cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2rbnzs7pb
title: Large herbivore biomass in protected areas

description: Large herbivores provide key ecosystem processes, but have experienced
 massive historical losses and are under intense pressure, leaving current
 ecosystems with dramatically simplified faunas relative to the long-term
 evolutionary norm. Hampered by a shifting baseline, natural levels of
 large-herbivore biomass are poorly understood and seldom targeted. Here,
 we present a collation of large-herbivore biomass data from
 published sources as well as personal communication. The data includes
 continent, ecosystem name, latitude, longitude, large
 herbivore biomass in kg/km2 and the source of the data.
 It can be used together with net primary productivity
 (e.g., using satellite-derived NPP retrieved from
 http://files.ntsg.umt.edu/data/NTSG_Products/MOD17/GeoTIFF/MOD17A3/GeoTIFF_30arcsec/) to explore the scaling relationship between producer and consumer.
description: We collated published empirical data on large-herbivore biomass
 (kg/km<sup>2</sup>) from Hatton<i> et al.</i>
 (2015), Rodriguez<i> et al.</i> (2014) and from personal
 communication. Hatton et al. reports wild large-herbivore biomass (≥5 kg)
 for 73 protected areas. Opposite to Hatton <i>et al.</i> we
 included the biomass of megaherbivores (i.e., herbivores ≥1000 kg, e.g.,
 elephants, rhinos, and hippos) and migratory species (species with
 seasonal, long-distance movement of individuals) weighted by the fraction
 of the year they spend in the ecosystem. Rodriguez <i>et
 al.</i> reports contemporary ungulate biomass of all species in the
 orders Perissodactyla, Artiodactyla or Proboscidea for 95 natural areas
 (national parks and protected areas with some degree of traditional
 pastoralism). We ensured no data overlap between Rodriguez et al and
 Hatton et al. From Rodriguez et al., we included the livestock biomass
 because grazing livestock in pastoralist systems also rely on the local
 primary production. In total, we included 289 data points from 146
 ecosystems across Africa, Asia, Europe, North America and South America.
 GPS positions were checked using Google maps satellite images and place
 names. Doubtful positions were checked against primary literature and
 either placed accordingly or moved to reserve centers. We used data from
 the years 1926-2009 as well as data from unknown years.
description: Refences: Hatton, I.A., McCann, K.S., Fryxell,
 J.M., Davies, T.J., Smerlak, M., Sinclair, A.R.E. & Loreau, M.
 (2015) The predator-prey power law: Biomass scaling across terrestrial and
 aquatic biomes. <i>Science,</i> 349.
 Rodriguez, J., Blain, H.A., Mateos, A., Martin-Gonzalez, J.A.,
 Cuenca-Bescos, G. & Rodriguez-Gomez, G. (2014) Ungulate carrying
 capacity in Pleistocene Mediterranean ecosystems: Evidence from the
 Atapuerca sites. <i>Palaeogeography Palaeoclimatology
 Palaeoecology,</i> 393, 122-134.
DOI: 10.5281/zenodo.18380404
title: Supporting data for Matsuzawa, Zhu, et al., "Nonlinear Diffusion and Decay of a Blob of Turbulence Spreading Into a Quiescent Fluid", PNAS, (2026)

description: Paper: Nonlinear Diffusion and Decay of a Blob of Turbulence Spreading Into a Quiescent Fluid

Authors: Takumi Matsuzawa, Minhui Zhu, Nigel Goldenfeld, William T. M. Irvine

Description:This repository contains the data presented in Figures 1–5 of the paper, which examine the decay and propagation of turbulence generated by repeatedly colliding vortex rings. In the study, we also explored turbulence decay generated by oscillating a double grid.

Each folder contains the data used to produce the main figures. For Figures 1C–F and 4C–F, we present time slices of ensemble-averaged fields, including energy and enstrophy.

The original velocity field data is approximately 10 GB per sample. We performed 21, 10, and 10 replications for the blob, double oscillating grid, and single oscillating grid configurations, respectively. From these, Reynolds averaging was applied to extract the turbulent (fluctuating) components. 

Contents:Each folder contains HDF5 files with relevant data that made it into the plot.

E.g. Figure 2B_tegral_lengthscale.h5 contains/blob/t_t0: t-t0/blob/ell: ell (Integral length scale) from the blob experiments/blob/ell_scaled: ell / Lbox (Scaled integral length scale)...
DOI: 10.5281/zenodo.18380405
title: Supporting data for Matsuzawa, Zhu, et al., "Nonlinear Diffusion and Decay of a Blob of Turbulence Spreading Into a Quiescent Fluid", PNAS, (2026)

description: Paper: Nonlinear Diffusion and Decay of a Blob of Turbulence Spreading Into a Quiescent Fluid

Authors: Takumi Matsuzawa, Minhui Zhu, Nigel Goldenfeld, William T. M. Irvine

Description:This repository contains the data presented in Figures 1–5 of the paper, which examine the decay and propagation of turbulence generated by repeatedly colliding vortex rings. In the study, we also explored turbulence decay generated by oscillating a double grid.

Each folder contains the data used to produce the main figures. For Figures 1C–F and 4C–F, we present time slices of ensemble-averaged fields, including energy and enstrophy.

The original velocity field data is approximately 10 GB per sample. We performed 21, 10, and 10 replications for the blob, double oscillating grid, and single oscillating grid configurations, respectively. From these, Reynolds averaging was applied to extract the turbulent (fluctuating) components. 

Contents:Each folder contains HDF5 files with relevant data that made it into the plot.

E.g. Figure 2B_tegral_lengthscale.h5 contains/blob/t_t0: t-t0/blob/ell: ell (Integral length scale) from the blob experiments/blob/ell_scaled: ell / Lbox (Scaled integral length scale)...
DOI: 10.5061/dryad.7pvmcvdtj
title: Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies

description: Infections early in life can have enduring effects on an organism’s
 development and immunity. In this study, we show that this equally applies
 to developing “superorganisms” – incipient social insect
 colonies. When we exposed newly mated Lasius niger ant
 queens to a low pathogen dose, their colonies grew more slowly than
 controls before winter, but reached similar
 sizes afterwards. Independent of exposure, queen hibernation
 survival improved when the ratio of pupae to workers was small.
 Queens that reared fewer pupae before worker emergence exhibited
 lower pathogen levels, indicating that high brood rearing efforts
 interfere with the ability of the queen’s immune system to suppress
 pathogen proliferation. Early-life queen pathogen-exposure also
 improved the immunocompetence of her worker offspring, as demonstrated by
 challenging the workers to the same pathogen a year later.
 Transgenerational transfer of the queen’s pathogen experience to
 her workforce can hence durably reduce the disease
 susceptibility of the whole superorganism.
description: All experimental procedures are described in the main manuscript
 text or supplemental material. Data collectors: Barbara Casillas-PÈrez,
 Christopher D. Pull, Elisabeth Naderlinger
description: ReadMe file has been provided; files names indicate the figures
 produced with each dataset.
DOI: 10.21979/n9/iys0ze
title: Longitudinal Wastewater-Based Surveillance for SARS-CoV-2 in High-Density Student Dormitories in Singapore

description: Environmental surveillance of wastewater from student dormitories was carried out over an academic year at a university campus in Singapore. During the surveillance period, SARS-CoV-2 trends in campus wastewater levels closely resembled Singapore’s combined national wastewater levels and clinical COVID-19 cases. In the examined sewer sheds, larger student populations significantly increased both the odds and duration of detecting SARS-CoV-2 RNA (p-value &lt; 0.001 for both measures). However, the type of building corridor did not have a statistically significant impact on either the duration of detection (p-value = 0.716) or the odds of detecting the virus (p-value = 0.067). This study exemplifies the use of a decentralized and high-resolution surveillance system for the twice-weekly detection of viral shedding in high-density living conditions to support public health decisions and management.
DOI: 10.5061/dryad.dncjsxm0s
title: Evolutionary modularity, integration and disparity in an accretionary skeleton: Analysis of venerid Bivalvia

description: Modular evolution, the relatively independent evolution of body parts, may
 promote high morphological disparity in a clade. Conversely, integrated
 evolution via the stronger covariation of parts may limit disparity.
 However, integration can also promote high disparity by channeling
 morphological evolution along lines of least resistance—a process that may
 be particularly important in the accumulation of disparity among organisms
 with accretionary growth, as in many invertebrate systems. We use a
 time-calibrated phylogenetic hypothesis and high-density, 3D
 semilandmarking to analyze the relationship between modularity,
 integration, and disparity in the most diverse extant bivalve family: the
 Veneridae. In general, venerids have a simple, two-module parcellation of
 body features that is divided into features of the calcium carbonate shell
 and features of the internal soft anatomy. This division falls more along
 developmental than functional lines when placed in the context of bivalve
 evolutionary-development and biomechanics. While the venerid body is
 tightly integrated in absolute terms, increasing modularity strength among
 subclades and ecologies appears to correlate with increasing disparity,
 indicating that shifts towards more mosaic evolution beget higher
 morphologic variance in this speciose family.
DOI: 10.5061/dryad.crjdfn34x
title: Data from: Endophytes shape the legacy left by the above- and below ground litter of the host affecting the establishment of a legume

description: Plant litter is a key component of plant-soil feedback (PSF), given its
 strong potential impacts on plant establishment and growth, through
 chemical and physical pathways. Although PSF of the layer of dead plant
 material on the soil surface (aboveground litter) has been widely studied
 little is known about the role of dead roots (belowground litter) and the
 impact of plant symbionts on host litter legacy. Here, we examined whether
 the fungal endophyte Epichloë occultans changed the effects of above and
 belowground litter of Lolium multiflorum plants on the establishment of
 Trifolium repens. We hypothesized that both types of litter deposited by
 the grass-endophyte symbiosis reduce the establishment of the legume due
 to the release of allelopathic compounds during the decomposition and
 leaching processes. To test this, we performed two experiments with
 different quantities of litter produced by plants of the same grass
 population, with high and low levels of endophyte infection (E+ and E-).
 Seeds of T. repens were exposed to the aboveground litter with or without
 the addition of belowground litter, or to their leachates, to separate the
 physical and chemical pathways. We found that the treatments with the
 combination of the above and belowground litter produced by E+ plants,
 increased the germination speed and seedling emergence of T. repens by 56%
 compared with both types of litter produced by E- plants. A similar effect
 was also observed with only the aboveground litter. However, the
 belowground litter of E+ plants reduced the germination speed, seedling
 emergence by 76% and establishment of T. repens by 73% compared with the
 belowground litter of E- plants. Besides, the belowground litter had
 positive effects on the root colonization by arbuscular mycorrhizal fungi
 and reduced the root nodulation of T. repens. The quantity of litter did
 not affect any of these responses. Our results suggest that these litter
 legacy effects could be due to the release of endophyte induced secondary
 metabolites, such as phenolic and flavonoid compounds. Changes in host
 plant litter inputs may have consequences for the prevalence of legume
 plants in grasslands and pastures, affecting their quality and dynamics.
description: See manuscript for methods details.
description: The data is divided according to the
 experiments that were carried out. These include the final data used to
 generate the figures and tables.
DOI: 10.5061/dryad.73n5tb2xv
title: Three phylogenetically distinct and culturable diazotrophs are perennial symbionts of leaf-cutting ants

description: The obligate mutualistic basidiomycete fungus, Leucocoprinus
 gongylophorus, mediates nutrition of leaf-cutting ants with carbons from
 vegetal matter. In addition, diazotrophic Enterobacteriales in the fungus
 garden and intestinal Rhizobiales supposedly mediate assimilation of
 atmospheric nitrogen; and Entomoplasmatales in the genus Mesoplasma, as
 well as other yet unidentified strains, supposedly mediate ant
 assimilation of other compounds from vegetal matter, such as citrate,
 fructose and aminoacids. Together, these nutritional partners
 would support the production of high yields of leafcutter biomass. In the
 present investigation, we propose that three phylogenetically distinct and
 culturable diazotrophs in the genera Ralstonia, Methylobacterium and
 Pseudomonas integrate this symbiotic nutrition network, facilitating ant
 nutrition on nitrogen. Strains in these genera were often isolated and
 directly sequenced in 16S rRNA libraries from the ant abdomen, together
 with the non-diazotrophs Acinetobacter and Brachybacterium. These five
 isolates were underrepresented in libraries, suggesting that none of them
 is dominant in vivo. Libraries have been dominated by four uncultured
 Rhizobiales strains in the genera Liberibacter, Terasakiella and
 Bartonella and, only in Acromyrmex ants, by the Entomoplasmatales in the
 genus Mesoplasma. Acromyrmex also presented small amounts of two other
 uncultured Entomoplasmatales strains, Entomoplasma and Spiroplasma. The
 absence of Entomoplasmatales in Atta workers implicates that association
 with these bacteria is not mandatory for ant biomass production. Most of
 the strains that we detected in South American ants were genetically
 similar with strains previously described in association with leafcutters
 from Central and North America, indicating wide geographic dispersion, and
 suggesting fixed ecological services.
DOI: 10.7280/d1nx1w
title: Fine resolution flood forecasts and hindcast of Hurricane Harvey for Harris County, TX using PRIMo

description: Urban flooding from extreme precipitation has emerged as a major threat to
 metropolitan regions of the United States. There is a pressing need for
 flood inundation forecasts capable of meeting emergency response needs for
 public safety and damage reduction from the household scale
 upwards to the entire region. Leveraging the computational efficiency of
 the numerical hydrodynamic model PRIMo (University of California Irvine),
 we present a flood inundation forecasting system that
 ingests short-range quantitative precipitation forecast data
 provided by the National Weather Service, 3 m resolution
 topographic data available from the 3D Elevation Program of the
 United States Geologic Survey, and other data to simulate flooding at
 fine-resolution (3 m) at the county/regional scale, and inform emergency
 management at household scales. With an application to Metropolitan
 Houston and 5-day simulations of Hurricane Harvey, the forecast system is
 shown to capture flood peaks with a mean absolute error (MAE) of 0.86 m,
 hourly streamflow stage is captured with a median MAE and Nash Sutcliffe
 Efficiency (NSE) of 0.90 m and 0.41, respectively, and high water marks
 (HWMs) are captured with a MAE of 0.77 m. The forecast system also
 achieves hit rates of 90% and 73% predicting 3-1-1- distress calls and
 FEMA property damage claims, respectively, based on simulated flood
 depth. Based on fast model speeds made possible by upscaling and
 parallel computing, these results demonstrate the potential to
 operationally forecast flood inundation and its impacts in the U.S. for
 emergency management. This dataset contains a Hurricane Harvey hindcast as
 well as three forecast scenarios at 3 m linear
 resolution using different levels of PRIMo's computational grid
 upscaling technology. The data represents maximum accumulated flood depths
 over the period August 26 2017 - August 30 2017 as a result of heavy
 precpitation and storm surge. The spatial extent of the flood hazard
 layers is approximately 9,000 km2 encompassing Harris
 County, Texas.
description: Included GeoTIFF files (.tif extension) may be opened directly in
 any geospatial data visualization software supporting rasterized data
 including but not limited to ArcGIS and QGIS. The metadata standard
 includes spatial projection of the flood hazard rasters for overlay with
 other spatial information. To access the data contained
 in the zipped Geo-database (.gdb.zip extension), first decompress the
 archive file (e.g. using 7Zip). Subsequently the geodatabase may be opened
 directly in most GIS software including ArcGIS and QGIS.
DOI: 10.5061/dryad.pzgmsbcn5
title: Genetic variation in sea otters (Enhydra lutris) from the North Pacific with relevance to the threatened Southwest Alaska distinct population segment

description: For the sea otter (Enhydra lutris), genetic population structure is an
 area of research that has not received significant attention, especially
 in Southwest Alaska where that distinct population segment has been listed
 as threatened since 2005 pursuant to the U.S. Endangered Species Act. In
 this study, 501 samples from 14 locations from Prince William Sound,
 Alaska to the Commander Islands in Russia were analyzed for variation at
 13 microsatellite loci. Our results indicate a high degree of genetic
 divergence among the 14 locations (FST = 0.12) with gene flow conforming
 to the isolation by distance (IBD) model (r2 = 0.491, p &lt; 0.05).
 The 14 sampling locations formed six geographic associations in clustering
 and ordination analyses that likely correspond to remnant population
 lineages: 1) Southcentral Alaska, 2) Kodiak and North Alaska Peninsula, 3)
 South Alaska Peninsula and Bristol Bay, 4) Eastern Aleutian, 5) Western
 Aleutian, and 6) the Commander Islands. Except for South Alaska Peninsula
 and Bristol Bay, these clusters closely agree with previously defined
 stock and management unit boundaries. Our results reveal significant
 genetic population structure and are generally congruent with current
 management strategies for the threatened Southwest Alaska distinct
 population segment.
description: The file contains microsatellite data from 13 loci for 501 sea
 otters collected from 14 locations in Alaska and Russia. The
 individual's sex and latitude and longitude of sample collection are
 included with the multilocus genotype. Missing data are coded as
 "0" and "U" indicates that the sex of the individual
 is unknown.
DOI: 10.5061/dryad.31zcrjdmf
title: Genome content flat files for comparative genomic analysis of seadragons and relatives

description: Seadragons are widely recognized for their derived and novel traits.
 Research and conservation efforts involving these unique fish species and
 their relatives have been hindered by a lack of genomic resources. From
 this project we present full, annotated genomes of leafy and
 weedy seadragons, which help uncover surprising features of gene family
 and genome architecture evolution that likely relate to extreme phenotypic
 traits in seadragons, pipefishes, and seahorses. These genomes are
 important research resources for the Syngnathidae, a diverse,
 morphologically exceptional group of vertebrates, and for comparative
 genomic study of vertebrates in general.
description: Genome annotations (genes and repetitive DNA) for
 seadragons and other teleost fishes using standard tools (e.g. Braker,
 RepeatModeler, RepeatMasker) Custom compartive
 genomic analysis and visualization using R scripts, and associated data
 files 10x draft genome assembly for
 <em>Doryrhamphus excisus</em> de novo
 transcriptome assemblies for <em>Syngnathus scovelli</em>
description: The contents of this data set are organized into three high-level
 directories: analysis_code/ (contains R
 scripts and data files to perform downstream analyses described in the
 manuscript) summary_files/ (contains braker gene
 annotations for 5 syngnathiform genomes and repeat annotations for 16
 teleost genomes) supplementary_assemblies/ (contains
 a draft 10x genome assembly for bluestripe pipefish -
 BP1_comb_355M_pseudohap.2.fasta.gz, and two de novo Trinity transcriptome
 assemblies for Gulf pipefish)
DOI: 10.5061/dryad.n8pk0p2wc
title: Data from: The first phylogeny of Australasian Lamiinae longhorn beetles

description: We used phylogenomic data and information from the beetle fossil record to
 reconstruct the phylogeny and historical biogeography of Australasian
 longhorn beetles (Cerambycidae) in the subfamily Lamiinae. We further
 focused our study on the distribution of proposed diagnostic morphological
 characters in Lamiinae, and on the phylogeny of Rhytiphora
 Audinet-Serville, Australia’s most species-rich genus of longhorn beetles.
 Lamiinae was monophyletic, but the majority of tribes were poly- or
 paraphyletic. Within Lamiinae, we recovered four main clades, including
 one clade mostly comprised of Australian endemic genera of probable
 Gondwanan origin. This clade also contained taxa that dispersed from
 Australia to New Zealand and experienced multiple independent instances of
 wing loss. Another of the four clades contained Australian genera that
 colonised the region from Asia, including Rhytiphora. The defining feature
 of Rhytiphora, the setose “sex patches” on the male abdomen, was shared
 with many other Asian lamiine genera recovered in the same clade. Our
 results shed new light on the geographic and temporal origins of
 Australian Lamiinae, revealing an unexpected mixture of both ancient
 Gondwanan and recent Asian origins. Moreover, we confirmed rampant
 non-monophyly at the tribal level among the Australasian genera of
 Lamiinae. Based on our results, we move 17 genera into Lamiinae incertae
 sedis and six genera into the tribe Ancitini Aurivillius. We also
 reinstate the tribe Niphonini Pascoe for part of the Asian-Australian
 Pteropliini Thomson and synonymise Achriotypa Pascoe with Rhytiphora.
description: <strong>Alignment files</strong>
 Lam_138tax_concat_aa.nex (concatenated alignment of amino
 acids)<br> Lam_138tax_concat_nt.nex (concatenated alignment of
 nucleotides)<br> Lam_138tax_concat_nt-degen.nex (concatenated
 alignment of degeneracy-recoded nucleotides)<br>
 Lam_138tax_concat_nt-noLR.nex (concatenated alignment of nucleotides with
 third codon positions, Leu and Arg removed)
 <strong>Maximum likelihood phylogenies
 (IQ-TREE)</strong> Lam_IQ_aa.tree (Newick-format
 tree from amino acid dataset)<br> Lam_IQ_degen.tree (Newick-format
 tree from degeneracy-recoded nucleotide dataset)<br> Lam_IQ_nt.tree
 (Newick-format tree from nucleotide dataset)
 <strong>Dated phylogenies
 (MCMCTree)</strong> Lam_MCMC_noLR_alt-cauch.tre
 (Nexus-format tree from alternate fossil arrangement and truncated Cauchy
 priors)<br> Lam_MCMC_noLR_alt-unif.tre (Nexus-format tree from
 alternate fossil arrangement and uniform priors)<br>
 Lam_MCMC_noLR_cauch.tre (Nexus-format tree from original fossil
 arrangement and truncated Cauchy priors)<br> Lam_MCMC_noLR_unif.tre
 (Nexus-format tree from original fossil arrangement and uniform
 priors) <strong>README
 file</strong> Lamiinae_Dryad_metadata.txt
 (detailed information on the data package)