cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.394hm
title: Data from: Body length of bony fishes was not a selective factor during the biggest mass extinction of all time

description: The Permo-Triassic mass extinction devastated life on land and in the sea,
 but it is not clear why some species survived and others went extinct. One
 explanation is that lineage loss during mass extinctions is a random
 process in which luck determines which species survive. Alternatively, a
 phylogenetic signal in extinction may indicate a selection process
 operating on phenotypic traits. Large body size has often emerged as an
 extinction risk factor in studies of modern extinction risk, but this is
 not so commonly the case for mass extinctions in deep time. Here, we
 explore the evolution of non-teleostean Actinopterygii (bony fishes) from
 the Devonian to the present day, and we concentrate on the Permo-Triassic
 mass extinction. We apply a variety of time-scaling metrics to date the
 phylogeny, and show that diversity peaked in the latest Permian and
 declined severely during the Early Triassic. In line with previous
 evidence, we find the phylogenetic signal of extinction increases across
 the mass extinction boundary: extinction of species in the earliest
 Triassic is more clustered across phylogeny compared to the more randomly
 distributed extinction signal in the late Permian. However, body length
 plays no role in differential survival or extinction of taxa across the
 boundary. In the case of fishes, size did not determine which species
 survived and which went extinct, but phylogenetic signal indicates that
 the mass extinction was not a random field of bullets.
description: Puttick_et_al_2017Example R code to date trees, run analysis of phylogenetic signal of extinction, and run analysis of length and extinctionPuttick_et_al_2017_functionsR functionsfullTree_noBLUndated, unresolved, full phylogeny used as input for dating trees using different methodsageStagesAges of taxa used to date phylogenieshedmanTreesDated trees using the Hedman methodmblTreesDated trees using the mbl method in Newick formatequalTreesDated trees using the equal method in Newick formathedmanReScaleHedman rescale values to get tree to absolute timeequalReScaleEqual rescale values to get tree to absolute timemblReScalembl rescale values to get tree to absolute timehedmanDataTip and internal node reconstructions of body lengths on Hedman treesequalDataTip and internal node reconstructions of body lengths on equal treesmblDataTip and internal node reconstructions of body lengths on mbl treeshedmanLengthsbody lengths from Hedman treesequalLengthsbody lengths from equal treesmblLengthsbody lengths from mbl treesPuttick_et_al_2017_SupplementaryInformation
DOI: 10.5064/f6vanjl8/7vq98g
title: Silan-Ciruelas_FRA_Opt1_6B_1_5_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/2sud73
title: Silan-Ciruelas_FRA_Opt1_16B_10-20_High_Median-High.pdf
DOI: 10.5061/dryad.508j2
title: Data from: Misinformed leaders lose influence over pigeon flocks

description: In animal groups where certain individuals have disproportionate influence
 over collective decisions, the whole group's performance may suffer
 if these individuals possess inaccurate information. Whether in such
 situations leaders can be replaced in their roles by better-informed group
 mates represents an important question in understanding the adaptive
 consequences of collective decision-making. Here, we use a clock-shifting
 procedure to predictably manipulate the directional error in navigational
 information possessed by established leaders within hierarchically
 structured flocks of homing pigeons (Columba livia). We demonstrate that
 in the majority of cases when leaders hold inaccurate information they
 lose their influence over the flock. In these cases, inaccurate
 information is filtered out through the rearrangement of hierarchical
 positions, preventing errors by former leaders from propagating down the
 hierarchy. Our study demonstrates that flexible decision-making structures
 can be valuable in situations where ‘bad’ information is introduced by
 otherwise influential individuals.
description: GPS csv files for tracks
 of all birdsThe data is saved in the
 formate 01_"flock number"_"bird
 ID"_"release". For example, 01_08_S01_12 is flock 8, bird
 S01 and release 12. The data are in CSV files with all columns named.
 There are 8 flocks with 5 birds.Data.zip
DOI: 10.5064/f6vanjl8/o8tuwr
title: Silan-Ciruelas_Opt1_Therapist9.pdf
DOI: 10.5061/dryad.vf1jj
title: Data from: Molecular phylogeny, revised higher classification, and implications for conservation of endangered Hawaiian leaf-mining moths (Lepidoptera: Gracillariidae: Philodoria)

description: The leaf-mining moth genus Philodoria Walsingham (Lepidoptera:
 Gracillariidae) is composed of 30 described species, all of which are
 endemic to the Hawaiian Islands. Philodoria is known to feed on 10
 families of endemic Hawaiian host plants, with several species recorded
 only from threatened or endangered hosts. Beyond their dependence on these
 plants, little is known of their evolutionary history and conservation
 status. We constructed a molecular phylogeny of Philodoria to assess
 validity of its current subgeneric classification and to help guide future
 work on this threatened Hawaiian lineage. Mitochondrial and nuclear DNA
 sequences from three genes (CO1, CAD, EF-1α) combining for a total of
 2,041 base pairs, were collected from 11 Philodoria species, incorporating
 taxa from both currently recognized subgenera. These data were analyzed
 using both parsimony and model-based phylogenetic approaches. Contrary to
 the most recent systematic treatment of Philodoria, our results indicate
 strongly that the two currently recognized Philodoria subgenera are not
 monophyletic and that morphological characters used to classify them are
 homoplasious. Based on our robust results, we revised the higher
 classification of Philodoria: the subgenus Eophilodoria Zimmerman, 1978 is
 established as subjective junior synonym of Philodoria Walsingham, 1907.
 We also present new host plant and distribution data and discuss host
 range of Philodoria as it pertains to endangered Hawaiian plants.
description: Concatenated alignment
 of CO1, CAD, and EF1aConcatenated alignment
 of CO1, CAD, and EF1a for Philodoria leaf mining moth species and
 outgroupsConcatenated alignments for
 HPC.phy3GENE
 PhotosPhotos of sequenced
 Philodoria leaf miner tissue
DOI: 10.5064/f6vanjl8/cxhoka
title: Silan-Ciruelas_FRA_Opt1_23A_LGBT_Low_Median-High.pdf
DOI: 10.5064/f6vanjl8/ritqg0
title: Silan-Ciruelas_FRA_Opt1_19A_20+_Low_Median-High.pdf
DOI: 10.5064/f6vanjl8/3rnvnh
title: Silan-Ciruelas_USA_Opt2_14A_Haley_5-10_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/wstq6t
title: Silan-Ciruelas_TUR_Opt2_22A_Anil_LGBT_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/4tsnsb
title: Silan-Ciruelas_BRA_Opt2_21A_Camilla_LGBT_Low_Low-Median.pdf
DOI: 10.5061/dryad.2jr1648
title: Data from: Past distribution of epiphyllous liverworts in China: the usability of historical data

description: Epiphyllous liverworts form a special group of bryophytes that primarily
 grow on the leaves of understory vascular plants in tropical and
 subtropical evergreen broadleaf forests. Being sensitive to moisture and
 temperature changes, epiphyllous liverworts are often consider to be good
 indicators of climate change and forest degradation. However, they are a
 poorly collected and taxonomically complicated group, with an only partly
 identified distribution pattern. In this study, we built four models based
 on 24 environmental variables at four different spatial resolutions (i.e.,
 1 km, 5 km, 10 km, and 15 km) to predict the past distribution of
 epiphyllous liverworts in China, using Maxent model and 63 historical
 location records (i.e., presence-only data). Both area under the curve of
 the receiver operating characteristic (AUC) and true skill statistic (TSS)
 methods are used to assess the model performance. Results showed that the
 model with the predictors at a 15-km resolution achieved the highest
 predictive accuracy (AUC=0.946; TSS=0.880), although there was no
 statistically significant difference between the four models (p &gt;
 0.05). The most significant environmental variables included aridity,
 annual precipitation, precipitation of wettest month, precipitation of
 wettest quarter, precipitation of warmest quarter, annual mean NDVI, and
 minimum NDVI. The predicted suitable areas for epiphyllous liverworts were
 mainly located in the south of Yangtze River and seldom exceeds 35° N,
 which were consistent with the museum and herbarium records, as well as
 the historical records in scientific literatures. Our study further
 demonstrated the value of historical data to ecological and evolutionary
 studies.
description: Historical presence data
 and environmental variables used in MaxentHistorical presence
 localities were present in file of historical_presence.csv, and 28
 environmental varibales with resolution of 1km were provided in a document
 of China_1km. These are the files that can be directly used in the Maxent
 model.Data
 for submission.zip
DOI: 10.5064/f6vanjl8/gpacfo
title: Silan-Ciruelas_PHL_Opt2_20A_Rissa_20_years_High_Med-High.pdf
DOI: 10.5064/f6vanjl8/zmvsx5
title: Silan-Ciruelas_USA_Opt1_15A_Haley_10-20_Low_Median-High.pdf
DOI: 10.5061/dryad.96584
title: Data from: Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data

description: Background: A variety of bacteria are known to influence carcinogenesis.
 Therefore, we sought to investigate if publicly available whole genome and
 whole transcriptome sequencing data generated by large public cancer
 genome efforts, like The Cancer Genome Atlas (TCGA), could be used to
 identify bacteria associated with cancer. The Burrows-Wheeler aligner
 (BWA) was used to align a subset of Illumina paired-end sequencing data
 from TCGA to the human reference genome and all complete bacterial genomes
 in the RefSeq database in an effort to identify bacterial read pairs from
 the microbiome. Results: Through careful consideration of all of the
 bacterial taxa present in the cancer types investigated, their relative
 abundance, and batch effects, we were able to identify some read pairs
 from certain taxa as likely resulting from contamination. In particular,
 the presence of Mycobacterium tuberculosis complex in the ovarian serous
 cystadenocarcinoma (OV) and glioblastoma multiforme (GBM) samples was
 correlated with the sequencing center of the samples. Additionally, there
 was a correlation between the presence of Ralstonia spp. and two specific
 plates of acute myeloid leukemia (AML) samples. At the end, associations
 remained between Pseudomonas-like and Acinetobacter-like read pairs in
 AML, and Pseudomonas-like read pairs in stomach adenocarcinoma (STAD) that
 could not be explained through batch effects or systematic contamination
 as seen in other samples. Conclusions: This approach suggests that it is
 possible to identify bacteria that may be present in human tumor samples
 from public genome sequencing data that can be examined further
 experimentally. More weight should be given to this approach in the future
 when bacterial associations with diseases are suspected.
description: Additional file 1:
 Metadata and taxonomic assignments for TCGA bacterial read
 pairsSummary of TCGA data by
 bacterial read pair. This file is a tab-delimited text file of all TCGA
 read pairs and their corresponding metadata and bacterial taxonomic
 assignments from the first release of TCGA data. Comments are denoted by a
 #. Abbreviations for sequencing center and tissue source site are as
 follows: BCGSC—British Columbia Genome Sequencing Center; Broad—The Broad
 Institute of MIT and Harvard; Fox Chase—Fox Chase Cancer Center;
 MSKCC—Memorial Sloan Kettering Cancer Center; UCSF—University of
 California San Francisco; UNC—University of North Carolina; Wash Univ St.
 Louis—Washington University in St. Louis.microview-v1-all-reads-comment-header.txt.gz
DOI: 10.5064/f6vanjl8/znzbw8
title: Silan-Ciruelas_USA_Opt1_17B_Engy_20_years_Low_Low-Median.pdf
DOI: 10.5064/f6vanjl8/4gghpl
title: Silan-Ciruelas_FRA_Opt1_21B_Hector_LGBT_Low_Low-Median.pdf
DOI: 10.5064/f6vanjl8/j2mhrp
title: Silan-Ciruelas_USA_Opt1_17A_Engy_20_years_Low_Low-Median.pdf
DOI: 10.5061/dryad.fm28d
title: Data from: "Characterization of two Iberian freshwater fish transcriptomes, Squalius carolitertii and Squalius torgalensis, living in distinct environmental conditions" in Genomic Resources Notes Accepted 1 April 2015 to 31 May 2015

description: The advance of NGS technologies opened exciting research avenues, as for
 example expanding the study of the mechanisms underlying adaptation from
 model organisms to natural systems. We used NGS technologies to sequence
 12 RNA-seq libraries, and provide the first transcriptomes of two endemic
 Iberian Cyprinids. The species Squalius carolitertii and S. torgalensis
 inhabit different regions of Portugal with distinct climate types,
 Atlantic in the North and Mediterranean in the South, respectively. While
 northern regions present mild temperatures, in southern regions fish are
 often under harsh temperatures and droughts. Herein, we sequenced the
 transcriptome from three tissues (skeletal muscle, liver and fins) in an
 Illumina HiSeq2000 of fish exposed to different temperatures: 18ºC
 (control) and 30ºC (test). Around 200 million raw reads were generated for
 each species, with similar number of reads per library (approximately 30
 million), rendering de novo assemblies with a total of 145975 and 137303
 contigs, for S. carolitertii and S. torgalensis, respectively. Gene
 ontology showed that around 60% of the annotated genes belonged to four
 biological processes and approximately 75% to two molecular functions.
 Besides, this study provides, for the first time, the transcriptome
 characterization of two endemic fish from Iberian freshwater basins, S.
 carolitertii and S. torgalensis, and constitutes a valuable resource for
 understanding environmental adaptations of Iberian Cyprinids.
description: assembly_carolitertiicd-hit-est_carolitertii.fastaassembly_torgalensiscd-hit_torgalensis.fastatop_blasthit_torgtop_blasthit_carolS.carolitertii annotationscarolitertii.annotS.torgalensis annotationstorgalensis.annot
DOI: 10.5064/f6vanjl8/areile
title: Silan-Ciruelas_BRA_Opt2_22B_Camilla_LGBT_High_Low-Median.pdf
DOI: 10.5281/zenodo.18377525
title: SpatialFusion additional data

description: This repository contains additional data described in the manuscript: 'SpatialFusion: A lightweight multimodal foundation model for pathway-informed spatial niche mapping' by Yates et al.It contains: - annotated cell types for the HEST1k Xenium cohort (https://arxiv.org/abs/2406.16192), manually annotated using canonical markers and the help of ChatGPT- the processed data from the CRC cohort (https://www.nature.com/articles/s41588-025-02193-3), with cell segmented, manual annotation of cell types, and PROGENy estimated pathways.
DOI: 10.5061/dryad.4jm83
title: Data from: Exploring evolutionary relationships across the genome using topology weighting

description: We introduce the concept of topology weighting, a method for quantifying
 relationships between taxa that are not necessarily monophyletic, and
 visualising how these relationships change across the genome. A given set
 of taxa can be related in a limited number of ways, but if each taxon is
 represented by multiple sequences, the number of possible topologies
 becomes very large. Topology weighting reduces this complexity by
 quantifying the contribution of each 'taxon topology' to the
 full tree. We describe our method for topology weighting by iterative
 sampling of sub-trees (Twisst), and test it on both simulated and real
 genomic data. Overall, we show that this is an informative and versatile
 approach, suitable for exploring relationships in almost any genomic
 dataset. Scripts to implement the method described are available at
 github.com/simonhmartin/twisst.
description: Simulation
 DataGenotypes, trees and
 weights for all simulations.sim.tar.gzNeurospora DataGenotypes, trees and weights for Neurospora analyses, based on data originally from Corcoran et al. 2016: http://datadryad.org/resource/doi:10.5061/ dryad.162mhneurospora.tar.gzHeliconius DataGenotypes, trees and weights for Heliconius analyses, based on data originally from Martin et al. 2013 Genome Res. 23: 1817–1828, European Nucleotide Archive, study accession no. ERP002440.Martin2013_data.tar.gz
DOI: 10.5064/f6vanjl8/8a31zs
title: Silan-Ciruelas_BRA_Opt2_23B_Camilla_LGBT_Low_Median-High.pdf
DOI: 10.5281/zenodo.18377524
title: SpatialFusion additional data

description: This repository contains additional data described in the manuscript: 'SpatialFusion: A lightweight multimodal foundation model for pathway-informed spatial niche mapping' by Yates et al.It contains: - annotated cell types for the HEST1k Xenium cohort (https://arxiv.org/abs/2406.16192), manually annotated using canonical markers and the help of ChatGPT- the processed data from the CRC cohort (https://www.nature.com/articles/s41588-025-02193-3), with cell segmented, manual annotation of cell types, and PROGENy estimated pathways.
DOI: 10.5064/f6vanjl8/7yxkyv
title: Silan-Ciruelas_USA_Opt2_18A_Marina_20_High_Low-Median.pdf
DOI: 10.5061/dryad.r60sv
title: Data from: Rapid evolutionary response to a transmissible cancer in Tasmanian devils

description: Although cancer rarely acts as an infectious disease, a recently emerged
 transmissible cancer in Tasmanian devils (Sarcophilus harrisii) is
 virtually 100% fatal. Devil facial tumour disease (DFTD) has swept across
 nearly the entire species’ range, resulting in localized declines
 exceeding 90% and an overall species decline of more than 80% in less than
 20 years. Despite epidemiological models that predict extinction,
 populations in long-diseased sites persist. Here we report rare genomic
 evidence of a rapid, parallel evolutionary response to strong selection
 imposed by a wildlife disease. We identify two genomic regions that
 contain genes related to immune function or cancer risk in humans that
 exhibit concordant signatures of selection across three populations. DFTD
 spreads between hosts by suppressing and evading the immune system, and
 our results suggest that hosts are evolving immune-modulated resistance
 that could aid in species persistence in the face of this devastating
 disease.
description: Genotype calls from
 Stacks for Tasmanian devil RAD-seqThis VCF file contains
 raw genotype calls produced by Stacks as described in Epstein et al. 2016.
 Very briefly, the genotyping workflow was quality control -&gt; PCR
 de-duplication (for paired-end samples) -&gt; Alignment to reference -&gt;
 Filter out MAPQ &lt; 40 -&gt; Stacks.devils_radseq_stacks_snpcalls_360_samples.vcf.gz
DOI: 10.5064/f6vanjl8/momqnz
title: Silan-Ciruelas_TUR_Opt2_13B_NejlaNaz_10-20_Low_Low-Median.pdf
DOI: 10.5064/f6vanjl8/kk3voj
title: Silan-Ciruelas_PHL_Opt2_16A_Rozel_10-20_High_Median-High.pdf
DOI: 10.5064/f6vanjl8/mwn03b
title: Silan-Ciruelas_PHL_Opt2-19B-Christelle_20years_Low_Med-High.pdf
DOI: 10.5061/dryad.4ch98
title: Data from: Speed dependency in α-motoneuron activity and locomotor modules in human locomotion: indirect evidence for phylogenetically conserved spinal circuits

description: Coordinated locomotor muscle activity is generated by the spinal central
 pattern generators (CPGs). Vertebrate studies have demonstrated the
 following two characteristics of the speed control mechanisms of the
 spinal CPGs: (i) rostral segment activation is indispensable for achieving
 high-speed locomotion; and (ii) specific combinations between spinal
 interneuronal modules and motoneuron (MN) pools are sequentially activated
 with increasing speed. Here, to investigate whether similar control
 mechanisms exist in humans, we examined spinal neural activity during
 varied-speed locomotion by mapping the distribution of MN activity in the
 spinal cord and extracting locomotor modules, which generate basic MN
 activation patterns. The MN activation patterns and the locomotor modules
 were analysed from multi-muscle electromyographic recordings. The
 reconstructed MN activity patterns were divided into the following three
 patterns depending on the speed of locomotion: slow walking, fast walking
 and running. During these three activation patterns, the proportion of the
 activity in rostral segments to that in caudal segments increased as
 locomotion speed increased. Additionally, the different MN activation
 patterns were generated by distinct combinations of locomotor modules.
 These results are consistent with the speed control mechanisms observed in
 vertebrates, suggesting phylogenetically conserved spinal mechanisms of
 neural control of locomotion.
description: EMG_and_force_dataThis zip file includes time, EMG signals (14 muscles) and force data (vertical component) for each subject.
DOI: 10.5064/f6vanjl8/tsrpvb
title: Silan-Ciruelas_InformedConsent-DataNotice.pdf
DOI: 10.5064/f6vanjl8/ojtvus
title: Silan-Ciruelas_TUR_Opt2_20B_Kerem_Over20_High_Median-High.pdf
DOI: 10.5061/dryad.gf246
title: Data from: Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

description: DNA metabarcoding is a promising approach for rapidly surveying
 biodiversity and is likely to become an important tool for measuring
 ecosystem responses to environmental change. Metabarcoding markers need
 sufficient taxonomic coverage to detect groups of interest, sufficient
 sequence divergence to resolve species, and will ideally indicate relative
 abundance of taxa present. We characterized zooplankton assemblages with
 three different metabarcoding markers (nuclear 18S rDNA, mitochondrial
 COI, and mitochondrial 16S rDNA) to compare their performance in terms of
 taxonomic coverage, taxonomic resolution, and correspondence between
 morphology- and DNA-based identification. COI amplicons sequenced on
 separate runs showed that operational taxonomic units representing
 &gt;0.1% of reads per sample were highly reproducible, although
 slightly more taxa were detected using a lower annealing temperature.
 Mitochondrial COI and nuclear 18S showed similar taxonomic coverage across
 zooplankton phyla. However, mitochondrial COI resolved up to threefold
 more taxa to species compared to 18S. All markers revealed similar
 patterns of beta-diversity, although different taxa were identified as the
 greatest contributors to these patterns for 18S. For calanoid copepod
 families, all markers displayed a positive relationship between biomass
 and sequence reads, although the relationship was typically strongest for
 18S. The use of COI for metabarcoding has been questioned due to lack of
 conserved primer-binding sites. However, our results show the taxonomic
 coverage and resolution provided by degenerate COI primers, combined with
 a comparatively well-developed reference sequence database, make them
 valuable metabarcoding markers for biodiversity assessment.
description: 46vsTD_fastqRaw FASTQ files for COI marker PCR-amplified using either the published touchdown (TD) or a single annealing temperature (46) thermal cycling protocol.Cop16S_fastqRaw FASTQ files for Storm Bay zooplankton assemblages amplified with the Cop16S marker.Uni18S_fastqRaw FASTQ files for Storm Bay zooplankton assemblages amplified with the Uni18S marker.LerayCOI_fastqRaw FASTQ files for Storm Bay zooplankton assemblages amplified with the Uni18S marker.OTU_tablesOTU tables for Storm Bay zooplankton assemblages amplified using three metabarcoding markers (mitochondrial COI, 16S, and nuclear 18S), and the comparison of the COI marker using two different thermal cycling protocols.
DOI: 10.5064/f6vanjl8/rwow7m
title: Silan-Ciruelas_TUR_Opt1_6B_EdaDamla_1-5_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/r09lse
title: Silan-Ciruelas_PHL_Opt2_4B_Nica_1_High_Median-High.pdf