cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9cnp5hqnt
title: Geographic variability of hybridization between red-breasted and red-naped sapsuckers

description: Hybrid zones reveal the strength of reproductive isolation between
 populations undergoing speciation and are a key tool in evolutionary
 biology research. Multiple replicate transects across the same hybrid zone
 offer insight into the dynamics of hybridization in different
 environments, clarifying the role of extrinsic forces on the speciation
 process. Red-breasted and red-naped sapsuckers (Sphyrapicus ruber and S.
 nuchalis) have a long zone of contact over approximately 1,600 km from
 central British Columbia, Canada to central California, USA. We used
 Genotyping-by-Sequencing data from three independent sapsucker hybrid zone
 transects to compare hybridization dynamics between these species under
 variable geoclimatic conditions. We generated geographic clines of the
 genomic data to compare hybrid zone widths and used Random Forest models
 and linear regression to assess the relationship between climate and
 sapsucker ancestry along each transect. Our results show variation in the
 directionality of backcrossing, often indicative of moving hybrid zones.
 We note variable cline widths among transects, indicating differences in
 selection maintaining hybrid zone dynamics. Furthermore, Random Forest
 models identified different variables in close association with sapsucker
 ancestry across each transect. These results indicate a lack of
 repeatability across replicate transects and a strong influence of local
 environment on hybrid zone dynamics.
description: Please see the Natola et al. 2022 Evolution paper for
 methodology, and the README.md and tassel_filter_admixture_scripts.txt
 files for additional details. 
description: The README contains a list of files used and the figures/contexts
 they appear in the publication text. The file
 tassel_filter_admixture_scripts.txt outlines steps to convert raw Illumina
 GBS reads to genotype files in the program Tassel, filter reads, and run
 ADMIXTURE on a remote server. Raw Illumina fastq.gz files can be
 downloaded from NCBI's Sequence Read Archive (SRA BioProject numbers
 PRJNA326842 - Northern, PRJNA896571 - Central, PRJNA521235 -
 Southern).
DOI: 10.5061/dryad.0k6djhb3r
title: Testing the chilling: Before drought-tolerance hypothesis in Pooideae grasses

description: Temperate Pooideae are a large clade of economically important grasses
 distributed in some of the Earth’s coldest and driest terrestrial
 environments. Previous studies have inferred that Pooideae diversified
 from their tropical ancestors in a cold montane habitat, suggesting that
 above-freezing cold (chilling) tolerance evolved early in the subfamily.
 By contrast, drought tolerance is hypothesized to have evolved multiple
 times independently in response to global aridification that occurred
 after the split of Pooideae tribes. To independently test predictions of
 the chilling before-drought hypothesis in Pooideae, we assessed the
 conservation of whole plant and gene expression traits in response to
 chilling versus drought. We demonstrated that both trait responses are
 more similar across tribes in cold as compared to drought, suggesting that
 chilling responses evolved before, and drought responses after, tribe
 diversification. Moreover, we found significantly more overlap between
 drought and chilling-responsive genes within a species than between
 drought-responsive genes across species, providing evidence that chilling
 tolerance genes acted as precursors for the novel acquisition of increased
 drought tolerance multiple times independently, partially through the
 cooption of chilling responsive genes.
DOI: 10.5061/dryad.jh9w0vtfp
title: Supplementary materials for: CNN-based surrogate for the phase field damage mode

description: We investigate the generalization of a CNN-based surrogate for the phase
 field model in predicting both damage and maximum/peak load, given the
 image of an arbitrary 2D microstructure of a unidirectional
 fiber-reinforced composite. We first discuss the phase field model and the
 numerical procedure to generate training and test data from synthetic
 microstructures with different volume fractions and fiber radii. We next
 present a two-stage approach for predicting peak load, achieved by first
 transforming a given fiber-encoded microstructure image to a continuous
 damage field; and second, predicting peak load from the damage field. A
 key finding is that the direct approach for predicting peak load from the
 microstructure image using a standard regression model fails to
 generalize. Instead, the damage field, even if imperfectly predicted,
 provides valuable cues for the CNN in generalizing across new
 microstructures. We describe several case studies to demonstrate the
 capability of the surrogate model to predict damage and peak load and to
 interpolate over fiber radii and volume fractions. 
description: The data in damage_prediction_X are predicted by our CNN-based
 Image-to-Image model given microstructure geometries.
 "geometry.th" is the geometry image of microstructure generated
 by our Python code with different volume fractions and fiber radii.
 "max_f.th" and "resampled_damage.th" are the peak load
 value and damage field calculated by FEniCS for corresponding
 microstructures. 
description: All .th files can be loaded by PyTorch commend torch.load("filename.th").
DOI: 10.5061/dryad.pk0p2ngs0
title: Expectation-Maximization enables phylogenetic dating under a Categorical Rate Model

description: Dating phylogenetic trees to obtain branch lengths in the unit of time is
 essential for many downstream applications but has remained challenging.
 Dating requires inferring mutation rates that can change across the tree.
 While we can assume to have information about a small subset of nodes from
 the fossil record or sampling times (for fast-evolving organisms),
 inferring the ages of the other nodes essentially requires extrapolation
 and interpolation. Assuming a clock model that defines a distribution over
 rates, we can formulate dating as a constrained maximum likelihood (ML)
 estimation problem. While ML dating methods exist, their accuracy degrades
 in the face of model misspecification where the assumed parametric
 statistical clock model vastly differs from the true distribution.
 Notably, existing methods tend to assume rigid, often unimodal rate
 distributions. A second challenge is that the likelihood function involves
 an integral over the continuous domain of the rates and often leads to
 difficult non-convex optimization problems. To tackle these two
 challenges, we propose a new method called Molecular Dating using
 Categorical-models (MD-Cat). MD-Cat uses a categorical model of rates
 inspired by non-parametric statistics and can approximate a large family
 of models by discretizing the rate distribution into k categories. Under
 this model, we can use the Expectation-Maximization (EM) algorithm to
 co-estimate rate categories and branch lengths in the time unit. Our model
 has fewer assumptions about the true clock model than parametric models
 such as Gamma or LogNormal distribution. Our results on two simulated and
 real datasets of Angiosperms and HIV and a wide selection of rate
 distributions show that MD-Cat is often more accurate than the
 alternatives, especially on datasets with nonmodal or multimodal clock
 models.
DOI: 10.5061/dryad.63xsj3v5z
title: Fluctuations in resource availability shape the competitive balance among non-native plant species

description: Fluctuating resource availability plays a critical role in determining
 non-native plant invasions by mediating the competitive balance between
 non-native and native species. However, the impact of fluctuating resource
 availability on interactions among non-native species remains largely
 unknown. This represents a barrier to understanding invasion mechanisms,
 particularly in habitats that harbor multiple non-native species with
 different responses to fluctuating resource availability. To examine the
 responses of non-native plant species to nutrient fluctuations, we
 compared the growth of each of 12 non-native species found to be common in
 local natural areas to nutrients supplied at a constant rate or supplied
 as a single large pulse in a pot experiment. We found that seven species
 produced more biomass with pulsed nutrients compared to constant nutrients
 (hereafter ‘benefitting species’), while the other five species did not
 differ between nutrient enrichment treatments (hereafter ‘non-benefitting
 species’). To investigate how nutrient fluctuations influence the
 interactions among non-native plant species, we established experimental
 non-native communities in the field with two benefitting and two
 non-benefitting non-native species. Compared with constant nutrient
 supply, the single large pulse of nutrients did not influence community
 biomass, but strongly increased the biomass and cover of the benefitting
 species and decreased those of the non-benefitting species. Furthermore,
 the benefitting species had higher leaf N content and greater plant height
 when nutrients were supplied as a single large pulse than at a constant
 rate, whereas the non-benefitting species showed no differences in leaf N
 content and were shorter when nutrients were supplied as a single large
 pulse than at a constant rate. Our results add to the growing evidence
 that the individual responses of non-native species to nutrient
 fluctuation are species-specific. More importantly, benefitting species
 were favored by nutrients coming in a pulse, while non-benefitting ones
 were favored by nutrients coming constantly when they grew together. This
 suggests that nutrient fluctuations can mediate the competitive balance
 among non-native plants and may thus determine their invasion success in a
 community harbouring multiple non-native plant species.
DOI: 10.6076/d17304
title: Genome-wide DDR protein Association Score (DAS) network

description: The DNA damage response (DDR) ensures error-free DNA replication and
 transcription and is disrupted in numerous diseases. An ongoing challenge
 is to determine the proteins orchestrating DDR and their organization into
 complexes, including constitutive interactions and those induced by
 genomic insults. Here we use multi-conditional network analysis to
 systematically map DDR assemblies at multiple scales. Affinity
 purifications of 21 DDR proteins, with/without genotoxin exposure, are
 combined with multi-omics data to reveal a hierarchical organization of
 605 proteins in 109 assemblies. Assemblies capture canonical repair
 mechanisms and propose new DDR-associated proteins extending to stress,
 transport, and chromatin functions. We find significant associations
 between protein assemblies and genetic dependencies in processing
 different genotoxic agents and that multiple-assembly proteins can act
 pleiotropically in multiple-agent responses. Protein assignments are
 further supported by specific DDR readouts, implicating twelve new
 proteins in double-strand-break repair. The DNA Damage Response Assemblies
 Map is available for interactive visualization and query
 (ccmi.org/DDRAM/).
DOI: 10.5061/dryad.18931zd1m
title: Input data to model multiple effects of large-scale deployment of grass in crop-rotations at European scale

description: This is the input dataset to a Python script
 (https://github.com/oskeng/MF-bio-grass) used to model the effects of
 widespread deployment of grass in rotations with annual crops to provide
 biomass while remediating soil organic carbon (SOC) losses and other
 environmental impacts. For more information about the dataset and the
 study, see the original article: Englund, O., Mola-Yudego, B., Börjesson,
 P., Cederberg, C., Dimitriou, I., Scarlat, N., Berndes, G. Large-scale
 deployment of grass in crop rotations as a multifunctional climate
 mitigation strategy. GCB Bioenergy
description: See original article: Englund, O.,
 Mola-Yudego, B., Börjesson, P., Cederberg, C., Dimitriou, I., Scarlat, N.,
 Berndes, G. Large-scale deployment of grass in crop rotations as a
 multifunctional climate mitigation strategy. GCB Bioenergy
 Preprint: Englund, O., Mola-Yudego, B.,
 Börjesson, P., Cederberg, C., Dimitriou, I., Scarlat, N., Berndes, G.,
 (2022). Large-scale deployment of grass in crop rotations as a
 multifunctional climate mitigation strategy. EarthArXiv. Sept. 23.
 https://doi.org/10.31223/X5KW5J
description: The data file (Geopackage) can be opened using standard GIS
 software, preferably GRASS GIS or QGIS (both open source).
 This dataset is intended as input to a Python script (https://github.com/oskeng/MF-bio-grass) that must be run from within a GRASS GIS session.
DOI: 10.25824/redu/co4iqx
title: CPVfromFSI: CP violation from final state interactions

description: Wolfram Mathematica package developed to calculate CP asymmetries in two-body D0 decays through a phenomenological model.
DOI: 10.5061/dryad.kh189329h
title: Data from: Heat tolerance variation reveals vulnerability of tropical herbivore-parasitoid interactions to climate change

description: Assessing the heat tolerance (CTmax) of organisms is central to understand
 the impact of climate change on biodiversity. While both environment and
 evolutionary history affect CTmax, it is unclear how these factors and
 their interplay influence ecological interactions, communities, and
 ecosystems under climate change. We collected and reared caterpillars and
 parasitoids from canopy and ground layers in different seasons in a
 tropical rainforest. We tested the CTmax and Thermal Safety Margins (TSM)
 of these food webs with implications for how species interactions could
 shift under climate change. We identified strong influence of phylogeny in
 herbivore-parasitoid community heat tolerance. The TSM of all insects were
 narrower in the canopy and parasitoids had lower heat tolerance compared
 to their hosts. Our CTmax-based simulation showed higher
 herbivore-parasitoid food web instability under climate change than
 previously assumed, highlighting the vulnerability of parasitoids and
 related herbivore control in tropical rainforests, particularly in the
 forest canopy.
description: This dataset include two parts: 1) heat
 tolerance data (CTmax) of herbivores and associated parasitoids, body size
 of herbivores and parasitoids, the season and forest layers they were
 sampled collected also included. These heat tolerance data were measured
 with a Grant-TX200 water bath (accuracy 0.01 °C) at ramping speed of f 0.2
 °C per min and recorded as the temperature they lost musle movements.
 Detailed morpho-species codes, parameter and descriptions of the CTmax
 measurement methodology were listed in the associated study.
 2) three herbivore-parasitoid food webs from rearing. These food
 webs are from quantative sampling of forest canopy in the hot season,
 forest understory in the hot season, and forest understory in the cool
 season. Column names are parasitoids and rows names are herbivore.
 Detailed morpho-species codes, description of survey, food web assemble
 forest layers, and seasons could be found in the associated
 study.
description: Microsoft Excel
DOI: 10.5061/dryad.s1rn8pkcc
title: Reducing pesticides without organic certification? Potentials and limits of an intermediate form of agricultural production

description: A growing number of farmer cooperatives cultivate crops without chemical
 pesticides, but also without organic certification. How does this
 intermediate form of agriculture between conventional and organic
 production function? What are the outcomes of this production form on
 cropland biodiversity? How does this model contribute to the transition
 toward more sustainable forms of agriculture? We address these research
 questions using original data collected in the AgroBioDiv project from the
 farmers’ cooperative “KraichgauKorn” based in the German State of
 Baden-Württemberg. This cooperative is a collection of conventional
 farmers, who refrain from pesticide use during cultivation periods for
 KraichgauKorn grains, with products being produced without pesticide
 inputs in the growing season. Our study finds higher levels of weed
 species biodiversity on KGK cereal fields compared to conventional fields,
 but lower than organic fields. In addition, more endangered wild species
 monitored by the State of Baden-Württemberg were found on KGK fields than
 on conventional fields, with organic fields exhibiting the highest
 presence of endangered flora. We conclude that such kinds of enterprises
 may indeed contribute substantially to a successful transformation toward
 sustainable agricultural systems.
description: Supplementary data files can be opened using Microsoft Excel
 and/or a normal Text-Editor.
DOI: 10.5061/dryad.nk98sf7wz
title: Lianas rapidly colonize early stages of tropical forests, presumably through leaf trait diversification

description: Questions: Ecological succession is the process during which ecosystems
 recover after disturbances. Studies investigating community re-assembly
 during tropical forest succession have rarely compared lianas to trees. We
 addressed two questions: (1) How do changes in stem density, total basal
 area, and species richness of lianas and trees compare throughout a
 secondary succession, and to what extent does the relative basal area of
 lianas change along a secondary succession? (2) How do the successional
 trajectories of functional community trait values of lianas and trees
 compare? Location: Yoko forest reserve, central Congo basin. Methods:
 Using univariate Bayesian modeling techniques, we analyzed differences in
 successional pathways between lianas and trees in terms of community
 structure, and functional assembly in a replicated chronosequence spanning
 from young to old-growth forests. Results: We found divergent structural
 trajectories between lianas and trees along the forest chronosequence. The
 stem density of lianas peaked at the intermediate stage, while that of
 trees almost linearly decreased from the early to late stages of
 succession. The basal area of lianas increased at a higher rate than that
 of trees, which translated into a marginal increase of liana relative
 basal area over succession. On the contrary, we observed a lower rate of
 increase in species richness for lianas than trees over succession. We
 found a progressive convergence in the responses of lianas and trees to
 changes with succession in terms of specific leaf area and leaf nitrogen
 content, but a diverging response in terms of leaf phosphorus content.
 These functional composition patterns most probably resulted from
 environmental filtering, induced by a change from nitrogen to phosphorus
 limitation as the succession progressed to mature forest. 
 Conclusions: These findings underscore the rapid colonization of tropical
 forests by lianas after agricultural abandonment, presumably by deploying
 a more diverse leaf economic spectrum early in succession.
DOI: 10.5281/zenodo.15470319
title: Carbon sequestration along a gradient of tidal marsh degradation in response to sea level rise; supporting data

description: This dataset contains the results from a fieldstudy in the Blackwater marshes, in Maryland, USA, supporting the paper 'Carbon sequestration along a gradient of tidal marsh degradation in response to sea level rise', submitted to Biogeoscience in 2025.

The dataset is organised in 6 tabs: 



Sediment samples: results for carbon content (%), bulk density (g/cm³) and the isotopic signature (‰)  of the sediment samples.

Vegetation: results of the vegetation biomass survey (g/m²) and their isotopic signature (‰).

Belowground biomass: results of the belowground biomass samples (g/cm³).

Accertion rates: sediment accretion rates at each location, including the standard error.

Elevation: elevation data collected with an RTK GPS (m).

Suspended sediment data: suspended sediment concentration (mg/l) and the isotopic signature (‰).
DOI: 10.5281/zenodo.15470320
title: Carbon sequestration along a gradient of tidal marsh degradation in response to sea level rise; supporting data

description: This dataset contains the results from a fieldstudy in the Blackwater marshes, in Maryland, USA, supporting the paper 'Carbon sequestration along a gradient of tidal marsh degradation in response to sea level rise', submitted to Biogeoscience in 2025.

The dataset is organised in 6 tabs: 



Sediment samples: results for carbon content (%), bulk density (g/cm³) and the isotopic signature (‰)  of the sediment samples.

Vegetation: results of the vegetation biomass survey (g/m²) and their isotopic signature (‰).

Belowground biomass: results of the belowground biomass samples (g/cm³).

Accertion rates: sediment accretion rates at each location, including the standard error.

Elevation: elevation data collected with an RTK GPS (m).

Suspended sediment data: suspended sediment concentration (mg/l) and the isotopic signature (‰).
DOI: 10.5061/dryad.dv41ns22m
title: Louisiana black-bellied whistling-duck clutch characteristics in the presence of conspecific and interspecific brood parasitism

description: Black-bellied Whistling-Ducks (Dendrocygna autumnalis; hereafter
 Whistling-Duck) are undergoing a rapid range expansion northward and now
 breed throughout the southeastern United States. As a facultative
 cavity-nesting species, they have the potential to compete with Wood Ducks
 (Aix sponsa) and Hooded Mergansers (Lophodytes cucullatus) for nest sites.
 Little is known about Whistling-Duck breeding biology, and estimates of
 clutch characteristics and rates of conspecific and interspecific brood
 parasitism (hereafter, CBP and IBP respectively) are lacking. We monitored
 Whistling-Duck nests in Louisiana to describe nesting chronology, clutch
 size of parasitized and unparasitized (hereafter, normal) nests, and
 hatchability (i.e., the portion of eggs that hatched) for clutches of
 different sizes and types. We monitored a total of 558 nest boxes
 2020–2021 and determined the presence of brood parasitism for 231
 Whistling-Duck nests. CBP was detected in 73 (31.6%) nests, and IBP was
 observed in 51 (22.1%) nests parasitized by Wood Ducks, 2 (0.9%) nests
 parasitized by Hooded Mergansers, and 1 nest contained eggs from all three
 species. Normal clutches were smaller (15.4 ± 4.4 eggs) than CBP clutches
 (26.1 ± 8.8 eggs) and mixed clutches (22.2 ± 5.3 eggs; clutches containing
 Wood Duck or Hooded Merganser eggs; all pairwise P &lt; 0.0001).
 However, within-clutch repeatability estimates for egg morphology data
 (i.e., length, width, and mass) were low (&lt; 0.40) for normal
 clutches, suggesting CBP went undetected. Of 180 fated nests used to
 determine hatchability, 66 (36.7%) were successful, 49 (27.2%) were
 abandoned, 64 (35.6%) were depredated, and 1 (0.6%) was nonviable.
 Considering successful nests, hatchability was high for all clutch size
 bins ranging from 67.4% (41-45 eggs) to 81.6% (11-15 eggs). This study is
 the first to document Whistling-Ducks successfully hatching mixed-species
 broods, and such high productivity could be contributing to whistling-duck
 range expansion.