cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d2547d80q
title: Data from: Upgrades of coastal protection infrastructure affect benthic communities

description: Sea level rise, storm surges, aging and wear are forcing upgrades to
 breakwaters and seawalls to protect coastal areas from erosion and
 inundation. Such upgrades involve the introduction of new material which
 may consequently act as an ecological disturbance that can alter
 established marine communities and ecosystem function. Mitigating
 ecological impacts requires an understanding of how species assemblages
 are affected by such works. Here, we use the major upgrade of a regularly
 wave-overtopped breakwater as a case study to evaluate the impacts of
 upgrades to hard coastal protection structure on benthic rocky reef
 communities. An asymmetrical Before-After Control-Impact (BACI)
 experimental design was used to test interactive effects of the
 infrastructure upgrades on benthic communities. While benthic assemblages
 were not significantly different from controls prior to the upgrade,
 improving the defensive capacity of the breakwater significantly changed
 community structure. Notably, most taxonomic groups showed higher cover at
 the control sites than at the impacted site post-upgrade, with articulated
 calcareous algae (e.g. Corallina officinalis and Amphiroa anceps) showing
 an opposite trend. Synthesis and applications: Ecological implications and
 structural limitations make regular upgrading of existing infrastructure
 unsuitable as a long-term management strategy. More sustainable
 alternatives need to be considered, such as decommissioning of structures
 and retreat from flood-prone areas. This transition, however, will take
 time and requires a change of mindset and policies. Where upgrades are
 urgent, eco-engineering techniques can mitigate impacts to habitats and
 associated taxa.
DOI: 10.5061/dryad.m63xsj3zs
title: Paleobiogeography, paleoecology, diversity, and speciation patterns in the Eublastoidea (Blastozoa: Echinodermata)

description: Understanding the distribution of taxa in space and time is key to
 understanding diversity dynamics. The fossil record provides an avenue to
 assess these patterns on vast timescales and through major global changes.
 The Eublastoidea were a conservatively plated Paleozoic echinoderm clade
 that range from the middle Silurian to the end Permian. The geographic
 distribution of the eublastoids, as a whole, has been qualitatively
 assessed but has historically lacked a quantitative analysis. This is the
 first examination of the Eublastoidea using probabilistic methods within
 the R package BioGeoBEARS to assess macroevolutionary trends. Results
 provide an updated understanding of eublastoid diversity with new peaks
 and troughs in diversity through their evolutionary history. Lithology is
 examined in an evolutionary framework and does not have clear evolutionary
 trends and there is much work to be done regarding environmental
 preferences. Biogeographic patterns do not recover precise group origins
 but do support the previous work that outlines Eublastoidea as a
 Laurentian clade. Sympatric speciation events dominant the clade’s history
 but are likely exaggerated due to the highly combined areas. Vicariance
 events are rare and restricted to the Silurian and Devonian and dispersal
 events are more common throughout the evolutionary history. Pathways
 allowing for lineage migrations are noted between Southern Laurussia and
 China in the Devonian and Carboniferous, and Southern Laurussia and
 Eastern Gondwana in the Carboniferous. Future work will include the
 addition of more non-Laurentian species into the estimated phylogeny to
 better estimate these global patterns.
description: This is abbreviated and without references, please see the
 manuscript for full details. Occurrence and Area Data:
 Geographic data were compiled for each species using published literature
 and online biodiversity data aggregators, specifically iDigBio (www.idigbio.org) and
 the Paleobiology Database (www.paleobiodb.org; Supplemental Table 1). Phylogenetic Inference: Character matrix compiled by Bauer through dissertation work (Bauer 2018) following updated homology schemes. The Nexus file was compiled in Mesquite and executed in RevBayes. Diversity and Ecology: Lineage diversity was estimated using paleotree; phytools was used to map environmental preference; Pagel’s lambda and K-statistic were employed using the phylosig function in the R package phytools. Biogeographic Analyses: Ancestral geographic ranges were inferred through probabilistic methods within the R package BioGeoBEARS.
description: There are readme files in both sets of data.
DOI: 10.5061/dryad.ht76hdrcg
title: Data from: Miniaturization, genome size, and biological size in a diverse clade of salamanders

description: Genome size (C-value) can affect organismal traits across levels of
 biological organization, from tissue complexity to metabolism. Neotropical
 salamanders show wide variation in genome and body sizes, including
 several clades with miniature species. Because miniaturization imposes
 strong constraints on morphology and development, and genome size is
 strongly correlated with cell size, we hypothesize that body size has
 played an important role in the evolution of genome size in bolitoglossine
 salamanders. If this hypothesis is correct, then genome size and body size
 should be correlated in this group. Using Feulgen Image Analysis
 Densitometry (FIAD), we estimated genome sizes for 60 species of
 neotropical salamanders. We also estimated the “biological size” of
 species by comparing genome size and physical body sizes in a phylogenetic
 context. We found a significant correlation between C-value and physical
 body size using optimal regression with an Ornstein-Uhlenbeck model, and
 report the smallest salamander genome found to date. Our index of
 biological size showed that some salamanders with large physical body size
 have smaller biological body size than some miniature species, and that
 several clades showed patterns of increased or decreased biological size
 compared to their physical size. Our results suggest a causal relationship
 between physical body size and genome size and show the importance of
 considering the impact of both on the biological size of organisms.
 Indeed, biological size may be a more appropriate measure than physical
 size when considering phenotypic consequences of genome size evolution in
 many groups.
description: We generated a Sanger sequence dataset by sequencing some taxa of
 Neotropical salamanders for two mitochondrial genes (cytochrome b and 16S)
 and combined these data with data from Genbank for these two genes and
 three nuclear genes (RAG1, SLC8A3, POMC). We concatenated these data and
 estimated a phylogeny using BEAST. We estimated the maximum clade
 credibility tree from the posterior distribution of this analysis as well
 as a file of 100 trees from the posterior distribution of this analysis.
 We also include a file of measurements of body size and head size taken
 from museum specimens using Vernier calipers.
DOI: 10.15468/dl.9yrq2u
title: Occurrence Download

description: A dataset containing 269 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Augouardia letestui",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 269 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002394-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.t76hdr7z3
title: High-throughput discovery of phage receptors using transposon insertion sequencing of bacteria

description: As the most abundant microbes on earth, novel bacteriophage (phage;
 bacteria-specific viruses) are readily isolated from environmental
 samples. However, it remains challenging to characterize phage-bacteria
 interactions, such as the host receptor(s) phage bind to initiate
 infection. Here, we tested whether transposon insertion sequencing, INSeq,
 could be used to identify bacterial genes involved in phage binding. As
 proof of concept, results showed that INSeq screens successfully
 identified genes encoding known receptors for previously characterized
 viruses of Escherichia coli (phage T6, T2, T4 and T7). INSeq screens were
 then used to identify genes involved during infection of six newly
 isolated coliphage. Results showed that candidate receptors could be
 successfully identified for the majority (five of six) of the phage;
 furthermore, genes encoding the phage receptor(s) were the top hit(s) in
 the analyses of the successful screens. INSeq screens provide a generally
 useful method for high-throughput discovery of phage receptors. We discuss
 limitations of our approach when examining uncharacterized phage, as well
 as usefulness of the method for exploring the evolution of broad versus
 narrow use of cellular receptors among phage in the biosphere.
DOI: 10.5061/dryad.f7m0cfxsk
title: Data for assessment of damage to residential dwellings using artificial neural networks

description: The data provided and the associated MATLAB code were used to build an
 Artificial Neural Network Model to capture damage to residential home
 subjected to tornado events in the State of Missouri. The ANN model
 utilizes relevant tornado, societal demographic, and structural data to
 determine a building’s resulting damage state from an extreme wind
 event.
DOI: 10.5061/dryad.18931zctb
title: Analysis of airline boarding changes in response to COVID-19

description: Airlines have introduced a back-to-front boarding process in response to
 the COVID-19 pandemic. We performed pedestrian dynamics simulation using
 the Constrained Linear Movement (CALM) model to simulate people boarding a
 144-seat Airbus 320 airplane using different boarding procedures,
 including back to front. This data set contains input files, code, and
 output files from the simulations containing the trajectories of
 passengers for a parameter sweep consisting of thousands of simulations.
 It also contains code to perform analysis of the output to determine
 passenger contacts.
description: We used pedestrian dynamics to simulate people boarding a
 144-seat Airbus 320 airplane using different boarding procedures.
 Simulations start with input files provided here, specifying the initial
 positions of passengers. The Constrained Linear Movement (CALM) model is
 used to compute passenger trajectories, which are then output. A parameter
 sweep is performed to explore the space of possible passenger behavior,
 thus leading to thousands of simulations. Each simulation is then analyzed
 to determine the number of contacts arising from it. Each contact
 corresponds to 1.125 person seconds of contact. It is a function of the
 contact threshold, which is an input parameter to the code.
description: 1. A user will need to run the codes on machines with the Message
 Passing Interface (MPI) installed. 2. It will help a
 user to read the following paper. M.S. Lahijani, T.
 Islam, A. Srinivasan, and S. Namilae. Constrained Linear Movement Model
 (CALM): Simulation of passenger movement in airplanes. PLoS ONE 15(3):
 e0229690 (2020). https://doi.org/10.1371/journal.pone.0229690.
DOI: 10.5061/dryad.9zw3r22bj
title: Pleistocene persistence and expansion in tarantulas on the Colorado Plateau and the effects of missing data on phylogeographical inferences from RADseq

description: Few phylogeographical studies exist for taxa inhabiting the Colorado
 Plateau province. We combined mitochondrial and genomic data with species
 distribution modeling to test Pleistocene hypotheses for Aphonopelma
 marxi, a large tarantula endemic to the plateau region. Mitochondrial and
 genomic analyses revealed that the species comprises at least three main
 clades that diverged in the Pleistocene. A clade distributed along the
 Mogollon Rim appears to have persisted in place during the last glacial
 maximum, whereas the other two clades probably colonized the central and
 northeastern portion of the species’ range from small refugial areas along
 river-carved canyons. Climate models support this hypothesis for the
 Mogollon Rim, but late glacial climate data appear too coarse to detect
 suitable areas in canyons. Locations of canyon refugia could not be
 inferred from genomic analyses due to missing data, encouraging us to
 explore the effect of missing loci in phylogeographical inferences using
 RADseq. In phylogenetic analyses, node support for major clades decreased
 with the addition of samples with significant amounts of missing data
 (more than 30%). Population genomic structure was greatly influenced by
 missing data, with the group membership of many taxa changing as samples
 with missing loci were added. Results from DAPC, a distance-based method,
 did not change as samples with significant amounts missing data were
 added. We conclude that the specific loci that are missing matters more
 than the number of missing loci, and that samples with missing data can
 still add information to RADseq-based analyses as long as results are
 interpreted cautiously.
DOI: 10.5061/dryad.sqv9s4n1n
title: Mechanochemical exfoliation of graphite

description: A facile method to produce few-layer graphene (FLG) nanosheets is
 developed using protein-assisted mechanical exfoliation. The predominant
 shear forces that are generated in a planetary ball mill facilitates
 exfoliation of graphene layers from graphite flakes. The process employs a
 commonly known protein, Bovine Serum Albumin (BSA), which not only acts as
 an effective exfoliation agent but also provide stability by preventing
 restacking of the graphene layers. The latter is demonstrated by the
 excellent long-term dispersibility of exfoliated graphene in an aqueous
 BSA solution, which exemplifies a common biological medium. Development of
 such potentially scalable and toxin-free methods are critical for
 producing cost-effective biocompatible graphene, enabling numerous
 possible biomedical and biological applications. A methodical study was
 performed to identify effect of time and varying concentrations of BSA
 towards graphene exfoliation. The fabricated product has been
 characterized using Raman spectroscopy, powder X-Ray diffraction,
 transmission electron microscopy and scanning electron microscopy. The
 BSA-FLG dispersion was then placed in media containing Astrocyte cells to
 check for cytotoxicity. It was found that lower concentrations of BSA-FLG
 dispersion had only minute cytotoxic effects on the Astrocyte cells.
DOI: 10.5061/dryad.7pvmcvdqj
title: Disentangling leaf morphology in Daustinia montana (Convolvulaceae)

description: Daustinia montana (Convolvulaceae) is the only species of the genus, and
 is notable for its wide leaf variability. To understand whether this
 plasticity is correlated with the distribution of the species, linear
 morphometric and leaf contour analyses were performed. Specimens from
 herbaria were photographed, and pre-established linear measurements were
 made. A multivariate analysis was then performed to test the strength of
 associations among morphological characteristics, climatic variables, and
 distribution of the species. Elliptic Fourier analysis based on 20
 harmonics was used to generate shape descriptors, resulting in nine main
 components. With elliptic Fourier descriptors, a grouping tree was created
 that suggests the existence of six morphotypes in D. montana. Moreover,
 clustering analysis revealed two large groups distinguished mainly by leaf
 width. The present findings indicate that the morphotypes are strongly
 related to latitude and that other characteristics such as the type of
 indumentum are related to climatic variables.  
description: Field expeditions were performed out to collect and herbarium
 specimens were analyzed. Specimens were collected using standard
 techniques in taxonomy (Mori et al.1989). The coordinates were matching
 the labels of the herbarium specimens, of the field collections or Google
 Earth.  Climate data from the geographic locations was obtained from the
 WorldClim Global Climate databank (Fick and Hijmans 2017). The extraction
 of the climate data was performed with the aid of QGIS Development Team
 (2015). The images were captured using a digital camera, according to
 created protocol. Linear measurements were performed on the photographed
 material using ImageJ (Schneider et al. 2012). The images of the leaves
 were processed using Adobe Photoshop CS6 for the isolation of the leaves,
 subtraction of the petioles, digitization of the contours, and
 uniformization of the background. The images were processed using the
 SHAPE v. 1.3 computational package (Iwata and Ukai 2002) for the
 evaluation of the contour shape based on elliptical Fourier
 analysis.<br>  
description: All data used in the analyzes are available.
DOI: 10.5061/dryad.x95x69pfm
title: Data from: Implications of acute temperature and salinity tolerance thresholds for the persistence of intertidal invertebrate populations experiencing climate change

description: To predict whether populations of marine animals will persist in the face
 of changing climate conditions, it is informative to understand how past
 climate conditions have shaped present-day tolerance thresholds. We
 examined 4 species of intertidal invertebrates (Nucella lamellosa,
 Littorina scutulata, Littorina sitkana and Balanus glandula) inhabiting
 the coasts of Vancouver Island, Canada, where the east coast experiences
 historically warmer sea surface temperature (SST), warmer low tide (i.e.
 emersion) rock surface temperature (RST), and lower sea surface salinity
 (SSS) than the west coast. To determine if east coast populations have
 higher tolerance thresholds to acute stress than west coast populations,
 animals from 3 sites per coast were exposed to stressful temperatures and
 salinities in common garden experiments. Emersion temperature tolerance
 differed between populations only in N. lamellosa and B. glandula,
 tolerance thresholds being 1.4-1.5 °C higher on the east coast. Water
 temperature tolerance differed between populations only in B. glandula and
 L. scutulata but was highest on the west coast. No differences in salinity
 tolerance were observed within any species. Thus, there is limited
 evidence of divergence among east and west coast populations in tolerance
 of acute stress despite the substantial historical differences in extreme
 temperature and salinity conditions between coasts. However, based on
 present-day summertime SST and RST and known rates of change in these
 parameters, we predict present-day tolerance thresholds would be
 sufficient to allow adults of these populations to tolerate extreme
 temperatures predicted for the next several hundred years, and that even a
 slow rate of change in acute tolerance thresholds might suffice to keep up
 with future temperature extremes.
DOI: 10.5061/dryad.xd2547ddw
title: Delayed adaptive radiation among New Zealand stream fishes: joint estimation of divergence time and trait evolution in a newly delineated island species flock

description: Adaptive radiations are generally thought to occur soon after a lineage
 invades a region offering high levels of ecological opportunity. However,
 few adaptive radiations beyond a handful of exceptional examples are
 known, so a comprehensive understanding of their dynamics is still
 lacking. Here, we present a novel case of an island species flock of
 freshwater fishes with a radically different tempo of adaptive history
 than that found in many popular evolutionary model systems. Using a
 phylogenomic dataset combined with simultaneous Bayesian estimation of
 divergence times and trait-based speciation and extinction models, we show
 that the New Zealand Gobiomorphus gudgeons comprise a
 monophyletic assemblage, but surprisingly, the radiation did not fully
 occupy freshwater habitats and explosively speciate until more than ten
 million years after the lineage invaded the islands. This shift in
 speciation rate was not accompanied by an acceleration in the rate of
 morphological evolution in the freshwater crown clade relative to the
 other species, but is correlated with a reduction in head pores and scales
 as well as an increase in egg size. Our results challenge the notion that
 clades always rapidly exploit ecological opportunities in the absence of
 competing lineages. Instead, we demonstrate that adaptive radiation can
 experience a slow start before undergoing accelerated diversification and
 that lineage and phenotypic diversification may be uncoupled in young
 radiations.
description: Methods are described in the publication, with additional details
 in the deposited file Gobiomorphussupplementalmethods.docx.
 UCE raw reads are available under NCBI BioProjects PRJNA348720
 (<em>Mogurnda adspersa</em>) and PRJNA659476 (all other
 samples).
description: Supplemental Figures and Tables are identified by number (S1-S3
 and T1-T4) Gobiomorphus1_1000_95p.phylip and
 Gobiomorphus1_1000_75p.phylip are the 95% and 75% taxon complete UCE
 alignments, and Gobiomorphus1_1000_75p.charsets and
 Gobiomorphus1_1000_95p.charsets are the files listing partitions for each
 UCE locus InstructionsforRevBayes.txt details how to
 prepare datafiles and run the RevBayes analysis (gobiomorphustreePLconfig
 is used in preparing the ultrametric tree).
 RevBayesfiles.tar contains the scripts and datafiles for running
 the RevBayes analyses. gobiomorphusdata.xls is
 the spreadsheet of morphometric measurements for Gobiomorphus species,
 including ln transformed values
 Gobiomorphussupplementalmethods.docx is the methods supplement,
 describing details of UCE sequencing and alignment and phylogenetic
 analyses
DOI: 10.5061/dryad.4j0zpc885
title: Males adjust their manipulation of female remating in response to sperm competition risk

description: To reduce the potential for sperm competition, male insects are thought to
 inhibit the post-mating reproductive behaviour of females through
 receptivity inhibiting compounds transferred in the ejaculate. Selection
 is expected to favour phenotypic plasticity in male post-copulatory
 expenditure, with males investing strategically in response to their
 perceived risk of sperm competition. However, the impact that socially
 cued strategic allocation might have on female post-mating behaviour has
 rarely been assessed. Here, we varied male perception of sperm competition
 risk, both prior to and during mating, to determine if a male’s
 competitive environment impacts the extent to which he manipulates female
 remating behaviour. We found that female Australian field crickets
 (Teleogryllus oceanicus) mated to males that were reared under sperm
 competition risk emerged from a shelter in search of male song sooner than
 did females mated to males reared without risk, but only when mating
 occured in a risk free environment. We also found that females reared in a
 silent environment where potential mates were scarce displayed greater
 post-mating mate searching behaviour than females exposed to male calls
 during development. Collectively, our findings suggest complex interacting
 effects of male and female sociosexual environments on female post-mating
 sexual receptivity.