cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sxksn031w
title: Data from: Trematode parasites exceed aquatic insect biomass in Oregon stream food webs

description: 1) Although parasites are increasingly recognized for their ecosystem
 roles, it is often assumed that free-living organisms dominate animal
 biomass in most ecosystems and therefore provide the primary pathways for
 energy transfer. 2) To examine the contributions of parasites to ecosystem
 energetics in freshwater streams, we quantified the standing biomass of
 trematodes and free-living organisms at nine sites in three streams in
 western Oregon, USA. We then compared rates of biomass flow from snails
 (Juga plicifera) into trematode parasites relative to aquatic vertebrate
 predators (sculpin, cutthroat trout, and Pacific giant salamanders). 3)
 The trematode parasite community had the fifth highest dry biomass density
 among stream organisms (0.40 g m-2) and exceeded the combined biomass of
 aquatic insects. Only host snails (3.88 g m-2), sculpin (1.11 g m-2),
 trout (0.73 g m-2), and crayfish (0.43 g m-2) had a greater biomass. The
 parasite 'extended phenotype', consisting of trematode plus
 castrated host biomass, exceeded the individual biomass of every taxonomic
 group other than snails. The substantial parasite biomass stemmed from the
 high snail density and infection prevalence, and the large proportional
 mass of infected hosts that consisted of trematode tissue (mean = 31% per
 snail). 4) Estimates of yearly biomass transfer from snails into
 trematodes were slightly higher than the combined estimate of snail
 biomass transfer into the three vertebrate predators. Pacific giant
 salamanders accounted for 90% of the snail biomass consumed by predators.
 5) These results demonstrate that trematode parasites play
 underappreciated roles in the ecosystem energetics of some freshwater
 streams.
DOI: 10.5061/dryad.70rxwdbwc
title: Assembly of Aegilops umbellulata chromosomes

description: We sequenced and assembled seven chromosomes of Aegilops umbellulata. The
 assembly with Meraculous resulted in ~ 101k - 191k scaffolds per
 chromosome with N50 size 2.9kb – 4.0kb. The scaffold sequences were used
 for development of molecular markers specific for cDNAs sequences mapped
 on Ae. umbellulata chromosomes Pairwise alignment of wheat cDNA-sequences
 and the chromosomal scaffolds of Ae. umbellulata identified candidate
 sequences. In order to analyze the structure and homeology of Aegilops
 chromosomes, forty-three mapped wheat cDNAs covering all seven chromosome
 groups were localized by FISH.
description: Flow-sorted chromosomes were treated with proteinase K and their
 DNA was amplified by multiple displacement amplification (MDA) using
 Illustra GenomiPhi V2 DNA Amplification Kit (GE Healthcare, Chalfont St.
 Giles, United Kingdom) as described by Šimková et al. (2008). Three
 independent amplifications from each chromosome were pooled to reduce
 amplification bias and 2µg of amplified DNA were fragmented and used to
 prepare Illumina sequencing libraries with TruSeq DNA PCR-Free Library
 Preparation Kit (Illumina, Inc., San Diego, USA). All samples were
 sequenced on Illumina HiSeq 2000 according manufacturer's instruction
 to produce 2x100 bp paired-end reads. Each chromosome or chromosome arm
 was sequenced on a separate lane of the instrument to obtain ~130 millions
 of pair-end read (~26 Gbp) for each chromosome/arm. De novo assembly was
 done with MaSuRCA assembler (Zimin et al. 2013) using default parameters.
 Finally, contigs shorter than 200 bp were removed from the assembly of
 each chromosome prior further analysis.
DOI: 10.5061/dryad.c59zw3r68
title: Electric vehicle synthetic trips

description: This dataset contains four files: - a trip diary that was synthesized for
 electric vehicle drivers in the area of Westfield Shopping Center, London.
 - a trip diary that was synthesized for electric vehicle drivers in the
 area of Canary Wharf, London. - A set of EV charging packages that were
 used to optimize charging prices for a Charging Service Provider - A
 readme file with details and variable definitions for the contained
 datasets The original trip sample that was used for the synthesis of the
 two travel diaries is part of the London Travel Demand
 Survey (LTDS)
 - https://tfl.gov.uk/corporate/about-tfl/how-we-work/planning-for-the-future/consultations-and-surveys
DOI: 10.5061/dryad.v9s4mw6tm
title: Brewster angle optical reflection observation of self-limiting nanoparticle monolayer self-assembly at a liquid/liquid interface

description: Real-time optical reflection of incident p-polarized light near
 Brewster’s angle shows that after drop-casting iron oxide nanoparticles
 (NPs) in heptane on top of a diethylene glycol (DEG) liquid substrate, an
 iron oxide NP layer forms at the DEG/heptane interface, and it self-limits
 to a monolayer even when there are excess NPs dispersed in the upper
 heptane phase. Most modes of NP self-assembly do not self-limit growth
 after the formation of a single monolayer. Observations are compared to a
 reflection model incorporating the reflectances expected at each
 interface. An effective medium model of the dielectric constant is used to
 model the reflectance of the NP layer at the DEG/heptane interface.
description: To form these NP assemblies, 2 mL of DEG were first deposited
 into a glass Petri dish (diameter = 3.45 cm) to form a ∼2.14 mm-thick
 liquid substrate (if the surface were flat).
 A <i>p</i>-polarized He-Ne laser (632.8 nm, plasma filter) was
 expanded from below to form a 2.21 cm × 1.32 cm elliptical beam at the
 center of the DEG/air interface, to average over this region, and all
 reflected beams other than those from the glass bottom of the Petri dish
 were imaged on a photodiode, on which they overlap. The laser was adjusted
 to hit the DEG/air interface at Brewster’s angle (34.65°) to minimize
 reflectance from this interface. Then, 1400 μL of heptane were deposited
 on the DEG substrate to form a ∼1.50 mm-thick upper layer reservoir and,
 finally, 120 μL of a heptane colloid of NPs were drop-cast on top. This
 quickly mixed with the heptane reservoir to form a more dilute, ∼1.63
 mm-thick heptane colloid layer. The Petri dish was then capped to slow the
 heptane evaporation. The NPs were spherical iron oxide NPs
 (Fe<sub>2</sub>O<sub>3</sub>, 11.8 nm core
 diameter, capped by oleate) synthesized by standard methods. The number of
 NPs in the heptane colloid drop was characterized by the number of
 close-packed NP MLs that would be expected to form on the DEG substrate
 after heptane evaporation, averaged over the surface; this is termed the
 number of ML-equivalents being drop-cast. The light
 beams reflected from the DEG/heptane colloid and heptane colloid/air
 interfaces were monitored by a photodiode for 240 min, way before the
 heptane upper layer evaporated. Before the heptane was added, the
 reflected fraction from the DEG/air interface was very small, but not
 zero, because of the surface and laser beam curvatures. After it was added
 and before the NPs were drop-cast, the reflectances from the DEG/heptane
 and heptane/air interfaces were still very small because the refractive
 indices of pure DEG and heptane are nearly the same (below). After the NPs
 were added and a NP layer formed at the DEG/heptane colloid interface, the
 reflectance from that interface was expected to initially increase
 monotonically and linearly with layer thickness at the interface (for up
 to ∼6 MLs, corresponding to ∼ a quarter wavelength in this
 medium).
DOI: 10.5061/dryad.cz8w9gj2g
title: Population ecology and dynamics of a remnant natural population of European yew (Taxus baccata) in a lowland temperate forest – implications for use in reforestation

description: There is increasing focus on reforestation, but the efforts still often
 include limited subsets of species despite evidence that tree diversity
 promote biodiversity and ecological resilience. In addition to these
 benefits, greater inclusion of rare native species in reforestation
 efforts would also help conserve these species in an uncertain future.
 Here, we investigate the population ecology and dynamics of the only
 remaining historical population of the shade-adapted under- and mid-story
 tree European yew (Taxus baccata) in Denmark to inform its potential usage
 in reforestation. The species has been widely extirpated from European
 landscapes, and while much used in horticulture, is hardly used in
 reforestation, so there is limited experience with its requirements and
 performance. We collected data on all individuals in 2015 and compared
 them with results from a previous census in 1999. Furthermore, we used
 boosted regression trees (BRT) modelling to investigate the ecological
 drivers of the distributions of its different life stages. Our results
 show a stable T. baccata population, with much regeneration in areas of
 more open-canopy conditions that also support high survival between
 life-stages. The BRT results show that moss-dominated microhabitats under
 moderately shaded conditions are important for T. baccata seedling
 establishment, while higher light availability is important for survival
 from sapling to adult life-stages. For use in reforestation, we recommend
 providing moderately shaded microhabitats to allow the seedlings and small
 saplings to escape competition while also acting as protection from
 herbivores. Through their long-lived nature, low stature and evergreen
 foliage, T. baccata would increase the structural complexity of young
 woodlands, likely enhancing their value for biodiversity, their ecological
 resilience, as well as their amenity value. Inclusion of T. baccata in
 reforestation efforts would also aid its spontaneous recolonization of
 woodland areas, helping it to build larger, more widespread populations
 with greater resilience to future pressures.
description: Metadata file is included in the excel workbook.
description: Metadata file is included in the excel workbook.
DOI: 10.5061/dryad.w6m905qns
title: Data for: Benchmarking Oxford Nanopore read assemblers for high-quality molluscan genomes

description: Choosing the optimum assembly approach is essential to achieving a
 high-quality genome assembly suitable for comparative and evolutionary
 genomic investigations. Significant recent progress in long-read
 sequencing technologies such as PacBio and Oxford Nanopore Technologies
 (ONT) also brought about a large variety of assemblers. Although these
 have been extensively tested on model species such as Homo sapiens and
 Drosophila melanogaster, such benchmarking has not been done in Mollusca
 which lacks widely adopted model species. Molluscan genomes are
 notoriously rich in repeats and are often highly heterozygous, making
 their assembly challenging. Here, we benchmarked 10 assemblers based on
 ONT raw reads from two published molluscan genomes of differing
 properties, the gastropod Chrysomallon squamiferum (356.6Mb, 1.59%
 heterozygosity) and the bivalve Mytilus coruscus (1593Mb, 1.94%
 heterozygosity). By optimising the assembly pipeline, we greatly improved
 both genomes from previously published versions. Our results suggested
 that 40-50X of ONT reads are sufficient for high-quality genomes, with
 Flye being the recommended assembler for compact and less heterozygous
 genomes exemplified by C. squamiferum, while NextDenovo excelled for more
 repetitive and heterozygous molluscan genomes exemplified by M. coruscus.
 A phylogenomic analysis utilising the two updated genomes with other 32
 published high-quality lophotrochozoan genomes resulted in maximum support
 across all nodes, and we show that improved genome quality also leads to
 more complete matrices for phylogenomic inferences. Our benchmarking will
 ensure the efficiency in future assemblies for molluscs and perhaps also
 other marine phyla with few genomes available.
DOI: 10.5061/dryad.sf7m0cg4w
title: Supplementary material for: Exploring the impact of unstable terminals on branch support values in paleontological data

description: The dataset consists of a PDF file and two plain-text TNT scripts (*.run
 files). The PDF includes supporting Figures for the additional analyses
 conducted by Flores et al. on paleontological datasets. The TNT scripts
 conduct two complementary sets of analyses: (a) evaluation of
 taxon instability relative to the incompleteness ("mc.run"), and
 (b) changes in branch support values after pruning unstable taxa
 ("avmc.run"). To properly run these files in TNT, the name of
 the matrix files should be given as arguments (see the TNT
 documentation webpage for details on the usage of script files). The
 scripts generate CSV-formatted output for being subsequently read
 into any other software. Script files are provided as
 "ready-for-use", and are freely distributable and modifiable. We
 request that you cite the respective paper and dataset.
DOI: 10.5061/dryad.5x69p8d20
title: Datasets supporting: Coastal regions of the northern Antarctic Peninsula are key for gentoo populations

description: Southern Ocean ecosystems are rapidly changing due to climate variability.
 An apparent beneficiary of such change in the western Antarctic Peninsula
 (WAP) is the gentoo penguin Pygoscelis papua, which has increased its
 population size and expanded its range southward in the last 20 years. To
 better understand how this species has responded to large-scale changes,
 we tracked individuals during the non-breeding winter period from five
 colonies across the latitudinal range of breeding sites in the WAP,
 including from a recently-established colony. Results highlight
 latitudinal gradients in movement; strong associations with shallow,
 coastal habitats along the entire Antarctic Peninsula; and movements that
 are independent of, yet constrained by, sea ice. It is clear that coastal
 habitats essential to gentoo penguins during the breeding season are
 similarly critical during winter. Larger movements of birds from northern
 colonies in the WAP further suggest that leap-frog migration may influence
 colonization events by facilitating nest-area prospecting and use of new
 haul-out sites. Our results support efforts to develop a marine protected
 area around the WAP. Winter habitats used by gentoo penguins outline high
 priority areas for improving management of the spatiotemporally
 concentrated krill (Euphausia superba) fishery that operates in this
 region during winter.
description: This data set contains a zipped file with 71 individual .csv file
 used to support the analysis of winter movements of penguins presented by
 Korczak-Abshire et al. 2021, " Coastal regions of the northern
 Antarctic Peninsula are key for gentoo populations." Data include
 geographical position estimates from satellite telemetry studies on gentoo
 (<em>P. papua</em>) penguins tracked from the Antarctic
 peninsula region,  sea ice concentration, and depth of the sea floor at
 the position, colony identifier for where tracking commenced, the binary
 identifier of life stage of the investigated individuals.
description: A read me file is included with the data to identify fields,
 units, and study locations.
DOI: 10.5061/dryad.w3r2280pj
title: Paracoccidioides genomes reveal divergence

description: The fungus Paracoccidioides spp. is a prevalent human pathogen endemic to
 South America. The genus is composed of five species. In this report, we
 use 37 whole genome sequences to study the allocation of genetic variation
 in Paracoccidioides. We tested three genome-wide predictions of advanced
 speciation, namely, that all species should be reciprocally monophyletic,
 that species pairs should be highly differentiated along the whole genome,
 and that there should be low rates of interspecific gene exchange. We find
 support for these three hypotheses. Species pairs with older divergences
 show no evidence of gene exchange, while more recently diverged species
 pairs show evidence of modest rates of introgression. Our results indicate
 that as divergence progresses, species boundaries become less porous among
 Paracoccidioides species. Our results suggest that species in
 Paracoccidioides are at different stages along the divergence continuum.
description: Ploidy plots for six additional lines and a genome-wide
 phylogenetic tree.
DOI: 10.5061/dryad.2rbnzs7mk
title: Images of loop-mediated isothermal amplification (LAMP) for SARS-CoV-2 testing and optimized 'Cap-iLAMP'

description: Here we present images of loop-mediated isothermal
 amplification (LAMP) and optimized Cap-iLAMP (capture and
 improved ‎loop-mediated isothermal amplification).
 Cap-iLAMP combines a hybridization capture-based RNA extraction
 of gargle lavage samples with an improved colorimetric RT-LAMP assay and
 smartphone-based color scoring. Cap-iLAMP is compatible with point-of-care
 testing and enables the detection of SARS-CoV-2 positive samples in less
 than one hour. The sensitivity is 97% and the specificity is 99%.
DOI: 10.15468/dl.qyw2z2
title: Occurrence Download

description: A dataset containing 1482715 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "TaxonKey is Piranga olivacea",
 "Year 2010-2025"
 ]
}

 The dataset includes 1482715 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002668-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.t1g1jwt1c
title: Benthic foraminiferal raw counts and manuscript data

description: Quantitative palaeobathymetric reconstructions based on foraminiferal
 proxies have been used in a wide variety of geological studies on
 tectonic, climatic and environmental changes in sedimentary basins.
 However, palaeo-water depth estimates are frequently biased due to
 taphonomic processes (dissolution, transport) as well as local conditions
 (primary productivity, oxygen content, and organic matter fluxes). This
 study evaluated the level of reliability of three commonly used transfer
 equations based on planktic and benthic foraminiferal proxies that produce
 different palaeobathymetric results. The most trustworthy method involves
 removing abundant infaunal benthic foraminifera before applying the
 paleo-water depth equation based on benthic foraminiferal water-depth
 ranges and presence/absence of species. This new approach provides sound
 palaeobathymetric results that improve estimations of long- and short-term
 relative sea-level changes with negligible influence of taphonomic as well
 as ecological factors. In case of using one equation based on
 planktic/benthic ratios (P/B ratios), removing all infaunal benthic
 foraminiferal species improves the accuracy of P/B ratios, which yields
 more accurate palaeodepth reconstructions despite the low level of
 trustworthiness of this equation for both long- and short-term relative
 sea-level variations.
description: This
 database includes all benthic foraminiferal raw counts, and manuscript
 data including: 1) paleobathymetric data; 2) foraminiferal and stable
 isotope data used in figure 8; and 3) PCA assemblages loadings.
DOI: 10.5061/dryad.6t1g1jwxm
title: Raster layers of prioritisation analyses for current and future conditions based on phylogenetic diversity of Neotropical palms

description: Aim: Palms are an ecologically and societally important plant group, with
 high diversity in the Neotropics. Here, we estimated the impacts of future
 climate change on phylogenetic diversity (PD) of Neotropical palms under
 varying climatic and dispersal scenarios, assessed the effectiveness of
 the established network of protected areas (PAs) for conserving palms PD
 today and in 2070, and identified priority areas for the conservation of
 palm species and their evolutionary history in the face of climate change.
 Location: Neotropics. Methods: We used ecological niche modelling to
 estimate the distribution of 367 species in the present and for 2070 based
 on two greenhouse gas emission and two dispersal scenarios. We calculated
 Faith’s PD within each five arc-minute grid cell to evaluate the
 effectiveness of PAs relative to null models and used phylogenetic spatial
 prioritisation analysis to detect priority areas. Results: We found that
 even under the most optimistic climatic and dispersal scenarios, the
 established network of PAs performed poorly in safeguarding palms PD under
 both current conditions and those projected for 2070. Significant losses
 in PD inside PAs are expected under future climate conditions, especially
 if species are unable to disperse to suitable areas. Nevertheless, a
 modest and strategic increase in the number of PAs could considerably
 improve the protection of palms PD in the present and 2070. Main
 conclusions: The PD of Neotropical palms is poorly represented within the
 established network of PAs, at both present and in 2070. A higher realised
 dispersal rates would diminish PD losses inside the network of PAs. The
 conservation of palm PD can be improved through the expansion of PAs in
 strategic regions such as the upper portion of the Amazon Basin, Tropical
 Andes, and Mesoamerica.
description: Raster layers of
 prioritisation analyses for current and future conditions based on
 phylogenetic diversity of Neotropical palms to expand current network of
 protected area. Future scenarios were represented by different combination
 between dispersal rates and representative concentration
 pathways. Layer
 descriptions: Prioritisation_CurrentConditions.tif: prioritisation for current climatic conditions Prioritisation_Dispersal-0_RCP-45.tif: prioritisation for a negligible dispersal scenario (0 km/decade) and a representative concentration pathway of 4.5 Prioritisation_Dispersal-0_RCP-85.tif: prioritisation for a negligible dispersal scenario (0 km/decade) and a representative concentration pathway of 8.5 Prioritisation_Dispersal-50_RCP-45.tif: prioritisation for a human assisted dispersal scenario (50 km/decade) and a representative concentration pathway of 4.5 Prioritisation_Dispersal-50_RCP-85.tif prioritisation for a human assisted dispersal scenario (50 km/decade) and a representative concentration pathway of 8.5