cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.brv15dvf8
title: When is warmer better? Disentangling within- and between-generation effects of thermal history on early survival

description: Understanding the fitness consequences of thermal history is necessary to
 predict organismal responses to global warming. This is especially
 challenging for ectotherms with complex life cycles, where distinct life
 stages can differ in thermal sensitivity, acclimate to different thermal
 environments, and accrue responses to acclimation within and between
 generations. Although acclimation is often hypothesized to benefit
 organisms by helping them (or their offspring) to compensate for negative
 impacts of environmental change, mixed support for this hypothesis
 highlights the need to assess alternatives. Assessments that explicitly
 dissect responses across life stages and generations, however, remain
 limited.  We assess alternative hypotheses of acclimation (none,
 beneficial, colder-is-better, and warmer-is-better) within and between
 generations of a marine tubeworm whose vulnerability to warming rests on
 survival at early planktonic stages (gametes, embryos, and larvae). First,
 we acclimate parents, gametes, and embryos to ambient and projected warmer
 temperatures (17°C and 22°C) factorially by life stage. Next, we rear
 offspring with differing acclimation histories to the end of larval
 development at test temperatures from 10°C to 28°C (lower and upper
 survival limits, respectively). Last, we estimate thermal survival curves
 for development and compare them among thermal histories.   We
 show that survival curves are most responsive to parental acclimation
 followed by acclimation at embryogenesis, but are buffered against
 acclimation at fertilization. Moreover, curves respond independently to
 acclimation within and between generations and respond largely as
 predicted by the warmer-is-better hypothesis, despite the semblance of
 beneficial acclimation after successive doses of warmer
 temperature.  Our study demonstrates the varied nature of thermal
 acclimation and the importance of considering how responses aggregate
 across complex life cycles when predicting vulnerability to warming.
DOI: 10.5061/dryad.n2z34tn2h
title: Data from: Conserving habitat for migratory ungulates: how wide is a migration corridor?

description: Conserving migratory ungulates relies on the analysis of GPS collar data
 and associated maps of migration corridors to inform management and policy
 actions. Current methods for identifying migratory corridors use complex
 statistical models designed to account for movement uncertainty rather
 than estimating the amount of space required by animals to migrate.
 Further, such methods can complicate conservation efforts by producing
 highly variable corridor widths and non-contiguous corridors that do not
 fully connect seasonal ranges. To remedy this, we propose an intuitive
 line buffer approach for delineating individual migration corridors that
 is simple to implement and focuses on the functional corridor widths
 needed by migratory ungulates.  By buffering a line that connects
 successive GPS locations, we can delineate individual migration corridors
 with consistent widths that are robust to variable parameters (GPS
 fix-rate, travel speed, tortuosity) and provide contiguous connection
 between seasonal ranges. Using a combination of expert knowledge,
 simulation, and 10-min GPS collar data collected from mule deer
 (Odocoileus hemionus) and pronghorn (Antilocapra americana), we suggest
 400 to 600 m are reasonable estimates of functional migration corridor
 widths for individuals of those species. Our line buffer approach is
 intended to simplify migration corridor delineation, improve transparency,
 and encourage a broader discussion of functional corridor widths. These
 considerations help advance efforts to conserve habitat within migration
 corridors and prioritize conservation efforts within a single corridor or
 across multiple corridors.
description: We collected 10-min data from GPS collars (model G5-D; Advanced
 Telemetry Systems, Isanti, MN) for a single spring migration in 2022 from
 2 female mule deer and 2 female pronghorn in Wyoming, USA. Animals were
 captured using a netgun shot from a helicopter in March 2022 following
 capture and handling methods approved by the University of Wyoming Animal
 Care and Use Committee (protocols 20200302MK00411-01 and
 20210301MK00461-02) and Wyoming Department of Game and Fish (permits
 33-937 and 33-1162). 
description: The dataset is a comma-delimited file with 5 columns and 6,444
 rows. The species column represents either mule deer
 (<em>Odocoileus</em> <em>hemionus</em>) or
 pronghorn (<em>Antilocapra</em>
 <em>americana</em>). The id column represents a unique animal
 id. The x and y columns represent easting and northing of the relocations
 in ESPG: 5072. The date column represents the date and time (in
 'Year-Month-Day Hour:Minute:Second' format) of the relocation in
 local time (MST or MDT). The dataset is only the 10-min relocation data
 from the 4 animals during their spring migration in 2022. Note that these
 data do not encompass the entire spring migration of these animals, as we
 remotely programmed the collars (which have a delay of a day or two) to
 collect 10-min data after they seemingly began migrating.
DOI: 10.5061/dryad.7pvmcvf00
title: Pesticide exposure enhances dominance patterns in a zooplankton community

description: Exposure to pesticides can profoundly alter community dynamics. It is
 expected that dominance patterns will be enhanced or reduced depending on
 whether the dominant species is less or more sensitive to the pesticide
 than the subdominant species. Community dynamics are, however, also
 determined by processes linked to population growth as well as competition
 at carrying capacity. Here, we used a mesocosm experiment to quantify the
 effect of chlorpyrifos exposure on the population dynamics of four
 cladoceran species (Daphnia magna, D. pulicaria, D. galeata and
 Scapholeberis mucronata) in mixed cultures, testing for direct effects of
 chlorpyrifos and indirect effects mediated by interactions with other
 species on timing of population growth and dominance at carrying capacity.
 We also quantified whether the pesticide-induced changes in community
 dynamics affect top-down control of phytoplankton. By adding a treatment
 in which we used different genotype combinations of each species, we also
 tested to what extent genetic composition affects community responses to
 pesticide exposure. Immobilization tests showed that D. magna is the least
 sensitive to chlorpyrifos of the tested species. Chlorpyrifos exposure
 first led to a reduction in the abundance of D. galeata to the benefit of
 D. pulicaria, and subsequently to a reduction in densities of D. pulicaria
 to the benefit of D. magna. This resulted in D. magna being more dominant
 in the pesticide than in the control treatment by the end of the
 experiment. There was no effect of genotypic differences on community
 patterns, and top-down control of phytoplankton was high in all
 treatments. Our results suggest that in this community dominance patterns
 are enhanced in line with the observed among-species differences in
 sensitivity to the pesticide. Our results also show that the development
 of the community in the pesticide treatment is a complex interaction
 between direct and indirect effects of the pesticide.
DOI: 10.5061/dryad.4tmpg4fgq
title: Data from: A test of the green wave hypothesis in omnivorous brown bears across North America

description: Herbivorous animals tend to seek out plants at intermediate phenological
 states to improve energy intake while minimizing consumption of fibrous
 material. In some ecosystems, the timing of green-up is heterogeneous and
 propagates across space in a wave-like pattern, known as the green wave.
 Tracking the green wave allows individuals to prolong access to
 higher-quality forage. While there is a plethora of empirical support for
 such behavior in herbivorous taxa, the green wave hypothesis (GWH) is
 nuanced based on factors such as body morphometrics and digestive
 capacity. Furthermore, little is known about whether other taxa, such as
 omnivores, track the green wave. Our objective was to assess whether the
 GWH can be extended to explain the movements of omnivores. Using GPS
 collar data from seven populations (n = 127 individuals) of brown bears
 (Ursus arctos) across their entire North American range, we first tested
 whether bears tracked the green wave. Using conditional resource selection
 functions, we found that variation in proxies of vegetative forage quality
 better-explained movement and habitat selection than proxies of forage
 biomass in over half of the bears in our study, providing evidence of
 green wave tracking. Second, we assess factors that explained variation in
 green wave tracking using linear mixed-effects models. Green wave tracking
 in brown bears was explained by the variation in availability of green-up
 within spring home ranges, and how green-up transitioned across those home
 ranges. Our results demonstrate that the GWH can partially explain
 movement of a non-migratory omnivorous species, extending the generality
 of the GWH as a broad predictor of animal space use. The green wave is
 another resource wave brown bears track, and our findings help predict
 brown bear space use, which can be used to guide conservation and habitat
 restoration efforts.
description: This dataset was developed by merging GPS location data from
 collared grizzly bears with environmental data. See methods section of
 Bowersock et al. 2023 in Ecography for details. 
description: Both datasets do not require specific programs or software to
 open. They are in the comma-delimited format (CSV).
DOI: 10.5061/dryad.70rxwdc3x
title: Genetic differentiation and evolution of broad-leaved evergreen shrub and tree varieties of Daphniphyllum macropodum (Daphniphyllaceae)

description: Tree form evolution is an important ecological specialization for woody
 species, but its evolutionary process with adaptation is poorly
 understood, especially on the microevolutionary scale. Daphniphyllum
 macropodum comprises two varieties: a tree variety growing in a warm
 temperate climate with light snowfall and a shrub variety growing in a
 cool temperate climate with heavy snowfall of Japan. Chloroplast DNA
 variations and genome-wide single nucleotide polymorphisms across D.
 macropodum populations and D. teijsmannii as an outgroup were used to
 reveal evolutionary process of the shrub variety. Population genetic
 analysis indicated that the two varieties diverged but were weakly
 differentiated. Approximate Bayesian computation analysis supported a
 scenario, which assumed migration between the tree variety and the
 southern populations of the shrub variety. We found migration between the
 two varieties where the distributions of the two varieties are in contact,
 it is concordant with higher tree height in the southern populations of
 the shrub variety than the northern populations. The genetic divergence
 between the two varieties was associated with snowfall. The heavy snowfall
 climate is considered to have developed since the middle Quaternary in
 this region. The estimated divergence time between the two varieties
 suggests that the evolution of the two varieties may be concordant with
 such paleoclimatic change.
description: Please read the README document ("README.md") and the
 accompanying published article: Yoichi W, Matsuzawa S, Tamaki I, Nagano
 AJ, Oh S-H. 2023. Genetic differentiation and evolution of broad-leaved
 evergreen shrub and tree varieties of Daphniphyllum macropodum
 (Daphniphyllaceae). Heredity.
DOI: 10.5061/dryad.qjq2bvqn0
title: The weaken-ﬁll-repair model for cell budding: Linking cell wall biosynthesis with mechanics

description: The interplay between cellular mechanics and other biochemical processes
 leading to the cell cycle is poorly understood. Here, we propose a
 quantitative model of the mechanism of cell budding, particularly for
 Saccharomyces cerevisiae, as a ''weaken-ﬁll-repair''
 process. This model links Newtonian mechanics over the cell wall with
 biochemical processes that change the mechanical properties of the wall.
 Our model shows that: (1) The oscillatory behavior in the size of the
 mother compartment during cell division, as observed experimentally, is an
 inevitable consequence of the budding mechanism; (2) The asymmetry of cell
 division is necessary for the daughter cell to maintain mechanical
 stiffness; (3) Although different aspects of a cell are strictly
 constrained and intricately interconnected, the budding process is
 governed by a single reduced parameter that, when at an appropriate value,
 can automatically achieve homeostasis. Our quantitative model of the
 evolution of cell walls and their impact on cell division could provide
 valuable insights into cell morphology from a system perspective. This
 knowledge could be instrumental in developing effective antimicrobial
 treatments against microorganisms with cell walls and even in building
 synthetic cells.
DOI: 10.5061/dryad.7h44j100g
title: Diet of Curruca melanocephala in north Portugal

description: Metadata of foraging interaction between Sardinian Warblers and animal and
 plant prey items in north Portugal. Data was obtained through DNA
 metabarcoding analysis using the primers FwhF2-R2n and UniPlantF-R.
 Contains the diet of 234 individuals sampled across 12 months and four
 sites. It includes the code to replicate the methods described in the
 article "DNA metabarcoding, diversity partitioning and null models
 reveal mechanisms of seasonal trophic specialisation in a Mediterranean
 warbler" currently in the process of publishing.
description: # Diet of Curruca melanocephala in north Portugal Description: Metadata of
 foraging interaction between Sardinian Warblers and animal and plant prey
 items in north Portugal. Data was obtained through DNA metabarcoding
 analysis using the primers FwhF2-R2n and UniPlantF-R. Contains the diet of
 234 individuals sampled across 12 months and four sites. Each row belongs
 to an interaction between one sample and a haplotype (prey item). It
 includes the code to replicate the methods described in the article
 "DNA metabarcoding, diversity partitioning and null models reveal
 mechanisms of seasonal trophic specialisation in a Mediterranean
 warbler" published in Molecular Ecology (2023). Required software: R.
 Cite as: \[dataset] Velarde-Garcéz, D., Mata, V. A., Beja, P., &
 Silva, L. P. (2023). Data from: DNA metabarcoding, diversity partitioning
 and null models reveal mechanisms of seasonal trophic specialisation in a
 Mediterranean warbler. Dryad Digital Repository.
 Columns: * primerset: name
 of primer * seq: nucletotide sequence of the identified haplotype *
 seq.len: number of nucleotides in the sequence * sample: sample code *
 clean.reads: number of reads after filtering of the haplotype in the
 sample * kingdom: kingdom identification according to BOLD * phylum:
 phylum identification according to BOLD * class: class identification
 according to BOLD * order: order identification according to BOLD *
 family: family identification according to BOLD * genus: genus
 identification according to BOLD * species: species identification
 according to BOLD * id.level: lowest taxonomic level obtained in the
 identification. * match.bold: percentage of the match according to BOLD. *
 match.ncbi: percentage of the match according to ncbi. * otu.id:
 Operational Taxonomic Unitd ID * date: Date of the sample collection *
 month.cat: Month category of the sample collection * C/R: Capture or
 Recapture * ring: Code of the individual * age.ca: Category of age (1cy:
 first year birds; 2cy+ second year birds or older) * sex: sex (M: male; F:
 female; unk: unknown) * site: Locality were the sample was collected. *
 interaction: sample and OTU
DOI: 10.5061/dryad.t4b8gtj6q
title: Competition is a major limiting factor of refueling in migratory passerines during stopover

description: For an avian migrant, refueling capacity attainable during stopovers
 governs the entire migration schedule and, ultimately, its fitness.
 Specifically, timely replenishing energy stores is critical when migration
 involves crossing ecological barriers, within which refueling may be
 limited. Here, we tested the hypothesis that fuel deposition rates (FDRs)
 of migratory passerines within barrier-edge stopover sites are constrained
 by the density of potential competitors, irrespective of migration season,
 phenology, and local environmental conditions. We also evaluated diverse
 intra- and inter-specific competition scenarios and explored a potential
 mediation of density-dependence by environmental factors. The analyzed
 data, collected by us over 13 consecutive years (2009–2022), contains
 information on seven species of long-distance migratory insectivorous
 passerines measured within eight desert-edge habitats throughout autumn
 and spring migrations. As predicted, our analyses revealed negative
 density-dependence regulation of FDRs, consistent across species and
 migration seasons. Notably, bird density exerted its effect above and
 beyond the other factors known to influence FDR, such as relative ambient
 temperature, phenology, temporal progress of stopover, and body mass next
 to landfall. As expected, FDR increased at higher relative ambient
 temperatures and with the stopover’s progress. In spring, FDR also rose as
 the season advanced. These findings signify the substantial impact of
 competition on the refueling performance of migratory passerines during
 their stopover on an ecological barrier’s edge, acting over and above the
 other environmental factors. The detected importance of competition and
 its interrelation with other predictors provides an insight into
 stopover’s functioning; environmentally imposed and inescapable
 interspecific interference is thus a significant limiting factor of FDR, a
 deleterious relationship potentially remediable by informed habitat
 restoration and planning.
DOI: 10.25338/b8gs95
title: Documenting twenty years of the contracted labor-intensive forestry workforce on National Forest System lands in the United States

description: This paper presents the first nationwide analysis detailing the scope and
 scale of labor-intensive forestry contracts performed on National Forest
 System lands and examines the businesses contracted, location and types of
 work performed, and distance traveled by businesses between 2001 and 2020.
 During the study period, 61,698 contracts were awarded to 7,896
 businesses, totaling $12,917,907,763, to perform labor-intensive forestry
 work, with most work being contracted for wildfire-related activities.
 Businesses were typically located in western states and nonminority owned
 businesses received the majority of contracts. Of minority-owned
 businesses, Hispanic American–owned businesses received the most
 contracts. The median distance that businesses traveled to accomplish work
 increased significantly through time but differed by business type.
 Understanding the scope and work of businesses awarded contracts provides
 insight into the workforce and its relationship to marginalized
 populations. Strategic investment in this workforce may have widespread
 impacts on federal, state, and local economies and the livelihoods of
 forest workers.
description: All contract data reports with the USFS listed as the contracting
 agency between federal fiscal years 2001 and 2020 from the System for
 Award Management (SAM.gov), the federally managed website that
 consolidates data from the Federal Procurement Data System. All data
 processing, analyses, and visualization were completed using R v4.1.3 in
 RStudio v2022.2.3.492 using the dplyr, ggplot2, sf, and FSA
 packages.
description: Please see the README document and the accompanying published
 article: Deak, A., Huber-Stearns, H., Crandall, M., Poudel, K., Davis,
 E.J., Coughlan, M.R., and Wilmsen, C. 2023. Documenting twenty years of
 the contracted labor-intensive forestry workforce on National Forest
 System lands in the United States. Journal of Forestry. Accepted. DOI:
 10.1093/jofore/fvad026
DOI: 10.25349/d9k330
title: Measures and models of visual acuity in epipelagic and mesopelagic teleosts and elasmobranchs

description: Eyes in low-light environments typically must balance sensitivity and
 spatial resolution. Vertebrate eyes with large "pixels" (e.g.
 retinal ganglion cells with inputs from many photoreceptors) will be
 sensitive but provide coarse vision. Small pixels can render finer detail,
 but each pixel will gather less light and thus have poor signal
 relative-to-noise, leading to lower contrast sensitivity. This balance is
 particularly critical in oceanic species at mesopelagic depths (200-1000
 m) because they experience low light and live in a medium that
 significantly attenuates contrast. Depending on the spatial frequency and
 inherent contrast of a pattern being viewed, the viewer’s pupil size and
 temporal resolution, and the ambient light level and water clarity, an
 optimal visual acuity exists that maximizes the distance at which the
 pattern can be discerned. We develop a model that predicts this optimal
 acuity for common conditions in the open ocean, and compare it to visual
 acuity in marine teleost fishes and elasmobranchs found at various depths
 in productive and oligotrophic waters. Visual acuity in epipelagic and
 upper mesopelagic species aligned well with model predictions, but species
 at lower mesopelagic depths (&gt;600 m) had far higher measured
 acuities than predicted. This is consistent with the prediction that
 animals found at lower mesopelagic depths operate in a visual world
 consisting primarily of bioluminescent point sources, where high visual
 acuity helps localize targets of this kind. Overall, the results suggest
 that visual acuity in oceanic fish and elasmobranchs is under
 depth-dependent selection for detecting either extended patterns or point
 sources.
description: The data analyzed here are primarily derived from a literature
 synthesis in which we searched for published measures of visual acuity
 (measured morphologically) in fishes. We also searched for published
 daytime depth ranges and values of lens diameter for each species. Fish
 were assigned habitat designations based on information from FishBase.org
 and confirmed by author TS. Some data are also the result of an optical
 model created to determine optimal visual acuity under a set of visual
 parameters. Lastly, phylogenies used to make Figure 3 were derived from
 Rabosky et al. 2018 (for teleost fishes) and VertLife.org (for
 elasmobranchs).
description: All files are .csv files, openable with Microsoft Excel. Custom
 analysis codes can be run using the open-source R coding
 software.