cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3n6qm3p
title: Data from: Estimating the impact of divergent mating phenology between residents and migrants on the potential for gene flow

description: Gene flow between populations can allow the spread of beneficial alleles
 and genetic diversity between populations, with importance to
 conservation, invasion biology, and agriculture. Levels of gene flow
 between populations vary not only with distance, but also with divergence
 in reproductive phenology. Since phenology is often locally adapted,
 arriving migrants may be reproductively out of synch with residents, which
 can depress realized gene flow. In flowering plants, the potential impact
 of phenological divergence on hybridization between populations can be
 predicted from overlap in flowering schedules—the daily count of flowers
 capable of pollen exchange—between a resident and migrant population. The
 accuracy of this prospective hybridization estimate, based on parental
 phenotypes, rests upon the assumptions of unbiased pollen transfer between
 resident and migrant active flowers. We tested the impact of phenological
 divergence on resident–migrant mating frequencies in experiments that
 mimicked a single large gene flow event. We first prospectively estimated
 mating frequencies two lines of Brassica rapaselected or early and late
 flowering. We then estimated realized mating frequencies retrospectively
 through progeny testing. The two estimates strongly agreed in a greenhouse
 experiment, where procedures ensured saturating, unbiased pollination.
 Under natural pollination in the field, the rate of resident–migrant
 mating, was lower than estimated by phenological divergence alone,
 although prospective and retrospective estimates were correlated. In both
 experiments, differences between residents and migrants in flowering
 schedule shape led to asymmetric hybridization. Results suggest that a
 prospective estimate of hybridization based on mating schedules can be a
 useful, although imperfect, tool for evaluating potential gene flow. They
 also illustrate the impact of mating phenology on the magnitude and
 symmetry of reproductive isolation.
description: DataAll data files
 pertaining to the submitted manuscript, with analyses and R scripts for
 graphs where appropriate.To
 Dryad.rarExperiment
 1All
 files pertaining to results from Experiment 1.Experiment 2 Chi
 SquaredAll files pertaining to
 the chi squared analysis of experiment 2.Experiment 2 General
 FilesRaw data, R scripts, and
 graphs pertaining to experiment 2.Experiment 2
 LDAFiles pertaining to the
 LDA analysis of experiment 2, including data files and R
 script.
DOI: 10.5061/dryad.t778h30
title: Data from: Female choice for related males in wild red-backed toadlets (Pseudophryne coriacea)

description: Mate choice for genetic benefits is assumed to be widespread in nature,
 yet very few studies have comprehensively examined relationships between
 female mate choice and male genetic quality in wild populations. Here, we
 use exhaustive sampling and single nucleotide polymorphisms (SNPs) to
 provide a partial test of the “good genes as heterozygosity” hypothesis
 and the “genetic compatibility” hypothesis in an entire population of
 terrestrial breeding red-backed toadlets, Pseudophryne coriacea. We found
 that successful males did not display higher heterozygosity, despite a
 positive relationship between male heterozygosity and offspring
 heterozygosity. Rather, in the larger of two breeding events, we found
 that successful males were more genetically similar to their mate than
 expected under random mating, indicating that females can use pre- or
 post-copulatory mate choice mechanisms to bias paternity towards more
 related males. These findings provide no support for the good genes as
 heterozygosity hypothesis but lend support to the genetic compatibility
 hypothesis. A complete test of this hypothesis will now require evaluating
 how parental genetic similarity impacts offspring fitness. Terrestrial
 toadlets show a high degree of site fidelity, high levels of genetic
 structuring between populations, and frequently hybridise with sister
 species. As such, female mate choice for related males may be an adaptive
 strategy to reduce outbreeding depression. Our findings provide the first
 population-wide evidence for non-random preferential inbreeding in a wild
 amphibian. We argue that such reproductive patterns may be common in
 amphibians because extreme genetic differentiation within meta-populations
 creates an inherently high risk of outbreeding depression.
description: O'BrienEtAl_HammingDistanceMatrix&SNPscoringO'BrienEtAl_Supplymentary materialSUPPLEMENTARY MATERIAL Table S1. Repeated measures incurred by polyandrous females were avoided by only including one male mate, chosen randomly (a), for each polyandrous female when calculating mean HDV-mated and variance of HDV-mated. Alternatively, HDV-mated and variance of HDV-mated was calculated by including only the least related mate (b) and only the most related mate (c), per polyandrous female. Significance level different from those presented in the main document are highlighted in bold. Table S2. Mean ± SD, variance and range of relatedness (HDV) for all actual female-male mates (identified by offspring genetic parentage) during each breeding event. Table S3. Mean relatedness (HDV) and variance generated from 10,000 simulations of random pairings between all assigned mothers and all potential mates from each breeding event. Two-tailed 95% confidence intervals and significance values (HDV P-value and Variance P-value) indicate whether HDV mean and variance of actual mates (see Table 2) differed from randomly generated mean and variance values. Note: lower HDV equals greater relatedness.
DOI: 10.5061/dryad.911161j
title: Data from: The cephalic anatomy of workers of the ant species Wasmannia affinis (Formicidae, Hymenoptera, Insecta) and its evolutionary implications

description: Despite the ecological significance of ants and the intensive research
 attention they have received, thorough treatments of ant anatomy and
 functional morphology are still scarce. In this study we document the head
 morphology of workers of the myrmicine Wasmannia affinis with optical
 microscopy, µ-computed tomography, scanning electron microscopy, and 3D
 reconstruction, providing the first complete anatomical treatment of an
 ant head with a broad array of modern techniques. We discuss the potential
 of the applied methods to generate detailed and well-documented
 morphological data sets with increased efficiency. We also address
 homology problems, particularly in the context of the cephalic digestive
 tract. According to our analyses the “pharynx” of previous ant studies is
 homologous to the prepharynx of other insects. We also discuss the
 phylogenetic potential and functional significance of the observed
 characters, with internal features such as tentorium and musculature
 discussed for the first time. Our investigation underlines that detailed
 anatomical data for Formicidae are still very fragmentary, which in turn
 limits our understanding of the major design elements underlying the ant
 bauplan. We attempt to provide a template for further anatomical studies,
 which will help to understand the evolution of this fascinating group on
 the phenotypic level.
description: Wasmannia
 affinis_nova_036a_data_part 1Part 1 of volumetric
 micro-CT scanning dataset for Wasmannia affinis Santschi, 1929 worker
 (nova_036a) in TIFF format (300 slices)Wasmannia
 affinis_nova_036a_part 1.zipWasmannia
 affinis_nova_036a_part 2Part 2 of volumetric
 micro-CT scanning dataset for Wasmannia affinis Santschi, 1929 worker
 (nova_036a) in TIFF format (300 slices)Wasmannia
 affinis_nova_036a_part 3Part 3 of volumetric
 micro-CT scanning dataset for Wasmannia affinis Santschi, 1929 worker
 (nova_036a) in TIFF format (300 slices)Wasmannia
 affinis_nova_036a_part 4Part 4 of volumetric
 micro-CT scanning dataset for Wasmannia affinis Santschi, 1929 worker
 (nova_036a) in TIFF format (300 slices)Wasmannia
 affinis_nova_036a_part 5Part 5 of volumetric
 micro-CT scanning dataset for Wasmannia affinis Santschi, 1929 worker
 (nova_036a) in TIFF format (328 slices)
DOI: 10.5281/zenodo.18350564
title: KEYS_BRAND7_450F_7_23C_0k_EDLC_single
DOI: 10.5061/dryad.sh00j9s
title: Data from: The effect of a transient immune activation on subjective health perception in two placebo controlled randomised experiments

description: Background Patient-reported outcomes predict mortality and play
 increasingly important roles in care, but factors that modify central
 measures such as health ratings have been little investigated. Building on
 designated immune-to-brain pathways, we aimed to determine how a
 short-term induced inflammation response impacts self-reported health
 status. Methods Lipopolysaccharide injections were used to provoke acute
 systemic inflammatory responses in healthy men and women and were compared
 to placebo in two double-blind randomized experiments. In Experiment 1, 8
 individuals (mean 24 years; SD=3.7) received lipopolysaccharide 0.8 ng/kg
 once and placebo once in a cross-over design, and in Experiment 2, 52
 individuals received either lipopolysaccharide 0.6 ng/kg or placebo once
 in a non-cross-over design (28.6 years; SD=7.1). Main outcomes were
 perceived health (general and current), sickness behaviour (like fatigue,
 pain and negative affect), and plasma interleukin (IL)-6, IL-8 and TNF-α,
 before and after injection. Results Compared to placebo,
 lipopolysaccharide lead to a deterioration in both self-rated general
 (Experiment 1, b=1.88 for 0.8 ng/kg) and current health (Experiment 1
 b=-3.00; and Experiment 2 b=-1.79) 1.5h after injection (p’s&lt;0.01),
 effects that remained after 4.5 to 5 hours (p’s&lt;0.05). The effect
 on current health in Experiment 2 was mediated by increased inflammation
 and sickness behaviour in response to lipopolysaccharide injection
 (β=-0.28, p=0.01). Conclusion Health is drastically re-evaluated during
 inflammatory activation. The findings are consistent with notions that
 inflammation forms part of health-relevant interoceptive computations of
 bodily state, and hint at one mechanism as to why subjective health
 predicts longevity.
description: Endotoxin_self-rated
 healthData from Experiment 1
 and 2 in The effect of a transient immune activation on subjective health
 perception in two placebo controlled randomised experiments by Andreasson
 et al
DOI: 10.5281/zenodo.18350563
title: KEYS_BRAND7_450F_7_23C_0k_EDLC_single
DOI: 10.5061/dryad.gg3g3s5
title: Data from: Linking DNA methylation with performance in a woody plant species

description: Epigenetic factors are increasingly being viewed as important mechanisms
 in organism performance. However, advances in plant epigenetics rely
 mostly on studies of short-lived model or cultivated species and there is
 a current gap in knowledge on wild plants, especially on woody plant
 species, that still needs to be addressed via empirical studies. Through a
 greenhouse experiment we compared the genetic (microsatellites) and
 epigenetic (methylation-sensitive amplified polymorphisms) variation in
 mother plants and their open-pollinated offspring of the Mediterranean
 woody plant Pistacia lentiscus. We also assessed whether the inherited DNA
 methylation patterns were related to the early offspring performance. Our
 results revealed (i) higher levels of relative DNA methylation in mother
 plants than in their offspring, although the amount of methylation in the
 offspring was remarkable; (ii) a significant relationship between relative
 methylation levels between the two life stages; (iii) a high epigenetic
 structure among families that was decoupled to the genetic structure; and
 (iv) a significant relationship between the relative DNA methylation
 levels and seedling phenotypic trait variation with higher levels of
 methylation in the genome being associated to a poorer performance. Our
 results stress the impact that epigenetic inheritance might have in
 evolution through its influence in seedling development, and that
 epigenetic effects can be detected even at early stages of the life cycle
 of woody long-lived species.
description: AlbaladejoRG_PistaciaZip file contains each of the datasets that accompany: Albaladejo et al. 2019 (https://doi.org/10.1007/s11295-019-1325-x) Linking DNA methylation with performance in a woody plant species. See README for variable definitions.
DOI: 10.5061/dryad.fp26p04
title: Data from: Warming enhances sedimentation and decomposition of organic carbon in shallow macrophyte-dominated systems with zero net effect on carbon burial

description: Temperatures have been rising throughout recent decades and are predicted
 to rise further in the coming century. Global warming affects carbon
 cycling in freshwater ecosystems, which both emit and bury substantial
 amounts of carbon on a global scale. Currently, most studies focus on the
 effect of warming on overall carbon emissions from freshwater ecosystems,
 while net effects on carbon budgets may strongly depend on burial in
 sediments. Here, we tested whether year‐round warming increases the
 production, sedimentation, or decomposition of particulate organic carbon
 and eventually alters the carbon burial in a typical shallow freshwater
 system. We performed an indoor experiment in eight mesocosms dominated by
 the common submerged aquatic plant Myriophyllum spicatum testing two
 temperature treatments: a temperate seasonal temperature control and a
 warmed (+4°C) treatment (n = 4). During a full experimental year, the
 carbon stock in plant biomass, dissolved organic carbon in the water
 column, sedimented organic matter, and decomposition of plant detritus
 were measured. Our results showed that year‐round warming nearly doubled
 the final carbon stock in plant biomass from 6.9 ± 1.1 g C in the control
 treatment to 12.8 ± 0.6 g C (mean ± SE), mainly due to a prolonged growing
 season in autumn. DOC concentrations did not differ between the
 treatments, but organic carbon sedimentation increased by 60% from 96 ±
 9.6 to 152 ± 16 g C m−2 year−1 (mean ± SE) from control to warm
 treatments. Enhanced decomposition of plant detritus in the warm
 treatment, however, compensated for the increased sedimentation. As a
 result, net carbon burial was 40 ± 5.7 g C m−2 year−1 in both temperature
 treatments when fluxes were combined into a carbon budget model. These
 results indicate that warming can increase the turnover of organic carbon
 in shallow macrophyte‐dominated systems, while not necessarily affecting
 net carbon burial on a system scale.
description: Velthuis et al., 2018,
 GCBData and R-scripts
 belonging to the published manuscript. For more detailed information see
 the README file.Velthuis et al., 2018
 GCB.zip
DOI: 10.5061/dryad.1540502
title: Data from: The consequences of land sparing for birds in the United Kingdom

description: 1. Land sparing has been proposed as a strategy to reconcile biodiversity
 conservation with agricultural production, with empirical studies on five
 continents indicating that most species would benefit if food demand was
 met through high-yield farming combined with the protection or restoration
 of natural habitat. 2. Most such studies come from landscapes covered by
 large areas of natural habitat and without a long history of intense human
 modification. However, much of Europe, consists of human-dominated
 landscapes, where biodiversity responses to land sparing may differ. To
 test this, we use estimates of bird population density in different
 (semi-)natural habitats, and forecasts of population density in farmland
 habitat, to assess the future consequences for birds of land-sparing
 scenarios in the United Kingdom. 3. Our scenarios predict that whilst up
 to 18 of the 156 species assessed (predominantly farmland associated
 species) might decline in UK conservation status under land sparing, up to
 35 UK bird species (mainly woodland and wetland species) might improve in
 status. This contrasts with a maximum of 8 species likely to improve in
 conservation status without land sparing, with up to 7 species
 deteriorating. 4. Combining land sparing with demand management measures
 (reducing food waste and the consumption of animal products) led to more
 positive population changes under all scenarios. 5. Synthesis and
 applications. Land sparing has the potential to benefit UK bird
 populations in aggregate but would likely have negative impacts on
 farmland bird species. These findings are likely to be applicable across
 human-dominated landscapes beyond the UK, though effects on other taxa,
 implementation mechanisms, and the sustainability of higher yields all
 require careful consideration.
description: Supplementary data
 fileThis .xlsx file shows,
 for each of 156 focal species: A) species traits (conservation status,
 habitat association, farmland dependency, wintering zone [for migrants],
 surrogate species [if applicable] and additional notes); B) habitat terms
 in the RSPB habitat-specific density model; C) predicted 2050 relative
 population size in each scenario; D) predicted 2050 conservation status in
 each scenario.
DOI: 10.5281/zenodo.18225906
title: Natural Gas compressibility factor and associated ML-based codes (ANN +GMDH+GP)
title: The results  of all applied models for prediction of Z-factor
title: Developed best ANN model (2-45-1)
title: Developed GP model
title: Developed GMDH model

description: This repository provides a curated databank of dry-gas compressibility factor (Z-factor) measurements compiled from multiple literature sources, alongside the code and trained models used in our head-to-head evaluation of modern machine-learning approaches versus classical equations of state and correlations.

The dataset contains 1,079 data points with pressures and temperatures harmonised to MPa and K. Pseudo-reduced variables were recomputed consistently (Ppr = P/Pc, Tpr = T/Tc) and Z was obtained/reconciled using standard industry practice. The data span approximately 0.2 ≤ Ppr ≤ 30 and 1.05 ≤ Tpr ≤ 3. Model development and validation in the accompanying code were conducted within the subset 0.162 < Ppr < 25.821 and 1.357 < Tpr < 2.42.

Included scripts implement three predictive models—ANN with Levenberg–Marquardt (ANN-LM), Group Method of Data Handling (GMDH), and Genetic Programming (GP)—together with example outputs, weights/biases, and tabulated results to facilitate replication and extension. Users are encouraged to adapt and improve these models for their own dry-gas systems.

Contents





Data: Dry-gas Z-factor databank (CSV/XLSX), with P, T, Pc, Tc, Ppr, Tpr, and Z.




Code:





developed_best_ANNLM.m (ANN-LM model and training script)




GMDH_DevelopedModel.m (GMDH model and sensitivity options)




Developed GP model (GP expression / notes)






Results:





All models results_Weights and Biased of ANN.xlsx (trained weights/biases and model performance tables

How to use





Open the scripts in MATLAB (R2020b or later recommended).




Load the provided data file; paths are relative to the repository root.




Run each script to reproduce training, testing, and the reported metrics; adjust hyperparameters as needed.




For deployment, apply models only within the validated range (0.162 < Ppr < 25.821; 1.357 < Tpr < 2.42).



Potential applications





Rapid Z-factor estimation for dry-gas reservoirs




Benchmarking new ML models against published baselines




Sensitivity analysis and uncertainty quantification




Teaching materials for data-driven thermophysical modelling
DOI: 10.5061/dryad.2s5h8k7
title: Data from: Population structure and male-biased dispersal in the short-tail stingray Bathytoshia brevicaudata (Myliobatoidei: Dasyatidae)

description: Selective pressures driving dispersal in vagile species often differ
 between males and females, resulting in sex-biased dispersal. Male-biased
 dispersal is common in mammals, where there is greater reproductive
 investment by females, and there is emerging evidence for a similar
 pattern in elasmobranchs. We examine the population structure of the
 short-tail stingray (Bathytoshia brevicaudata), a large, viviparous
 coastal species common in southern hemisphere waters. Using 11 nuclear
 (nDNA) microsatellite markers from 202 individuals in comparison to
 mitochondrial (mtDNA) data reported by Le Port and Lavery (J Hered
 103:174–185, 2012), we elucidate patterns of dispersal at both southern
 hemisphere and New Zealand scales. At a global scale, estimates of
 population differentiation were comparable across marker types
 (microsatellite FST = 0.148, p &lt; 0.001, mtDNA ϕST = 0.67,
 p &lt; 0.001). In contrast, New Zealand structure was much weaker for
 microsatellite markers (FST = 0.0026, p &gt; 0.05) than for mtDNA
 (ϕST = 0.054, p &lt; 0.05). Female-only data displayed a greater
 degree of population differentiation from both nDNA and mtDNA compared to
 male-only data, and population assignment tests indicated that males were
 significantly more likely to be immigrants to the population from which
 they were sampled. We estimate that within New Zealand, male-mediated gene
 flow is at least fivefold greater than female-mediated gene flow. This
 molecular evidence for sex-biased dispersal in a batoid species adds
 further support to male-biased dispersal as a recurrent pattern in
 viviparous elasmobranchs. Many elasmobranch species are vulnerable to
 extinction, and understanding movement patterns is crucial to management
 of threatened populations.
description: B_brevicaudata
 _microsat_genontypesMicrosatellite genotypes
 for 11 polymorphic loci from 202 Bathytoshia brevicaudata individuals,
 from New Zealand, Australia and South Africa (location info
 included)D.brev ALL SAMPLES genotypes -
 FINAL.csv