cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5kv72
title: Data from: Systematics of organic-walled microfossils from the ca. 780–740 Ma Chuar Group, Grand Canyon, Arizona

description: he ca. 780–740 Ma Chuar Group, Grand Canyon, Arizona, provides an
 exceptional record of life during the diversification of crown-group
 eukaryotes, just prior to the first Cryogenian glaciation. We document in
 detail the assemblage of organic-walled microfossils preserved in
 fine-grained siliciclastics throughout the unit. In contrast with earlier
 studies, we primarily used SEM to document fossil morphologies, augmented
 by transmitted light microscopy, FIB-SEM, and TEM. This resulted in the
 discovery of new species and the recognition of broad-ranging,
 intraspecific biological and taphonomic variation in other species.
 Twenty-two species and five unnamed morphotypes are described, including
 three new species: Kaibabia gemmulella, Microlepidopalla mira, and
 Volleyballia dehlerae; two new combinations: Galerosphaera walcottii and
 Lanulatisphaera laufeldii; and 17 previously described forms. The possible
 colonial green alga Palaeastrum dyptocranum Butterfield in Butterfield,
 Knoll, and Swett, 1994 and the index fossil Cerebrosphaera globosa
 (Ogurtsova and Sergeev, 1989) Sergeev and Schopf, 2010 (=C. buickii
 Butterfield, 1994) are described for the first time from Chuar rocks.
 Lanulatisphaera laufeldii, a locally abundant and globally widespread
 species characterized by submicrometer filamentous processes that form a
 reticulate network, may be a useful marker for the time interval just
 before the appearance of vase-shaped microfossils (VSMs) ca. 740 Ma.
 Organic-walled microfossil assemblages decline in diversity upsection,
 coincident with the appearance of VSMs and intermittent euxinia within the
 basin. Whether this pattern is due to preservational bias related to
 greater water depth or the higher TOC of upper Chuar rocks or instead
 reflects biotic turnover related to the spread of euxinic water masses in
 the basin is unknown.
description: Supplemental Data Table.
 Fossil occurrence data within the Chuar GroupLists sample names,
 their stratigraphic height, and the species, if any, that occur in each
 sample. Figure 2 in Porter and Riedman is based on these
 data.Supplemental
 data-Porter.xlsFig. S1. Map of SEM stub
 showing the location of holotype of Microlepidopalla mira Porter and
 RiedmanA high resolution tiff
 file showing an image of fossils on an SEM stub; the location of the
 holotype of Microlepidopalla mira Porter and Riedman is indicated in white
 text. (Other white text indicates the location of other specimens
 photographed by the authors.)Supplemental
 FigS1-Porter.tif
DOI: 10.5061/dryad.s30t4
title: Data from: Diabolical survival in Death Valley: recent pupfish colonization, gene flow, and genetic assimilation in the smallest species range on earth

description: One of the most endangered vertebrates, the Devils Hole pupfish Cyprinodon
 diabolis, survives in a nearly impossible environment: a narrow
 subterranean fissure in the hottest desert on earth, Death Valley. This
 species became a conservation icon after a landmark 1976 U.S. Supreme
 Court case affirming federal groundwater rights to its unique habitat.
 However, one outstanding question about this species remains unresolved:
 how long has diabolis persisted in this hellish environment? We used
 next-generation sequencing of over 13,000 loci to infer the demographic
 history of pupfishes in Death Valley. Instead of relicts isolated 2-3 Mya
 throughout repeated flooding of the entire region by inland seas as
 currently believed, we present evidence for frequent gene flow among Death
 Valley pupfish species and divergence after the most recent flooding 13
 kya. We estimate that Devils Hole was colonized by pupfish between 105 –
 830 years ago, followed by genetic assimilation of pelvic fin loss and
 recent gene flow into neighboring spring systems. Our results provide a
 new perspective on an iconic endangered species using the latest
 population genomic methods and support an emerging consensus that
 timescales for speciation are overestimated in many groups of rapidly
 evolving species.
description: Phylogenetic
 analysesfasta, nexus, and xml
 files used for phylogenetic analyses.phylogenetic
 analyses.zipSNP matrices used for
 PCA STRUCTURE TREEMIXplink and structure data
 formats with various filtering criteria.SNP
 matrices.zipdadi files for
 demographic analysisfasta and plink files
 used for dadi analysis of divergence time.
DOI: 10.5061/dryad.pr065
title: Data from: Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics

description: Understanding how environmental variation influences population genetic
 structure is important for conservation management because it can reveal
 how human stressors influence population connectivity, genetic diversity,
 and persistence. We used riverscape genetics modeling to assess whether
 climatic and habitat variables were related to neutral and adaptive
 patterns of genetic differentiation (population specific and pairwise FST)
 within five metapopulations (79 populations, 4,583 individuals) of
 steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA.
 Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found
 that climate-related variables (winter precipitation, summer maximum
 temperature, winter highest 5% flow events, and summer mean flow) often
 explained neutral and adaptive patterns of genetic differentiation within
 metapopulations, suggesting that climatic variation likely influences both
 demography (neutral variation) and local adaptation (adaptive variation).
 However, we did not observe consistent relationships between climate
 variables and FST across all metapopulations, underscoring the need for
 replication when extrapolating results from one scale to another (e.g.,
 basin-wide to the metapopulation scale). Sensitivity analysis
 (leave-one-population-out) revealed consistent relationships between
 climate variables and FST within three metapopulations; however, these
 patterns were not consistent in two metapopulations likely due to small
 sample sizes (N = 10). These results provide correlative evidence that
 climatic variation has shaped the genetic structure of steelhead
 populations and highlight the need for replication and sensitivity
 analyses in land and riverscape genetics.
description: Environmental, Genotype
 and GESTE input filesDataforDryad.zip
DOI: 10.5061/dryad.pc6sd
title: Data from: Genetic diversity of oilseed rape fields and feral populations in the context of coexistence with GM crops

description: Despite growing concern about transgenes escaping from fields, few studies
 have analysed the genetic diversity of crops in an agroecosystem over
 several years. Accurate information about the dynamics and relationship of
 the genetic diversity of crops in an agroecosystem is essential for risk
 assessment and policies concerning the containment of genetically modified
 crops and their coexistence with crops grown by conventional practices.
 Here, we analysed the genetic diversity of oilseed rape plants from fields
 and feral populations over 4 years in an agricultural landscape of 41 km2.
 We used exact compatibility and maximum likelihood assignment methods to
 assign these plants to cultivars. Even pure lines and hybrid cultivar seed
 lots contained several genotypes. The cultivar diversity in fields
 reflected the conventional view of agroecosystems quite well: that is,
 there was a succession of cultivars, some grown for longer than others
 because of their good performance, some used for one year and then
 abandoned, and others gradually adopted. Three types of field emerged:
 fields sown with a single cultivar, fields sown with two cultivars, and
 unassigned fields (too many cultivars or unassigned plants to reliably
 assign the field). Field plant diversity was higher than expected,
 indicating the persistence of cultivars that were grown for only one year.
 The cultivar composition of feral populations was similar to that of field
 plants, with an increasing number of cultivars each year. By using genetic
 tools, we found a link between the cultivars of field plants in a
 particular year and the cultivars of feral population plants in the
 following year. Feral populations on road verges were more diverse than
 those on path verges. All of these findings are discussed in terms of
 their consequences in the context of coexistence with genetically modified
 crops.
description: fields_Selommes_2002_to_2005Genotypes of OSR plants of fields from 2002 to 2005. S is for Seed, L for Leaf.pop_Selommes_2002_to_2005Genotypes of OSR plants from feral populations from 2002 to 2005. S is for seed and L for leaf.var_Selommes_2002_2005Genotypes of cultivars seed lots potentially sown from 2002 to 2005. Some cultivar names were changed due to confidentiality agreement with seeders.pop_caract_2002_to_2005Feral populations characteristics as Number of plants, Density and Threatments.sub_experiment_2007Genotypes of OSR plants sampled in S1 Appendix.
DOI: 10.5061/dryad.jb17n
title: Data from: On the accuracy of genomic selection

description: Genomic selection is focused on prediction of breeding values of selection
 candidates by means of high density of markers. It relies on the
 assumption that all quantitative trait loci (QTLs) tend to be in strong
 linkage disequilibrium (LD) with at least one marker. In this context, we
 present theoretical results regarding the accuracy of genomic selection,
 i.e., the correlation between predicted and true breeding values.
 Typically, for individuals (so-called test individuals), breeding values
 are predicted by means of markers, using marker effects estimated by
 fitting a ridge regression model to a set of training individuals. We
 present a theoretical expression for the accuracy; this expression is
 suitable for any configurations of LD between QTLs and markers. We also
 introduce a new accuracy proxy that is free of the QTL parameters and
 easily computable; it outperforms the proxies suggested in the literature,
 in particular, those based on an estimated effective number of independent
 loci (Me). The theoretical formula, the new proxy, and existing proxies
 were compared for simulated data, and the results point to the validity of
 our approach. The calculations were also illustrated on a new perennial
 ryegrass set (367 individuals) genotyped for 24,957 single nucleotide
 polymorphisms (SNPs). In this case, most of the proxies studied yielded
 similar results because of the lack of markers for coverage of the entire
 genome (2.7 Gb).
description: Data_files_Lolium_perenne_Rabier_et_al_2015_PLOS_ONEThe .zip file inclosed two files: Phenotypic_data_RGA_PBarre_12112015 with the Plant growth rate of 405 genotypes of perennial ryegrass and Genotypic_data_RGA_PBarre_12112015 with the genotypic data (SNP scoring 0, 1, 2 and the average per marker for missing data) of the same 405 genotypes.Data_files_Lolium_perenne_Rabier_etal_2015.zip
DOI: 10.5061/dryad.jk53j
title: Data from: Ants determine their next move at rest: motor planning and causality in complex systems

description: To find useful work to do for their colony, individual eusocial animals
 have to move, somehow staying attentive to relevant social information.
 Recent research on individual Temnothorax albipennis ants moving inside
 their colony’s nest found a power-law relationship between a movement’s
 duration and its average speed; and a universal speed profile for
 movements showing that they mostly fluctuate around a constant average
 speed. From this predictability it was inferred that movement durations
 are somehow determined before the movement itself. Here, we find similar
 results in lone T. albipennis ants exploring a large arena outside the
 nest, both when the arena is clean and when it contains chemical
 information left by previous nest-mates. This implies that these movement
 characteristics originate from the same individual neural and/or
 physiological mechanism(s), operating without immediate regard to social
 influences. However, the presence of pheromones and/or other cues was
 found to affect the inter-event speed correlations. Hence we suggest that
 ants’ motor planning results in intermittent response to the social
 environment: movement duration is adjusted in response to social
 information only between movements, not during them. This environmentally
 flexible, intermittently responsive movement behaviour points towards a
 spatially allocated division of labour in this species. It also prompts
 more general questions on collective animal movement and the role of
 intermittent causation from higher to lower organizational levels in the
 stability of complex systems.
description: Ant exploration
 trajectories36 ant exploration
 trajectories, each ant tracked for 45 minutes. First column is time,
 columns 2 and 3 are coordinates x and y. (0,0) is centre of arena (nest
 entrance). File names indicate treatment 'NC' - no cleaning and
 'C' - cleaning, and colony, e.g. 'C1' is colony 1. For
 example, 'C-C1-1' - cleaning treatment, colony 1, ant 1. Note
 that the first ants for NC were not used in the study (first ant of
 sequence enters a clean arena).
DOI: 10.5061/dryad.5d3rq
title: Data from: A simple approach for maximizing the overlap of phylogenetic and comparative data

description: Biologists are increasingly using curated, public data sets to conduct
 phylogenetic comparative analyses. Unfortunately, there is often a
 mismatch between species for which there is phylogenetic data and those
 for which other data are available. As a result, researchers are commonly
 forced to either drop species from analyses entirely or else impute the
 missing data. A simple strategy to improve the overlap of phylogenetic and
 comparative data is to swap species in the tree that lack data with
 ‘phylogenetically equivalent’ species that have data. While this procedure
 is logically straightforward, it quickly becomes very challenging to do by
 hand. Here, we present algorithms that use topological and taxonomic
 information to maximize the number of swaps without altering the structure
 of the phylogeny. We have implemented our method in a new R package
 phyndr, which will allow researchers to apply our algorithm to empirical
 data sets. It is relatively efficient such that taxon swaps can be quickly
 computed, even for large trees. To facilitate the use of taxonomic
 knowledge, we created a separate data package taxonlookup; it contains a
 curated, versioned taxonomic lookup for land plants and is interoperable
 with phyndr. Emerging online data bases and statistical advances are
 making it possible for researchers to investigate evolutionary questions
 at unprecedented scales. However, in this effort species mismatch among
 data sources will increasingly be a problem; evolutionary informatics
 tools, such as phyndr and taxonlookup, can help alleviate this issue.
description: Land plant taxonomic
 lookup tableThis dataset is a stable
 version (version 1.0.1) of the dataset contained in the taxonlookup R
 package (see https://github.com/traitecoevo/taxonlookup for the most
 recent version). It contains a taxonomic reference table for 16,913 genera
 of land plants along with the number of recognized species in each
 genus.plant_lookup.csv
DOI: 10.5061/dryad.55758
title: Data from: Climate interacts with anthropogenic drivers to determine extirpation dynamics

description: Theoretical studies suggest that the dynamics of a species’ range during a
 period of climate change depends upon the existence and interplay of
 various ecological and evolutionary processes. Here we tested how
 anthropogenic pressures contribute to climate-mediated extirpation
 patterns of 32 freshwater fish species over the last 20 yr. We contrasted
 two extreme cases to determine whether extirpations were governed by
 patterns of climate exposure, assuming full adaptation of species to local
 climate, or instead by the interplay between climate exposure and the
 distance from the centroid of species’ climatic niches, assuming a fixed
 niche, and asked whether anthropogenic disturbances interact with these
 climatic drivers. We found strong support for the fixed niche hypothesis,
 but showed that species-specific local adaptation to climate may also be
 important in determining extirpation dynamics. We also demonstrated that
 anthropogenic disturbance acted in concert with climate, ultimately
 determining population changes. Our results add novel evidence that
 unravelling the direct links between range dynamics and climate requires a
 multifaceted treatment, and that accounting for the cumulative effects of
 anthropogenic pressures deserves special attention in the context of
 climate change.
description: Temporal dynamics for
 the 32 speciesTemporal dynamics for
 the 32 species between 8 consecutives time periods at 794 sites across the
 French hydrographic network.data_Species_dynamics.txtEnvironmental characteristics of the sitesSpatial and environmental characteristics of the 794 sites.data_Env.txtDataset 1980-1991Temporally independent dataset composed of 3347 sites collected before major climatic changes (1980-1991)data_Pref.txtSpeciesCodes
DOI: 10.5281/zenodo.18339116
title: Research data for publication "Phenotype switching in highly invasive resistant to vemurafenib and cobimetinib melanoma cells"

description: This research aimed to determine and characterize the features related to phenotype switching occurring in melanoma cells due to the acquisition of resistance to clinically used BRAF/MEK inhibitors. We derived two melanoma cell lines resistant to vemurafenib (a BRAF inhibitor) and cobimetinib (an MEK inhibitor). Due to the significant impact of invasion on cancer progression, we focused our further research on this process.

Our analysis showed a greater capacity for migration and invasion of resistant melanoma cells compared to controls, as well as an increase in the level of RUNX2 (runt-related transcription factor 2). Moreover, examined cells exhibited higher adhesion to the surface and were more spread. These cells also formed more focal adhesions. Furthermore, we noticed an increased level of α-parvin and vinculin in resistant cells, as well as an elevated activation of FAK (focal adhesion kinase). Resistance was additionally accompanied by rearrangement of the actin cytoskeleton. Examined cells formed more stress fibers compared to control cells. YAP/TAZ localization became much more nuclear in the resistant ones. The amount of invadopodia was increased, which was reflected by elevated secretion and activation of proteases, as well as altered expression of their inhibitors.

Data submitted to the repository are initial, unprocessed experiment results. Individual folders (named after the type of research they concern) contain the output data for all technical repetitions of the experiments performed, and a .docx file with a description of the samples and the research method used. Data concerning the adhesion assay are numerical values of the obtained XTT test results. Data concerning the Western blotting method are photos of membranes with bands present on them corresponding to specific proteins. Data concerning the protease array are photos of membranes with dots present on them corresponding to specific proteases. Data obtained as a result of qPCR analysis are presented in the form of Excel files containing Ct (threshold cycle) values for selected genes expressed by cells at the mRNA level. Data concerning qualitative and quantitative analysis of microscopic images are photos of cells (tiff) and Excel files with quantitative data. Data concerning the 2D and 3D wound healing assay are photos of cells (tiff) and Excel files with quantitative data. Data concerning the gelatin zymography method are photos of gels with bands present on them corresponding to specific proteases. Data concerning the matrix metalloproteinase 14 activity assay are numerical values of obtained results in an Excel file.
DOI: 10.5281/zenodo.18339115
title: Research data for publication "Phenotype switching in highly invasive resistant to vemurafenib and cobimetinib melanoma cells"

description: This research aimed to determine and characterize the features related to phenotype switching occurring in melanoma cells due to the acquisition of resistance to clinically used BRAF/MEK inhibitors. We derived two melanoma cell lines resistant to vemurafenib (a BRAF inhibitor) and cobimetinib (an MEK inhibitor). Due to the significant impact of invasion on cancer progression, we focused our further research on this process.

Our analysis showed a greater capacity for migration and invasion of resistant melanoma cells compared to controls, as well as an increase in the level of RUNX2 (runt-related transcription factor 2). Moreover, examined cells exhibited higher adhesion to the surface and were more spread. These cells also formed more focal adhesions. Furthermore, we noticed an increased level of α-parvin and vinculin in resistant cells, as well as an elevated activation of FAK (focal adhesion kinase). Resistance was additionally accompanied by rearrangement of the actin cytoskeleton. Examined cells formed more stress fibers compared to control cells. YAP/TAZ localization became much more nuclear in the resistant ones. The amount of invadopodia was increased, which was reflected by elevated secretion and activation of proteases, as well as altered expression of their inhibitors.

Data submitted to the repository are initial, unprocessed experiment results. Individual folders (named after the type of research they concern) contain the output data for all technical repetitions of the experiments performed, and a .docx file with a description of the samples and the research method used. Data concerning the adhesion assay are numerical values of the obtained XTT test results. Data concerning the Western blotting method are photos of membranes with bands present on them corresponding to specific proteins. Data concerning the protease array are photos of membranes with dots present on them corresponding to specific proteases. Data obtained as a result of qPCR analysis are presented in the form of Excel files containing Ct (threshold cycle) values for selected genes expressed by cells at the mRNA level. Data concerning qualitative and quantitative analysis of microscopic images are photos of cells (tiff) and Excel files with quantitative data. Data concerning the 2D and 3D wound healing assay are photos of cells (tiff) and Excel files with quantitative data. Data concerning the gelatin zymography method are photos of gels with bands present on them corresponding to specific proteases. Data concerning the matrix metalloproteinase 14 activity assay are numerical values of obtained results in an Excel file.