cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gr656gk
title: Data from: Real-time decision-making during emergency disease outbreaks

description: In the event of a new infectious disease outbreak, mathematical and
 simulation models are commonly used to inform policy by evaluating which
 control strategies will minimize the impact of the epidemic. In the early
 stages of such outbreaks, substantial parameter uncertainty may limit the
 ability of models to provide accurate predictions, and policymakers do not
 have the luxury of waiting for data to alleviate this state of
 uncertainty. For policymakers, however, it is the selection of the optimal
 control intervention in the face of uncertainty, rather than accuracy of
 model predictions, that is the measure of success that counts. We simulate
 the process of real-time decision-making by fitting an epidemic model to
 observed, spatially-explicit, infection data at weekly intervals
 throughout two historical outbreaks of foot-and-mouth disease, UK in 2001
 and Miyazaki, Japan in 2010, and compare forward simulations of the impact
 of switching to an alternative control intervention at the time point in
 question. These are compared to policy recommendations generated in
 hindsight using data from the entire outbreak, thereby comparing the best
 we could have done at the time with the best we could have done in
 retrospect. Our results show that the control policy that would have been
 chosen using all the data is also identified from an early stage in an
 outbreak using only the available data, despite high variability in
 projections of epidemic size. Critically, we find that it is an improved
 understanding of the locations of infected farms, rather than improved
 estimates of transmission parameters, that drives improved prediction of
 the relative performance of control interventions. However, the ability to
 estimate undetected infectious premises is a function of uncertainty in
 the transmission parameters. Here, we demonstrate the need for both
 real-time model fitting and generating projections to evaluate alternative
 control interventions throughout an outbreak. Our results highlight the
 use of using models at outbreak onset to inform policy and the importance
 of state-dependent interventions that adapt in response to additional
 information throughout an outbreak.
description: Parameter estimates and
 simulation outputThese data include
 parameter estimates and simulation output for two outbreaks of
 foot-and-mouth disease (FMD): the outbreak in UK in 2001 and the outbreak
 in Miyazaki, Japan in 2010. Parameters are estimated at several time
 points throughout both outbreaks. Simulation of several control
 interventions from these time points onwards was also performed and the
 simulated total number of culled livestock is recorded. Details of the
 model structure and parameterisation of the model are described in the
 Methods section of the manuscript.data.zip
DOI: 10.5061/dryad.1qp358p
title: Data from: Mapping the expansion of coyotes (Canis latrans) across North and Central America

description: The geographic distribution of coyotes (Canis latrans) has dramatically
 expanded since 1900, spreading across much of North America in a period
 when most other mammal species have been declining. Although this
 considerable expansion has been well documented at the state/provincial
 scale, continent-wide descriptions of coyote spread have portrayed
 conflicting distributions for coyotes prior to the 1900s, with popularly
 referenced anecdotal accounts showing them restricted to the great plains,
 and more obscure, but data-rich accounts suggesting they ranged across the
 arid west. To provide a scientifically credible map of the coyote’s
 historical range (10,000 – 300 BP) and describe their range expansion from
 1900 to 2016, we synthesized archaeological and fossil records, museum
 specimens, peer-reviewed reports, and records from wildlife management
 agencies. Museum specimens confirm that coyotes have been present in the
 arid west and California throughout the Holocene, well before European
 colonization. Their range in the late 1800s was undistinguishable from
 earlier periods, and matched the distribution of non-forest habitat in the
 region. Coyote expansion began around 1900 as they moved north into taiga
 forests, east into deciduous forests, west into costal temperate rain
 forests, and south into tropical rainforests. Forest fragmentation and the
 extirpation of larger predators probably enabled these expansions. In
 addition, hybridization with wolves (C. lupus, C. lycaon, and/or C. rufus)
 and/or domestic dogs has been documented in the east, and suspected in the
 south. Our detailed account of the original range of coyotes and their
 subsequent expansion provides the core description of a large scale
 ecological experiment that can help us better understand the predator-prey
 interactions, as well as evolution through hybridization.
description: Coyote locations from
 VertnetLocation and date for
 verified coyote records from Museum specimens (zoology collections) as
 downloaded from VertnetHody_Kays_coyote_data_vertnet.csvHody_Kays_coyote_data_FaunmapFossil coyote locations as downloaded from FaunmapHody_Kays_coyote_data_faunmap.csvHody_Kays_coyote_data_literature_mx_camerica_modernModern location records for coyotes in Central America and Mexico as pulled from the literatureHody_Kays_coyote_data_literature_mx_camerica_historichistoric records of coyotes in Mexico and Central America as pulled from the literature
DOI: 10.5061/dryad.t12dr12
title: Data from: Penguin ectoparasite panmixia suggests extensive host movement within a colony

description: Parasite population structure can be used to infer fine-scale movement in
 host species. Many penguin species form large social colonies, and are
 highly philopatric, returning to the same nest or burrow, along the same
 route, after each trip to sea. Within a colony, however, the local
 abundance, physical similarity, and nocturnal habits of penguins hinder
 the observation of fine-scale movements. To determine the extent of
 movement and interaction of penguins within colonies, a genotyping by
 sequencing (GBS) approach was used to study the fine-scale structure of
 ticks—which depend on host movements for dispersal—exploiting the largest
 Little Penguin (Eudyptula novaehollandiae) colony in Australia (Phillip
 Island, Victoria). No barriers to tick gene flow were identified, and we
 infer that extensive penguin movement occurs throughout the colony. Our
 findings support the hypothesis that some penguin species are highly
 gregarious, socializing widely within colonies despite strong nest-site
 philopatry.
description: Compressed folder with
 Fasta files containing SNPs for each cladeThe attached zipped
 folder is comprised of two Fasta files, each containing the SNPs
 identified in the ticks from Clade A and Clade B respectively. In order to
 have been called, the SNPs had to be present in at least 20% of
 individuals.Data Files KLM The
 Auk.zip
DOI: 10.5061/dryad.q4f4ns6
title: Data from: A spatial kernel density method to estimate diet composition of fish

description: We present a novel spatially-explicit kernel density approach to estimate
 the proportional contribution of a prey to a predator’s diet by weight.
 First, we compare the spatial estimator to a traditional cluster-based
 approach using a Monte Carlo simulation study. Next we compare the diet
 composition of three predators from Pamlico Sound, North Carolina to
 evaluate how ignoring spatial correlation affected diet estimates. The
 spatial estimator had lower MSE values compared to the traditional
 cluster-based estimator for all Monte Carlo simulations. Incorporating
 spatial correlation when estimating the predator’s diet resulted in a
 consistent increase in precision across multiple levels of spatial
 correlation. Bias was often similar between the two estimators but when it
 differed it mostly favored the spatial estimator. The two estimators
 produced different estimates of proportional contribution of prey to the
 diets of the three field-collected predator species, especially when
 spatial correlation was strong and prey were consumed in patchy areas. Our
 simulation and empirical data provide strong evidence food habits data
 should be modeled using spatial approaches and not treated as
 spatially-independent.
description: Pam_Lat_LongsList of latitude and longitude coordinates for Pamlico Sound, NC. This file is used when generating ss_predictLocations for s, needed when estimating the diet using the spatial estimator and for simulating diet data across the Pamlico Sound surface.spot_trawlData used for estimating Spot diet using the spatial and non-spatial estimators.Creating S Predict GridsR code for generating sCross Validation using Grid SearchR code for cross validation using manual grid searchCross Validation using OptimizationR code for cross validation using an optimization routine.Data SimulationR code for simulating predator diet data.Estimating Diet using NonSpatial EstimatorR code for estimating predator diet composition using the nonspatial estimator.Estimating Diet using Spatial Estimator (SDKE)R code for estimating predator diet composition using the spatial estimator.Monte Carlo Simulation Study and Sample Size ComparisonR code for conducting Monte Carlo simulation study.Bhattacharyya DistanceR code for calculating Bhattacharyya Distance.Pamlico_Waters_Extended_wgs
DOI: 10.5061/dryad.j6s420k
title: Data from: Chorea, psychosis, acanthocytosis, and prolonged survival associated with ELAC2 mutations

description: Biallelic mutations in the elaC ribonuclease Z 2 (ELAC2) gene cause a rare
 mitochondrial disease, the main features of which are hypertrophic
 cardiomyopathy, delayed psychomotor development, and usually death during
 childhood. Only 20 families have been reported with this syndrome. Neither
 movement disorders nor psychotic features have been described as part of
 the spectrum of ELAC2 mutations. We describe a patient with a complex
 hyperkinetic syndrome and acanthocytosis, harboring biallelic ELAC2
 mutations.
description: Supplemental data ELAC2
 clean versionAppendix
 documentSupplemental data
 ELAC2.docxFigure e-1 Brain
 MRIFigure e-2
 PETFigure e-3:
 AcanthocytesFigure e-3
 Acanthocytes.docxFigure e-4:
 ElectropherogramFigure e-4
 Electropherogram.docxLegend to the
 videoComplex movement
 disorderTable
 e-1Table
 e-2201712041122 Consent
 NeurologyConsent_for_Publication_of_Photos_and (6).doc201804111900 Consent examining physician
DOI: 10.5061/dryad.3mn2402
title: Data from: The role of geography in adaptive radiation

description: Although the importance of biogeography in the speciation process is
 well-recognized, the fundamental role of geographic diversification during
 adaptive radiations has not been studied to determine its importance
 during the adaptive radiation process. We examined the relationship
 between lineage and regional diversification patterns in the South
 American rodent subfamily Sigmodontinae, one of the best candidates for an
 adaptive radiation in mammals, to propose a conceptual framework for
 geographic transitions during adaptive radiations. We reconstructed a
 time-calibrated phylogeny from four nuclear and one mitochondrial gene for
 77% of sigmodontine diversity. Historical biogeography was reconstructed
 among 14 regions, to which we applied a sliding-window approach to
 estimate regional transition rates through time. We compared these rate
 patterns and measured whether regions consisted of species that were more
 phylogenetically related than expected by chance. Following the initial
 South American colonization around 7 million years ago, multiple
 expansions from northern regions correlated with a burst of speciation.
 Subsequently, both diversification and regional transition rates decreased
 overall and within the majority of regions. Despite high regional
 transition rates, nearly all regional assemblages were phylogenetically
 clustered, indicating within-region diversification was common. We
 conclude that biogeographic complexity and partitioning played a profound
 role in the adaptive radiation of the South American Sigmodontinae
 (Oryzomyalia), the degree to which is determined by the relative scales of
 spatial variation and dispersal abilities.
description: Sequence alignment and
 Beast input fileXML file formatted to
 execute with Beast v1.8.4. This file was ran to generate Figure
 2.Schenk&Steppan.Beast_Input.xmlBeast output treeTree file of the 95% HPD tree, which is the result of the Beast analysis. File opens best in FigTree. Tree file used in Figures 2 and S2.Schenk&Steppan.Beast_Output.treAlignment fileNexus alignment file formatted for MrBayes, including partition boundaries.700.Sigmo.BI.nexSlidingWindow.RR code to conduct sliding window analysis. Code is duplicated at https://github.com/johnjschenk/RcodeSlidingWindowSimulations.RR code written to generate simulated data to compare again empirical data. Code can also be accessed at https://github.com/johnjschenk/Rcode.
DOI: 10.5281/zenodo.18389220
title: Dataset for "Pair-induced quenching in holmium doped fiber lasers and its impact on efficiency and operating wavelength"

description: This dataset includes relevant data and figures associated with the manuscript " Pair-induced quenching in holmium doped fiber lasers and its impact on efficiency and operating wavelength ".

The Figures are in .png formats and all relevant data are in .csv formats. 

Data files are labeled according to the corresponding figure in the manuscript (e.g., Fig2a_clad-pumped_anlOptim.csv contains the data used to generate the analytical model plots in Figure 2a). The dataset is organized in 3 folders, each of which is named after a Figure in the manuscript. 

 Only figures reporting simulation results are included in the dataset. The schematic Figure 1 is excluded.

Each folder reports processed Data related to a specific Figure (included in the folder). 

The labels of the axes and the units are indicated in the headers of individual columns of each .csv file

Full context and detailed analysis of the provided raw and processed Data can be found in the manuscript.
DOI: 10.5281/zenodo.18389221
title: Dataset for "Pair-induced quenching in holmium doped fiber lasers and its impact on efficiency and operating wavelength"

description: This dataset includes relevant data and figures associated with the manuscript " Pair-induced quenching in holmium doped fiber lasers and its impact on efficiency and operating wavelength ".

The Figures are in .png formats and all relevant data are in .csv formats. 

Data files are labeled according to the corresponding figure in the manuscript (e.g., Fig2a_clad-pumped_anlOptim.csv contains the data used to generate the analytical model plots in Figure 2a). The dataset is organized in 3 folders, each of which is named after a Figure in the manuscript. 

 Only figures reporting simulation results are included in the dataset. The schematic Figure 1 is excluded.

Each folder reports processed Data related to a specific Figure (included in the folder). 

The labels of the axes and the units are indicated in the headers of individual columns of each .csv file

Full context and detailed analysis of the provided raw and processed Data can be found in the manuscript.
DOI: 10.5061/dryad.hc54664
title: Data from: Order-level fern plastome phylogenomics: new insights from Hymenophyllales

description: PREMISE OF THE STUDY: Filmy ferns (Hymenophyllales) are a highly
 specialized lineage, having mesophyll one cell layer thick and inhabiting
 particularly shaded and humid environments. The phylogenetic placement of
 Hymenophyllales has been inconclusive, and while over 87 whole fern
 plastomes have been published, none was from Hymenophyllales. To better
 understand the evolutionary history of filmy ferns, we sequenced the first
 complete plastome for this order. METHODS: We compiled a plastome
 phylogenomic dataset encompassing all eleven fern orders, and
 reconstructed phylogenies using different data types (nucleotides, codons,
 and amino acids) and partition schemes (codon positions and loci). To
 infer the evolution of fern plastome organization, we coded plastomic
 features, including inversions, inverted repeat boundary shifts, gene
 losses, and tRNA anticodon sequences as characters, and reconstructed the
 ancestral states for these characters. KEY RESULTS: We discovered a suite
 of novel, Hymenophyllales-specific plastome structures that likely
 resulted from repeated expansions and contractions of the inverted repeat
 regions. Our phylogenetic analyses reveal that Hymenophyllales is highly
 supported as either sister to Gleicheniales or to Gleicheniales + the
 remaining non-Osmundales leptosporangiates, depending on the data type and
 partition scheme. CONCLUSIONS: Although our analyses could not confidently
 resolve the phylogenetic position of Hymenophyalles, the results here
 highlight the danger of drawing conclusions from "all-in"
 phylogenomic dataset without exploring potential inconsistencies in the
 data. Finally, our first order-level reconstruction of fern plastome
 structural evolution provides a useful framework for future plastome
 research.
description: alignments and partition
 schemesThe alignments and their
 partitions/models used in this study. For content of each alignment,
 please check the details in the original publication.
DOI: 10.5061/dryad.fj53jq3
title: Data from: Climatic adaptation and ecological descriptors of wild beans from Mexico

description: Despite its economic, social, biological, and cultural importance, wild
 forms of the genus Phaseolus are not well represented in germplasm banks,
 and they are at great risk due to changes in land use as well as climate
 change. To improve our understanding of the potential geographical
 distribution of wild beans (Phaseolus spp.) from Mexico and support in
 situ and ex situ conservation programs, we determined the climatic
 adaptation ranges of 29 species and two subspecies of Phaseolus collected
 throughout Mexico. Based on five biotic and 117 abiotic variables obtained
 from different databases—WorldClim, Global‐Aridity, and Global‐PET—we
 performed principal component and cluster analyses. Germplasm was
 distributed among 12 climatic types from a possible 28. The general
 climatic ranges were as follows: 8–3,083 m above sea level; 12.07–26.96°C
 annual mean temperature; 10.33–202.68 mm annual precipitation; 9.33–16.56
 W/m2 of net radiation; 11.68–14.23 hr photoperiod; 0.06–1.57 aridity
 index; and 10–1,728 mm/month of annual potential evapotranspiration. Most
 descriptive variables (25) clustered species into two groups: One included
 germplasm from semihot climates, and the other included germplasm from
 temperate climates. Species clustering showed 45% to 54% coincidence with
 species previously grouped using molecular data. The species P.
 filiformis, P. purpusii, and P. maculatus were found at low‐humidity
 locations; these species could be used to improve our understanding of the
 extreme aridity adaptation mechanisms used by wild beans to avoid or
 tolerate climate change as well as to introgress favorable alleles into
 new cultivars adapted to hot, dry environments.
description: S1S2
DOI: 10.5061/dryad.3k888n7
title: Data from: Extensive hybridization following a large escape of domesticated Atlantic salmon in the Northwest Atlantic

description: [No abstract entered]
description: SNP genotype
 dataSNP genotype data for 95
 SNPs for juvenile and baseline samples.2014_2015_data.csvGeographic distance from escape event to each riverGeographic distance from escape event to each riverDistance_from_escape.csvRiver Axial Distances and Catch
DOI: 10.5061/dryad.3d8332h
title: Data from: The spatial structure of phylogenetic and functional diversity in the United States and Canada: an example using the sedge family (Cyperaceae)

description: Systematically quantifying diversity across landscapes is necessary to
 understand how clade history and ecological heterogeneity contribute to
 the origin, distribution, and maintenance of biodiversity. Here, we chart
 the spatial structure of diversity among all species in the sedge family
 (Cyperaceae) throughout the USA and Canada. We first identify areas of
 remarkable species richness, phylogenetic diversity, and functional trait
 diversity, and highlight regions of conservation priority. We then test
 predictions about the spatial structure of this diversity based on the
 historical biogeography of the family. Incorporating a phylogeny, over
 400,000 herbarium records, and a database of functional traits mined from
 online floras, we find that species richness and functional trait
 diversity peak in the Northeastern USA, while phylogenetic diversity peaks
 along the Gulf of Mexico. Floristic turnover among assemblages increases
 significantly with distance, but phylogenetic turnover is twice as rapid
 along latitudinal gradients as along longitudinal gradients. These
 patterns reflect the expected distribution of Cyperaceae, which originated
 in the tropics but radiated in temperate regions. We identify assemblages
 with an abundance of rare, range-restricted lineages, and assemblages
 composed of species generally lacking from diverse regions. We argue that
 both of these metrics are useful for developing targeted conservation
 strategies. We use the data generated here to establish future research
 priorities, including the testing of a series of hypotheses regarding the
 distribution of chromosome numbers, photosynthetic pathways, and resource
 partitioning in sedges.
description: Species_coordinatesNA_CyperaceaePhylogeny of North American Cyperaceae