cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q2h4s
title: Stage-specific changes in the water, Na+, Cl- and K+ contents of organelles during apoptosis, demonstrated by a targeted cryo correlative analytical approach

description: Many studies have demonstrated changes in the levels of several ions
 during apoptosis, but a few recent studies have reported conflicting
 results concerning the changes in water content in apoptotic cells. We
 used a correlative light and cryo-scanning transmission electron
 microscopy method to quantify water and ion/element contents
 simultaneously at a nanoscale resolution in the various compartments of
 cells, from the onset to the end of apoptosis. We used stably transfected
 HeLa cells producing H2B-GFP to identify the stages of apoptosis in cells
 and for a targeted elemental analysis within condensed chromatin,
 nucleoplasm, mitochondria and the cytosol. We found that the compartments
 of apoptotic cells contained, on average, 10% more water than control
 cells. During mitochondrial outer membrane permeabilization, we observed a
 strong increase in the Na+ and Cl- contents of the mitochondria and a
 strong decrease in mitochondrial K+ content. During the first step in
 apoptotic volume decrease (AVD), Na+ and Cl- levels decreased in all cell
 compartments, but remained higher than those in control cells. Conversely,
 during the second step of AVD, Na+ and Cl- levels increased considerably
 in the nucleus and mitochondria. During these two steps of AVD, K+ content
 decreased steadily in all cell compartments. We also determined in vivo
 ion status during caspase-3 activity and chromatin condensation. Finally,
 we found that actinomycin D-tolerant cells had water and K+ contents
 similar to those of cells entering apoptosis but lower Na+ and Cl-
 contents than both cells entering apoptosis and control cells.
description: Figure
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DOI: 10.5061/dryad.q62j0
title: Data from: Exploration of genetic architecture through sib-ship reconstruction in advanced breeding population of Eucalyptus nitens

description: Accurate inference of relatedness between individuals in breeding
 population contributes to the precision of genetic parameter estimates,
 effectiveness of inbreeding management and the amount of genetic progress
 delivered from breeding programs. Pedigree reconstruction has been proven
 to be an efficient tool to correct pedigree errors and recover hidden
 relatedness in open pollinated progeny tests but the method can be limited
 by the lack of parental genotypes and the high proportion of alien pollen
 from outside the breeding population. Our study investigates the
 efficiency of sib-ship reconstruction in an advanced breeding population
 of Eucalyptus nitens with only partially tracked pedigree. The sib-ship
 reconstruction allowed the identification of selfs (4% of the sample) and
 the exploration of their potential effect on inbreeding depression in the
 traits studied. We detected signs of inbreeding depression in diameter at
 breast height and growth strain while no indications were observed in wood
 density, wood stiffness and tangential air-dry shrinkage. After the
 application of a corrected sib-ship relationship matrix, additive genetic
 variance and heritability were observed to increase where signs of
 inbreeding depression were initially detected. Conversely, the same
 genetic parameters for traits that appeared to be free of inbreeding
 depression decreased in size. It therefore appeared that greater genetic
 variance may be due, at least in part, to contributions from inbreeding in
 these studied populations rather than a removal of inbreeding as is
 traditionally thought.
description: PedigreePedigree for the studied populationPhenotype fileFile containing phenotypic data for the studied populationPhen_for_Publication.csvGenotypic dataData folder containing genotypes and their associated qualitative scores (GenTrain score and GenCall)GenData.zip
DOI: 10.5061/dryad.fh0m2
title: Data from: Quantification and statistical analysis methods for vessel wall components from stained images with Masson's trichrome

description: Purpose: To develop a digital image processing method to quantify
 structural components (smooth muscle fibers and extracellular matrix) in
 the vessel wall stained with Masson’s trichrome, and a statistical method
 suitable for small sample sizes to analyze the results previously
 obtained. Methods: The quantification method comprises two stages. The
 pre-processing stage improves tissue image appearance and the vessel wall
 area is delimited. In the feature extraction stage, the vessel wall
 components are segmented by grouping pixels with a similar color. The area
 of each component is calculated by normalizing the number of pixels of
 each group by the vessel wall area. Statistical analyses are implemented
 by permutation tests, based on resampling without replacement from the set
 of the observed data to obtain a sampling distribution of an estimator.
 The implementation can be parallelized on a multicore machine to reduce
 execution time. Results: The methods have been tested on 48 vessel wall
 samples of the internal saphenous vein stained with Masson’s trichrome.
 The results show that the segmented areas are consistent with the
 perception of a team of doctors and demonstrate good correlation between
 the expert judgments and the measured parameters for evaluating vessel
 wall changes. Conclusion: The proposed methodology offers a powerful tool
 to quantify some components of the vessel wall. It is more objective,
 sensitive and accurate than the biochemical and qualitative methods
 traditionally used. The permutation tests are suitable statistical
 techniques to analyze the numerical measurements obtained when the
 underlying assumptions of the other statistical techniques are not met.
description: Vessel wall images from
 the great saphenous vein stained with Masson's
 trichromeMicroscopic images of
 the vessel wall segments from the great saphenous vein stained with
 Masson's trichrome and taken with 4x magnification. Control samples
 come from subjects undergoing judicial autopsy. After checking through the
 medical history and physical inspection that the body showed no signs of
 venous insufficiency, internal saphenous vein segments were removed and
 immediately processed for histological studies. Samples classified as
 "competent" (normal venous flow) and "incompetent"
 (retrograde venous flow, reflux) were obtained from patients diagnosed
 with venous insufficiency of the great saphenous vein. The diagnosis was
 made by venous Doppler ultrasound. The tissue samples were taken and
 immediately processed for histological studies according to standard
 techniques.ImageDatabase.zip
DOI: 10.5061/dryad.t77q4
title: Data from: A phylogenomic analysis of turtles

description: Molecular analyses of turtle relationships have overturned prevailing
 morphological hypotheses and prompted the development of a new taxonomy.
 Here we provide the first genome-scale analysis of turtle phylogeny. We
 sequenced 2,381 ultraconserved element (UCE) loci representing a total of
 1,718,154 bp of aligned sequence. Our sampling includes 32 turtle taxa
 representing all 14 recognized turtle families and an additional six
 outgroups. Maximum likelihood, Bayesian, and species tree methods produce
 a single resolved phylogeny. This robust phylogeny shows that proposed
 phylogenetic names correspond to well-supported clades, and this topology
 is more consistent with the temporal appearance of clades and
 paleobiogeography. Future studies of turtle phylogeny using fossil turtles
 should use this topology as a scaffold for their morphological
 phylogenetic analyses. Molecular analyses of turtle relationships have
 overturned prevailing morphological hypotheses and prompted the
 development of a new taxonomy. Here we provide the first genome-scale
 analysis of turtle phylogeny. We sequenced 2,381 ultraconserved element
 (UCE) loci representing a total of 1,718,154 bp of aligned sequence. Our
 sampling includes 32 turtle taxa representing all 14 recognized turtle
 families and an additional six outgroups. Maximum likelihood, Bayesian,
 and species tree methods produce a single resolved phylogeny. This robust
 phylogeny shows that proposed phylogenetic names correspond to
 well-supported clades, and this topology is more consistent with the
 temporal appearance of clades and paleobiogeography. Future studies of
 turtle phylogeny using fossil turtles should use this topology as a
 scaffold for their morphological phylogenetic analyses.
description: Incomplete dataset -
 concatenated alignmentsDataset used to run
 analysis with MrBayes. Up to 25% missing data is allowed at each
 locus.incomplete_dataset2_partitioned_MrB2_500k_fixed.nexComplete dataset - concatenated alignmentsDataset used to run analysis with MrBayes. No missing data (e.g., taxa) was present at any locus.complete_dataset2_MrB500k.nexComplete dataset - individual mafft alignmentscomplete_dataset2_mafft-nexus.tar.gzIncomplete dataset - individual mafft alignmentsincomplete_dataset2_mafft-nexus.tar.gzMrBayes tree - incomplete datasetincomplete_dataset2_partitioned_MrB2_500k_final.treMrBayes tree - complete datasetcomplete_dataset2_MrB500_final.treRAxML tree - complete datasetcomplete_dataset2_clean_RAxML10k.treRAxML tree - incomplete datasetNote: 'autoMRE' was used to determine number of bootstrap replicates to run.incomplete_dataset2_RAx_autoMRE.trePhybase trees - complete datasetGenetrees, bootstraps, consensus treescomplete.phybase.zipPhybase trees - incomplete datasetgenetrees, bootstrap trees, consensus treesincomplete.phybase.zip
DOI: 10.5061/dryad.s5587
title: Data from: Spectral and temporal acoustic features modulate response irregularities within primary auditory cortex columns

description: Assemblies of vertically connected neurons in the cerebral cortex form
 information processing units (columns) that participate in the
 distribution and segregation of sensory signals. Despite well-accepted
 models of columnar architecture, functional mechanisms of inter-laminar
 communication remain poorly understood. Hence, the purpose of the present
 investigation was to examine the effects of sensory information features
 on columnar response properties. Using acute recording techniques,
 extracellular response activity was collected from the right hemisphere of
 eight mature cats (felis catus). Recordings were conducted with
 multichannel electrodes that permitted the simultaneous acquisition of
 neuronal activity within primary auditory cortex columns. Neuronal
 responses to simple (pure tones), complex (noise burst and frequency
 modulated sweeps), and ecologically relevant (con-specific vocalizations)
 acoustic signals were measured. Collectively, the present investigation
 demonstrates that despite consistencies in neuronal tuning (characteristic
 frequency), irregularities in discharge activity between neurons of
 individual A1 columns increase as a function of spectral (signal
 complexity) and temporal (duration) acoustic variations.
description: Multi-unit responses to
 acoustic signals within A1 columnsThe data set consists of
 eight multi-unit electrophysiology experiments located within a single
 .zip file. Acoustic feature (signal type and duration) are in subfolders
 where data rasters for each recording session conducted can be found.
 Columns represent time and rows trial number. Data is presented as Matlab
 files.DRYAD.zip
DOI: 10.5061/dryad.ht0hs
title: Data from: How does ascertainment bias in SNP analyses affect inferences about population history?

description: Background: The selection of variable sites for inclusion in genomic
 analyses can influence results, especially when exemplar populations are
 used to determine polymorphic sites. We tested the impact of ascertainment
 bias on the inference of population genetic parameters using empirical and
 simulated data representing the three major continental groups of cattle:
 European, African, and Indian. We simulated data under three demographic
 models. Each simulated data set was subjected to three ascertainment
 schemes: (I) random selection; (II) geographically biased selection; and
 (III) selection biased toward loci polymorphic in multiple groups.
 Empirical data comprised samples of 25 individuals representing each
 continental group. These cattle were genotyped for 47,506 loci from the
 bovine 50 K SNP panel. We compared the inference of population histories
 for the empirical and simulated data sets across different ascertainment
 conditions using FST and principal components analysis (PCA). Results:
 Bias toward shared polymorphism across continental groups is apparent in
 the empirical SNP data. Bias toward uneven levels of within-group
 polymorphism decreases estimates of F ST between groups.
 Subpopulation-biased selection of SNPs changes the weighting of principal
 component axes and can affect inferences about proportions of admixture
 and population histories using PCA. PCA-based inferences of population
 relationships are largely congruent across types of ascertainment bias,
 even when ascertainment bias is strong. Conclusions: Analyses of
 ascertainment bias in genomic data have largely been conducted on human
 data. As genomic analyses are being applied to non-model organisms, and
 across taxa with deeper divergences, care must be taken to consider the
 potential for bias in ascertainment of variation to affect inferences.
 Estimates of FST, time of separation, and population divergence as
 estimated by principal components analysis can be misleading if this bias
 is not taken into account.
description: Data from: How does
 ascertainment bias in SNP analyses affect inferences about population
 history?IPython notebooks
 containing the simulation and analyses code for the manuscript (named
 simulations.ipynb and analyses.ipynb respectively) and empirical and
 simulated data used in the manuscript.AscBiasDryad.zip
DOI: 10.5061/dryad.nf2c425n
title: Data from: Multilocus estimation of selfing and its heritability

description: We describe a new method of estimating the selfing rate (S) in a mixed
 mating population based on a population structure approach that accounts
 for possible intergenerational correlation in selfing rate, giving rise to
 an estimate of the upper limit for heritability of selfing rate (h^2). A
 correlation between generations in selfing rate is shown to affect one-
 and two-locus probabilities of identity by descent. Conventional estimates
 of selfing rate based on a population structure approach are positively
 biased by intergenerational correlation in selfing. Multilocus genotypes
 of individuals are used to give maximum-likelihood estimates of S and h^2
 in the presence of scoring artifacts. Our multilocus estimation of selfing
 rate and its heritability (MESH) method was tested with simulated data for
 a range of conditions. Selfing rate estimates from MESH have low bias and
 root mean squared error, while estimates of the heritability of selfing
 rate have more uncertainty. Increasing the number of individuals in a
 sample helps to reduce bias and root mean squared error more than
 increasing the number of loci of sampled individuals. Improved estimates
 of selfing rate, as well as estimates of its heritability, can be obtained
 with this method, although a large number of loci and individuals are
 needed to achieve best results.
description: READMEvariableSh2datavariablepopSizenumLocidata
DOI: 10.5061/dryad.sc193
title: Data from: Late Quaternary deep-sea ostracode taxonomy of the eastern North Atlantic Ocean

description: Taxonomic revision and re-evaluation of the eastern North Atlantic
 deep-sea ostracodes are conducted based on late Quaternary sediments from
 Ocean Drilling Program (ODP) Hole 982A, Rockall Plateau, eastern North
 Atlantic. Twenty one genera and 51 species were examined and
 (re-)illustrated with high-resolution scanning electron microscopy images.
 Six new species are described: Polycope lunaris, Argilloecia labri,
 Bythoceratina nuda, Cytheropteron colesoabyssorum, Cytheropteron
 colesopunctatum, and Cytheropteron paramediotumidum. Excellent fossil
 ostracode preservation in this sediment core enabled us to provide a
 robust taxonomic baseline of the eastern North Atlantic deep-sea
 ostracodes for application to palaeoceanographical, palaeoecological, and
 biogeographical studies.
description: High resolution Fig.
 2Yasuhara_Fig_2.tifHigh resolution Fig. 3Yasuhara_Fig_3.tifHigh resolution Fig. 4Yasuhara_Fig_4-1.tifHigh resolution Fig. 5Yasuhara_Fig_5.tifHigh resolution Fig. 6Yasuhara_Fig_6-1.tifHigh resolution Fig. 7Yasuhara_Fig_7.tifHigh resolution Fig. 8Yasuhara_Fig_8.tifHigh resolution Fig. 9Yasuhara_Fig_9.tifHigh resolution Fig. 10Yasuhara_Fig_10.tifHigh resolution Fig. 11Yasuhara_Fig_11.tifHigh resolution Fig. 12Yasuhara_Fig_12-1.tifHigh resolution Fig. 13Yasuhara_Fig_13-1.tifHigh resolution Fig. 14Yasuhara_Fig_14-1.tifHigh resolution Fig. 15Yasuhara_Fig_15-1.tifHigh resolution Fig. 16Yasuhara_Fig_16.tif
DOI: 10.5061/dryad.q2r3b1f
title: Data from: The choice of universal primers and the characteristics of the species mixture determines when DNA metabarcoding can be quantitative.

description: DNA metabarcoding is a technique used to survey biodiversity in many
 ecological settings, but there are doubts about whether it can provide
 quantitative results, i.e. the proportions of each species in the mixture
 as opposed to a species list. While there are several experimental studies
 that report quantitative metabarcoding results, there are a similar number
 that fail to do so. Here we provide the rationale to understand under what
 circumstances the technique can be quantitative. Basically, we simulate a
 mixture of DNA of S species with a defined initial abundance distribution.
 In the simulated PCR, each species increases its concentration following a
 certain amplification efficiency. The final DNA concentration will reflect
 the initial one when the efficiency is similar for all species; otherwise,
 the initial and final DNA concentrations would be poorly related. Although
 there are many known factors that modulate amplification efficiency, we
 focused on the number of primer-template mismatches, arguably the most
 important one. We used 15 common primers pairs targeting the mitochondrial
 COI region and the mitogenomes of ca. 1200 insect species. The results
 showed that some primers pairs produced quantitative results under most
 circumstances, whereas some other primers failed to do so. Many species,
 and a high diversity within the mixture, helped the metabarcoding to be
 quantitative. In conclusion, depending on the primer pair used in the PCR
 amplification and on the characteristics of the mixture analysed (i.e.,
 high species richness, low evenness), DNA metabarcoding can provide a
 quantitative estimate of the relative abundances of different species.
description: R scripts and data
 filesPinol_etal.zip
DOI: 10.5061/dryad.v883p
title: Data from: Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila

description: In many species, genomic data have revealed pervasive adaptive evolution
 indicated by the fixation of beneficial alleles. However, when selection
 pressures are highly variable along a species' range or through time
 adaptive alleles may persist at intermediate frequencies for long periods.
 So called “balanced polymorphisms” have long been understood to be an
 important component of standing genetic variation, yet direct evidence of
 the strength of balancing selection and the stability and prevalence of
 balanced polymorphisms has remained elusive. We hypothesized that
 environmental fluctuations among seasons in a North American orchard would
 impose temporally variable selection on Drosophila melanogaster that would
 drive repeatable adaptive oscillations at balanced polymorphisms. We
 identified hundreds of polymorphisms whose frequency oscillates among
 seasons and argue that these loci are subject to strong, temporally
 variable selection. We show that these polymorphisms respond to acute and
 persistent changes in climate and are associated in predictable ways with
 seasonally variable phenotypes. In addition, our results suggest that
 adaptively oscillating polymorphisms are likely millions of years old,
 with some possibly predating the divergence between D. melanogaster and D.
 simulans. Taken together, our results are consistent with a model of
 balancing selection wherein rapid temporal fluctuations in climate over
 generational time promotes adaptive genetic diversity at loci underlying
 polygenic variation in fitness related phenotypes.
description: Liftover file to convert
 D. simulans version 2 genome coordinates to D. melanogaster v5 (dm3)
 coordinatesLiftover file for use
 with UCSC liftOver utility for converting genomic coordinates of the
 version 2 D. simulans genome (Hu et al 2012) to version 5 (dm3) D.
 melanogaster genome.ds2_to_dm3.liftOver.gzAnntotated VCF fileAnnotated VCF file containing allele frequency and read depths of the 14 samples described in Bergland et al. Annotations include p- and q-values from models of seasonality and clinality; genic annotations; average frequencies; and, quality filters. This VCF file only contains SNPs with average minor allele frequency &gt; 0.15.6d_v7.3_output.vcf.gz
DOI: 10.5061/dryad.t430k
title: Data from: Testing the role of ecology and life history in structuring genetic variation across a landscape: a trait-based phylogeographic approach

description: Hypotheses to explain phylogeographic structure traditionally invoke
 geographic features, but often fail to provide a general explanation for
 spatial patterns of genetic variation. Organisms' intrinsic
 characteristics might play more important roles than landscape features in
 determining phylogeographic structure. We developed a novel comparative
 approach to explore the role of ecological and life-history variables in
 determining spatial genetic variation and tested it on frog communities in
 Panama. We quantified spatial genetic variation within 31 anuran species
 based on mitochondrial DNA sequences, for which hierarchical approximate
 Bayesian computation analyses rejected simultaneous divergence over a
 common landscape. Regressing ecological variables, on genetic divergence
 allowed us to test the importance of individual variables revealing that
 body size, current landscape resistance, geographic range, biogeographic
 origin and reproductive mode were significant predictors of spatial
 genetic variation. Our results support the idea that phylogeographic
 structure represents the outcome of an interaction between organisms and
 their environment, and suggest a conceptual integration we refer to as
 trait-based phylogeography.
description: Alignments_COI_16S_Per_comparisonAlignment of COI and 16S mitochondrial genes per comparison and per species. Two comparisons were performed, comparison 1 between Cana and Brewster (15 species) and comparison 2 between El Copé and Brewster (30 species).Paz_et_al_locality_data_for_ENMThis excel file has georeferenced locality data used to construct ENM´s for all 30 species. It also describes wether data points were used for model training or model testing.GLM code and data fileR code to replicate GLM construction and evaluation and database used to perform the analyses.GLMs.zipBioclimatic data used for ENM´sBioclimatic data used for model construction and projection to the last glacial maximum was obtained from the worldclim database (worldclim.org). Both present and past layers were cropped to the study area.used_cropped_bioclimatic_data.zip