cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6d3m0
title: Data from: The effect of selection history on extinction risk during severe environmental change

description: Environments rarely remain the same over time, and populations are
 therefore frequently at risk of going extinct when changes are significant
 enough to reduce fitness. While many studies have investigated what
 attributes of the new environments and of the populations experiencing
 these changes will affect their probability of going extinct, limited work
 has been directed toward determining the role of population history on the
 probability of going extinct during severe environmental change. Here we
 compare the extinction risk of populations with a history of selection in
 a benign environment, to populations with a history of selection in one or
 two stressful environments. We exposed spores and lines of the green alga
 Chlamydomonas reinhardtii from these three different histories to a range
 of severe environmental changes. We found that the extinction risk was
 higher for populations with a history of selection in stressful
 environments compared to populations with a history of selection in a
 benign environment. This effect was not due to differences in initial
 population sizes. Finally, the rates of extinction were highly repeatable
 within histories, indicating strong historical contingency of extinction
 risk. Hence, information on the selection history of a population can be
 used to predict their probability of going extinct during environmental
 change.
description: Extinction
 dataThis data file contains
 the extinction dynamics. For each culture, at each time point in the
 experiment, it says whether the culture is alive or extinct. The
 'plate' column contains an identifier for the 96-well plate on
 which the culture was propagated; 'Environment' describes the
 assay environment; 'Well' is the well in which the culture was
 propagated; 'Selection' is the selection history of the culture;
 'Line' is the line number out of 5 from each selection history;
 'Spore' is the spore number out of 4 from each line;
 'Replicate' is the replicate out of 3 for each spore;
 'State' is a brief description of the density of the culture as
 observed under a microscope; 'Time' is the cycle number of the
 experiment; 'Extinct' is whether the culture is alive (1) or
 extinct (0).extinction.data.csvYield dynamicsThis data file contains the yield dynamics. For each culture at each time point it contains the optical density ('absorbance') read at 750 nm. The 'Plate' column contains the identifier of the 96-well in which the culture was propagated; 'Environment' is the assay environment; 'Well' is the well in which the culture was propagated; 'Selection' is the selection history of the culture; 'Line' is the line number out of 5 from each selection history; 'Spore' is the spore number out of 4 from each line; 'Replicate' is the replicate number out of 3 from each spore; 'Time' is the cycle number of the experiment; 'absorbance' is the optical density reading at 750 nm, a proxy for yield.yield.data.csv
DOI: 10.5061/dryad.966qt
title: Data from: Early-life disease exposure and associations with adult survival, cause of death, and reproductive success in preindustrial humans

description: A leading hypothesis proposes that increased human life span since 1850
 has resulted from decreased exposure to childhood infections, which has
 reduced chronic inflammation and later-life mortality rates, particularly
 from cardiovascular disease, stroke, and cancer. Early-life cohort
 mortality rate often predicts later-life survival in humans, but such
 associations could arise from factors other than disease exposure.
 Additionally, the impact of early-life disease exposure on reproduction
 remains unknown, and thus previous work ignores a major component of
 fitness through which selection acts upon life-history strategy. We
 collected data from seven 18th- and 19th-century Finnish populations
 experiencing naturally varying mortality and fertility levels. We
 quantified early-life disease exposure as the detrended child mortality
 rate from infectious diseases during an individual’s first 5 y,
 controlling for important social factors. We found no support for an
 association between early-life disease exposure and all-cause mortality
 risk after age 15 or 50. We also found no link between early-life disease
 exposure and probability of death specifically from cardiovascular
 disease, stroke, or cancer. Independent of survival, there was no evidence
 to support associations between early-life disease exposure and any of
 several aspects of reproductive performance, including lifetime
 reproductive success and age at first birth, in either males or females.
 Our results do not support the prevailing assertion that exposure to
 infectious diseases in early life has long-lasting associations with
 later-life all-cause mortality risk or mortality putatively linked to
 chronic inflammation. Variation in adulthood conditions could therefore be
 the most likely source of recent increases in adult life span.
description: Data on early-life
 disease exposure, mortality and reproductive successThe data supplied are
 sufficient to repeat all analyses in the paper. Individual identities,
 maternal identities, and birth years have been assigned random numbers to
 protect the identities of the individuals involved. Since these are fitted
 as random effects, this will not affect any analyses. Data on the
 calculation of the early-life disease exposure measure can be found in the
 Supporting Information of the paper itself.Hayward et al_Early disease and
 later fitness_DATA.csv
DOI: 10.5061/dryad.59g2911
title: Data from: Fine-scale temperature associated genetic structure between inshore and offshore populations of sea scallop (Placopecten magellanicus)

description: In the northwest Atlantic Ocean, sea scallop (Placopecten magellanicus)
 have been characterized by a latitudinal genetic cline with a breakpoint
 between northern and southern genetic clusters occurring at ~45°N along
 eastern Nova Scotia, Canada. Using 96 diagnostic single nucleotide
 polymorphisms (SNPs) capable of discriminating between northern and
 southern clusters, we examined fine-scale genetic structure of scallops
 among 27 sample locations, spanning the largest geographic range evaluated
 in this species to date (~37-51°N). Here, we confirmed previous
 observations of northern and southern groups, but we show that the
 boundary between northern and southern clusters is not a discrete
 latitudinal break. Instead, at latitudes near the previously described
 boundary, we found unexpected patterns of fine-scale genetic structure
 occurring between inshore and offshore sites. Scallops from offshore
 sites, including St. Pierre Bank and the eastern Scotian Shelf, clustered
 with southern stocks, whereas inshore sites at similar latitudes clustered
 with northern stocks. Our analyses revealed significant genetic divergence
 across small spatial scales (i.e., 129 to 221 km distances), and that
 spatial structure over large and fine scales was strongly associated with
 temperature during seasonal periods of thermal minima. Clear temperature
 differences between inshore and offshore locations may explain the
 fine-scale structuring observed, such as why southern lineages of scallop
 occur at higher latitudes in deeper, warmer offshore waters. Our study
 supports growing evidence that fine-scale population structure in marine
 species is common, often environmentally associated, and that
 consideration of environmental and genomic data can significantly enhance
 the identification of marine diversity and management units.
description: Scallop_all2012-2016_genopop-27popsGenepop file with all scallops (adults and juveniles)Scallop Environmental dataEnvironmental data for 27 scallop locations with latitude, longitude and corresponding cartesian coordinates. Data includes averaged annual maximum and minimum and seasonally averaged temperature and salinity from the sea surface (SST, SSS) and bottom (BT, BS) for all scallop sites between 2011 and 2015.Scallop_Environmental_Data.csv
DOI: 10.6084/m9.figshare.29509628
title: Grading rubrics for 2026 paper "Computer Science Achievement and Writing Skills Predict Vibe Coding Proficiency".

description: This is the grading rubric for 2026 paper "Computer Science Achievement and Writing Skills Predict Vibe Coding Proficiency". Private link created on 2025-07-09; link published on 2026-01-26.
DOI: 10.6084/m9.figshare.29509628.v1
title: Grading rubrics for 2026 paper "Computer Science Achievement and Writing Skills Predict Vibe Coding Proficiency".

description: This is the grading rubric for 2026 paper "Computer Science Achievement and Writing Skills Predict Vibe Coding Proficiency". Private link created on 2025-07-09; link published on 2026-01-26.
DOI: 10.5061/dryad.79411
title: Data from: Molecular phylogeny of rhynchonellide articulate brachiopods (Brachiopoda, Rhynchonellida)

description: We present here the first report based on phylogenetic analyses of small
 subunit (SSU/18S) and large subunit (LSU/28S) ribosomal DNA (rDNA)
 sequences from a wider-than-token sample of rhynchonellide articulate
 brachiopods, with data from 11 of ∼20 extant genera (12 species) belonging
 to all four extant superfamilies. Data exploration by network and
 saturation analyses shows that the molecular sequence data are free from
 major aberrations and are suitable for phylogenetic reconstruction despite
 the presence of large deletions in four SSU rDNA sequences. Although
 molecular sequence analyses cannot directly illuminate the systematics of
 fossils, the independent, genealogical evidence and phylogenetic
 inferences about extant forms that they make possible are highly relevant
 to paleontological systematics because they highlight the limitations of
 evolutionary inference from morphology. Parsimony, distance, maximum
 likelihood (no clock) and Bayesian (relaxed-clock) analyses all find a
 tree topology that disagrees strongly with the existing superfamily
 classification. All tested phylogenetic reconstructions agree that the
 taxa analyzed fall into three clades designated A1, A2, and B that reflect
 two major divergence events. The relaxed-clock analysis indicates that
 clades A and B diverged in the Paleozoic, while clades A1 and A2 reflect
 Permo-Triassic (and later) events. Morphological homoplasy and possible
 gene co-option are suggested as the main sources for the discord between
 the morpho-classification, the results of cladistic analyses of
 morphology, and the relationships reconstructed from molecular sequences.
 The origin, function and evolutionary implications of the deletion-bearing
 rhynchonellide SSU rDNA sequences are briefly discussed in relation to
 pseudogenes and concerted evolution in the rDNA genomic region.
description: Executable Nexus file of
 sequence alignmentsAligned rDNA sequences
 from PAUP*4 with PAUP block giving optimal maximum likelihood model from
 Modeltest 3.06Supplemental data
 1.nexusSupplemental data
 2Output of GBlocks
 showing alignment sites included in and excluded from
 analysisSupplemental data
 3.docA brief account of
 deletions and pseudogenes
DOI: 10.5281/zenodo.18381226
title: Eye-tracking biomarkers in multiple sclerosis
DOI: 10.5281/zenodo.18381227
title: Eye-tracking biomarkers in multiple sclerosis
DOI: 10.5061/dryad.hh650
title: Data from: Genetically integrated traits and rugged adaptive landscapes in digital organisms

description: Background: When overlapping sets of genes encode multiple traits, those
 traits may not be able to evolve independently, resulting in constraints
 on adaptation. We examined the evolution of genetically integrated traits
 in digital organisms—self-replicating computer programs that mutate,
 compete, adapt, and evolve in a virtual world. We assessed whether overlap
 in the encoding of two traits – here, the ability to perform different
 logic functions – constrained adaptation. We also examined whether strong
 opposing selection could separate otherwise entangled traits, allowing
 them to be independently optimized. Results: Correlated responses were
 often asymmetric. That is, selection to increase one function produced a
 correlated response in the other function, while selection to increase the
 second function caused a complete loss of the ability to perform the first
 function. Nevertheless, most pairs of genetically integrated traits could
 be successfully disentangled when opposing selection was applied to break
 them apart. In an interesting exception to this pattern, the logic
 function AND evolved counter to its optimum in some populations owing to
 selection on the EQU function. Moreover, the EQU function showed the
 strongest response to selection only after it was disentangled from AND,
 such that the ability to perform AND was lost. Subsequent analyses
 indicated that selection against AND had altered the local adaptive
 landscape such that populations could cross what would otherwise have been
 an adaptive valley and thereby reach a higher fitness peak. Conclusions:
 Correlated responses to selection can sometimes constrain adaptation.
 However, in our study, even strongly overlapping genes were usually
 insufficient to impose long-lasting constraints, given the input of new
 mutations that fueled selective responses. We also showed that detailed
 information about the adaptive landscape was useful for predicting the
 outcome of selection on correlated traits. Finally, our results illustrate
 the richness of evolutionary dynamics in digital systems and highlight
 their utility for studying processes thought to be important in biological
 systems, but which are difficult to investigate in those systems.
description: avida_dataTAR archive containing data from Ostrowski et al. (2015). Genetically integrated traits and rugged adaptive landscapes in digital organisms. Archive contains configuration files, a list of run commands, an Excel spreadsheet showing the phenotypes of the evolved organisms, lineages, and organisms.
DOI: 10.5061/dryad.2517b
title: Data from: Change in fasting plasma glucose and incident type 2 diabetes mellitus: results from a prospective cohort study

description: Objective: To investigate the association between changes of fasting
 plasma glucose (FPG) values and incident type 2 diabetes (T2D) in a cohort
 of the Iranian population. Design: Prospective cohort study. Setting: This
 study was conducted within the framework of the Tehran Lipid and Glucose
 Study (TLGS) to investigate the association between change of FPG between
 baseline examination (1999-2001) and the second visit (2002-2005), with
 incident T2D. Participants: A total of 3981 non-diabetic participants aged
 20 years. Outcome measure: Type 2 diabetes was defined if the participant
 was using anti diabetic drugs, or if FPG was ≥ 7mmol L-1 or if the 2-h
 post challenge plasma glucose (2-hPCG) was ≥ 11.1 mmol L-1. Results:
 During a median follow-up of 6.17 years, after second examination, 288 new
 cases of T2D were identified. In the multivariable Cox proportional hazard
 analysis using age as timescale, we presented a simple model, including
 the FPG change (HR: 1.19, 95% CI: 1.07-1.33) and baseline waist
 circumference (WC) (HR: 1.004, 95% CI: 1.001-1.008) with a discriminative
 power (C-index) of 72%. Furthermore, we showed that the highest quartile
 of FPG change enhanced the T2D risk to 1.65 (95% CI: 1.2-2.27) compared to
 the lowest quartile (P for trend=0.004).The independent risk of FPG change
 resisted further adjustment with 2-hPCG change. Adding the 2-hPCG change
 only, slightly increased the discrimination power of the model, including
 FPG change and baseline value of WC (0.73 vs. 0.72 %). After limiting the
 study population to those with normal fasting glucose/normal glucose
 tolerance, FPG change still remained as an independent predictor (HR :
 1.57, 95% CI: 1.31-1.88). Conclusions: Two measurements of FPG obtained
 about 3 years apart can help to identify populations at risk for incident
 T2D; independent of important traditional risk factors and their changes
 including 2-hPCG change.
description: main data for fasting
 plasma glucose changefirst data
 file_3981.savsub-study sample for
 fasting plasma changesecond data
 file_3131.sav
DOI: 10.5061/dryad.48nv3
title: Data from: Disparities in influenza mortality and transmission related to sociodemographic factors within Chicago in the pandemic of 1918

description: Social factors have been shown to create differential burden of influenza
 across different geographic areas. We explored the relationship between
 potential aggregate-level social determinants and mortality during the
 1918 influenza pandemic in Chicago using a historical dataset of 7,971
 influenza and pneumonia deaths. Census tract-level social factors,
 including rates of illiteracy, homeownership, population, and
 unemployment, were assessed as predictors of pandemic mortality in
 Chicago. Poisson models fit with generalized estimating equations (GEEs)
 were used to estimate the association between social factors and the risk
 of influenza and pneumonia mortality. The Poisson model showed that
 influenza and pneumonia mortality increased, on average, by 32.2% for
 every 10% increase in illiteracy rate adjusted for population density,
 homeownership, unemployment, and age. We also found a significant
 association between transmissibility and population density, illiteracy,
 and unemployment but not homeownership. Lastly, analysis of the point
 locations of reported influenza and pneumonia deaths revealed fine-scale
 spatiotemporal clustering. This study shows that living in census tracts
 with higher illiteracy rates increased the risk of influenza and pneumonia
 mortality during the 1918 influenza pandemic in Chicago. Our observation
 that disparities in structural determinants of neighborhood-level health
 lead to disparities in influenza incidence in this pandemic suggests that
 disparities and their determinants should remain targets of research and
 control in future pandemics.
description: 1918 Pandemic Influenza
 Mortality, Chicago USAPoint location and week
 of epidemic of 8,031 influenza and pneumonia deaths recorded during the
 1918 Spanish flu pandemic within the city of Chicago. Data was digitized
 from 1920 City of Chicago Department of Health annual report Date last
 modified: 25-10-2016. Fields include: ID (FID), indicator of pneumonia (0
 or 1, 0 indicates an influenza death, 1 an influenza and pneumonia death),
 x and y coordinates (with units in meters), and week (sequential week of
 epidemic). See paper for more details.points.csvFine-scale sociodemographics of Chicago, USA, 1920Socio-demographic data (including population size, illiteracy, unemployment) of 496 census tracts within the City of Chicago. Data was collected from the 1920 national census.tracts.csvShapefile of census tract boundaries in Chicago in 1920Shapefile of census tract boundaries in Chicago in 1920. File included in zip file include IL_tract_a.dbf, IL_tract_a.prj, IL_tract_a.sbn, IL_tract_a.sbx, IL_tract_a.shp, IL_tract_a.shp.xml, IL_tract_a.shxshapefile.zip
DOI: 10.5061/dryad.362kt4r5
title: Data from: The evolution of trade-offs under directional and correlational selection

description: Using quantitative genetic theory we develop predictions for the evolution
 of trade-offs in response to directional and correlational selection. We
 predict that directional selection favoring an increase in one trait in a
 trade-off will result in change in the intercept but not the slope of the
 trade-off function, with the mean value of the selected trait increasing
 and that of the correlated trait decreasing. Natural selection will
 generally favor an increase in some combination of trait values, which can
 be represented as directional selection on an index value. Such selection
 induces both directional and correlational selection on the component
 traits. Theory predicts that selection on an index value will also change
 the intercept but not the slope of the trade-off function but because of
 correlational selection, the direction of change in component traits may
 be in the same or opposite directions. We test these predictions using
 artificial selection on the well-established trade-off between fecundity
 and flight capability in the cricket, Gryllus firmus and compare the
 empirical results with a priori predictions made using genetic parameters
 from a separate half-sib experiment. Our results support the predictions
 and illustrate the complexity of trade-off evolution when component traits
 are subject to both directional and correlational selection.
description: Data for Roff and
 Fairbairn Evolution 2012Excel file with data and
 descriptions
DOI: 10.5061/dryad.4df8k
title: Data from: Noisy neighbors can hamper the evolution of reproductive isolation by reinforcing selection

description: Reinforcement is the process by which selection against hybridization
 leads to an increase in reproductive isolation. The influence of
 reinforcing selection can be detected when sympatric individuals (those
 from areas of secondary contact) show a higher degree of prezygotic
 isolation than allopatric individuals (those from areas outside each
 other’s range). In areas of secondary contact with Drosophila santomea,
 Drosophila yakuba females show reinforcement of gametic isolation but not
 behavioral isolation, despite the fact that both behavioral and gametic
 isolation evolve in D. yakuba in experimental sympatry. Using behavioral
 assays and experimental evolution, I studied how both gametic and
 behavioral isolation are affected by biotic factors that the two species
 encounter in their natural environment. I show that if D. yakuba females
 are in environments where D. yakuba, D. santomea, and males from other
 species coexist, these females cannot fully discern between conspecific
 and heterospecific males. In such complex environments, gametic but not
 behavioral isolation evolves. The presence of nonhybridizing species can
 constrain the effect of reinforcement on behavioral isolation.
description: Matute. Noisy Neighbors.
 Am. Nat. Raw dataMatute_NN_raw_data.zip