cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6f27f
title: Data from: Weak phylogenetic signal in physiological traits of methane-oxidizing bacteria

description: The presence of phylogenetic signal is assumed to be ubiquitous. However,
 for microorganisms, this may not be true given that they display high
 physiological flexibility and have fast regeneration. This may result in
 fundamentally different patterns of resemblance, that is, in variable
 strength of phylogenetic signal. However, in microbiological inferences,
 trait similarities and therewith microbial interactions with its
 environment are mostly assumed to follow evolutionary relatedness. Here,
 we tested whether indeed a straightforward relationship between
 relatedness and physiological traits exists for aerobic methane-oxidizing
 bacteria (MOB). We generated a comprehensive data set that included 30 MOB
 strains with quantitative physiological trait information. Phylogenetic
 trees were built from the 16S rRNA gene, a common phylogenetic marker, and
 the pmoA gene which encodes a subunit of the key enzyme involved in the
 first step of methane oxidation. We used a Blomberg's K from
 comparative biology to quantify the strength of phylogenetic signal of
 physiological traits. Phylogenetic signal was strongest for physiological
 traits associated with optimal growth pH and temperature indicating that
 adaptations to habitat are very strongly conserved in MOB. However, those
 physiological traits that are associated with kinetics of methane
 oxidation had only weak phylogenetic signals and were more pronounced with
 the pmoA than with the 16S rRNA gene phylogeny. In conclusion, our results
 give evidence that approaches based solely on taxonomical information will
 not yield further advancement on microbial eco-evolutionary interactions
 with its environment. This is a novel insight on the connection between
 function and phylogeny within microbes and adds new understanding on the
 evolution of physiological traits across microbes, plants and animals.
description: Trait_data_JEB_krauseThis file includes the raw physiological trait data used for phylogenetic signal calculations.Phylogenetic_signal_blomberg_JEBThis file includes the results of each individual Blomberg's K signal calculation used to create figure 1 and table S1. In addition test statistic values are given as well.Read.meThis file includes a description of sequences which have been used.
DOI: 10.5061/dryad.1cn02
title: Data from: Colour in a new light: a spectral perspective on the quantitative genetics of carotenoid coloration

description: 1. Carotenoid-based colours are model traits for research on animal
 signalling and sexual selection but, whereas the consequences of variable
 expression have been extensively studied, its causes are rarely
 quantified. This issue is complicated by the composite nature of
 carotenoid-based colour patches, which combine pigments and a reflective
 background. Ultimately, the evolution of such colours will be determined
 by the processes that govern variable expression of these mechanisms. 2.
 We present a novel approach to assessing the quantitative genetics of
 colour expression, in which reflectance spectra are analysed directly,
 thereby avoiding the data loss and inherent subjectivity of summary colour
 variables. Further, the influence of the multiple component mechanisms can
 be distinguished in spectral analyses due to their contrasting
 wavelength-dependencies. 3. Using data from a six-year study of
 carotenoid-based plumage reflectance in wild great tits (Parus major), we
 employ a multi-parallel 'animal modelling' approach to estimate
 sources of variance for narrow (2nm) wavebands across the visible
 spectrum. 4. Moderate heritability estimates were limited to the
 violet-blue region of the spectrum, diagnostic of the carotenoid content
 of plumage being heritable. The natal environment effect was limited
 entirely to the violet-blue, again indicating that it relates to variation
 in carotenoid content of feathers. Other wavelengths were sensitive to
 annual and permanent environmental variation but only marginally
 influenced by additive genetic variation. Hence background reflectance is
 the component that is more sensitive to the environment. 5. Analysing
 reflectance spectra directly provided an objective perspective of the
 dynamics of colour expression that is not apparent when relying on summary
 colour scores. In this case, our results suggest that carotenoid
 deposition may be an effective target of selection and hence could explain
 the important role carotenoids frequently play in intraspecific
 signalling.
description: Wavelength-specific
 quantitative genetics datasheetFile containing
 reflectance measurements and other phenotypic data for all
 samples.Bagley great tit
 pedigreePedigree file (up to and
 including individuals first marked in 2013)Code for
 wavelength-specific analysesR code (running ASReml-R
 package) for parallel animal modelling analysis of 2nm
 wavebands.
DOI: 10.5061/dryad.3df32
title: Data from: The rise of army ants and their relatives: diversification of specialized predatory doryline ants

description: Background Army ants are dominant invertebrate predators in tropical and
 subtropical terrestrial ecosystems. Their close relatives within the
 dorylomorph group of ants are also highly specialized predators, although
 much less is known about their biology. We analyzed molecular data
 generated from 11 nuclear genes to infer a phylogeny for the major
 dorylomorph lineages, and incorporated fossil evidence to infer divergence
 times under a relaxed molecular clock. Results Because our results
 indicate that one subfamily and several genera of dorylomorphs are
 non-monophyletic, we propose to subsume the six previous dorylomorph
 subfamilies into a single subfamily, Dorylinae. We find the monophyly of
 Dorylinae to be strongly supported and estimate the crown age of the group
 at 87 (74–101) million years. Our phylogenetic analyses provide only weak
 support for army ant monophyly and also call into question a previous
 hypothesis that army ants underwent a fundamental split into New World and
 Old World lineages. Outside the army ants, our phylogeny reveals for the
 first time many old, distinct lineages in the Dorylinae. The genus
 Cerapachys is shown to be non-monophyletic and comprised of multiple
 lineages scattered across the Dorylinae tree. We recover, with strong
 support, novel relationships among these Cerapachys-like clades and other
 doryline genera, but divergences in the deepest parts of the tree are not
 well resolved. We find the genus Sphinctomyrmex, characterized by
 distinctive abdominal constrictions, to consist of two separate lineages
 with convergent morphologies, one inhabiting the Old World and the other
 the New World tropics. Conclusions While we obtain good resolution in many
 parts of the Dorylinae phylogeny, relationships deep in the tree remain
 unresolved, with major lineages joining each other in various ways
 depending upon the analytical method employed, but always with short
 internodes. This may be indicative of rapid radiation in the early history
 of the Dorylinae, but additional molecular data and more complete species
 sampling are needed for confirmation. Our phylogeny now provides a basic
 framework for comparative biological analyses, but much additional study
 on the behavior and morphology of doryline species is needed, especially
 investigations directed at the non-army ant taxa.
description: Phylogenetic data
 matrixThe full, aligned
 phylogenetic data matrix, including definitions of character partitions
 and exclusion sets, in Nexus format.Additional file
 4.txtTree
 filesThis file contains
 phylogenetic tree files for all reported phylogenetic analyses. See the
 attached ReadMe file for more information.Tree_files.zip
DOI: 10.5061/dryad.f4ks8
title: Data from: Phylogeny of Mycoplasma bovis isolates from Hungary based on multi locus sequence typing and multiple-locus variable-number tandem repeat analysis

description: Background: Mycoplasma bovis is an important pathogen causing pneumonia,
 mastitis and arthritis in cattle worldwide. As this agent is primarily
 transmitted by direct contact and spread through animal movements,
 efficient genotyping systems are essential for the monitoring of the
 disease and for epidemiological investigations. The aim of this study was
 to compare and evaluate the multi locus sequence typing (MLST) and the
 multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA)
 through the genetic characterization of M. bovis isolates from Hungary.
 Results: Thirty one Hungarian M. bovis isolates grouped into two clades by
 MLST. Two strains had the same sequence type (ST) as reference strain
 PG45, while the other twenty nine Hungarian isolates formed a novel clade
 comprising five subclades. Isolates originating from the same herds had
 the same STs except for one case. The same isolates formed two main clades
 and several subclades and branches by MLVA. One clade contained the
 reference strain PG45 and three isolates, while the other main clade
 comprised the rest of the strains. Within-herd strain divergence was also
 detected by MLVA. Little congruence was found between the results of the
 two typing systems. Conclusions: MLST is generally considered an
 intermediate scale typing method and it was found to be discriminatory
 among the Hungarian M. bovis isolates. MLVA proved to be an appropriate
 fine scale typing tool for M. bovis as this method was able to distinguish
 closely related strains isolated from the same farm. We recommend the
 combined use of the two methods for the genotyping of M. bovis isolates.
 Strains have to be characterized first by MLST followed by the fine scale
 typing of identical STs with MLVA.
description: Mycoplasma bovis MLST
 concatanate alignmentMycoplasma bovis MLST
 concatenate alignmentM.bovis_concatanate_alignment_02.06.fasFigure1Mycoplasma bovis MLST phylogenetic treeFigure2Mycoplasma bovis MLVA phylogenetic treeFigure3Mycoplasma bovis MLST and MLVA phylogenetic treesMLVA data
DOI: 10.5061/dryad.65364
title: Data from: Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast

description: Aneuploidy causes severe developmental defects and is a near universal
 feature of tumor cells. Despite its profound effects, the cellular
 processes affected by aneuploidy are not well characterized. Here, we
 examined the consequences of aneuploidy on the proteome of aneuploid
 budding yeast strains. We show that although protein levels largely scale
 with gene copy number, subunits of multi-protein complexes are notable
 exceptions. Posttranslational mechanisms attenuate their expression when
 their encoding genes are in excess. Our proteomic analyses further
 revealed a novel aneuploidy-associated protein expression signature
 characteristic of altered metabolism and redox homeostasis. Indeed
 aneuploid cells harbor increased levels of reactive oxygen species (ROS).
 Interestingly, increased protein turnover attenuates ROS levels and this
 novel aneuploidy-associated signature and improves the fitness of most
 aneuploid strains. Our results show that aneuploidy causes alterations in
 metabolism and redox homeostasis. Cells respond to these alterations
 through both transcriptional and posttranscriptional mechanisms.
description: Figure 1-Source Data
 1TMT
 and SILAC proteomeTable
 S1.xlsxFigure 2-Source Data
 1Transcriptome of
 aneuploid cellsTable
 S2.xlsxFigure 3-Source Data
 1Footprinting of disome
 VTable
 S3.xlsxFigure 5-Source Data
 1Macromolecular Complexes
 in aneuploid cellsTable
 S4b.xlsxFigure 6-Source Data
 1Aneuploid protein
 responseTable
 S5.xlsxFigure 7-Source Data
 1Proteome of disomes
 harboring the UBP6 deletionTable
 S6.xlsxFigure 8-Source Data
 1Strains
 utilizedTable
 S7.xlsxFigure 4-Source Data
 1Protein abundance of WT,
 disome II and disome V upon inhibition of protein turnover
 pathwaysSource Data
 4.xlsx
DOI: 10.5061/dryad.5nc25
title: Data from: A set of plastid loci for use in multiplex fragment length genotyping for intraspecific variation in Pinus (Pinaceae)

description: Premise of the study: Recently released Pinus plastome sequences support
 characterization of 15 plastid Simple Sequence Repeat (ptSSR) loci
 originally published for P. contorta and P. thunbergii. This allows
 selection of loci for single-tube PCR multiplexed genotyping in any
 subsection of the genus. Methods: Unique placement of primers and primer
 conservation across the genus were investigated, and a set of six loci
 were selected for single-tube multiplexing. We compare interspecific
 variation between ptSSRs and nucleotide sequences of ycf1 then test
 intraspecific variation for ptSSRs using 911 samples in the P. ponderosa
 species complex. Results: The ptSSR loci contain mononucleotide and
 complex repeats with additional length variation in flanking regions. They
 are not located in hypervariable regions and most primers are conserved
 across the genus. A single PCR per sample multiplexed for six loci yielded
 45 alleles in 911 samples. Discussion: The protocol allows efficient
 genotyping of many samples. The ptSSR loci are too variable for Pinus
 phylogenies but are useful for the study of genetic structure within and
 among populations. The multiplex method could easily be extended to other
 plant groups by choosing primers for ptSSR loci in a plastome alignment
 for the target group.
description: Alignment of 15 cpSSR
 primer pairs with Pinus plastomesThe published nucleotide
 sequences for 15 cpSSR primer pairs located within the aligned plastomes
 of 107 species of Pinus and six Pinaceae outgroups (TreeBase
 S12640).Wofford_APPS_alignment.fas
DOI: 10.5061/dryad.9g3cm
title: Data from: Genomic support for a moa-tinamou clade and adaptive morphological convergence in flightless ratites

description: One of the most startling discoveries in avian molecular phylogenetics is
 that the volant tinamous are embedded in the flightless ratites, but this
 topology remains controversial because recent morphological phylogenies
 place tinamous as the closest relative of a monophyletic ratite clade.
 Here, we integrate new phylogenomic sequences from 1,448 nuclear DNA loci
 totalling almost one million base pairs from the extinct little bush moa,
 Chilean tinamou and emu with available sequences from ostrich, elegant
 crested tinamou, four neognaths and the green anole. Phylogenetic analysis
 using standard homogeneous models and heterogeneous models robust to
 common topological artefacts recovered compelling support for ratite
 paraphyly with the little bush moa closest to tinamous within ratites.
 Ratite paraphyly was further corroborated by eight independent CR1
 retroposon insertions. Analysis of morphological characters reinterpreted
 on a 27-gene paleognath topology indicates that many characters are
 convergent in the ratites, probably as the result of adaptation to a
 cursorial life style.
description: UCE_concat_annotatedConcatenated nucleotide alignment for 854 ultraconserved genomic elements (UCEs) in nine avian species and green anole reptilian outgroupexons_concat_annotatedConcatenated nucleotide alignment for 594 protein-coding gene sequences in seven avian species and green anole reptilian outgroupretroelements.tarAligned palaeognath sequences for eight retroelement insertions and surrounding flanking sequence shared by moa and tinamous, and for one retroelement insertion shared by ratites (including moa) to the exclusion of tinamous (locus 7292)
DOI: 10.5061/dryad.d7639
title: Data from: A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0

description: We introduce molecularevolution.org, a publicly available gateway for
 high-throughput, maximum likelihood phylogenetic analysis powered by grid
 computing. The gateway features a garli 2.0 web service that enables a
 user to quickly and easily submit thousands of maximum likelihood tree
 searches or bootstrap searches that are executed in parallel on
 distributed computing resources. The garli web service allows one to
 easily specify partitioned substitution models using a graphical
 interface, and it performs sophisticated post-processing of phylogenetic
 results. Although the garli web service has been used by the research
 community for over three years, here we formally announce the availability
 of the service, describe its capabilities, highlight new features and
 recent improvements, and provide details about how the grid system
 efficiently delivers high-quality phylogenetic results.
description: Supplemental
 MaterialSupplemental material
 associated with the Systematic Biology article, "A Gateway for
 Phylogenetic Analysis Powered by Grid Computing Featuring GARLI
 2.0".garli_gateway_supplemental.pdfSupplemental Table 1A snapshot of information associated with The Lattice Project grid resources. The resources are shown sorted by composite throughput rating.supplemental_table_1.pdfSupplemental Figure 1The file repository belonging to an example registered user. Registered users may select from among the files found in their repository when specifying input files for a GARLI analysis, in addition to being able to upload new files.supplemental_figure_1.pdfSupplemental Figure 2The create job page found at molecularevolution.org, as viewed by a registered user.supplemental_figure_2.pdfSupplemental Figure 3The job status page found at molecularevolution.org, as viewed by a registered user.supplemental_figure_3.pdfSupplemental Figure 4The job details page found at molecularevolution.org, as viewed by a registered user.supplemental_figure_4.pdfSupplemental Figure 5The partitioned analysis portion of the create job page, currently showing a guided mode specification of two character sets and two data subsets.supplemental_figure_5.pdfSupplemental Figure 6Partial output summarizing the results of 100 search replicates for the best tree. Among the results of the post-processing displayed here are summary statistics that characterize the distribution of log-likelihood scores, symmetric tree distances (raw and normalized), and estimates of the number of search replicates required to recover the best tree topology at three probability levels.supplemental_figure_6.pdf
DOI: 10.5061/dryad.2b2dj
title: Data from: Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants

description: Microbial communities in plant roots provide critical links between above
 and belowground processes in terrestrial ecosystems. Variation in root
 communities has been attributed to plant host effects and microbial host
 preferences, as well as to factors pertaining to soil conditions,
 microbial biogeography and the presence of viable microbial propagules. To
 address hypotheses regarding the influence of plant host and soil
 biogeography on root fungal and bacterial communities we designed a
 trap-plant bioassay experiment. Replicate Populus, Quercus, and Pinus
 plants were grown in three soils originating from alternate field sites.
 Fungal and bacterial community profiles in the root of each replicate were
 assessed through multiplex 454 amplicon sequencing of 4 loci (i.e. 16S,
 SSU, ITS, LSU rDNA). Soil origin had a larger effect on fungal community
 composition than did host species, but the opposite was true for bacterial
 communities. Populus hosted the highest diversity of rhizospheric fungi
 and bacteria. Root communities on Quercus and Pinus were more similar to
 each other than to Populus. Overall, fungal root symbionts appear to be
 more constrained by dispersal and biogeography than by host availability.
description: PopulusBioassayGrowthHere are raw data pertaining to plant survivorship & height (growth) during the course of this experiment.16S_host_denoised_by_sampleID.fastafastq file with all denoised 16S sequences produced in this study16S_host_denoised_by_SampleID.fasta.tar.gz28S_host_denoised_by_SampleID.fasta.tarAll denoised 28S (rDNA) sequences produced in this study in fasta formatITS1_host_denoised_by_SampleID.fasta.tarAll denoised ITS1 sequences produced in this study in fasta format and by Sample IDITS2_host_denoised_by_SampleID.fasta.tarAll denoised ITS2 sequences produced in this study in fasta format and by Sample ID18S_host_denoised_by_SampleID.fasta.tarAll denoised 18S rDNA sequences produced in this study in fasta format and by Sample IDSampleMetadata_GenBank_AccessionsIncludes all the sample metadata associated with each sample, and BioProject data.bonito_samples_GB.xlsxITS1.fna_rep_setITS1 rep set of OTUs corresponding to OTUs in supplement 3ITS1_otu_tableSortedSoilITS1 OTU table (.xls format) corresponding to ITS1 OTU fasta fileGlomeromycota_454_Host_AllNexus file including 54 representative OTU sequences from this experiment and reference sequences
DOI: 10.82294/dvndi81gh
title: COPUS. Territorio: Caquetá. Sector: Educación. Año: 2025
title: Dato. Observación estructurada con el protocolo COPUS.

description: Información recopilada durante el año 2025 a partir de observaciones estructuradas realizadas con el protocolo COPUS, dirigidas a educadores artísticos pertenecientes a programas de formación en educación artística y cultural del sector Educación (educación formal) en el departamento de Caquetá.
DOI: 10.5061/dryad.6r52k
title: Data from: The founding of Mauritian endemic coffee trees by a synchronous long-distance dispersal event

description: The stochastic process of long-distance dispersal is the exclusive means
 by which plants colonize oceanic islands. Baker's rule posits that
 self-incompatible plant lineages are unlikely to successfully colonize
 oceanic islands because they must achieve a coordinated long-distance
 dispersal of sufficiently numerous individuals to establish an outcrossing
 founder population. Here, we show for the first time that Mauritian Coffea
 species are self-incompatible and thus represent an exception to
 Baker's rule. The genus Coffea (Rubiaceae) is composed of
 approximately 124 species with a paleotropical distribution. Phylogenetic
 evidence strongly supports a single colonization of the oceanic island of
 Mauritius from either Madagascar or Africa. We employ Bayesian divergence
 time analyses to show that the colonization of Mauritius was not a recent
 event. We genotype S-RNase alleles from Mauritian endemic Coffea, and
 using S-allele gene genealogies, we show that the Mauritian allelic
 diversity is confined to just seven deeply divergent Coffea S-RNase
 allelic lineages. Based on these data, we developed an individual-based
 model and performed a simulation study to estimate the most likely number
 of founding individuals involved in the colonization of Mauritius. Our
 simulations show that to explain the observed S-RNase allelic diversity,
 the founding population was likely composed of fewer than 31 seeds that
 were likely synchronously dispersed from an ancestral mainland species.
description: NowakPlastidData_4DryadPlastid sequence alignment used for divergence time estimation in the genus Coffea.NowakSAlleles_4DryadAlignment of Coffea S-RNase allele sequences used for evaluating the extent of trans-specific polymorphism between Madagascan/African Coffea and Mauritian Coffea.Nowak2014_DryadResults of individual-based simulations conducted to estimate the number of founding individuals responsible for the colonization of Mauritius by Coffea.