cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s1rn8pkct
title: Patterns of host plant use do not explain mushroom body expansion in Heliconiini butterflies

description: The selective pressures leading to the elaboration of downstream,
 integrative processing centres, such as the mammalian neocortex or insect
 mushroom bodies, are often unclear. In Heliconius butterflies, the
 mushroom bodies are three to four times larger than their Heliconiini, and
 the largest known in Lepidoptera. Heliconiini lay almost exclusively on
 Passiflora, which exhibit a remarkable diversity of leaf shape, and it has
 been suggested that the mushroom body expansion of Heliconius may have
 been driven by the cognitive demands of recognising and learning the leaf
 shapes of local host plants. We test this hypothesis using two
 complementary methods: i) phylogenetic comparative analyses to test
 whether variation in mushroom body size is associated with the
 morphological diversity of host plants exploited across the Heliconiini;
 and ii) shape learning experiments using six Heliconiini species. We found
 that variation in the range of leaf morphologies used by Heliconiini was
 not associated with mushroom body volume. Similarly, we find interspecific
 differences in shape learning ability, but Heliconius are not overall
 better shape learners than other Heliconiini. Together these results
 suggest that the visual recognition and learning of host plants was not a
 main factor driving the diversity of mushroom body size in this tribe.
description: This dataset consists of a previously collected dataset of
 Heliconiini hostplant use, voumetric brain data, morphometric
 quantifications of <em>Passiflora</em> leaf shape, and
 Heliconiini shape learning data collected from behavioural
 experiments.
description: All data were analysed in R. Code is included.
DOI: 10.5061/dryad.5qfttdzb1
title: Data of sperm competition experiments between Lampetra planeri and L. fluviatilis

description: The following data come from a study on the effects of sperm competition
 and cryptic female choice as putative postmating barriers in two lamprey
 ecotypes (Lampetra planeri and L. fluviatilis) with a partial reproductive
 isolation. We measured sperm traits in both ecotypes and designed sperm
 competition experiments to test the occurrence of cryptic female choice.
 Sperm competition experiments either at equal semen volume or equal sperm
 number were realized to investigate the role of sperm velocity on
 fertilization success.
description: All the data were collected in April and May 2021 in
 France. Adult lampreys were caught in the river by
 electrofishing in the Oir River (France). In the following days, sperm
 traits were assessed. Sperm number was assessed using a Thomas cell
 counting chamber and sperm velocity was measured by using a
 Computer-assisted Sperm Analysis System.  Then
 <em>in vitro</em> fertilizations were realized among and
 between ecotypes.
DOI: 10.5061/dryad.3r2280gmm
title: Laminar phase coupling data for: Spike-phase coupling patterns reveal laminar identity in primate cortex

description: The cortical column is one of the fundamental computational circuits in
 the brain. In order to understand the role neurons in different layers of
 this circuit play in cortical function it is necessary to identify the
 boundaries that separate the laminar compartments. While histological
 approaches can reveal ground truth they are not a practical means of
 identifying cortical layers in vivo. The gold standard for identifying
 laminar compartments in electrophysiological recordings is current-source
 density (CSD) analysis. However, laminar CSD analysis requires averaging
 across reliably evoked responses that target the input layer in cortex,
 which may be difficult to generate in less well-studied cortical regions.
 Further, the analysis can be susceptible to noise on individual channels
 resulting in errors in assigning laminar boundaries. Here, we have
 analyzed linear array recordings in multiple cortical areas in both the
 common marmoset and the rhesus macaque. We describe a pattern of laminar
 spike-field phase relationships that reliably identifies the transition
 between input and deep layers in cortical recordings from multiple
 cortical areas in two different non-human primate species. This measure
 corresponds well to estimates of the location of the input layer using
 CSDs but does not require averaging or specific evoked activity. Laminar
 identity can be estimated rapidly with as little as a minute of ongoing
 data and is invariant to many experimental parameters. This method may
 serve to validate CSD measurements that might otherwise be unreliable or
 to estimate laminar boundaries when other methods are not practical.
description: Data was collected from linear electrode arrays recording spiking
 and local field potential activity from macaque and marmoset monkeys
 performing behavorial tasks. Electrode voltages were recorded at 30 KHz
 and downsampled to 1000 Hz and low-pass filtered at 200 Hz. Spike times
 are time stamps for multiunit spiking activity during the LFP segments.
 Channel map indicated the linear position of each electrode from the
 tip.
description: Datafiles are in .mat format and can be opened with MATLAB.
DOI: 10.5061/dryad.9kd51c5nw
title: Data from: Biofilms as self-shaping growing nematics

description: Active nematics are the nonequilibrium analog of passive liquid crystals
 in which anisotropic units consume free energy to drive emergent behavior.
 Similar to liquid crystal (LC) molecules in displays, ordering and
 dynamics in active nematics are sensitive to boundary conditions; however,
 unlike passive liquid crystals, active nematics, such as those composed of
 living matter, have the potential to regulate their boundaries through
 self-generated stresses.  Here, using bacterial biofilms confined
 by a hydrogel as a model system, we show how a three-dimensional, living
 nematic can actively shape itself and its boundary in order to regulate
 its internal architecture through growth-induced stresses. We show that
 biofilms exhibit a sharp transition in shape from domes to lenses upon
 changing environmental stiffness or cell-substrate friction, which is
 explained by a theoretical model considering the competition between
 confinement and interfacial forces. The growth mode defines the
 progression of the boundary, which in turn determines the trajectories and
 spatial distribution of cell lineages. We further demonstrate that the
 evolving boundary defines the orientational ordering of cells and the
 emergence of topological defects in the interior of the biofilm. Our
 findings reveal novel self-organization phenomena in confined active
 matter and provide strategies for guiding the development of programmed
 microbial consortia with emergent material properties.
description: The dataset was acquired using a Yokogawa CSU-W1 spinning-disk
 confocal scanning unit mounted on a Nikon Ti2-E microscope body, using the
 Nikon perfect focus system and images were acquired using Nikon Elements
 5.20. For high-resolution, single-cell level imaging, a 100× silicon oil
 immersion objective (Lambda S 100XC Sil, numerical aperture = 1.35) was
 used. A z-step size of 0.195 μm was used. The green mNeonGreen fluorophore
 was excited using a 488 nm laser. For time course imaging, cells were
 incubated in a Tokai-Hit stage-top incubator at a temperature of 30°C.
 Provided here are raw data without any postprocessing.
description: The dataset was aqcuired and can be opened with Nikon Elements
 5.20. Alternatively, free software such as FIJI can also open it (https://imagej.net/software/fiji/).
DOI: 10.5066/p13vbqmf
title: Drought-related responses of stream flow, climate, and vegetation productivity from the Donner und Blitzen watershed, Great Basin Desert, USA (1988-2020)

description: Indicators of climatic, hydrologic, and ecological drought responses in water-related terrestrial and aquatic conditions within a single catchment in the northwestern Great Basin Desert and its associated stream network were developed from stream flow, climate and remote sensing sources for the time period of 1988 to 2020.
DOI: 10.7280/d1md7p
title: Dataset for: Impacts of a Cascadia subduction zone earthquake on water levels and wetlands of the lower Columbia river and estuary

description: Subsidence after a subduction zone earthquake can cause major changes in
 estuarine bathymetry. Here, we quantify the impacts of earthquake-induced
 subsidence on hydrodynamics and habitat distributions in a major system,
 the Lower Columbia River Estuary, using a hydrodynamic and habitat model.
 Model results indicate that coseismic subsidence increases tidal range,
 with the smallest changes at the coast and a maximum increase of ~10% in a
 region of topographic convergence. All modeled scenarios reduce intertidal
 habitat by 24-25%, and shifts ~93% of estuarine wetlands to
 lower-elevation habitat bands. Incorpating dynamic effects of tidal change
 from subsidence yields higher estimates of remaining habitat by multiples
 of 0-3.7, dependent on the habitat type. The persistent tidal change and
 chronic habitat disturbance after an earthquake poses strong challenges
 for estuarine management and wetland restoration planning, particularly
 when coupled with future sea-level rise effects.
DOI: 10.5061/dryad.v6wwpzh1c
title: Data from: Seed removal, seed dispersers, and the allocation of tissues in Myrtaceae seeds

description: To avoid seed predation, plants may invest in protective seed tissues.
 Often related to seed size, allocation in seeds’ physical defenses can
 also be influenced by dispersers. We explore the relationships between
 seed traits (seed mass and hardness) and seed removal in 22 Myrtaceae
 species of the Brazilian Atlantic Forest, a dominant and diverse
 fleshy-fruited taxon dispersed by birds, rodents, and other mammals. Our
 goal is to understand how seed traits influence seed removal rates, and
 whether dispersers can affect tissue allocation in the seed coat. Seeds
 were exposed to field removal experiments. In the lab, total seed mass and
 seed coat mass were obtained. To evaluate the influence of seed traits on
 removal, we performed Kruskal-Wallis and Simple Linear Regression tests.
 We assessed seed coat and seed mass covariation through standardized
 major-axis allometric regressions. Harder seeds were larger than softer
 ones. Seed traits affect removal rates, as tougher and heavier seeds had
 lower removal. Seed mass significantly predicts seed coat proportion in
 seven of the 14 species tested. Bird-dispersed species tend to exhibit
 lower proportions of seed coat as seed mass increases, whereas
 rodent-dispersed species apparently present the opposite trend, with seed
 coat proportion increasing with seed mass. Such difference may be caused
 by the contrasting seed predation pressure represented by birds and
 rodents. Energy allocation for defense, expressed in seed coat proportion,
 is greater in large seeds, as these are mostly dispersed by rodents whose
 propensity to cache and disperse seeds is greater for large and
 well-protected seeds.
DOI: 10.5061/dryad.xgxd254mb
title: Data from: Exceptions to the temperature-size rule: No Lilliput effect in end-Permian ostracods (Crustacea) from Aras Valley (NW Iran)

description: The body size of marine ectotherms is often negatively correlated with
 ambient water temperature, as seen in many clades during the hyperthermal
 crisis of the end-Permian mass extinction (c. 252 Mya). However, in the
 case of ostracods, size changes during ancient hyperthermal events are
 rarely quantified. In this study, we evaluate the body size changes of
 ostracods in the Aras Valley section (NW Iran) in response to the drastic
 warming during the end-Permian mass extinction at three taxonomic levels
 (class, order, species). On the assemblage level, the warming triggers a
 complete species turnover in the Aras Valley section, with larger, newly
 emerging species dominating the immediate post-extinction assemblage for a
 short time. Individual ostracod species and instars do not show dwarfing
 or a change in body size as an adaptation to the temperature stress during
 the end-Permian crisis. This may indicate that ostracods might be
 exceptions to the temperature-size rule (TSR), using an adaptation
 mechanism that does not involve a decrease in body size. Many recent
 experimental studies show that accelerated development without size
 changes is a common response of modern ostracods to thermal stress.
description: R/R Studio, any PDF reader, Microsoft Excel or an open-source
 alternative.
DOI: 10.5061/dryad.0p2ngf25g
title: Mechanisms of simultaneous linear and nonlinear computations at the mammalian cone photoreceptor synapse

description: Neurons enhance their computational power by combining linear and
 nonlinear transformations in extended dendritic trees. Rich, spatially
 distributed processing is rarely associated with individual synapses, but
 the cone photoreceptor synapse may be an exception. Graded voltages
 temporally modulate vesicle fusion at a cone’s ~20 ribbon active zones.
 The transmitter then flows into a common, glia-free volume where bipolar
 cell dendrites are organized by type in successive tiers. Using
 super-resolution microscopy and tracking vesicle fusion and postsynaptic
 response at the quantal level in the thirteen-lined ground
 squirrel, Ictidomys tridecemlineatus, we show that certain
 bipolar cell types respond to individual fusion events in the stream while
 other types respond to degrees of locally coincident events, creating a
 gradient across tiers that are increasingly nonlinear. Nonlinearities
 emerge from a combination of factors specific to each bipolar cell type
 including diffusion distance, contact number, receptor affinity, and
 proximity to transporters. Complex computations related to feature
 detection begin within the first visual synapse.
description: Whole-cell patch clamp recording, dual cell, triple, cell, rapid
 perfusion, capacitance measurements, processed using Igor 8.0 from
 Wavemetrics Super-resolution imaging with a Leica SP8
 3D-STED microscope processed with Fiji and Imaris 10.0.0
 software MCELL 3.4 Monte Carlo simulation
 program
description: Microsoft Excel or similar. Fiji or similar. MCELL 3.4.
DOI: 10.5061/dryad.15dv41p2c
title: Head shape predicts isotopic diet in anoles and day geckos

description: Trophic morphology affects resource acquisition; therefore, species
 differences in such traits may be informative for inferring resource use
 overlap and potential species interactions.  In lizards, head
 size and shape determine the size and hardness of prey that can be
 consumed. Lizards with large differences in head morphology are expected
 to overlap less in prey use than lizards with more similar
 traits.  Stable isotopes are increasingly being used to describe
 diet, yet how traditional functional traits affect isotopic diet is often
 not clear a priori.  We measured head size, head shape,
 ?15N, and ?13C under controlled resource availability in an enclosure
 experiment using introduced lizards in Hawaiʻi to test whether functional
 traits predict isotopic diet.  Brown anoles (Anolis sagrei) had
 the tallest and narrowest heads, the highest values
 of ?13C, and the lowest values of ?15N. Gold
 dust day geckos (Phelsuma laticauda) had the shortest and widest heads,
 the lowest values of ?13C, and the highest values of ?15N. Green
 anoles (Anolis carolinensis) were intermediate in both diet and
 morphology.  As a result of isotopic diet overlap, green anoles
 have reduced competitor-free resource space in the presence of both of the
 other lizard species.  Head shape was the best predictor of diet
 and the only trait that explained variation within as well as among
 species. Head size was sexually dimorphic, and therefore the weaker diet
 correlations with this trait may be explained by sexual selection. Breadth
 in morphospace did not correlate with isotopic diet breadth, nor did the
 amount of overlap in morphospace predict the amount of overlap in isotopic
 diet space.  While lizards were able to locally depress prey in
 experimental enclosures, no shifts in diet were detected in response to
 the presence of heterospecifics.  The generality of head shape in
 predicting isotopic diet, and whether it does so independent of habitat
 use, warrants additional study. Head shape provides a potentially fruitful
 avenue for trait-based approaches to studying ecology and evolution in
 lizards.
DOI: 10.5061/dryad.h18931zrg
title: Diversification and change in the R programming language

description: Languages change over time, driven by creation of new words and cultural
 pressure to optimise communication. Programming languages resemble written
 language but communicate primarily with computer hardware rather than a
 human audience. I tested for changes over time in use of R, a mature,
 open-source programming language used for scientific computing. Across
 393,142 GitHub repositories published between 2014 and 2021, I extracted
 143,409,288 R functions, programming “verbs”, and paired linguistic and
 ecological approaches to estimate change in the diversity and composition
 of function use over time. I found that the number of R functions in use
 increased and underwent substantial change, driven primarily by the
 popularity of the “tidyverse” collection of community-written extensions.
 I provide evidence that users can directly change the nature of
 programming languages, with patterns that match known processes from
 natural languages and genetic evolution. In the case of R, patterns
 suggested there are selective pressures for increased analytic complexity
 and R functions in decline but not extinct (“extinction debts”). R’s
 evolution towards the tidyverse may also represent the start of a division
 into two distinct dialects, which may impact the readability and
 continuity of analytic and scientific inquiries codified in R, as well as
 the language’s future.
description: Full methodology for this dataset is available in the manuscript,
 and the R code to process this is located in a GitHub repository: https://github.com/TimothyStaples/Revolution
description: This is a comma-separated values file intended for use in the
 galaxy_analysis.R script in https://github.com/TimothyStaples/Revolution
DOI: 10.5061/dryad.3ffbg79p5
title: Data from: Estimating phenology and phenological shifts with hierarchical modeling

description: This dataset contains daily counts of juvenile chum salmon (Oncorhynchus
 keta) from the Skagit River, WA between 1990–2019. The analyzed dataset
 contains 30 years and 4,636 monitoring days in which 2,358,284 migrating
 chum salmon were counted. This dataset is the companion dataset for
 phenomix R package.
description: Juvenile chum salmon were intercepted
 in the mainstem of the Skagit River during their spring migration to the
 ocean. Every spring between late January and late July from 1990–2019, the
 Washington Department of Fish and Wildlife has operated an incline plane
 trap and an eight-foot diameter rotary screw trap, fished in tandem on the
 mainstem of the Skagit River (-122.34° E, 48.44° N). Traps were monitored
 and fish were counted nightly and every third day. The dataset provided is
 of raw daily counts and is not adjusted for capture efficiency. For
 purposes of estimating migration timing, this assumes that capture
 efficiency does not change throughout the season. Given that these data
 are catch counts, we advise not to use them for estimating total migration
 abundance without an estimate of trap efficiency.  More information on the
 Skagit River juvenile fish trap operation can be found in Zimmerman et al.
 2015 TAFS 144:627-641.
DOI: 10.5061/dryad.8w9ghx3rq
title: Linking trait network parameters with plant growth across light gradients and seasons

description: 1. Reduced light availability induced by eutrophication has dramatically
 affected the growth of submerged macrophytes and caused their rapid
 decline globally in lakes. Functional traits have usually been used to
 predict ecological processes and explain plant adaptation. Trait networks,
 which are constructed from a series of nodes (traits) and edges
 (trait-trait correlations), can reveal complex relationships among traits.
 Plant traits belonging to different organs are considered relevant for
 overall plant performance. Therefore, variation in trait network topology
 at the whole-plant level can better reflect plant adaptation and response
 to environments than traditional methods, but the mechanisms underlying
 the decline of plants from a trait network perspective are not well
 understood. 2. In this study, based on a one-year manipulation experiment
 for Potamogeton maackianus cultured with four levels of light intensity,
 we constructed trait networks from 20 traits belonging to different
 organs. 3. Our results showed that trait network connectivity decreases in
 harsh environments, probably due to increased trait modules responding
 independently to stress. Network connectivity was positively related to
 the plant relative growth rate (RGR), as high trait connectivity and
 coordination should be beneficial for plants to acquire and transport
 resources efficiently across the whole plant. Additionally, we found that
 specific stem length, leaf:root mass ratios, and leaf total nonstructural
 carbohydrates were hub traits with high connectivity. These hub traits
 expressed high phenotypic plasticity, had close links with plant growth,
 and consistently held their higher importance within the network across
 light gradients or seasons. 4. We found that low phenotypic integration in
 stressful environments may constrain plant growth, which can provide
 important implications for understanding plant adaptation strategies to
 low-light stress and even predicting community dynamics in the context of
 global environmental change.