cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.45gb4
title: Data from: Quantitative ornithology with a commercial marine radar: standard-target calibration, target detection and tracking, and measurement of echoes from individuals and flocks

description: Marine surveillance radars are commonly used for radar ornithology, but
 they are rarely calibrated. This prevents them from measuring the radar
 cross-sections (RCS) of the birds under study. Furthermore, if the birds
 are aggregated too closely for the radar to resolve them individually, the
 bulk volume reflectivity cannot be translated into a numerical density. We
 calibrated a commercial off-the-shelf marine radar using a standard
 spherical target of known RCS. Once calibrated, the radar was used to
 measure the RCS of common and roseate terns (Sterna hirundo L. and Sterna
 dougallii Montagu) tracked from a land-based installation at their
 breeding colony on Great Gull Island, NY, USA. We also integrated echoes
 from flocks of terns, comparing these total flock cross-sections with
 visual counts from photos taken at the same time as the radar
 measurements. The radar's calibration parameters were determined with
 1% error. RCS measurements made after calibration were expected to be
 accurate within ±2 dB. Mean tern RCS was estimated at -28 dB relative to
 one square meter (dBsm), agreeing in magnitude with a simple theoretical
 model. RCS was 3-4 dB higher when birds’ aspect angles were broadside to
 the radar beam compared with head- or tail-on. Integrated flock
 cross-section was linearly related to the number of birds. The slope of
 this line, an independent estimate of RCS, was -32 dBsm, within an order
 of magnitude of the estimate from individual birds, and near the middle of
 the frequency distribution of RCS values. These results indicate that a
 calibrated marine radar can count the birds in an aggregation via echo
 integration. Field calibration of marine radars is practical, enables
 useful measurements, and should be done more often.
description: Raw radar files from
 tern colony on Great Gull Island, NYZipped archive
 containing 200 raw radar sweeps recorded as NetCDF files on 22 July 2014
 on Great Gull Island, NY. Each file contains a single sweep of the
 radar's antenna, with three variables. The variable
 "amplitude" contains 2-D array of radar reflectivities in polar
 coordinates. Amplitudes are recorded as 16-bit signed integer values from
 the digitizer: to convert them to voltages, divide by the variable's
 "max_counts" metadata value (which is equal to 32764 for all
 files in this archive). The other two variables, "pulse_number"
 and "range", are the values corresponding to the amplitude
 array's azimuth and radial axes. Analysis scripts for these files are
 found in the article's supplementary online
 information.raw_radar.zip
DOI: 10.5061/dryad.q447c
title: Data from: Who's downloading pirated papers? Everyone

description: In increasing numbers, researchers around the world are turning to
 Sci-Hub, the controversial website that hosts 50 million pirated papers
 and counting. Now, with server log data from Alexandra Elbakyan, the
 neuroscientist who created Sci-Hub in 2011 as a 22-year-old graduate
 student in Kazakhstan, Science addresses some basic questions: Who are
 Sci-Hub's users, where are they, and what are they reading? The
 Sci-Hub data provide the first detailed view of what is becoming the
 world's de facto open-access research library. Among the revelations
 that may surprise both fans and foes alike: Sci-Hub users are not limited
 to the developing world. Some critics of Sci-Hub have complained that many
 users can access the same papers through their libraries but turn to
 Sci-Hub instead—for convenience rather than necessity. The data provide
 some support for that claim. Over the 6 months leading up to March,
 Sci-Hub served up 28 million documents, with Iran, China, India, Russia,
 and the United States the leading requestors.
description: Sci-Hub download
 dataThese data include 28
 million download request events from the server logs of Sci-Hub from 1
 September 2015 through 29 February 2016. The uncompressed 2.7 gigabytes of
 data are separated into 6 data files, one for each month, in tab-delimited
 text format.scihub_data.zipIPython Notebook for Sci-Hub raw dataIPython Notebook used to process the raw server log data (processing the GIS files into CSV, scraping DOI metadata, etc.).Sci-Hub.htmlSci-Hub.ipynbSci-Hub publisher DOI prefixesData scraped from the CrossRef website which can be used to replicate the analysis of downloads by publisher.publisher_DOI_prefixes.csv
DOI: 10.15468/dl.2h8p5d
title: Occurrence Download

description: A dataset containing 9770 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aquilegia coerulea"
 ]
}

 The dataset includes 9770 records from 182 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000354-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.60qm3
title: Data from: The influence of wind selectivity on migratory behavioral strategies

description: Air and water currents affect the timing and energy expenditure of many
 migratory animals, and therefore selection of favorable currents is
 important for optimal migratory performance. However, waiting for
 favorable currents also incurs costs. Here we conduct an optimality
 analysis to determine how wind selectivity affects three migratory
 currencies: time, energy, and risk. To describe variation in these metrics
 under varying degrees of selectivity, we constructed an individual-based
 model to simulate fall migration of passerines across eastern North
 America, allowing birds to use different thresholds of wind profit as the
 criterion for daily departure. A gradient of thresholds were tested across
 a range of realistic wind currents, from initiating flights only on nights
 when winds were directed in their preferred migratory direction (highly
 selective), to flying under most wind conditions (low selectivity). Our
 analysis indicated that relative mortality risk was lowest at intermediate
 selectivity; energy expended during flight was least for the most
 selective individuals; and of those that successfully completed migration,
 time spent on migration was lowest for the least selective birds. We
 solved for the optimal range of wind selectivity and show that this
 departure criterion alone can produce a tradeoff between time and energy
 that has been seen in many other behavioral contexts. While we solved for
 optima using some conditions specific to eastern North America, we show
 that variation in wind selectivity at departure can produce migratory
 behaviors that mimic the classic “time-minimizer” and “energy-minimizer”
 strategies developed from measurements of wild birds across multiple
 continents.
description: simulated
 datasetThis file contains all
 the simulated data resulting from our individual based migration model.
 Wind profit values from -40 to 10 m/s-1 across all starting
 locations.dataset.csv
DOI: 10.5061/dryad.mp745
title: Data from: Causes and consequences of large clonal assemblies in a poplar hybrid zone

description: Asexual reproduction is a common and fundamental mode of reproduction in
 plants. Although persistence in adverse conditions underlies most known
 cases of clonal dominance, proximal genetic drivers remain unclear, in
 particular for populations dominated by a few large clones. In this study,
 we studied a clonal population of the riparian tree Populus alba in the
 Douro river basin (northwestern Iberian Peninsula) where it hybridizes
 with Populus tremula, a species that grows in highly contrasted ecological
 conditions. We used 73 nuclear microsatellites to test whether genomic
 background (species ancestry) is a relevant cause of clonal success, and
 to assess the evolutionary consequences of clonal dominance by a few
 genets. Additional genotyping-by-sequencing data were produced to estimate
 the age of the largest clones. We found that a few ancient (over a few
 thousand years old) and widespread genets dominate the population, both in
 terms of clone size and number of sexual offspring produced.
 Interestingly, large clones possessed two genomic regions introgressed
 from P. tremula, which may have favoured their spread under stressful
 environmental conditions. At the population level, the spread of large
 genets was accompanied by an overall ancient (&gt;0.1 Myr) but soft
 decline of effective population size. Despite this decrease, and the high
 clonality and dominance of sexual reproduction by large clones, the Douro
 hybrid zone still displays considerable genetic diversity and low
 inbreeding. This suggests that even in extreme cases as in the Douro,
 asexual and sexual dominance of a few large, geographically extended
 individuals does not threaten population survival.
description: Datafile_21SSRs_533rametsGenotype of 533 ramets with 21 nuclear SSRsDatafile_21x533.xlsxDatafile_52SSRs_137indsGenotype of 137 individuals with 52 nuclear SSRsDatafile_52x137.xlsxPopulation map files for STACKSVery simple text file needed to run 'populations' command of STACKSGBS_population_maps.tar.gzBarcodes files for STACKSVery simple text files needed to run 'process_radtags' command of STACKSGBS_barcodes.tar.gzGBS fastq files (1/2)Raw GBS compressed fastq files (n=10), to process with STACKSGBS_raw_data_1.tar.gzScripts compressedIncludes ones bash script to run STACKS and trimmomatic and six R scripts to process the info from STACKS and calculate age of the genetsScripts.tar.gz
DOI: 10.5061/dryad.6kn93
title: Data from: Genomic divergence in a ring species complex

description: Ring species provide particularly clear demonstrations of how one species
 can gradually evolve into two, but are rare in nature. In the greenish
 warbler (Phylloscopus trochiloides) species complex, a ring of populations
 wraps around Tibet. Two reproductively isolated forms co-exist in central
 Siberia, with a gradient of genetic and phenotypic characteristics through
 the southern chain of populations connecting them. Previous genetic
 evidence has proven inconclusive, however, regarding whether species
 divergence took place in the face of continuous gene flow and whether
 hybridization between the terminal forms of the ring ever occurred. Here
 we use genome-wide analyses to show that, although spatial patterns of
 genetic variation are currently mostly as expected of a ring species,
 historical breaks in gene flow have existed at more than one location
 around the ring, and the two Siberian forms have occasionally interbred.
 Substantial periods of geographical isolation occurred not only in the
 north but also in the western Himalayas, where there is now an extensive
 hybrid zone between genetically divergent forms. Limited asymmetric
 introgression has occurred directly between the Siberian forms, although
 it has not caused a blending of those forms, suggesting selection against
 introgressed genes in the novel genetic background. Levels of reproductive
 isolation and genetic introgression are consistent with levels of
 phenotypic divergence around the ring, with phenotypic similarity and
 extensive interbreeding across the southwestern contact zone and strong
 phenotypic divergence and nearly complete reproductive isolation across
 the northern contact zone. These results cast doubt on the hypothesis that
 the greenish warbler should be viewed as a rare example of speciation by
 distance, but demonstrate that the greenish warbler displays a continuum
 from slightly divergent neighbouring populations to almost fully
 reproductively isolated species.
description: Greenish warbler
 sequences and SNPs mapped on zebra finch genomeGreenish warbler
 sequences mapped on zebra finch genome assembly (pink annotations). The
 physical location of SNP markers is also indicated. Grey annotations refer
 to the set of 81,034 SNPs with data in at least 80% of individuals (N=95
 birds). Yellow annotations refer to the subset of 2,334 SNPs with no
 missing data and minimum coverage = 3 reads. Blue annotations refer to the
 1,827 SNP markers used during the chromosome-by-chromosome introgression
 analysis. These assemblies can be inspected in the free version of the
 Geneious genomic workbench, which can be downloaded from
 http://www.geneious.com/download.Greenish Warbler Assemblies on
 ZF.geneiousGreenish Warbler De Novo
 Assembly DraftDe Novo Assembly of a
 whole-genome sequencing library from one Phylloscopus trochiloides
 viridanus bird (SRA accession number: SRX473141). De Novo Assembly was
 carried out in the CLC genomic workbench and following the default
 parameters set by the developer.GWDeNovoAssembly.gz
DOI: 10.15468/9ek5m8
title: Vermont Wild Bee Survey: Miscellaneous Records

description: Incidental wild bee records recorded by the Vermont Wild Bee Survey from 2023 onward. These records Include incidental visual observations by experts not recorded elsewhere and miscellaneous pinned specimens.
DOI: 10.5061/dryad.fb1fq
title: Data from: The impact of the tree prior on molecular dating of data sets containing a mixture of inter- and intraspecies sampling

description: In Bayesian phylogenetic analyses of genetic data, prior probability
 distributions need to be specified for the model parameters, including the
 tree. When Bayesian methods are used for molecular dating, available tree
 priors include those designed for species-level data, such as the
 pure-birth and birth-death priors, and coalescent-based priors designed
 for population-level data. However, molecular dating methods are
 frequently applied to data sets that include multiple individuals across
 multiple species. Such data sets violate the assumptions of both the
 speciation and coalescent-based tree priors, making it unclear which
 should be chosen and whether this choice can affect the estimation of node
 times. To investigate this problem, we used a simulation approach to
 produce data sets with different proportions of within- and
 between-species sampling under the multispecies coalescent model. These
 data sets were then analysed under pure-birth, birth-death, constant-size
 coalescent, and skyline coalescent tree priors. We also explored the
 ability of Bayesian model testing to select the best-performing priors. We
 confirmed the applicability of our results to empirical data sets from
 cetaceans, phocids, and coregonid whitefish. Estimates of node times were
 generally robust to the choice of tree prior, but some combinations of
 tree priors and sampling schemes led to large differences in the age
 estimates. In particular, the pure-birth tree prior frequently led to
 inaccurate estimates for data sets containing a mixture of inter- and
 intraspecific sampling, whereas the birth-death and skyline coalescent
 priors produced stable results across all scenarios. Model testing
 provided an adequate means of rejecting inappropriate tree priors. Our
 results suggest that tree priors do not strongly affect Bayesian molecular
 dating results in most cases, even when severely misspecified. However,
 the choice of tree prior can be significant for the accuracy of dating
 results in the case of data sets with mixed inter- and intraspecies
 sampling.
description: Ritchie_TreePrior_OnlineAppendixOnline Supplementary Information for "The Impact of the Tree Prior on Molecular Dating of Heterogeneous Inter- and Intraspecies Data Sets". Contains Table S1, Figures S2-S4.Cetacea_TreePriors_AnalysesAlignment and BEAST files for analysis of tree prior impact on Cetacean date estimates.Coregonus_TreePriors_AnalysesAlignments and analysis files for investigation of tree prior impact on whitefish (Coregonus) date estimates.Phocid_TreePriors_AnalysesAlignments and BEAST analysis files for investigation of tree prior impact on phocid date estimates.All Simulation DataLARGE FILE. Alignments, true tree files, phylograms showing branch rates, and BEAST analysis files for all simulated analyses. The analysis number in the filename refers to the index of the true tree in the relevant .trees file.HeteregeneousDataSims.zip
DOI: 10.5061/dryad.m0q5s
title: Data from: Understanding the genomic basis of adaptive response to variable osmotic niches in freshwater prawns: a comparative intraspecific RNA-Seq analysis of Macrobrachium australiense

description: Understanding the molecular basis of adaptive response to variable
 environmental conditions is a central goal of evolutionary biology. Here
 we sought to identify potential outlier SNPs (single nucleotide
 polymorphisms) in three wild populations of a freshwater prawn
 (Macrobrachium australiense) that are exposed to differing osmotic niches
 by using a comparative transcriptomics approach. De novo assembly of
 approximately 542 million (75 nt) pair end reads collected from 10
 individuals revealed 123,396 longer contigs/transcripts of variable
 length, that showed 97.38% transcriptome assembly completeness.
 Differential gene expression (DGE) analysis of major osmoregulatory genes
 revealed that Calreticulin, Na+/H+ exchanger and V-type (H+) ATPase showed
 the highest expression levels in the Blunder Creek (low ionic) population,
 while Crustacean cardiovascular peptide (CCP), Na+/K+-ATPase, Na+/K+/2Cl-
 Co-transporter (NKCC) and Na+/HCO3 exchanger showed the highest expression
 levels in the Bulimba Creek (higher ionic) population. In total, 16 gene
 ontology (GO) term categories were functionally enriched among the three
 studied populations. We identified 4144 raw and 835 high quality filtered
 SNPs in the three M. australiense populations, of which 84 SNPs were
 identified as outliers. Outliers were detected in 4 important
 osmoregulatory genes that include: Calreticulin, Na+/H+ exchanger,
 Na+/K+-ATPase and V-type-(H+)-ATPase. All outliers in the osmoregulatory
 genes were located in non-coding regulatory regions (untranslated regions,
 UTRs) of the gene. We hypothesize that the outlier SNPs identified here in
 M. australiense populations exposed naturally to different osmotic
 conditions influence specific gene expression patterns that allow
 individuals to respond to local environmental conditions.
description: M_australiense-ForwardReadsM_australiense-ReverseReads
DOI: 10.5061/dryad.bp11m
title: Data from: Composite measures of selection can improve the signal-to-noise ratio in genome scans

description: The growing wealth of genomic data is yielding new insights into the
 genetic basis of adaptation, but it also presents the challenge of
 extracting the relevant signal from multi-dimensional datasets. Different
 statistical approaches vary in their power to detect selection depending
 on the demographic history, type of selection, genetic architecture and
 experimental design. Here, we develop and evaluate new approaches for
 combining results from multiple tests, including multivariate distance
 measures and methods for combining P-values. We evaluate these methods on
 (i) simulated landscape genetic data analysed for differentiation outliers
 and genetic-environment associations and (ii) empirical genomic data
 analysed for selective sweeps within dog breeds for loci known to be
 selected for during domestication. We also introduce and evaluate how
 robust statistical algorithms can be used for parameter estimation in
 statistical genomics. On the simulated data, many of the composite
 measures performed well and had decreased variation in outcomes across
 many sampling designs. On the empirical dataset, methods based on
 combining P-values generally performed better with clearer signals of
 selection, higher significance of the signal, and in closer proximity to
 the known selected locus. Although robust algorithms could identify
 neutral loci in our simulations, they did not universally improve power to
 detect selection. Overall, a composite statistic that measured a robust
 multivariate distance from rank-based P-values performed the best. We
 found that composite measures of selection could improve the signal of
 selection in many cases, but they were not a panacea and their power is
 limited by the power of the univariate statistics they summarize. Since
 genome scans are widely used, improving inference for prioritizing
 candidate genes may be beneficial to medicine, agriculture, and breeding.
 Our results also have application to outlier detection in high-dimensional
 datasets and to combining results in meta-analyses in many disciplines.
 The compound measures we evaluate are implemented in the r package
 minotaur.
description: Data and
 scriptsZip file containing data
 files and scripts for analysis. Please see the README file within the
 compressed file for a description of all scripts.CodeforDryad_MEE.zip
DOI: 10.5061/dryad.jv1vf
title: Data from: Processing of simple and complex acoustic signals in a tonotopically organized ear

description: Processing of complex signals in the hearing organ remains poorly
 understood. This paper aims to contribute to this topic by presenting
 investigations on the mechanical and neuronal response of the hearing
 organ of the tropical bushcricket species Mecopoda elongata to simple pure
 tone signals as well as to the conspecific song as a complex acoustic
 signal. The high-frequency hearing organ of bushcrickets, the crista
 acustica (CA), is tonotopically tuned to frequencies between about 4 and
 70 kHz. Laser Doppler vibrometer measurements revealed a strong and
 dominant low-frequency-induced motion of the CA when stimulated with
 either pure tone or complex stimuli. Consequently, the high-frequency
 distal area of the CA is more strongly deflected by low-frequency-induced
 waves than by high-frequency-induced waves. This low-frequency dominance
 will have strong effects on the processing of complex signals. Therefore,
 we additionally studied the neuronal response of the CA to native and
 frequency-manipulated chirps. Again, we found a dominant influence of
 low-frequency components within the conspecific song, indicating that the
 mechanical vibration pattern highly determines the neuronal response of
 the sensory cells. Thus, we conclude that the encoding of communication
 signals is modulated by ear mechanics.
description: Rohdaten_BereitstellungMeasured mechanical data (Polytec Software). Polytec Scan Viewer may be used to visualize scanning vibrometer (.svd) files - available for download at Questions about data may be directed to Dr. Manuela Nowotny at