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202 results for “phylogenomic analysis”
Data set: Australia's hidden radiation - phylogenomic analysis reveals rapid Miocene radiation of blindsnakes
<p>This repository contains the additional raw data to accompany our paper entitled "Australia’s hidden radiation: phylogenomic analysis reveals rapid Miocene radiation of blind snakes."</p> <p>This project is part of the AusARG Initiative funded by BioPlatforms Australia.</p> <p>Raw sequences data can be downloaded from the BioPlatforms downloads portal: https://data.bioplatforms.com/dataset?q=ticket%3ABPAOPS-1196</p> <p><strong>Information about files</strong></p> <ol> <li>ASTRAL_tree_SqCL_AHE.tre - output from ASTRAL-III just with SqCL data + outgroups</li> <li>ASTRAL_tree_SqCL_AHE_Ramphotyphlops.tre - same with above but also including additional <em>Ramphotyphlops </em>genes.</li> <li>mcmctree_1.txt - mcmcfile output from MCMCTree analysis using all SkewT or SkewNormal distribution priors.</li> <li>mcmctree_2.txt - mcmcfile output from MCMCTree analysis using SkewT, SkewNormal, and cauchy distribution priors. **This is the tree used in our publication**</li> <li>mcmctree_strategy1.tre - output phylogeny 1</li> <li>mcmctree_strategy2.tre - output phylogeny 2</li> <li>IQTREE_gcf_scf.nex - gene concordance and site factors for mcmctree_strategy2.tre</li> </ol> <p>tree_data/ folder contains concatenated gene trees (IQTREE) and corresponding shortcut coalescent method (ASTRAL-III) tree.</p> <p>Should there be questions regarding the code and data set, please contact the corresponding author.</p>
Phylogenomic analysis of cell-surface receptors and downstream signaling components in the plant lineage
<p>Here we identified cell-surface receptors and downstream signaling components from the genomes of 350 plant species. </p><p>Zip file contains:</p><p>Folder 'seqeunces for downstream signaling components' - FASTA and TREE files of the identified downstream signaling components.</p><p>Folder 'sequences for cell-surface receptors' - FASTA and TREE files of the identified cell-surface receptors.</p><p>Folder 'Specific analysis' - Contains specific analysis for the identified cell-surface receptors.</p><p>Subfolder 'ID analysis' - Contains information on ID clusters and motifs analysis in IDs.</p><p>Subfolder 'LRR motif gap analysis' - Contains information on small (10-29 aa) and large (30-90) gaps between LRR motifs in RLPs and RLKs.</p><p>Subfolder 'LRR-RLK & LRR-RLP phylogenetic analysis' - Contains FASTA and TREE files of the specific domain/regions (C3, C3-F, eJM-TM-cJM, and all) in LRR-RLPs and LRR-RLKs. This subfolder also contains the specific amino acid, charge and motif analysis in this region (see C3F-end features.xlsx).</p><p>Protein counts per species file - Contains the total number of each protein family/subfamily in each of the 350 species.</p><p>simpleToFullNames (translator file)- Translator file for the original ID of each gene. </p>
Data from: Revised evolutionary and taxonomic synthesis for parrots (order: Psittaciformes) guided by phylogenomic analysis
<p>Parrots (Order: Psittaciformes) are a diverse clade that are easily distinguishable from other birds. Despite the clear characters that define the Psittaciformes (hooked bills, zygodactylous feet, and plumage that is often predominantly green or red), relative morphological uniformity among parrots has made taxonomic classification a fraught endeavor for over a century. Parrot systematics were propelled forward when DNA sequencing data shed insights into higher- and species-level relationships. However, despite these significant advances, major gaps in taxon sampling and uncertainty in relationships remained due to inferring phylogenetic relationships with short fragments of DNA. Recent work using genome-wide molecular markers with nearly complete parrot species-level sampling has brought clarity to many of the remaining outstanding questions on taxonomic relationships. Here, we build on this work by including four additional species to present a taxonomic revision of Psittaciformes better aligned with its evolutionary tree. We infer maximum likelihood and time-calibrated phylogenies for parrots, present accounts for 106 genera, compare how our findings relate to previous work, and highlight future areas of research. The family-group nomenclature we propose reflects deep evolutionary divergences with diagnosable synapomorphies that are commensurate across comparable ranks in psittaciform clades. We erect three new family-group names at the rank of tribe (Brotogerini Smith, Thom and Joseph, 2024; Neophemini Schodde, Smith, Thom and Joseph, 2024; Bolbopsittacini Smith, Thom and Joseph, 2024). We elevate one tribe to subfamily rank for the cacatuid genus <em>Probosciger</em> and we restrict usage of the recently introduced tribe Touitini to its type-genus <em>Touit</em>. At shallower taxonomic scales, recognition of more rather than fewer genera addresses issues of paraphyly or high discordance in morphological and genomic characters at those levels. We support many reinstatements of older generic names advocated in recent decades and we further reinstate five valid, available generic names not widely used in recent literature if at all (<em>Licmetis</em>, <em>Gymnopsittacus</em>, <em>Clarkona</em>, <em>Suavipsitta</em>, <em>Cardeos</em>). We advocate the retention of <em>Vini</em> Lesson, 1833 over <em>Coriphilus</em> Wagler, 1832 based on preliminary examination showing substantially more frequent usage of the former. We redraw generic limits in some other cases (e.g., <em>Bolborhynchus</em> parrotlets and allies) and this includes recognizing fewer genera than recently proposed for the <em>Psittacula</em> <em>sensu lato</em> ringneck parakeets. Our revised classification of parrots addresses many longstanding taxonomic questions including those that have arisen through the acquisition of genetic data. It provides context for the temporal origins of psittaciform clades and the taxonomic and phenotypic diversification throughout their evolutionary history. We hope that it will be a benchmark guiding further taxonomic study as well as for downstream analyses in many other fields.</p>
Supplementary materials for Phylogenomics and genetic analysis of solvent-producing Clostridium species
<p>The genus <em>Clostridium</em> is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 <em>C. beijerenckiI, </em>57 <em>C. saccharobutylicum</em>, 4 <em>C. saccharoperbutylacetonicum</em>, 5 <em>C. butyricum</em>, 7 <em>C. acetobutylicum</em>, and 3 <em>C. tetanomorphum </em>genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or <em>Escherichia coli </em>for enhanced chemical production. Recently, gene sequences from this collection were used to engineer <em>Clostridium autoethanogenum</em>, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production<em>, </em>as well as butanol, butanoic acid, hexanol and hexanoic acid production. </p>
Data for phylogenomic analysis of chelicerate gene family evolution
<p>We used phylogenomics to investigate patterns of gene family evolution across ticks and other chelicerates, which include a diverse array of parasites. We used phylogenetic profiling and trait-association tests to predict gene families that may enable parasitic species to feed on hosts undetected for prolonged periods (>1 day). This release accompanies the pub, “<a href="https://doi.org/10.57844/arcadia-4e3b-bbea">Comparative phylogenomic analysis of Chelicerates points to gene families associated with long-term suppression of host detection</a>." Please see the pub for more information.</p> <ul> <li>chelicerata-v1-10062023.zip contains the outputs from NovelTree that are needed as inputs for phylogenetic profiling.</li> <li>annotated.zip contains gene annotations used to do orthogroup filtering.</li> <li>tx2gene.tsv has presence/absence of expression for each Amblyomma americanum transcript. </li> <li>chelicerate_proteome_preprocessing_outputs.zip contains the outputs of chelicerate protein data curation.</li> <li>chelicerata-v1-parameterfile.json & chelicerata-v1-samplesheet.csv were inputs for setting up the initial NovelTree run.</li> <li>2024-06-24-all-chelicerate-noveltree-proteins.fasta has the full set of chelicerate protein sequences.</li> <li>summary_of_noveltree_results.zip contains summary figures from the outputs of the NovelTree run.</li> <li>chelicerate-samples.tsv is the sample sheet used in proteome curation upstream of NovelTree.</li> </ul>
FIGURE 3 in Revised Evolutionary And Taxonomic Synthesis For Parrots (Order: Psittaciformes) Guided By Phylogenomic Analysis
FIGURE 3. Species-level topology of Psittacinae. Support values come from the maximum likelihood tree. Nodes have ultrafast bootstrap values of ≥95% otherwise noted.
FIGURE 8 in Revised Evolutionary And Taxonomic Synthesis For Parrots (Order: Psittaciformes) Guided By Phylogenomic Analysis
FIGURE 8. Photographs (not to scale) of Calyptomena hosii (left photo: Dubi Shapiro) a suboscine passerine of Borneo (Brunei, Indonesia) and Triclaria malachitacea (right photo: Marcos Eugênio) of southeastern Brazil showing presumably convergent evolution in ventral coloring. See text for discussion. Photographs reproduced with permission from the photographers.
FIGURE 16 in Revised Evolutionary And Taxonomic Synthesis For Parrots (Order: Psittaciformes) Guided By Phylogenomic Analysis
FIGURE 16. Dorsal view of specimens of Glossopsitta concinna from the Australian National Wildlife Collection (ANWC) showing variation within and between sexes and within and between mainland southeastern Australia versus Tasmania. Note the bluer coronal color in mainland males. Registration numbers from the bird collection at ANWC are shown. Photograph: Gordon Gullock.
FIGURE 78 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 78. Mantidactylus manerana fotaka ssp. nov. in life. (a,b) Adult female from Sorata in dorsolateral and ventral view. Specimen probably corresponding to a voucher deposited in the UADBA collection.
FIGURE 77 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 77. Audiospectrogram and corresponding oscillogram of one advertisement call of the holotype of Mantidactylus manerana manerana, recorded on 17 November 2016 at Camp Simpona, Marojejy National Park (ca 20°C air temperature). Recording bandpass-filtered at 350–6000 Hz.
FIGURE 76 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 76. Mantidactylus manerana manerana sp. nov. from Marojejy in life, in dorsolateral and ventral view. (a,b) Adult male (holotype ZSM 500/2016 = ZCMV 15162), photographed in 2016. (c,d). Adult male (ZSM 209/2005 = FGZC 2881), photographed in 2005. (e,f) Adult male (ZSM 207/2005 = FGZC 2846), photographed in 2005.
FIGURE 73 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 73. Preserved lectotype of Mantidactylus inaudax, and holotype specimens of newly named species and subspecies in the M. inaudax clade. Scale bars equal 5 mm.
FIGURE 71 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 71. Audiospectrogram and corresponding oscillogram of a 1000 ms section of a series of advertisement calls (three calls figured) tentatively allocated to Mantidactylus glosi, recorded on 26 February 2006 at Ambatovory (air temperature not measured). Recording bandpass-filtered at 640–2300 Hz.
FIGURE 70 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 70. Mantidactylus glosi sp. nov. (a) Adult female (possibly corresponding to ZSM 433/2006 = ZCMV 3364), from Ambatovory, Ranomafana, in dorsolateral view, photographed in 2003. (b). Specimen from Ambatovory, Ranomafana, in dorsolateral view, photographed in 2003 and only tentatively attributed to this species. (c, d) Female JCR328 from Andalangina, Ranomafana, in dorsolateral and ventral views.
FIGURE 75 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 75. Audiospectrogram and corresponding oscillogram of one advertisement call of Mantidactylus inaudax, recorded on 23 June 2009 at Makira West (air temperature estimated at 20–25°C). Recording bandpass-filtered at 640–6500 Hz.
FIGURE 69 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 69. Mantidactylus eulenbergeri sp. nov. in life, in dorsolateral and ventral view. (a,b) Adult male (holotype ZSM 85/2002 = FGMV 2001.1092) from Andasibe.
FIGURE 68 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 68. Mantidactylus brevirostris sp. nov. from Betampona in life, in dorsolateral view. (a) Unsexed individual (ACP5444 = Bet76). (b) Unsexed individual (ACP5463 = Bet101). (c) Unsexed individual (ACP5463 = Bet68). (d) Unsexed individual (ACP5467 = Bet91).
FIGURE 72 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 72. Mantidactylus stelliger sp. nov. from Ambohitsara in life, in dorsolateral, ventral, and anterior view. (a,b) Adult male (holotype ZSM 2381/2007 = ZCMV 5932), photographed in 2007. (c,d) Adult male (ZSM 2380/2007 = ZCMV 5922), photographed in 2007. (e,f) Adult female (ZSM 2379/2007 = ZCMV 5870), photographed in 2007.
FIGURE 66 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 66. Audiospectrogram and corresponding oscillogram of a 1000 ms section of a series of advertisement calls (four calls figured) of Mantidactylus augustini sp. nov., recorded on 16 December 2001 at Andranofotsy (25.4°C air temperature). Recording bandpass-filtered at 500–3500 Hz.
FIGURE 65 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 65. Mantidactylus augustini sp. nov. from Andranofotsy in life, in dorsolateral and ventral view. (a,b,c) Adult female (FGMV 2001.1431, voucher deposited in UADBA), photographed in 2001. (d,e) Adult male (holotype ZSM 122/2002 = FGMV 2001.1388 = 2002.A4), photographed in 2001.
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