cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.785cv
title: Data from: Northeastern North America as a potential refugium for boreal forests in a warming climate

description: High precipitation in boreal northeastern North America could help forests
 withstand the expected temperature-driven increase in evaporative demand,
 but definitive evidence is lacking. Using a network of tree-ring
 collections from 16,450 stands across 583,000 km2 of boreal forests in
 Québec, Canada, we observe a latitudinal shift in the correlation of black
 spruce growth with temperature and reduced precipitation, from negative
 south of 49°N to largely positive to the north of that latitude. Our
 results suggest that the positive effect of a warmer climate on growth
 rates and growing season length north of 49°N outweighs the potential
 negative effect of lower water availability. Unlike the central and
 western portions of the continent’s boreal forest, northeastern North
 America may act as a climatic refugium in a warmer climate.
description: Black spruce
 standardized chronologiesThe file contains the
 standardized growth indices (chronologies) for 378 black spruce
 populations across Quebec, Canada, for the period 1960-2004. Each
 chronology in identified by its lat-lon coordinates. In addition, the file
 displays the soil type (deposit, texture, drainage) associated with each
 chronology.DRYADchrons.csvHistorical monthly climateThis file contains the average monthly temperature, precipitation and soil moisture index, identified by their lon-lat coordinates, corresponding to the black spruce chronologies (1960-2004).DRYADclim.csvBaseline and future climate simulationsSpatially-explicit climate data (Shape files) from the NEX-GDDP dataset, prepared by the Climate Analytics Group and NASA Ames Research Center using the NASA Earth Exchange, distributed by the NASA Center for Climate Simulation (NCCS), and transformed by Travis Logan at Ouranos, Montreal, Canada. The data cover the southern part of Quebec, Canada, and summarize the outputs of 21 climate simulations and two greenhouse gas emission scenarios (RCP). The data are divided in three sets: historical (1970-2000), future (2041-2070) with a 4.5 RCP and future (2041-2070) with a 8.5 RCP.FinalShapefiles.zip
DOI: 10.5061/dryad.2rb57
title: Data from: The peripheral olfactory code in Drosophila larvae contains temporal information and is robust over multiple timescales

description: We studied the electrophysiological activity of two classes of Drosophila
 melanogaster larval olfactory sensory neurons (OSNs), Or24a and Or74a, in
 response to 1 s stimulation with butanol, octanol, 2-heptanone, and propyl
 acetate. Each odour/OSN combination produced unique responses in terms of
 spike count and temporal profile. We used a classifier algorithm to
 explore the information content of OSN activity, and showed that as well
 as spike count, the activity of these OSNs included temporal information
 that enabled the classifier to accurately identify odours. The responses
 of OSNs during continuous odour exposure (5 and 20 min) showed that both
 types of neuron continued to respond, with no complete adaptation, and
 with no change to their ability to encode temporal information. Finally,
 we exposed larvae to octanol for 3 days and found only minor quantitative
 changes in OSN response to odours, indicating that the larval peripheral
 code is robust when faced with long-term exposure to odours, such as would
 be found in a natural context.
description: Electrophysiological
 dataExcel file containing
 raw electrophysiological responses from identified OSNs in response to
 identified odours.raw data for Proc Roy
 Soc.xls
DOI: 10.5061/dryad.g703s
title: Data from: Open water camouflage via 'leaky' light guides in the midwater squid Galiteuthis

description: Galiteuthis, a midwater squid, has photophores on the ventral surfaces of
 its eyes. These photophores emit bioluminescence to counter-illuminate the
 shadows cast by the eyes in downwelling sunlight, thereby hiding the eyes
 from upward-looking predators. The photophores consist of laminated
 fibre-like cells with semi-coaxial protein-dense layers around axial
 cytoplasm. These cells have been suggested to function as light guides:
 bioluminescence is an isotropic process used to hide in an anisotropic
 light environment, so any emission must be reshaped to be effective. We
 found a wide variation in cross-sectional geometries of photophore cells;
 some were more efficient at light guiding than others. We used a set of
 optical models to place these photophores in the context of the radiance
 where Galiteuthis lives and discovered a possible adaptive reason for this
 variation. In Galiteuthis's horizontal and vertical range, ocean
 radiance is also quite variable. For complete camouflage, photophores must
 reproduce this variation in radiance using an isotropic source. Our models
 show that variation in the geometry of the photophore light guides
 reproduces the predicted variation in ocean radiance experienced by this
 species. By selectively activating geometrically distinct populations of
 photophore cells, the animal may reproduce the angular distribution of
 light at all positions in its habitat.
description: Meep front end control
 file for FDTD calculationThis the scheme code
 written for calculating transmittance down biological fibers using Meep,
 the open source Finite Difference Time Domain (FDTD) software. The output
 of this code are absolute flux values through each defined flux plane
 determined using FDTD.eps3Dtrans3.ctlh5 files for input in eps3Dtrans3.ctlThese h5 files are files necessary for inputing arbitrary dielectric structure to front end code for meep. These files were generated from binary TEM images of biological light guides. Transmittance through fibers with these cross sections were described in the paper.h5files.zipTEM imagesThese are TEM images in tiff format described by the paper. These images were made binary and de-speckled for use in Meep FDTD code.TEMimages.zipHydrolight Calculation fileMatlab file containing Hydrolight runs for 480 nm using ac-9 casts from NASA's SeaBASS ocean optics database.HydrolightCalcs.mat
DOI: 10.5061/dryad.8j36j
title: Data from: Commensal associations and benthic habitats shape macroevolution of the bivalve clade Galeommatoidea

description: The great diversity of marine life has been shaped by the interplay
 between abiotic and biotic factors. Among different biotic interactions,
 symbiosis is an important yet less studied phenomenon. Here, we tested how
 symbiotic associations affected marine diversification, using the bivalve
 superfamily Galeommatoidea as a study system. This superfamily contains
 large numbers of obligate commensal as well as free-living species and is
 therefore amenable to comparative approaches. We constructed a global
 molecular phylogeny of Galeommatoidea and compared macroevolutionary
 patterns between free-living and commensal lineages. Our analyses inferred
 that commensalism/sediment-dwelling is likely to be the ancestral
 condition of Galeommatoidea and that secondary invasions of hard-bottom
 habitats linked to the loss of commensalism. One major clade containing
 most of the free-living species exhibits a 2–4 times higher
 diversification rate than that of the commensals, likely driven by
 frequent niche partitioning in highly heterogeneous hard-bottom habitats.
 However, commensal clades show much higher within-clade morphological
 disparity, likely promoted by their intimate associations with diverse
 hosts. Our study highlights the importance of interactions between
 different ecological factors in shaping marine macroevolution and that
 biotic factors cannot be ignored if we wish to fully understand processes
 that generate marine biodiversity.
description: 1000 posterior BEAST
 phylogenies of Galeommatoidea1ktree_final_fix118.treesConsensus BEAST phylogeny of Galeommatoideafinal_BEAST.treLandmarks and semi-landmarks for all specimensTPS file containing one landmark and 45 semi-landmarks for all specimens. Image IDs correspond to phylogenetic tip IDs on the phylogeny.all_side.tps
DOI: 10.5061/dryad.3393k
title: Data from: Whole genome sequence resource of Indian Zaprionus indianus

description: The present article documents the whole genome sequence information of the
 Indian Zaprionus indianus, a member of the fruit fly family Drosophilidae.
 The sequences were generated on an Illumina platform and reads and whole
 genome sequence submitted to NCBI to the SRA and BioProject databases
 respectively. This is the first Indian Z. indianus whole genome (draft)
 submitted to the sequence repository with SRA reads. The details of
 methodology, assembly statistics and functional annotation are presented
 in this paper.
description: Total CDS predicted in
 Zaprionus indianus genome of Indian originTotal CDS predicted in
 Zaprionus indianus genome of Indian origin using Augustus
 software.ZP_IN_CDS.faPathway analysis of Indian Zaprionus indianusThe mapping of the CDS of Indian Zaprionus indianus was done with the biological pathway using Blast2GO PRO-KEGG annotation server.ZP_IN_PathwayAnalysis.xls
DOI: 10.5061/dryad.1f5h4
title: Data from: The wings before the bird: an evaluation of flapping-based locomotory hypotheses in bird antecedents

description: Background. Powered flight is implicated as a major driver for the success
 of birds. Here we examine the effectiveness of three hypothesized pathways
 for the evolution of the flight stroke, the forelimb motion that powers
 aerial locomotion, in a terrestrial setting across a range of stem and
 basal avians: flap running, Wing Assisted Incline Running (WAIR), and
 wing-assisted leaping. Methods. Using biomechanical mathematical models
 based on known aerodynamic principals and in vivo experiments and ground
 truthed using extant avians we seek to test if an incipient flight stroke
 may have contributed sufficient force to permit flap running, WAIR, or
 leaping takeoff along the phylogenetic lineage from Coelurosauria to
 birds. Results. None of these behaviours were found to meet the
 biomechancial threshold requirements before Paraves. Neither was there a
 continuous trend of refinement for any of these biomechanical performances
 across phylogeny nor a signal of universal applicability near the origin
 of birds. None of these flap-based locomotory models appear to have been a
 major influence on pre-flight character acquisition such as pennaceous
 feathers, suggesting non-locomotory behaviours, and less stringent
 locomotory behaviours such as balancing and braking, played a role in the
 evolution of the maniraptoran wing and nascent flight stroke. We find no
 support for widespread prevalence of WAIR in non-avian theropods, but
 can’t reject its presence in large winged, small-bodied taxa like
 Microraptor and Archaeopteryx. Discussion. Using our first principles
 approach we find that “near flight” locomotor behaviors are most sensitive
 to wing area, and that non-locomotory related selection regimes likely
 expanded wing area well before WAIR and other such behaviors were possible
 in derived avians. These results suggest that investigations of the
 drivers for wing expansion and feather elongation in theropods need not be
 intrinsically linked to locomotory adaptations, and this separation is
 critical for our understanding of the origin of powered flight and avian
 evolution.
description: Supporting documents and
 tables for Dececchi et al. 2016This includes all 15
 supporting tables, 2 supporting nexus files, the supporting calculation
 spreadsheet for Dececchi et al. 2016Supporting files for Dececchi
 et al. 2016.zip
DOI: 10.5061/dryad.c78k5
title: Data from: Herbivorous dinosaur jaw disparity and its relationship to extrinsic evolutionary drivers

description: Morphological responses of nonmammalian herbivores to external ecological
 drivers have not been quantified over extended timescales. Herbivorous
 nonavian dinosaurs are an ideal group to test for such responses, because
 they dominated terrestrial ecosystems for more than 155 Myr and included
 the largest herbivores that ever existed. The radiation of dinosaurs was
 punctuated by several ecologically important events, including extinctions
 at the Triassic/Jurassic (Tr/J) and Jurassic/Cretaceous (J/K) boundaries,
 the decline of cycadophytes, and the origin of angiosperms, all of which
 may have had profound consequences for herbivore communities. Here we
 present the first analysis of morphological and biomechanical disparity
 for sauropodomorph and ornithischian dinosaurs in order to investigate
 patterns of jaw shape and function through time. We find that
 morphological and biomechanical mandibular disparity are decoupled:
 mandibular shape disparity follows taxonomic diversity, with a steady
 increase through the Mesozoic. By contrast, biomechanical disparity builds
 to a peak in the Late Jurassic that corresponds to increased functional
 variation among sauropods. The reduction in biomechanical disparity
 following this peak coincides with the J/K extinction, the associated loss
 of sauropod and stegosaur diversity, and the decline of cycadophytes. We
 find no specific correspondence between biomechanical disparity and the
 proliferation of angiosperms. Continual ecological and functional
 replacement of pre-existing taxa accounts for disparity patterns through
 much of the Cretaceous, with the exception of several unique groups, such
 as psittacosaurids that are never replaced in their biomechanical or
 morphological profiles.
description: MacLaren_etal_SupplementaryInformation_FinalThis MS Word document offers additional information to support the main document. It describes the study materials used and specific methodology used to attain the specimen information; descriptions of landmark placements; in-depth explanations of continuous functional characters and the method by which they were calculated; extended analytical methodology; additional graphical results which augment those in the main text; a list of specimens involved in the study; and a supplementary list of references and specimen sources.MacLaren_etal_SupplementaryInformation_JM edit_3.pdfMacLaren_etal_SupplementaryInformation_RawDataThis MS Excel document lists raw and calculated data for the specimens used in this study. This includes relative warp scores (used for morphological analysis); biomechanical character scores; and raw measurements from specimens (used to calculate biomechanical character scores).
DOI: 10.25824/redu/4dskrf
title: Replication data containing the HPLC and NMR files for: "Methanol, ethylene glycol, and glycerol photoelectrochemical oxidation reactions on BiVO4: Zr,Mo/Pt thin films: a comparative study"

description: Replication data containing the HPLC and NMR files for: "Methanol, ethylene glycol, and glycerol photoelectrochemical oxidation reactions on BiVO4: Zr,Mo/Pt thin films: A comparative study" published in Electrochimica Acta (https://doi.org/10.1016/j.electacta.2024.145300)
DOI: 10.5061/dryad.46vf8
title: Data from: A toolkit for optimizing fish passage barrier mitigation actions

description: The presence of dams, stream–road crossings and other infrastructure often
 compromises the connectivity of rivers, leading to reduced fish abundance
 and diversity. The assessment and mitigation of river barriers is critical
 to the success of restoration efforts aimed at restoring river integrity.
 In this study, we present a combined modelling approach involving
 statistical regression methods and mixed integer linear programming to
 maximize resident fish species richness within a catchment through
 targeted barrier mitigation. Compared to existing approaches, our proposed
 method provides enhanced biological realism while avoiding the use of
 complex and computationally intensive population/ecosystem models. To
 estimate barrier passability quickly and at low cost, we further outline a
 rapid barrier assessment methodology. The methodology is used to
 characterize potential passage barriers for various fish species common to
 the UK but can be readily adapted to different planning areas and other
 species of interest. We demonstrate the applicability of our barrier
 assessment and prioritization approach based on a case study of the River
 Wey, located in south-east England. We find that significant increases in
 species richness can be achieved for modest investment in barrier
 mitigation. In particular, dams and weirs with low passability located on
 mid- to high-order streams are identified as top priorities for
 mitigation. Synthesis and applications. Our study shows the benefits of
 combining a coarse resolution barrier assessment methodology with
 state-of-the-art optimization modelling to cost-effectively plan fish
 passage barrier mitigation actions. The modelling approach can help inform
 on-the-ground river restoration decision-making by providing a recommended
 course of action that best allocates limited resources in order to restore
 longitudinal connectivity and maximize ecological gains.
description: River Wey Fish Sampling
 DataRiver Wey fish sampling
 dataset used in species richness regression analysis (King et al.
 2016).River Wey Barrier
 DataRiver Wey barrier
 dataset used in barrier optimization analysis (King et al.
 2016).OPL
 modelCPLEX Studio OPL
 project, including (.mod), data (.dat), settings (.ops) files, and Excel
 (.xlsx) files, used in performing optimization analysis (King et al.
 2016).
DOI: 10.5061/dryad.cc5v0
title: Data from: Population dynamics and life history of Euphorbia rosescens, a perennial herb endemic to florida scrub

description: Euphorbia rosescens is a recently described plant that is narrowly endemic
 to the Lake Wales Ridge. Little is known of the ecology or life history of
 this diminutive, deeply rooted polygamodioecious perennial. We studied 13
 subpopulations of this species from 2004-2012 from five habitats, sampling
 monthly during its growing season. Subpopulations were stable year-to-year
 with annual survivals &gt; 90%, but with considerable within-year
 dynamics, peaking in density in April and dying back in the fall and
 winter. Stem densities did not vary among subpopulations, habitats, or by
 subpopulation gender. Annual plant dormancy was common and decreased
 subsequent survival. Belowground biomass averaged almost 50 times higher
 than aboveground biomass. Subpopulations either consisted of entirely
 female individuals or a mixture of male and functionally andromonoecious
 individuals and these subpopulation genders remained stable across years.
 Overall, flowering has been dominated by female plants. Plants produced
 modest numbers of inflorescences (cyathia), and fruit production was very
 low. Although most plants survived fire by resprouting, fire decreased
 survival and had a short-term positive effect on floral production. Lack
 of fecundity and recruitment are concerns for this state-endangered
 species, but more information is needed on its breeding system and
 clonality to make specific management recommendations.
description: Euphorbia rosescens
 demography datasetDataset includes vital
 rates (survival, # stems, reproductive stage, flowering sex, stem length
 and # cyathia) collected for a demographic study of Euphorbia rosescens
 from 2004-2012. Data were collected on 1567 individuals among 13
 subpopulations that encompassed a variety of habitats and fire
 histories.eupros_demog.csvEuphorbia rosescens excavationDataset includes stem length of above- and belowground plant material collected in a single excavation of 68 Euphorbia rosescens individuals. Above- and belowground root weights were used to calculate below- to aboveground ratios.eupros_excavation.csv
DOI: 10.5061/dryad.3rt26
title: Data from: Detecting evolutionarily significant units above the species level using the Generalized Mixed Yule Coalescent method

description: 1. There is renewed interest in inferring evolutionary history by
 modelling diversification rates using phylogenies. Understanding the
 performance of the methods used under different scenarios is essential for
 assessing empirical results. Recently we introduced a new approach for
 analysing broadscale diversity patterns, using the Generalized Mixed Yule
 Coalescent (GMYC) method to test for the existence of evolutionarily
 significant units above the species (higher ESUs). This approach focuses
 on identifying clades as well as estimating rates and we refer to it as
 clade-dependent. However, the ability of the GMYC to detect the
 phylogenetic signature of higher ESUs has not been fully explored, nor has
 it been placed in the context of other, clade-independent approaches. 2.
 We simulated &gt;32,000 trees under two clade-independent models:
 constant-rate birth-death (CRBD) and variable-rate birth-death (VRBD),
 using parameter estimates from nine empirical trees and more general
 parameter values. The simulated trees were used to evaluate scenarios
 under which GMYC might incorrectly detect the presence of higher ESUs. 3.
 The GMYC null model was rejected at a high rate on CRBD-simulated trees.
 This would lead to spurious inference of higher ESUs. However, the support
 for the GMYC model was significantly greater in most of the empirical
 clades than expected under a CRBD process. Simulations with empirically
 derived parameter values could therefore be used to exclude CRBD as an
 explanation for diversification patterns. In contrast, a VRBD process
 could not be ruled out as an alternative explanation for the apparent
 signature of hESUs in the empirical clades, based on the GMYC method
 alone. Other metrics of tree shape, however, differed notably between the
 empirical and VRBD-simulated trees. These metrics could be used in future
 to distinguish clade-dependent and clade-independent models. 4. In
 conclusion, detection of higher ESUs using the GMYC is robust against some
 clade-independent models, as long as simulations are used to evaluate
 these alternatives, but not against others. The differences between
 clade-dependent and clade-independent processes are biologically
 interesting, but most current models focus on the latter. We advocate more
 research into clade-dependent models for broad diversity patterns.
description: Humphreysetal_MEE_CRBD_treesTrees simulated using a constant-rate birth-death model, using parameter values estimated for each of 9 clades. The file contains 9 x 500 trees.Humphreysetal_MEE_VRBD_treesTrees simulated using a variable-rate birth-death model, using parameter values estimated for each of 9 clades. The file contains 9 x 100 trees.Humphreysetal_MEE_Gnetales_cycads_treesMaximum clade credibility trees for Gnetales and cycads based on Beast analysis of published matK, rbcL, 18S and, for cycads, PHYP sequences.