cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8kc1v
title: Data from: Prediction of phylogeographic endemism in an environmentally complex biome.

description: Phylogeographic endemism, the degree to which the history of recently
 evolved lineages is spatially restricted, reflects fundamental
 evolutionary processes such as cryptic divergence, adaptation and
 biological responses to environmental heterogeneity. Attempts to explain
 the extraordinary diversity of the tropics, which often includes deep
 phylogeographic structure, frequently invoke interactions of climate
 variability across space, time and topography. To evaluate historical
 versus contemporary drivers of phylogeographic endemism in a tropical
 system, we analyse the effects of current and past climatic variation on
 the genetic diversity of 25 vertebrates in the Brazilian Atlantic
 rainforest. We identify two divergent bioclimatic domains within the
 forest and high turnover around the Rio Doce. Independent modelling of
 these domains demonstrates that endemism patterns are subject to different
 climatic drivers. Past climate dynamics, specifically areas of relative
 stability, predict phylogeographic endemism in the north. Conversely,
 contemporary climatic heterogeneity better explains endemism in the south.
 These results accord with recent speleothem and fossil pollen studies,
 suggesting that climatic variability through the last 250 kyr impacted the
 northern and the southern forests differently. Incorporating sub-regional
 differences in climate dynamics will enhance our ability to understand
 those processes shaping high phylogeographic and species endemism, in the
 Neotropics and beyond.
description: Current Species
 ModelsThese are Maxent outputs
 of each species for present day climate conditions. These outputs are used
 to determine distribution presence/absence for phylogeographic endemism
 calculations in Biodiverse.current_species_models.zipStability ModelsThese are the processed stability estimates of the Atlantic Forest used in Figure 2, and Supplemental Figure S2. They are again grouped by forest region (entire forest, northern forest, southern forest) and into 0-21kybp and 0-120kybp analyses, and additionally by dispersal level (0m/year, 5m/year & 10m/year).stability_models.zipClimate DataClimate and paleoclimatic data (Bioclim - see www.worldclim.org) for the Atlantic Forest. Folders are organized by climate age - e.g. 0 is present, 21 is 21 kybp, and 120 is 120kyp.climate_data.zipRaw Stability ModelsThese are Maxent outputs of the Atlantic Forest over many timeslices used to determine forest stability. The outputs are grouped by forest region (entire forest, northern forest, southern forest) and into 0-21kybp and 0-120kybp analyses.raw_stability_models.zip
DOI: 10.5061/dryad.1h1f2
title: Data from: Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of single nucleotide polymorphisms

description: Assessing the genetic variability of the tick Ixodes ricinus - an
 important vector of pathogens in Europe - is an essential step for
 setting-up anti-tick control methods. Here, we report the first
 identification of a set of SNPs isolated from the genome of I. ricinus,
 carried out by applying a genomic complexity reduction step, followed by
 pyrosequencing and the use new bioinformatics tools. Almost 1.4 million
 reads (average length : 528 nt) were generated with a full Roche 454 GS
 FLX run on two Reduced Representation Libraries of I. ricinus. 321,088
 putative SNPs were isolated using the newly developed bioinformatics tool
 READ2SNPS, which identifies SNPs without requiring a reference genome.
 Stringent selection criteria were applied in a bioinformatics pipeline to
 select 1,768 SNPs for the development of specific primers. Among 384
 randomly selected SNPs, tested by Fluidigm genotyping technology on 464
 individual ticks, 368 SNPs loci (96%) exhibited the presence of the two
 expected alleles. Hardy-Weinberg equilibrium tests conducted on 6 natural
 populations of ticks showed that from 26 to 46 of the 384 loci exhibited
 significant heterozygote deficiencies. The generated SNP resource
 described here will be useful for a variety of applications such as the
 assessment of the genetic structure of I. ricinus populations.
description: output_read2snps_cov4_10_Q30output data generated by Read2snps tool. This file contain only SNPs sequences with SNPs with a depth sequencing between 4 and 10 for a minimum quality of 30. This file have been used to select and to design primers.assembling_Ixodes_ricinus_RRLBioinformatic_scripts
DOI: 10.5061/dryad.ns315
title: Data from: Revealing the biochemical and genetic basis of color variation in a polymorphic lizard

description: Determining the mechanistic and genetic basis of animal coloration is
 essential to understand the costs and constraints on colour production,
 and the evolution and maintenance of phenotypic variation. However, genes
 underlying structural colour and widespread pigment classes apart from
 melanin remain largely uncharacterised, in part due to restricted
 taxonomic focus. We combined liquid chromatography-mass spectrometry and
 RNA-seq gene expression analyses to characterise the pigments and genes
 associated with skin colour in the polymorphic lizard, Ctenophorus
 decresii. Throat coloration in male C. decresii may be a combination of
 orange, yellow, grey or ultra-violet blue. We confirmed the presence of
 two biochemically different pigment classes, pteridines (self-synthesised)
 and carotenoids (acquired through the diet), in all skin colours. Orange
 skin had the highest levels of pteridine pigments while yellow skin tended
 to have higher levels of carotenoids, of which the vitamin A precursors
 β-carotene and β-cryptoxanthin have not been previously confirmed in
 reptiles. These results were confirmed by gene expression analyses, which
 detected 489 genes differentially expressed between the skin colours,
 including genes associated with pteridine production, provitamin A
 carotenoid metabolism, iridophore-specific synthesis, melanin synthesis
 and steroid hormone pathways. For the majority of these 489 genes,
 however, our study reveals a new association with colour production in
 vertebrates. These data represent a significant contribution to
 understanding the genetic basis of colour variation in vertebrates and a
 rich resource for further studies.
description: Gene_Differential_Expression_ResultsSpreadsheet showing the reletive expression levels of genes (in transcripts per million reads, TPM) in skin and non-skin tissue samples estimated using RSEM and Bowtie 2. Differentially expressed genes between skin colours and skin and non-skin were identified using edgeR.Genes_More_Highly_Expressed_in_SkinList of genes more highly expressed in at least one skin colour (blue, grey, yellow, orange) than in non-skin samples. Data are transcripts per million reads (TPM) estimated using RSEM.RSEM_ReferenceCtenophorus decresii specific reference for downstream mapping (for estimating gene expression) consisting of 19,407 protein coding regions annotated for Pogona vitticeps (the closest con-familial species for which a fully annotated genome is available).decresii_pogona_eo.fastaEdgeR_MatrixGene count matrix for differential expression analysis.EdgeR_ScriptR script for differential expression analysis using EdgeR.AssembliesTrinity assemblies for each transcriptome used in this study.
DOI: 10.5061/dryad.5d972
title: Data from: Automated reconstruction of three-dimensional fish motion, forces, and torques

description: Fish can move freely through the water column and make complex
 three-dimensional motions to explore their environment, escape or feed.
 Nevertheless, the majority of swimming studies is currently limited to
 two-dimensional analyses. Accurate experimental quantification of changes
 in body shape, position and orientation (swimming kinematics) in three
 dimensions is therefore essential to advance biomechanical research of
 fish swimming. Here, we present a validated method that automatically
 tracks a swimming fish in three dimensions from multi-camera high-speed
 video. We use an optimisation procedure to fit a parameterised,
 morphology-based fish model to each set of video images. This results in a
 time sequence of position, orientation and body curvature. We post-process
 this data to derive additional kinematic parameters (e.g. velocities,
 accelerations) and propose an inverse-dynamics method to compute the
 resultant forces and torques during swimming. The presented method for
 quantifying 3D fish motion paves the way for future analyses of swimming
 biomechanics.
description: Fish tracker source code
 and example dataThis repository contains
 the source code of the fish tracker, and its post-processor, described in
 the associated article. It also includes the code of a reference data
 generator, to create synthetic data used to test the fish tracker.
 Finally, it contains a set of example data of a 3 days post fertilisation
 zebrafish larva.Voesenek_Pieters_VanLeeuwen_tracking_source_data.zip
DOI: 10.5061/dryad.n3jk5
title: Data from: Gene duplication, population genomics and species-level differentiation within a tropical mountain shrub

description: Gene duplication leads to paralogy, which complicates the de novo assembly
 of genotyping-by-sequencing (GBS) data. The issue of paralogous genes is
 exacerbated in plants, because they are particularly prone to gene
 duplication events. Paralogs are normally filtered from GBS data before
 undertaking population genomics or phylogenetic analyses. However, gene
 duplication plays an important role in the functional diversification of
 genes and it can also lead to the formation of postzygotic barriers. Using
 populations and closely related species of a tropical mountain shrub, we
 examine: (1) the genomic differentiation produced by putative orthologs,
 and (2) the distribution of recent gene duplication among lineages and
 geography. We find high differentiation among populations from isolated
 mountain peaks and species-level differentiation within what is
 morphologically described as a single species. The inferred distribution
 of paralogs among populations is congruent with taxonomy and shows that
 GBS could be used to examine recent gene duplication as a source of
 genomic differentiation of non-model species.
description: Demultiplexing and de
 novo assembly detailsContains demultiplexing
 and de novo assembly details of data used for paralogs filtering and
 subsequent population genomics analyses.1stacksContains data directories used by scripts from the section "3Berberis_phylogeo" of this repository for running the *populations* program of *Stacks* after putative paralogous loci have been filtered.3Berberis_phylogeoContains scripts for paralogous loci filtering, output data from the *populations* program of *Stacks*, as well as R scripts used for analyses and plotting.
DOI: 10.5061/dryad.s29j7
title: Data from: Modelling enrolment in Cambrian trilobites

description: Trilobites were capable of enroling in different ways based on the
 flexible articulation of thoracic segments and associated interlocking
 devices; the type of enrolment (spiral or sphaeroidal) is thought to have
 largely depended on the coaptative devices that each trilobite used to
 enclose the body. Based on X-ray microtomography scans of complete
 enrolled specimens from the Cambrian, we created three-dimensional (3D)
 computer models to assess the kinematics needed to achieve both enrolment
 types. We demonstrate that closely related trilobites with little
 morphological variation (Bailiaspis?, Conocoryphe and Parabailiella)
 developed different enrolment types as a result of small variations in the
 number of thoracic segments and the angle between adjacent segments.
 Moreover, our models indicate that sphaeroidal enrolment, which is
 associated with a smaller number of thoracic segments, enabled faster
 encapsulation. This supports the hypothesis that there was a trend in the
 evolution of trilobites towards reduction in the number of thoracic
 segments in phylogenetically derived taxa in order to enhance the
 efficiency of enrolment.
description: Supplementary+Data+1Slices from XMT scan of two enrolled specimens of Bailiaspis? glabrata (MPZ2017/310-311).Supplementary+Data+2Slices from XMT scan of one enrolled specimen of Parabailella languedocensis (C-12).Supplementary+Model+1Interactive 3-D reconstruction of Bailiaspis? glabrata (MPZ2017/310) in VAXML format.Supplementary+Model+2Interactive 3-D reconstruction of Bailiaspis? glabrata (MPZ2017/311) in VAXML format.Supplementary+Model+3Interactive 3-D reconstruction of Parabailella languedocensis (C-12) in VAXML format.Supplementary+Movie+1Movie showing in real-time the logarithm curve of the spiral and sphaeroidal enrolment mechanism of the 3D model created using Bailiaspis? grabata.CompEnroll.movSupplementary+Movie+23-D model of Bailiaspis? glabrata showing the enrolment procedure.Supplementary+Movie.mov
DOI: 10.5281/zenodo.14361228
title: [Dataset & Models] Online material to publication "Self-consistent models of Earth's mantle and core from long-period seismic and tidal constraints"

description: Supporting material for publication "Self-consistent models of Earth's mantle and core from long-period seismic and tidal constraints" (Munch, Kemper, Khan, Helffrich & Giardini, 2025, JGR Solid Earth).

This repository contains:



SCEM_nmodes_catalog.xls: Compilation of normal mode centre frequencies and quality (attenuation) factors used on the study. 

forward_calculator.zip: Python script to compute normal mode centre frequencies and quality factors for a given 1D model (in .bm format) and compare predictions with observations (in .csv format). Running this script locally requires installation of package specnm (https://johkem1.gitlab.io/specnm/). Alternatively, the script can also be run online on the following link: https://colab.research.google.com/drive/1jaFiMHTlUW_kTOdtLCyOpN5StGxWtqk7?usp=sharing

specnm_predictions_PREM: Predicted normal mode centre frequencies and quality factors for PREM. Calculations performed using the specnm tool.

Kernel_Gallery.zip: Gallery of normal modes sensitivity kernels (pdf format). 

models.zip: self-consistent (SCEM) and polynomially-parameterized (P-PEM) Earth models in .bm format. The zip file contains three folders with:



MAP: Maximum a-posteriori models (MAP)

bounds: upper and lower bounds of Vs, Vp, and density as a function of depth/radius. For SCEM, we also provide temperature (when available) and pressure.

SCEM/PPEM: subset of models representative of the posterior probablity distribution




 

Citation:

Munch, F. D., Kemper, J., Khan, A., Helffrich, G., & Giardini, D. (2026). Self‐consistent models of Earth's mantle and core from long‐period seismic and tidal constraints. Journal of Geophysical Research: Solid Earth, 131, e2024JB030971. https://doi.org/10.1029/2024JB030971
DOI: 10.5281/zenodo.18386410
title: [Dataset & Models] Online material to publication "Self-consistent models of Earth's mantle and core from long-period seismic and tidal constraints"

description: Supporting material for publication "Self-consistent models of Earth's mantle and core from long-period seismic and tidal constraints" (Munch, Kemper, Khan, Helffrich & Giardini, 2025, JGR Solid Earth).

This repository contains:



SCEM_nmodes_catalog.xls: Compilation of normal mode centre frequencies and quality (attenuation) factors used on the study. 

forward_calculator.zip: Python script to compute normal mode centre frequencies and quality factors for a given 1D model (in .bm format) and compare predictions with observations (in .csv format). Running this script locally requires installation of package specnm (https://johkem1.gitlab.io/specnm/). Alternatively, the script can also be run online on the following link: https://colab.research.google.com/drive/1jaFiMHTlUW_kTOdtLCyOpN5StGxWtqk7?usp=sharing

specnm_predictions_PREM: Predicted normal mode centre frequencies and quality factors for PREM. Calculations performed using the specnm tool.

Kernel_Gallery.zip: Gallery of normal modes sensitivity kernels (pdf format). 

models.zip: self-consistent (SCEM) and polynomially-parameterized (P-PEM) Earth models in .bm format. The zip file contains three folders with:



MAP: Maximum a-posteriori models (MAP)

bounds: upper and lower bounds of Vs, Vp, and density as a function of depth/radius. For SCEM, we also provide temperature (when available) and pressure.

SCEM/PPEM: subset of models representative of the posterior probablity distribution




 

Citation:

Munch, F. D., Kemper, J., Khan, A., Helffrich, G., & Giardini, D. (2026). Self‐consistent models of Earth's mantle and core from long‐period seismic and tidal constraints. Journal of Geophysical Research: Solid Earth, 131, e2024JB030971. https://doi.org/10.1029/2024JB030971
DOI: 10.5061/dryad.v5gd2
title: Data from: Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers

description: New sequencing technologies allow development of genome-wide markers for
 any genus of ecological interest, including plant genera such as Betula
 (birch) that have previously proved difficult to study due to widespread
 polyploidy and hybridisation. We present a de novo reference genome
 sequence assembly, from 67X short read coverage, of Betula nana (dwarf
 birch) – a diploid that is the keystone woody species of sub-arctic scrub
 communities but of conservation concern in Britain. We also present 100bp
 PstI RAD markers for B. nana and closely related Betula tree species.
 Assembly of RAD markers in 15 individuals by alignment to the reference B.
 nana genome yielded 44k-86k RAD loci per individual, whereas de novo RAD
 assembly yielded 64k-121k loci per individual. Of the loci assembled by
 the de novo method, 3k homologous loci were found in all 15 individuals
 studied, and 35k in 10 or more individuals. Matching of RAD loci to RAD
 locus catalogs from the B. nana individual used for the reference genome,
 showed similar numbers of matches from both methods of RAD locus assembly
 but indicated that the de novo RAD assembly method may over-assemble some
 paralogous loci. In 12 individuals hetero-specific to B. nana 37k-47k RAD
 loci matched a catalog of RAD loci from the B. nana individual used for
 the reference genome, whereas 44k-60k RAD loci aligned to the B. nana
 reference genome itself. We present a preliminary study of allele sharing
 among species, demonstrating the utility of the data for introgression
 studies and for the identification of species-specific alleles.
description: Diagram-of-bioinformatic-pipelinesbowtie-sstacks-MatchesTo097Catalogbowtie-cstacks-IndividualCatalogsdenovo-sstacks-MatchesToUniversalCatalogsdenovo-sstacks-MatchesTo097Catalogsdenovo-ustacks-cstacks-IndividualAndUniversalCatalogsBetulaNana1.0Betula nana genome assembly 1.0
DOI: 10.57841/casdc.0007100
title: 研制出高场下高性能ReBCO超导带材
DOI: 10.5061/dryad.39272
title: Data from: Computer simulations show that Neanderthal facial morphology represents adaptation to cold and high energy demands, but not heavy biting

description: Three adaptive hypotheses have been forwarded to explain the distinctive
 Neanderthal face: 1) an improved ability to accommodate high anterior bite
 forces, 2) more effective conditioning of cold and/or dry air, and, 3)
 adaptation to facilitate greater ventilatory demands. We test these
 hypotheses using three-dimensional models of Neanderthals, modern humans,
 and a close outgroup (H. heidelbergensis), applying finite element
 analysis (FEA) and computational fluid dynamics (CFD). This is the most
 comprehensive application of either approach applied to date and the first
 to include both. FEA reveals few differences between H. heidelbergensis,
 modern humans and Neanderthals in their capacities to sustain high
 anterior tooth loadings. CFD shows that the nasal cavities of Neanderthals
 and especially modern humans condition air more efficiently than does that
 of H. heidelbergensis, suggesting that both evolved to better withstand
 cold and/or dry climates than less derived Homo. We further find that
 Neanderthals could move considerably more air through the nasal pathway
 than could H. heidelbergensis or modern humans, consistent with the
 propositions that, relative to our outgroup Homo, Neanderthal facial
 morphology evolved to reflect improved capacities to better condition
 cold, dry air, and, to move greater air volumes in response to higher
 energetic requirements.
description: FEA
 dataFEA data
 xlsAfrican_American_Airway_ExpirationComputational Fluid Dynamics data - African_American_Airway_Expiration [csv format]African_American_Airway_InspirationCFD [computational fluid dynamics data] for African_American_Airway_Inspiration [csv format]Broken_Hill_1_ExpirationCFD [computational fluid dynamics data] for Broken Hill 1_expiration [csv format]Broken_Hill_1_InspirationCFD [computational fluid dynamics data] for Broken Hill_1_Inspiration [csv format]European_American_Airway_ExpirationCFD [computational fluid dynamics data] for European_American_Airway_Exspiration [csv format]European_American_Airway_InspirationCFD [computational fluid dynamics data] for European_American_Airway_inspiration [csv format]Neanderthal_Airway_ExpirationCFD [computational fluid dynamics data] for Neanderthal_Airway_Expiration [csv format]Neanderthal_Airway_InspirationCFD [computational fluid dynamics data] for Neanderthal_Airway_Inspiration [csv format]