cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.142p9j6
title: Data from: Sexual conflict and sexually transmitted infections (STIs): coevolution of sexually antagonistic host traits with an STI

description: In many taxa, there is a conflict between the sexes over mating rate. The
 outcome of sexually antagonistic coevolution depends on the costs of
 mating and natural selection against sexually antagonistic traits. A
 sexually transmitted infection (STI) changes the relative strength of
 these costs. We study the three-way evolutionary interaction among male
 persistence, female resistance, and STI virulence for two types of STIs: a
 viability-reducing STI and a reproduction-reducing STI. A
 viability-reducing STI escalates conflict between the sexes. This leads to
 increased STI virulence (i.e., full coevolution) if the costs of sexually
 antagonistic traits occur through viability but not through reproduction.
 In contrast, a reproduction-reducing STI de-escalates the sexual conflict,
 but STI virulence does not coevolve in response. We also investigated the
 establishment probability of STIs under different combinations of
 evolvability. Successful invasion by a viability-reducing STI becomes less
 likely if hosts (but not parasites) are evolvable, especially if only the
 female trait can evolve. A reproduction-reducing STI can almost always
 invade because it does not kill its host. We discuss how the evolution of
 host and parasite traits in a system with sexual conflict differs from a
 system with female mate choice.
description: Analytical
 ModelMathematica notebook
 outlining the analytical model described in the appendix and the functions
 used to determine numerical solutions appearing in Figures A3 and
 A4.sexualConflictSTIs_WardlawAgrawal_AmNat.nbPython scripts that runs all parameter combinations.Python script that takes a text file of all parameter combinations to be run and runs them in the command line automatically.lazyLoopTheBest.pyBash script that runs the simulations.This bash script takes the name of the text file containing parameters to be run, as well as the name of the database and .csv file where output data will be stored. It runs all parameter combinations through lazyLoopTheBest.py and then uses SQL to make a .csv file for import into R for plotting.runStuffWithCommandLinePrompts.bashText file with parameters to be runThis text file specifies all parameter combinations to be run, as well as the number of replicates of each parameter combination, and the number of processors to use.runAll.txtPython script that exports output data to a databasePython script called by IBM.py that adds output data to a database. While IBM.py is run separately for each parameter combination, the database contains the output of all parameter combinations contained in the runAll.txt file.sexualConflictDatabaseHandler.pyIndividual Based Simulation ModelSource code for the simulation model.IBM_WardlawAgrawal_AmNat.pyREADMEDescription of how to use the program package.
DOI: 10.5061/dryad.c54h30c
title: Data from: Parameterizing the robust design in the BUGS language: lifetime carry‐over effects of environmental conditions during growth on a long‐lived bird

description: 1. Since the initial development of the robust design, this
 capture‐recapture model structure has been modified to estimate temporary
 emigration, and expanded to include auxiliary information such as band
 recovery and live resight data using maximum likelihood approaches. These
 developments have allowed investigators to separately assess individual
 and group effects on true survival, site fidelity, and temporary
 emigration. Additionally, recent advances in the BUGS language have
 allowed researchers to develop increasingly complex, user‐specified models
 in Bayesian frameworks. 2. The robust design has rarely been implemented
 in the BUGS language, and previous attempts to parameterize the robust
 design in BUGS exhibited strong bias in estimates of temporary emigration
 rates. Given the limitations of current parameterizations of the robust
 design in Bayesian frameworks, and our research objectives, we have
 developed a parameterization of the robust design in the BUGS language
 that produces unbiased estimates of all model parameters. 3. We use this
 novel model structure to examine lifetime carry‐over effects of
 environmental conditions during early life on annual breeding
 probabilities of Pacific black brent (Branta bernicla nigricans) breeding
 on the Yukon‐Kuskokwim River Delta in western Alaska. We found that
 individuals that were more structurally developed as goslings bred at
 increased rates as adults (β = 0.14, f = 0.94), with no effect on adult
 survival (β = 0.01, f = 0.62). Additionally, we provide evidence for
 long‐term declines in apparent survival of breeding adult females at the
 population level (β = ‐0.01, f = 0.90). 4. This novel model structure can
 be easily expanded (Gibson et al., in review), and has important
 implications for population modelling at broad scales, where we apply it
 to a declining population of Pacific black brent. Given long‐term declines
 in gosling growth on the Yukon‐Kuskokwim Delta, we predict future declines
 in population trajectories as a result of lifetime carry‐over effects of
 environmental conditions during growth on adult fecundity, and long‐term
 declines in adult survival.
description: Riecke_RDataRData file containing the capture-recapture and covariate data required to run the Bayesian RD model described in Riecke et al., Methods in Ecology and Evolution.biological_modelBayesian model used to estimate survival and breeding propensity of black brent nesting on the Yukon-Kuskokwim River Delta, Alaska, 1988-2014. From Riecke et al., Methods in Ecology and Evolution.Riecke_et al_supplementary_material_1This R script simulates and analyzes robust design data with random emigration. The model estimates detection at the population level.Riecke_et al_supplementary_material_2This script simulates and analyzes data with Markovian emigration. The model is parameterized with separate process and observation states, and detection is estimated at the population level.
DOI: 10.5061/dryad.8gb685k
title: Data from: A coupled soil water balance model for simulating depression-focused groundwater recharge

description: In arid and semi-arid environments focussed infiltration of rain and
 snowmelt water under topographic depressions is an important mechanism of
 groundwater recharge. Quantifying the aggregated recharge from numerous
 small depressions is a major challenge in water resource management.
 Building on field-based investigations into the surface water-groundwater
 interaction of individual depressions and their catchments (i.e. uplands)
 in the Canadian Prairies, we have developed a simple water balance model
 to simulate groundwater recharge considering the hydrological coupling of
 a depression-upland system. The model is based on the Versatile Soil
 Moisture Budget (VSMB), which has been widely used in the Canadian
 Prairies to simulate soil moisture conditions. We evaluated the new model,
 VSMB Depression-Upland System (VSMB-DUS) using field data consisting of an
 artificial flooding experiment and long-term monitoring of a depression in
 Alberta, Canada. The model captured surface water level, soil moisture,
 and groundwater responses to the artificial flooding with a reasonable
 accuracy, and also represented the inter-annual variability of recharge
 fluxes during a five year period (2007-2011) including dry and wet years.
 Simulated annual recharge varied between 12 and 45 mm, whereas annual
 precipitation varied between 453 and 597 mm during the five-year period.
 The VSMB-DUS tends to over- or under-estimate snowmelt runoff in
 individual years, however, simulated recharge was only slightly impacted
 by the errors in snowmelt runoff estimation. Due to its computational
 efficiency and robust algorithms, the VSMB-DUS will provide a useful tool
 for estimating aggregated recharge in a large-scale model grid cell
 containing hundreds of depression-upland systems.
description: 2004_InfiltrationExperimentContains the observation data related to the 2004 Infiltration experiment at the C24 depression at the Spy Hill site, Alberta, Canada.2006_2011_dataContains observation data (pond depth, runoff, piezometer level and meteorological data) for the C24 depression from Nov 2006 - Dec 2011.GIS_Data.zip file containing GIS files for the C24 depression, West Nose Creek catchment and digital elevation model of the area.
DOI: 10.5061/dryad.5ft0368
title: Data from: Phenological responses of 215 moth species to interannual climate variation in the Pacific Northwest from 1895 through 2013

description: Climate change has caused shifts in the phenology and distributions of
 many species but comparing responses across species is challenged by
 inconsistencies in the methodology and taxonomic and temporal scope of
 individual studies. Natural history collections offer a rich source of
 data for examining phenological shifts for a large number of species. We
 paired specimen records from Pacific Northwest insect collections to
 climate data to analyze the responses of 215 moth species to interannual
 climate variation over a period of 119 years (1895–2013) during which
 average annual temperatures have increased in the region. We quantified
 the effects of late winter/early spring temperatures, averaged annually
 across the region, on dates of occurrence of adults, taking into account
 the effects of elevation, latitude, and longitude. We assessed whether
 species-specific phenological responses varied with adult flight season
 and larval diet breadth. Collection dates were significantly earlier in
 warmer years for 36.3% of moth species, and later for 3.7%. Species
 exhibited an average phenological advance of 1.9 days/°C, but
 species-specific shifts ranged from an advance of 10.3 days/°C to a delay
 of 10.6 days/°C. More spring-flying species shifted their phenology than
 summer- or fall-flying species. These responses did not vary among groups
 defined by larval diet breadth. The highly variable phenological responses
 to climate change in Pacific Northwest moths agree with other studies on
 Lepidoptera and suggest that it will remain difficult to accurately
 forecast which species and ecological interactions are most likely to be
 affected by climate change. Our results also underscore the value of
 natural history collections as windows into long-term ecological trends.
description: Moth occurrence dataset
 before removal of pseudoreplicatesOccurrence records from
 the Pacific Northwest Moths (http://pnwmoths.biol.wwu.edu) database used
 for analyses in this paper. The Pacific Northwest Moths database is
 largely built from natural history collection specimen records, but it
 also includes some records from field notes, the literature, and
 photograph-vouchered specimens. See README.txt for information about the
 column headings.Maurer_et_al_2018_Pacific
 Northwest_moth_phenology_climate_variation_occurrence_records_GLMM.csv
DOI: 10.5061/dryad.7kj7t1q
title: Data from: Validity of the Diplostomoidea and Diplostomida (Digenea, Platyhelminthes) upheld in phylogenomic analysis

description: Higher systematics within the Digenea, Carus 1863 have been relatively
 stable since a phylogenetic analysis of partial nuclear ribosomal markers
 (rDNA) led to the erection of the Diplostomida Olson, Cribb, Tkach, Bray,
 and Littlewood, 2003. However, recent mitochondrial (mt) genome
 phylogenies suggest this order might be paraphyletic. These analyses show
 members of two diplostomidan superfamilies are more closely related to the
 Plagiorchiida La Rue, 1957 than to other members of the Diplostomida. In
 one of the groups implicated, the Diplostomoidea Poirier, 1886, a recent
 phylogeny based on mt DNA also indicates the superfamily as a whole is
 non-monophyletic. To determine if these results were robust to additional
 taxon sampling, we analyzed mt genomes from seven diplostomoids in three
 families. To choose between phylogenetic alternatives based on mt genomes
 and the prior rDNA-based topology, we also analyzed hundreds of
 ultra-conserved elements (UCEs) assembled from shotgun sequencing. The
 Diplostomida was paraphyletic in the mt genome phylogeny, but supported in
 the UCE phylogeny. We speculate this mitonuclear discordance is related to
 ancient, rapid radiation in the Digenea. Both UCEs and mt genomes support
 the monophyly of the Diplostomoidea and show congruent relationships
 within it. The Cyathocotylidae Muhling, 1898 are early diverging
 descendants of a paraphyletic clade of Diplostomidae Poirier, 1886, in
 which were nested members of the Strigeidae Railliet, 1919; the results
 support prior suggestions that the Crassiphialinae Sudarikov, 1960 will
 rise to the family level. Morphological traits of diplostomoid
 metacercariae appear to be more useful for differentiating higher taxa
 than those of adults. We describe a new species of Cotylurus Szidat, 1928,
 resurrect a species of Hysteromorpha Lutz, 1931, and find support for a
 species of Alaria Schrank, 1788 of contested validity. Complete rDNA
 operons are provided as a resource for future studies.
description: UCE probes for
 Platyhelminthes especially Diplostomoideafasta file with UCE
 probesplatyhelminthes-v2-master-probe-list-DUPE-SCREENED.fastaDiplostoloidea_archive_UCEUCE loci fasta files extracted from draft genomes via the PHYLUCE pipeline.Diplostomoidea_alignment_archivePhylip file and associated characters sets used in the phylogenomic analyses.
DOI: 10.5061/dryad.369417f
title: Data from: Nationwide prevalence and incidence study of neuromyelitis optica spectrum disorder in Denmark

description: Objectives: To estimate the nationwide population-based incidence,
 prevalence, and geographical distribution of neuromyelitis optica spectrum
 disorder in Denmark based on the 2015 International Panel for NMO
 Diagnosis (IPND) criteria Methods: We conducted a multicentre,
 historically prospective study. Data were sourced from the Danish National
 Patient Registry, the Danish Multiple Sclerosis Registry, departments of
 neurology and laboratories providing aquaporin 4 (AQP4) antibody test.
 Cases were selected based on the 2006 Wingerchuk and the 2015 IPND
 criteria and were individually validated by an expert panel. Results: We
 confirmed NMO in 30 cases (2006 criteria), and NMOSD in 56 cases (2015
 IPND criteria) between 2007 and 2014. Defined by the 2006 criteria, the
 incidence of NMO was 0.029 per 100,000 person-years (95% CI;0.014 -
 0.051), and the prevalence (age ≥ 16) was 0.566 per 100,000 (95% CI;0.370
 - 0.830). Based on the 2015 IPND criteria, the incidence of NMOSD was
 0.070 per 100,000 person-years (95% CI;0.046 - 0.102), and the prevalence
 (age ≥ 16) was 1.09 per 100,000 (95% CI;0.808 - 1.440), without regional
 differences. Conclusions: Our estimates of incidence and prevalence are
 similar to other Caucasian population-based studies using the 2015 IPND
 criteria. We found no geographical clustering in Denmark.
description: Description of cases -
 Appendix 1Appendix 1. -
 NEUROLOGY-2018-900159.docx
DOI: 10.5061/dryad.18cg032
title: Data from: Origin and hidden diversity within the poorly known Galápagos snake radiation (Serpentes: Dipsadidae)

description: Galápagos snakes are among the least studied terrestrial vertebrates of
 the Archipelago. Here, we provide a phylogenetic analysis and a time
 calibrated tree for the group, based on a sampling of the major
 populations known to occur in the Archipelago. Our study revealed the
 presence of two previously unknown species from Santiago and Rábida
 Islands, and one from Tortuga, Isabela, and Fernandina. We also recognize
 six additional species of Pseudalsophis in the Galápagos Archipelago
 (Pseudalsophis biserialis from San Cristobal, Floreana and adjacent
 islets; Pseudalsophis hoodensis from Española and adjacent islets;
 Pseudalsophis dorsalis from Santa Cruz, Baltra, Santa Fé, and adjacent
 islets; Pseudalsophis occidentalis from Fernandina, Isabela, and Tortuga;
 Pseudalsophis slevini from Pinzon, and Pseudalsophis steindachneri from
 Baltra, Santa Cruz and adjacent islets). Our time calibrated tree suggests
 that the genus Pseudalsophis colonized the Galápagos Archipelago through a
 single event of oceanic dispersion from the coast of South America that
 occurred at approximately between 6.9 Ma and 4.4 Ma, near the
 Miocene/Pliocene
 boundary.www.zoobank.org/urn:lsid:zoobank.org:pub:2679FD19-
 01E5-48FE-A0DA-A88FF145DE56
description: Alignment used to
 produce Figure 1 - RAxML treeInformation of loci
 partitions mtdna_12S= 1-492; mtdna_16S= 493-1071; mtdna_cytb = 1072-2159;
 ncdna_bdnf= 2160-2834; ncdna_cmos= 2835-3415; ncdna_nt31=
 3416-3943;RAxML_alignment_for_Figure-1.phyAlignment used to produce Figure 2 - RAxML treeInformation of loci partitions mtdna_12S= 1-492; mtdna_16S= 493-1071; mtdna_cytb = 1072-2159; ncdna_bdnf= 2160-2834; ncdna_cmos= 2835-3415; ncdna_nt31= 3416-3943;RAxML_alignmnet_for_Figure-2.phyXML file used to produce Figure 3 - BEAST treeBEAST_input_file_for_Figure-3.xmlBEAST tree file - Figure 3BEAST_tree_for_Figure-3.treRAxML tree file - Figure 1RAxML_tree_for_Figure-1.treRAxML tree file - Figure 2RAxML_tree_for_Figure-2.trecharacter set file for analysis using RAxMLRAxML_charset_for_Figure-1.txt
DOI: 10.5061/dryad.b7q3g2q
title: Data from: Increase in crop losses to insect pests in a warming climate

description: Insect pests substantially reduce yields of three staple grains—rice,
 maize, and wheat—but models assessing the agricultural impacts of global
 warming rarely consider crop losses to insects. We use established
 relationships between temperature and the population growth and metabolic
 rates of insects to estimate how and where climate warming will augment
 losses of rice, maize, and wheat to insects. Global yield losses of these
 grains are projected to increase by 10 to 25% per degree of global mean
 surface warming. Crop losses will be most acute in areas where warming
 increases both population growth and metabolic rates of insects. These
 conditions are centered primarily in temperate regions, where most grain
 is produced.
description: Climate impact on crop
 yieldsProjected impact of
 climate warming on yield losses to insect pests among 3 major grain crops:
 wheat, rice, and maize.Crop_impact_results.mat
DOI: 10.5061/dryad.8mj8fc5
title: Data from: Improving short-term information spreading efficiency in scale-free networks by specifying top large-degree vertices as the initial spreaders.

description: The positive function of initially influential vertices could be exploited
 to improve spreading efficiency for short-term spreading in scale-free
 networks. However, the selection of initial spreaders depends on the
 specific scenes. The selection of initial spreaders needs to offer low
 complexity and low power consumption for short-term spreading. In this
 paper, we propose a selection strategy for efficiently spreading
 information by specifying a set of top large-degree vertices as the
 initially informed vertices. The essential idea behind the proposed
 selection strategy is to exploit the significant diffusion of the top
 large-degree vertices at the beginning of spreading. To evaluate the
 positive impact of initially influential vertices, we first build an
 information spreading model in the Barabási-Albert (BA) scale-free
 network; next, we design 54 comparative Monte Carlo experiments based on a
 benchmark strategy and the proposed selection strategy in different BA
 scale-free network structures. Experimental results indicate that (1) the
 proposed selection strategy significantly can improve spreading efficiency
 in the short-term spreading and (2) both network size and number of hubs
 have a strong impact on spreading efficiency, while the number of
 initially informed vertices has a weak impact. The proposed selection
 strategy can be employed in short-term spreading, such as sending warnings
 or crisis information spreading or information spreading in emergency
 training or realistic emergency scenes.
description: Short-term spreading
 time in different BA scale-free networksShort-term spreading
 time with different numbers of initial spreaders and different structures
 of BA scale-free networks.Data_Handle.opj
DOI: 10.5061/dryad.5gj7056
title: Data from: Gut microflora may facilitate adaptation to anthropic habitat: a comparative study in Rattus

description: Anthropophilic species (‘commensal’ species) that are completely dependent
 upon anthropic habitats experience different selective pressures
 particularly in terms of food than their non-commensal counterparts. Using
 a next-generation-sequencing approach, we characterized and compared the
 gut microflora community of 53 commensal Rattus rattus and 59
 non-commensal Rattus satarae captured in 10 locations in the Western
 Ghats, India. We observed that while species identity was important in
 characterizing the microflora communities of the two Rattus hosts,
 environmental factors also had a significant effect. While there was
 significant geographic variation in the microflora of the non-commensal R.
 satarae, there was no effect of geographic distance on gut microflora of
 the commensal R. rattus. Interestingly, host genetic distance did not
 significantly influence the community in either Rattus hosts.
 Collectively, these results indicate that a shift in habitat is likely to
 result in a change in the gut microflora community and imply that the gut
 microflora is a complex trait, influenced by various parameters in
 different habitats.
description: Final OTU
 tableTable of Operational
 Taxonomic Units (OTUs) created using the uclust algorithm at a 97%
 similarity threshold and filtering unclassifiable and unalignable reads as
 well as singletons.otu_table_biomv1.biomMapping fileMapping file with sample descriptions and metadata.mapping_assembly_corrected.txtFasta file containing aligned representative sequencesFor each OTU, longest read was chosen as the representative sequence. All representative sequences were aligned using the PyNAST algorithm and filtered the alignment using a lane mask file.filtered_nochim_rep_set.fastaPhylogenetic treePhylogenetic tree was constructed for the representative sequences using FastTree.tree_filtered.tre
DOI: 10.5281/zenodo.18389208
title: JSAP v1.0 Experimental Logs: Constructive Alignment via Judge–Shift and Anchor Density

description: JSAP v1.0 Experimental Logs

This dataset contains reproducible experimental logs for the Judge–Shift Alignment Protocol (JSAP v1.0), a constructive alignment method that constrains model judgments through explicit anchor-trace mapping and external-anchor density thresholds.

Package Contents





Protocol specification (one-pager)




Fixed test set (20 items across empirical, rule-based, and ethical domains)




System prompt template with mandatory output format




Raw model outputs (JSONL) for all three experimental phases




Quantitative compliance metrics



Models Tested




Model
Vendor
JSAP Compliance




Copilot Deep Research
Microsoft
1.00 🏆


Gemini 1.5 Flash
Google
0.95


Llama 3.1
Meta
0.94


Claude Opus 4.5
Anthropic
0.93


GPT-4o
OpenAI
0.91


GPT-5.2 Thinking
OpenAI
0.91


Perplexity
Perplexity
0.90


Claude Sonnet 4
Anthropic
0.79


GPT-5.2 Auto
OpenAI
0.73




Key Findings





9 models from 6 vendors tested




JSAP Compliance range: 0.73–1.00




7/9 models achieve ≥0.90 compliance




Trace Score explains 43% of model variance




OSS matches proprietary: Llama 3.1 (0.94) ≈ Claude Opus 4.5 (0.93)



Scientific Contribution

This release provides the first cross-model empirical evidence that:





A deterministic external-anchor density threshold (D_ext < θ) can forcibly suppress confident judgments at the output level




This suppression operates without access to internal representations or training-time modification




The mechanism functions consistently across multiple vendors and architectures



License

CC-BY-4.0