cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f4qrfj707
title: High-resolution 3D forest structure explains ecomorphological trait variation in assemblages of saproxylic beetles

description: Climate, topography, and the 3D structure of forests are major drivers
 affecting local species communities. However, little is known about how
 the specific functional traits of saproxylic (wood-living) beetles,
 involved in the recycling of wood, might be affected by those
 environmental characteristics. Here we combine ecological and
 morphological traits available for saproxylic beetles and airborne laser
 scanning (ALS) data in Bayesian trait-based joint species distribution
 models to study how traits drive the distributions of more than 230
 species in temperate forests of Europe. We found that elevation (as a
 proxy for temperature and precipitation) and the proportion of conifers
 played important roles in species occurrences while variables related to
 habitat heterogeneity and forest complexity were less relevant. Further,
 we showed that local communities were shaped by environmental variation
 primarily through their ecological traits whereas morphological traits
 were involved only marginally. As predicted, ecological traits influenced
 species’ responses to forest structure, and to other environmental
 variation, with canopy niche, wood decay niche, and host preference as the
 most important ecological traits. Conversely, no links between
 morphological traits and environmental characteristics were observed. Both
 models, however, revealed strong phylogenetic signal in species’ response
 to environmental characteristics. These findings imply that alterations of
 climate and tree species composition have the potential to alter
 saproxylic beetle communities in temperate forests. Additionally,
 ecological traits help explain species’ responses to environmental
 characteristics and thus should prove useful in predicting their responses
 to future change. It remains challenging, however, to link simple
 morphological traits to species’ complex ecological niches.
description: See manuscript for methods details. 
 Species traits - from references cited in manuscript (Hagge et
 al., 2021; Köhler, 2000; Seibold et al., 2015)
 Environmental variables - from multiple local and remote
 measurements Species detections - presence/absence of
 species captured in window traps at each plot
description: Microsoft Excel / Libre Office
DOI: 10.5061/dryad.msbcc2g27
title: The genomic landscapes of desert birds form over multiple time scales

description: Spatial models show that genetic differentiation between populations can
 be explained by factors ranging from geographic distance to environmental
 resistance across the landscape. However, genomes exhibit a landscape of
 differentiation, which could indicate that multiple spatial models better
 explain divergence in different portions of the genome. We test whether
 alternative geographic predictors of intraspecific differentiation vary
 across the genome in ten bird species that co-occur in Sonoran and
 Chihuahuan Deserts of North America. Using population-level genomic data,
 we characterized the genomic landscapes across species and modeled five
 predictors that represented historical and contemporary mechanisms. The
 characteristics of genomic landscapes differed across the ten species,
 influenced by varying levels of population structuring and admixture
 between deserts. General dissimilarity matrix modeling indicated that the
 best-fit models differed from the whole genome and partitions along the
 genome. Almost all of the historical and contemporary mechanisms were
 important in explaining genetic distance, particularly historical and
 contemporary environment, while contemporary abundance, position of the
 barrier to gene flow, and distance explained relatively less. Individual
 species have significantly different patterns of genomic variation. These
 results illustrate that the genomic landscape of differentiation was
 influenced by alternative geographic factors operating on different
 portions of the genome.
DOI: 10.5061/dryad.8cz8w9gv6
title: Climate mitigation potential and soil microbial response of cyanobacteria-fertilized bioenergy crops in a cool semi-arid cropland

description: Bioenergy carbon capture and storage (BECCS) systems can serve as
 decarbonization pathways for climate mitigation. Perennial grasses are a
 promising second-generation lignocellulosic bioenergy feedstock, but
 optimizing their sustainability, productivity, and climate mitigation
 potential requires an evaluation of how nitrogen (N) fertilizer strategies
 interact with greenhouse gas (GHG) and soil organic carbon (SOC) dynamics.
 Further, crop and fertilizer choice can affect the soil microbiome which
 is critical to soil organic matter turnover, nutrient cycling, and
 sustaining crop productivity but these feedbacks are poorly
 understood due to the paucity of data from agroecosystems. Here, we
 examine the climate mitigation potential and soil microbiome response to
 establishing two functionally different perennial grasses, switchgrass
 (Panicum virgatum, C4), and tall wheatgrass (Thinopyrum ponticum, C3), in
 a cool semi-arid agroecosystem under two fertilizer applications, a novel
 cyanobacterial biofertilizer (CBF) and urea. Finally, we examine shifts in
 soil microbial composition resulting from crop establishment and
 fertilizer regime. We find that in contrast to the C4 crop, the C3 crop
 achieved 98% greater productivity and had a higher N use efficiency when
 fertilized and the CBF produced the same biomass enhancement as urea.
 Non-CO2 greenhouse gas fluxes across all treatments were low and we
 observed a three-year net loss of SOC under the C4 crop and a net increase
 under the C3 crop at a 0-30 cm soil depth regardless of fertilization.
 Further, we detected crop-specific changes in the soil microbiome,
 including an increased relative abundance of arbuscular mycorrhizal fungi
 under the C3, and potentially pathogenic fungi in the C4 grass. Taken
 together, these findings highlight the potential of CBF-fertilized C3
 crops as a second-generation bioenergy feedstock in semiarid regions as a
 part of a climate mitigation strategy.
description: The dataset was collected and compiled between 2017 and 2020.
 Soil carbon and nitrogen data from 2017 were collected at two depths
 (0-15cm) and (15-30cm). Soil carbon and nitrogen data from 2020 were
 collected at three depths (0-5cm), (5-15cm), and (15-30cm). A weighted
 average was used to compare the three-year change. Greenhouse gas flux
 data (CO2, CH4, and N2O) were collected in 2020 acoss multiple sampling
 periods from March to October using a Picarro G2508 analyzer. Both
 aboveground biomass (equal mix of stem + leaf + infloresence) data are
 from two perennial grasses, switchgrass and tall wheatgrass, that were
 harvested in September 2020.  Root biomass and chemistry data are from the
 top 15 cm of the soil of both switchgrass and tall wheatgrass.
description: The data were compiled in microsoft excel and processed in R
 using packages cited in the manuscript.
DOI: 10.5061/dryad.3n5tb2rmb
title: Video recording of the collective display of Photuris frontalis fireflies

description: Photuris frontalis fireflies are known for their synchronous flashing when
 swarming in large numbers. Here, we provide a continuous, high-resolution
 video recording of their collective display. This recording was obtained
 at Congaree National Park, South Carolina, USA, on May 23, 2021, in the
 fireflies' natural habitat. It started at 8:38 pm EDT and continued
 for about 130 min without human interference. The flashes seen in the
 video appear usually synchronous, and at times produce more complex
 patterns akin to the mathematical phenomenon known as "chimera
 state".
description: This movie was recorded with a α7R4 Sony camera with
 settings: 60 fps
 Exposure time: 1/60 s Aperture:
 f/1.4 ISO = 32,000 
 The camera was mounted with a Rokinon 35mm AS UMC lens, which is
 a wide-angle lens (63°). Focus was at infinity.<br><br>The
 camera was placed on a tripod about 1m50 above ground.
 The movie was produced by the camera as a .MP4 file. It was
 automatically split after 100min.
description: The video files can be read with most usual MP4 reader
 software.
DOI: 10.15468/dl.h87sph
title: Occurrence Download

description: A dataset containing 37423 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Alternanthera philoxeroides",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation, Occurrence evidence)"
 ]
}

 The dataset includes 37423 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003285-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.wdbrv15s5
title: SO2 and copper tolerance exhibit an evolutionary trade-off in Saccharomyces cerevisiae

description: Copper tolerance and sulfite tolerance are two well-studied phenotypic
 traits of Saccharomyces cerevisiae. The genetic bases of these traits are
 derived from allelic expansion at the CUP1 locus and reciprocal
 translocation at the SSU1 locus, respectively. Previous work identified a
 negative association between sulfite and copper tolerance in S. cerevisiae
 wine yeasts. Here we probe the relationship between sulfite and copper
 tolerance and show that an increase in CUP1 copy number does not impart
 copper tolerance in all S. cerevisiae wine yeast.  Bulk-segregant
 QTL analysis was used to identify variance at SSU1 as a causative factor
 in copper sensitivity, which was verified by reciprocal hemizygosity
 analysis in a strain carrying 20 copies of CUP1. Transcriptional and
 proteomic analysis demonstrated that SSU1 over-expression did not suppress
 CUP1 transcription or constrain protein production but suggested that SSU1
 overexpression induced sulfur limitation during exposure to copper.
 Finally, an SSU1 over-expressing strain exhibited increased sensitivity to
 moderately elevated copper concentrations in sulfur-limited medium,
 demonstrating that SSU1 over-expression burdens the sulfate assimilation
 pathway. Over-expression of MET 3/14/16, genes upstream of H2S production
 in the sulfate assimilation pathway increased the production of SO2 and
 H2S but did not improve copper sensitivity in an SSU1 overexpressing
 background. We conclude that copper and sulfite tolerance are conditional
 traits in S. cerevisiae and provide evidence of the metabolic basis for
 their mutual exclusivity. These findings suggest an evolutionary basis for
 the extreme amplification of CUP1 observed in some yeasts.
description: A complete description of how the data was collected and the
 methods used to process it is provided in the associated
 manuscript.
description: All data is provided as tab-delimited text.
DOI: 10.5061/dryad.ffbg79czg
title: Data from: Rapid flower closure of Drosera tokaiensis deters caterpillar herbivory

description: Certain plants exhibit rapid movement in response to mechanical
 stimulation; however, the ecological functions of this behaviour are
 largely unknown. Here, we show that the rapid flower closure of Drosera
 tokaiensis (Droseraceae) in response to mechanical stimulation functions
 as a physical defence against a specialist herbivore Buckleria paludum
 (Pterophoridae) caterpillar. Following feeding damage on fruits, flowers,
 flower stalks, and buds by B. paludum, D. tokaiensis closed its flowers
 nine times faster than during natural circadian closure. The extent of
 damage to ovules was significantly reduced when the flowers were able to
 close compared with the condition in which closure was physically
 inhibited by application of a resin. Nonetheless, flower closure had no
 effect on the feeding damage to stamens and pistils and promoted further
 damage to petals. Given that feeding on petals, stamens, and pistils had
 no significant effect on the number of mature seeds, rapid flower closure
 leading to the protection of ovules had an overall positive effect on the
 reproductive success of D. tokaiensis. Our study showed rapid plant
 movement as a novel case of induced physical defence against herbivory.
DOI: 10.5061/dryad.1vhhmgqws
title: Data from: The origin of a new chromosome in gerbils

description: Gerbil genomes have both an extensive set of GC-rich genes and chromosomes
 strikingly enriched for constitutive heterochromatin. We sought to
 determine if there was a link between these two phenomena and found that
 the two heterochromatic chromosomes of the Mongolian gerbil (Meriones
 unguiculatus) have distinct underpinnings: chromosome 5 has a large block
 of intra-arm heterochromatin as the result of a massive expansion of
 centromeric repeats (probably due to centromeric drive); while chromosome
 13 is comprised of extremely large (&gt;150kb) repeated sequences. We
 suggest that chromosome 13 originated when a functionally important ‘seed’
 broke off from another chromosome and underwent multiple
 breakage-fusion-bridge cycles. Genes with the most extreme GC skew are
 encoded on this chromosome, most likely due to the restriction of
 recombination to a narrow permissive region (since GC bias is linked with
 recombination-associated processes). Our results demonstrate the
 importance of including karyotypic features such as chromosome number and
 the locations of centromeres in the interpretation of genome sequence
 data, and highlight novel patterns involved in the evolution of
 chromosomes.
description: Here are a gff (gene annotation) file, a vcf (list of single
 nucleotide variants) for genetic map markers in a F2 mapping panel, a
 second gff containing repetitive elements, and a genetic map. Also
 included is the codebase for the project (i.e. Supplemental Material
 3) All of these files correspond with the
 chromosome-scale <em>Meriones unguiculatus</em> genome that we
 published which is available at NCBI (bioproject PRJNA397533). Methods are described in the manuscript "The origin of a new chromosome in gerbils". The gene annotation was done with the maker pipeline and RNAseq data from kidney and testis. The VCF was based on the sequence data from the manuscript (Brekke et al 2019) and contains genotype data for the entire mapping panel at the genetic markers. The physical and genetic positions of the markers are given in the genetic map. The repetitive element annotation file was created with the EarlGrey pipeline. Brekke, T. D., S. Supriya, M. G. Denver, A. Thom, K. A. Steele, and J. F. Mulley. 2019. A high-density genetic map and molecular sex-typing assay for gerbils. Mamm Genome 30:63–70.
description: These are all flat-text files in standard gff3 and vcf
 format. The code is in bash, R, and Python3 and
 Processing.
DOI: 10.5061/dryad.k98sf7m92
title: Limited movement of an avian hybrid zone in relation to regional variation in magnitude of climate change

description: Studies of natural hybrid zones can provide documentation of range shifts
 in response to climate change and identify loci important to reproductive
 isolation. Using a temporal (36–38 years) comparison of the black-capped
 (Poecile atricapillus) and Carolina (P. carolinensis) chickadee hybrid
 zone, we investigated movement of the western portion of the zone (western
 Missouri) and assessed whether loci and pathways underpinning reproductive
 isolation were similar to those in the eastern portion of the hybrid zone.
 Using 92 birds sampled along the hybrid zone transect in 2016 and 68 birds
 sampled between 1978 and 1980, we generated 11,669 SNPs via ddRADseq.
 These SNPs were used to assess movement of the hybrid zone through time
 and to evaluate variation in introgression among loci. We demonstrate that
 the interface has moved ~5 km to the northwest over the last 36–38 years,
 i.e., at only one-fifth the rate at which the eastern portion (e.g.,
 Pennsylvania, Ohio) of the hybrid zone has moved. Temperature trends over
 the last 38 years reveal that eastern areas have warmed 50% more than
 western areas in terms of annual mean temperature, possibly providing an
 explanation for the slower movement of the hybrid zone in Missouri. Our
 results suggest hybrid zone movement in broadly distributed species, such
 as chickadees, will vary between areas in response to local differences in
 the impacts of climate change.
description: Please see the README document
 ("README_chickadee_9Oct2022.txt") and the accompanying published
 article: Alexander, A., Robbins, M., Holmes, J., Moyle, R. and Peterson,
 T. Limited movement of an avian hybrid zone in relation to regional
 variation in magnitude of climate change. Molecular Ecology.
description: Please see the README document
 ("README_chickadee_9Oct2022.txt") and the accompanying published
 article: Alexander, A., Robbins, M., Holmes, J., Moyle, R. and Peterson,
 T. Limited movement of an avian hybrid zone in relation to regional
 variation in magnitude of climate change. Molecular Ecology.
DOI: 10.5281/zenodo.18401731
title: Cloud Workload and Resource Utilization Dataset for RL-Based Resource Allocation

description: This dataset contains workload traces and system performance metricsused for training and evaluating a reinforcement learning-basedcloud resource allocation framework.

It supports the study:“A Flexible Reinforcement Learning Framework for Smart Resource Allocation in Cloud Computing”.
DOI: 10.5281/zenodo.18401732
title: Cloud Workload and Resource Utilization Dataset for RL-Based Resource Allocation

description: This dataset contains workload traces and system performance metricsused for training and evaluating a reinforcement learning-basedcloud resource allocation framework.

It supports the study:“A Flexible Reinforcement Learning Framework for Smart Resource Allocation in Cloud Computing”.
DOI: 10.5061/dryad.pzgmsbcqh
title: Interest in insect die-off and intention for action using Google trends

description: 1. The publication of “More than 75 percent decline over 27 years in total
 flying insect biomass in protected areas” by Hallmann et al. in October
 2017 gained vast media coverage in Germany. The insect crisis as
 conservation topic has received little attention among the public before,
 but since media influences people’s awareness, we investigated i) whether
 the study publication induced increased awareness among the German public
 for insect die-off, and ii) whether it contributed to people’s intentions
 to undertake insect protecting actions. 2. We used Google Trends to
 examine the people’s internet activity in terms of keywords relevant to
 our research question. 3. A high peak in Google searches for insect
 die-off (Insektensterben) was indeed visible just after the study
 publication, and search volume remained significantly higher for the
 following six months, confirming that the topic gained attention. 4.
 Searches for the three keywords insect hotel, bee friendly and bee meadow
 increased significantly over the summers of the years 2017 to 2019. This
 suggests that intentions to undertake these simple insect protecting
 actions rose as well. The results propose that media should use the window
 of opportunity opened by shocking news about a crisis to spread
 information on feasible counteractions. 5. Due to the prevailing
 topicality in the media and the already increased awareness and
 willingness to action among the population, conservation organizations can
 take advantage of the situation by communicating practical conservation
 measures to the general public in cooperation with media agencies or via
 own channels such as press releases and social media campaigns.
description: The data was downloaded from Google Trends. It was searched for
 the index of search activity for the four German keywords
 "Insektensterben" ("insect die-off"),
 "Insektenhotel" ("insect hotel"),
 "bienenfreundlich" ("bee friendly") and
 "Bienenweide" ("bee meadow"). For all four keywords,
 query data was used rather than query collections, which is an additional
 feature of Google trends that includes related searches. The geographical
 range was restricted to Germany, and data was downloaded for the time span
 between January 3, 2016, and December 22, 2019. It was
 then analyzed with R, where the data sets were divided into different
 sections and compared with each other.
DOI: 10.5061/dryad.w9ghx3fsb
title: Estimating fine-scale changes in turbulence using the movements of a flapping flier

description: All animals that operate within the atmospheric boundary layer need to
 respond to aerial turbulence. Yet little is known about how flying animals
 do this because evaluating turbulence at fine scales (tens to ~ 300 m) is
 exceedingly difficult. Recently, data from animal-borne sensors have been
 used to assess wind and updraft strength, providing a new possibility for
 sensing the physical environment. We tested whether highly-resolved
 changes in altitude and body acceleration measured onboard solo-flying
 pigeons (as model flapping fliers) can be used as qualitative proxies for
 turbulence. A range of pressure and acceleration proxies performed well
 when tested against independent turbulence measurements from a tri-axial
 anemometer mounted onboard an ultralight flying the same route, with
 stronger turbulence causing increasing vertical displacement. The best
 proxy for turbulence also varied with estimates of both convective
 velocity and wind shear. The approximately- linear relationship between
 most proxies and turbulence levels suggests this approach should be widely
 applicable, providing insight into how turbulence changes in space and
 time. Furthermore, pigeons were able to fly in levels of turbulence that
 were unsafe for the ultralight, paving the way for the study of how
 freestream turbulence affects the costs and kinematics of animal flight.
description: For information on data collection and processing please see the
 methods section and the supplementary information of the
 manuscript: <strong>"Estimating fine-scale
 changes in turbulence using the movements of a flapping
 flier"</strong> Because of the large number
 and diversity of attibutes used across datasets, a specific summary of
 attributes and description ("Attribute Summary.txt")
 is included in each folder and subfolder for each dataset. For
 dataset and code organisation, please see the main "README.docx"
 file first.
DOI: 10.5061/dryad.59zw3r2bn
title: Ecological determinants of variation in phenotypic selection on quantitative immune defence traits

description: Immune defence is an important determinant of organismal fitness. While
 theoretical models based on trade-offs in resource allocation predict
 quantitative immune traits to be subject to stabilizing selection due to
 associated energetic costs and self-harm, empirical studies report mainly
 positive directional selection. This discrepancy may arise from multiple
 ecological factors that vary in nature and could influence selection. We
 examined if selection on immune activity varies depending on immune
 challenge/infection risk, between immune traits, and among populations in
 the freshwater snail Lymnaea stagnalis. We assessed selection on the
 phenoloxidase-like and antibacterial activity of snail haemolymph while
 manipulating the level of immune challenge imposed by environmental
 microbes. We did this using snails from multiple populations and also
 quantified within-population family-level variation (i.e., evolutionary
 potential) in the snails’ immune activity. We found that the strength of
 immune challenge and the examined immune trait determined selection on the
 snails’ immune function. Thus, variation in infection risk can be an
 important factor in maintaining genetic variation in defence traits.
 Additionally, immune traits showed low among-population differentiation
 but high within-population genetic variation. This pattern could arise if
 natural snail populations are exposed to higher temporal than spatial
 variation in infection risk.