cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9cnp5hqgh
title: Experimental evidence for stabilising selection on virulence in a bacterial pathogen

description: The virulence-transmission trade-off hypothesis has provided a dominant
 theoretical basis for predicting pathogen virulence evolution, but
 empirical tests are rare, particularly at pathogen emergence. We
 conducted an infection experiment in a North American songbird
 using 55 distinct isolates of its emerging infectious bacterial pathogen
 that differed in virulence. We demonstrate that more virulent variants
 transmitted faster, but had shorter infection durations, leading to
 variants of intermediate virulence being more evolutionarily successful.
 Interestingly, we did not find support for the common suggestion that the
 number of pathogen cells underpins their virulence and transmission
 rate. 
description: Wild house finches from populations that are outside the current
 range of <i>M. gallisepticum</i>, and have thus not evolved
 genetic resistance, were captured in Arizona during summer 2015 (N = 118,
 64 males and 54 females). The birds were divided into 2 groups of 59
 birds. Each of 55 <i>M. gallisepticum </i>isolates sampled
 over the course of the epidemic was inoculated into one bird selected at
 random from the 59 birds of the first group (30 males and 29 females),
 with 4 isolates inoculated in two birds each. Birds from the second group
 served as uninfected sentinels. Protocols were approved by Institutional Animal Care and Use Committees (IACUC) of Arizona State University (permit #15-1438R), as well as by Institutional Biological Use Authorizations to Auburn University (# BUA 500), and the University of Exeter’s ethics committee. Putative host mortality was determined <i>in situ</i> on days 3, 6, 8, 14, 21, 25, 28 and 34 post-infection, with infection considered lethal when birds lost the avoidance response to hand capture. A quantitative proxy for virulence was also obtained from the extent of conjunctival swelling measured from photographs taken at 6, 13, 25 and 34 days post-inoculation (dpi) from a standardized distance. Transmission rate to the sentinel was determined by amplification of <i>M. gallisepticum</i> DNA from conjunctival and tracheal swabs obtained from the sentinel at 2, 3, 4, 5, 6, 7, 8, 11, 14, 17, 20, 23, 26, 29, 32 and 35 days post-inoculation. Fitness was calculated as the product of infection duration (in days to putative mortality) and transmission rate (in days<sup>-1</sup>). Bacterial load was measured by quantitative amplification of <i>M. gallisepticum</i> DNA from pooled conjunctival and tracheal swabs obtained at 8, 14, 21 and 28 dpi. 
description: To test the associations between transmission rate and mortality,
 transmisssion rate and conjunctival swelling, and fitness and conjunctival
 swelling, we considered only the isolates that had successfully
 established an infection (infection =1). To test the association
 between pathogen load/replication rate and transmission, we considered
 only the isolates that successfully replicated during the experiment
 (included =1).
DOI: 10.5061/dryad.8w9ghx3kf
title: Landscape-level toxicant exposure mediates infection impacts on wildlife populations

description: Anthropogenic landscape modification such as urbanization can expose
 wildlife to toxicants, with profound behavioural and health effects.
 Toxicant exposure can alter local transmission of wildlife diseases by
 reducing survival or altering immune defence. However, predicting the
 impacts of pathogens on wildlife across their ranges is complicated by
 heterogeneity in toxicant exposure across the landscape, especially if
 toxicants alter wildlife movement from toxicant-contaminated to
 uncontaminated habitats. We developed a mechanistic model to explore how
 toxicant effects on host health and movement propensity influence
 range-wide pathogen transmission, and zoonotic exposure risk, as an
 increasing fraction of the landscape is toxicant-contaminated. When
 toxicant-contaminated habitat is scarce on the landscape, costs to
 movement and survival from toxicant exposure can trap infected animals in
 contaminated habitat and reduce landscape-level transmission. Increasing
 the proportion of contaminated habitat causes host population declines
 from combined effects of toxicants and infection. The onset of host
 declines precedes an increase in the density of infected hosts in
 contaminated habitat, and thus may serve as an early warning of increasing
 zoonotic spillover risk in urbanizing landscapes. These results highlight
 how sublethal effects of toxicants can determine pathogen impacts on
 wildlife populations that may not manifest until landscape contamination
 is widespread.
description: R code with ODEs and sensitivity analyses to reproduce all
 results and figures in the figure.
DOI: 10.5061/dryad.ghx3ffbmg
title: Shade is the most important factor limiting growth of a woody range expander

description: The expansion of woody plants into grasslands and old fields is often
 ascribed to fire suppression and heavy grazing, especially by domestic
 livestock. However, it is also recognized that nutrient availability and
 interspecific competition with grasses and other woody plants play a role
 in certain habitats. I examined potential factors causing range- and niche
 expansion by the eastern redcedar Juniperus virginiana, the most
 widespread conifer in the eastern United States, in multifactorial
 experiments in a greenhouse. Historical records suggest that the eastern
 redcedar is a pioneer forest species, and may be replaced as the forest
 increases in tree density due to shading. Another possible factor that
 affects its distribution may be nutrient availability, which is higher in
 old fields and other disturbed lands than in undisturbed habitats. In its
 historic range, eastern redcedars are particularly abundant on limestone
 outcrops, often termed ‘cedar barrens’. However, the higher abundance on
 limestone could be due to reduced interspecific competition rather than a
 preference for high pH substrates. I manipulated shade, fertilization,
 lime, and interspecific competition with a common dominant tree, the post
 oak Quercus stellata . In a separate experiment, I manipulated fire and
 grass competition. I measured growth rates (height and diameter) and
 above- and belowground biomass at the end of both experiments. I also
 measured total non-structural carbohydrates and nitrogen in these plants.
 Shade was the most important factor limiting the growth rates and biomass
 of eastern redcedars. I also found that there were significant declines in
 nitrogen and non-structural carbohydrates when shaded. These results are
 consistent with the notion that the eastern redcedar is a pioneer forest
 species, and that shade is the reason that these redcedars are replaced by
 other tree species. In the second experiment, I found that a single fire
 had a negative effect on young trees. There was no significant effect of
 competition with grass, perhaps because the competitive effect was shading
 by grasses and not nutrient depletion. Overall, the effects of shade were
 far more apparent than the effects of fire.
description: Split-plot design, with shade as the split-plot ("ERC Tree
 Data") Completely randomized design ("ERC
 Burning Experiment")
description: No missing values Two EXCEL files. The 1st
 experiment: Data included the effects of shade, fertilizer, competition
 with a tree, and lime on eastern redcedar growth ("ERC Tree
 Data".) The 2nd experiment: Data included the effects of fire and
 grass competition on eastern redcedar growth ("ERC Burning
 Experiment")
DOI: 10.5061/dryad.xgxd254f4
title: Song recordings and annotation files of 3 canaries used to evaluate training of TweetyNet models for birdsong segmentation and annotation

description: Many analyses of birdsong require time-consuming manual annotation of the
 individual elements of song, known as syllables or notes. We developed the
 first automated algorithm for birdsong annotation, "TweetyNet",
 that is applicable to complex song such as canary song. TweetyNet is
 trained with a small amount of hand-labeled data using supervised learning
 methods. We evaluate the amount of data required for training TweetyNet
 models using vocalizations of two songbird species - Bengalese finches and
 Canaries. This dataset contains song audio files and their accompanying
 annotation files for the three canaries used in this analysis.
description: This dataset was acquired between late April and early May 2018 -
 a period during which canaries perform their mating season songs. Birds
 were individually housed in soundproof boxes and recorded for 7-10 days
 (Audio-Technica AT831B Lavalier Condenser Microphone, M-Audio M-track
 amplifiers, and VOS games' Boom Recorder software on a Mac Pro
 desktop computer). In-house software was used to detect and save only
 sound segments that contained vocalizations.
description: The vocalizations of 3 canaries are in 3 separate
 folders. Two annotation files describe all the labeled
 vocalization segments of each animal in two formats: 1.
 A .csv file contains the annotations as a table with a row for each
 annotated canary syllable and columns: 
 label - Identity of syllable onset_s - Time
 (sec from file onset) of the syllable onset
 offset_s - Time (sec from file onset) of the syllable
 offset onset_Hz
 offset_Hz audio_file - Path to audio
 file annot_file - Path to annotation file
 sequence - n.a. annotation - number of
 audio files 2. A Matlab file containing 2
 cell arrays: keys - cell array of srtings -
 audio file names. elements - cell array if structs
 (matching the files in 'keys') with fields: 
 filenum: file number segFileStartTimes
 (vector): Time (sec from file onset) of the syllable onsets
 segFileEndTimes (vector): Time (sec from file onset) of the
 syllable offsets segType (vector): syllable
 identities
DOI: 10.5061/dryad.7wm37pvrj
title: Extensive hybridization reveals multiple coloration genes underlying a complex plumage phenotype

description: Coloration is an important target of both natural and sexual selection.
 Discovering the genetic basis of colour differences can help us to
 understand how this visually striking phenotype evolves. Hybridizing taxa
 with both clear colour differences and shallow genomic divergences are
 unusually tractable for associating coloration phenotypes with their
 causal genotypes. Here, we leverage the extensive admixture between two
 common North American woodpeckers—yellow-shafted and red-shafted
 flickers—to identify the genomic bases of six distinct plumage patches
 involving both melanin and carotenoid pigments. Comparisons between
 flickers across ~7.25 million genome-wide SNPs show that these two forms
 differ at only a small proportion of the genome (mean FST = 0.008). Within
 the few highly differentiated genomic regions, we identify 368 SNPs
 significantly associated with four of the six plumage patches. These SNPs
 are linked to multiple genes known to be involved in melanin and
 carotenoid pigmentation. For example, a gene (CYP2J19) known to cause
 yellow to red colour transitions in other birds is strongly associated
 with the yellow versus red differences in the wings and tail feathers of
 these flickers. Additionally, our analyses suggest novel links between
 known melanin genes and carotenoid coloration. Our finding of
 patch-specific control of plumage coloration adds to the growing body of
 literature suggesting colour diversity in animals could be created through
 selection acting on novel combinations of coloration genes.
description: <b>Northern flicker reference genome</b> (NOFL.pseudochromosomes.fasta.gz) gzipped file containing the northern flicker (<i>Colaptes auratus</i>) reference genome that was sequenced and assembled in this study. The sampled individual was a male from the yellow-shafted subspecies group.   <b>Reference genome annotations </b>(nofl_maker_annotation.gff.gz) gzipped file of the MAKER annotations of the northern flicker (<i>Colaptes auratus</i>) reference genome.   <b>Northern flicker SNP dataset </b>(RSFL-YSFL_WGS_missing80_mindepth3.vcf.gz) gzipped file containing the SNP dataset used in this study (7,233,334 biallelic SNPs). The data is from whole genome re-sequencing of 10 red-shafted flickers, 10 yellow-shafted flickers, and 48 red-shafted x yellow-shafted flicker hybrids, as described in the manuscript.   <b>Sample information </b>(sample_info.txt) Sample metadata to link the VCF file to individuals described in Supplementary Table 2 of the study.   <b>Northern flicker reference genome not aligned to zebra finch </b>(NOFL.scaffolds.fasta.gz) gzipped file containing the scaffold version of the northern flicker reference genome that was not aligned to the zebra finch genome using Satsuma. This reference was not used in this study, but is provided to allow for use by others.   Data processing scripts are available at https://github.com/stepfanie-aguillon/. Note that file names are consistent with those used in the GitHub Repository.
DOI: 10.5061/dryad.7sqv9s4r4
title: Data for: The scales of coevolution: comparative phylogeography and genetic demography of a locally adapted venomous predator and its prey

description: Coevolutionary theory predicts that differences in the genetic demography
 of interacting species can influence patterns of local adaptation by
 affecting the potential of local populations to respond to selection. We
 conducted a comparative phylogeographic study of venomous rattlesnakes and
 their venom-resistant ground squirrel prey across California, and assessed
 how effective population size (Ne) estimates correspond with a previously
 documented pattern of rattlesnake local adaptation. Using RAD-seq markers,
 we detected lineage relationships among both the rattlesnakes (Crotalus
 oreganus ssp.) and ground squirrels (Otospermophilus sp.) that are
 incongruent with previous phylogenetic hypotheses. Both rattlesnakes and
 squirrels share a deep divergence at the Sacramento-San Joaquin River
 Delta. At this broad phylogeographic scale, we found that the locally
 adapted rattlesnakes had higher Ne than squirrels. At the population
 scale, snakes also had larger Ne accompanied by larger values of several
 metrics of population genetic diversity. However, the specific magnitude
 of local adaptation of venom activity to ground squirrel venom resistance
 was not significantly correlated with local differences in Ne or other
 diversity statistics between predator and prey populations, suggesting
 other factors in the geographic mosaic of coevolution contribute to the
 specific local-scale outcomes of this interaction. These results suggest
 an evolutionary mechanism that may explain some (but clearly not all) of
 rattlesnake local adaptation in this coevolutionary interaction – larger
 population sizes raise adaptive potential of rattlesnakes compared to
 ground squirrels.
description: Double digest RAD-seq data processed using AftrRAD v. 5.0.1.
description: See README.txt in the zip drive for all relevant information
 about directory contents.
DOI: 10.6078/d1gd8s
title: Matlab applications for: A mechanical model to interpret distributed fiber optic strain measurement at displacement discontinuities

description: This repository publishes the data and Matlab app for the paper titled,
 "A Mechanical Model to Interpret Distributed Fiber Optic Strain
 Measurement at Displacement Discontinuities" published in Structural
 Health Monitoring. Distributed fiber optic (strain) sensing (DFOS), which
 provides the unique advantage of sensing damage (e.g. cracking) at
 locations that are not known a priori, has been increasingly used in civil
 engineering. Quantitative crack measurement requires the translation of a
 discontinuous displacement field at the crack to a continuous strain
 deformation in the fiber. The mechanical model contributes to the
 explanation of Distributed Fiber Optic (strain) Sensing (DFOS)
 results on concrete sensing. The crack sensing results with
 DFOS of one RC specimen under tension and the corresponding
 visualization app are also included in this repository.
DOI: 10.5061/dryad.vx0k6djq7
title: Regional effect of visual clutter

description: Stabilizing responses to disturbances are a critical part of the flight
 control system in flies. While strongly mediated by mechanoreception, much
 of the final steering response results from the wide field motion
 detection system associated with vision. The accuracy of the optomotor
 responses is affected when the characteristics of the visual input exceed
 the dynamic range of the motion detecting system. This has been
 demonstrated for stimulus parameters such as contrast, brightness,
 velocity, and spatial and temporal frequencies in gratings, but less is
 known about the effect of variables in more complex moving stimuli. By
 presenting laterally-moving dotfields of different densities we found
 that, in Drosophila melanogaster, the amplitude of the optomotor response
 is significantly affected by the level of visual clutter in the stimulus.
 Flies countersteer strongly within a relatively low and narrow range of
 element densities. But this effect is exclusive to the ventral region of
 the eye, and dorsal stimuli elicit an unaltered and stereotypical response
 throughout levels of visual clutter. This highlights local specialization
 of the eye and suggests the lower region may play a more critical role in
 translational flight-stabilization.
description: We recorded the steering responses of <em>Drosophila
 melanogaster</em> when presented with ventral and dorsal visual
 stimuli in a rigid tether virtual arena. Tethered flies were illuminated
 from above with an infrared light, while photodiodes below measured the
 shadow produced by each wing beat. Since flies steer by changing the
 relative amplitudes of left and right wing beats, attempts to turn produce
 a differential voltage by the sensor pair, and is reported as the voltage
 difference in wing beat amplitude, ΔWBA. This information is saved in
 a binary file per experiment and per fly. The data stored here has not
 been processed. We provide a Python code that can be used to read it,
 analyze it and reproduce the figures we present in our paper.
description: The files are
 compressed as a zip file. Once unpacked they provide the file structure
 required by the script to read them. Feel free to contact C. Ruiz if you
 have any questions regarding the dataset. The analysis
 is written as a Python script that can be called from the command line or
 imported using an interpreter such as Spyder. It is necessary to have
 Python installed already in the system and some basic packages. Follow
 these instructions in order to generate the plots used to compose the
 figures in the paper and examine the data: Unpack the
 compressed ZIP file preserving the folder structure.
 Open a terminal window or an interpreter such as Spyder and run
 the code<br> The code will load the binary files that contain the
 WVA values, process the data and generate the plots presented in the
 manuscript for publication. It will also show some lines of text at the
 end offering the results of the statisticts tests ran on the
 data.
DOI: 10.5281/zenodo.18396187
title: Successional development and structural complexity regulate forest carbon accumulation under climatic constraints
DOI: 10.5281/zenodo.18396186
title: Successional development and structural complexity regulate forest carbon accumulation under climatic constraints
DOI: 10.15468/dl.anu44e
title: Occurrence Download

description: A dataset containing 159276 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Spiranthes"
 ]
}

 The dataset includes 159276 records from 1272 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002560-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25326/4mhv-jx20
title: Prosulfocarb + ozone

description: Publication of the dataset
DOI: 10.25326/yk9m-da75
title: Pirimiphos-methyl + OH

description: Publication of the dataset
DOI: 10.25326/ncvq-3j17
title: Pirimiphos-methyl + OH

description: Publication of the dataset
DOI: 10.25326/zzby-bj73
title: Pirimiphos-methyl + OH

description: Publication of the dataset
DOI: 10.25326/4qym-1417
title: Pirimiphos-methyl + OH

description: Publication of the dataset
DOI: 10.25326/m0g9-0v28
title: Pirimiphos-methyl + OH

description: Publication of the dataset
DOI: 10.25326/9cn3-yt51
title: prosulfocarb + OH

description: Publication of the dataset
DOI: 10.25326/8n8y-rd78
title: prosulfocarb + OH

description: Publication of the dataset
DOI: 10.25326/hfj7-ch20
title: prosulfocarb + OH

description: Publication of the dataset
DOI: 10.25326/akqd-f907
title: alpha-pinene+ammonium sulphate + None - Aerosol study - particle formation - 2019-02-12

description: Publication of the dataset
DOI: 10.25326/sw72-n595
title: alpha-pinene+NO + None - Gas-phase oxidation - product study - 2019-01-18

description: Publication of the dataset
DOI: 10.25326/6mdf-ve68
title: alpha-pinene+NO + None - Gas-phase oxidation - product study - 2019-02-19

description: Publication of the dataset
DOI: 10.25326/sfk3-5j81
title: propene+NO + None - Gas-phase oxidation - product study - 2018-10-01

description: Publication of the dataset
DOI: 10.25326/ph3t-mr90
title: alpha-pinene+ozone + O3 - Gas-phase oxidation - product study - 2019-02-14

description: Publication of the dataset
DOI: 10.15468/dl.ae5pn7
title: Occurrence Download

description: A dataset containing 2347248 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "Geometry POLYGON((-99.77735 18.84631,-98.2838 18.96974,-98.27763 20.14853,-99.83289 20.0683,-99.77735 18.84631))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2347248 records from 873 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024749-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v3cnzh
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Winteria telescopa Brauer, 1901",
 "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 ((17.949 -34.5253,17.9648 -34.5378,17.9648 -34.1504,17.8905 -34.1504,17.949 -34.5253))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009972-250525065834625/datasets/export for details.
DOI: 10.5281/zenodo.15472561
title: Loghub-2.0-Revised

description: This database contains Loghub-2.0-Revised data. For more details, please visit https://github.com/Dyed-Heart/Loghub-2.0-Revised
DOI: 10.5281/zenodo.15472562
title: Loghub-2.0-Revised

description: This database contains Loghub-2.0-Revised data. For more details, please visit https://github.com/Dyed-Heart/Loghub-2.0-Revised
DOI: 10.15468/dl.t84k8u
title: Occurrence Download

description: A dataset listing the 4064451 species recorded in GBIF matching the query:
{ }

 The dataset's 4064451 records were derived from 72670 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001586-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.