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142 results for “Cytochrome oxidase I”
FIGURE 3 in Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene
FIGURE 3. Phylogeny of the Chinese Prionini based on partial sequences of 16S rRNA. A: Bootstrap 50% majority-rule consensus tree of distance method by PAUP* with bootstrap values (%), Wtd. S.S. = 0.1041, APSD = 5.454, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; B: Bootstrap 50% majority-rule consensus tree of maximum likelihood method by PAUP* with bootstrap values (%), -Ln likelihood = 1754.1334, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; C: Bootstrap 50% majority-rule consensus tree of parsimony method by PAUP* with bootstrap values (%), tree length = 280, CI = 0.7429, RI = 0.4586, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; D: Bayesian tree by MrBayes with Bayesian posterior probabilities (%), the scale bar in the bottom left corner of the tree meaning 0.1 nucleotide substitutions per site.
FIGURE 2 in Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene
FIGURE 2. Phylogeny of the Chinese Prionini based on partial sequences of 12S rRNA (excluding Priotyrannus closteroides). A: Bootstrap 50% majority-rule consensus tree of distance method by PAUP* with bootstrap values, Wtd. S.S. = 0.0266, APSD = 3.139, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; B: Bootstrap 50% majority-rule consensus tree of maximum likelihood method by PAUP* with bootstrap values, -Ln likelihood = 2474.8359, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; C: Bootstrap 50% majority-rule consensus tree of parsimony method by PAUP* with bootstrap values, tree length =431, CI = 0.7425, RI = 0.4158, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; D: Bayesian tree by MrBayes with Bayesian posterior probabilities, the scale bar in the bottom left corner of the tree meaning 0.1 nucleotide substitutions per site.
FIGURE 1 in Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene
FIGURE 1. Phylogeny of the Chinese Prionini based on partial sequences of 12S rRNA. A: Bootstrap 50% majority-rule consensus tree of distance method by PAUP* with bootstrap values, Wtd. S.S. = 0.0787, APSD = 4.741, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; B: Bootstrap 50% majority-rule consensus tree of maximum likelihood method by PAUP* with bootstrap values, -Ln likelihood = 2748.8839, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; C: Bootstrap 50% majority-rule consensus tree of parsimony method by PAUP* with bootstrap values, tree length = 499, CI = 0.7054, RI = 0.3849, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; D: Bayesian tree by MrBayes with Bayesian posterior probabilities, the scale bar in the bottom left corner of the tree meaning 0.1 nucleotide substitutions per site.
FIGURE 7 in Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene
FIGURE 7. Phylogeny of the Chinese Prionini based on combined sequences of 12S rRNA and 16S rRNA (excluding Priotyrannus closteroides). A: Bootstrap 50% majority-rule consensus tree of distance method by PAUP* with bootstrap values (%), Wtd. S.S. = 0.0251, APSD = 3.047, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; B: Bootstrap 50% majority-rule consensus tree of maximum likelihood method by PAUP* with bootstrap values (%), -Ln likelihood = 4077.7392, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; C: Bootstrap 50% majority-rule consensus tree of parsimony method by PAUP* with bootstrap values (%), tree length =682, CI = 0.7405, RI = 0.3723, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; D: Bayesian tree by MrBayes with Bayesian posterior probabilities (%), the scale bar in the bottom left corner of the tree meaning 0.1 nucleotide substitutions per site.
Figure 2. Minimum-evolution tree deduced from cytochrome c oxidase subunit I in DNA barcoding and morphology reveal exceptional species diversity of Scoparia (Lepidoptera: Crambidae) from the Hailuogou Glacier area, China
Figure 2. Minimum-evolution tree deduced from cytochrome c oxidase subunit I (COI) gene sequences. Sequences were corrected with the Kimura two-parameter substitution model. Codon positions included were 1st + 2nd + 3rd + noncoding. Values represented at the nodes of branches are bootstrap values (1000 replicates).
Figure 1. Neighbour-joining tree deduced from the cytochrome c oxidase subunit I in DNA barcoding and morphology reveal exceptional species diversity of Scoparia (Lepidoptera: Crambidae) from the Hailuogou Glacier area, China
Figure 1. Neighbour-joining tree deduced from the cytochrome c oxidase subunit I (COI) gene sequences using MEGA 5. Sequences were corrected with the Kimura two-parameter substitution model. Codon positions included were 1st + 2nd + 3rd + noncoding. Values represented at the nodes of branches are bootstrap values (1000 replicates).
Figure 3. Cytochrome c oxidase subunits I and II in Songs, genetics, and morphology: revealing the taxonomic units in the European Cicadetta cerdaniensis cicada group, with a description of new taxa (Hemiptera: Cicadidae)
Figure 3. Cytochrome c oxidase subunits I and II (COI and COII) mitochondrial DNA concatenated phylogeny of the Cicadetta cerdaniensis song group. Maximum-likelihood (ML, GARLI) phylogenies are shown with ML branch lengths (box on the left) and ML bootstrap support. Nodes with less than 50% bootstrap support have been collapsed. Cicadetta fangoana was selected as the out-group taxon; taxa colours correspond to Figure 9. Specimen names include two-letter country codes followed by species or informal names (later in this study: 'cerdaniensis'-like = Cicadetta sibillae sp. nov., 'intermediate' = Cicadetta anapaistica lucana ssp. nov.). Specimen identification numbers are congruent with the type series for undescribed taxa. Cicadetta cantilatrix specimens originate from Switzerland, France, Poland, Slovenia, Macedonia, and Bulgaria. Type localities of Cicadetta cantilatrix, Cicadetta cerdaniensis, and Cicadetta anapaistica are included.
Figure 10. Haplotype parsimonious networks constructed from cytochrome c oxidase subunit I in A new genus of large hydrothermal vent-endemic gastropod (Neomphalina: Peltospiridae)
Figure 10. Haplotype parsimonious networks constructed from cytochrome c oxidase subunit I sequences of 30 specimens of: A, Gigantopelta chessoia sp. nov.; B, Gigantopelta aegis sp. nov. Open circles are represented haplotypes, number inside the circles and sizes of the circles correspond to number of individuals sharing the haplotype. Filled circles are hypothesized intermediate haplotypes that are not represented by sequences.
Figure 3. Maximum likelihood topologies. A, cytochrome oxidase 1 fragments. B, internal transcribed spacer fragment. C, combined data set. Bootstrap supports over 75 in Integrative taxonomy of Parasabella and Sabellomma (Sabellidae: Annelida) from Australia: description of new species, indication of cryptic diversity, and translocation of some species out of their natural distribution range
Figure 3. Maximum likelihood topologies. A, cytochrome oxidase 1 fragments. B, internal transcribed spacer fragment. C, combined data set. Bootstrap supports over 75% shown on nodes. Scale bar, average of nucleotide substitutions per site.
Figure 8. Cytochrome oxidase I in Mimetic colour pattern evolution in the highly polymorphic Bombus trifasciatus (Hymenoptera: Apidae) species complex and its comimics
Figure 8. Cytochrome oxidase I (COI) + 16S genetic distances between pairs of individuals from Figure 6 compared to their geographical distances. Distances between unique sublineages coloured in Figure 6 are in grey. Inferred withinlineage distances are coloured here by lineage. The line represents the trend of isolation by distance within Bombus trifasciatus s.s.
Figure 5. Phylogenetic relationships inferred from cytochrome c oxidase subunit I in Pseudocryptic speciation of Chrysochroa fulgidissima (Coleoptera: Buprestidae) with two new species from Korea, China and Vietnam
Figure 5. Phylogenetic relationships inferred from cytochrome c oxidase subunit I + 16S ribosomal RNA gene (1193 bp). Labelling as in Figure 3.
Figure 3. Phylogenetic relationships inferred from cytochrome c oxidase subunit I in Pseudocryptic speciation of Chrysochroa fulgidissima (Coleoptera: Buprestidae) with two new species from Korea, China and Vietnam
Figure 3. Phylogenetic relationships inferred from cytochrome c oxidase subunit I (664 bp). Colours represented within each terminal taxa denote biogeographical populations of Chrysochroa fulgidissima as given in Table 1. Numbers above branches are indicated by the neighbour-joining bootstrap value, Bayesian posterior probabilities, and the maximum likelihood bootstrap proportions. Numbers cited under branches are parsimony bootstrap symmetric resampling and jackknife support, respectively. The topology was constructed by Bayesian phylogenetic analysis.
Figure 2. Cytochrome oxidase c subunit I in An integrative approach to characterize cryptic species in the Thoracostoma trachygaster Hope, 1967 complex (Nematoda: Leptosomatidae)
Figure 2. Cytochrome oxidase c subunit I. Neighbourjoining tree based on P-distances with haplotypes from 2007 and the new haplotypes found in 2009 and 2010 (represented by numbers followed by clade – I, II, or III). The haplotypes from clade I and II that were recovered from 2007 appear underlined in the tree. The corresponding taxon names of the other clades can be found in Derycke et al. (2010a).
Figure 3. Ninety per cent majority rule consensus cytochrome oxidase I in Swima (Annelida, Acrocirridae), holopelagic worms from the deep Pacific
Figure 3. Ninety per cent majority rule consensus cytochrome oxidase I (COI) gene tree from Bayesian analyses of cirratuliform annelids, showing Swima as part of Acrocirridae and support for Swima monophyly. Unsupported branches were collapsed. Support indicated as posterior probabilities. Asterisks indicate 1.0 or 100% support.
Figure 1. Best selected tree from a maximum likelihood reconstruction for the cytochrome c oxidase subunit I in Integrating DNA and morphological taxonomy to describe diversity in poorly studied microscopic animals: new species of the genus Abrochtha Bryce, 1910 (Rotifera: Bdelloidea: Philodinavidae)
Figure 1. Best selected tree from a maximum likelihood reconstruction for the cytochrome c oxidase subunit I data set under the general time reversible model with gamma distribution, displaying all compatible groupings and with average branch lengths proportional to numbers of substitutions per site, indicated by the scale bar. Bootstrap support values above 80% are shown below each branch; posterior probabilities above 0.8 from 36 000 sampled trees from the Bayesian analysis are shown above each branch. Support values for within-species relationships are not shown. Filled circles indicate clades (and singlets) identified by the 4¥ rule; open diamonds indicate clades (and singlets) identified by the generalized mixed yule coalescent model. Names refer to the species and the clonal populations.
FIGURE 3. Neighbor-joining tree for Cytochrome C Oxidase Subunit I in Two new species and three new provincial records of Neoperla (Plecoptera: Perlidae) from Nanling Mountains, China
FIGURE 3. Neighbor-joining tree for Cytochrome C Oxidase Subunit I (COI) sequences (659 bp) from Neoperla annulatispina Mo, Li & Wang, sp. nov. and N. nigromarginata Li & Zhang, 2014, modeled by Kimura-2-parameter (K2P).
FIGURE 1. Neighbor-joining tree derived from mitochondrial cytochrome oxidase 1 in Identification of early life-history stages of Caribbean Apogon (Perciformes: Apogonidae) through DNA Barcoding
FIGURE 1. Neighbor-joining tree derived from mitochondrial cytochrome oxidase 1 sequences showing genetic lineages of Apogon species from Bahamas (BAH), Belize (BLZ), Curaçao (CUR), Florida (FCC, FWRI, SMS), and Saba Bank (SAB). L = larva, J = juvenile, A = adult.
Figure 2. The cytochrome c oxidase 1 in Evidence Of A Putative Novel Species Of Avian Schistosome Infecting Planorbella Trivolvis
Figure 2. The cytochrome c oxidase 1 (COI) phylogenetic tree including members of the avian Schistosomatidae. Nodal support indicated by Bayesian posterior probabilities. GenBank accession numbers precede taxon names. The representative sample from this study is in bold.
FIGURE 8—Phylogenetic tree inferred using Bayesian Inference derived from cytochrome c oxidase subunit I in How many species of genus Lernaeopoda Blainville, 1822 (Siphonostomatoida: Lernaeopodidae) are there in the southwestern Atlantic?
FIGURE 8—Phylogenetic tree inferred using Bayesian Inference derived from cytochrome c oxidase subunit I (COI) gene dataset. Numbers in the nodes represent posterior probability (<0.95 are not shown).
Supplementary material 2 from: Hrabina P, Pernerová L, Suchomel J, Robovský J (2023) Utility of cytochrome c oxidase I for the deciphering of unstable phylogeny and taxonomy of gorals, genus Nemorhaedus Hamilton Smith, 1827 (Bovidae, Ovibovina). ZooKeys 1181: 81-110. https://doi.org/10.3897/zookeys.1181.108019
List of taxa and GenBank accession numbers used for the original gene analysis with 134 COI sequences
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