cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3xsj3txmn
title: Pattern variation is linked to anti-predator colouration in butterfly larvae

description: Prey animals typically try to avoid being detected and/or advertise to
 would-be predators that they should be avoided. Both anti-predator
 strategies primarily rely on colour to succeed, but the specific
 patterning used is also important. While the role of patterning in
 camouflage is relatively clear, the design features of aposematic patterns
 are less well understood. Here, we use a comparative approach to
 investigate how pattern use varies across a phylogeny of 268 species of
 cryptic and aposematic butterfly larvae, which also vary in social
 behaviour. We find that longitudinal stripes are used more frequently by
 cryptic larvae and that patterns putatively linked to crypsis are more
 likely to be used by solitary larvae. In contrast, aposematic larvae are
 more likely to use horizontal bands and spots, but we find no differences
 in the use of individual pattern elements between solitary and gregarious
 aposematic species. However, solitary aposematic larvae are more likely to
 display multiple pattern elements, whereas those with no pattern are more
 likely to be gregarious. Our study advances our understanding of how
 pattern variation, colouration and social behaviour co-vary across
 lepidopteran larvae, and highlights new questions about how patterning
 affects larval detectability and predator responses to aposematic prey.
description: The data was collected by mining online sources. It has been
 processed and analysed in R.
description: The data was analysed in R requiring the following
 packages: ape
 geiger MCMCglmm
 openxlsx
DOI: 10.15468/dl.3a24rz
title: Occurrence Download

description: A dataset containing 22801903 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Sweden",
 "Geometry POLYGON((17.37308 58.55154,19.29389 58.55154,19.29389 60.60106,17.37308 60.60106,17.37308 58.55154))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 22801903 records from 655 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002985-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4xgxd25f9
title: THz optical solitons from dispersion-compensated antenna-coupled planarized ring quantum cascade lasers

description: Quantum Cascade Lasers (QCL) constitute an intriguing opportunity for the
 production of on-chip optical Dissipative Kerr Solitons (DKS):
 self-organized optical waves which can travel while preserving their shape
 thanks to the interplay between Kerr effect and dispersion. Originally
 demonstrated in passive microresonators, DKS were recently observed in
 mid-IR ring QCL paving the way for their achievement even at longer
 wavelengths. To this end we realized defect-less THz ring QCLs featuring
 anomalous dispersion leveraging on a technological platform based on
 waveguide planarization. A concentric coupled-waveguide approach is
 implemented for dispersion compensation whilst a passive broadband
 bullseye antenna improves the device power extraction and far field. In
 these devices, comb spectra featuring sech2 envelopes are presented for
 free-running operation. This first hint of the presence of solitons is
 further supported by the observation of highly hysteretic behaviour and by
 phase-sensitive measurements which show the presence of self-starting 12
 ps-long pulses in the reconstructed time profile of the emission
 intensity. These observations are in very good agreement with our numeric
 simulations based on a Complex Ginzburg-Landau equation time-domain
 solver. Such devices constitute a new experimental platform for the study
 of soliton phenomena in the THz range, allowing as well on-chip, passive
 ultrashort THz pulse generation appealing for a variety of applications.
DOI: 10.15468/dl.shssxk
title: Occurrence Download

description: A dataset containing 29035 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aegilops geniculata"
 ]
}

 The dataset includes 29035 records from 416 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003491-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jwstqjqfg
title: MALDI imaging analysis of complex carbohydrates in human and mouse models pulmonary fibrosis

description: Human lung fibrosis samples. Mouse models of lung fibrosis in WT and
 Epm2a, and Gaa knockout strains were analyzed using MALDI-MSI. Analytes
 analyzed were N-linked glycans and glycogen.
description: Tissues were sectioned at 4 μm and mounted on positively charged
 glass slides for MALDI imaging as previously described. Slides were heated
 at 60°C for 1 hr. After cooling, tissue sections were deparaffinized by
 washing twice in xylene (3 min each). Tissue sections were then rehydrated
 by washing slides twice in 100% ethanol (1 min each), once in 95% ethanol
 (1 min), once in 70% ethanol (1 min), and twice in water (3 min each).
 Following washes, slides were transferred to a coplin jar containing
 citraconic anhydride buffer for antigen retrieval and the jar was placed
 in a vegetable steamer for 25 min. Citraconic anhydride buffer was
 prepared by adding 25 µL citraconic anhydride in 50 mL water and adjusted
 to pH 3.0 with HCl. After antigen retrieval, slides were dried in a vacuum
 desiccator prior to enzymatic digestion. An HTX spray station (HTX) was
 used to coat the slide with a 0.2 ml aqueous solution of isoamylase (3
 units/slide) and PNGase F (20 mg total/ slide). The spray nozzle was
 heated to 45˚C with a spray velocity of 900 m/min. Following enzyme
 application, slides were incubated at 37˚C for 2 hr in a humidified
 chamber, and dried in a vacuum desiccator prior to matrix application
 [a-cyano-4-hydroxycinnamic acid matrix (0.021 g CHCA in 3 ml 50%
 acetonitrile/50% water and 12 µL 25%TFA) applied with HTX sprayer]. For
 detection and separation of glycogen and N-glycans, a Waters SynaptG2-Si
 high-definition mass spectrometer equipped with traveling wave ion
 mobility was used. The laser was operating at 1000 Hz with an energy of
 200 AU and spot size of 75 µm, mass range is set at 500–3000m/z.
 Ion mobility settings were done according to previously established
 parameters with a trap entrance energy of 2V, trap bias of 85V, and
 DC/exist of 0V. Wave velocity settings were set to: trap 9.6 m/s, IMS
 4.6m/s, transfer 17.4 m/s. Wave height settings were set to: trap 4V,
 IMS,42.7, transfer 4V, and additional settings are variable wave ramp down
 of 1400 m/s. Data was acquired with Masslynx v4.2. MALDI images were
 produced using the HDI software v1.5 (Waters Corp) following built-in peak
 integration function to account for mass drift over the MALDI run. All
 MALDI images were normalized to total ion current (TIC) within each
 pixel.
DOI: 10.5061/dryad.hmgqnk9ng
title: Data for: Simulated climate change causes asymmetric responses in insect life history timing potentially disrupting a classic ecological speciation system

description: Climate change may alter phenology within populations with cascading
 consequences for community interactions and ongoing evolutionary
 processes. Here, we measured the response to climate change in two
 sympatric, recently diverged (~170 years) populations of Rhagoletis
 pomonella flies specialized on different host fruits (hawthorn and apple)
 and their parasitoid wasp communities. We tested whether warmer
 temperatures affect dormancy regulation and its consequences for synchrony
 across trophic levels and temporal isolation between divergent
 populations. Under warmer temperatures, both fly populations developed
 earlier. However, warming significantly increased the proportion of
 maladaptive pre-winter development in apple, but not hawthorn, flies.
 Parasitoid phenology was less affected, potentially generating ecological
 asynchrony. Observed shifts in fly phenology under warming may decrease
 temporal isolation, potentially limiting ongoing divergence. Our findings
 of complex sensitivity of life-history timing to changing temperatures
 predict that coming decades may see multifaceted ecological and
 evolutionary changes in temporal specialist communities.
description: These are laboratory eclosion data for
 <em>Rhagoletis</em> <em>pomonella</em> flies and
 their community of parasitoid wasps from an a climate warming simulation
 study. See Lackey, Deneen, Feder, Ragland, Hahn, and Powell,
 "Simulated climate change causes asymmetric responses in insect life
 history timing potentially disrupting a classic ecological speciation
 system" BioRxiv: https://doi.org/10.1101/2022.12.06.519222 for detailed methods.
description: These data are presented in a tab-delimited R dataframe, which
 can be opened with a text editor or a spreadsheet program.
DOI: 10.5061/dryad.kprr4xh8z
title: Assessment of targeted enrichment locus capture across time and museums using odonate specimens

description: The use of gDNA isolated from museum specimens for high throughput
 sequencing, especially targeted sequencing in the context of
 phylogenetics, is a common practice. Yet, little understanding has been
 focused on comparing the quality of DNA and the results of sequencing
 museum DNAs. Dragonflies and damselflies are ubiquitous in freshwater
 ecosystems and are commonly collected and preserved insects in museum
 collections hence their use in this study. However, the history of odonate
 preservation across time and museums have resulted in wide variability in
 the success of viable DNA extraction, necessitating an assessment of their
 usefulness in genetic studies. Using Anchored Hybrid Enrichment probes, we
 sequenced DNA from samples at two museums, 48 from the American Museum of
 Natural History (AMNH) in NYC, USA, and 46 from the Naturalis Biodiversity
 Center (RMNH) in Leiden, Netherlands ranging from global collection
 localities and across a 120-year time span. We recovered at least 4 loci
 out of an &gt;1000 locus probe set for all samples, with the average
 capture being ~385 loci. Neither specimen age nor size was a good
 predictor of locus capture, but recapture rates differed significantly
 between museums. Samples from the AMNH had lower overall locus capture
 than the RMNH, perhaps due to differences in specimen storage over time.
description: For taxon sampling, damselflies and dragonflies from the RMNH and AMNH were selected with an emphasis on having a breadth of sizes, families, and ages. We initially selected samples that ranged in age from 2001 (~20 years old) to 1909 (~112 years old). We chose 94 specimens; 64 were Anisoptera and 30 were Zygoptera, from 48 AMNH and 46 RMNH. Genomic DNA was isolated and sent to RAPID Genomics (Gainesville Florida) for library preparation and sequencing using Anchored Hybrid Enrichment probes. We trimmed adapters from raw reads for each sample using <em>fastp</em> and checked quality using <em>multiQC</em>. Following trimming, we assembled and assigned orthology to each targeted capture locus. Following assembly, we screened each locus for orthology by ensuring that the locus did not have BLAST hits to multiple places in the genome and, by ensuring the best reciprocal hits between the reference and the query sequence. We generated a multiple sequence alignment and concatenated the alignments using <em>FASconCAT</em> (Kück and Meusemann 2010) and generated an optimal partitioning scheme using relaxed clustering with the model fixed to GTR+G for each subset in IQtree v.2.1.3 (Minh et al. 2020). We selected a model for each subset in the partitioning scheme using ModelFinder and estimated a maximum likelihood tree with 1,000 ultrafast bootstrap replicates in IQtree.
description: IQ-Tree v.2.1.3 (Data matrix - fasta file)
 UNIX/Command line or a Text Editor for viewing (fastq files - raw
 data) FigTree (Tree file - .treefile)
 BBEdit (Partition files - Nexus)
DOI: 10.5061/dryad.jsxksn0fn
title: Regional and local factors interact to shape colonization and extinction dynamics of invasive Hydrilla verticillata in a patchy landscape

description: Understanding the response of species to global change requires
 disentangling the drivers of their distributions across landscapes.
 Colonization and extinction processes, shaped by the interplay of
 landscape-level and local patch-level factors, are key determinants of
 these distributions. However, disentangling the influence of these
 factors, when larger-scale processes manifest at local scales, remains a
 challenge. We addressed this challenge by investigating the colonization
 and extinction dynamics of the aquatic plant, Hydrilla verticillata, in a
 complex riverine rock pool system. This system, with hundreds of rock
 pools experiencing varying flooding frequencies, provided a natural
 laboratory to examine how a single landscape-level disturbance can
 differentially impact colonization and extinction depending on local patch
 characteristics to shape species distributions. Using five years of data
 across over 500 sites and more than 5,000 surveys, we employed dynamic
 occupancy models to model colonization, extinction, and changes in
 Hydrilla patch occupancy while accounting for imperfect detection. Our
 results revealed that larger, infrequently flooded pools closer to the
 river were more likely to be colonized. In contrast, local extinction of
 Hydrilla was more likely in smaller pools closer to the river that flooded
 frequently. These findings underscore the importance of considering
 context-dependence in species distribution models. The same
 landscape-level disturbance (flooding) had opposing effects on
 colonization and extinction, with the direction and magnitude of these
 effects varying with local patch characteristics. Our study highlights the
 need for integrating local and landscape-level factors, and considering
 how larger-scale processes play out at the patch level, to understand the
 complex dynamics that shape species distributions.
description: Excel and R are required to open the data files included in this
 submission.
DOI: 10.5061/dryad.34tmpg4qf
title: High latitude ocean habitats are a crucible of fish body shape diversification

description: A strong decline in species richness from the equator to the poles is a
 common feature of Earth’s biodiversity. However, little is known about how
 phenotypic diversity varies across the same latitudinal gradient. Here, we
 examine body shape diversity in marine fishes across latitudes and explore
 the role of time and evolutionary rate in explaining the diversity
 gradient. Marine fishes' occupation of upper latitude environments
 has increased substantially over the last 55 million years. Latitude
 strongly affects the rate of body shape evolution and its disparity.
 Fishes in the highest latitudes exhibit nine times the rate of body shape
 evolution and one and a half times the disparity compared to equatorial
 latitudes. The more dynamic evolution of body shape may be due to
 increased ecological opportunity in polar and subpolar oceans due to (1)
 the evolution of anti-freeze proteins in certain temperate clades that
 allowed them to invade regions of cold water, and (2) periodic
 environmental disturbances driven by cyclical warming and cooling in upper
 latitudes. Our results suggest that decreasing water temperature, through
 its effects on the activity levels of fishes, may have elevated the
 relative frequency of body shapes associated with less-active lifestyles.
description: High latitude ocean habitats are a crucible of fish body shape
 diversification Michael D. Burns University of California, Davis
 [burnsmic01@gmail.com](mailto:burnsmic01@gmail.com) File 1: dat_final.csv
 Data file containing species name (tree_Name), latitude centroid
 (lat_centroid), latitude minimum (lat_min), latitude maximum (lat_max), 
 standard length (Standard_length in millimeters and log-transformed),
 Maximum body depth (Max_body_depth in millimeters and log-transformed),
 maximum fish width (Max_fish_width in millimeters and log-transformed),
 head depth (Head_depth in millimeters and log-transformed), lower jaw
 length (Lower_jaw_length in millimeters and log-transformed), mouth width
 (Mouth_width in millimeters and log-transformed), caudal peduncle depth
 (Min_caudalpeduncle_depth in millimeters and log-transformed) , and caudal
 peduncle width (Min_caudalpeduncle_width in millimeters and
 log-transformed) File 2: Rabosky_et_al_2018.nexus A phylogenetic tree from
 Rabosky et al. 2018 "An inverse latitudinal gradient in speciation
 rate for marine fishes", trimmed to our dataset. File 3 (on Zenodo):
 Burns et al. 2024_code.R R code that runs all of the analyses in the
 manuscript.
DOI: 10.5061/dryad.h70rxwdpd
title: Morphometric and phylogeny data for: Morphology, variation, and systematics of the late Cambrian Laurentian dikelocephalid trilobite Walcottaspis vanhornei

description: These pages provide details of the taxa, characters and character states
 used in the phylogenetic analyses of Walcottaspis vanhornei (Walcott,
 1914) and relatives in the accompanying paper.  Phylogenetic
 information included here provides details of characters and taxa used for
 both the parsimony-based and Bayesian analyses and documents levels of
 support of two types (Bremer and bootstrap) for the parsimony analysis.
 Also included here is the result of Bayesian maximum likelihood analysis
 that provides further support to the results of parsimony analysis. We
 include bivariate plots of the variance explained by each relative warp
 for the sclerites analyzed and morphometric measurement error analysis.
description: Please see README.md file included with the dataset for
 explanation of data files and softwares required/used to open and analyse
 the files.
DOI: 10.5061/dryad.6m905qg4p
title: Elevated atmospheric CO2 suppresses silicon accumulation and exacerbates endophyte reductions in plant phosphorus

description: Many temperate grasses are both hyper-accumulators of silicon (Si) and
 hosts of Epichloë fungal endophytes; functional traits which may alleviate
 environmental stresses such as herbivore attack. Si accumulation and
 endophyte infection may operate synergistically, but this has not been
 tested in a field setting, nor in the context of changing environmental
 conditions. Predicted increases in atmospheric CO2 concentrations can
 affect both Si accumulation and endophyte function, but these have not
 been studied in combination. We investigated how elevated atmospheric CO2
 (eCO2), Si supplementation, endophyte-presence and insect herbivory
 impacted plant growth, stoichiometry (C, N, P and Si), leaf gas exchange
 (rates of photosynthesis, stomatal conductance, transpiration rates) and
 endophyte production of anti-herbivore defences (alkaloids) of an
 important pasture grass (tall fescue; Lolium arundinaceum) in the field.
 eCO2 and Si supplementation increased shoot biomass (+52% and +31%,
 respectively), whereas herbivory reduced shoot biomass by at least 35% and
 induced Si accumulation by 24%. Shoot Si concentrations, in contrast,
 decreased by 17–21% under eCO2. Si supplementation and herbivory reduced
 shoot C concentrations. eCO2 reduced shoot N concentrations which led to
 increased shoot C:N ratios. Overall, shoot P concentrations were 26% lower
 in endophytic plants compared to non-endophytic plants, potentially due to
 decreased mass flow (i.e. observed reductions in stomatal conductance and
 transpiration). Alkaloid production was not discernibly affected by any
 experimental treatment. The negative impacts of endophytes on P uptake
 were particularly strong under eCO2. We show that eCO2 and insect
 herbivory reduce and promote Si accumulation, respectively, incorporating
 some field conditions for the first time. This indicates that these
 drivers operate in a more realistic ecological context than previously
 demonstrated. Reduced uptake of P in endophytic plants may adversely
 affect plant productivity in the future, particularly if increased demand
 for P due to improved plant growth under eCO2 cannot be met.
description: Microsoft Excel, Microsoft Word
DOI: 10.25338/b8x35s
title: Data from: Epidemiology of skin changes in endangered Southern Resident killer whales

description: Photographic identification catalogs of individual killer whales (Orcinus
 orca) over time provide a tool for remote health assessment. We
 retrospectively examined digital photographs of Southern Resident killer
 whales in the Salish Sea to characterize skin changes and to determine if
 they could be an indicator of individual, pod, or population health. Using
 photographs collected from 2004 through 2016 from 18,697 individual whale
 sightings, we identified six lesions (cephalopod, erosions, gray patches,
 gray targets, orange on gray, and pinpoint black discoloration). Of 141
 whales that were alive at some point during the study, 99% had
 photographic evidence of skin lesions. Using a multivariate model
 including age, sex, pod, and matriline across time, the point prevalence
 of the two most prevalent lesions, gray patches and gray targets, varied
 between pods and between years and showed small differences between stage
 classes. Despite minor differences, we document a strong increase in point
 prevalence of both lesion types in all three pods from 2004 through 2016.
 The health significance of this is not clear, but the possible
 relationship between these lesions and decreasing body condition and
 immunocompetence in an endangered, non-recovering population is a concern.
 Understanding the etiology and pathogenesis of these lesions is important
 to better understand the health significance of these skin changes that
 are increasing in prevalence.
description: We evaluated digital photographs of surfacing Southern Resident
 killer whales taken by the Center for Whale Research (CWR). Specifically,
 photographs collected for identification purposes focused on the left and
 right saddle patch and dorsal fin. Every in-focus, clear photograph taken
 between 2004–2016 was evaluated for skin abnormalities. Four
 veterinarians, two veterinary pathologists specializing in marine mammals
 and two veterinarians with expertise in cetacean clinical medicine,
 collectively reviewed all images of skin lesions on high-definition
 screens. Distinct lesions were identified and differentiated by typical
 pathologic qualifiers. A name and morphologic description were given for
 each distinct lesion type and every lesion present in an image was
 recorded by lesion type, date, and individual animal.