cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3rq51
title: Data from: Phylogenetic informativeness reconciles ray-finned fish molecular divergence times

description: Discordance among individual molecular age estimates, or between molecular
 age estimates and the fossil record, is observed in many clades across the
 Tree of Life. This discordance is attributed to a variety of variables
 including calibration age uncertainty, calibration placement, nucleotide
 substitution rate heterogeneity, or the specified molecular clock model.
 However, the impact of changes in phylogenetic informativeness of
 individual genes over time on phylogenetic inferences is rarely analyzed.
 Using nuclear and mitochondrial sequence data for ray-finned fishes
 (Actinopterygii) as an example, we extend the utility of phylogenetic
 informativeness profiles to predict the time intervals when nucleotide
 substitution saturation results in discordance among molecular ages
 estimated. Results: We demonstrate that even with identical calibration
 regimes and molecular clock methods, mitochondrial based molecular age
 estimates are systematically older than those estimated from nuclear
 sequences. This discordance is most severe for highly nested nodes
 corresponding to more recent (i.e., Jurassic-Recent) divergences. By
 removing data deemed saturated, we reconcile the competing age estimates
 and highlight that the older mtDNA based ages were driven by nucleotide
 saturation. Conclusions: Homoplasious site patterns in a DNA sequence
 alignment can systematically bias molecular divergence time estimates. Our
 study demonstrates that PI profiles can provide a non-arbitrary criterion
 for data exclusion to mitigate the influence of homoplasy on time
 calibrated branch length estimates. Analyses of actinopterygian molecular
 clocks demonstrate that scrutiny of the time scale on which sequence data
 is informative is a fundamental, but generally overlooked, step in
 molecular divergence time estimation.
description: ALLalignwithcichlidcali_MTDNAtre file based on analysis of all mtDNA data and all calibrationsPrunedalignwithcichlidcali_MTDNAnewick file tree of divergence times estimated with pruned mtDNA alignment and all calibrationsxmlDornburgPruned_ALLmtxml file used in this study for the pruned mtDNA alignmentxmlDornburg_all_mtxml file used to generate divergence times using all mtDNA and all calibrationsAll_calisNuc_AllTree file from beast analysis of all nDNA data with all calibrationsAll_calisNuc_7PartTree file from beast analysis of the pruned nDNA datasetxmlDornburg_allnucxml file used to generate divergence times using all nDNA dataxmlDornburg_pruned_nDNAxml file used to generate divergence times using pruned nDNA data
DOI: 10.6084/m9.figshare.31158467
title: AI-Assisted MI diagnosis from echocardiogram videos: does explainability enhance human-AI collaborative accuracy?

description: Echocardiography after myocardial infarction (MI) provides clinically useful information through assessment of regional wall motion abnormalities, but interpretation requires expertise and remains subject to observer variability. Artificial intelligence (AI) shows promise in automatic interpretation, but it is unclear how explainability affects human-AI collaborative performance. A ResNet18-LSTM model was trained to classify normal vs MI on 127 apical four chamber (A4C) and 120 apical two chamber (A2C) echocardiogram videos from the HMC-QU dataset. Gradient-weighted Class Activation Mapping (Grad-CAM provided visual explanations. Eight cardiology trainees compared diagnostic performance across three conditions: (a) echo clips alone, (b) echo clips with AI predictions, and (c) echo clips with AI predictions plus Grad-CAM explanations. The AI models demonstrated strong discriminative performance with AUCs of 0.9429 (A2C) and 0.9250 (A4C). AI alone achieved 80.0% accuracy versus 77.0% for clinicians alone. Surprisingly, combining AI with human judgment did not improve performance, and introducing visual explanations reduced accuracy to 72% and specificity from 93.8% to 83.8% (p = 0.046). While AI models can effectively detect MI on echocardiographic videos, current explainability techniques may misalign with clinical reasoning, potentially impairing diagnostic performance. Future integration requires AI visual explanation strategies that complement clinician expertise. Heart attacks (myocardial infarction) remain a leading cause of death worldwide. Doctors use ultrasound videos of the heart (echocardiograms) to detect damage from heart attacks, but interpreting these videos requires significant expertise and results can vary between doctors. Artificial intelligence (AI) shows promise in helping doctors analyze these videos, but it is unclear whether showing doctors how the AI makes its decisions improves diagnostic accuracy. In this study, we trained an AI system to detect heart attack damage from echocardiogram videos using 247 recordings from two standard heart views. We then tested whether providing visual explanations of the AI’s reasoning (heat maps highlighting important regions) would help eight trainee cardiologists make better diagnoses. The AI achieved 80% accuracy on its own, slightly better than the doctors’ 77% accuracy. Surprisingly, when doctors saw the AI’s predictions, their accuracy did not improve. Even more unexpectedly, adding visual explanations reduced their accuracy to 72% and made them more likely to misidentify healthy hearts as abnormal. Our findings suggest that simply making AI systems transparent does not guarantee better decision-making. Future AI tools for heart imaging will need visual explanations specifically designed to match how doctors think and work, not just show where the AI is looking.
DOI: 10.5061/dryad.6kp2j
title: Data from: Demographic variation in the U.K. serotine bat: filling gaps in knowledge for management

description: Species of conservation concern, or those in conflict with man, are most
 efficiently managed with an understanding of their population dynamics.
 European bats exemplify the need for successful and cost-effective
 management for both reasons, often simultaneously. Across Europe, bats are
 protected, and the concept of Favourable Conservation Status (FCS) is used
 as a key tool for the assessment and licensing of disruptive actions to
 populations. However, for efficient decision-making, this assessment
 requires knowledge on the demographic rates and long-term dynamics of
 populations. We used capture–mark–recapture to describe demographic rates
 for the Serotine bat (Eptesicus serotinus) at two sites in England and
 investigate the transition rates between three stages: juveniles,
 immatures, and breeders. We then use these rates in an individual-based
 population dynamics model to investigate the expected trajectories for
 both populations. Our results demonstrate for the first time the presence
 and scale of temporal variation in this species' demography. We
 describe the lengthy prereproductive period (3.5 years) that female
 Serotines experience. Finally, we show how site-specific variation in
 demographic rates can produce divergent population trajectories. Effective
 management of European bat populations can be achieved through the
 understanding of life histories, and local demographic rates and
 population dynamics, in order to anticipate the presence of source and
 sink sites in the landscape. Using the Serotine bat in England, we show
 that these can be obtained from rigorous and systematic studies of
 long-term demographic datasets.
description: IBM for two populations
 of UK Serotine batsFemale-only
 Individual-Based Model for two populations of Serotine bats in the UK:
 Hollingbury (H) and Crundale (C). Demographic rates were estimated using
 capture-mark-recapture.IBM_Chauvenet et al. 2014 Ecol
 Evol.RFiles for CMR analysis
 using POPAN modelThis folder contains the
 raw capture records for the Crundale and Hollingbury Serotine bats
 population (females only); they are formatted to be read in MARK and RMark
 (in R) and modelled using a POPAN approach. In addition, the folder also
 contains the R scripts for analysing the two datasets in R using the RMark
 package.POPAN
 analysis.zipFiles for CMR analysis
 with CJS model- Hollingbury onlyThis folder contains the
 raw capture record for the Hollingbury Serotine bats population (females
 only), formatted to be read in MARK or RMark (in R) and modelled using a
 CJS approach. In addition, the folder also contains the MARK files for the
 CJS models that were run.CJS analysis-
 Hollingbury.zipFiles for CMR analysis
 with CJS model- Crundale onlyThis folder contains the
 raw capture record for the Crundale Serotine bats population (females
 only), formatted to be read in MARK or RMark (in R) and modelled using a
 CJS approach. In addition, the folder also contains the MARK files for the
 CJS models that were run.CJS analysis-
 Crundale.zip
DOI: 10.6084/m9.figshare.31158467.v1
title: AI-Assisted MI diagnosis from echocardiogram videos: does explainability enhance human-AI collaborative accuracy?

description: Echocardiography after myocardial infarction (MI) provides clinically useful information through assessment of regional wall motion abnormalities, but interpretation requires expertise and remains subject to observer variability. Artificial intelligence (AI) shows promise in automatic interpretation, but it is unclear how explainability affects human-AI collaborative performance. A ResNet18-LSTM model was trained to classify normal vs MI on 127 apical four chamber (A4C) and 120 apical two chamber (A2C) echocardiogram videos from the HMC-QU dataset. Gradient-weighted Class Activation Mapping (Grad-CAM provided visual explanations. Eight cardiology trainees compared diagnostic performance across three conditions: (a) echo clips alone, (b) echo clips with AI predictions, and (c) echo clips with AI predictions plus Grad-CAM explanations. The AI models demonstrated strong discriminative performance with AUCs of 0.9429 (A2C) and 0.9250 (A4C). AI alone achieved 80.0% accuracy versus 77.0% for clinicians alone. Surprisingly, combining AI with human judgment did not improve performance, and introducing visual explanations reduced accuracy to 72% and specificity from 93.8% to 83.8% (p = 0.046). While AI models can effectively detect MI on echocardiographic videos, current explainability techniques may misalign with clinical reasoning, potentially impairing diagnostic performance. Future integration requires AI visual explanation strategies that complement clinician expertise. Heart attacks (myocardial infarction) remain a leading cause of death worldwide. Doctors use ultrasound videos of the heart (echocardiograms) to detect damage from heart attacks, but interpreting these videos requires significant expertise and results can vary between doctors. Artificial intelligence (AI) shows promise in helping doctors analyze these videos, but it is unclear whether showing doctors how the AI makes its decisions improves diagnostic accuracy. In this study, we trained an AI system to detect heart attack damage from echocardiogram videos using 247 recordings from two standard heart views. We then tested whether providing visual explanations of the AI’s reasoning (heat maps highlighting important regions) would help eight trainee cardiologists make better diagnoses. The AI achieved 80% accuracy on its own, slightly better than the doctors’ 77% accuracy. Surprisingly, when doctors saw the AI’s predictions, their accuracy did not improve. Even more unexpectedly, adding visual explanations reduced their accuracy to 72% and made them more likely to misidentify healthy hearts as abnormal. Our findings suggest that simply making AI systems transparent does not guarantee better decision-making. Future AI tools for heart imaging will need visual explanations specifically designed to match how doctors think and work, not just show where the AI is looking.
DOI: 10.5061/dryad.js5d3
title: Data from: Movement propensity and ability correlate with ecological specialisation in European land snails: comparative analysis of a dispersal syndrome

description: Intra- and inter-specific differences in movement behaviour play an
 important role in the ecology and evolution of animals, particularly in
 fragmented landscapes. As a consequence of rarer and generally more
 fragmented habitat, and because dispersal tends to disrupt benefits
 brought by local adaptation, theory predicts that mobility and dispersal
 should be counter-selected in specialists. Using experimental data and
 phylogenetic comparative tools, we analysed movement propensity and
 capacity, as well as dispersal-related phenotypic traits, in controlled
 conditions in 20 species of European land snails from the Helicoidea
 superfamily. Costs of movement in terrestrial gastropods are among the
 highest in animals, which make them a potentially powerful model to test
 these predictions. Habitat specialists were indeed less likely to cross a
 boundary between a familiar and an unfamiliar substrate than generalists.
 They also had smaller feet, after accounting for size. Furthermore,
 exploring specialists were slower than generalists, and had more tortuous
 trajectories, leading them to stay closer to the familiar patch. Movement
 traits were generally evolutionary labile, but some were constrained by
 body size, a phylogenetically conserved trait. High specialisation and low
 dispersal ability are two traits often considered to increase species
 vulnerability to fragmentation, climate changes and extinction. This study
 confirms they should not be considered separately, due to their
 integration in a dispersal syndrome. Therefore, specialist species face
 double penalty under habitat loss and other environmental changes, making
 them more vulnerable to extinction and contributing to the biotic
 homogenization of communities.
description: Individual relocation
 data for the 20 species of helicoid land snailsraw_relocations.txtSpecies- and Individual-level traits for the 20 species of helicoid land snailsraw_individual_synthetic_data.txt
DOI: 10.34740/kaggle/dsv/14640232
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.603d2
title: Data from: Parallel genome-wide fixation of ancestral alleles in partially outcrossing experimental populations of Caenorhabditis elegans

description: Experimental evolution studies, coupled with new advances in DNA
 sequencing technology, have become a powerful tool for exploring how
 populations respond to selection at the genomic level. Recent experiments
 in microbes typically have found evidence for multiple novel mutations,
 which are usually fixed. In contrast, in animal model systems,
 evolutionary responses seem to involve more modest changes in the
 frequencies of pre-existing alleles, probably because these populations
 outcross and are usually initialized with greater levels of standing
 variation. In this experiment, I used whole-genome rese- quencing to
 estimate allele frequencies and look for novel substitutions in
 experimentally evolved popu- lations of Caenorhabditis elegans. These
 populations were founded with a fixed pair of deleterious mutations
 introgressed into multiple wild genetic backgrounds and allowed to evolve
 for 50 generations with a mixed mating system. There is evidence for some
 recombination between ancestral haplotypes, but selective sweeps seem to
 have resulted in the fixation of large chromosomal segments throughout
 most of the genome. In addition, a few new mutations were detected.
 Simulations suggest that strong selection and low outcrossing rates are
 likely explanations for the observed outcomes, consistent with earlier
 work show- ing large fitness increases in these populations over 50
 generations. These results also show clear parallels to population genetic
 patterns in C. elegans in nature: recent selective sweeps, high linkage
 disequilibrium, and low effective recombination rates. Thus, the genomic
 consequences of selection depend heavily on the biology of the organism in
 question, including its mating system and levels of genetic variation.
description: CHC G3
 DryadZipped scripts and
 processed data. Please see additional archives described in paper for raw
 sequence data.
DOI: 10.5061/dryad.60j76
title: Data from: Heritability of seed weight in Maritime pine, a relevant trait in the transmission of environmental maternal effects

description: Quantitative seed provisioning is an important life-history trait with
 strong effects on offspring phenotype and fitness. As for any other trait,
 heritability estimates are vital for understanding its evolutionary
 dynamics. However, being a trait in between two generations, estimating
 additive genetic variation of seed provisioning requires complex
 quantitative genetic approaches for distinguishing between true genetic
 and environmental maternal effects. Here, using Maritime pine as a
 long-lived plant model, we quantified additive genetic variation of cone
 and seed weight (SW) mean and SW within-individual variation. We used a
 powerful approach combining both half-sib analysis and parent–offspring
 regression using several common garden tests established in contrasting
 environments to separate G, E and G × E effects. Both cone weight and SW
 mean showed significant genetic variation but were also influenced by the
 maternal environment. Most of the large variation in SW mean was
 attributable to additive genetic effects (h2=0.55–0.74). SW showed no
 apparent G × E interaction, particularly when accounting for cone weight
 covariation, suggesting that the maternal genotypes actively control the
 SW mean irrespective of the amount of resources allocated to cones.
 Within-individual variation in SW was low (12%) relative to
 between-individual variation (88%), and showed no genetic variation but
 was largely affected by the maternal environment, with greater variation
 in the less favourable sites for pine growth. In summary, results were
 very consistent between the parental and the offspring common garden
 tests, and clearly indicated heritable genetic variation for SW mean but
 not for within-individual variation in SW.
description: Seed weights of Pinus
 pinaster genotypes and open pollinated familiesSee Readme
 fileHDY-14-OR0070RR
 DATA.xls
DOI: 10.15468/dl.stkk9k
title: Occurrence Download

description: A dataset containing 38299 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is BEL",
 "OccurrenceStatus is Present",
 "TaxonKey is Fraxinus",
 "Year 1926-2026"
 ]
}

 The dataset includes 38299 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001620-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5878/002852
title: The Class SOM Survey 2008
title: SOM-undersökningen Klass-SOM 2008
title: Klass-SOM 2008

description: The Class SOM questionnaire consisted of typical SOM questions about politics, society, media and leisure habits but also a large set of work-related questions. The study was carried out alongside National SOM 2008.

Purpose:
The purpose of the survey is to explore working life and job conditions in Sweden.
description: Klass-SOM-studien innehöll typiska SOM-frågor om politik, samhälle, medier och fritidsvanor men hade dessutom ett större block med yrkes- och arbetsrelaterade frågor.
Formuläret innehåller åtta olika frågeområden: nyheter och medier; politik, samhälle och demokrati; radio, tv och internet; samhälle och service; aktiviteter, intressen och värderingar; ditt arbetsliv; din arbetssituation; samt bakgrundsfrågor.
Undersökningen genomfördes parallellt med Riks-SOM 2008.

Syfte:
Undersökningens syfte är att få veta mera om svenskars yrkesliv och arbetsförhållanden.
DOI: 10.5878/002820
title: The Class SOM Survey 2008
title: SOM-undersökningen Klass-SOM 2008
title: Klass-SOM 2008

description: The Class SOM questionnaire consisted of typical SOM questions about politics, society, media and leisure habits but also a large set of work-related questions. The study was carried out alongside National SOM 2008.

Purpose:
The purpose of the survey is to explore working life and job conditions in Sweden.
description: Klass-SOM-studien innehöll typiska SOM-frågor om politik, samhälle, medier och fritidsvanor men hade dessutom ett större block med yrkes- och arbetsrelaterade frågor.
Formuläret innehåller åtta olika frågeområden: nyheter och medier; politik, samhälle och demokrati; radio, tv och internet; samhälle och service; aktiviteter, intressen och värderingar; ditt arbetsliv; din arbetssituation; samt bakgrundsfrågor.
Undersökningen genomfördes parallellt med Riks-SOM 2008.

Syfte:
Undersökningens syfte är att få veta mera om svenskars yrkesliv och arbetsförhållanden.
DOI: 10.5061/dryad.84ph3
title: Data from: Real-time assessment of hybridization between wolves and dogs: combining non-invasive samples with ancestry informative markers

description: Wolves and dogs provide a paradigmatic example of the ecological and
 conservation implications of hybridization events between wild and
 domesticated forms. However, our understanding of such implications has
 been traditionally hampered by both high genetic similarity and the
 difficulties in obtaining tissue samples (TS), which limit our ability to
 assess ongoing hybridization events. To assess the occurrence and
 extension of hybridization in a pack of wolf-dog hybrids in Northwestern
 Iberia, we compared the power of 52 nuclear markers implemented on TS with
 a subset of 13 ancestry informative markers (AIMs) typed in non-invasive
 samples (NIS). We demonstrate that the 13 AIMs are as accurate as the 52
 markers that were chosen without regard to the power to differentiate
 between wolves and dogs, also having the advantage of being rapidly
 screened on NIS. The efficiency of AIMs significantly outperformed ten
 random sets of similar size and an additional commercial set of 18
 markers. Bayesian clustering analysis implemented on AIMs and NIS
 identified nine hybrids, two wolves and two dogs. Four hybrids were
 unambiguously assigned to F1xWolf backcrosses. Our approach (AIMs + NIS)
 overcomes previous difficulties related to sample availability and
 informative power of markers, allowing a quick identification of wolf-dog
 hybrids in the first phases of hybridization episodes. This provides
 managers with a reliable tool to evaluate hybridization, and estimate the
 success of their actions. This approach may be easily adapted for other
 pairs of wild/domesticated species, thus improving our understanding of
 the introgression of domestication genes into natural populations.
description: Genotypes for Iberian
 Wolves and DogsThis file contains
 Iberian wolves, dogs and Barbanza individuals’ genotypes. Sheet “52 loci”
 contains genotypes for the whole set of markers on our dataset. Sheet “13
 loci” contains genotypes for the 13 AIMs selected as the most suitable for
 studying wolfxdog hybridization in this project.Simulated genotypes for
 wolves and dogsThis file contains 13
 sets of loci for 1000 simulated genotypes of wolves and dogs. Sheet “52
 loci” contains simulated genotypes for the whole set of markers on our
 dataset. Sheet “13 AIMs” contains simulated genotypes for the 13 AIMs
 selected as the most suitable for studying hybridization in this project.
 Sheet “Set Finnzymes” contains simulated genotypes for the 18 markers
 available on a commercial kit for dog microsatellites genotyping. Sets 1
 to 10 are subsets of 13 random selected markers across the whole dataset
 of 52 loci.