cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fxpnvx0wq
title: COMSOL simulation & example datasets for: Nonuniform structural properties of wings confer sensing advantages

description: Sensory feedback is essential to both animals and robotic systems for
 achieving coordinated, precise movements. Mechanosensory feedback, which
 provides information about body deformation, depends not only on the
 properties of sensors but also on the structure in which they are
 embedded. In insects, wing structure plays a particularly important role
 in flapping flight: in addition to generating aerodynamic forces, wings
 provide mechanosensory feedback necessary for guiding flight while
 undergoing dramatic deformations during each wingbeat. However, the role
 that wing structure plays in determining mechanosensory information is
 relatively unexplored. Insect wings exhibit characteristic stiffness
 gradients and are subject to both aerodynamic and structural damping. Here
 we examine how both of these properties impact sensory performance, using
 finite element analysis combined with sensor placement optimization
 approaches. We show that wings with nonuniform stiffness exhibit several
 advantages over uniform stiffness wings, resulting in higher accuracy of
 rotation detection and lower sensitivity to the placement of sensors on
 the wing. Moreover, we show that higher damping generally improves the
 accuracy with which body rotations can be detected. These results
 contribute to our understanding of the evolution of the nonuniform
 stiffness patterns in insect wings, as well as suggest design principles
 for robotic systems.
DOI: 10.5061/dryad.m0cfxpp7c
title: Individual variation in spawning migration timing in a salmonid fish—exploring roles of environmental and social cues

description: Describing and explaining patterns of individual animal behaviors in situ,
 and their repeatability over the annual cycle, is an emerging field in
 ecology owing largely to advances in tagging technology. We describe
 individual movements of adult Sakhalin taimen, Parahucho perryi, an
 endangered salmonid fish, in the headwaters of a river in northern Japan
 during the spring spawning season over two years. Migration timing,
 separated into stages prior to, during, and following the spawning period,
 was found to be more consistent and repeatable for females than males. We
 hypothesized that the observed coordinated movement within seasons, and
 repeatability in migration timing across seasons, could result from 1)
 individual-specific responsiveness resulting from endogenous, biological
 traits that are mediated by environmental factors, or 2) social
 interactions among comigrating individuals. We found that water
 temperature and water level experienced by fish near the river mouth
 approximately a week before arrival at the spawning ground explained
 variability in run timing between years for females but not males. We
 found no evidence of conspecific attraction or repulsion resulting from
 social interactions among the spawners and post-spawners. We conclude that
 individual-specific responsiveness to environmental cues was the likely
 mechanism underpinning the observed migration timing and movement
 patterns.
description: R Markdown codes uploaded can be viewed and executed by using
 RStudio software.
DOI: 10.5061/dryad.x3ffbg7pf
title: Chamaeleo africanus DNA sequencing purity results and statistics

description: Conservation of wildlife often depends on high quality molecular data to
 establish reliable species identification. Traditional approaches in
 extracting material (DNA) for phylogenetic studies on chameleons have
 relied on removed, euthanized or preserved/museum specimens, while field
 sampling usually takes the form of tail clippings from living individuals
 and their subsequent release. In this article, we propose an alternative
 to these approaches for field sampling, towards isolation of nuclear and
 mitochondrial DNA with oral (buccal) swabs, a methodology already been
 demonstrated as effective in other taxa. Options of sampling, storage,
 transport, extraction of DNA are presented and the quality and quantity of
 extracted material (using venipuncture as a positive control) was
 demonstrated as sufficient for downstream applications, including
 sequencing thereby presenting a practical field alternative. The
 advantages and limitations of this minimally invasive and non-destructive
 method applied to Chamaeleo africanus are further discussed.
description: Quality scores and statistical evaluation of 16S mtDNA and
 RAG1nuDNA amplicons between whole blood and buccal swab samples.
 Sequencing quality scores (defined as Q = -10log10(e)) were obtained from
 the sequencing software.
DOI: 10.5061/dryad.0p2ngf253
title: Data from: Influence of abiotic and biotic factors on benthic marine community composition, structure and stability: a multidisciplinary approach to molluscan assemblages from the Miocene of northern Germany

description: The Miocene mica-clay deposits of Groß Pampau (northern Germany) are well
 known for their diverse assemblages of marine mammals, particularly
 whales. Despite numerous systematic and biostratigraphic studies, an
 in-depth palaeoecological analysis of its diverse molluscan assemblages
 and a comprehensive palaeoenvironmental reconstruction are lacking. Here,
 we integrated new faunal, sedimentological, and geochemical data to
 reconstruct the marine palaeo-ecosystem of the late Miocene sedimentary
 succession of Groß Pampau, and to identify the drivers controlling the
 composition, ecological structure and temporal dynamics of its
 macrobenthic molluscan assemblages. Fossil evidence, coupled with analyses
 of clay mineral composition, grain size distribution, and geochemical data
 (total organic carbon, total nitrogen, δ13C, δ18O, δ15N of sediment and
 shells), suggest a warm-temperate, mesotrophic, low-energy, offshore
 marine setting mostly below storm wave base and a pronounced
 surface-to-bottom water temperature gradient. Low variability in
 sedimentological and geochemical signals indicates generally stable
 physico-chemical conditions, whereas occurrences of opportunistic species
 (Varicorbula gibba) point at occasionally less favourable bottom
 conditions, possibly related to transient hypoxia. Canonical
 correspondence analysis reveals that the distribution of molluscan
 assemblages correlates with total organic carbon and nitrogen content,
 suggesting organic matter availability at the seafloor as a controlling
 factor. A pattern of repetitive punctuated stasis of molluscan assemblages
 is defined by the temporal persistence in taxonomic and ecological
 composition, occasionally interrupted by shifts to a different faunal
 configuration. We suggest that both stable environmental conditions and
 biotic interactions, i.e. the top-down control exerted by carnivorous
 gastropods and environmental modification by ubiquitous burrowing deposit
 feeders, probably contributed to the observed temporal stability. Whereas
 comparison with Miocene molluscan assemblages of Gram, Denmark, revealed
 differences in the presence and relative abundance of genera, functional
 congruence indicates that offshore benthic ecosystems of the southern
 North Sea Basin functioned similarly.
DOI: 10.5061/dryad.37pvmcvpz
title: Are trapping data suited for home-range estimation?

description: Modern home-range estimation typically relies on data derived from
 expensive radio- or GPS-tracking. Although trapping represents a low-cost
 alternative to telemetry, there lacks an evaluation of the performance of
 home-range estimators on trap-derived data. Using simulated data, we
 evaluate three variables reflecting the key trade-offs ecologists face
 when designing a trapping study: 1) the number of observations obtained
 per individual, 2) the trap density, and 3) the proportion of the home
 range falling inside the trapping area. We compare the performance of five
 home-range estimators (MCP, LoCoH, KDE, AKDE, bicubic interpolation). We
 further explore the potential benefits of combining these estimators with
 asymptotic models, which leverage the saturating behavior of changes in
 the estimated home-range area as the number of observations increases to
 improve accuracy, as well as different data ordering procedures. We then
 quantified the bias in home-range size under the different scenarios
 investigated. The number of observations and the proportion of the home
 range within the trapping grid were the most important predictors of the
 accuracy and the precision of home-range estimates. The use of asymptotic
 models helped obtain accurate estimates at smaller sample sizes, while
 distance-ordering improved the precision and asymptotic consistency of
 estimates. While AKDE was the best-performing estimator under most
 conditions evaluated, bicubic interpolation was a viable alternative under
 common real-world conditions of low trap density and area covered. A case
 study using empirical data from white-tailed deer in Florida and another
 from jaguars in Belize demonstrated support for the findings of our
 simulation results. Although researchers with trap data often overlook
 home-range estimation, our results indicate that these data have the
 capacity to yield accurate estimates of home-range size. Trapping data can
 therefore lower the economic costs of home-range analysis, potentially
 enlarging the span of species, researchers and questions studied in
 ecology and conservation.
description: Using an I.I.D. movement model, we simulated captures in
 different trapping conditions and compared the home range size obtained
 with different methods. We analyzed real-world trapping data for
 white-tailed deer (Florida) and jaguars (Belize) from publicly available
 repositories and compared the home range sizes obtained with those
 predicted based on our simulations. 
description: All data can be opened with R. All R scripts to create and
 analyze the data can be found at https://github.com/llsociasmartinez/home-range-trapping-data.
DOI: 10.5061/dryad.b5mkkwhh7
title: Data from: Demographic consequences of an extreme heatwave are mitigated by spatial heterogeneity in an annual monkeyflower

description: This repository includes three different datasets as well as associated
 readme files. One dataset contains fitness data for
 individuals planted within a common garden experiment planted near the
 Browder Ridge Trailhead, Oregon USA in 2019. The second dataset contains
 fecundity data from 12 populations in the Central Oregon Cascades in 2018
 and 2019. The final dataset contains demographic and phenological
 data from eleven populations in the Central Oregon Cascades in
 2019. 
description: Please see methodology in McDonald et al. 2023 as well as
 information within ReadMe files. Briefly, this was fitness and phenology
 data collected from a field common garden experiment and natural
 populations in central Oregon.
DOI: 10.5061/dryad.b2rbnzskk
title: Genetic evidence for widespread population size expansion in North American boreal birds prior to the Last Glacial Maximum

description: Pleistocene climate cycles are well known to have shaped contemporary
 species distributions and genetic diversity. Northward range expansions in
 response to deglaciation following the Last Glacial Maximum (LGM; ~21,000
 years ago) have been surmised to lead to population size expansions in
 terrestrial taxa and changes in seasonal migratory behaviour. Recent
 findings, however, suggest that some northern temperate populations may
 have been more stable than expected through the LGM. We modelled the
 demographic history of twenty co-distributed boreal-breeding bird species
 of North America from full mitochondrial gene sets and species-specific
 molecular rates. We used these demographic reconstructions to test how
 species with different migratory strategies were affected by glacial
 cycles. Our results suggest that effective population sizes increased in
 response to deglaciation during the middle Wisconsin period (~45,000 years
 ago) whereas genetic diversity was maintained throughout the LGM despite
 shifts in geographic range. We conclude that earlier glacial cycles prior
 to the LGM have most strongly shaped contemporary genetic diversity in
 these high-latitude species. We did not find differences in historic
 population dynamics between species differing in migratory behaviour,
 contributing to growing evidence that major switches in migratory strategy
 during the Last Glacial Maximum are unnecessary to explain contemporary
 migratory patterns.
DOI: 10.5061/dryad.zpc866tcd
title: Gut microbiome composition associated with Plasmodium infection in the Eurasian tree sparrow

description: Recent expansion of microbiome research has uncovered connections between
 resident microbial communities and blood parasite risk, establishing the
 potential for microbial disease treatments such as probiotics in the
 future. However, this field has largely focused on humans and model
 organisms, leaving much unknown about how microbial communities might
 directly or indirectly impact parasite infection in wild populations and
 non-mammals. To contribute to this knowledge base in wild birds, we
 collected fecal and blood samples from wild Eurasian tree sparrows (Passer
 montanus) in the United States to test for associations between blood
 parasite infection and the gut microbiome. We used a widespread molecular
 approach to test 81 samples from peripheral blood for Plasmodium and
 Haemoproteus, and we characterized the gut microbiome using fecal samples
 as a proxy. Neither alpha nor beta diversity significantly varied with
 detected Plasmodium infection. However, differential abundance analysis
 highlighted a number of significantly varying bacteria, with the greatest
 representation within the phyla Proteobacteria and Firmicutes in
 Plasmodium-infected birds. These differentially abundant taxa offer a
 starting point for experimental work establishing the relationship between
 microbial abundance and Plasmodium infection.
description: Eurasian tree sparrows were sampled in Missouri, USA during 2020
 and 2021. Fecal and blood samples were collected from each individual,
 birds were tagged with numbered color bands, and basic body measurements
 were taken. DNA was extracted from fecal and blood samples.
 Blood sample DNA was tested for haemosporidian parasites, and the
 positive amplicons were sequenced. Parasite sequence files are included
 here. Parasite lineage results are included in the metadata
 files.  Fecal sample DNA was sequenced using 16S rRNA
 gene sequencing and the sequence files are uploaded on the NCBI SRA under
 the project number PRJNA825312. R code is uploaded here as an HTML file.
 Metadata files are included for 2020 and 2021 as excel sheets. 
description: R (https://www.r-project.org/) may be used to run all of the scripts included in the Dada2_plasmodium.html file. The parasite lineages may be examined using a tool such as Gear-Genomics (https://www.gear-genomics.com/).
DOI: 10.25349/d9r626
title: Data from: Quantum disordered ground state in the triangular-lattice magnet NaRuO2

description: It has long been hoped that spin liquid states might be observed in
 materials that realize the triangular-lattice Hubbard model. However, weak
 spin–orbit coupling and other small perturbations often induce
 conventional spin freezing or magnetic ordering. Sufficiently strong
 spin–orbit coupling, however, can renormalize the electronic wavefunction
 and induce anisotropic exchange interactions that promote magnetic
 frustration. Here we show that the cooperative interplay of spin–orbit
 coupling and correlation effects in the triangular-lattice magnet NaRuO2
 produces an inherently fluctuating magnetic ground state. Despite the
 presence of a charge gap, we find that low-temperature spin excitations
 generate a metal-like term in the specific heat and a continuum of
 excitations in neutron scattering, reminiscent of spin liquid states
 previously found in triangular-lattice organic magnets. Further cooling
 produces a crossover into a different, highly disordered spin state whose
 dynamic spin autocorrelation function reflects persistent fluctuations.
 These findings establish NaRuO2 as a cousin to organic, Heisenberg spin
 liquid compounds with a low-temperature crossover in quantum disorder.
description: Data can be accessed using text editors and Microsoft Excel.
DOI: 10.5061/dryad.zkh1893dj
title: Multiplying the impact of biodiversity conservation funding using spatial exchange rates

description: Funding available to support conservation must be invested effectively
 given declines in biodiversity and ecosystem services. Unfortunately,
 conservation dollars often come with restrictions on where they can be
 spent. We introduce a method to demonstrate to supporters of conservation
 how much more could be achieved if they allow greater flexibility over
 conservation funding. Specifically, we calculate conservation exchange
 rates that summarize gains in conservation outcomes available if funding
 originating in one location can be invested elsewhere. We illustrate our
 approach by considering NGO funding and major federal programs within the
 United States and a range of conservation objectives focused on
 biodiversity and ecosystem services. We show that large improvements in
 biodiversity and ecosystem service provision are available if geographic
 restrictions on conservation funding can be loosened. We demonstrate how
 conservation exchange rates can be used to spotlight promising
 opportunities for relaxing geographic funding restrictions.
DOI: 10.5061/dryad.k3j9kd5c1
title: Flight initiation distances of birds

description: Habitat destruction and fragmentation increasingly brings humans into
 close proximity with wildlife, particularly in urban contexts. Animals
 respond to humans using nuanced anti-predator responses, especially
 escape, with responses influenced by behavioural and life history traits,
 the nature of the risk, and aspects of the surrounding environment.
 Although many studies examine associations between broad-scale habitat
 characteristics (i.e., habitat type) and escape response, few investigate
 the influence of fine-scale aspects of the local habitat within which
 escape occurs. We test the ‘habitat connectivity hypothesis’ which
 suggests that, given the higher cost of escape within less connected
 habitats (due to the lack of protective cover), woodland birds should
 delay escape (tolerate more risk) than when in more connected habitat. We
 analyse flight-initiation distances (FIDs) of five species of woodland
 birds in urban Melbourne, south-eastern Australia. A negative effect of
 habitat connectivity (the proportion of the escape route with
 shrubs/trees/perchable infrastructure) on distance fled was evident for
 all study species, suggesting a higher cost of escape associated with
 lower connectivity. FID did not vary with connectivity at the location at
 which escape was initiated (four species), apart from a positive effect of
 habitat connectivity on FID for Noisy Miner Manorina melanocephala. We
 provide some support for two predictions of the ‘habitat connectivity
 hypothesis’ in at least some taxa, and conclude it warrants further
 investigation across a broader range of taxa inhabiting contrasting
 landscapes. Increasing habitat connectivity within urban landscapes may
 reduce escape stress experienced by urban birds.
description: See Radvan et al for details.
description: The CSV file is suitable for R
DOI: 10.5061/dryad.stqjq2c72
title: CA3 axonal calcium imaging

description: Memorizing locations that are harmful or dangerous is a key capability of
 all organisms, and requires an integration of affective and spatial
 information. In mammals, the dorsal hippocampus mainly processes spatial
 information, while the intermediate to ventral hippocampal divisions
 receive affective information via the amygdala. However, how spatial and
 aversive information is integrated is currently unknown. To address this
 question, we recorded the activity of hippocampal long-range CA3 axons at
 single axon resolution in mice forming an aversive spatial memory. We show
 that intermediate CA3 to dorsal CA3 (i-dCA3) projections rapidly
 overrepresent areas preceding the location of an aversive stimulus, due to
 a spatially selective addition of newly place-coding axons, followed by a
 spatially nonspecific stabilization. This sequence significantly improves
 the encoding of location by the i-dCA3 axon population. These results
 suggest that i-dCA3 axons transmit a precise, denoised and stable signal
 indicating imminent danger to dorsal hippocampus.
description: The calcium imaging data was obtained through chronic two-photon
 awake imaging of CA3 axons within the murine hippocampus. Concurrently,
 behavioral data was gathered from the experimental setup using a
 LabView-based customized software. The analysis of the imaging data was
 performed in MATLAB, utilizing standard toolboxes, open-access toolboxes,
 and custom-written code. The treadmill behavioral data was partially
 analyzed in MATLAB and partially in Python.
description: # CA3 axonal calcium imaging
 [https://doi.org/10.5061/dryad.stqjq2c72](https://doi.org/10.5061/dryad.stqjq2c72) This data set contains the calcium imaging and behavioral data used in Nikbakht et al.,'s "**Efficient encoding of aversive location by CA3 long-range projections**". The data set contains the preprocessed imaging and behavior data for 8 animals over 8 behavioral sessions. The formatting of the data set is MATLAB files (*.m). Code available on: [https://github.com/negarniki/Efficient-encoding-of-aversive-location-by-CA3-long-range-projections](https://github.com/negarniki/Efficient-encoding-of-aversive-location-by-CA3-long-range-projections) ## Description of the data and file structure The **BigFatCluster.m** is structured in a way that the columns represent 8 animals (1-4: i-d, 5-8:d-d) over 8 behavioral sessions. **cclustID.m** contains the table guide headers. The tracked data over session pairs are named after the respective sessions. **BigFatPCA.m** contains the results of GLM analysis.