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370 results for “plant material”
Figure S13 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S13 (lef).'oot-to-tip length variances per gene tree. The cut-off of 0.009 is indicated with a dashed vertical line.
Figure S26 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S26. Tanglegram comparing the ASTRAL single-copy genes phylogeny (Figure S14) with the PhyloBayes phylogeny (Figure S23).
Figure S23 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S23. Phylogeny of Caesalpinioideae. PhyloBayes species tree. Posterior probability support values are only shown for nodes with a posterior probability <1.
Figure S10 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S10 (lef). Numbers of genes with potential paralogs per sample. The eleven samples with the most potential paralogs are labelled.
Figure S25 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S25. Tanglegram comparing the ASTRAL single-copy genes phylogeny (Figure S14) with the RAxML amino acid single-copy genes phylogeny (Figure S20).
Figure S28 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S28. Levels of topological congruence between phylogenies generated in different ways, estimated as Robinson-Foulds (RF) distances between species trees. Exact values are in Table S17. Thickness of the connecting lines reflects RF distance. Abbreviations are as follows 'AS' = ASTRAL-3; 'RA' = RAxML; '997' = all genes without paralogs, '997p'= all genes with paralogs, 'SC' = single-copy genes; 'NT' = nucleotide alignment; 'AA' = amino acid alignment; 'PB' = PhyloBayes phylogeny; 'CP' = chloroplast phylogeny.
Figure S40 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S40. Phyloregionalization of Australia using the metachronogram. Subfigures show clustering results with two to eight phyloregions, as well as the results of phyloregionalization analyses using the geographic residuals of phylogenetic turnover, and ancient phylogenetic turnover with a cut-off of 5, 10, and 20 million years.
Figure S44 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S44. Phyloregionalization per continent using the genus-level Mimosoid phylogeny (rather than the metachronogram). Caption otherwise as for Figure 3.
Figure S41 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S41. Phyloregionalization of the global tropics using the metachronogram. Subfigures show clustering results with two to eight phyloregions, as well as the results of phyloregionalization analyses using the geographic residuals of phylogenetic turnover, and ancient phylogenetic turnover with a cut-off of 5, 10, and 20 million years.
Figure S39 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S39. Phyloregionalization of Asia using the metachronogram. Subfigures show clustering results with two to eight phyloregions, as well as the results of phyloregionalization analyses using the geographic residuals of phylogenetic turnover, and ancient phylogenetic turnover with a cut-off of 5, 10, and 20 million years.
Figure S32 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S32 (lef). Internode certainty values based on the 821 single-copy gene trees mapped onto the single-copy genes ASTRAL species tree (Figure S14). For each node, the upper number shows the quartet-based Extended Quadripartition Internode Certainty (EQP-IC) score calculated with QuartetScores, and the lower number shows the bipartition-based Internode Certainty All score calculated with PhyParts, both rounded down to two digits. Boxes are coloured based on unrounded values: green for values ≥ 0.5, yellow for values ≥ 0 and <0.5, and red for values <0. Branch lengths are set equal for easier visualisation. Inset depicts a correlation plot between the two measures.
Figure S33 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S33 (right).'esults of ASTRAL's polytomy test based on the 821 single-copy gene trees mapped onto the single-copy genes ASTRAL species tree (Figure S14). Node numbers are tests of the null hypothesis that a branch should be replaced by a polytomy. Only node numbers> 0.05 are shown. Branch lengths are set equal for easier visualisation.
Figure S31 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S31. Gene tree incongruence mapped onto the time-calibrated version of the phylogenomic backbone of Caesalpinioideae. Each branch is coloured to reflect the ratio of total supporting versus total conflicting gene trees as determined by PhyParts. Clades named by Koenen et al. (24) are labelled. Two recent radiations in Madagascar, one in the Dichrostachys clade and one in Albizia, are highlighted.
Figure S36 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S36. Phyloregionalization of North America using the metachronogram. Subfigures show clustering results with two to eight phyloregions, as well as the results of phyloregionalization analyses using the geographic residuals of phylogenetic turnover, and ancient phylogenetic turnover with a cut-off of 5, 10, and 20 million years.
Figure S14 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S14. Phylogeny of Caesalpinioideae. ASTRAL species tree based on the 821 single-copy gene trees. Local posterior probability support values are only shown for nodes with a local posterior probability <1. Branch lengths are expressed in coalescent units. Terminal branches were assigned an arbitrary uniform length for visual clarity.
Supplementary materials to: Nano-Strainer: a workflow for identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads
<p>In the paper associated with this dataset, a workflow is presented which enables the identification of single-/low-copy nuclear molecular markers for a plant group of interest, by mining data from a small representative target capture experiment done using a commercial probe kit and Oxford Nanopore long-read sequencing. The proposed pipeline first assesses sequence variability contained in the data from targeted loci and assigns reads to their respective genes, via a combined BLAST/clustering procedure. Cluster consensus sequences are then examined based on four pre-defined criteria presumably indicative for absence of paralogy. This is done by calculating four specialized indices; loci are ranked according to their performance in these indices, and top-scoring loci are considered putatively single- or low-copy. The approach can be applied to any probe set. As it relies on long reads, the contribution also provides template workflows for processing Nanopore-based target capture data. Identified loci can be used for NGS amplicon sequencing. For detection of possibly remaining paralogy in these data, which might occur in groups with rampant paralogy, the long-read assembly tool CANU is employed. The presented workflow can be useful for researchers dealing with reticulate or polyploidization phylogenetic histories in plants.</p> <p>The present dataset contains several documents supplementing the original paper. Its most important elements are a detailed description (alongside two graphical workflow figures) of all methods employed in the study, suitable for reproducing the steps of the workflow and also the wet-lab work. The workflow employs a collection of BASH, Python and R scripts which is available here, together with a detailed account on command line use in Linux. Also, reference sequences for the identified markers can be found as well as sequence alignments derived from the amplicon sequencing.</p>
Dataset for manuscript "Plants as inspiration for material‑based sensing and actuation in soft robots and machines"
<p>The dataset includes data for Figure 2 in the article "Plants as inspiration for material-based sensing and actuation in soft robots and machines<em>" MRS Bulletin</em> (2023). https://doi.org/10.1557/s43577-022-00470-8</p>
Supplementary materials to: Nano-Strainer: a workflow for identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads
Open the record for dataset details and reuse information.
Supplementary Material for Frontiers Plant Genetics and Genomics 'Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality'
<p>Authors</p> <p>Zhian N. Kamvar, Jonah C. Brooks, and Niklaus J. Grünwald</p>
Data for article Pesticide seed dressings can affect the activity of various soil organisms and reduce decomposition rate of plant material, BMC Ecology
<p>Raw data for article "Pesticide seed dressings can affect the activity of various soil organisms and reduce decomposition rate of plant material" published in BMC Ecology</p>
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