cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3bk3j9knw
title: Data from: Multiple origins of lipid-based structural colors contribute to a gradient of fruit colors in Viburnum (Adoxaceae)

description: Structural color is poorly known in plants relative to animals. In fruits,
 only a handful of cases have been described, including in Viburnum tinus
 where the blue color results from a disordered multilayered reflector made
 of lipid droplets. Here, we examine the broader evolutionary context of
 fruit structural color across the genus Viburnum. We obtained fresh and
 herbarium fruit material from 30 Viburnum species spanning the phylogeny
 and used transmission electron microscopy, optical simulations, and
 ancestral state reconstruction to (1) identify the presence/absence of
 photonic structures in each species, (2) understand the mechanism
 producing structural color in newly identified species, (3) relate the
 development of cell wall structure to reflectance in V. dentatum, and (4)
 describe the evolution of cell-wall architecture across Viburnum. We
 identify at least two (possibly three) origins of blue fruit color in
 Viburnum, both of which produce large photonic structures made of lipid
 droplets embedded in the cell wall and which reflect blue light. Examining
 species that may exhibit structural color in combination with anthocyanin
 and carotenoid pigments, rather than focusing on the most extreme
 examples, will yield further insights into the diversity, ecology and
 evolution of fruit color.
description: The datasets included are reflectance measurements of
 <em>Viburnum</em> <em>dentatum</em> fruits during
 development, as well as measurements of fruit length and width during
 development.  Additionally, we include measurements of the cell wall
 components (cell wall, globular region, and cuticle) across 30 species of
 <em>Viburnum</em>. The reflectance
 measurements were made using a Jaz spectrometer (OceanOptics, Dunedin, FL)
 equipped with a deuterium-halogen lamp and a UV detector. To hold the
 probe at 45˚ consistently across samples, we used an anodized aluminum
 probe holder, which also eliminated background radiation. Reflectance
 measurements were calibrated against a Spectralon white standard
 (Labsphere, North Sutton, NH). The measurements of
 fruit length and width were made using Mitutoyo calipers.
 The measurements of cell wall components across 30
 <em>Viburnum</em> species were made using TEM images imported
 into the program Fiji (a wrapper for ImageJ), where we calibrated the
 measurements and then made 3 measurements per cell per species, with at
 least 3 cells per species (1 for <em>V</em>.
 <em>jucundum</em>, 2 for <em>V</em>.
 <em>venustum</em>).
DOI: 10.5061/dryad.wpzgmsbr0
title: Supplementary information for: Redundancy analysis, genome-wide association studies, and the pigmentation of brown trout (Salmo trutta L.)

description: The association of molecular variants to phenotypic variation is a main
 issue in biology, often tackled with genome-wide association studies
 (GWAS). GWAS are challenging, with increasing, but still limited use in
 evolutionary biology. We used redundancy analysis (RDA) as a complimentary
 ordination approach to single- and multi-trait GWAS to explore the
 molecular basis of pigmentation variation in brown trout (Salmo trutta)
 belonging to wild populations impacted by hatchery fish. Based on 75,684
 single nucleotide polymorphic (SNP) markers, RDA, single- and multi-trait
 GWAS allowed us to extract 337 independent “colour patterning loci” (CPLs)
 associated with trout pigmentation traits, such as the number of red and
 black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of
 40 brown trout linkage groups indicating a polygenic genomic architecture
 of pigmentation, (ii) were found associated with 218 candidate genes,
 including 197 genes formerly mentioned in the literature dealing with skin
 pigmentation, skin patterning, differentiation or structure notably in a
 close relative, the rainbow trout (Onchorhynchus mykiss), and (iii)
 related to functions relevant to pigmentation variation (e.g., calcium-
 and ion-binding, cell adhesion). Annotated CPLs include genes with
 well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also
 markers associated with genes formerly found expressed in rainbow or brown
 trout skins. RDA was also shown useful to investigate management issues,
 especially the dynamics of trout pigmentation submitted to several
 generations of hatchery introgression.
description: The data set (pictures) was acquired during field or hatchery
 sampling of trout in order to collect phenotypic data on slightly
 anesthetized individual trout des cibed in the paper (N = 112).
 The metadata file contains the description of the data that were
 acquired: mostly colour patterns as described in the paper, plus fish
 size, plus sex.
description: No specific programs, individual examination of trout pictures
 was made to acquire the data. Pictures might be accessed using common
 softwares implements on most computers.
DOI: 10.5061/dryad.2z34tmpqc
title: Data for: Nitrogen deposition in forests: Statistical modeling of total deposition from throughfall loads

description: Introduction: Nitrogen (N) gradient studies in some cases use N deposition
 in throughfall as measure of N deposition to forests. For evaluating
 critical loads of N, however, information on total N deposition is
 required, i.e., the sum of estimates of dry, wet and occult deposition.
 Methods: The present paper collects a number of studies in Europe where
 throughfall and total N deposition were compared in different forest
 types. From this dataset a function was derived which allows to estimate
 total N deposition from throughfall N deposition. Results: At low
 throughfall N deposition values, the proportion of canopy uptake is high
 and thus the underestimation of total deposition by throughfall N needs to
 be corrected. At throughfall N deposition values &gt;20 kg N ha-1 yr-1
 canopy uptake is getting less important. Conclusions: This work shows that
 throughfall clearly underestimates total deposition of nitrogen. With the
 present data set covering large parts of Europe it is possible to derive a
 critical load estimate from gradient studies using throughfall data.
description: This is a meta analysis of various datasets collected in European
 forests, with the author of the study given in the table.
description: Rmd file can be accessed using R and reproduces the commands used
 to analyse the data. The PDF file gives a description to the steps
 involved. The two files belong together.
DOI: 10.15468/dl.x76a7b
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euchresta horsfieldii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 29 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003303-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kprr4xh7w
title: Predation patterns on the tundra – genetic barcoding of scats from two sympatric fox species

description: In the Arctic tundra, climate-induced emergence of the red fox (Vulpes
 vulpes), a competitor to the Arctic fox (Vulpes lagopus), is predicted to
 influence predation patterns of both fox mesopredators. In this study, we
 i) identified predator species from scats through an established barcoding
 approach, and ii) explored the use of a cheap, quick barcoding method of
 fox feces (n = 103). We investigated differences in diet between the red
 fox (predicted generalist predator) and Arctic fox (predicted specialist
 predator) over two years with varying prey abundance. We amplified short
 DNA fragments (&lt; 200 bp) from small rodents, birds and hares. For
 both predators, there was a high frequency of occurrence of rodents (38 -
 69 %) identifying them as primary prey species and birds as secondary prey
 species (13-31%). This demonstrates the strength of a straightforward DNA
 barcoding method for dietary analyses in sympatric fox predators, with
 species-level resolution of prey. Barcoding is a promising tool for future
 dietary studies, however a few methodological improvements, along with
 extended sampling, are needed for a more complete assessment of fox
 predation patterns. Integrating high-resolution dietary analyses has great
 potential to enhance our understanding of predation patterns in Arctic
 tundra communities.
DOI: 10.5061/dryad.cjsxksn8z
title: Data of two neotropical Colaptes woodpeckers' nests fate and environmental features associated with them

description: Understanding factors affecting nest survival of woodpeckers in threatened
 landscapes is a key tool for land managers, particularly when conservation
 depends on public policies. However, information of Neotropical
 woodpeckers breeding in southern temperate forests is noticeably sparse
 despite the worrying conservation status of these ecosystems and
 woodpeckers’ key role as cavity providers. Our objective was to assess the
 relationship between tree cavity features, vegetation structure, and
 landscape configuration on the nest survival of the Green-barred
 Woodpecker (Colaptes melanochloros) and the Campo Flicker (C. campestris).
 We monitored nests of these woodpeckers during three breeding seasons from
 2015–2018 in a woodland of east-central Argentina threatened by selective
 tree logging and soil material extraction. We recorded features that
 presumably influence nest survival at a micro-scale (cavity, cavity-tree
 features, and foliage cover around the cavity) and a macro-scale (forest
 cover and shape index within a 500 m circle around the nest). We did not
 find support for a relationship between daily nest survival rates (DSR)
 and cavity features, vegetation structure, or landscape configuration.
 However, new cavities were more successful than reused ones for the
 Green-barred Woodpecker. We also found a surprisingly high rate (~33% of
 nest failures) of nest abandonment for both species. Abandonment may be a
 factor regulating this population and causes of abandonment warrants
 further investigation. Given the importance of new cavities to the success
 of Green-barred Woodpeckers, our results indicate the preservation of
 medium-size trees (20 cm &lt; DBH &lt; 50 cm) with wood softened
 by degradation processes (preferred by the species to excavate cavities)
 would facilitate persistence of both of this woodpecker and the
 cavity-nesting community. Effective audit of soil material extraction and
 controlled selective timber logging practices (including preservation of
 mature trees) in compliance with existing regulations could contribute to
 this type of habitat maintenance.
description: Data were collected in Punta Indio,Buenos Aires, Argentina. We
 searched for nests of <em>Colaptes</em>
 <em>campestris</em> and <em>Colaptes</em>
 <em>melanochloros</em> (two Neotropical woodpeckers) during
 three breeding seasons. We monitored them until the nesting attempt
 finished (successful or failed) and then registered cavity and landscape
 features to later assess whether fate is related to environmental
 characteristics at two spatial scales. 
description: R software is required to run analyses
DOI: 10.15468/dl.z8uab3
title: Occurrence Download

description: A dataset containing 1498 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Haemadipsa",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1498 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003304-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rxwdbrvct
title: Deep learning training data (JOVE)

description: Cryo-electron tomography (cryo-ET) allows researchers to image cells in
 their native, hydrated state at the highest resolution currently possible.
 However, the technique has several limitations that make analyzing the
 data it generates time-intensive and difficult. Hand-segmenting a single
 tomogram can take hours to days of human effort, but the microscope can
 easily generate 50 or more tomograms a day. Current deep learning
 segmentation programs for cryo-ET do exist but are limited to segmenting
 one structure at a time. Here multi-slice U-Net convolutional neural
 networks are trained and applied to automatically segment multiple
 structures simultaneously within cryo-tomograms. With proper
 preprocessing, these networks can be robustly inferred to many tomograms
 without the need for training individual networks for each tomogram. This
 workflow dramatically improves the speed with which cryo-electron
 tomograms can be analyzed by cutting segmentation time down to under 30
 min in most cases. Further, segmentations can be used to improve the
 accuracy of filament tracing within a cellular context and to rapidly
 extract coordinates for subtomogram averaging.
description: This data set was collected on a Titan Krios G3i using TFS
 Tomography 5.0. It was aligned and reconstructed using IMOD, and the
 multi-ROI was hand-segmented by the authors using Dragonfly
 2022.1. The data comes two forms. 1)
 An ORS object file that contains the unprocessed tomogram, the ground
 truth multi-ROI, and mask used to train the network used in our JOVE
 protocol. This is a ready-to-use format that can be imported to Dragonfly
 very simply. 2) A set of .MRC files containing the
 unprocessed tomogram (pixel size 13.6 ang/pix), and binary masks for the
 groud truth input classes we used to train the data. These allow users to
 use the dataset outside of the Dragonfly environment.
description: To open the ORS object, you will need the ORS Dragonfly software
 suite. MRC files are readily opened in free software
 such as ImageJ and IMOD ImageJ Reference
 Schneider, C. A., Rasband, W. S., & Eliceiri, K. W.
 (2012). NIH Image to ImageJ: 25 years of image analysis. Nature
 Methods, 9(7), 671–675. doi:10.1038/nmeth.2089 IMOD Reference Kremer J.R., D.N. Mastronarde and J.R. McIntosh (1996) Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116:71-76.
DOI: 10.5061/dryad.37pvmcvpk
title: Limited recovery following a massive seagrass decline in subarctic eastern Canada

description: Over the last few decades, there has been increasing recognition of
 seagrasses' contribution to the functioning of nearshore ecosystems
 and climate change mitigation. Nevertheless, seagrass ecosystems have been
 deteriorating globally at an accelerating rate during recent decades. In
 2017, research into the condition of eelgrass (Zostera marina) along the
 eastern coast of James Bay, Canada, was initiated in response to reports
 of eelgrass decline by the Cree First Nations of Eeyou Istchee. As part of
 this research, we compiled and analyzed two decades of eelgrass cover data
 and three decades of eelgrass monitoring data (biomass and density) to
 detect changes and assess possible environmental drivers. We detected a
 major decline in eelgrass conditions between 1995 and 1999, which
 encompassed the entire east coast of James Bay. Surveys conducted in 2019
 and 2020 indicated limited changes post-decline, e.g., low eelgrass cover
 (&lt;25%), low aboveground biomass, smaller shoots than before 1995,
 and marginally low densities persisted at most sites. Overall, the
 synthesized datasets show a 40 % loss of eelgrass meadows with &gt;
 50% cover in eastern James Bay since 1995, representing the largest scale
 eelgrass decline documented in eastern Canada since the massive die-off
 event that occurred in the 1930s along the North Atlantic coast. Using
 biomass data collected since 1982, but geographically limited to the
 sector of the coast near the regulated La Grande River, generalized
 additive modeling revealed eelgrass meadows are affected by local sea
 surface temperature, early ice breakup, and higher summer freshwater
 discharge. Our results caution against assuming subarctic seagrass
 ecosystems have avoided recent global declines or will benefit from
 ongoing climate warming.
description: The methods used to collect and process the data are described in
 Leblanc et al. 2022 <strong>Limited recovery following a massive
 seagrass decline in subarctic eastern Canada</strong>. Global Change
 Biology, <em>accepted</em>. 
description: All files are in .csv format.
DOI: 10.5061/dryad.5hqbzkh91
title: Complex urban environments provide Apis mellifera with a richer plant forage than suburban and more rural landscapes

description: Growth in the global development of cities, and increasing public interest
 in beekeeping, has led to rises in the numbers of urban apiaries. Towns
 and cities can provide an excellent diet for managed bees, with a diverse
 range of nectar and pollen available throughout a long flowering season
 and are often more ecologically diverse than the surrounding rural
 environments. Accessible urban honeybee hives are a valuable research
 resource to gain insights into the diet and ecology of wild pollinators in
 urban settings. We used DNA metabarcoding of the rbcL and ITS2 gene
 regions to characterise the pollen community in Apis mellifera honey,
 inferring the floral diet, from 14 hives across an urban gradient around
 Greater Manchester, UK. We found that the proportion of urban land around
 a hive is significantly associated with an increase in the diversity of
 plants foraged, and that invasive and non-native plants appear to play a
 critical role in the sustenance of urban bees, alongside native plant
 species. The proportion of improved grassland, typical of suburban lawns
 and livestock farms, is significantly associated with decreases in the
 diversity of plant pollen found in honey samples. These findings are
 relevant to urban landscape developers motivated to encourage biodiversity
 and bee persistence, in line with global bio-food security agendas.
description: Honey samples were sourced from 14 <em>Apis</em>
 <em>mellifera</em> hives; 12 from Greater Manchester, one from
 Cheshire and one from Lancashire. Honey samples were diluted in molecular
 grade water (4x 10g/25ml per sample) centrifuged at 15,000 x g for 30
 minutes. DNA was then extracted from the pellet, the rbcL and ITS gene
 regions were amplified and PCR products sequenced on an Illumina HiSeq
 using a V2 flowcell. Sequencing data were analysed using the DADA2
 functionality in the QIIME2 package and taxa assigned using previously
 published databases and the NBCI nucleotide database. Species and genus
 assignments were checked for plausibility in the UK using the Royal
 Horticultural Society Horticultural Database, the Biological Records
 Centre Atlas of the British and Irish Flora and the Plants for a Future
 database, as well as online searches of UK garden centres.
description: Data were processed and analysed using the R statistical platform
 (version 4.0.4). R scripts are included in the data files and software
 required is included in the scripts.
DOI: 10.5061/dryad.83bk3j9vp
title: Combining camera trap surveys and IUCN range maps to improve knowledge of species distributions

description: Reliable maps of species distributions are fundamental for biodiversity
 research and conservation. Range maps created by the International Union
 for Conservation of Nature (IUCN) Red List are often considered
 authoritative but may not match species occurrence data. We tested
 concordance between occurrences from camera trap surveys and predicted
 occurrence from IUCN maps for 510 medium- to large-bodied mammalian
 species in 80 camera-trap sampling areas. Across all areas, cameras
 detected 39% of the species that were expected to occur based on IUCN
 ranges.  The probability of mismatches between camera traps and
 IUCN range maps was significantly higher for smaller-bodied mammals and
 habitat specialists in the Neotropics and Indomalaya, and in areas with
 shorter canopy forests. Our results indicate that in many areas within
 their range map distributions species may be rare or absent. We suggest
 that combining range map data with accumulating data from ground-based
 biodiversity sensors, such as camera traps, acoustic recorders, and eDNA
 surveys, provides a richer knowledge base for conservation mapping and
 planning.
description: Minimal reproducible code for modelling in Chen et al. 2022, Combining
 camera trap surveys and IUCN range maps can improve knowledge of species
 distributions Code to run binomial regression models Dataframe has 2967
 obs. of 16 variables Name Type Unit Explanatation speciesScientificName
 Character NA scientific name of the species type Character NA three
 categories of species occurrences: A-camera only, B-Both, C-IUCN only
 projectID\ Character NA project ID ForStrat.Value Binomial NA Foraging
 stratum:G (1) species restricted to terrestrial surfaces, Semi-Ar (0) -
 Semi-arboreal BodyMass.Value Numerical g Mean adult body mass of a species
 (g) Activity.Nocturnal Binomial NA Nocturnality (1), other (0); IUCN_frq\
 Numerical\ NA\ Total IUCN assessments of a species IUCN_year\ Numerical NA
 Year of latest IUCN assessments of a species IUCN_cat\ Numerical NA The
 extinction risk of species assessed by IUCN Red List. Categories were
 coded as integers: Least Concern (LC -1), Near Threatened (NT-2),
 Vulnerable (VU-3), Endangered (EN -4), Critically Endangered (CR - 5), and
 Data Deficient (NA) realm\ Character NA The zoogeographical realm where a
 camera trap survey was conducted Tree_mean Numerical meter Forest canopy
 height (m) sampling_effort_t Numerical camera trap days The total camera
 days of a camera trap project hab_breadth Numerical NA The number of IUCN
 habitats listed as suitable. Ranging from 1-35. Species without habitat
 breadth data are coded as: NA range_area\ Numerical km2 Range area of IUCN
 range map (km2) order\ Character NA The order of the species
DOI: 10.5061/dryad.s1rn8pkc5
title: Alternating regimes of shallow and deep-sea diversification explain a species-richness paradox in marine fishes

description: The deep sea contains a surprising diversity of life, including iconic
 fish groups such as anglerfishes and lanternfishes. Still, &gt; 65% of
 marine teleost fish species are restricted to the photic zone &lt; 200
 m, which comprises less than 10% of the ocean’s total volume. From a
 macroevolutionary perspective, this paradox may be explained by three
 hypotheses: 1) shallow-water lineages have had more time to diversify than
 deep-sea lineages, 2) shallow-water lineages have faster rates of
 speciation than deep-sea lineages, or 3) shallow-to-deep sea transition
 rates limit deep-sea richness. Here we use phylogenetic comparative
 methods to test among these three non-mutually exclusive hypotheses. While
 we found support for all hypotheses, the disparity in species richness is
 better described as the uneven outcome of alternating phases that favored
 shallow or deep diversification over the past 200 million y. Shallow
 marine teleosts became incredibly diverse 100 million years ago during a
 period of warm temperatures and high sea level, suggesting the importance
 of reefs and epicontinental settings. Conversely, deep-sea colonization
 and speciation were favored during brief episodes when cooling
 temperatures increased the efficiency of the ocean’s carbon pump. Finally,
 time-variable ecological filters limited shallow-to-deep colonization for
 much of teleost history, which helped maintain higher shallow richness. A
 pelagic lifestyle and large jaws were associated with early deep-sea
 colonists, while a demersal lifestyle and a tapered body plan were typical
 of later colonists. Therefore, we also suggest that some hallmark
 characteristics of deep-sea fishes evolved prior to colonizing the deep
 sea.
description: R scripts and R packages