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342 results for “DNA phylogeny”
Phylogeny of "Philoceanus complex" seabird lice (Phthiraptera: Ischnocera) inferred from mitochondrial DNA sequences
<p>Data from "Phylogeny of “<em>Philoceanus </em>complex” seabird lice (Phthiraptera: Ischnocera) inferred from mitochondrial DNA sequences". See the file index.html for details. Data includes NEXUS files for sequences, tree files output by MrBayes and PAUP, and host-parasite association files for TreeMap.</p>
Fig. 3 in Application Of Dna Barcoding In Taxonomy And Phylogeny: An Individual Case Of Coi Partial Gene Sequencing From Seven Animal Species
Fig. 3. Phylogenetic position of Macrobiotus sp., Bayesian inference phylogenetic tree. Sequences obtained by us are written in bold.
Fig. 1 in Application Of Dna Barcoding In Taxonomy And Phylogeny: An Individual Case Of Coi Partial Gene Sequencing From Seven Animal Species
Fig. 1. Phylogenetic position of D. lindholmi and L. a. exigua, Bayesian inference phylogenetic tree. Sequences obtained by us are written in bold.
Fig. 3. Maximum likelihood tree constructed from 38 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and relatives using a in Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences
Fig. 3. Maximum likelihood tree constructed from 38 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and relatives using a transition/transversion rate ratio of 1.6. Branch lengths are proportional to the number of expected nucleotide substitutions per site.
Fig. 2 in Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences
Fig. 2. Neighbor-joining tree inferred form the analysis of 39 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and its relatives using a transition/transversion rate ratio of 1.6. Branch lengths are proportional to distance estimated from the two parameter method of Kimura. Numbers at nodes indicate bootstrap values for 100 replicate analyses. On this tree, bootstrap values <20% are not indicated.
Fig. 1 in Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences
Fig. 1. Strict consensus of 11 parsimony trees derived from equally-weighted parsimony analysis of combined nuclear DNA ITS1 and ITS2 sequences from Daucus and its relatives using all unambiguously-aligned positions (CIs with and without uninformative characters= 0.6613 and 0.5817; RI=0.8387). From the left to the right, names of taxa, sections, and clades are given. Numbers above the nodes indicate the number of times a monophyletic group occurred in 100 bootstrap replicates; AutoDecay values are given below.
Linked collectors and determiners for: Revision of the Nearctic species of Gimnomera Rondani (Diptera: Scathophagidae) with morphological phylogeny and DNA barcodes.
Natural history specimen data linked to collectors and determiners held within, "Revision of the Nearctic species of Gimnomera Rondani (Diptera: Scathophagidae) with morphological phylogeny and DNA barcodes". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/e1297bcb-24e9-4306-8210-068cc6f5f482">https://bionomia.net/dataset/e1297bcb-24e9-4306-8210-068cc6f5f482</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/e1297bcb-24e9-4306-8210-068cc6f5f482">https://gbif.org/dataset/e1297bcb-24e9-4306-8210-068cc6f5f482</a>. Formatted as a Frictionless Data package.
Figure 2. Phylogenetic relationships among the 29 in Molecular phylogeny and phylogeography of the Greek populations of the genus Orthometopon (Isopoda, Oniscidea) based on mitochondrial DNA sequences
Figure 2. Phylogenetic relationships among the 29 specimens of Orthometopon species. Individuals from two other terrestrial isopod species were used as outgroup taxa: Ligidium sp. and Armadillidium vulgare. Phylogenetic analyses, maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI), all produced trees with the same topology. Only the BI tree is presented here. Numbers above the branches indicate bootstrap values in the MP and ML analyses, respectively (MP/ML). Numbers below the branches indicate the posterior probabilities of the Bayesian analysis (BI).
Figure 1 in Molecular phylogeny and phylogeography of the Greek populations of the genus Orthometopon (Isopoda, Oniscidea) based on mitochondrial DNA sequences
Figure 1. Map showing the sampling localities of the 29 specimens used for the DNA analysis. The numbers correspond to those listed in Table 1.
Supplementary data for: DNA sequences are as useful as protein sequences for inferring deep phylogenies
<p>Inference of deep phylogenies has almost exclusively used protein rather than DNA sequences, based on the perception that protein sequences are less prone to homoplasy and saturation or to issues of compositional heterogeneity than DNA sequences. Here we analyze a model of codon evolution under an idealized genetic code and demonstrate that those perceptions may be misconceptions. We conduct a simulation study to assess the utility of protein versus DNA sequences for inferring deep phylogenies, with protein-coding data generated under models of heterogeneous substitution processes across sites in the sequence and among lineages on the tree, and then analyzed using nucleotide, amino acid, and codon models. Analysis of DNA sequences under nucleotide-substitution models (possibly with the third codon positions excluded) recovered the correct tree at least as often as analysis of the corresponding protein sequences under modern amino acid models. We also applied the different data-analysis strategies to an empirical dataset to infer the metazoan phylogeny. Our results from both simulated and real data suggest that DNA sequences may be as useful as proteins for inferring deep phylogenies and should not be excluded from such analyses. Analysis of DNA data under nucleotide models has a major computational advantage over protein-data analysis, potentially making it feasible to use advanced models that account for among-site and among-lineage heterogeneity in the nucleotide-substitution process in inference of deep phylogenies.</p>
Supplementary data for: DNA sequences are as useful as protein sequences for inferring deep phylogenies
Open the record for dataset details and reuse information.
Genus level DNA sequence data for three genes (matK, rbcL, trnH-psbA) for the paper: A comprehensive, genus-level time-calibrated phylogeny of the tree flora of Mediterranean Europe and an assessment of its vulnerability
<p>This data file contains the consensus DNA sequences in fasta format, of 64 tree genera found in Mediterranean Europe, following the checklist of Médail et al. (2019). </p> <p>The data are used in a manuscript submitted for publication to Botany Letters and currently under revision. The manuscript is entitled: "<em>A comprehensive, genus-level time-calibrated phylogeny of the tree flora of Mediterranean Europe and an assessment of its vulnerability</em>". Its authors are: Marwan Cheikh Albassatneh, Marcial Escudero, Loic Ponge<sup>*</sup>, Anne-Christine Monnet, Juan Arroyo, Toni Nikolic, Gianluigi Bacchetta, Francesca Bagnoli, Panayotis Dimopoulos, Agathe Leriche, Frédéric Médail, Anne Roig, Ilaria Spanu, Giovanni Giuseppe Vendramin, Arndt Hampe, Bruno Fady.</p>
The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data
<p>The angiosperm family Primulaceae is morphologically diverse and distributed nearly worldwide. However, phylogenetic uncertainty has limited the ability to identify major morphological and biogeographic transitions. We used target capture sequencing with the Angiosperms353 kit for over 300 species across Ericales, tree-based sequence curation, and multiple phylogenetic approaches to investigate the phylogenetics of the major clades of Primulaceae and their relationship to other Ericales. The study included 150 samples of Primulaceae comprising nearly all recognized genera of the family, with a particular focus on the most diverse subfamily, Myrsinoideae, for which previous phylogenetic knowledge was poor. We used fossil and secondary calibrations to generate dated phylogenetic trees and conducted broad-scale biogeographic analyses as well as ancestral state reconstructions of plant habit.</p>
Expanded phylogeny of Nomadinae (Hymenoptera: Apidae) with integration of UCE and DNA barcode sequence data
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The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data
Open the record for dataset details and reuse information.
FIGURE 40 in Revision of the Nearctic species of Gimnomera Rondani (Diptera: Scathophagidae) with morphological phylogeny and DNA barcodes
FIGURE 40. One of the four most parsimonious cladograms produced by analysing the data in Table 1 and obtained by reweighting characters using the rescaled consistency index (RCI). Character distributions represented by black blocks are for uniquely derived states; grey blocks are for homoplasious states.
FIGURE 41 in Revision of the Nearctic species of Gimnomera Rondani (Diptera: Scathophagidae) with morphological phylogeny and DNA barcodes
FIGURE 41. Neighbour-joining tree of 51 specimens of Gimnomera and one outgroup specimen with COI sequences, including unique voucher number (numbers starting with CCDB are from this study), sequence length, locality and GenBank accession number. Current species concepts shown by different colours, with the exception of G. tibialis and G. sibirica, where colours represent different populations (dark brown = G. tibialis east population, dark red = G. tibialis north population, orange = G. sibirica, light brown = G. cerea, light blue = G. subvittata, purple = G. aquilonia, light red = G. sp A, dark pink = G. terrywheeleri, navy blue = G. cuneiventris, light pink = G. vockerothi).
FIGURE 39 in Revision of the Nearctic species of Gimnomera Rondani (Diptera: Scathophagidae) with morphological phylogeny and DNA barcodes
FIGURE 39. Strict consensus tree of four most parsimonious cladograms of species of Gimnomera and outgroups, produced by analysing the data matrix in Table 1. Bremer support values are shown at each internode.
FIGURES 37–38 in Revision of the Nearctic species of Gimnomera Rondani (Diptera: Scathophagidae) with morphological phylogeny and DNA barcodes
FIGURES 37–38. Known distribution of Gimnomera. 37. G. tibialis (Malloch); 38. G. vockerothi sp. nov..
FIGURES 17–20 in Revision of the Nearctic species of Gimnomera Rondani (Diptera: Scathophagidae) with morphological phylogeny and DNA barcodes
FIGURES 17–20. Male and female Gimnomera, lateral views. 17. G. subvittata (Malloch), male; 18. Female of possible ninth species of Nearctic Gimnomera (Gimnomera sp. A); 19. G. tibialis (Malloch), female; 20. G. vockerothi sp. nov., female.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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