cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gb5mkkwmw
title: Data from: Insectivorous birds can see and smell systemically herbivore‐induced pines

description: Several studies have shown that insectivorous birds are attracted to
 herbivore-damaged trees even when they cannot see or smell the actual
 herbivores or their faeces. However, it often remained an open question
 whether birds are attracted by herbivore-induced changes in leaf odour or
 in leaf light reflectance or by both types of changes. Our study addressed
 this question by investigating the response of great tits (Parus major)
 and blue tits (Cyanistes caeruleus) to Scots pine (Pinus sylvestris)
 damaged by pine sawfly larvae (Diprion pini). We released the birds
 individually to a study booth, where they were simultaneously offered a
 systemically herbivore-induced and a non-infested control pine branch. In
 the first experiment, the birds could see the branches, but not smell
 them, because each branch was kept inside a transparent, air-tight
 cylinder. In the second experiment, the birds could smell the branches,
 but not see them, because each branch was placed inside a non-transparent
 cylinder with a mesh lid. The results show that the birds were more
 attracted to the herbivore-induced branch in both experiments. Hence,
 either type of the tested cues, the herbivore-induced visual plant cue
 alone as well as the olfactory cues per se, is attractive to the birds.
description: Birds were tested individually in a booth with two branches
 inside cylinders. One cylinder had a systemically herbivore-induced branch
 and one had an intact control branch. In the vision experiment birds could
 see, but not smell the branches. In the olfaction experiment birds could
 smell, but not see the branches. In the analyses we
 used the "raw" values of first choice, time spent on cylinders
 and number of visits on the cylinders.
description: Birds that did not calm down were left out from the analyses (two
 individuals in vision experiment and four in the olfaction
 experiment).
DOI: 10.5061/dryad.xpnvx0kcg
title: Differences in ontogenetic and diurnal microhabitat selection by sympatric live-bearing fish species with different reproductive modes

description: A pregnancy imposes a heavy reproductive burden on females. Some
 live-bearing species have evolved reproductive adaptations to reduce this
 burden, which may influence their ability to utilize specific
 microhabitats. We investigate whether two such reproductive adaptations,
 placentation (embryo provisioning via a placenta) and superfetation (the
 ability to carry multiple broods at various developmental stages),
 influence microhabitat selection by five sympatric Costa Rican
 live-bearing fish species (family Poeciliidae). Theory predicts that
 placentation and superfetation should both reduce the reproductive burden
 of females during pregnancy, improve their body streamlining, and swimming
 performance, and consequently allow them to utilize ‘more
 performance-demanding’ microhabitats. Here we apply underwater visual fish
 surveys to test a key prediction of this hypothesis, which is that the
 presence of these two reproductive adaptations is correlated with the
 utilization of microhabitats in the river that are characterized by a
 higher-flow velocity. Consistent with our predictions, we observed
 significant interspecific differences in daytime microhabitat use: species
 that had both placentation and superfetation were found in deeper and
 faster-flowing parts of the river, species that lacked both adaptations
 were confined to shallow slow-flowing areas, and species with one
 adaptation (i.e. only superfetation) inhabited intermediate areas. This
 interspecific daytime microhabitat use was strongest in reproductive
 adults, intermediate in immatures, and absent in juveniles (the latter of
 which were all found in shallow low-velocity zones), suggesting that
 ontogeny influences species-specific microhabitat use. Finally, at night,
 all fishes, regardless of the species or age-class, congregated in shallow
 slow-flowing waters to rest (sleep) on the river bottom. Taken together,
 our results suggest that placentation and superfetation may be hitherto
 unrecognized reproductive features that help to understand differences in
 ontogenetic and diurnal microhabitat preferences between sympatric
 live-bearing fish species living in environments characterized by large
 flow variation.
DOI: 10.5061/dryad.g79cnp5n8
title: First use of acoustic calls to distinguish cryptic fish species: Dascyllus aruanus complex as a case study

description: From a practical point of view, the determination of species in the wild
 is based on their phenotypes. Consequently, many species remain unknown
 because they are visually indistinguishable from described species.
 Although molecular methods and advances in bioacoustical analysis have
 been extensively used to uncover cryptic species, the combination of both
 methodologies is still rare and concerns only some terrestrial taxa such
 as insects, bats, frogs and birds. In this study, we aim to determine
 whether the sounds produced by different populations of fish can also be a
 tool to distinguish and identify cryptic species. The humbug damselfish
 complex, Dascyllus aruanus, is widely distributed across the Indo-Pacific
 Ocean and, since 2019, is thought to be composed of at least two species
 with Dascyllus aruanus in the Pacific Ocean and Dascyllus abudafur in the
 Indian Ocean. Recordings were made over a large geographical area with
 populations from Madagascar (Indian Ocean), Taiwan (Pacific Ocean) and
 French Polynesia (Society Islands). Two kinds of sounds were used for
 analysis: sounds associated with conspecific chases, and sounds produced
 during the “signal jump” of courtship behaviour. The sounds associated
 with signal jumps differ geographically. Acoustic feature differences
 between Taiwan and Madagascar align with the existence of genetic
 differences confirming specific status and supporting for the first time
 that sounds can help to discriminate cryptic species in Teleosts. However,
 differences in both acoustic features and genetic data can also be found
 between Taiwan and French Polynesia suggesting two clearly distinct
 populations. Using the same reasoning, we propose to resurrect the epithet
 “emamo” (Lesson 1830) for the Society Island humbug damselfish.
 Interestingly, sounds associated to conspecific chases are more variable
 than sounds related to signal jumps, suggesting that there are more
 constraints on sounds related to courtship since they would serve as
 indicators for species identity and contribute to premating isolation.
DOI: 10.5061/dryad.9ghx3fffh
title: Gene Delivery to Neurons in the Auditory Brainstem of Barn Owls using Standard Recombinant Adeno-associated Virus Vectors

description: Recombinant adeno-associated virus (rAAV) vectors are a commonly used tool
 for gene delivery. There is a large choice of different serotypes whose
 transduction efficiency varies for different animal species. In this
 study, three rAAV vectors were tested for transduction efficiency in the
 auditory brainstem of adult barn owls (Tyto alba) which are not standard
 laboratory animals. Injections with rAAV serotypes 2/1 and 2/5 resulted in
 reliable expression in various nuclei of the auditory brainstem of barn
 owls. Both vectors showed evidence of being spread by axonal transport.
 However, only rAAV2/5 also showed expression in regions far distant from
 the injection site, suggesting long-range axonal transport in connections
 along the auditory pathway. In contrast, injections with rAAV2/9 resulted
 in no expression. Our results demonstrate for the first time that
 commercially available rAAV vectors can be used for reliable gene
 expression in the barn owl auditory brainstem and pave the way toward
 optogenetic manipulation of neural activity in this important animal
 species in neuroethology and auditory physiology.
description: See attached Readme_CRNEUR-D-20-00004.pdf for additional
 information.
DOI: 10.5061/dryad.0k6djh9xf
title: Rearing environment affects the genetic architecture and plasticity of DNA methylation in Chinook salmon

description: Genetic architecture and phenotypic plasticity are important
 considerations when studying trait variation within and among populations.
 Since environmental change can induce shifts in the genetic architecture
 and plasticity of traits, it is important to consider both genetic and
 environmental sources of phenotypic variation. While there is overwhelming
 evidence for environmental effects on phenotype, the underlying mechanisms
 are less clear. Variation in DNA methylation is a potential mechanism
 mediating environmental effects on phenotype due to its sensitivity to
 environmental stimuli, transgenerational inheritance, and influences on
 transcription. To characterize the effect of environment on methylation,
 we created two 6x6 (North Carolina II) Chinook salmon breeding crosses and
 reared the offspring in two environments: uniform hatchery tanks and
 semi-natural stream channels. We sampled the fish twice during
 development, at the alevin (larval) and fry (juvenile) stages. We measured
 DNA methylation at 13 genes using a PCR-based bisulfite sequencing
 protocol. The genetic architecture of DNA methylation differed between
 rearing environments, with greater additive and non-additive genetic
 variance in hatchery fish and greater maternal effects in semi-natural
 channel fish, though gene-specific variation was evident. We observed
 plasticity in methylation across all assayed genes, as well as
 gene-specific effects at two genes in alevin and six genes in fry,
 indicating developmental stage-specific effects of rearing environment on
 methylation. Characterizing genetic and environmental influences on
 methylation is critical for future studies on DNA methylation as a
 potential mechanism for acclimation and adaptation.
description: This Dryad entry contains bisulfite sequencing data for Chinook
 salmon reared in the semi-natural channel. For hatchery-reared fish data,
 see https://doi.org/10.5061/dryad.5x69p8d07.
DOI: 10.5061/dryad.mw6m905tx
title: Comparative analysis of angiogenesis models: MATLAB data files

description: This data set contains the MATLAB files that were used to generate figures
 located in the article "Comparative analysis of angiogenesis
 models" (J. Math. Biol, in press). The
 article's abstract may be found below.  Although
 discrete approaches are increasingly employed to model biological
 phenomena, it remains unclear how complex, population-level behaviours in
 such frameworks arise from the rules used to represent interactions
 between individuals. Discrete-to-continuum approaches, which are used to
 derive systems of coarse-grained equations describing the mean-field
 dynamics of a microscopic model, can provide insight into such emergent
 behaviour. Coarse-grained models often contain nonlinear terms that depend
 on the microscopic rules of the discrete framework, however, and such
 nonlinearities can make a model difficult to mathematically analyse. By
 contrast, models developed using phenomenological approaches are typically
 easier to investigate but have a more obscure connection to the underlying
 microscopic system. To our knowledge, there has been little work done to
 compare solutions of phenomenological and coarse-grained models. Here we
 address this problem in the context of angiogenesis (the creation of new
 blood vessels from existing vasculature). We compare asymptotic solutions
 of a classical, phenomenological "snail-trail" model for
 angiogenesis to solutions of a nonlinear system of partial differential
 equations (PDEs) derived via a systematic coarse-graining procedure
 (Pillay, 2017). For distinguished parameter regimes corresponding to
 chemotaxis-dominated cell movement and low branching rates, both continuum
 models reduce at leading order to identical PDEs within the domain
 interior. Numerical and analytical results confirm that pointwise
 differences between solutions to the two continuum models are small if
 these conditions hold, and demonstrate how perturbation methods can be
 used to determine when a phenomenological model provides a good
 approximation to a more detailed coarse-grained system for the same
 biological process.
description: These data were produced and processed using MATLAB 2018b
 (Mathworks), using codes "ABM_2D_Model.m" and
 "Larger_Domain_Angiogenesis_Models.m" listed
 at https://github.com/wdmartinson/comparative-analysis-of-continuum-angiogenesis-models. Partial differential equations were solved using the method of lines (Sciesser, 1991, The numerical method of lines: Integration of partial differential equations). For further details on the equations and rules used to simulate the models, we refer to the article by Martinson et al. (in press, J. Math. Biol., DOI: 10.1007/s00285-021-01570-w).
description: Please see the attached README file
 (MARTINSON_DATASET_MATLAB_CAAM_README.txt) for further details on how the
 data in the collection were generated, information on the files contained
 in this dataset, and descriptions of the meanings of the variables and
 parameter values contained within the dataset.
DOI: 10.5061/dryad.c59zw3r50
title: Psocodea Phylogenomic dataset from: Phylogenomics of parasitic and non-parasitic lice (Insecta: Psocodea): combining sequence data and Exploring compositional bias solutions in Next Generation Datasets

description: This dataset includes all alignments used for the phylogenomic analysis of
 Psocodea. In this dataset, includes all result files of phylogenomic
 analyses completed. This includes maximum likelihood, astral, MCMCtree,
 quartet sampling, and all gene trees. Any relevant input files are
 included, and any materials are available upon request. The insect order
 Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and
 non-parasitic members (Psocoptera). The extreme age and ecological
 diversity of the group may be associated with major genomic changes, such
 as base compositional biases expected to affect phylogenetic inference.
 Divergent morphology between parasitic and non-parasitic members has also
 obscured the origins of parasitism within the order. We conducted a
 phylogenomic analysis on the order Psocodea utilizing both transcriptome
 and genome sequencing to obtain a data set of 2,370 orthologous genes. All
 phylogenomic analyses, including both concatenated and coalescent methods
 suggest a single origin of parasitism within the order Psocodea, resolving
 conflicting results from previous studies. This phylogeny allows us to
 propose a stable ordinal level classification scheme that retains
 significant taxonomic names present in historical scientific literature
 and reflects the evolution of the group as a whole. A dating analysis,
 with internal nodes calibrated by fossil evidence, suggests an origin of
 parasitism that predates the K-Pg boundary. Nucleotide compositional
 biases are detected in third and first codon positions and result in the
 anomalous placement of the Amphientometae as sister to Psocomorpha when
 all nucleotide sites are analyzed. Likelihood-mapping and quartet sampling
 methods demonstrate that base compositional biases can also have an effect
 on quartet-based methods.
description: Please refer to the publication for details.
DOI: 10.5281/zenodo.17981383
title: Critical Reassessment of Gallium and Reactor Neutrino Anomalies in 3+2 Sterile Neutrino Models: Incorporating Recent Exclusions, Bayesian Analyses, and Alternative Hypotheses

description: This study proposes and critically evaluates a 3+2 sterile neutrino framework to address the gallium anomaly (20--24% deficit at >4σ from BEST and prior experiments [barinov2022results,semenov2023revised]) and the reactor antineutrino anomaly (reduced to <1.5σ with refined flux models [giunti2022reactor,berryman2022reactor]). The model includes an eV-scale sterile neutrino for anomalies and a keV-scale for dark matter, but recent exclusions from MicroBooNE, KATRIN, and SBN at ≥95% CL [microboone2021,abrams2022katrin,acero2022nova] render it untenable. We perform Bayesian fits to raw BEST data, yielding posterior odds of 1:15 against sterile vs. cross-section alternatives. Oscillation parameters (Δm²₄₁ = 1.3 ± 0.5 eV², sin² 2θ₁₄ = 0.26 ± 0.09) are tested against Lyman-α bounds (m_th > 4.1 keV [irsic2017lyman]) and NuSTAR limits [roach2020nustar]. Numerical simulations confirm 20.5% monoenergetic gallium deficit and 16.3% spectrum-averaged, with χ²/d.o.f. = 1.12. Matter effects are negligible (A ∼ 10⁻¹⁵ eV²), proven via exact MSW derivations. For keV sterile, corrected QKE yield Ω_s h² ≈ 0.12, but ΔN_eff > 0.3 tensions persist. Monte Carlo sensitivity (10,000 draws) quantifies degeneracies. We derive self-interaction potentials and TOV modifications rigorously. Supernova and neutron star implications are detailed, but limited by exclusions. Falsifiable predictions for DUNE and XRISM are provided, favoring non-sterile resolutions like wave function corrections [semenov2023revised]. This work quantifies systematics, advocating peer-reviewed alternatives with full derivations and verifiable codes.
DOI: 10.5281/zenodo.18395684
title: Critical Reassessment of Gallium and Reactor Neutrino Anomalies in 3+2 Sterile Neutrino Models: Incorporating Recent Exclusions, Bayesian Analyses, and Alternative Hypotheses

description: This study proposes and critically evaluates a 3+2 sterile neutrino framework to address the gallium anomaly (20--24% deficit at >4σ from BEST and prior experiments [barinov2022results,semenov2023revised]) and the reactor antineutrino anomaly (reduced to <1.5σ with refined flux models [giunti2022reactor,berryman2022reactor]). The model includes an eV-scale sterile neutrino for anomalies and a keV-scale for dark matter, but recent exclusions from MicroBooNE, KATRIN, and SBN at ≥95% CL [microboone2021,abrams2022katrin,acero2022nova] render it untenable. We perform Bayesian fits to raw BEST data, yielding posterior odds of 1:15 against sterile vs. cross-section alternatives. Oscillation parameters (Δm²₄₁ = 1.3 ± 0.5 eV², sin² 2θ₁₄ = 0.26 ± 0.09) are tested against Lyman-α bounds (m_th > 4.1 keV [irsic2017lyman]) and NuSTAR limits [roach2020nustar]. Numerical simulations confirm 20.5% monoenergetic gallium deficit and 16.3% spectrum-averaged, with χ²/d.o.f. = 1.12. Matter effects are negligible (A ∼ 10⁻¹⁵ eV²), proven via exact MSW derivations. For keV sterile, corrected QKE yield Ω_s h² ≈ 0.12, but ΔN_eff > 0.3 tensions persist. Monte Carlo sensitivity (10,000 draws) quantifies degeneracies. We derive self-interaction potentials and TOV modifications rigorously. Supernova and neutron star implications are detailed, but limited by exclusions. Falsifiable predictions for DUNE and XRISM are provided, favoring non-sterile resolutions like wave function corrections [semenov2023revised]. This work quantifies systematics, advocating peer-reviewed alternatives with full derivations and verifiable codes.
DOI: 10.5061/dryad.v6wwpzgsv
title: Data from: Stopover refueling, movement, and departure decisions in the White-throated Sparrow: the influence of intrinsic and extrinsic factors during spring migration

description: 1. Differential migration timing between sex or age classes are examples
 of how migratory movement strategies can differ among sub-groups within a
 population. However, in songbirds, evidence for intrinsic differences in
 en route migratory behavior is often mixed, suggesting that the local
 environmental context may play a role in accentuating or diminishing
 patterns. 2. We evaluated how multiple intrinsic and extrinsic variables
 influenced refueling rates, local movement behavior, and departure
 decisions in the White-throated Sparrow (Zonotrichia albicollis) during
 spring migration. This species exhibits a unique genetically-based plumage
 dimorphism, providing a unique class of individual in which to evaluate
 patterns and processes of differential migration, in addition to sex, age,
 and migration distance. 3. At a migratory stopover site, plasma metabolite
 analysis was used to quantify individual variation in stopover refueling
 rate. In after second year adults, automated and manual radio telemetry
 was used to quantify daily activity timing, daily movement distances,
 stopover duration, and departure time. Arrival timing to the stopover site
 was determined using capture data. Non-breeding and previous
 breeding/natal latitude were determined using analysis of hydrogen
 isotopes in claws and feathers. 4. Males arrived at the stopover site 11
 days on average before females, but no difference in migration timing was
 observed between plumage morph or age classes. After second year adults
 with more southern previous breeding latitudes arrived at stopover earlier
 whereas second year birds making their first return migration arrived at
 stopover in an inverse relationship to non-breeding latitude. Stopover
 refueling rate did not differ between ages, sexes, or plumage morphs, and
 daily departure probability of adults was higher under warmer temperatures
 and favorable tailwinds. White-striped morphs moved greater distances
 during stopover, initiated daily activity earlier in the morning, and
 departed for migration earlier in the evening than tan-striped morphs. 5.
 Our results show that while individual phenotype can influence some
 aspects of local stopover-scale movement behavior, evidence for
 differential stopover behavior was weak. Differential migration timing is
 unlikely to result from intrinsic differences in en route refueling rate
 and departure decisions, especially because the latter is strongly
 influenced by meteorological conditions. 
description: Complete data was not collected for every bird processed during
 the spring of 2017. As such, there are missing values in the WTSP dataset.
 Missing values in the manual telemetry dataset are primarily associated
 with the time of release at the release point.
DOI: 10.5061/dryad.bvq83bk6c
title: Data sets used in the manuscript titled "Ecosystem-level energy and water budgets are resilient to canopy mortality in sparse semi-arid biomes"

description: This data set reports water and energy fluxes, soil water content and sap
 fluxes measured at two adjacent pinon-juniper woodlands in central New
 Mexico from January 2009 to December 2016.  This data set was
 used for the analysis in the manuscript titled “Ecosystem-level energy and
 water budgets are resilient to canopy mortality in sparse semi-arid
 biomes” submitted to JGR-Biogeosciences.
DOI: 10.5061/dryad.47d7wm3b4
title: Long-term outcome in patients with aneurysmal subarachnoid hemorrhage requiring mechanical ventilation

description: Patients with aneurysmal subarachnoid hemorrhage (aSAH) requiring
 mechanical ventilation have distinctive outcome from less severe patients.
 We aimed to precise the long-term outcome of these patients with critical
 aSAH and to identify factors associated with poor outcome. We conducted a
 retrospective study in a neuro-ICU of a university hospital in France.
 Patients with aSAH requiring mechanical ventilation hospitalized from 2010
 to 2015 were included. At least one year after the initial bleeding,
 survival and degree of disability were measured using the modified Rankin
 Scale (mRS) via  phone interviews. A multivariate logistic
 regression analysis was performed to define independent factors associated
 with poor outcome defined as mRS&gt;2. Among aSAH patients requiring
 assisted ventilation, two-thirds of them had survived at one year, and
 one-third had a good long-term outcome. Attention should be paid to DCI,
 which is a treatable independent factor associated with poor outcome.
description: An analytic retrospective study was conducted in an academic
 center in Montpellier, France. This observational study was performed
 according to the STROBE guidelines.