cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.15dv41p1d
title: LiDAR reveals a preference for intermediate visibility by a forest-dwelling ungulate species: Deer locational data

description: Visibility (viewshed) plays a significant and diverse role in animals’
 behavior and fitness. Understanding how visibility influences animal
 behavior requires the measurement of habitat visibility at spatial scales
 commensurate to individual animal choices. However, measuring habitat
 visibility at a fine spatial scale over a landscape is a challenge,
 particularly in highly heterogeneous landscapes (e.g., forests). As a
 result, our ability to model the influence of fine-scale visibility on
 animal behavior has been impeded or limited. In this study, we demonstrate
 the application of the concept of 3D cumulative viewshed in the study of
 animal spatial behavior at a landscape level. Specifically, we employed a
 newly described approach that combines terrestrial and airborne LiDAR to
 measure fine-scale habitat visibility (3D cumulative viewshed) on a
 continuous scale in forested landscapes. We applied the LiDAR-derived
 visibility to investigate how visibility in forests affects the summer
 habitat selection and the movement of 20 GPS-collared female red deer
 Cervus elaphus in a temperate forest in Germany. We used integrated step
 selection analysis to determine whether red deer show any preference for
 fine-scale habitat visibility and whether visibility is related to the
 rate of movement of red deer. We found that red deer selected intermediate
 habitat visibility. Their preferred level of visibility during the day was
 substantially lower than that of night and twilight, whereas the
 preference was not significantly different between night and twilight. In
 addition, red deer moved faster in high-visibility areas, possibly mainly
 to avoid predation and anthropogenic risk. Furthermore, red deer moved
 most rapidly between locations in the twilight. For the first time, the
 preference for intermediate habitat visibility and the adaption of
 movement rate to fine-scale visibility by a forest-dwelling ungulate
 species at a landscape scale was revealed. The LiDAR technique used in
 this study offers fine-scale habitat visibility at the landscape level in
 forest ecosystems, which would be of broader interest in the fields of
 animal ecology and behavior.
description: The locational data were collected from GPS-collared red deer in
 Bavaria Forest National Park (Germany). The data were processed as
 described in detail in the Methods and Materials section of the article
 "LiDAR reveals a preference for intermediate visibility by a
 forest-dwelling ungulate species".
description: This dataset was used to perform integrated step selection
 analysis for red deer in the article "LiDAR reveals a preference for
 intermediate visibility by a forest-dwelling ungulate species". The
 meaning of each column in the dataset can be found in the related article
 and accompanying README file.
DOI: 10.5061/dryad.v41ns1s0v
title: How do host-plant use and seasonal life cycle relate to insect body size: A case study on European geometrid moths (Lepidoptera: Geometridae)

description: We used European geometrid moths (&gt; 630 species) as a model group
 to investigate how life history traits linked to larval host plant use
 (i.e., diet breadth and host-plant growth form) and seasonal life cycle
 (i.e., voltinism, overwintering stage, and caterpillar phenology) are
 related to adult body size in holometabolous insect herbivores. To do so,
 we applied phylogenetic comparative methods to account for shared
 evolutionary history among herbivore species. We further categorised
 larval diet breadth based on the phylogenetic structure of utilised host
 plant genera. Our results indicate that species associated with woody
 plants are, on average, larger than herb feeders and increase in size with
 increasing diet breadth. Obligatorily univoltine species are larger than
 multivoltine species, and attain larger sizes when their larvae are
 restricted to the early season. Furthermore, adult body size is
 significantly smaller in species that overwinter in the pupal stage
 compared to those that overwinter as egg or caterpillar. In summary, our
 results indicate that the ecological niche of an holometabolous insect
 herbivore is strongly interrelated with its size at maturity.
description: We compiled information on overwintering stage (546 species) and
 caterpillar phenology (138 species) for European geometrid moths
 (Lepidoptera: Geometridae). Information was compiled based on available
 literature and reliable online sources.
DOI: 10.5061/dryad.tqjq2bw38
title: Open forest successional stages and landscape heterogeneity promote wild bee diversity in temperate forests

description: Recent studies have emphasized forests as crucial habitat for wild bees.
 In Europe, most forests are managed following the principles of
 close‐to‐nature silviculture, which combine timber production and nature
 conservation. However, open late and early successional stages within
 these forests are largely missing, which could be important for wild bees.
 This highlights that close‐to‐nature silviculture alone might not be
 sufficient to conserve bees within temperate forests. Open structures such
 as canopy gaps and road verges in forests could improve habitat for bees.
 To provide management recommendations for wild bee conservation in
 temperate forests, we analyzed how components of bee beta diversity varied
 between forest management types and tested how open structures, namely
 clear‐cuts, canopy gaps, and forest road verges influenced bee abundance,
 richness, and diversity. In addition, we analyzed the abundance and
 percent of red‐listed bee species at different scales. Bees were sampled
 using 90 pan traps on 45 (1 ha) plots in 2019 and 2020 in the Black
 Forest, Germany. Plots were selected in 15 triplets each consisting of
 three management types related to different successional stages:
 unmanaged, close‐to‐nature, and small clear‐cut. Beta diversity was not
 consistently nested highlighting the importance of different management
 and successional stages within the landscape to support bees in forests.
 Abundance, species richness, and Shannon diversity of bees were highest on
 clear‐cuts, compared to unmanaged‐ and close‐to‐nature plots. At landscape
 scale, wild bee abundance increased with canopy openness while wild bee
 diversity increased with landscape heterogeneity. Abundance‐ and percent
 of red‐listed bee species increased with the length of forest road verges.
 We advocate creating habitats at local scales which offer flowering and
 nesting resources by providing canopy gaps. At landscape scale,
 heterogeneity created through different forest successional stages is
 needed to conserve the entire community of wild bees.
description: Please see README.md document and read the published article for
 further information: Eckerter, T., Braunisch, V., Buse, J., Klein, AM.
 (2022). Open forest successional stages and landscape heterogeneity
 promote wild bee diversity in temperate forests. <em>Conservation
 Science and Practice</em>. Accepted DOI:10.1111/csp2.12843
description: You will need any spreadsheet programm to open the data files
 such as Microsoft Excel, Mac Numbers, Open Office or Google Sheets. The
 Readme file can be opened using the Editor.
DOI: 10.5061/dryad.5x69p8d72
title: Demographic changes and life-history strategies predict the genetic diversity in crabs

description: Uncovering what predicts genetic diversity (GD) within species can help us
 access the status of populations and their evolutionary potential. Traits
 related to effective population size show a proportional association to
 GD, but evidence supports life-history strategies and habitat as the
 drivers of GD variation. Instead of investigating highly divergent taxa,
 focusing on one group could help to elucidate the factors influencing the
 GD. Additionally, most empirical data is based on vertebrate taxa;
 therefore, we might be missing novel patterns of GD found in neglected
 invertebrate groups. Here, we investigated the predictors of the GD in
 crabs (Brachyura) by compiling the most comprehensive cytochrome c oxidase
 subunit I (COI) available. Eight predictor variables were analyzed across
 150 species (16,992 sequences) using linear models (multiple linear
 regression) and comparative methods (PGLS). Our results indicate that
 population size fluctuation represents the most critical trait predicting
 GD, with species that have undergone bottlenecks followed by population
 expansion showing lower GD. Egg size, pelagic larval duration, and habitat
 might play a role probably because of their association with how species
 respond to disturbances. Ultimately, K-strategists that have undergone
 bottlenecks are the species showing lower GD. Some variables do not show
 an association with GD as expected, most likely due to the taxon-specific
 role of some predictors, which should be considered in further
 investigations and generalizations.  This work highlights the
 complexity underlying the predictors of GD and adds results from a marine
 invertebrate group to the current understanding of this topic.
DOI: 10.5061/dryad.0rxwdbs4c
title: Within-generation and transgenerational social plasticity interact during rapid adaptive evolution

description: The effects of within-generation plasticity versus transgenerational
 plasticity on trait expression are poorly understood, but important for
 evaluating plasticity’s evolutionary consequences. We tested how genetics,
 within-generation plasticity, and transgenerational plasticity jointly
 shape traits influencing rapid evolution in the field cricket Teleogryllus
 oceanicus. In Hawaiian populations attacked by acoustically-orienting
 parasitoid flies, a protective, X-linked variant (“flatwing”) eliminates
 male acoustic sexual signals. Silent males rapidly spread to fixation,
 dramatically changing the acoustic environment. First, we found evidence
 supporting flatwing-associated pleiotropy in juveniles: pure-breeding
 flatwing males and females exhibit greater locomotion than those with
 normal-wing genotypes. Second, within-generation plasticity caused
 homozygous-flatwing females developing in silence, which mimics
 all-flatwing populations, to attain lower adult body condition and
 reproductive investment than those experimentally exposed to song. Third,
 maternal song exposure caused transgenerational plasticity in offspring,
 affecting adult, but not juvenile, size, condition, and reproductive
 investment. This contrasted with behavioral traits, which were only
 influenced by within-generation plasticity. Fourth, we matched and
 mismatched maternal and offspring social environments and found that
 transgenerational plasticity sometimes interacted with within-generation
 plasticity and sometimes opposed it. Our findings stress the importance of
 evaluating the plasticity of different traits and stages across
 generations when evaluating their fitness consequences and role in
 adaptation.
description: Locomotion activity data was measured from a 5-minute open-field
 test video, from which coordinates were extracted using DORIS (v.0.0.17).
 Coordinates were then smoothed and distances were computed using a custom
 script in R. Size data (pronotum length and width) were measured from
 images of individual crickets using ImageJ (v.1.8.0_112). The reproductive
 investment was measured by weighting ovary and egg tissue in females or
 testes in males. The somatic condition was calculated from somatic weight
 (total weight - reproductive tissue weight) separately for each sex using
 the smatr package in R. 
description: All data files can be opened using Excel. Scripts can be opened
 using R.
DOI: 10.5061/dryad.8pk0p2nrj
title: Disturbing the spatial structure of biofilms affects the expression of agr regulated virulence factors in Staphylococcus aureus

description: Staphylococcus aureus uses quorum sensing and nutrient
 availability to control the expression of agr-regulated virulence
 factors. Quorum sensing is mediated by autoinducing peptide
 (AIP), which at high concentration, reduces expression of surface
 attachment proteins (coa, fnbpA), and increases expression of
 exotoxins (lukS) and proteases (splA). Nutrient availability can be sensed
 through the saeS/saeR system. Low nutrients increase
 expression of saeR, which augments expression
 of coa and fnbpA distinct from
 AIP. The formation of spatial structure, such as biofilms, can
 alter quorum sensing and nutrient acquisition. In natural environments,
 biofilms encounter forces that may alter their spatial structure. This may
 impact quorum sensing and/or nutrient acquisition, and thus affect the
 expression of agr-regulated virulence factors. However, this has
 not been studied. We show that periodically disturbing biofilms composed
 of S. aureus using a physical force affects the
 expression of agr-regulated virulence factors. In nutrient-poor
 environments, disturbance increased the expression of
 coa, fnbpA, lukS, and splA. Disturbance into a
 nutrient-rich environment at low or high disturbance amplitudes moderately
 reduced expression of coa and fnbpA but
 increased expression of lukS and splA.
 Interestingly, at an intermediate amplitude, the overall expression
 of agr-regulated virulence factors was the lowest; expression
 of lukS and splA remained unchanged
 relative to an undisturbed biofilm while expression
 of coa and fnbpA significantly decreased. We
 hypothesize that these changes are a result of disturbance-driven changes
 in access to AIP and nutrients. Our results may allow the identification
 of environments where virulence is enhanced, or reduced, owing to
 disturbance.
DOI: 10.6078/d1mh7p
title: Data from: Sugar pine association genetics and performance in a post-fire restoration planting

description: Climate change is motivating a reassessment of how seeds are selected for
 reforestation, as rapid environmental change can lead to local
 maladaptation in trees. Genetic association studies and past seed source
 climate both have the potential to help identify appropriate planting
 stock, but these techniques have not been compared and tested as part of
 an operational planting program. In this study, we combined an analysis of
 SNPs associated with environmental gradients in sugar pine (P.
 lambertiana) with an analysis of post-fire seedling survival and growth in
 a restoration experiment. Our genotype-environment association (GEA) tests
 revealed 829 SNPs (single nucleotide polymorphisms) with significant
 association with climate gradients – especially April snowpack – 323 of
 which either had annotations that suggested potential functional
 importance or were identified by two different methods. We then built
 Bayesian models of survival and growth for all seedlings to test the
 effects of source elevation, a common proxy for climate. For the subset of
 seedlings alive and genotyped in 2020 (1–3 years after planting), we
 tested the relative predictive ability of source elevation versus the
 proportion of seedling alleles expected to be locally advantageous. We
 found that source elevation was generally better at predicting seedling
 performance than genotype indices, perhaps because of the limited scope of
 the association analysis. Seed sources from 500–1500 feet lower in
 elevation and one seed zone further south generally performed as well or
 better than local seed sources. This is likely because the temperatures in
 the planting area closely resemble that of those source regions in the
 mid-20th century, allowing seedlings to survive and exhibit the higher
 growth potential often seen in warmer-climate populations. By contrast,
 seedlings from cooler, wetter sources tended to perform poorly. This
 result, and those of similar previous studies, suggest that “climate
 matching” using past climate information for existing seed sourcing units
 is a reasonable starting point for finding seedlings suited to
 already-altered planting site climate conditions. However, further tests
 with more extensive genomic and performance data may improve the utility
 of genotype information for seed selection.
DOI: 10.5061/dryad.0cfxpnw6c
title: Data set for: Genetic dissection of marker trait associations for grain micro-nutrients and thousand grain weight under heat and moisture deficit stress conditions in wheat

description: The study material in the GWAS panel with 193 bread wheat genotypes from
 Indian and exotic collections was selected to map the genomic regions
 responsible for grain iron and Zinc content under drought and heat stress
 treatments. Phenotypic data: The GWAS panel was evaluated at IARI, New
 Delhi - DL (28.6550° N, 77.1888° E, MSL 228.61 m) under Irrigated (IR),
 Restricted Irrigated (RI) and Late sown (LS) treatment conditions over 2
 years i.e. 2020 and 2021 with augmented RCBD design. Data was collected on
 Grain Iron and Grain zinc content along with thousand-grain weight. Around
 20 g of grain sample from each of 282 genotypes from the GWAS panel under
 all three conditions were used for phenotyping GFeC and GZnC through
 high-throughput Energy Dispersive X-ray Fluorescence (ED-XRF) machine
 (model X-Supreme 8000; Oxford Instruments plc, Abingdon, United Kingdom)
 calibrated with glass beads-based values. To record TGW, manual counting
 of grains was followed and the weight of the grains was recorded in grams
 with an electronic balance. Genotypic data: Genomic DNA of the GWAS panel
 was extracted from the leaves of seedlings by Cetyl Trimethyl Ammonium
 Bromide (CTAB) method. The panel was genotyped using Axiom Wheat Breeder’s
 Genotyping Array (Aﬀymetrix, Santa Clara, CA, United States) having 35,143
 genome-wide SNPs. The monomorphic, markers with minor allele frequency
 (MAF) of &lt;5%, missing data of &gt;10%, and heterozygote
 frequency &gt;50% were removed from the analysis. The remaining set of
 13,947 high-quality SNPs was used in GWAS analysis.
description: Description of methods used for collection/generation of data:
 Around 20 g of grain sample from each of 193 genotypes from the GWAS panel
 under all three conditions over 2 seasons were used for phenotyping GFeC
 and GZnC through high-throughput Energy Dispersive X-ray Fluorescence
 (ED-XRF) machine (model X-Supreme 8000; Oxford Instruments plc, Abingdon,
 United Kingdom) calibrated with glass beads-based values. To record TGW,
 manual counting of grains was followed and the weight of the grains was
 recorded in grams with an electronic balance. The genotypes were genotyped
 using Axiom Wheat Breeder’s Genotyping Array (Aﬀymetrix, Santa Clara, CA,
 United States) having 35,143 genome-wide SNPs. Methods
 for processing the data: The GWAS panel of 193 genotypes was genotyped
 using Axiom Wheat Breeder’s Genotyping Array (Aﬀymetrix, Santa Clara, CA,
 United States) having 35,143 genome-wide SNPs. The monomorphic, markers
 with minor allele frequency (MAF) of &lt;5%, missing data of
 &gt;10%, and heterozygote frequency &gt;50% were removed from the
 analysis. The remaining set of 13,947 high-quality SNPs was used in GWAS
 analysis. For more detail please see the README
 file.
description: Microsoft Excel
DOI: 10.5061/dryad.k98sf7m9c
title: Supplementary materials: Indirect effects of trophic interactions govern carbon circulation in two beech forest soil ecosystems

description: 1. Forests soils harbour a vast array of organisms that govern the
 processing of organic matter. Through their trophic interactions, they
 give rise to carbon flows that sustain soil ecosystem functioning.
 Understanding how soil food webs shape carbon flows may enhance our
 knowledge about the role of biodiversity on soil processes. 2. In this
 work, we assembled trophic networks representing soil food webs of two
 beech forests during spring and autumn and compiled mass-balanced models
 quantifying carbon flows between their components. These models were
 investigated using network analysis to identify the role of the components
 on carbon flow, cycling and functional trophic relationships. Moreover, we
 explored how the structure of carbon exchanges promote efficiency and
 stability. 3. Results indicate the importance of indirect interactions.
 Most trophic groups exhibit a diffuse dependency on all the compartments
 for their carbon requirement although certain groups such as Collembola
 play the role of hubs in distributing carbon. Indirect interactions often
 reverse the impacts of direct trophic relationships being antagonistic to
 the direction of change predicted based on predator-prey interactions. The
 high incidence of generalist feeding habits increases the redundancy of
 energy channels thereby making such food webs more resilient against
 perturbations but at the expense of carbon transfer efficiency. 4.
 Although differences can be observed across sites and periods, food web
 structure rather than environmental variability seems to be the main
 factor responsible for patterns of carbon flows in the two beech forests.
description: Biomass data were collected from field samplings. Metabolic data
 were assessed to biomass data by using metabolic parameters extracted from
 bibliography (see appendix). Provided data are the
 adjacency matrices from both northern and southern forests in spring and
 autumn seasons, together with biomasses of each compartment. These
 matrices were used to build the models and make the analysis.
description: We used R to perform the analysis.
DOI: 10.5061/dryad.xwdbrv1h9
title: Data for: Climate and forest attributes influence aboveground biomass of deciduous broadleaf forests in China

description: Forests provide a huge carbon pool, a substantial portion of which is
 stored in aboveground biomass (AGB). Deciduous broadleaf forests in China
 are an essential component of global deciduous broadleaf forests, yet the
 impacts of climate and forest attributes on their AGB are not well
 understood. Using a comprehensive forest inventory database available from
 772 plots distributed across the temperate and subtropical deciduous
 broadleaf forests in China (23.51°-42.53° N and 104.24°-128.27° E), we
 applied variance partitioning analysis, model selection analysis and
 structural equation models to explore how AGB was associated with climate
 and forest attributes (species diversity, community-level functional
 traits, and stand structures) in different climatic regions (semi-arid
 forests, semi-humid forests and humid forests). Community-level functional
 traits and stand structures together explained a great portion of the
 variance in AGB. The effect of community-level functional traits was
 greater than that of stand structures in semi-arid forests and semi-humid
 forests, but smaller in humid forests. Further analyses showed that
 community-level maximum tree height, stem density and tree size inequality
 were the best explanatory variables. Although climate and species
 diversity had only minor effects, the direct positive effect of mean
 annual precipitation (MAP) was still important, especially in semi-arid
 forests. Synthesis. Community-level functional traits but not species
 diversity were key drivers of AGB, indicating that tree species diversity
 loss may not impair AGB substantially in deciduous broadleaf forests in
 China. Moreover, stand structures had also strong effects on AGB in both
 semi-arid forests and humid forests, highlighting the importance of
 structural complexity. In addition, MAP had a direct positive effect on
 AGB in semi-arid forests and semi-humid forests, and a future predicted
 increase in drought might potentially reduce carbon storage in these
 forests.