cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9jk90f6
title: Data from: Contrasting processes drive ophiuroid phylodiversity across shallow and deep seafloors

description: Our knowledge of the distribution and evolution of deep-sea life is
 limited, impeding our ability to identify priority areas for conservation.
 Here we analyse, for the first time, large integrated phylogenomic and
 distributional datasets of seafloor fauna from sea surface to abyss and
 equator to pole of the Southern Hemisphere for an entire class of
 invertebrates (Ophiuroidea). We find that latitudinal diversity gradients
 are assembled through contrasting evolutionary processes for shallow
 (0-200 m) and deep (&gt; 200 m) seas. The shallow-water
 tropical-temperate realm broadly reflects a tropical
 diversification-driven process but with exchange in both directions.
 Diversification rates are reversed for the realm containing the deep sea
 and Antarctica, being highest at polar and lowest at tropical latitudes,
 and net exchange is from high to low latitudes. The tropical upper bathyal
 (200-700 m deep), with its rich ancient phylodiversity, is characterised
 by relatively low diversification and moderate immigration rates.
 Conversely, the young specialised Antarctic fauna is inferred to be
 rebounding from regional extinction associated with the rapid cooling of
 polar waters over the mid-Cenozoic.
description: Bathyplot_dataExcel spread sheets with basic taxa, grid cell and biome informationphylo-DryadZipped folder containing phylogenetic supermatix data and associated information and treescode-DryadZipped folder containing Unix and R scripts for various macro-evolutionary analysesbamm4zipped folder containing BAMM input and output filesBathome_ReadMeWord file with information on the contents of this Dryad packagedist-Dryadzipped folder containing distribution and grid cell data
DOI: 10.5061/dryad.tt743
title: Data from: Young inversion with multiple linked QTLs under selection in a hybrid zone

description: Fixed chromosomal inversions can reduce gene flow and promote speciation
 in two ways: by suppressing recombination and by carrying locally favoured
 alleles at multiple loci. However, it is unknown whether favoured
 mutations slowly accumulate on older inversions or if young inversions
 spread because they capture pre-existing adaptive quantitative trait loci
 (QTLs). By genetic mapping, chromosome painting and genome sequencing, we
 have identified a major inversion controlling ecologically important
 traits in Boechera stricta. The inversion arose since the last glaciation
 and subsequently reached local high frequency in a hybrid speciation zone.
 Furthermore, the inversion shows signs of positive directional selection.
 To test whether the inversion could have captured existing, linked QTLs,
 we crossed standard, collinear haplotypes from the hybrid zone and found
 multiple linked phenology QTLs within the inversion region. These findings
 provide the first direct evidence that linked, locally adapted QTLs may be
 captured by young inversions during incipient speciation.
description: Young inversion with
 multiple linked QTLs under selection in a hybrid zone
DOI: 10.5061/dryad.b6091
title: Data from: Do small swarms have an advantage when house hunting? The effect of swarm size on nest-site selection by Apis mellifera

description: Reproductive swarms of honeybees are faced with the problem of finding a
 good site to establish a new colony. We examined the potential effects of
 swarm size on the quality of nest-site choice through a combination of
 modelling and field experiments. We used an individual-based model to
 examine the effects of swarm size on decision accuracy under the
 assumption that the number of bees actively involved in the
 decision-making process (scouts) is an increasing function of swarm size.
 We found that the ability of a swarm to choose the best of two nest sites
 decreases as swarm size increases when there is some time-lag between
 discovering the sites, consistent with Janson & Beekman (Janson
 & Beekman 2007 Proceedings of European Conference on Complex
 Systems, pp. 204–211.). However, when simulated swarms were faced with a
 realistic problem of choosing between many nest sites discoverable at all
 times, larger swarms were more accurate in their decisions than smaller
 swarms owing to their ability to discover nest sites more rapidly. Our
 experimental fieldwork showed that large swarms invest a larger number of
 scouts into the decision-making process than smaller swarms. Preliminary
 analysis of waggle dances from experimental swarms also suggested that
 large swarms could indeed discover and advertise nest sites at a faster
 rate than small swarms.
description: Experimental and
 simulation data of nest-site selection by Apis melliferaThis zip folder contains
 three major sub-folders with experimental and simulation data from our
 study. The folder "RateofNewDancers" contains a summary
 spreadsheet of our field observations of new dancers appearing on the
 surface of 8 small and 8 large artificial swarms of Apis mellifera, along
 with reduced data and the MATLAB code we used for analysis. Swarm
 experiments were performed between the 28th of September 2009 and the 20th
 of January 2010 at the University of Sydney's Crommelin Field
 Station, Pearl Beach, New South Wales, Australia (Latitude: 33.55 degrees
 South, Longitude: 151.30 degrees East). The folder
 "VideoAnalysisofWaggleDances" contains the raw data files
 generated by our MATLAB programme to aid in the analysis of waggle dances
 on two small and one large experimental swarm. Also provided in
 "VideoAnalysisofWaggleDances" are MATLAB files to analyse the
 distinct sites danced for by bees in each of the three swarms.
 "ExampleSimulationCodesandData" contains the MATLAB codes used
 to perform all the individual-based simulations described in our main
 manuscript and sections S5-S7 of our online supplementary material. Also
 contained in "ExampleSimulationCodesandData" is the output data
 from all the simulations and the MATLAB codes used to analyse that
 data.OnlineDataforSchaerfMakinsonMyerscoughBeekman.zip
DOI: 10.5061/dryad.56g7v08
title: Data from: Theoretical conditions for the coexistence of viral strains with differences in phenotypic traits: a bifurcation analysis

description: We investigate the dynamics of a wild-type viral strain which generates
 mutant strains differing in phenotypic properties for infectivity,
 virulence, and mutation rates. We study, by means of a mathematical model
 and bifurcation analysis, conditions under which the wild-type and mutant
 viruses, which compete for the same host cells, can coexist. The
 coexistence conditions are formulated in terms of the basic reproductive
 numbers of the strains, a maximum value of the mutation rate, and the
 virulence of the pathogens. The analysis reveals that parameter space can
 be divided into five regions, each with distinct dynamics, that are
 organised around degenerate Bogdanov-Takens and zero-Hopf bifurcations,
 the latter of which gives rise to a curve of transcritical bifurcations of
 periodic orbits. These results provide new insights into the conditions by
 which viral populations may contain multiple coexisting strains in a
 stable manner.
description: figure_dataEach subfolder has a name of a figure. In every such subfolder, Matlab code for the figure is provided, and named "...maker.m", alongside its data folder. The data is obtained using MATCONT6p10 (free Matlab software project for the numerical continuation and bifurcation study).MATCONT_systemsTwo systems were studied, numbered (2.4) and (3.19) in the paper. The codes for MATCONT6p10 for both systems are provided.
DOI: 10.5061/dryad.hm573
title: Data from: Avoiding topsy-turvy: how Anna's Hummingbirds (Calypte anna) fly through upward gusts

description: Flying organisms frequently confront the challenge of maintaining
 stability when moving within highly dynamic airflows near the Earth's
 surface. Either aerodynamic or inertial forces generated by appendages and
 other structures, such as the tail, may be used to offset aerial
 perturbations, but these responses have not been well characterized. To
 better understand how hummingbirds modify wing and tail motions in
 response to individual gusts, we filmed Anna's Hummingbirds as they
 negotiated an upward jet of fast moving air. Birds exhibited large
 variation in wing elevation, tail pitch, and tail fan angles among
 transits as they repeatedly negotiated the same gust, and often exhibited
 a dramatic decrease in body angle (28 ± 6 degrees) post-transit. After
 extracting three-dimensional kinematic features, we identified a spectrum
 of control strategies for gust transit, with one extreme involving
 continuous flapping, no tail fanning, and little disruption to body
 posture (23 ± 3 degrees downward pitch), and the other extreme
 characterized by dorsal wing pausing, tail fanning, and greater downward
 body pitch (38 ± 4 degrees). The use of a deflectable tail on a glider
 model transiting the same gust resulted in enhanced stability and can
 easily be implemented in design of aerial robots.
description: Glider_tracked_pointsZip file containing raw tracked xy and reconstructed 3D position files for each glider trial.Glider_Data_Analysis_12.17.17R script that conducts all analyses involving glider responses the air gust.gustDataForR_2018-06-25_21-11-15Data file in .mat form with one row for each trial (for loading into R workspace).Bird_tracked_pointsZip file containing manually digitized xy and reconstructed xyz points for each bird gust transit.Bird_trajectories_and_kinematicsZip file containing a MATLAB Struct file with trajectory and kinematics data.Kinematics_Processing_Code_MATLABMATLAB scripts for calculating body, wing, and tail kinematics from raw 3D point trajectories.Hummingbird flight through gusts Badger et al 2018Movie 1: Hummingbird and glider transits through a fast upward gust.Initialize_AirKnife_Data_11.30.18R script for importing and pre-processing data (including clustering).AirKnife_Data_Analysis_11.30.18R script that conducts all analyses involving bird responses to the air gust.AirKnife_Data_R_Workspace_11.30.18R workspace after running Initialize_AirKnife_Data.AirKnife_Data_R_Workspace_11.30.18_Results_CalculatedR workspace after running AirKnife_Data_Analysis
DOI: 10.5061/dryad.8jd18
title: Data from: SNP discovery and gene annotation in the surf clam Mesodesma donacium

description: The main objective of this research was to identify single-nucleotide
 polymorphisms (SNPs) from an Expressed Sequences Tags (EST) data set
 generated by 454 pyrosequencing in the soft clam Mesodesma donacium. A
 total of 180 159 ESTs were yielded from a M. donacium cDNA library. De
 novo assembly was performed using stringent calling parameters, producing
 10 178 contigs and 41 765 singletons. Here, a total of 2594 SNPs were
 discovered related to 613 consensus sequences, achieving a frequency of 1
 SNPs per 260 bp. SNP variants showed that A/G, A/T and C/T were the most
 abundant among the identified polymorphisms. We validated a total of 12
 SNPs loci by HRMA for annotated genes such as heat shock protein-70 and
 the translation elongation factor 1-alpha. The Gene Ontology analysis
 regarding molecular function level revealed that sequences with SNPs were
 mainly classified to protein and nucleotide binding, as well hydrolase
 activity, ion binding and oxidoreductase activity. Further, biological
 processes like cellular and metabolic process, biogenesis, localization
 and biological regulation were highly annotated. The most expressed genes
 were related to the mitochondrial electron transport chain,
 senescence-associated protein, ubiquitin and actin. Interestingly, some
 relevant genes related to immune response and biomineralization showed a
 high abundance, such as tumor necrosis factor (TNF)-alpha-receptor-like
 protein, serine protease inhibitor, heat shock protein, aragonite-binding
 protein and ferritin. This study contributes to relevant genes associated
 with functional polymorphisms and gives an overview for future genetic
 investigations.
description: ContigSNP_annotated_Md
 (613 seq)613 concensus sequences
 annotated with SNPs variants from Mesodesma donacium
 transcriptome.Raw data of 454
 transcriptome pyrosequencing from M. donaciumFASTA file with 180,159
 ESTs.Md.faMulti BLAST (613 sequences)_MmSNPBLAST results for the 613 sequences with SNP annotationsGOAnalysis MmSNPsGO analysis from contigs annotated with SNP variants.
DOI: 10.5061/dryad.57j1t
title: Data from: Flow cytometric methods for indirect analysis and quantification of gametogenesis in Chlamydomonas reinhardtii (Chlorophyceae)

description: Induction of sexual reproduction in the facultatively sexual Chlamydomonas
 reinhardtii is cued by depletion of nitrogen. We explore the capacity for
 indirect monitoring of population variation in the gametogenic process
 using flow cytometry. We describe a high-throughput method capable of
 identifying fluorescence, ploidy and scatter profiles that track
 vegetative cells entering and undergoing gametogenesis. We demonstrate for
 the first time, that very early and late growth phases reduce the capacity
 to distinguish putative gametes from vegetative cells based on scatter and
 fluorescence profiles, and that early/mid-logarithmic cultures show the
 optimal distinction between vegetative cells and gamete scatter profiles.
 We argue that early/mid logarithmic cultures are valuable in such high
 throughput comparative approaches when investigating optimisation or
 quantification of gametogenesis based on scatter and fluorescence
 profiles. This approach provides new insights into the impact of culture
 conditions on gametogenesis, while documenting novel scatter and
 fluorescence profile shifts which typify the process. This method has
 potential applications to; enabling quick high-throughput monitoring, uses
 in increasing efficiency in the quantification of gametogenesis, as a
 method of comparing the switch between vegetative and gametic states
 across treatments, and as criteria for enrichment of gametic phenotypes in
 cell sorting assays.
description: Chlamydomonas flow data
 files
DOI: 10.5061/dryad.178n3
title: Data from: The future of evolutionary diversity in reef corals

description: One-third of the world's reef-building corals are facing heightened
 extinction risk from climate change and other anthropogenic impacts.
 Previous studies have shown that such threats are not distributed randomly
 across the coral tree of life, and future extinctions have the potential
 to disproportionately reduce the phylogenetic diversity of this group on a
 global scale. However, the impact of such losses on a regional scale
 remains poorly known. In this study, we use phylogenetic metrics in
 conjunction with geographical distributions of living reef coral species
 to model how extinctions are likely to affect evolutionary diversity
 across different ecoregions. Based on two measures—phylogenetic diversity
 and phylogenetic species variability—we highlight regions with the largest
 losses of evolutionary diversity and hence of potential conservation
 interest. Notably, the projected loss of evolutionary diversity is
 relatively low in the most species-rich areas such as the Coral Triangle,
 while many regions with fewer species stand to lose much larger shares of
 their diversity. We also suggest that for complex ecosystems like coral
 reefs it is important to consider changes in phylogenetic species
 variability; areas with disproportionate declines in this measure should
 be of concern even if phylogenetic diversity is not as impacted. These
 findings underscore the importance of integrating evolutionary history
 into conservation planning for safeguarding the future diversity of coral
 reefs.
description: Reef ecoregion occupancy
 data for all scleractinian corals based primarily on the Coral Geographic
 database (Veron et al. 2009)Huang&Roy_Distribution.csvConservation status of all scleractinian corals based on the IUCN Red List of Threatened Species (Carpenter et al. 2008)Huang&Roy_Species.csvBEAST input file used to fit the DNA sequence data onto the coral supertree topology with fossil node calibrations (Stolarski et al. 2011)Huang&Roy_Molecular.xmlPhylogeny with the DNA sequence data fit onto the coral supertree topologyHuang&Roy_Molecular.treBEAST input file for randomly resolving polytomies on the strict consensus supertree generated by PolytomyResolver (Kuhn et al. 2011)Huang&Roy_Supertree.xmlSupertree randomly resolved for analyses of evolutionary diversity (1000 posterior trees)Huang&Roy_Supertree.treR code used to compute and compare evolutionary diversity metrics in each ecoregion before and after the projected extinction of threatened speciesHuang&Roy_Analyses.R
DOI: 10.5061/dryad.8bp16
title: Data from: Magnetic resonance and ultrasound contrast imaging of polymer-shelled microbubbles loaded with iron oxide nanoparticles

description: Dual-mode contrast agents (CAs) have great potential for improving
 diagnostics. However, the effectiveness of CAs is strictly related to both
 the solution adopted to merge the two agents into a single probe unit, and
 the ratio between the two agents. In this study, two dual-mode CAs for
 simultaneous magnetic resonance imaging (MRI) and ultrasound imaging (UI)
 were assessed. For this purpose, different densities of superparamagnetic
 iron oxide nanoparticles (SPIONs) were anchored to the external surface of
 polymer-shelled microbubbles (MBs) or were physically entrapped into the
 shell. In vitro static and dynamic experiments were carried out with a
 limited concentration of modified MBs (106 bubbles ml−1) by avoiding
 destruction during UI (performed at a peak pressure lower than 320 kPa)
 and by using a low-field MRI system (with a magnetic flux density equal to
 0.25 T). Under these conditions, different imaging techniques, set-up
 parameters and SPION densities were used to achieve satisfactory detection
 of the CAs by using both UI and MRI. However, when the SPION density was
 increased, the MRI contrast improved, whereas the UI contrast worsened due
 to the reduced elasticity of the MB shell. For both UI and MRI, MBs with
 externally anchored SPIONs provided better performance than MBs with
 SPIONs entrapped into the shell. In particular, a SPION density of 29%
 with respect to the mass of the MBs was successfully tested.
description: Ultrasound data
 (two-dimensional matrices of data)A MATLAB (The MathWorks,
 Inc., MA, USA) script reads the RF frames that were acquired by the
 ultrasound scanner. The acquired RF signals were processed and converted
 to a two-dimensional matrix M(i,j) (i.e., “file_name.mat”) where i
 represents the ith line of sight of the image (x axis) and j is the index
 of the time samples of each line of sight (y axis). The chosen
 “file_name.mat” can be defined as follows: “a_b_c.mat” where a stands for
 the dual-mode microbubble (MB) type that was analysed (i.e., MB-plain,
 MBN-into15, MBN-into38, and MBN-on29); b describes the imaging technique
 that was applied (CPS3 or Chirp CPS3); c represents the negative peak
 pressure at the focus depth (230 or 320 kPa). The ultrasound images were
 generated by processing the two-dimensional matrices by implementing the
 same functions as those used on the back end of the scanner system (i.e.,
 envelope detection and logarithmic compression). Finally, the data can be
 used to calculate the contrast-to-tissue ratio (CTR), following the
 procedure described in the manuscript.US_data.mat
DOI: 10.5061/dryad.9b8tt
title: Data from: A new species of the paper wasp genus Polistes (Hymenoptera, Vespidae, Polistinae) in Europe revealed by morphometrics and molecular analyses

description: We combine multivariate ratio analysis (MRA) of body measurements and
 analyses of mitochondrial and nuclear data to examine the status of
 several species of European paper wasps (Polistes Latreille, 1802) closely
 related to P. gallicus. Our analyses unambiguously reveal the presence of
 a cryptic species in Europe, as two distinct species can be recognized in
 what has hitherto been considered Polistes bischoffi Weyrauch, 1937. One
 species is almost as light coloured as P. gallicus, and is mainly recorded
 from Southern Europe and Western Asia. The other species is darker and has
 a more northern distribution in Central Europe. Both species occur
 syntopically in Switzerland. Given that the lost lectotype of P. bischoffi
 originated from Sardinia, we selected a female of the southern species as
 a neotype. The northern species is described as P. helveticus sp. n. here.
 We also provide a redescription of P. bischoffi rev. stat. and an
 identification key including three more closely related species, P.
 biglumis, P. gallicus and P. hellenicus.
description: Neumeyer et al European
 Polistes data used for morphometryA tab delimited text
 file including all body measurements in micrometers used for morphometric
 analyses. In addition, images showing the exact character
 definitions.Neumeyer et al European
 Polistes raw data file and illustration of body
 measurements.zip
DOI: 10.5061/dryad.fn203
title: Data from: Three-dimensional visualization of the internal plastid membrane network during runner bean chloroplast biogenesis: dynamic model of the tubular-lamellar transformation

description: Chloroplast biogenesis is a complex process integrated with plant
 development, leading to fully differentiated and functionally mature
 plastids. In this paper, the process of structural membrane transformation
 during the etioplast - chloroplast transition is reconstructed with the
 help of electron tomography and confocal microscopy. 3D reconstruction is
 the only method that leads to an understanding of the transformation of
 the regular, tubular network of paracrystalline prolamellar bodies (PLB)
 and prothylakoids (PT), flattened porous membranes, to the chloroplast
 thylakoids. We provide spatial models of the bean chloroplast biogenesis
 that allow such reconstruction of the internal membranes of the developing
 chloroplast and visualize the transformation from the tubular arrangement
 to the linear system of parallel lamellae. We prove that the tubular
 structure of the PLB transforms directly to flat slats, without dispersion
 to vesicles. We demonstrate that the grana/stroma thylakoid connections
 have a helical character starting from the early stages of appressed
 membrane formation. Moreover, we point out the importance of particular
 chlorophyll-protein (CP) complex components in the membrane stacking
 during the biogenesis. The main stages of chloroplast internal membrane
 biogenesis are presented in a movie that shows the time development of the
 chloroplast biogenesis as a 'dynamic' model of this process.
description: Dynamic Model of the
 Chloroplast BiogenesisVideo (MOV) File
 Presenting the Dynamic Model of the Chloroplast Biogenesis Based on the
 Electron Tomography Reconstructions of Seven Subsequent Developmental
 Stages and on 2D Theoretical Modelstpc01053_SupplementalMovie1.mov