cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pv332
title: Data from: Dated plant phylogenies resolve Neogene climate and landscape evolution in the Cape Floristic Region

description: In the context of molecularly-dated phylogenies, inferences informed by
 ancestral habitat reconstruction can yield valuable insights into the
 origins of biomes, palaeoenvironments and landforms. In this paper, we use
 dated phylogenies of 12 plant clades from the Cape Floristic Region (CFR)
 in southern Africa to test hypotheses of Neogene climatic and geomorphic
 evolution. Our combined dataset for the CFR strengthens and refines
 previous palaeoenvironmental reconstructions based on a sparse, mostly
 offshore fossil record. Our reconstructions show remarkable consistency
 across all 12 clades with regard to both the types of environments
 identified as ancestral, and the timing of shifts to alternative
 conditions. They reveal that Early Miocene land surfaces of the CFR were
 wetter than at present and were dominated by quartzitic substrata. These
 conditions continue to characterize the higher-elevation settings of the
 Cape Fold Belt, where they have fostered the persistence of ancient fynbos
 lineages. The Middle Miocene (13–17 Ma) saw the development of perennial
 to weakly-seasonal arid conditions, with the strongly seasonal rainfall
 regime of the west coast arising ~6.5–8 Ma. Although the Late Miocene may
 have seen some exposure of the underlying shale substrata, the present-day
 substrate diversity of the CFR lowlands was shaped by Pliocene-Pleistocene
 events. Particularly important was renewed erosion, following the
 post-African II uplift episode, and the reworking of sediments on the
 coastal platform as a consequence of marine transgressions and tectonic
 uplift. These changes facilitated adaptive radiations in some, but not
 all, lineages studied.
description: Georeferenced locality
 databaseThis file contains
 accurate point locality data for the taxa used in the study. Collection
 records with locality descriptions were obtained from various herbaria in
 South Africa (BOL, NBG, PRE) or from individual authors (e.g. G
 Galley).CFRGeorefDatabase_2014.xlsx
DOI: 10.5061/dryad.d048q
title: Data from: Covariation in abscission force and terminal velocity of wind-borne sibling seeds alters long distance dispersal projections

description: 1. Despite the fact that seeds are unlikely to be identical—even among
 siblings within a maternal individual—dispersal models typically use one
 mean trait value to represent the ability of an entire species to
 disperse. Previous work has shown that the environmental conditions under
 which individuals leave the maternal site strongly affect how far seeds
 will travel. However, less is known about how trait variation within
 individuals contributes to dispersal or how such variation might interact
 with abiotic factors. 2. Here, we develop the use of an ergometer in a
 novel application to investigate variation in seed traits, specifically
 the force required for seed abscission and seed terminal velocity,
 exhibited by seeds from different locations within maternal capitula of
 the invasive species Carduus nutans (Asteraceae). 3. We find that seeds
 from the center of capitula are significantly easier to liberate and have
 slower falling velocities than siblings found near the edge of capitula.
 When abscission force is positively correlated with terminal velocity,
 slowly falling, easily abscised seeds are projected to travel much further
 than the average seed on slow winds. 4. Our experimental and theoretical
 results, which together show that within-individual variation can strongly
 affect model projections of species dispersal, have important implications
 for our broader understanding of population spread rates, the spatial
 structure of populations, metapopulation connectivity, and gene flow in
 the landscape.
description: SeedPulls_dataThis file contains the raw and synthesized data from laboratory trials in which the force required to remove a seed from C, nutans capitula was measured with an ergometer.TVdrops_dataThis data is comprised of terminal velocity trials on seeds extracted from maternal capitula in different regions of the capitular disk.
DOI: 10.5061/dryad.7gg25
title: Data from: Previously unknown evolutionary groups dominate the ssDNA gokushoviruses in oxic and anoxic waters of a coastal marine environment

description: Metagenomic studies have revealed that ssDNA phages from the family
 Microviridae subfamily Gokushovirinae are widespread in aquatic
 ecosystems. It is hypothesized that gokushoviruses occupy specialized
 niches, resulting in differences among genotypes traversing water column
 gradients. Here, we use degenerate primers that amplify a fragment of the
 gene encoding the major capsid protein to examine the diversity of
 gokushoviruses in Saanich Inlet, a seasonally anoxic fjord on the coast of
 Vancouver Island, British Columbia. Amplicon sequencing of samples from
 the mixed oxic surface (10 m) and deeper anoxic (200 m) layers indicated a
 diverse assemblage of gokushoviruses, with greater richness at 10 m than
 200 m. A comparison of amplicon sequences with sequences selected on the
 basis of RFLP patterns from eight surface samples collected over a
 one-year period revealed that gokushovirus diversity was higher in spring
 and summer during stratification, and lower in fall and winter after
 deep-water renewal, consistent with seasonal variability within
 gokushovirus populations. Phylogenetic analysis of clustered amplicons
 revealed at least five new phylogenetic clades of previously unknown
 sequences, with the most abundant group associated with viruses that
 infect SUP05, a ubiquitous and abundant member of marine oxygen minimum
 zones. Our results provide persuasive evidence that, while specific
 gokushovirus genotypes may have a narrow host range, hosts for
 gokushoviruses in Saanich Inlet consist of a wide range of bacterial taxa,
 including SUP05, a taxonomic clade of gamma proteobacterial sulfur
 oxidizers. Members of SUP05 are abundant in Saanich Inlet and involved in
 carbon, nitrogen, and sulfur cycling along the redoxline; thus,
 gokushoviruses are likely important mortality agents of these bacteria and
 have consequent influences on biogeochemical cycling in this system.
description: raw_readsRaw reads divided by primers of 454 pyrosequencing of gokushovirus degenerate PCR products from Saanich Inlet (raw_reads.zip).OTUsOTUs at 97% for each of the primer bins (OTUs.zip).alignments_and_treesAlignment and tree of the major capsid protein phylogeny (alignments_and_trees.zip).
DOI: 10.5061/dryad.sv70f
title: Data from: Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly

description: A comprehensive in silico analysis of 71 species representing the
 different taxonomic classes and physiological genre of the domain Archaea
 was performed. These organisms differed in their physiological attributes,
 particularly oxygen tolerance and energy metabolism. We explored the
 diversity and similarity in the codon usage pattern in the genes and
 genomes of these organisms, emphasizing on their core cellular pathways.
 Our thrust was to figure out whether there is any underlying similarity in
 the design of core pathways within these organisms. Analyses of codon
 utilization pattern, construction of hierarchical linear models of codon
 usage, expression pattern and codon pair preference pointed to the fact
 that, in the archaea there is a trend towards biased use of synonymous
 codons in the core cellular pathways and the Nc-plots appeared to display
 the physiological variations present within the different species. Our
 analyses revealed that aerobic species of archaea possessed a larger
 degree of freedom in regulating expression levels than could be accounted
 for by codon usage bias alone. This feature might be a consequence of
 their enhanced metabolic activities as a result of their adaptation to the
 relatively O2-rich environment. Species of archaea, which are related from
 the taxonomical viewpoint, were found to have striking similarities in
 their ORF structuring pattern. In the anaerobic species of archaea, codon
 bias was found to be a major determinant of gene expression. We have also
 detected a significant difference in the codon pair usage pattern between
 the whole genome and the genes related to vital cellular pathways, and it
 was not only species-specific but pathway specific too. This hints towards
 the structuring of ORFs with better decoding accuracy during translation.
 Finally, a codon-pathway interaction in shaping the codon design of
 pathways was observed where the transcription pathway exhibited a
 significantly different coding frequency signature.
description: Codon pair
 ratioThe pathway/system -wise
 codon pair ratio data for all the species generated using
 Anaconda.codon pair
 ratio.xlsxCodon
 CountThe total codon counts
 for each of the 71 organsim per pathway.All 71 genomes 5
 pathwaysThis archive contains
 the different codon usage indices value for all the 71 species calculated
 separately for each of the five pathway systems and curated
 individually.All 71 Whole
 GenomesThis archive contains
 the different codon usage indices values for the whole genome of the 71
 species separately.
DOI: 10.82294/dvnu7i4sy
title: COPUS. Territorio: Barrancabermeja. Sector: Cultura. Año 2024
title: Dato. Observación estructurada con el protocolo COPUS.

description: Información recopilada durante el año 2024 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 Cultura (educación informal) en la ciudad de Barrancabermeja.
DOI: 10.5061/dryad.38417
title: Data from: Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa

description: Squamate reptiles (lizards and snakes) are a pivotal group whose
 relationships have become increasingly controversial. Squamates include
 &gt;9000 species, making them the second largest group of terrestrial
 vertebrates. They are important medicinally and as model systems for
 ecological and evolutionary research. However, studies of squamate biology
 are hindered by uncertainty over their relationships, and some consider
 squamate phylogeny unresolved, given recent conflicts between molecular
 and morphological results. To resolve these conflicts, we expand existing
 morphological and molecular datasets for squamates (691 morphological
 characters and 46 genes, for 161 living and 49 fossil taxa, including a
 new set of 81 morphological characters and adding two genes from published
 studies) and perform integrated analyses. Our results resolve higher-level
 relationships as indicated by molecular analyses, and reveal hidden
 morphological support for the molecular hypothesis (but not vice-versa).
 Furthermore, we find that integrating molecular, morphological, and
 paleontological data leads to surprising placements for two major fossil
 clades (Mosasauria and Polyglyphanodontia). These results further
 demonstrate the importance of combining fossil and molecular information,
 and the potential problems of estimating the placement of fossil taxa from
 morphological data alone. Thus, our results caution against estimating
 fossil relationships without considering relevant molecular data, and
 against placing fossils into molecular trees (e.g. for dating analyses)
 without considering the possible impact of molecular data on their
 placement.
description: combined-all-taxa-ML.phyCombined DNA and morphological data for all taxa of squamate studyweighted combined analysesData files used in the combined data weighted analyses where the DNA data was recoded to 63 binary characters.morphological partition analysesData sets used in the morphological partition analysessquamateDNA-BayesThis data file used for the DNA only Bayesian analyses of extant taxa. The same data and alignments used in the ML and parsimony analyses.morphology_alltaxaMrBayes formatted file for Bayesian analyses including ordered multistate characters. The same character matrix was also used in the Bayesian analyses and parsimony analyses with all characters as unordered.morphology_alltaxa_MLMorphological data matrix for ML analyses of all taxa.
DOI: 10.5061/dryad.7qc22
title: Data from: Evolution of the bamboos (Bambusoideae; Poaceae): a full plastome phylogenomic analysis

description: Background: Bambusoideae (Poaceae) comprise three distinct and
 well-supported lineages: tropical woody bamboos (Bambuseae), temperate
 woody bamboos (Arundinarieae) and herbaceous bamboos (Olyreae).
 Phylogenetic studies using chloroplast markers have generally supported a
 sister relationship between Bambuseae and Olyreae. This suggests either at
 least two origins of the woody bamboo syndrome in this subfamily or its
 loss in Olyreae. Results: Here a full chloroplast genome (plastome)
 phylogenomic study is presented using the coding and noncoding regions of
 13 complete plastomes from the Bambuseae, eight from Olyreae and 10 from
 Arundinarieae. Trees generated using full plastome sequences support the
 previously recovered monophyletic relationship between Bambuseae and
 Olyreae. In addition to these relationships, several unique plastome
 features were uncovered including the first mitogenome-to-plastome
 horizontal gene transfer observed in monocots. Conclusions: Phylogenomic
 agreement with previous published phylogenies reinforces the validity of
 these studies. Additionally, this study presents the first published
 plastomes from Neotropical woody bamboos and the first full plastome
 phylogenomic study performed within the herbaceous bamboos. Although the
 phylogenomic tree presented in this study is largely robust, additional
 studies using nuclear genes support monophyly in woody bamboos as well as
 hybridization among previous woody bamboo lineages. The evolutionary
 history of the Bambusoideae could be further clarified using
 transcriptomic techniques to increase sampling among nuclear orthologues
 and investigate the molecular genetics underlying the development of woody
 and floral tissues.
description: Full plastome
 matrixThis matrix contains
 full aligned plastomes for 31 bamboo species and two outgroup taxa
 (Pooideae, Ehrhartoideae). Gapped positions have been removed along with
 one inverted repeat region.Bamboo33sppmatrix.phy
DOI: 10.5061/dryad.49q24
title: Data from: The phylogenetic utility and functional constraint of microRNA flanking sequences

description: MicroRNAs (miRNAs) have recently risen to prominence as novel factors
 responsible for post-transcriptional regulation of gene expression. miRNA
 genes have been posited as highly conserved in the clades in which they
 exist. Consequently, miRNAs have been used as rare genome change
 characters to estimate phylogeny by tracking their gain and loss. However,
 their short length (21–23 bp) has limited their perceived utility in
 sequenced-based phylogenetic inference. Here, using reference taxa with
 established phylogenetic relationships, we demonstrate that miRNA
 sequences are of high utility in quantitative, rather than in qualitative,
 phylogenetic analysis. The clear orthology among miRNA genes from
 different species makes it straightforward to identify and align these
 sequences from even fragmentary datasets. We also identify significant
 sequence conservation in the regions directly flanking miRNA genes, and
 show that this too is of utility in phylogenetic analysis, as well as
 highlighting conserved regions that will be of interest to other fields.
 Employing miRNA sequences from 12 sequenced drosophilid genomes, together
 with a Tribolium castaneum outgroup, we demonstrate that this approach is
 robust using Bayesian and maximum-likelihood methods. The utility of these
 characters is further demonstrated in the rhabditid nematodes and
 primates. As next-generation sequencing makes it more cost-effective to
 sequence genomes and small RNA libraries, this methodology provides an
 alternative data source for phylogenetic analysis. The approach allows
 rapid resolution of relationships between both closely related and rapidly
 evolving species, and provides an additional tool for investigation of
 relationships within the tree of life.
description: All sequences and
 alignments used in studyZipped sequences (fasta)
 and alignments (multiple formats) for all genes used in
 analysesSupplementaryFile3.zip
DOI: 10.5061/dryad.2s361
title: Data from: Pseudomonas putida and Pseudomonas fluorescens species group recovery from human homes varies seasonally and by environment

description: By shedding light on variation in time as well as in space, long-term
 biogeographic studies can help us define organisms’ distribution patterns
 and understand their underlying drivers. Here we examine distributions of
 Pseudomonas in and around 15 human homes, focusing on the P. putida and P.
 fluorescens species groups. We describe recovery from 10,941 samples
 collected during up to 8 visits per home, occurring on average 2.6 times
 per year. We collected a mean of 141 samples per visit, from sites in most
 rooms of the house, from the surrounding yards, and from human and pet
 occupants. We recovered Pseudomonas in 9.7% of samples, with the majority
 of isolates being from the P. putida and P. fluorescens species groups
 (approximately 62% and 23% of Pseudomonas samples recovered respectively).
 Although representatives of both groups were recovered from every season,
 every house, and every type of environment sampled, recovery was highly
 variable across houses and samplings. Whereas recovery of P. putida group
 was higher in summer and fall than in winter and spring, P. fluorescens
 group isolates were most often recovered in spring. P. putida group
 recovery from soils was substantially higher than its recovery from all
 other environment types, while higher P. fluorescens group recovery from
 soils than from other sites was much less pronounced. Both species groups
 were recovered from skin and upper respiratory tract samples from healthy
 humans and pets, although this occurred infrequently. This study indicates
 that even species that are able to survive under a broad range of
 conditions can be rare and variable in their distributions in space and in
 time. For such groups, determining patterns and causes of stochastic and
 seasonal variability may be more important for understanding the processes
 driving their biogeography than the identity of the types of environments
 in which they can be found.
description: Data - Remold etal
 Seasonal Diffs in Household PUG and PFG DistributionsRaw data describing
 sampled sites and strains recoveredGenbank Accession Nos -
 Remold etal Seasonal Diffs in Household PUG and PFG
 DistributionsGenbank Accession
 Numbers associated with each Pseudomonas strain (SRP)
DOI: 10.15159/phytop.161
title: Jõksi

description: Phytoplankton biomass, diversity and abundance in samples collected from Lake Jõksi during the period 1953-1991.
DOI: 10.5061/dryad.b91t7
title: Data from: High precipitation and seeded species competition reduce seeded shrub establishment during dryland restoration

description: Drylands comprise 40% of Earth's land mass and are critical to food
 security, carbon sequestration, and threatened and endangered wildlife.
 Exotic weed invasions, overgrazing, energy extraction, and other factors
 have degraded many drylands, and this has placed an increased emphasis on
 dryland restoration. The increased restoration focus has generated a
 wealth of experience, innovations and empirical data, yet the goal of
 restoring diverse, native, dryland plant assemblages composed of grasses,
 forbs, and shrubs has generally proven beyond reach. Of particular concern
 are shrubs, which often fail to establish or establish at trivially low
 densities. We used data from two Great Plains, USA coal mines to explore
 factors regulating shrub establishment. Our predictor data related to
 weather and restoration (e.g., seed rates, rock cover) variables, and our
 response data described shrub abundances on fields of the mines. We found
 that seeded non-shrubs, especially grasses, formed an important
 competitive barrier to shrub establishment: With every one standard
 deviation increase in non-shrub seed rate, the probability shrubs were
 present decreased ~0.1 and shrub cover decreased ~35%. Since new fields
 were seeded almost every year for &gt;20 years, the data also provided
 a unique opportunity to explore effects of stochastic drivers (i.e.,
 precipitation, year effects). With every one standard deviation increase
 in precipitation the first growing season following seeding, the
 probability shrubs were present decreased ~0.07 and shrub cover decreased
 ~47%. High precipitation appeared to harm shrubs by increasing grass
 growth/competition. Also, weak evidence suggested shrub establishment was
 better in rockier fields where grass abundance/competition was lower.
 Multiple lines of evidence suggest reducing grass seed rates below levels
 typically used in Great Plains restoration would benefit shrubs without
 substantially impacting grass stand development over the long term. We
 used Bayesian statistics to estimate effects of seed rates and other
 restoration predictors probabilistically to allow knowledge of the
 predictors' effects to be refined through time in an adaptive
 management framework. We believe this framework could improve restoration
 planning in a variety of systems where restoration outcomes remain highly
 uncertain and ongoing restoration efforts are continually providing new
 data of value for reducing the uncertainty.
description: montana weather
 dataThis is the
 precipitation data used in the papervegThis file contains the
 plant and rock cover data used in the paper.rec
 historyThis file contains data
 on reclamation practices used on the fields in the
 study.seed mixes shrub
 projectThis file provides the
 seed mixes used on fields in the studies. The rec history file can be used
 to link seed mixes to fields.