cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1040d
title: Data from: Body mass-corrected molecular rate for bird mitochondrial DNA

description: Mitochondrial DNA remains one of the most widely used molecular markers to
 reconstruct the phylogeny and phylogeography of closely related birds. It
 has been proposed that bird mitochondrial genomes evolve at a constant
 rate of ~0.01 substitution per site per million years, that is that they
 evolve according to a strict molecular clock. This molecular clock is
 often used in studies of bird mitochondrial phylogeny and molecular
 dating. However, rates of mitochondrial genome evolution vary among bird
 species and correlate with life history traits such as body mass and
 generation time. These correlations could cause systematic biases in
 molecular dating studies that assume a strict molecular clock. In this
 study, we overcome this issue by estimating corrected molecular rates for
 birds. Using complete or nearly complete mitochondrial genomes of 475
 species, we show that there are strong relationships between body mass and
 substitution rates across birds. We use this information to build models
 that use bird species’ body mass to estimate their substitution rates
 across a wide range of common mitochondrial markers. We demonstrate the
 use of these corrected molecular rates on two recently published data
 sets. In one case, we obtained molecular dates that are twice as old as
 the estimates obtained using the strict molecular clock. We hope that this
 method to estimate molecular rates will increase the accuracy of future
 molecular dating studies in birds.
description: Full nucleotide
 sequences alignmentAlignments of the 12
 H-stranded protein-coding genes (i.e. all the protein-coding genes except
 NADH-dehydrogenase 6, ND6) for 475 speciesmito.fastaPhylogenetic treePhylogenetic tree of 475 species following the topology of Prum et al. (2015)mito.treeChronogram Calibration sets 2Chronogram estimated using the calibration sets 2 (see table 1 of Nabholz et al. 2016)Chronogram_Calibration_sets_2.treeChronogram Calibration sets 4Chronogram estimated using the calibration sets 4 (see table 1 of Nabholz et al. 2016)Chronogram_Calibration_sets_4.treeR script to convert branch length in divergence datesA R script to compute the mass-corrected substitution rate and compute the divergence dates. This program convert branch length in divergence dates by computing the mass-corrected molecular rates as described in Nabholz et al. 2016. Header of the script contains useful informations.applyMassCorrectedRates.RHarrier_Oatley_2015This dataset is used as the first working example in Nabholz et al. 2016Xiphorhynchus_Rocha_2015This dataset is used as the second working example in Nabholz et al. 2016
DOI: 10.5061/dryad.5kc40
title: Data from: Importance of deep water uptake in tropical eucalypt forest

description: Climate models predict that the frequency, intensity and duration of
 drought events will increase in tropical regions. Although water
 withdrawal from deep soil layers is generally considered to be an
 efficient adaptation to drought, there is little information on the role
 played by deep roots in tropical forests. Tropical Eucalyptus plantations
 managed in short rotation cycles are simple forest ecosystems that may
 provide an insight into the water use by trees in tropical forests. The
 contribution made by water withdrawn from deep soil layers to the water
 required for evapotranspiration was quantified daily from planting to
 harvesting age for a Eucalyptus grandis stand using a soil water transfer
 model coupled with an ecophysiological forest model (MAESPA). The model
 was parameterized using an extensive data set and validated using time
 series of the soil water content down to a depth of 10 m and water-table
 level, as well as evapotranspiration measured using eddy covariance. Fast
 root growth after planting provided access to large quantities of water
 stored in deep soil layers over the first 2 years. Eucalyptus roots
 reached the water-table at a depth of 12 m after 2 years. Although the
 mean water withdrawal from depths of over 10 m amounted to only 5% of
 canopy transpiration from planting to a harvesting age of 5 years, the
 proportion of water taken up near the water-table was much higher during
 dry periods. The water-table rose from 18 to 12 m below-ground over 2
 years after the harvest of the previous stand and then fell until
 harvesting age as evapotranspiration rates exceeded the annual rainfall.
 Deep rooting is an efficient strategy to increase the amount of water
 available for the trees, allowing the uptake of transient gravitational
 water and possibly giving access to a deep water-table. Deep soil layers
 have an important buffer role for large amounts of water stored during the
 wet season that is taken up by trees during dry periods. Our study
 confirms that deep rooting could be a major mechanism explaining high
 transpiration rates throughout the year in many tropical forests.
description: DATASET
DOI: 10.5061/dryad.80150
title: Data from: EMG versus torque control of human-machine systems: equalizing control signal variability does not equalize error or uncertainty

description: In this paper we asked the question: if we artificially raise the
 variability of torque control signals to match that of EMG, do subjects
 make similar errors and have similar uncertainty about their movements? We
 answered this question using two experiments in which subjects used three
 different control signals: torque, torque+noise, and EMG. First, we
 measured error on a simple target-hitting task in which subjects received
 visual feedback only at the end of their movements. We found that even
 when the signal-to-noise ratio was equal across EMG and torque+noise
 control signals, EMG resulted in larger errors. Second, we quantified
 uncertainty by measuring the just-noticeable difference of a visual
 perturbation. We found that for equal errors, EMG resulted in higher
 movement uncertainty than both torque and torque+noise. The differences
 suggest that performance and confidence are influenced by more than just
 the noisiness of the control signal, and suggest that other factors, such
 as the user’s ability to incorporate feedback and develop accurate
 internal models, also have significant impacts on the performance and
 confidence of a person’s actions. We theorize that users have difficulty
 distinguishing between random and systematic errors for EMG control, and
 future work should examine in more detail the types of errors made with
 EMG control.
description: TrajectoriesAFCProcessedDataDataReadMe
DOI: 10.5061/dryad.ft596
title: Data from: Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species

description: Today most population genomic studies of nonmodel organisms either
 sequence a subset of the genome deeply in each individual or sequence
 pools of unlabelled individuals. With a step-by-step workflow, we
 illustrate how low-coverage whole-genome sequencing of hundreds of
 individually barcoded samples is now a practical alternative strategy for
 obtaining genomewide data on a population scale. We used a highly
 efficient protocol to generate high-quality libraries for ~6.5 USD from
 each of 876 Atlantic silversides (a teleost fish with a genome size ~730
 Mb) that we sequenced to 1–4× genome coverage. In the absence of a
 reference genome, we developed a bioinformatic pipeline for mapping the
 genomic reads to a de novo assembled reference transcriptome. This
 provides an ‘in silico’ method for exome capture that avoids the
 complexities and expenses of using wet chemistry for target isolation.
 Using novel tools for analysis of low-coverage data, we extracted
 population allele frequencies, individual genotype likelihoods and
 polymorphism data for 2 504 335 SNPs across the exome for the 876 fish. To
 illustrate the use of the resulting data, we present a preliminary
 analysis of geographical patterns in the exome data and a comparison of
 complete mitochondrial genome sequences for each individual (constructed
 from the low-coverage data) that show population colonization patterns
 along the US east coast. With a total cost per sample of less than 50 USD
 (including sequencing) and ability to prepare 96 libraries in only 5 h,
 our approach adds a viable new option to the population genomics toolbox.
description: Commands for running the
 pipelineThis file contains a
 list of the programs and parameter values we used for the bioinformatic
 analysis pipeline described in the paper. Note that the sequence of steps
 described in this file was designed to carefully evaluate the quality of
 sequencing data generated with a new library preparation method. For
 routine applications (where it may not be necessary to quantify the loss
 of data at each individual filtering step), several steps can be skipped,
 optimized or combined for a more streamlined pipeline.QC_Stats_Therkildsen_and_PalumbiThis Excel file contains the raw data used to evaluate the quality of sequencing libraries. Please see the tab "Column title descriptions" for explanations of the column headers.RemoveSequencesFromFastq.pyA simple python script for removing specific sequences (named in an input file) from a fastq file. Our pipeline uses this script to removing potential contaminant reads prior to mapping to the reference.
DOI: 10.5281/zenodo.18371273
title: Conversation with Ana Martínez Arenaz and Jaime Oiza Galán

description: The discussion, held at A Coruña's Archaeology and History Museum, features museum manager Ana Martínez Arenaz and museum director Jaime Oiza Galán. The two museum staff members discuss the relationship between the museum and the UNESCO-listed lighthouse, and the city's cultural landscape.They explain how the Tower functions as A Coruña's primary monument in the absence of competing religious architecture, serving as the city's emblematic symbol and most visited site alongside the museum housed in the San Antón fortress.The conversation explores artefacts from the Tower of Hercules' excavation campaigns displayed in the museum, visitor engagement with A Coruña's legends, and personal memories about the lighthouse. The museum staff discuss the possible cultural barriers affecting visits to heritage sites by local residents.A significant theme emerges around Geryon's underrepresentation compared to Hercules, with participants discussing recent artistic attempts to reclaim this figure through street art (Xeriongram) and children's literature. Contemporary reinterpretations seek to rehabilitate Geryon as a relatable, non-threatening local character with Galician features, rather than Hercules' defeated antagonist.
DOI: 10.5281/zenodo.18371274
title: Conversation with Ana Martínez Arenaz and Jaime Oiza Galán

description: The discussion, held at A Coruña's Archaeology and History Museum, features museum manager Ana Martínez Arenaz and museum director Jaime Oiza Galán. The two museum staff members discuss the relationship between the museum and the UNESCO-listed lighthouse, and the city's cultural landscape.They explain how the Tower functions as A Coruña's primary monument in the absence of competing religious architecture, serving as the city's emblematic symbol and most visited site alongside the museum housed in the San Antón fortress.The conversation explores artefacts from the Tower of Hercules' excavation campaigns displayed in the museum, visitor engagement with A Coruña's legends, and personal memories about the lighthouse. The museum staff discuss the possible cultural barriers affecting visits to heritage sites by local residents.A significant theme emerges around Geryon's underrepresentation compared to Hercules, with participants discussing recent artistic attempts to reclaim this figure through street art (Xeriongram) and children's literature. Contemporary reinterpretations seek to rehabilitate Geryon as a relatable, non-threatening local character with Galician features, rather than Hercules' defeated antagonist.
DOI: 10.5061/dryad.tc29r
title: Data from: Methodological considerations for detection of terrestrial small-body salamander eDNA and implications for biodiversity conservation

description: Environmental DNA (eDNA) can be used as an assessment tool to detect
 populations of threatened species and provide fine-scale data required to
 make management decisions. The objectives of this project were to use
 quantitative PCR (qPCR) to: (i) detect spiked salamander DNA in soil, (ii)
 quantify eDNA degradation over time, (iii) determine detectability of
 salamander eDNA in a terrestrial environment using soil, faeces, and skin
 swabs, (iv) detect salamander eDNA in a mesocosm experiment. Salamander
 eDNA was positively detected in 100% of skin swabs and 66% of faecal
 samples and concentrations did not differ between the two sources.
 However, eDNA was not detected in soil samples collected from directly
 underneath wild-caught living salamanders. Salamander genomic DNA (gDNA)
 was detected in all qPCR reactions when spiked into soil at 10.0, 5.0, and
 1.0 ng/g soil and spike concentration had a significant effect on detected
 concentrations. Only 33% of samples showed recoverable eDNA when spiked
 with 0.25 ng/g soil, which was the low end of eDNA detection. To determine
 the rate of eDNA degradation, gDNA (1 ng/g soil) was spiked into soil and
 quantified over seven days. Salamander eDNA concentrations decreased
 across days, but eDNA was still amplifiable at day 7. Salamander eDNA was
 detected in two of 182 mesocosm soil samples over 12 weeks (n = 52 control
 samples; n = 65 presence samples; n = 65 eviction samples). The
 discrepancy in detection success between experiments indicates the
 potential challenges for this method to be used as a monitoring technique
 for small-bodied wild terrestrial salamander populations.
description: Walker_qPCR_dataThe zipped folder contains all qPCR profile files with corresponding labels to the manuscript.
DOI: 10.5061/dryad.m37gc
title: Data from: Badgers prefer cattle pasture but avoid cattle: implications for bovine tuberculosis control

description: Effective management of infectious disease relies upon understanding
 mechanisms of pathogen transmission. In particular, while models of
 disease dynamics usually assume transmission through direct contact,
 transmission through environmental contamination can cause different
 dynamics. We used Global Positioning System (GPS) collars and
 proximity-sensing contact-collars to explore opportunities for
 transmission of Mycobacterium bovis [causal agent of bovine tuberculosis]
 between cattle and badgers (Meles meles). Cattle pasture was badgers’ most
 preferred habitat. Nevertheless, although collared cattle spent 2914
 collar-nights in the home ranges of contact-collared badgers, and 5380
 collar-nights in the home ranges of GPS-collared badgers, we detected no
 direct contacts between the two species. Simultaneous GPS-tracking
 revealed that badgers preferred land &gt; 50 m from cattle. Very
 infrequent direct contact indicates that badger-to-cattle and
 cattle-to-badger M. bovis transmission may typically occur through
 contamination of the two species’ shared environment. This information
 should help to inform tuberculosis control by guiding both modelling and
 farm management.
description: badger habitat use
 observed and expectedThis excel file
 contains, for each GPS-collared badger, the proportions of locations
 falling into each land use type. These data were used to perform
 compositional analyses of badger habitat selection. Raw badger GPS-collar
 data are available on MoveBank.badger_habitat_use_obs_exp.xlsxsimultaneous badger cattle location pairsSimultaneous GPS-collar locations of badgers, and cattle within those badgers' home ranges, used to explore proximity between the two species. The expected distributions of separation distances were generated from these data by permutation. Raw GPS-collar data are available on MoveBank.simultaneous_location_pairs.xlsx
DOI: 10.34810/data1279
title: Partitura i enregistrament de "Cantate Domino. Motete a solo con dos violines, para Navidad" Joseph Pujol (actiu entre 1738-1787)

description: Sota el marc del projecte Estudi i Recuperació de Patrimoni Musical, aquest dataset conté dos arxius: 
&lt;p&gt;Transcripció del manuscrit original de Joseph Pujol
&lt;p&gt;Enregistrament de la peça interpretada per:
&lt;p&gt;- Eva del Campo, orgue positiu. Orgue positiu construït per Gerrit Klop el
2022.
&lt;p&gt;- Ricart Renart, violí I. Violí construït per Joseph Massaguer el 1753.
&lt;p&gt;- Marta Guillen, violí II. Violí construït per Giuseppe Tenneriello el 2009.
&lt;p&gt;- Guillermo Turina, violoncel. Violoncel construït per Marchal a finals del
segle XVIII.
&lt;p&gt;- Soledad Cardoso (soprano)
DOI: 10.5061/dryad.cj965
title: Data from: Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears

description: Ancient DNA studies have revolutionized the study of extinct species and
 populations, providing insights on phylogeny, phylogeography, admixture
 and demographic history. However, inferences on behaviour and sociality
 have been far less frequent. Here, we investigate the complete
 mitochondrial genomes of extinct Late Pleistocene cave bears and middle
 Holocene brown bears that each inhabited multiple geographically proximate
 caves in northern Spain. In cave bears, we find that, although most caves
 were occupied simultaneously, each cave almost exclusively contains a
 unique lineage of closely related haplotypes. This remarkable pattern
 suggests extreme fidelity to their birth site in cave bears, best
 described as homing behaviour, and that cave bears formed stable maternal
 social groups at least for hibernation. In contrast, brown bears do not
 show any strong association of mitochondrial lineage and cave, suggesting
 that these two closely related species differed in aspects of their
 behaviour and sociality. This difference is likely to have contributed to
 cave bear extinction, which occurred at a time in which competition for
 caves between bears and humans was likely intense and the ability to
 rapidly colonize new hibernation sites would have been crucial for the
 survival of a species so dependent on caves for hibernation as cave bears.
 Our study demonstrates the potential of ancient DNA to uncover patterns of
 behaviour and sociality in ancient species and populations, even those
 that went extinct many tens of thousands of years ago.
description: Fortes_et_al_2016_mtDNA_alignmentMtDNA sequence alignment used in Fortes et al. 2016 Mol Ecol. See README for further info.
DOI: 10.5061/dryad.1255v
title: Data from: Testing for biases in selection on avian reproductive traits and partitioning direct and indirect selection using quantitative genetic models

description: Key life history traits such as breeding time and clutch size are
 frequently both heritable and under directional selection, yet many
 studies fail to document micro-evolutionary responses. One general
 explanation is that selection estimates are biased by the omission of
 correlated traits that have causal effects on fitness, but few valid tests
 of this exist. Here we show, using a quantitative genetic framework and
 six decades of life-history data on two free-living populations of great
 tits Parus major, that selection estimates for egg-laying date and clutch
 size are relatively unbiased. Predicted responses to selection based on
 the Robertson-Price Identity were similar to those based on the
 multivariate breeder's equation, indicating that unmeasured covarying
 traits were not missing from the analysis. Changing patterns of phenotypic
 selection on these traits (for laying date, linked to climate change)
 therefore reflect changing selection on breeding values, and genetic
 constraints appear not to limit their independent evolution. Quantitative
 genetic analysis of correlational data from pedigreed populations can be a
 valuable complement to experimental approaches to help identify whether
 apparent associations between traits and fitness are biased by missing
 traits, and to parse the roles of direct versus indirect selection across
 a range of environments.
description: Hoge_Veluwe_Great_Tit_dataLife history data on great tits from Hoge Veluwe population, 1955-2013Pruned_pedigree_Hoge_VeluwePedigree for great tits Hoge Veluwe populationVlieland_East_Great_Tit_dataLife history data for Vlieland East population 1955-2013Pruned_pedigree_Vlieland_EastPedigree for Vlieland East great tit population
DOI: 10.5517/ccdc.csd.cc2nh2r0
title: CCDC 2457362: Experimental Crystal Structure Determination

description: Related Article: Phan N. Phu, Nathaniel S. Sickerman, Joseph W. Ziller, Michael P. Hendrich, A. S. Borovik
|2025|Z.Anorg.Allg.Chem.||e202500128|doi:10.1002/zaac.202500128
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pd059
title: CCDC 2484190: Experimental Crystal Structure Determination

description: Related Article: Tanawat Phumjan, Kasam Poonswat, Chatphorn Theppitak, Paratchata Batsomboon, Somsak Ruchirawat, Poonsakdi Ploypradith|2026|Chem.Asian J.|21|e70489|doi:10.1002/asia.70489
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pd07c
title: CCDC 2484192: Experimental Crystal Structure Determination

description: Related Article: Tanawat Phumjan, Kasam Poonswat, Chatphorn Theppitak, Paratchata Batsomboon, Somsak Ruchirawat, Poonsakdi Ploypradith|2026|Chem.Asian J.|21|e70489|doi:10.1002/asia.70489
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pd09f
title: CCDC 2484194: Experimental Crystal Structure Determination

description: Related Article: Tanawat Phumjan, Kasam Poonswat, Chatphorn Theppitak, Paratchata Batsomboon, Somsak Ruchirawat, Poonsakdi Ploypradith|2026|Chem.Asian J.|21|e70489|doi:10.1002/asia.70489
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.