sexual trait. We discuss the possible role of other biotic factors
 influencing selection on ornamental plumage.
description: The methods are described in detail in the manuscript.
description: # Data from: Phenotypic selection on an ornamental trait is not modulated
 by breeding density in a pied flycatcher population
 [https://doi.org/10.5061/dryad.zcrjdfnf5](https://doi.org/10.5061/dryad.zcrjdfnf5) ## Description of the data and file structure The variables included in the dataset are:  year = Sampling year MaleID= Male identity FemaleID =Female identity habitat= The study area containts two study plots, located in an oak (1) or coniferous (2) forest n.ficed = Number of nest-boxes occupied by pied flycatchers on the given plot and year  n.other_sp = Number of nest-boxes occupied by other species on the given plot and year n.Total = total number of nest-boxes installed on the given plot and year Agem = Male age Tarsusm = Tarsus lenght (mm) Dcolour =Dorsal brownness, defined as the percentage of the head and mantle area covered by non-black feathers (brownish, grey or white), excluding the rump and the white forehead patch  Ld = Laying date nr = number of recruits NA- missing data code
DOI: 10.5061/dryad.qfttdz0jw
title: Rapid evolution of seed dormancy during sunflower de-domestication

description: Hybridization between crops and their wild relatives may promote the
 evolution of de-domesticated (feral) weeds. Wild sunflower (Helianthus
 annuus L.) is typically found in ruderal environments, but crop-wild
 hybridization may facilitate the evolution of weedy populations. Using one
 crop-specific mitochondrial marker (CMS-PET1) and 14 nuclear SSR markers,
 we studied the origin and genetic diversity of a recently discovered weedy
 population of sunflower (named BRW). Then, using a resurrection approach,
 we tested for rapid evolution of weedy traits (seed dormancy, herbicide
 resistance, and competitive ability) by sampling weedy and wild
 populations 10 years apart (2007 and 2017). All the weedy plants present
 the CMS-PET1 cytotype, confirming their feral origin. At the nuclear
 markers, BRW showed higher genetic diversity than the cultivated lines and
 low differentiation with one wild population, suggesting that wild
 hybridization increased their genetic diversity. We found support for
 rapid evolution towards higher seed dormancy, but not for higher
 competitive ability or herbicide resistance. Our results highlight the
 importance of seed dormancy during the earliest stages of adaptation and
 show that crop-wild hybrids can evolve quickly in agricultural
 environments.
DOI: 10.5061/dryad.d51c5b05j
title: Twitter vaccine misinformation data

description: Anti-vaccine content is rapidly propagated via social media, fostering
 vaccine hesitancy, while pro-vaccine content has not replicated the
 opponent's successes. Despite this disparity in the dissemination of
 anti- and pro-vaccine posts, linguistic features that facilitate or
 inhibit the propagation of vaccine-related content remain less known.
 Moreover, most prior machine-learning algorithms classified social-media
 posts into binary categories (e.g., misinformation or not) and have rarely
 tackled a higher-order classification task based on divergent perspectives
 about vaccines (e.g., anti-vaccine, pro-vaccine, and neutral). Our
 objectives are (1) to identify sets of linguistic features that facilitate
 and inhibit the propagation of vaccine-related content and (2) to compare
 whether anti-vaccine, pro-vaccine, and neutral tweets contain either set
 more frequently than the others. To achieve these goals, we collected a
 large set of social media posts (over 120 million tweets) between Nov. 15
 and Dec. 15, 2021, coinciding with the Omicron variant surge. A two-stage
 framework was developed using a fine-tuned BERT classifier, demonstrating
 over 99 and 80 percent accuracy for binary and ternary classification.
 Finally, the Linguistic Inquiry Word Count text analysis tool was used to
 count linguistic features in each classified tweet. Our regression results
 show that anti-vaccine tweets are propagated (i.e., retweeted), while
 pro-vaccine tweets garner passive endorsements (i.e., favorited). Our
 results also yielded the two sets of linguistic features as facilitators
 and inhibitors of the propagation of vaccine-related tweets. Finally, our
 regression results show that anti-vaccine tweets tend to use the
 facilitators, while pro-vaccine counterparts employ the inhibitors. These
 findings and algorithms from this study will aid public health
 officials' efforts to counteract vaccine misinformation, thereby
 facilitating the delivery of preventive measures during pandemics and
 epidemics.
description: This dataset corresponds to social media posts collected from
 twitter that have been annotated as pro-vaccine (1), anti-vaccine (-1),
 and neutral or vaccine unrelated (0). There are 2 sets of data; with the
 first set collected in October, 2019 (before the pandemic) and the second
 set collected between November 15 to December 15, 2021 (during pandemic).
 The dataset was collected using the Twitter v2 API. For more information
 about the data collection and annotation process, please refer to the
 following publication: Argyris, Y.A.,
 Zhang, N., Bashyal, B., and Tan, P.-N. (2022). "Using Deep Learning
 to Identify Linguistic Features that Facilitate or Inhibit the Propagation
 of Anti- and Pro-Vaccine Content on Social Media". To appear in the
 Proceedings of the IEEE International Conference on Digital Health,
 Barcelona, Spain.
description: The data file is stored in CSV format. Due to Twitter policy
 about publishing tweets, we provide only the tweet ID and their
 classes.