cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.38r08
title: Data from: Tree phenology responses to winter chilling, spring warming, at north and south range limits

description: Increases in primary production may occur if plants respond to climate
 warming with prolonged growing seasons, but not if local adaptation, cued
 by photoperiod, limits phenological advance. It has been hypothesized that
 trees with diffuse porous xylem anatomy and early successional species may
 respond most to warming. Within species, northern populations may respond
 most due to the fact that growing seasons are relatively short. Species
 most sensitive to spring temperature may show little overall response to
 warming if reduced chilling in fall/winter offsets accelerated
 winter/spring development. Because current thermal models consider only
 highly aggregated variables, e.g., degree days or chilling units
 (temperature sums for a season or year) they may not accurately represent
 warming effects. We show that assumptions contained in current thermal
 (degree-day) models are unrealistic for climate change analysis. Critical
 threshold parameters are not identifiable, and they do not actually have
 much to do with thresholds for development. Traditional models further
 overlook the discrete nature of observations, observation error, and the
 continuous response of phenological development to temperature variation.
 An alternative continuous development model (CDM) that addresses these
 problems is applied to a large experimental warming study near northern
 and southern boundaries of 15 species in the eastern deciduous forest of
 the US, in North Carolina and Massachusetts. Results provide a detailed
 time course of phenological development, including vernalization during
 winter and warming in spring, and challenge the basic assumptions of
 thermal models. Where traditional models find little evidence of a
 chilling effect (most are insignificant or have the wrong sign), the
 continuous development model finds evidence of chilling effects in most
 species. Contrary to the hypothesis that northern populations respond
 most, we find southern populations are most responsive. Because northern
 populations already have a compressed period for spring development they
 may lack flexibility to further advance development. A stronger response
 in the southern range could allow residents to resist northward migration
 of immigrants as climate warms. If potential invaders fail to exploit a
 prolonged growing season to the same degree as residents, then there is a
 resident advantage. Hypothesized effects of warming for xylem anatomy and
 successional status are not supported by the 15 species in this study.
description: Spring Phenology
 DataPhenologyData.zip
DOI: 10.5061/dryad.774s8
title: Data from: The gravity of pollination: integrating at-site features into spatial analysis of contemporary pollen movement.

description: Pollen-mediated gene flow is a major driver of spatial genetic structure
 in plant populations. Both individual plant characteristics and
 site-specific features of the landscape can modify the perceived
 attractiveness of plants to their pollinators and thus play an important
 role in shaping spatial genetic variation. Most studies of landscape-level
 genetic connectivity in plants have focused on the effects of
 inter-individual distance using spatial and increasingly ecological
 separation; yet have not incorporated individual plant characteristics or
 other at-site ecological variables. Using spatially explicit simulations,
 we first tested the extent to which the inclusion of at-site variables
 influencing local pollination success improved the statistical
 characterization of genetic connectivity based upon examination of pollen
 pool genetic structure. The addition of at-site characteristics provided
 better models than those that only considered inter-individual spatial
 distance (e.g., IBD). Models parameterized using conditional genetic
 covariance (e.g., Population Graphs) also outperformed those assuming
 panmixia. In a natural population of Cornus florida L. (Cornaceae), we
 showed that the addition of at-site characteristics (clumping of primary
 canopy opening above each maternal tree and maternal tree floral output)
 provided significantly better models describing gene flow than models
 including only between-site spatial (IBD) and ecological (Isolation By
 Resistance) variables. Overall, our results show that including
 inter-individual and local ecological variation greatly aids in
 characterizing landscape-level measures of contemporary gene flow.
description: Simulation Gravity
 ModelSimulated genotypes for
 low and high density populations.Cornus Gravity
 ModelRaw data analyzed in the
 gravity model for flowering dogwood, Cornus florida.
DOI: 10.5061/dryad.79hn1
title: Data from: Controlling meiotic recombinational repair: specifying the roles of ZMMs, Sgs1 and Mus81/Mms4 in crossover formation

description: Crossovers (COs) play a critical role in ensuring proper alignment and
 segregation of homologous chromosomes during meiosis. How the cell
 balances recombination between CO vs. noncrossover (NCO) outcomes is not
 completely understood. Further lacking is what constrains the extent of
 DNA repair such that multiple events do not arise from a single
 double-strand break (DSB). Here, by interpreting signatures that result
 from recombination genome-wide, we find that synaptonemal complex proteins
 promote crossing over in distinct ways. Our results suggest that Zip3
 (RNF212) promotes biased cutting of the double Holliday-junction (dHJ)
 intermediate whereas surprisingly Msh4 does not. Moreover, detailed
 examination of conversion tracts in sgs1 and mms4-md mutants reveal
 distinct aberrant recombination events involving multiple chromatid
 invasions. In sgs1 mutants, these multiple invasions are generally
 multichromatid involving 3–4 chromatids; in mms4-md mutants the multiple
 invasions preferentially resolve into one or two chromatids. Our analysis
 suggests that Mus81/Mms4 (Eme1), rather than just being a minor resolvase
 for COs is crucial for both COs and NCOs in preventing chromosome
 entanglements by removing 3′- flaps to promote second-end capture.
 Together our results force a reevaluation of how key recombination enzymes
 collaborate to specify the outcome of meiotic DNA repair.
description: PGENETICS_ZMM_SGS1_MMS4_ReCombine_dataPGENETICS_ZMM_MMS4_ReCombine_data.zip
DOI: 10.5061/dryad.130pg
title: Data from: The impact of resources for clinical surveillance on the control of a hypothetical foot-and-mouth disease epidemic in Denmark

description: The objectives of this study were to assess whether current surveillance
 capacity is sufficient to fulfill EU and Danish regulations to control a
 hypothetical foot-and-mouth disease (FMD) epidemic in Denmark, and whether
 enlarging the protection and/or surveillance zones could minimize economic
 losses. The stochastic spatial simulation model DTU-DADS was further
 developed to simulate clinical surveillance of herds within the protection
 and surveillance zones and used to model spread of FMD between herds. A
 queuing system was included in the model, and based on daily surveillance
 capacity, which was 450 herds per day, it was decided whether herds
 appointed for surveillance would be surveyed on the current day or added
 to the queue. The model was run with a basic scenario representing the EU
 and Danish regulations, which includes a 3 km protection and 10 km
 surveillance zone around detected herds. In alternative scenarios, the
 protection zone was enlarged to 5 km, the surveillance zone was enlarged
 to 15 or 20 km, or a combined enlargement of the protection and
 surveillance zones was modelled. Sensitivity analysis included changing
 surveillance capacity to 200, 350 or 600 herds per day, frequency of
 repeated visits for herds in overlapping surveillance zones from every 14
 days to every 7, 21 and 30 days, and the size of the zones combined with a
 surveillance capacity increased to 600 herds per day. The results showed
 that the default surveillance capacity is sufficient to survey herds on
 time. Extra resources for surveillance did not improve the situation, but
 fewer resources could result in larger epidemics and costs. Enlarging the
 protection zone was a better strategy than the basic scenario. Despite
 that enlarging the surveillance zone might result in shorter epidemic
 duration, and lower number of affected herds, it resulted frequently in
 larger economic losses.
description: DataDryadthis Data includes 4 data types: 1) Text files and an excel file which are the output data (results) of study; 2) R files which are the code of the simulation model that was used (DTU-DADS, Version 0.14); 3) csv files that are the input data for the model, and 4) readme files in 2 word documents describing the content of the output data and the model.
DOI: 10.5061/dryad.8ct18
title: Data from: Adaptive evolution and environmental durability jointly structure phylodynamic patterns in avian influenza viruses

description: Avian influenza viruses (AIVs) have been pivotal to the origination of
 human pandemic strains. Despite their scientific and public health
 significance, however, there remains much to be understood about the
 ecology and evolution of AIVs in wild birds, where major pools of genetic
 diversity are generated and maintained. Here, we present comparative
 phylodynamic analyses of human and AIVs in North America, demonstrating
 (i) significantly higher standing genetic diversity and (ii) phylogenetic
 trees with a weaker signature of immune escape in AIVs than in human
 viruses. To explain these differences, we performed statistical analyses
 to quantify the relative contribution of several potential explanations.
 We found that HA genetic diversity in avian viruses is determined by a
 combination of factors, predominantly subtype-specific differences in host
 immune selective pressure and the ecology of transmission (in particular,
 the durability of subtypes in aquatic environments). Extending this
 analysis using a computational model demonstrated that virus durability
 may lead to long-term, indirect chains of transmission that, when coupled
 with a short host lifespan, can generate and maintain the observed high
 levels of genetic diversity. Further evidence in support of this novel
 finding was found by demonstrating an association between subtype-specific
 environmental durability and predicted phylogenetic signatures: genetic
 diversity, variation in phylogenetic tree branch lengths, and tree height.
 The conclusion that environmental transmission plays an important role in
 the evolutionary biology of avian influenza viruses—a manifestation of the
 “storage effect”—highlights the potentially unpredictable impact of
 wildlife reservoirs for future human pandemics and the need for improved
 understanding of the natural ecology of these viruses.
description: H1Aligned sequences for H1
 avian subtypeH2Aligned sequences for H1
 avian subtypeH3Aligned sequences for H3
 avian subtypeH4Aligned sequences for H4
 avian subtypeH5Aligned sequences for H5
 avian subtypeH6Aligned sequences for H6
 avian subtypeH7Aligned sequences for H7
 avian subtypeH9Aligned sequences for H9
 avian subtypeH10Aligned sequences for
 H10 avian subtypeH11Aligned sequences for
 H11 avian subtypeH12Aligned sequences for
 H12 avian subtype
DOI: 10.5061/dryad.56kf4
title: Data from: Three-dimensional reconstructions come to life – interactive 3D PDF animations in functional morphology

description: Digital surface mesh models based on segmented datasets have become an
 integral part of studies on animal anatomy and functional morphology;
 usually, they are published as static images, movies or as interactive PDF
 files. We demonstrate the use of animated 3D models embedded in PDF
 documents, which combine the advantages of both movie and interactivity,
 based on the example of preserved Trigonopterus weevils. The method is
 particularly suitable to simulate joints with largely deterministic
 movements due to precise form closure. We illustrate the function of an
 individual screw-and-nut type hip joint and proceed to the complex
 movements of the entire insect attaining a defence position. This posture
 is achieved by a specific cascade of movements: Head and legs interlock
 mutually and with specific features of thorax and the first abdominal
 ventrite, presumably to increase the mechanical stability of the beetle
 and to maintain the defence position with minimal muscle activity. The
 deterministic interaction of accurately fitting body parts follows a
 defined sequence, which resembles a piece of engineering.
description: Interactive animated 3D
 reconstruction of the metacoxal joint of Trigonopterus
 oblongusClick on the figure to
 start interactive 3D view; switch between views by using the menu (Adobe
 Reader 8.1 or higher required).fig_s1.pdfInteractive animated 3D reconstruction of Trigonopterus vandekampi simulating the movements from walking position to thanatosis postureDefault views illustrating the blocking mechanisms are provided. Click on the figure to start interactive 3D view; switch between views by using the menu (Adobe Reader 8.1 or higher required).fig_s2.pdf
DOI: 10.5061/dryad.d702p
title: Data from: Concentrations and ratios of particulate organic carbon, nitrogen, and phosphorus in the global ocean

description: Knowledge of concentrations and elemental ratios of suspended particles
 are important for understanding many biogeochemical processes in the
 ocean. These include patterns of phytoplankton nutrient limitation as well
 as linkages between the cycles of carbon and nitrogen or phosphorus. To
 further enable studies of ocean biogeochemistry, we here present a global
 dataset compiled from published literature and consisting of 60811
 measurements of particulate organic carbon, nitrogen, and phosphorus
 analyzed as part of 70 cruises or time-series. The data are globally
 distributed and represent all major ocean regions as well as different
 depths in the water column. The global median C:P, N:P, and C:N ratios are
 163, 22, and 6.6, respectively, but also includes a lot of variation
 between samples from different regions. Thus, this compilation will
 hopefully assist in a wide range of future studies of ocean elemental
 ratios.
description: Marine particulate
 organic matterThe dataset includes
 information about latitude, longitude,depth and time of sampling of marine
 particulate organic phosphorus, nitrogen, and carbonCNP_data_DRYAD_edit_2.csv
DOI: 10.6084/m9.figshare.31158421
title: Data set for "Fabrication and Wear Analysis of AA2024 Aluminium Hybrid Composites

description: This study aims to develop and assess the tribological performance of AA2024-based hybrid composites reinforced with waste industrial stainless steel (SS) grinding particles and eggshell (ES) particles. By utilizing waste materials, the research promotes a circular economy approach for sustainable and lightweight structural applications. Hybrid composites were fabricated using the hot press sintering method. Microstructural analysis was conducted to examine reinforcement distribution and porosity. The relative density was measured to assess densification. Microhardness tests were performed to evaluate strengthening mechanisms, while wear analysis was carried out to determine wear rate and the coefficient of friction (COF). Microstructural analysis confirmed a homogeneous distribution of reinforcements with minimal porosity (~5.12% in AA2024+3ES+4SS). The composites exhibited relative densities between 92% and 94.5%, demonstrating effective densification. Microhardness increased from 92.4 ± 3.1 HV (AA2024) to 128.6 ± 4.2 HV (AA2024+3ES+4SS), attributed to grain refinement and reinforcement hardening effects. The lowest wear volume loss (3.293 mm3), and the COF (0.38) in AA2024+3ES+4SS, indicating enhanced tribological performance. This study introduces a novel approach to developing hybrid aluminium composites using industrial and biowaste reinforcements, offering a sustainable and cost-effective alternative for aerospace and automotive applications.
DOI: 10.6084/m9.figshare.31158421.v1
title: Data set for "Fabrication and Wear Analysis of AA2024 Aluminium Hybrid Composites

description: This study aims to develop and assess the tribological performance of AA2024-based hybrid composites reinforced with waste industrial stainless steel (SS) grinding particles and eggshell (ES) particles. By utilizing waste materials, the research promotes a circular economy approach for sustainable and lightweight structural applications. Hybrid composites were fabricated using the hot press sintering method. Microstructural analysis was conducted to examine reinforcement distribution and porosity. The relative density was measured to assess densification. Microhardness tests were performed to evaluate strengthening mechanisms, while wear analysis was carried out to determine wear rate and the coefficient of friction (COF). Microstructural analysis confirmed a homogeneous distribution of reinforcements with minimal porosity (~5.12% in AA2024+3ES+4SS). The composites exhibited relative densities between 92% and 94.5%, demonstrating effective densification. Microhardness increased from 92.4 ± 3.1 HV (AA2024) to 128.6 ± 4.2 HV (AA2024+3ES+4SS), attributed to grain refinement and reinforcement hardening effects. The lowest wear volume loss (3.293 mm3), and the COF (0.38) in AA2024+3ES+4SS, indicating enhanced tribological performance. This study introduces a novel approach to developing hybrid aluminium composites using industrial and biowaste reinforcements, offering a sustainable and cost-effective alternative for aerospace and automotive applications.
DOI: 10.5061/dryad.t6js1
title: Data from: Expansion of genotypic diversity and establishment of 2009 H1N1 pandemic-origin internal genes in pigs in China

description: ‘Two-way' transmission of influenza viruses between humans and swine
 has been frequently observed and the occurrence of the 2009 H1N1 pandemic
 influenza (pdm/09) demonstrated that swine-origin viruses could facilitate
 the genesis of a pandemic strain. Although multiple introductions to and
 reassortment in swine of the pdm/09 virus have been repeatedly reported in
 both Eurasia and the Americas, its long-term impact on the development of
 swine influenza viruses (SIVs) has not been systematically explored. Our
 comprehensive evolutionary studies on the complete genomes of 387 SIVs
 obtained from 2009 to 2012 in influenza surveillance in China revealed 17
 reassortant genotypes with pdm/09-origin genes. Even though the entire
 2009 pandemic virus and its surface genes cannot persist, its internal
 genes have becoming established and are now the predominant lineages in
 pigs in the region. The main persistent pdm/09-origin reassortant forms
 had at least 5 pdm/09-origin internal genes and their surface genes
 primarily of European avian-like (EA) or human H3N2-like SIV origin. These
 findings represent a marked change to the evolutionary patterns and
 ecosystem of SIVs in China. It is possible that the pdm/09-origin internal
 genes may be in the process of replacing EA- or triple reassortant-like
 internal genes. These alterations to the SIV gene pool need to be
 continually monitored to assess changes in the potential for SIVs to
 transmit to humans. Importance: Shortly after the emergence of the 2009
 pandemic H1N1 (pdm/09) influenza virus, it was transmitted from humans to
 pigs and this continues to occur around the world. Many reassortants
 between pdm/09-origin viruses and enzootic swine influenza viruses (SIVs)
 have been detected. However, the long-term impact of pdm/09-origin viruses
 on the SIV gene pool, which could lead to the generation of influenza
 viruses with the potential to infect humans, has not been systematically
 examined. From extensive surveillance of SIVs over a 38-month period in
 southern China, it was found that, although neither complete pdm/09
 viruses nor their surface genes could persist in pigs, their internal
 genes did persist. Over the survey period, these internal genes became
 predominant, potentially replacing those of the enzootic SIV lineages. The
 altered diversity of the SIV gene pool needs to be closely monitored for
 changes in the potential of SIVs to transmit to humans.
description: Maximum likelihood trees
 and genotype table of swine influenza virusSup fig and
 table.pdf
DOI: 10.5061/dryad.d772v
title: Data from: Species delimitation of the cochineal insects (Dactylopius) using molecular phylogenetics and morphology (Ph.D. thesis)

description: Cochineal insects (Dactylopius: Dactylopiidae: Coccoidea) are strict
 cactus parasites that are both pests of agriculture, commercially grown
 themselves, and useful biological control agents. Any genetic framework
 for this genus is completely lacking at onset of this project. Work here
 is focused on species delimitation within the genus Dactylopius. In the
 first chapter I present a morphological description of a new species of
 Dactylopius from the Chihuahuan Desert. In the second chapter I delimit
 the cochineal insect (Dactylopius coccus) using mtDNA data using a variety
 of population genetic and phylogenetic approaches. Third chapter I use
 mtDNA and nuclear coding and non-coding DNA to delimit the other species
 found within the genus sampled from across their recorded geographic and
 host-plant range.
description: concatenated.matrix-vi-24-13.codon.posMulti-gene nexus file of all the data from my third chapter, it has the gene ID's and codon calls. It is a MrBayes file.i-26-13-final-mtDNA-outgroup_CPP_coalescence_clockNexus MrBayes file from the second chapter of my dissertation that describes how I set up the dated phylogeny along with the associated nucleotide data.x-5-13-D_coccus_CO1_CO2_combined_copy_for_Dryad.nex
DOI: 10.5061/dryad.jm6pj
title: Data from: Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds

description: Recent discoveries have highlighted the dramatic evolutionary
 transformation of massive, ground-dwelling theropod dinosaurs into light,
 volant birds. Here, we apply Bayesian approaches (originally developed for
 inferring geographic spread and rates of molecular evolution in viruses)
 in a different context: to infer size changes and rates of anatomical
 innovation (across up to 1549 skeletal characters) in fossils. These
 approaches identify two drivers underlying the dinosaur-bird transition.
 The theropod lineage directly ancestral to birds undergoes sustained
 miniaturization across 50 million years and at least 12 consecutive
 branches (internodes) and evolves skeletal adaptations four times faster
 than other dinosaurs. The distinct, prolonged phase of miniaturization
 along the bird stem would have facilitated the evolution of many novelties
 associated with small body size, such as reorientation of body mass,
 increased aerial ability, and paedomorphic skulls with reduced snouts but
 enlarged eyes and brains.
description: Dataset 1: Character
 ListCharacter list for
 Dataset 1, with references, in Word (doc) formatDryad1-characterList.docDataset 1: TerminalTaxaTerminal taxa in Dataset 1, with sources of anatomical information and references, in Word (doc) formatDryad2-TerminalTaxa.docStratigraphic and Size Data for Datasets 1 and 2Stratigraphic and size data for all taxa (from Datasets 1 and 2) in Excel (xls) formatDryad3-StratigraphicAndSize.xlsDataset 1 in PAUP formatDataset 1 in nexus format with PAUP commandsDryad4-paup.txtDataset 1 in BEAST formatDataset 1 with size and stratigraphic data in BEAST xml format (plain text file).Dryad5-Dataset1_BEAST.xmlDataset 2 in BEAST formatDataset 2 with size and stratigraphic data in BEAST xml format (plain text file).Dryad6_Dataset2_BEAST.xml