cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6078/d1z11p
title: Data from: Table-top extreme ultraviolet second harmonic generation

description: The lack of available table-top extreme ultraviolet (XUV) sources with
 high enough fluxes and coherence properties have limited the availability
 of nonlinear XUV and x-ray spectroscopies to free electron lasers (FEL).
 Here, we demonstrate second harmonic generation (SHG) on a table-top XUV
 source for the first time by observing SHG near the Ti M2,3-edge with a
 high-harmonic seeded soft x-ray laser (HHG-SXRL). Further, this experiment
 represents the first SHG experiment in the XUV. First-principles
 electronic structure calculations suggest the surface specificity and
 separate the observed signal into its resonant and non-resonant
 contributions. The realization of XUV-SHG on a table-top source opens up
 opportunities for the study of element-specific dynamics in
 multi-component systems where surface, interfacial, and bulk-phase
 asymmetries play a driving role in smaller-scale labs as opposed to FELs.
description: See associated journal article and supplementary
 information.
description: File contains data points for main text figures in tab-separated
 ASCII format. Subfolders contain raw data from the camera in Andor
 format.
DOI: 10.5061/dryad.5mkkwh75m
title: Microscale modelling of dielectrophoresis assembly processes

description: This work presents a microscale approach for simulating the
 dielectrophoresis (DEP) assembly of polarizable particles under an
 external electric field. The model is shown to capture interesting
 dynamical and topological features, such as the formation of chains of
 particles and their incipient aggregation into hierarchical structures. A
 quantitative characterization in terms of the number and size of these
 structures is also discussed. This computational model could represent a
 viable numerical tool to study the mechanical properties of particle-based
 hierarchical materials and suggest new strategies for enhancing their
 design and manufacture.
description: The simulations were obtained by LAMMPS.
description: The freeware PARAVIEW is adviced to open the vtk files.
DOI: 10.5061/dryad.2547d7wqc
title: Let it snow? Spring snowpack and microsite characterize the regeneration niche of high-elevation pines

description: Aim: The persistence potential of forests under rapid climate change will
 depend on species-specific tolerances to increasing growing season soil
 moisture stress as snowpack declines. High-elevation tree species may be
 particularly vulnerable to increasing water stress and associated changes
 to disturbance regimes because they occur at the environmental margins of
 tree distributions and are considered snowpack dependent. Here, we
 evaluate the interacting effects of climate, disturbance, and microsite
 conditions on tree regeneration in high-elevation, migration-limited pines
 that have experienced recent disturbance-induced tree mortality. Location:
 Great Basin (California & Nevada), USA Taxon: Gymnosperms;
 Pinaceae Methods: We used field observations from 70 sites that varied in
 climate, disturbance, and local site conditions across semi-arid,
 high-elevation forests of the Great Basin. We employed structural equation
 models to evaluate how climate and disturbance interact with microsite
 conditions to influence regeneration. Results: We found a broad range of
 establishment conditions of high-elevation conifers - whitebark, limber,
 and bristlecone pines – across climatic and disturbance gradients in the
 Great Basin, but our research detected clear differences in the
 regeneration niche for each species that may lead to differential survival
 as climate and disturbance conditions continue to change. Regeneration of
 whitebark and bristlecone pines diverged in their responses to spring
 snowpack conditions, with whitebark pine increasing and bristlecone pine
 decreasing with greater spring snowpack. Limber pine regenerated across a
 range of climatic and landscape conditions, and this generalist strategy
 may be advantageous if future climate and disturbance conditions exceed
 tolerances of more specialized species. Main Conclusions: Our findings
 highlight the critical role that spring snowpack, and consequently growing
 season soil moisture, plays in determining the persistence potential of
 high-elevation conifers. However, this role varies among species and thus
 may drive compositional changes as earlier snowmelt drives soil moisture
 declines across mountainous landscapes of the western United States.
DOI: 10.6078/d1t704
title: Strains and constructs for: A chimeric nuclease substitutes a phage CRISPR-Cas system to provide sequence specific immunity against subviral parasites

description: Mobile genetic elements, elements that can move horizontally between
 genomes, have profound effects on their hosts fitness. The PLE is a mobile
 element that integrates into the chromosome of Vibrio cholerae and
 parasitizes the bacteriophage ICP1 to move between cells. This parasitism
 by PLE is such that it abolishes the production of ICP1 progeny and
 provides a defensive boon to the host cell population. In response to the
 severe parasitism imposed by PLE, ICP1 has acquired an adaptive CRISPR-Cas
 system that targets the PLE genome during infection. However, ICP1
 isolates that naturally lack CRISPR-Cas are still able to overcome certain
 PLE variants, and the mechanism of this immunity against PLE has thus far
 remained unknown. Here we show that ICP1 isolates that lack CRISPR-Cas
 encode an endonuclease in the same locus, and that the endonuclease
 provides ICP1 with immunity to a subset of PLEs. Further analysis shows
 that this endonuclease is of chimeric origin, incorporating a DNA binding
 domain that is highly similar to some PLE replication origin binding
 proteins. This similarity allows the endonuclease to bind and cleave PLE
 origins of replication. The endonuclease appears to exert considerable
 selective pressure on PLEs and may drive PLE replication module swapping
 and origin restructuring as mechanisms of escape. This work demonstrates
 that new genome defense systems can arise through domain shuffling and
 provides a greater understanding of the evolutionary forces driving genome
 modularity and temporal succession in mobile elements.
description: These files represent strains and constructs cloned and assayed
 for the production of the associated manuscript. Primer sequences are
 annotated within each file. Construct sequence was validated through
 Sanger sequencing.
description: Files are named for the constructs they correspond to. Strains
 that contain each construct appear in parentheses after contruct
 name.
DOI: 10.5061/dryad.8w9ghx3md
title: Changes in fat mass and migratory restlessness in northern wheatears

description: To fuel their migratory endurance flights, most birds accumulate large
 quantities of fat prior to departure. It therefore seems logical that the
 decision to depart on a migratory flight depends on fuel stores, at least
 to some extent; very small fuel stores prohibit migratory endurance
 flight. However, studies linking migrants’ estimated fuel stores (or
 sometimes actual fat stores) to departure likelihood have provided
 inconsistent results. Fuel stores are not static though, but highly
 dynamic. Instead of investigating fuel stores at a given time, we
 therefore focussed on quantifying the dynamic process of fuelling and how
 it affects migrants’ motivation to depart. We did so by temporarily caging
 wild northern wheatears (Oenanthe oenanthe) at a stopover site during
 autumn migration. Birds were kept under controlled conditions, receiving
 ad libitum food. Changes in fat mass (measured by quantitative magnetic
 resonance) and migratory restlessness (an accurate proxy for migrants’
 motivation to depart from stopover) were closely monitored. We found that
 the change in fat mass was a good predictor of the change in migratory
 restlessness. Individuals accumulating little fat did not show much change
 in their restlessness, while individuals accumulating much fat showed a
 strong increase in restlessness. Our study therewith provides clear
 support for the idea that fat stores affect birds’ motivation to migrate,
 and shows that for migrating birds, increasing fat stores are an important
 cue to depart from stopover. Fat accumulation affected the change in
 migratory restlessness in the same manner for relatively lean and
 relatively fat birds. Additionally, food intake or changes therein did not
 explain the change in migratory restlessness we observed. We therefore
 hypothesize that the fat tissue itself signals changes in energetic state,
 likely through production and release of hormones, affecting birds’
 motivation to migrate.
DOI: 10.5061/dryad.zs7h44j85
title: Assortative mating can help adaptation of flowering time to a changing climate: insights from a polygenic model

description: Several empirical studies report fast evolutionary changes in flowering
 time in response to contemporary climate change. Flowering time is a
 polygenic trait under assortative mating, since flowering time of mates
 must overlap. Here we test whether assortative mating, compared to random
 mating, can help better track a changing climate. For each mating pattern,
 our individual-based model simulates a population evolving in a climate
 characterized by stabilizing selection around an optimal flowering time,
 which can change directionally and/or fluctuate. We also derive new
 analytical predictions from a quantitative genetics model for the expected
 genetic variance at equilibrium, and its components, the lag of the
 population to the optimum, and the population mean fitness. We compare
 these predictions between assortative and random mating, and to our
 simulation results. Assortative mating, compared to random mating, has
 antagonistic effects on genetic variance: it generates positive
 associations among similar allelic effects, which inflates the genetic
 variance, but it decreases genetic polymorphism, which depresses the
 genetic variance. In a stationary environment with substantial stabilizing
 selection, assortative mating affects little the genetic variance compared
 to random mating. In a changing climate, assortative mating however
 increases genetic variance compared to random mating, which diminishes the
 lag of the population to the optimum, and in most scenarios translates
 into a fitness advantage relative to random mating. The magnitude of this
 fitness advantage depends on the extent to which genetic variance limits
 adaptation, being larger for faster environmental changes and weaker
 stabilizing selection.
description: Please contact the corresponding author for the notebook (.nb)
 simulating the evolution of populations under assortative and random
 mating.
DOI: 10.5061/dryad.66t1g1k1x
title: Examples of misclassified images of papilledema severity by the Deep Learning System

description: The study's objective is to evaluate the performance of a deep
 learning system (DLS) in classifying the severity of papilledema
 associated with increased intracranial pressure, on standard retinal
 fundus photographs. A DLS was trained to automatically classify
 papilledema severity in 965 patients (2103 mydriatic fundus photographs),
 representing a multiethnic cohort of patients with confirmed elevated
 intracranial pressure. Training was performed on 1052 photographs with
 mild/moderate papilledema (MP) and 1051 photographs with severe
 papilledema (SP) classified by a panel of experts, and the performance of
 the DLS was tested in 111 patients (214 photographs, 92 with MP
 and 122 with SP). In this dataset, we provide illustrative examples of
 misclassified images by the DLS, two examples of images wrongly classified
 as moderate papilledema instead of severe (figure 1A and 1B), and two
 examples of images wrongly classified as severe papilledema instead of
 moderate (figure 2A and 2B). Unsurprisingly, DLS errors occurred more
 often in patients with moderate papilledema (Frisén 3 severity), a
 situation already encountered in clinical studies.
description: The study included de-identified unaltered digital ocular fundus
 photographs obtained in patients with confirmed intracranial hypertension
 and papilledema, from international neuro-ophthalmology centers. Two
 experts independently classified the fundus photographs into a simple
 two-grade papilledema severity classification; 1/ mild to moderate
 papilledema (Frisén 1-3), defined as disc edema with no obscuration of
 major blood vessels on the disc; 2/ severe papilledema (Frisén 4-5),
 defined as disc edema associated with any obscuration of major blood
 vessels on the disc. The fundus photographs were divided into 2 datasets,
 the training dataset used to teach the DLS to classify papilledema
 severity, and the testing dataset, used to evaluate the performance of the
 DLS. The fundus photographs included in this dataset
 are illustrative examples of papilledema images which were
 misclassified in terms of severity, according to the gold standard, by the
 deep learning system.
DOI: 10.5061/dryad.8kprr4xnb
title: Testing the effectiveness of the Forest Integrity Assessment: A field-based tool for estimating the condition of tropical forest

description: 1. Global targets to halt biodiversity losses and mitigate climate change
 will require protecting rainforest beyond current protected area networks,
 necessitating responsible forest stewardship from a diverse range of
 companies, communities and private individuals. Robust assessments of
 forest condition are critical for successful forest management, but many
 existing techniques are highly technical, time-consuming, expensive, or
 require specialist knowledge. 2. To make assessment of tropical forests
 accessible to a wide range of actors, many of whom may be limited by
 resources or expertise, the High Conservation Value Resource Network
 (HCVRN), with the SE Asia Rainforest Research Partnership (SEARRP),
 developed a South East Asian version of the Forest Integrity Assessment
 (FIA) tool as a rapid (&lt; 1 hour) method of assessing forest
 condition in the field, where non-experts respond to 50 questions about
 characteristics of the local environment while walking a site transect.
 Here, we examined the effectiveness of this survey tool by conducting ~
 1,000 assessments of forest condition at 16 tropical rainforest sites with
 varying levels of disturbance in Sabah, Malaysian Borneo. 3. We found good
 agreement (R-squared range: 0.50 – 0.78) between FIA survey scores and
 independent measures of forest condition, including biodiversity,
 vegetation structure, aboveground carbon, and other key metrics of
 ecosystem function, indicating that the tool performed well. Although
 there was variation among assessor responses when surveying the same
 forest sites, assessors were consistent in their ranking of those sites,
 and prior forest knowledge had a minimal effect on the FIA scores.
 Revisions or further training for questions where assessors disagree, for
 example on the presence of fauna at a site, could improve consistency. 4.
 We conclude that the FIA survey tool is a robust method of assessing
 forest condition, providing a rapid and accessible means of forest
 conservation assessment. The FIA tool could be incorporated into
 management practices in a wide range of forest conservation schemes, from
 sustainability standards, to community forestry and restoration
 initiatives. The tool will enable more organisations and individuals to
 understand the conservation value of the forests they manage, and to
 identify areas for targeted improvements.Minhyuk Seo
DOI: 10.5061/dryad.xwdbrv1d2
title: Temporal and sociocultural effects of human colonisation on native biodiversity: Filtering and rates of adaptation

description: Modern human societies have negatively impacted native species richness
 and their adaptive capacity on every continent, in clearly contrasting
 ways. We propose a general model to explain how the sequence, duration,
 and type of colonising society alter native species richness patterns
 through changes in evolutionary pressures. These changes cause different
 ‘filtering effects’ on native species, while simultaneously altering the
 capacity of surviving species to adapt to further anthropogenic pressures.
 This framework may better explain the observed native species extinction
 rates and extirpation legacies following human colonisation events, as
 well as better predict future patterns of human impact on biodiversity.
description: <b>Native
 biodiversity extinction</b>. We obtained the date of non-human
 Anthropocene megafauna (mammal and avifauna weighing &gt; 0.7 kg,
 based on Dirzo et al. 2014 ) considered as extinct or extirpated from four
 geographic regions, Africa (supplementary form Table 1), Europe
 (supplementary-form Table 2), North America (supplementary-form Table 3)
 and New Zealand (supplementary-form Table 4), from published information
 on IUCN (2015), New Zealand bird online (http://www.nzbirdsonline.org.nz), the sixth extinction (http://www.petermaas.nl) and in the primary literature (Kingdon 1997, Palumbo and Gallo-Orsi 1999, Reumer <i>et al.</i> 2003, Baillie <i>et al. </i>2004, Fontaine <i>et al.</i> 2007; Bover and Alcover 2008, Jackson and Nowell 2011). The pre-human native megafauna species richness for each geographical range was extracted from IUCN (2015). Species were included if they were either considered extinct or extirpated in the wild. Those species that were considered extirpated are those that are functionally extinct, such as species classified as extinct in the wild. The percentage of megafauna that went extinct for each time period was established based on the total population of megafauna during the pre-human period.
DOI: 10.5061/dryad.41ns1rnd4
title: Daphnia magna trade-off safety from UV radiation for food

description: Research on diel vertical migration (DVM) is generally conducted at the
 population level, whereas few studies have focused on how individual
 animals behaviorally respond to threats when also having access to
 foraging opportunities. We utilized a 3-D tracking platform to record the
 swimming behavior of Daphnia magna exposed to
 ultraviolet radiation (UVR) in the presence or absence of a food patch. We
 analyzed the vertical position of individuals before and during UVR
 exposure and found that the presence of food reduced the average swimming
 depth during both sections of the trial. Since UVR is a strong driver of
 zooplankton behavior, our results highlight that biotic factors, such as
 food patches, have profound effects on both the amplitude and the
 frequency of avoidance behavior. In a broader context, the trade-off
 between threats and food adds to our understanding of the strength and
 variance of behavioral responses to threats, including DVM.
DOI: 10.5061/dryad.9w0vt4bfd
title: Emergence rates of stink bugs and parasitoids under four heat wave conditions

description: Heat waves are becoming more frequent with climate change and their impact
 on lower and higher trophic levels can differ. Higher trophic levels, such
 as predators and parasitoids, are predicted to be more strongly affected
 by heat waves than herbivores because they may have smaller thermal
 windows and because of altered ecological interactions with lower trophic
 levels. We tested the effects of heat waves of varying intensity
 (36-42˚C), imposed for four hours during five consecutive days on the egg
 stage of an invasive herbivore, the brown marmorated stink bug
 (Halyomorpha halys) and on various developmental stages of its parasitoid,
 Trissolcus japonicus. Halyomorpha halys eggs had lower hatching success
 and fewer nymphs emerging with increasing intensity of heat stress, while
 exposure during the egg and larval stages of T. japonicus did not decrease
 adult emergence rates. Heat waves increased development time of
 parasitoids and decreased adult emergence when pupal stages were exposed.
 Adult parasitoids experiencing heat stress had lower survival, but their
 parasitism success overall was not affected. In addition, we detected
 transgenerational effects whereas emergence success and the number of
 adult parasitoids emerging in the second generation declined when the
 parental generation was exposed to 42˚C. Contrary to expectations, the
 results suggest that H. halys may be more sensitive to heat stress than T.
 japonicus, at least during early development. Our findings indicate that
 biological control services provided by T. japonicus can be maintained in
 the face of increasing heat wave events and point to the importance of
 following populations beyond the first generation to better understand the
 long-term consequences of heat stress.
description: Methods for data collection are described in the
 manuscript. 
description: The metadata for the dataset can be found in the first tab,
 called 'metadata' of the excel file. This explains which
 sections certain tabs of data belong to in the manuscript as well as what
 all the column names indicate in each tab. There are no
 missing values in the dataset. N/A has been inserted to data points where
 certain variables could not be calculated due to lack of emergence of
 parasitoids.
DOI: 10.5061/dryad.s4mw6m966
title: Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology

description: Karyotype, including the chromosome and arm numbers, is a fundamental
 genetic characteristic of all organisms and has long been used as a
 species-diagnostic character. Additionally, karyotype evolution plays an
 important role in divergent adaptation and speciation. Centric fusion and
 fission change chromosome numbers, whereas the intra-chromosomal movement
 of the centromere, such as pericentric inversion, changes arm numbers. A
 probabilistic model simultaneously incorporating both chromosome and arm
 numbers has not been established. Here, we built a probabilistic model of
 karyotype evolution based on the “karyograph”, which treats karyotype
 evolution as a walk on the two-dimensional space representing the
 chromosome and arm numbers. This model enables analysis of the stationary
 distribution with a stable karyotype for any given parameter. After
 evaluating their performance using simulated data, we applied our model to
 two large taxonomic groups of fish, Eurypterygii and series Otophysi, to
 perform maximum likelihood estimation of the transition rates and
 reconstruct the evolutionary history of karyotypes. The two taxa
 significantly differed in the evolution of arm number. The inclusion of
 speciation and extinction rates demonstrated possibly high extinction
 rates in species with karyotypes other than the most typical karyotype in
 both groups. Finally, we made a model including polyploidization rates and
 applied it to a small plant group. Thus, the use of this probabilistic
 model can contribute to a better understanding of tempo and mode in
 karyotype evolution and its possible role in speciation and extinction.
description: We upload scripts for phylogenetic comparative methods and
 subsequent analyses using our probabilistic model of karyotype evolution
 described in Yoshida and Kitano (2021, PLoS Genet). We also upload data
 set used for the analysis.
description: Please read "Ducuments_Yoshida_and_Kitano_2021.doc" for
 detailed information.