cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4mw6m90b9
title: Data and R scripts from: Assemblage reorganisation of South African dragonflies due to climate change

description: Aim: Climate change is expected to cause large shifts in species
 assemblages such as dragonflies and damselflies (Insecta: Odonata). Here
 we assess the influence of environmental drivers of turnover on Odonata
 assemblages. Secondly, we map the predicted spatial variation in species
 composition, first as a gradient of assemblage similarity, and then as
 discrete bioregions delineating major areas of odonate endemism. Finally,
 we map the magnitude of expected change in species turnover in response to
 climate change under two emission scenarios. Location: South Africa
 Methods: We used a spatial database comprising of 164 species of odonates
 and 20 covariates, to explore changes in compositional turnover using
 generalised dissimilarity models. Bioregions were compiled through various
 clustering techniques. Results: Present-day odonate bioregions correspond
 to climatic zones and are clearly separated by transitional zones with
 rapid spatial turnover. Present odonate bioregions are projected to
 undergo extensive reorganisation by 2050 and 2070. Temporal turnover in
 species composition is expected to reach up to 80% in the large arid
 interior and 64% along the coast. Half of all South Africa’s protected
 areas are likely to experience climate-induced changes to dragonfly
 bioregions in the near future. Main conclusions: Species assemblages are
 rapidly changing. This work highlights future shifts in climate will
 result in complex and non-linear responses in Odonata communities. With
 ongoing climate change, current odonate bioregions are predicted to expand
 while others will contract considerably in size within the next thirty
 years. The current demarcated protected areas may be inadequate to protect
 dragonflies as climates change. Odonata can be used to track forefronts of
 climate change, which will likely affect a larger array of taxa as well.
DOI: 10.5061/dryad.0gb5mkm21
title: Rare morph Lake Malawi mbuna cihclids benefit from reduced aggression from con- and heterospecifics

description: Balancing selection is important for the maintenance of polymorphism as it
 can prevent either fixation of one morph through directional selection or
 genetic drift, or speciation by disruptive selection. Polychromatism, the
 presence of multiple genetically determined colour phenotypes, can be
 maintained if the fitness of alternative morphs depends on the relative
 frequency in a population. In aggressive species, negative
 frequency-dependent antagonism can prevent an increase in the frequency of
 rare morphs as they would only benefit from increased fitness while they
 are rare. Heterospecific aggression is common in nature and has the
 potential to contribute to rare morph advantage. Here we carry out field
 observations and laboratory aggression experiments with mbuna cichlids
 from Lake Malawi, to investigate the role of con- and heterospecific
 aggression in the maintenance of polychromatism and identify benefits to
 rare morphs which are likely to result from reduced aggression. We
 hypothesise that rare morph individuals receive less aggression than
 common morph individuals and therefore have an ecological advantage.
 Within species we found that males and females bias aggression towards
 their own morph, adding to the evidence that inherent own-morph aggression
 biases can contribute to balancing selection. Over-representation of rare
 morph territory owners may be influenced by two factors; higher tolerance
 of different morph individuals as neighbours, and ability of rare morphs
 to spend more time feeding. Reduced aggression to rare morph individuals
 by heterospecifics may also contribute to rare morph advantage.
description: Methods of data collection/processing/analysis can be found in
 the paper: Tyers et al. 2021. Rare morph Lake Malawi mbuna cichlids
 benefit from reduced aggression from con- and heterospecifics. Journal of
 Evolutionary Biology.
description: see file "Tyers_mbuna-aggression_Readme.txt"
DOI: 10.5061/dryad.1ns1rn8v6
title: Data from: Inter-generational costs of oxidative stress: reduced fitness in daughters of mothers that experienced high levels of oxidative damage during reproduction

description: Parental condition transfer effects occur when the parents’ physiological
 state during reproduction affects offspring performance. Oxidative damage
 may mediate such effects, yet evidence that oxidative damage experienced
 by parents during reproduction negatively affects offspring fitness is
 scarce and limited to early life stages. We show in Japanese quail
 (Coturnix japonica) that maternal levels of oxidative damage, measured
 during reproduction, negatively predict the number of offspring produced
 by daughters. This maternal effect on the daughter’s reproductive success
 was mediated by an effect on hatching success, rather than the number of
 eggs laid by daughters. We also observed a negative association between
 the father’s oxidative damage levels and the number of eggs laid by
 daughters, but a positive association between the father’s oxidative
 damage levels and the hatching success of these eggs. These opposing
 paternal effects cancelled each other out, resulting in no overall effect
 on the number of offspring produced by daughters. No significant
 association between a female’s own level of oxidative damage during
 reproduction and her reproductive success was observed. Our results
 suggest that oxidative damage experienced by parents may be a better
 predictor of an individual’s reproductive performance than oxidative
 damage experienced by the individual itself. Although the mechanisms
 underlying these parental condition transfer effects are currently
 unknown, changes in egg composition or (epi-)genetic alterations of
 gametes may play a role. These findings highlight the importance of an
 inter-generational perspective when quantifying costs of physiological
 stress.
DOI: 10.5061/dryad.n02v6wwz2
title: Data from: Variation in male-built nest volume with nesting-support quality, colony and egg production in whiskered terns

description: Nest building can represent an energetically-costly activity for a variety
 of animal taxa. Besides, the determinants of within-species variation in
 the design of nests, notably with respect to natural and sexual selection,
 are still insufficiently documented. Based on an observational study, we
 examined the influence of nesting conditions (nesting-support quality,
 colony, laying date, and year) on male-built nest volume and also its
 potential role as a post-mating sexually-selected display in the whiskered
 tern Chlidonias hybrida. This tern species is a monogamous colonial bird
 with obligate bi-parental care breeding on aquatic vegetation. Hence,
 large nesting platforms are expected to be a selective advantage because
 they would better withstand adverse environmental conditions and provide a
 secure structure for eggs. Nest size may also serve as a post-mating
 sexual trait, and variation in egg production would be positively
 associated to nest size. We found that nest volume was adjusted to
 different environmental cues. A positive relationship was found between
 nest volume and nesting-support quality indicating that the leaf density
 of white waterlily is essential for nest stability. Variation in nest
 volume was not correlated to colony size but varied among colonies and
 years. Male-built nest volume was also positively associated with mean egg
 volume per clutch but not with clutch size. The fitness consequences of
 building a large nest are yet to be studied, and, additional
 investigations are recommended to better understand whether the activity
 of males early during breeding season (e.g. nest building and courtship
 feeding performance) really serves as post-mating sexually-selected
 signals.
description: The datasets were collected across a range of colonies for a
 3-year period before been processed by a series of linear and logistic
 regression models to test various hypotheses explaining variation in nest
 volume and females' reproductive traits.
description: The readme file contains an explanation of each variable of the
 three distinct datasets with its measurement units. Information on how the
 measurements were done can be found in the associated manuscript
 referenced above.
DOI: 10.5061/dryad.cjsxksn6d
title: Data from: Buxus and Tetracentron genomes

description: Ancient whole-genome duplications (WGDs) characterize many large clades of
 angiosperms, including angiosperms themselves. Prominently, the core
 eudicot clade accommodates 70% of all angiosperms and shares ancestral
 hexaploidy, termed gamma. Gamma arose via two WGDs that occurred early in
 eudicot history; however, the relative timing of these is unclear, largely
 due to the lack of high-quality genomes among early-diverging eudicots. We
 provide complete genomes for Buxus sinica (Buxales) and Tetracentron
 sinense (Trochodendrales), representing the lineages most closely related
 to core eudicots. We show that Buxus and Tetracentron are both
 characterized by independent WGDs, resolve relationships among
 early-diverging eudicots and their respective genomes, and use a new
 pipeline (RACCROCHE) to reconstruct ancestral genome structure at three
 key phylogenetic nodes of eudicot diversification. Our reconstructions
 indicate genome structure remained relatively stable during early eudicot
 diversification, and reject hypotheses of gamma arising via inter-lineage
 hybridization between ancestral eudicot lineages, involving, instead, only
 stem lineage core eudicot ancestors.
DOI: 10.5061/dryad.ffbg79cvz
title: Data from: Genome-wide assessment of kokanee salmon stock diversity, population history and hatchery representation at the northern range margin

description: Freshwater fisheries represent important natural resources, yet a vast
 majority are threatened by anthropogenic stressors. Accurate baseline
 information on stock diversity, population history and hatchery
 representation are required for implementing effective conservation and
 management strategies for mitigating declines. Genetic tools have played
 key roles for informing fisheries management, including for kokanee, the
 freshwater resident form of sockeye salmon (Oncorhynchus nerka),
 particularly in the southern portion of its North American range. Here, we
 investigated stock diversity, population history and hatchery
 representation of kokanee at the northern extent of its range in Canada in
 Kluane National Park and Reserve (KNPR) in the Yukon that underwent a
 12-year population crash followed by a rapid increase in numbers. Using
 restriction-site associated DNA sequencing, we genotyped individuals at
 11,442 single nucleotide polymorphisms (SNPs) that were sampled from
 putative reproductive ecotypes spawning on the shore of Sockeye Lake
 (n=26), within Sockeye Creek (n=20) or near an outlet in between (n=2), as
 well as broodstock from the Whitehorse Rapids Hatchery (n=29). We found no
 evidence of wild stock diversity or ecotype differentiation based on
 neutral SNPs nor outlier loci. Within-population genetic diversity and
 effective population size were substantially higher in the wild population
 relative to the hatchery and significant differentiation was detected,
 suggesting the hatchery population was not representative of wild stock
 diversity. Overall, our results suggest that separate management of
 kokanee in KNPR based on ecotype is not warranted at this time and that
 supplementation with the existing hatchery stock is not appropriate.
description: <strong>onco_77ind_11559snp.vcf</strong>: genotypic
 data for 77 individuals from Sockeye Lake (n=48) and the Whitehorse Rapids
 Hatchery (n=29) at 11,559 SNPs generated via RADseq
 <strong>11559_populations.loci.fa</strong>: fasta
 file containing sequences for 11,559 loci
DOI: 10.5061/dryad.dbrv15f25
title: Agreement rate data set for GENETEX manuscript

description: Objectives: Clinico-Genomic Data (CGD) acquired through routine
 clinical practice has the potential to improve our understanding of
 clinical oncology. However, these data often reside in heterogeneous and
 semi-structured data, resulting in prolonged time-to-analyses. Materials
 and Methods: We created GENETEX: an R package and Shiny
 application for text mining genomic reports from EHR and direct import
 into REDCap®. Results: GENETEX facilitates the abstraction of CGD
 from EHR and streamlines capture of structured data into REDCap®. Its
 functions include natural language processing of key genomic information,
 transformation of semi-structured data into structured data and
 importation into REDCap. When evaluated with manual abstraction, GENETEX
 had &gt;99% agreement and captured CGD in approximately one-fifth the
 time. Conclusions: GENETEX is freely available under the
 Massachusetts Institute of Technology license and can be obtained from
 GitHub. GENETEX is executed in R and deployed as a Shiny application for
 non-R users. It produces high-fidelity abstraction of CGD in a fraction of
 the time.
description: The dataset was collected during a study for the GENETEX
 manuscript. It contains the data used for the section on "Real-world
 deployment". In order to evaluate the performance of augmented
 abstraction with GENETEX in the real-world setting compared to manual
 capture, we selected 7 genomic reports at random (3 Guardant, 2
 Foundation Medicine, 1 MGH SNaPshot, and 1 BWH Oncopanel) for abstraction.
 Each report was abstracted independently by 2 data abstractors via manual
 abstraction, as well as with GENETEX. The data from that abstraction is
 conained in this csv file.
DOI: 10.5061/dryad.47d7wm3dw
title: Data from the article: Narrative Risk Communication as a Lingua Franca for Environmental Hazard Preparation

description: Incorporating narrative elements into risk communication may encourage
 preparation for environmental hazards in ways that scientific language
 alone does not. We integrate narrative theory, narrative persuasion, and
 risk theories into a Narrative Risk Communication Framework and then
 assess the effectiveness of character selection as a narrative mechanism
 in scientific risk communication as compared to conventional science
 messaging alone. We utilize a survey experiment with residents along the
 flood-prone Yellowstone River in Montana and analyze the resulting data
 with a parallel and serial mediation statistical model. We find that
 positive affective response mediates the influence of narratives featuring
 hero character language. Positive affective response appears to overcome
 the risk perception paradox both by circumventing rational analysis of
 risk and by shaping risk perception. Overall, the results suggest that
 inspirational hero language is superior to language of fear or
 victimization in encouraging preparation – an important lesson for
 practitioners working to help citizens prepare for environmental
 disasters.
description: The dataset resulted from a survey experiment conducted with
 residents who lived within 800 meters of the Yellowstone River in Montana.
 The survey yielded 3,320 responses out of 8,721 mailings, for a response
 rate of 38.1%. After cleaning to remove addresses that did not contain a
 residence or for which the respondent was not an owner, trustee, or
 administrator of the property, 2,901 responses remained as valid. The
 primary data analysis involved a parallel and serial mediation model. Data
 and instructions are supplied to replicate that model. The number of
 observations used in the modeling, after eliminating missing data, is
 1,938.
description: Observations with missing data have been removed from the
 comma-separated data file (Lingua_Franca_Dataset_REPLICATION.csv) for
 replication purposes. A codebook (Lingua_Franca_Codebook_REPLICATION.docx)
 and instructions for running the parallel and serial mediation model
 (Lingua_Franca_Instructions_REPLICATION.docx) are supplied along with the
 materials. The materials also include a more comprehensive ReadMe file
 (LINGUA_FRANCA_Readme.txt).
DOI: 10.5061/dryad.w3r2280rk
title: Data from: Spatial variation in bioclimatic relationships for a snow-adapted species along a discontinuous southern range boundary

description: Documenting variation in the relationship between climate variables and
 species occurence at range boundaries can help reveal how species will
 respond to global climate change. We collected snowshoe hare
 (Lepus americanus) presence-absence data from snow-track surveys conducted
 in the U.S. states of Michigan and Wisconsin in winters from 2012-2014 at
 their southern range boundary in the region. A series of 125m transects
 were walked at each site within a week of fresh snowfall, and the presence
 or absence of snowshoe hare tracks on each transect was recorded. Data set
 also includes the variables mean 5-year snow cover duration, mean 5-year
 maximum temperature, and percentage forest cover at each site. Each
 variable was used in data analysis for the related paper to relate
 snowshoe hare occurrence to climate and land cover variables at the
 southern edge of their distribution. Snowshoe hares in the region occur in
 areas with longer snow cover duration and lower maximum temperatures but
 these relationships vary across the study area such that maximum
 temperature was positively correlated with snowshoe hare occurrence in the
 northern portion of the study area (Upper Peninsula of Michigan).
description: Sites were selected based off historical locations of snowshoe
 hares from a peer-reviewed manusript in Wisconsin, or hunter surveys in
 Michigan. Snow tracking surveys were performed at sites during winters
 2012-13 and 2013-2014. A series of 125m transects were walked and we
 recoreded whether snowshoe hare tracks were present on each transect
 (Counts column).
description: Locations denoted 'mesh' in the Spp column are the
 nodes of the triangulated mesh used in the spatial SDM.
DOI: 10.5061/dryad.9kd51c5hz
title: Manipulating plant microbiomes in the field: native mycorrhizae advance plant succession and improve native plant restoration

description: The plant microbiome is critical to plant health and is degraded with
 anthropogenic disturbance. However, the value of re-establishing the
 native microbiome is rarely considered in ecological restoration.
 Arbuscular mycorrhizal (AM) fungi are particularly important microbiome
 components, as they associate with most plants, and later successional
 grassland plants are strongly responsive to native AM fungi. With five
 separate sites across the United States, we inoculated mid- and late
 successional plant seedlings with one of three types of native microbiome
 amendments: 1) whole rhizosphere soil collected from local old-growth,
 undisturbed grassland communities in Illinois, Kansas, or Oklahoma, 2)
 laboratory cultured AM fungi from these same old-growth grassland sites or
 3) no microbiome amendment. We also seeded each restoration with a diverse
 native seed mixture. Plant establishment and growth was followed for three
 growing seasons. The reintroduction of soil microbiome from native
 ecosystems improved restoration establishment. • Including only native
 arbuscular mycorrhizal fungal communities produced similar improvements in
 plant establishment as what was found with whole soil microbiome
 amendment. These findings were robust across plant functional groups.
 Inoculated plants (amended with either AM fungi or whole soil) also grew
 more leaves and were generally taller during the three growing seasons.
 Our research shows that mycorrhizal fungi can accelerate plant succession
 and that the reintroduction of both whole soil and laboratory cultivated
 native mycorrhizal fungi can be used as tools to improve native plant
 restoration following anthropogenic disturbance.
description: See manuscript methods.
DOI: 10.25338/b81m00
title: Anchorage by seed mucilage prevents seed dislodgement in high surface flow: a mechanistic investigation

description: Background and Aims: Seed mucilage is a common and highly diverse trait
 shared among thousands of angiosperm species. While long recognized that
 mucilage allows seeds to anchor to substrates (antitelechory), resisting
 abiotic and biotic dislodgement, we still lack a mechanistic understanding
 of this process. Methods: We propose a mechanistic model of how mucilage
 affects substrate anchorage and fluid resistance, ultimately contributing
 to dislodgement resistance. To test this model, we subjected mucilaginous
 seeds of 52 species, varying in eight measured seed traits, to seven days
 of continuous water flow at a range of dislodgement potentials. Key
 Results: Supporting our model, mucilage mass increased force necessary to
 dislodge both dry and wet seeds; our measurement of the dislodgement force
 of dry mucilage explained time to dislodgement well. The effect size was
 remarkably large; increasing the standardized mucilage mass by one
 standard deviation resulted in a 280-fold increase in the time to
 dislodgement. Fluid resistance was largely dependent on speed of water
 flow and the seed’s modified drag coefficient, but not seed traits.
 Neither mucilage expansion speed nor mucilage decay rate explained
 dislodgement potential well.  Conclusions: Our results suggest
 that the degree of anchorage to substrate, measured with a simple
 dislodgement force assay, is highly predictive of mucilaginous seed
 retention in highly erosive environments. In contrast, we found that other
 seed and mucilage traits are of lesser importance to anchorage.
description: See paper
description: See readme file