cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9jp26bk
title: Data from: Protocol dependence and state variables in the force-moment ensemble

description: Stress-based ensembles incorporating temperature-like variables have been
 proposed as a route to an equation of state for granular materials. To
 test the efficacy of this approach, we perform experiments on a
 two-dimensional photoelastic granular system under three loading
 conditions: uniaxial compression, biaxial compression, and simple shear.
 From the interparticle forces, we find that the distributions of the
 normal component of the coarse-grained force-moment tensor are
 exponential-tailed, while the deviatoric component is
 Gaussian-distributed. This implies that the correct stress-based
 statistical mechanics conserves both the force-moment tensor and the
 Maxwell-Cremona force-tiling area. As such, two variables of state arise:
 the tensorial angoricity and a new temperature-like quantity associated
 with the force-tile area which we name keramicity. Each quantity is
 observed to be inversely proportional to the global confining pressure;
 however only keramicity exhibits the protocol-independence expected of a
 state variable, while tensorial angoricity behaves as a variable of
 process.
description: Biaxial loading
 dataforce and volume data
 for each particle, at each loading stepbiaxial.tgzUniaxial loading dataforce and volume data for each particle, at each loading stepuniaxial.tgzShear loading dataforce and volume data for each particle, at each loading stepshear.tgzRaw figuresfiles in .eps and MATLAB .fig formatsfigures.tgz
DOI: 10.5061/dryad.37d5m
title: Data from: Homing pigeons (Columba livia) modulate wingbeat characteristics as a function of route familiarity

description: Mechanisms of avian navigation have received considerable attention, but
 whether different navigational strategies are accompanied by different
 flight characteristics is unknown. Managing energy expenditure is critical
 for survival, therefore understanding how flight characteristics, and
 hence energy allocation, potentially change with birds familiarity with a
 navigational task could provide key insights into the costs of
 orientation. We addressed this question by examining changes in wingbeat
 characteristics and airspeed of homing pigeons (Columba livia) as they
 learned a homing task. Twenty-one pigeons were released 20 times
 individually from either 3.85 km or 7.06 km from home. Birds were equipped
 with 5 Hz GPS trackers and 200 Hz tri-axial accelerometers. We found that,
 as the birds' route efficiency increased during the first six
 releases, their median peak-to-peak dorsal body (DB) acceleration and
 median DB amplitude also increased. This, in turn, led to higher
 airspeeds, suggesting that birds fly slower when traversing unfamiliar
 terrain. By contrast, after route efficiency stabilised, birds exhibited
 increasing wingbeat frequencies, which did not result in further increases
 in speed. Overall, higher wind support was also associated with lower
 wingbeat frequencies and with increased DB amplitude. Our study suggests
 that the cost of early flights from an unfamiliar location may be higher
 than subsequent flights both due to inefficient routes (increased
 distance) and lower airspeeds (increased time). Furthermore, the results
 indicate, for the first time, that birds modulate their wingbeat
 characteristics as a function of navigational knowledge, and suggest that
 flight characteristics may be used as "signatures" of
 birds' route familiarity.
description: Raw weather
 dataRaw weather data. Date
 and timestamp, wind speed and wind bearing.WeatherData_May-Sep2015_avwindbearing.csvRaw GPS dataRaw GPS data for the far siteRouteRecapping_GPS_farsite.zipRaw GPS dataRaw GPS data for the near site.RouteRecapping_GPS_nearsite.zipRaw accelerometer dataRaw accelerometer data from the far site. Column headings: Seconds, X-axis (g-force; forward-backward on the bird), Y-axis (g-force; left-right on the bird), Z-axis (g-force, up-down on the bird), light (LUX), temperature (degrees Celsius). Note: there appears to be some problems with the measurements from light and temperature so these were not used in our study.RouteRecapping_Accelerometer_farsite.zipRaw accelerometer dataRaw accelerometer data for the near site. Column headings: Seconds, X-axis (g-force; forward-backward on the bird), Y-axis (g-force; left-right on the bird), Z-axis (g-force, up-down on the bird), light (LUX), temperature (degrees Celsius). Note: there appears to be some problems with the measurements from light and temperature so these were not used in our study.RouteRecapping_Accelerometer_nearsite.zip
DOI: 10.5061/dryad.q4qb1
title: Data from: A molecular phylogeny of Staphyleaceae: implications for generic delimitation and classical biogeographic disjunctions in the family

description: Staphyleaceae traditionally comprises three genera of temperate and
 tropical trees and shrubs: Euscaphis Siebold & Zucc., Staphylea
 L., and Tuprinia Vent. These genera are clearly supported by morphology,
 but a recent classification based on four chloroplast genes and nuclear
 ITS treats Staphylea, Euscaphis, and New World Turpinia in Staphylea s.l.
 and Old World Turpinia in Dalrympelea Roxb. In this study, our objectives
 were to (1) resolve the phylogenetic relationships within Staphyleaceae
 using two nuclear and six chloroplast markers, (2) explore morphological
 synapomorphies that support major clades, and (3) discuss the implications
 of our results on generic delimitation and biogeography. Our phylogenetic
 results show five major clades in Staphyleaceae: (1) Old World Turpinia,
 (2) New World Turpinia, (3) a clade of exclusively Old World Staphylea,
 (4) an Asian-North American clade of Staphylea comprising all New World
 species and the rest of the Old World ones, and (5) Euscaphis. Within the
 two clades each of Staphylea and Turpinia, morphological features
 traditionally used for delimiting the genera may exhibit convergence.
 Among morphological features examined in this study, we found that pollen
 is not taxonomically informative, features of leaf teeth and epicuticular
 waxes show limited support for the traditional genera of Staphylea and
 Tuprinia, respectively, and petal length (i.e., flower size) is
 significantly smaller in Old World Turpinia compared to New World
 Turpinia. With respect to biogeography, our results support a rare
 disjunction between eastern North America and the Himalayas.
description: Staphyleaceae -
 micrographs of leaf surfacesAbaxial leaf surfaces of
 leaves of selected species of Staphyleaceae. Micrographs were taken using
 a XL-30 Philips scanning electron microscope.Staphyleaceae -
 micrographs of leaf teethMicrographs of leaf
 teeth of selected species of Staphyleaceae. Images were taken from slides
 of cleared leaves from the United States National Museum of Natural
 History cleared leaf collection.Staphyleaceae -
 alignments - finalSequence alignments of
 molecular markers used in this study. Alignments contain indels and a
 MrBayes block at the end.Staphyleaceae -
 alignments.zipStaphyleaceae -
 micrographs of pollen - finalScanning electron
 micrographs of pollen of Staphyleaceae taken with a Philips XL-30 scanning
 electron microscope.Staphyleaceae - micrographs of
 pollen.zipStaphyleaceae -
 micrographs of flowers - 11-1Micrographs of flowers
 of Turpinia. We captured the images using a Zeiss Stemi SV8
 stereomicroscope and a Retigna 1300i camera. We captured the images while
 the dehydrated flowers were floating in ethanol.
DOI: 10.13140/rg.2.2.36532.92808
title: Evolution in real time Jan 2026 Supplement1.pdf
DOI: 10.5061/dryad.pf150
title: Data from: Hierarchical influences of prey distribution on patterns of prey capture by a marine predator

description: 1. Prey distribution acts at multiple spatial scales to influence foraging
 success by predators. The overall distribution of prey may shape foraging
 ranges, the distance between patches may influence the ability of
 predators to detect and move between profitable areas, and individual
 patch characteristics may affect prey capture efficiency. 2. In this
 study, we assessed relationship between spatially-explicit patterns of
 prey capture by a central place forager, the little penguin (using GPS
 tracking and accelerometry), and the distribution of aggregations of
 potential forage fish prey (using boat-based active acoustics) in eastern
 Australia. We used complementary resource selection functions to estimate
 the distribution of both prey captures and aggregations across the study
 area, based on a suite of habitat characteristics. 3. We found that 99 %
 of prey captures by penguins occurred in the top 20 m of the water column.
 The estimated distribution of prey captures across the study area was
 similar to the distribution of aggregations above 20 m depth, indicating
 that penguins effectively matched the local distribution of their prey. 4.
 The distances between consecutive prey captures followed a bimodal
 distribution, with means of 8.1 ± 2.2 m and 57.4 ± 1.7 m. Based on the
 length of aggregations and the distances separating aggregations along
 survey transects, this implies that foraging behaviour occurs on multiple
 spatial scales corresponding to within-patch and between-patch movements
 respectively. 5. Morphological characteristics of aggregations above 20 m
 depth were important for explaining variance in the number of prey caught
 by penguins in an area, with penguins catching more prey where
 aggregations were relatively dense, compact and shallow. 6. These results
 reveal spatially explicit patterns of prey capture, and provide a
 framework for understanding how features of prey distribution influence
 prey intake by predators in patchy environments.
description: allPengLocsWk1GPS locations for penguins tracked from Montague Island, October 2015allAccelWk1Accelerometry data for penguins tracked in September/October 2015 from Montague Island, NSW, AustraliaaggregationsCharacteristics of potential forage fish aggregations detected around Montague Island, Australia in Sep/Oct 2016. Aggregations were identified from EK80 70KHz acoustic data using Echoview's 'schools detection' algorithm.svyTransect line coordinates with continuous seabed depth recordingsctdfWk1CTD data corresponding to acoustic survey around Montague Island, Sep/Oct 2016
DOI: 10.5061/dryad.s8v7q
title: Data from: Genome-wide signatures of local selection in the panmictic European eel

description: Next-generation sequencing and the collection of genome-wide data allow
 identifying adaptive variation and footprints of directional selection.
 Using a large SNP data set from 259 RAD-sequenced European eel individuals
 (glass eels) from eight locations between 34 and 64oN, we examined the
 patterns of genome-wide genetic diversity across locations. We tested for
 local selection by searching for increased population differentiation
 using FST-based outlier tests and by testing for significant associations
 between allele frequencies and environmental variables. The overall low
 genetic differentiation found (FST = 0.0007) indicates that most of the
 genome is homogenized by gene flow, providing further evidence for genomic
 panmixia in the European eel. The lack of genetic substructuring was
 consistent at both nuclear and mitochondrial SNPs. Using an extensive
 number of diagnostic SNPs, results showed a low occurrence of hybrids
 between European and American eel, mainly limited to Iceland (5.9%),
 although individuals with signatures of introgression several generations
 back in time were found in mainland Europe. Despite panmixia, a small set
 of SNPs showed high genetic differentiation consistent with
 single-generation signatures of spatially varying selection acting on
 glass eels. After screening 50 354 SNPs, a total of 754 potentially
 locally selected SNPs were identified. Candidate genes for local selection
 constituted a wide array of functions, including calcium signalling,
 neuroactive ligand–receptor interaction and circadian rhythm. Remarkably,
 one of the candidate genes identified is PERIOD, possibly related to
 differences in local photoperiod associated with the &gt;30°
 difference in latitude between locations. Genes under selection were
 spread across the genome, and there were no large regions of increased
 differentiation as expected when selection occurs within just a single
 generation due to panmixia. This supports the conclusion that most of the
 genome is homogenized by gene flow that removes any effects of
 diversifying selection from each new generation.
description: scriptpython script to
 establish the genomic position of candidate SNPs based on the gene
 predictions for the European eel genomeRaw_SNP_DataRAW SNP data on Genepop format for all individuals
DOI: 10.5061/dryad.35td0
title: Data from: Random-close packing limits for monodisperse and polydisperse hard spheres

description: We investigate how the densities of inherent structures, which we refer to
 as the closest jammed configurations, are distributed for packings of
 10000 frictionless hard spheres. A computational algorithm is introduced
 to generate closest jammed configurations and determine corresponding
 densities. Closest jamming densities for monodisperse packings generated
 with high compression rates using Lubachevsky–Stillinger and force-biased
 algorithms are distributed in a narrow density range from φ = 0.634-0.636
 to φ ≈ 0.64; closest jamming densities for monodisperse packings generated
 with low compression rates converge to φ ≈ 0.65 and grow rapidly when
 crystallization starts with very low compression rates. We interpret φ ≈
 0.64 as the random-close packing (RCP) limit and φ ≈ 0.65 as a lower bound
 of the glass close packing (GCP) limit, whereas φ = 0.634-0.636 is
 attributed to another characteristic (lowest typical, LT) density φLT. The
 three characteristic densities φLT, φRCP and φGCP are determined for
 polydisperse packings with log-normal sphere radii distributions.
description: Data
DOI: 10.5061/dryad.53mp5ng
title: Data from: Terrestrial species adapted to sea dispersal: differences in propagule dispersal of two Caribbean mangroves

description: A central goal of comparative phylogeography is to understand how
 species-specific traits interact with geomorphological history to govern
 the geographic distribution of genetic variation within species. One key
 biotic trait with an immense impact on the spatial patterns of
 intraspecific genetic differentiation is dispersal. Here we quantify how
 species-specific traits directly related to dispersal affect genetic
 variation in terrestrial organisms with adaptations for dispersal by sea,
 not land—the mangroves of the Caribbean. We investigate the phylogeography
 of white mangroves (Laguncularia racemosa, Combretaceae) and red mangroves
 (Rhizophora mangle, Rhizophoraceae) using chloroplast genomes and nuclear
 markers (thousands of RAD-Seq loci) from individuals throughout the
 Caribbean. Both coastal tree species have viviparous propagules that can
 float in salt water for months, meaning they are capable of dispersing
 long distances. Spatially explicit tests of the role of ocean currents on
 patterning genetic diversity revealed that ocean currents act as a
 mechanism for facilitating dispersal, but other means of moving genetic
 material are also important. We measured pollen- versus propagule-mediated
 gene flow and discovered that in white mangroves, seeds were more
 important for promoting genetic connectivity between populations, but in
 red mangroves, the opposite was true: pollen contributed more. This result
 challenges our concept of the importance of both proximity to ocean
 currents for moving mangrove seeds and the extent of long-distance pollen
 dispersal. This study also highlights the importance of spatially explicit
 quantification of both abiotic (ocean currents) and biotic (dispersal)
 factors contributing to gene flow to understand fully the phylogeographic
 histories of species.
description: Red mangrove chloroplast
 DNA sequence alignmentThis is a fasta
 alignment of the chloroplast genome sequences for 50 red mangrove
 individualsred_chloroplast.fastaWhite mangrove chloroplast DNA sequence alignmentThis is a fasta alignment of the chloroplast genome sequences for 50 white mangrove individualswhite_chloroplast.fastaRed mangrove nuclear DNA sequence alignmentThis is a fasta file containing nuclear (RAD-Seq) DNA sequences for 122 red mangrove individualsred_nuclear.fastaWhite mangrove nuclear DNA sequence alignmentThis is a fasta file containing nuclear (RAD-Seq) DNA sequences for 54 white mangrove individualswhite_nuclear.fastaVCF file of red mangrove SNPsThis is a VCF file containing SNP data for 122 red mangrove individualsred_SNPs.vcfSupplementThis supplement contains three Supplemental Tables and three Supplemental FiguresVCF file of white mangrove SNPsThis is a VCF file containing SNP data for 54 white mangrove individualswhite_SNPs.vcfOcean current layersZipped folder containing 24 .asc files with ocean current bearing (East, North) and velocity for the study regionocean_current_layers.zip
DOI: 10.5683/sp3/gldt0r
title: Balancing foraging opportunity and predation risk: Influence of dependent neonates on spatial co-occurrence of northern cervids and omnivorous predators

description: These data and associated R code were used for the analysis presented in Balancing foraging opportunity and predation risk: Influence of dependent neonates on spatial co-occurrence of northern cervids and omnivorous predators https://doi.org/10.1139/cjz-2025-0038
DOI: 10.5061/dryad.k3h89
title: Data from: Group foraging decisions in nutritionally differentiated environments

description: Foraging behaviour must be flexible enough to adapt to heterogeneities in
 the distribution and quality of food resources. Accurate models of optimal
 foraging behaviour should acknowledge the extent to which animals can
 detect and regulate their intake of food based on smaller scale
 differences in food types. In particular, consideration of macro-nutrient
 distribution and how animals perceive this is limited in studies of
 optimal foraging, particularly in vertebrates and for animals that forage
 in groups. Here, we track shoals of eight mosquitofish as they forage in
 two environments that contain equal amounts of available energy but differ
 in their distribution of macro-nutrients. We provide empirical evidence
 that fish will distribute themselves within an environment in relation to
 the distribution of specific macro-nutrients. Also, fish make foraging
 decisions based on the macronutrient composition of patches, such that
 their durations on patches are longer when they have a higher
 concentration of protein and lower concentration of carbohydrate. The
 ratio of protein to carbohydrate does not affect the probability of a fish
 joining a patch, however, with low numbers of fish on the patch the
 probability of a fish leaving is greater per unit time step in the patches
 with a low protein to carbohydrate ratio than the patches with a high
 protein to carbohydrate ratio. This study confirms the importance of
 considering the macro-nutrient composition of foods when considering the
 movement decisions of foraging groups and thus has important consequences
 for developing more accurate foraging models that take into account the
 distribution of macro-nutrients in the environment. The results suggest
 the spatial distribution of nutrients on a landscape scale could influence
 grouping patterns and social interactions, thus affecting population
 dynamics.
description: Data_Dryad.mat files with coord data, matlab scripts and excel work sheetsData_Dyad.zip
DOI: 10.5061/dryad.755d6
title: Data from: Body size evolution in an old insect order: no evidence for Cope’s Rule in spite of fitness benefits of large size

description: We integrate field data and phylogenetic comparative analyses to
 investigate causes of body size evolution and stasis in an old insect
 order: odonates (“dragonflies and damselflies”). Fossil evidence for
 “Cope's Rule” in odonates is weak or non-existent since the last
 major extinction event 65 million years ago, yet selection studies show
 consistent positive selection for increased body size among adults. In
 particular, we find that large males in natural populations of the banded
 demoiselle (Calopteryx splendens) over several generations have consistent
 fitness benefits both in terms of survival and mating success.
 Additionally, there was no evidence for stabilizing or conflicting
 selection between fitness components within the adult life-stage. This
 lack of stabilizing selection during the adult life-stage was
 independently supported by a literature survey on different male and
 female fitness components from several odonate species. We did detect
 several significant body size shifts among extant taxa using comparative
 methods and a large new molecular phylogeny for odonates . We suggest that
 the lack of Cope's rule in odonates results from conflicting
 selection between fitness advantages of large adult size and costs of long
 larval development. We also discuss competing explanations for body size
 stasis in this insect group.
description: Body SIze Evolution in
 Odonates Data Filedryad.zip
DOI: 10.5061/dryad.q5t5s
title: Data from: Mapping and analysis of the connectome of sympathetic premotor neurons in the rostral ventrolateral medulla of the rat using a volumetric brain atlas

description: Spinally projecting neurons in the rostral ventrolateral medulla (RVLM)
 play a critical role in the generation of vasomotor sympathetic tone and
 are thought to receive convergent input from neurons at every level of the
 neuraxis; the factors that determine their ongoing activity remain
 unresolved. In this study we use a genetically restricted viral tracing
 strategy to definitively map their spatially diffuse connectome. We
 infected bulbospinal RVLM neurons with recombinant rabies variant that
 drives reporter expression in monosynaptically connected input neurons and
 mapped their distribution using a MRI-based volumetric atlas and a novel
 image alignment and visualization tool that efficiently translates the
 positions of neurons captured in conventional photomicrographs to
 Cartesian coordinates. We identified prominent inputs from
 well-established neurohumoral and viscero-sympathetic sensory actuators,
 medullary autonomic and respiratory subnuclei, and supramedullary
 autonomic nuclei. The majority of inputs lay within the brainstem (88 –
 94%), and included putative respiratory neurons in the pre-Bötzinger
 Complex and post-inspiratory complex that are therefore likely to underlie
 respiratory-sympathetic coupling. We also discovered a substantial and
 previously unrecognized input from the region immediately ventral to
 nucleus prepositus hypoglossi. In contrast, RVLM sympathetic premotor
 neurons were only sparsely innervated by suprapontine structures including
 the paraventricular nucleus, lateral hypothalamus, periaqueductal grey and
 superior colliculus, and we found almost no evidence of direct inputs from
 the cortex or amygdala. Our approach can be used to quantify, standardize
 and share complete neuroanatomical datasets, and therefore provides
 researchers with a platform for presentation, analysis and independent
 analysis of connectomic data.
description: Waxholm Rat Calculation
 TemplateThis template will help
 you to translate pixel co-ordinates of cells identified from microscopy
 images to Waxholm co-ordinates. In needs to be used in conjunction with
 the AlignNii image anchoring tool, which aligns 2d histological images in
 the 3d MRI Waxholm rat brain. Access to this tool can be requested from
 Jan Bjaalie (j.g.bjaalie@medisin.uio.no).Waxholm volumetric
 atlasThis is the zipped
 Imaris file that contains the Waxholm MRI dataset, the corresponding
 segmented dataset, the volumetric segmentation model and all of
 connectomic data from this paper.Dempsey 2016 RVLM Connectome
 Resource.zip