cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rr4xgxd8f
title: Data from: Predator abundance drives the association between exploratory personality and foraging habitat risk in a wild marine meso-predator.

description: 1. In recent years, the incorporation of lower levels of organization to
 the understanding of population ecology, has led to an increase in
 interest for animal personality and individual foraging specialization.
 Despite these topics investigating comparable phenomena, i.e. individual
 consistency in behavior and in food resource use respectively, they have
 rarely been investigated together. 2. Food resource use is thought to be
 at the interface between personality and life-history. More explorative
 individuals in a population, for example, are thought to increase
 encounter rates with food resources and consequently have faster growth
 than less explorative conspecifics. 3. Such hypotheses have so far only
 received partial support, and the link between personality and
 life-history is increasingly speculated to be plastic and dependent on
 spatio-temporal variation in ecological conditions. Intra-specific
 competition and/or predation risk, for example are known to influence
 foraging specialization. 4. Here, we investigated the relationship between
 exploration personality of juvenile lemon sharks (Negaprion brevirostris)
 (measured in captivity) and foraging habitat use (high risk vs low risk;
 measured via stable isotope analysis in the field) in relation to
 conspecific and predator abundance. 5. We identified predator abundance as
 the main driver for the association between foraging habitat and
 exploration personality. When predators were less abundant, increased
 exploration was associated with foraging in riskier habitats. When
 predator abundance increased, an inverse relationship occurred, with less
 explorative individuals using more dangerous habitat. 6. We conclude that
 the relationship between personality and resource use is plastic and
 context dependent, which could explain the inconclusive results of
 previous studies investigating links between personality and life-history.
description: <strong>Dataset:
 Fun-eco-driver-data.txt</strong> Nursery: Area of
 capture (Either "Bimini - NS" (North Sound) or "Bimini -
 SL" (Sharkland)) Year: year of capture
 Pop.size: Number of sharks captured for a year and a
 Nursery Predator abundance: relative abundance of
 predators (Carcharhinus leucas, Carcharhinus limbatus and Negaprion
 brevirostris) for a year and a Nursery
 <strong>Dataset:
 Fun-eco-SI-data.txt</strong> ID: Unique
 individual identifier Sex: Sex Year:
 year of capture Nursery: Area of capture (Either
 "Bimini - NS" (North Sound) or "Bimini - SL"
 (Sharkland)) PCL: Pre-caudal length, nearest
 mm d13c: Carbon stable isotope value
 Explo: exploration score in a captive novel-open field
 test
DOI: 10.5061/dryad.jh9w0vtc2
title: Mullerian mimicry and the colouration patterns of sympatric coral snakes

description: This dataset cointains data used for the study of Müllerian mimicry in
 coral snakes. Coral snakes in the genus Micrurus are venomous,
 aposematic organisms that signal danger to predators through vivid
 colouration. Previous studies found that they serve as models to several
 harmless species of Batesian mimics. However, the extent to which Micrurus
 species engage in Müllerian mimicry remains poorly understood. We
 integrate detailed morphological and geographical distribution data to
 investigate if coral snakes are Müllerian mimics. We found that
 colouration is spatially structured and that Micrurus species tend to be
 more similar where they co-occur. Though long supposed, we empirically
 demonstrate Müllerian mimicry for the first time in coral snakes.
 Additionally, we found that the length of red-coloured rings in Micrurus
 is conserved, even at large geographic scales. This finding suggests that
 bright red rings may be under more substantial stabilizing selection than
 other aspects of colouration, and probably function as a generalized
 signal for deterring predators.
description: We examined museum specimens of <i>Micrurus brasiliensis,
 M. frontalis, M. ibiboboca, M. lemniscatus, </i>and<i> M.
 surinamensis </i>by taking high-quality digital photographs from the
 dorsum of 1528 preserved snakes. We measured the number of red rings,
 relative length of red rings (length of red ring / total length), relative
 length of external black rings ((length of black ring I + length of black
 ring III) / total length) / 2), relative length of white rings ((length of
 white ring I + length of white ring II / total length) / 2), and relative
 length of internal black rings (length of black ring II / total length).
 We calculated the colour variation through the geographic distribution of
 each species coupled with a multivariate spatial analysis
 approach.
DOI: 10.5061/dryad.z34tmpgdx
title: Landslide age, elevation and residual vegetation determine tropical montane forest canopy recovery and biomass accumulation after landslide disturbances in the Peruvian Andes

description: Landslides are common natural disturbances in tropical montane forests.
 While the geomorphic drivers of landslides in the Andes have been studied,
 factors controlling post-landslide forest recovery across the steep
 climatic and topographic gradients characteristic of tropical mountains
 are poorly understood. Here we use a LiDAR-derived canopy height map
 coupled with a 25-year landslide time series map to examine how landslide,
 topographic, and biophysical factors, along with residual vegetation,
 affect canopy height and heterogeneity in regenerating landslides. We also
 calculate aboveground biomass accumulation rates and estimate the time for
 landslides to recover to mature forest biomass levels. We find that age
 and elevation are the biggest determinants of forest recovery, and that
 the jump-start in regeneration that residual vegetation provides lasts for
 at least 18 years. Our estimates of time to biomass recovery (31.6-37.1
 years) are surprisingly rapid, and as a result we recommend that future
 research pair LiDAR with hyperspectral imagery to estimate forest
 aboveground biomass in frequently disturbed landscapes. Synthesis: Using a
 high-resolution LiDAR dataset and a time-series inventory of 608
 landslides distributed across a wide elevational gradient in Andean
 montane forest, we show that age and elevation are the most influential
 predictors of forest canopy height and canopy variability. Other features
 of landslides, in particular the presence of residual vegetation, shape
 post-landslide regeneration trajectories. LiDAR allows for a detailed
 analysis of forest structural recovery across large landscapes and numbers
 of disturbances, and provides a reasonable upper bound on aboveground
 biomass accumulation rates. However, because this method does not capture
 the effect of compositional change through succession on aboveground
 biomass, wherein high-wood density species gradually replace light-wooded
 pioneer species, it overestimates aboveground biomass. Given previously
 estimated stem turnover rates along this elevational gradient, we posit
 that aboveground biomass recovery takes at least three times as long as
 our recovery time estimates based on LiDAR-derived structure alone.
description: The bulk of the dataset was collected by overlaying landslide
 polygons onto various raster datafiles, then extracting the mean values of
 each parameter for each landslide. A portion of the dataset was generated
 by a support vector machine model. Methods for how each variable was
 collected are detailed in the manuscript and briefly in the
 "Information" tab of the Excel file. Where not noted, data were
 processed using various spatial data packages in R statistical
 software.
description: There is additional information about each tab and each variable
 in the dataset on the "Information" tab of the Excel
 file.
DOI: 10.5061/dryad.4j0zpc8bq
title: Data and code from: Evolution of brilliant iridescent feather nanostructures

description: The brilliant iridescent plumage of birds creates some of the most
 stunning color displays known in the natural world. Iridescent plumage
 colors are produced by nanostructures in feathers and have evolved in a
 wide variety of birds. The building blocks of these structures—melanosomes
 (melanin-filled organelles)—come in a variety of forms, yet how these
 different forms contribute to color production across birds remains
 unclear. Here, we leverage evolutionary analyses, optical simulations and
 reflectance spectrophotometry to uncover general principles that govern
 the production of brilliant iridescence. We find that a key feature that
 unites all melanosome forms in brilliant iridescent structures is thin
 melanin layers. Birds have achieved this in multiple ways: by decreasing
 the size of the melanosome directly, by hollowing out the interior, or by
 flattening the melanosome into a platelet. The evolution of thin melanin
 layers unlocks color-producing possibilities, more than doubling the range
 of colors that can be produced with a thick melanin layer and
 simultaneously increasing brightness. We discuss the implications of these
 findings for the evolution of iridescent structures in birds and propose
 two evolutionary paths to brilliant iridescence.
description: Please see the associated README files to see how datasets have
 been collected and processed.
description: Please see the associated README files for information on how to
 use code and data.
DOI: 10.5061/dryad.41ns1rndq
title: Datasets associated with: Late Holocene spread of pastoralism coincides with endemic megafaunal extinction on Madagascar

description: Recently expanded estimates for when humans arrived on Madagascar (up to
 ~10,000 years ago) highlight questions about the causes of the island’s
 relatively late megafaunal extinctions (~2000-500 years ago). Introduced
 domesticated animals could have contributed to extinctions, but the
 arrival times and past diets of exotic animals are poorly known. To
 conduct the first explicit test of the potential for competition between
 introduced livestock and extinct endemic megafauna in southern and western
 Madagascar, we generated new radiocarbon and stable carbon and nitrogen
 isotope data from the bone collagen of introduced ungulates (zebu cattle,
 ovicaprids, and bushpigs, n=66) and endemic megafauna (pygmy
 hippopotamuses, giant tortoises, and elephant birds, n=68) and combined
 these data with existing data from endemic megafauna (n=282, including
 giant lemurs). Radiocarbon dates confirm that introduced and endemic
 herbivores briefly overlapped chronologically in this region between 1000
 and 800 calibrated years before present (cal BP). Moreover, stable isotope
 data suggest that goats, tortoises, and hippos had broadly similar diets
 or exploited similar habitats. These data support the potential for both
 direct and indirect forms of competition between introduced and endemic
 herbivores. We argue that competition with introduced herbivores, mediated
 by opportunistic hunting by humans and exacerbated by environmental
 change, contributed to the late extinction of endemic megafauna on
 Madagascar.
description: Stable carbon isotope, stable nitrogen isotope, and radiocarbon
 data were collected using standard approaches.  Please see manuscript for
 details.
DOI: 10.15468/dl.efjmpy
title: Occurrence Download

description: A dataset containing 66859 records in GBIF matching the query:
SELECT
 '462' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 46.479780028101516
 AND decimalLatitude &lt;= 51.21395264452012
 AND decimalLongitude &gt;= -113.58444627864597
 AND decimalLongitude &lt;= -100.71036946873933
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 66859 records were derived from 159 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002878-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7272/q6qc01rn
title: Analysis of localized cAMP perturbations within a tissue reveal the effects of a local, dynamic gap junction state on ERK signaling

description: Beyond natural stimuli such as growth factors and stresses, the ability to
 experimentally modulate at will the levels or activity of specific
 intracellular signaling molecule(s) in specified cells within a tissue can
 be a powerful tool for uncovering new regulation and tissue behaviors.
 Here we perturb the levels of cAMP within specific cells of an epithelial
 monolayer to probe the time-dynamic behavior of cell-cell communication
 protocols implemented by the cAMP/PKA pathway and its coupling to the ERK
 pathway. The time-dependent ERK responses we observe in the perturbed
 cells for spatially uniform cAMP perturbations (all cells) can be very
 different from those due to spatially localized perturbations (a few
 cells). Through a combination of pharmacological and genetic
 perturbations, signal analysis, and computational modeling, we infer how
 intracellular regulation and regulated cell-cell coupling each impact the
 intracellular ERK response in single cells. Our approach reveals how a
 dynamic, gap junction state helps sculpt the intracellular ERK response
 over time in locally perturbed cells.
DOI: 10.5061/dryad.h70rxwdjs
title: Data from: Characterization of the abiotic drivers of abundance of nearshore Arctic fishes

description: Fish are critical ecologically and socioeconomically for subsistence
 economies in the Arctic, an ecosystem undergoing unprecedented
 environmental change. Our understanding of the responses of nearshore
 Arctic fishes to environmental change is inadequate because of limited
 research on the physicochemical drivers of abundance occurring at a fine
 scale. Here, high-frequency in-situ measurements of pH, temperature,
 salinity, and dissolved oxygen were paired with daily fish catches in
 nearshore Alaskan waters of the Beaufort Sea. This dataset
 includes hourly measurements of pH, temperature, salinity, and dissolved
 oxygen, which were collected and calibrated according to best practices in
 chemical oceanography, and daily catch-per-unit-effort data for
 18 nearshore Arctic fish species paired with daily averaged oceanographic
 data.
DOI: 10.5061/dryad.gxd2547md
title: Data from: Extensive sympatry and frequent hybridization of ecologically divergent aquatic plants on the Qinghai-Tibetan Plateau

description: Hybridization has fascinated biologists in recent centuries for its
 evolutionary importance, especially in plants. Hybrid zones are commonly
 located in regions across environmental gradients due to more
 opportunities to contact and ecological heterogeneity. For aquatic taxa,
 intrazonal character makes broad overlapping regions in intermediate
 environments between related species. However, we have limited information
 on the hybridization pattern of aquatic taxa in alpines, especially
 submerged macrophytes. In this study, we aimed to test the hypotheses that
 niche overlap and hybridization might be extensive in related aquatic
 plants across an altitudinal gradient. We evaluated the niche overlap in
 three related species pairs on the Qinghai-Tibetan Plateau and assessed
 the spatial pattern of hybrid populations. Obvious niche overlap and
 common hybridization were revealed in all three pairs of related aquatic
 plants. The plateau edge and river basins were broad areas for the
 sympatry of divergent taxa, where a large proportion of hybrid populations
 occurred. Hybrids are also discretely distributed in diverse habitats on
 the plateau. Differences in the extent of niche overlap, genetic
 incompatibility and phylogeographic history might lead to variations in
 hybridization patterns among the three species pairs. Our results
 suggested that plateau areas are a hotspot for ecologically divergent
 aquatic species to contact and mate and implied that hybridization may be
 important for the freshwater biodiversity of highlands.
description: A total of 15 indeterminate populations for related
 <em style="font-family:'Times New Roman' , serif;font-size:14.6667px;">Stuckenia </em>and<em style="font-family:'Times New Roman' , serif;font-size:14.6667px;"> </em><em style="font-family:'Times New Roman' , serif;font-size:11pt;">Ranunculus </em>(<em style="font-family:'Times New Roman' , serif;font-size:11pt;">Stuckenia</em>: 91 individuals of 8 populations;
 <em style="font-family:'Times New Roman' , serif;font-size:11pt;">Ranunculus</em>: 112 individuals of 7 populations),
 21 pure <em style="font-family:'Times New Roman' , serif;font-size:11pt;">Stuckenia</em> populations (75 individuals of
 <em style="font-family:'Times New Roman' , serif;font-size:11pt;">S. pectinata</em> and 131 individuals of <em style="font-family:'Times New Roman' , serif;font-size:11pt;">S. filiformis</em>) and 20 pure <em style="font-family:'Times New Roman' , serif;font-size:11pt;">Ranunculus</em> populations (110 individuals of
 <em style="font-family:'Times New Roman' , serif;font-size:11pt;">R. trichophyllus</em> and 215 individuals of <em style="font-family:'Times New Roman' , serif;font-size:11pt;">R. subrigidus</em>) were involved. All samples were collected
 on the Qinghai-Tibetan Plateau, and preserved in silica gel
 before total genomic DNA
 extractration. Microsatellite markers (7 loci for
 <em>Stuckenia,</em> 17 loci for
 <em>Ranunculus</em>) were used for genotyping.
DOI: 10.5061/dryad.9ghx3ffhp
title: Experimental evidence that effects of megaherbivores on mesoherbivore space use are influenced by species’ traits

description: The extinction of 80% of megaherbivore (&gt;1,000 kg) species towards
 the end of the Pleistocene altered vegetation structure, fire dynamics,
 and nutrient cycling worldwide. Ecologists have proposed (re)introducing
 megaherbivores or their ecological analogues to restore lost ecosystem
 functions and reinforce extant but declining megaherbivore populations.
 However, the effects of megaherbivores on smaller herbivores are poorly
 understood. We used long-term exclusion experiments and multispecies
 hierarchical models fitted to dung counts to test 1) the effect of
 megaherbivore (elephant and giraffe) presence-absence on the occurrence
 (dung presence) and use intensity (dung-pile density) of mesoherbivores
 (2–1,000 kg), and 2) the extent to which the responses of each
 mesoherbivore species was predictable based on their traits (diet and
 shoulder height) and phylogenetic relatedness. Megaherbivores increased
 the predicted occurrence and use intensity of zebras but reduced the
 occurrence and use intensity of several other mesoherbivore species. The
 negative effect of megaherbivores on mesoherbivore occurrence was stronger
 for shorter species, regardless of diet or relatedness. Megaherbivores
 substantially reduced the expected total use intensity (i.e., cumulative
 dung density of all species) of mesoherbivores, but only minimally reduced
 the expected species richness (i.e., cumulative predicted occurrence
 probabilities of all species) of mesoherbivores (by &lt;1 species).
 Simulated extirpation of megaherbivores altered use intensity by
 mesoherbivores, which should be considered during (re)introductions of
 megaherbivores or their ecological proxies. Species’ traits (in this case
 shoulder height) may be more reliable predictors of mesoherbivores’
 responses to megaherbivores than phylogenetic relatedness, and may be
 useful for predicting responses of data-limited species.
description: This dataset consists of dung surveys (belt transects) in two
 long-term herbivore exclosure experiments in a Kenyan savanna
 ecosystem. See the Materials and Methods section of the
 publication for more details.
description: Area surveyed ('AREA') is in
 m<sup>2</sup>. For megaherbivore
 accessibility ('MEGA'), 'YES' = accessible,
 'NO' = excluded.
DOI: 10.5061/dryad.4xgxd2599
title: Data for: Cdt1 inhibits CMG helicase in early S phase to separate origin licensing from DNA synthesis

description: Human cells license tens of thousands of origins of replication in G1 and
 then must stop all licensing before DNA synthesis in S phase to prevent
 re-replication and genome instability that ensue when an origin is
 licensed on replicated DNA. However, the E3 ubiquitin ligase
 CRL4Cdt2 only starts to degrade the licensing factor Cdt1 after
 origin firing, raising the question of how cells prevent re-replication
 before Cdt1 is fully degraded. Here, using quantitative microscopy and in
 vitro reconstituted human DNA replication, we show that Cdt1 inhibits DNA
 synthesis during an overlap period when Cdt1 is still present after origin
 firing. Cdt1 inhibits DNA synthesis by suppressing CMG helicase
 progression at replication forks, and DNA synthesis commences once Cdt1 is
 degraded. Thus, in contrast to the prevailing model that human cells
 prevent re-replication by strictly separating licensing from firing,
 licensing and firing overlap, and cells instead separate licensing from
 DNA synthesis.
description: Quantitative high-throughput microscopy was performed on human
 cell lines. Live-cell imaging of fluorescent cell cycle reporters in cell
 lines was quantified to study cell cycle dynamics, and this information
 was integrated together with fixed-cell imaging of immunofluorescene and
 other staining. Microscopy images were processed using a cell
 segmentation/tracking and quantification pipeline which automatically
 quantifies signals in single cells. The included data includes single-cell
 measurements for all experiments used to generate figures for Ratnayeke et
 al. 2022, as well as MATLAB scripts to generate the figures. 
description: Code repository to generate figures can be found at https://doi.org/10.5281/zenodo.7183751 or https://github.com/MeyerLab/image-analysis-ratnayeke-2022. See README in code repository for instructions. Figure generating scripts are directly executable once the path to the data folder in each script is edited.