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142 results for “Cytochrome oxidase I”
Figure 4 in Molecular characterisation of leeches (Clitellata, Annelida) based on the mitochondrial cytochrome oxidase I (COI) gene region for Turkish fauna
Figure 4. Maximum likelihood phylogeny for Helobdella species based on COI sequences. Bootstrap values are shown for 1000 replicates.
Figure 2 in Molecular characterisation of leeches (Clitellata, Annelida) based on the mitochondrial cytochrome oxidase I (COI) gene region for Turkish fauna
Figure 2. Maximum likelihood phylogeny for Glossiponia species based on COI sequences. Bootstrap values are shown for 1000 replicates.
FIGURE 7. Cytochrome oxidase subunit I in A new species of small-eared shrew of the genus Cryptotis (Mammalia, Eulipotyphla, Soricidae) from the northernmost Peruvian Andes
FIGURE 7. Cytochrome oxidase subunit I phylogenetic trees for Cryptotis genus. Bootstrap supports are indicated at each node for A. Maximum Likelihood; B. Posterior Probability values for Bayesian Inference.
FIG. 6. A majority-rule consensus gene tree reconstructed from mtDNA cytochrome oxidase 1 in Redescription and Recognition of Etheostoma cyanorum from Blue River, Oklahoma
FIG. 6. A majority-rule consensus gene tree reconstructed from mtDNA cytochrome oxidase 1 (CO1) sequence data obtained from the Barcode of Life Database (BOLD). Maximum-likelihood (ML) and Bayesian trees had identical topologies. Branch lengths are proportional to inferred mutations. Shading of lineages represents samples from E. whipplei (outgroup) in black, E. cyanorum in gray, and E. radiosum in white. ML bootstrap proportions/ Bayesian posterior probabilities are reported. See Data Accessibility for tree file.
Table 2. Genetic distances for mitochondrial DNA partial cytochrome c oxidase subunit I and cytochrome b in Molecular phylogeny of the Aplodactylidae (Perciformes: Cirrhitoidea), a group of Southern Hemisphere marine ® shes
<p>Table 2. Genetic distances for mitochondrial DNA partial cytochrome <i>c</i> oxidase subunit I and cytochrome <i>b</i> sequences when combined. Values are Kimura (1980) two-parameter percentage sequence divergences, obtained when using the optimum expected transition±transversion nucleotide substitution ratio of 3.0 from maximum likelihood analysis (fi gure 3).</p><table><tbody><tr><th></th><th></th><th>1</th><th>2</th><th>3</th><th>4</th><th>5</th><th>6</th><th>7</th></tr></tbody><tbody><tr><th>1</th><td><i>Aplodactylus arctidens</i></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>2</th><td><i>Aplodactylus punctatus</i></td><td>6.1</td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>3</th><td><i>Aplodactylus westralis</i></td><td>7.8</td><td>7.6</td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>4</th><td><i>Aplodactylus etheridgii</i></td><td>10.0</td><td>10.3</td><td>10.0</td><td></td><td></td><td></td><td></td></tr><tr><th>5</th><td><i>Aplodactylus lophodon</i></td><td>11.8</td><td>11.9</td><td>12.4</td><td>11.1</td><td></td><td></td><td></td></tr><tr><th>6</th><td><i>Chironemus marmoratus</i></td><td>20.0</td><td>18.7</td><td>18.3</td><td>19.3</td><td>19.5</td><td></td><td></td></tr><tr><th>7</th><td><i>Cheilodactylus fasciatus</i></td><td>21.8</td><td>21.0</td><td>20.5</td><td>22.6</td><td>20.2</td><td>21.2</td><td></td></tr><tr><th>8</th><td><i>Cirrhitus splendens</i></td><td>22.6</td><td>20.7</td><td>21.0</td><td>23.1</td><td>22.0</td><td>23.1</td><td>22.8</td></tr></tbody></table>
Data from: Site specific distribution of oak rhizosphere associated oomycetes revealed by cytochrome c oxidase subunit II metabarcoding
The phylum Oomycota comprises important tree pathogens like Phytophthora quercina, involved in central European oak decline, and P. cinnamomi shown to affect holm oaks among many other hosts. Despite the importance to study the distribution, dispersal and niche partitioning of this phylum, metabarcoding surveys and studies considering environmental factors that could explain oomycete community patterns are still rare. We investigated oomycetes in the rhizosphere of evergreen oaks in a Spanish oak woodland using metabarcoding based on Illumina sequencing of the taxonomic marker cytochrome c oxidase subunit II (cox2). We developed an approach amplifying a 333 bp long fragment using the forward primer Hud-F (Hudspeth, Nadler, & Hudspeth, 2000) and a reverse primer found using DegePrime (Hugerth et al., 2014). Factors reflecting topo-edaphic conditions and tree health were linked to oomycete community patterns. The majority of detected OTUs belonged to the Peronosporales. Most taxa were relatives of the Pythiaceae, but relatives of the Peronosporaceae and members of the Saprolegniales were also found. The most abundant OTUs were related to Globisporangium irregulare and Phytophthora cinnamomi, both displaying strong site specific patterns. Oomycete communities were strongly correlated with the environmental factors: altitude, crown foliation, slope and soil skeleton and soil nitrogen. Our findings illustrate the significance of small scale variation in habitat conditions for the distribution of oomycetes and highlights the importance to study oomycete communities in relation to such ecological patterns.
Figure 6. The maximum-likelihood phylogram for cytochrome oxidase subunit I in A case of biodiversity overestimation in the Balkan Belgrandiella A. J. Wagner, 1927 (Caenogastropoda: Hydrobiidae): molecular divergence not paralleled by high morphological variation
Figure 6. The maximum-likelihood phylogram for cytochrome oxidase subunit I (COI) haplotypes. Bootstrap support and Bayesian posterior probabilities are shown. Normal font indicates reference haplotypes, bold font indicates haplotypes obtained in present study.
Figure 5. Minimum spanning haplotype network derived from a 658 base-pair cytochrome c oxidase subunit I in Six degrees of separation in barnacles? Assessing genetic variability in the sea-turtle epibiont Stomatolepas elegans (Costa) among turtles, beaches and oceans
Figure 5. Minimum spanning haplotype network derived from a 658 base-pair cytochrome c oxidase subunit I (COI) fragment from 57 Stomatolepas elegans collected from nine different Lepidochelys olivacea nesting on Playa Teopa, Jalisco, Mexico, six S. elegans from Caretta caretta from the western Atlantic, and six S. praegustator from C. caretta from the western Atlantic. Circle sizes are proportional to the frequency of each haplotype, with haplotype 1 being most common. Coloured pie slices are also proportional, and represent the number of S. elegans from each turtle characterized by the respective haplotype. Colours represent the nine Mexican turtles randomly sampled for S. elegans populations. Open circles with numbers indicate Atlantic haplotypes. Solid black circles designate hypothetical missing haplotypes. The network includes S. elegans haplotypes 1–21, and S. praegustator haplotypes 19, 26–30. Haplotypes 1–17, shown in colour, represent Jalisco, Mexico specimens collected from nine different turtles in the Pacific, and haplotypes 18–21 and 26–30, shown as unshaded circles, represent southeastern United States Atlantic specimens collected from six different C. caretta (see Table 1).
Figure 7. Maximum likelihood phylogram for combined 18S and cytochrome oxidase subunit I in An unusual, flagellum-bearing hydrobiid snail (Gastropoda: Rissooidea: Hydrobiidae) from Greece, with descriptions of a new genus and a new species
Figure 7. Maximum likelihood phylogram for combined 18S and cytochrome oxidase subunit I (COI) sequences, bootstrap support.
Figure 6. Maximum likelihood phylogram for cytochrome oxidase subunit I in An unusual, flagellum-bearing hydrobiid snail (Gastropoda: Rissooidea: Hydrobiidae) from Greece, with descriptions of a new genus and a new species
Figure 6. Maximum likelihood phylogram for cytochrome oxidase subunit I (COI) sequences, bootstrap support (1000 replicates).
Figure 2. Cytochrome c oxidase I in Mosquito (Diptera: Culicidae) fauna of the Iranian islands in the Persian Gulf
Figure 2. Cytochrome c oxidase I (COI) sequence alignments, showing only variable bases generated in the study and available in GenBank, for (A) Anopheles stephensi (n = 2) from a colony derived from females collected at Bandar-Abbas in mainland Hormozgan Province and GenBank entries from India (Tamil Nadu, n = 3; Pondicherry, n = 2), colony material (University of Leeds, UK, n = 3) and another of unknown origin (n = 1), (B) Culex quinquefasciatus from the Persian Gulf Islands of Abu-Musa (n = 1),Larak(n = 1) and Qeshm (n = 1) and four GenBank entries from India (Kerala, Hyderabad, Pondicherry and south) and (C) Ochlerotatus caspius s.l. from Abu-Musa Island (n = 5) and GenBank entries from Ardebil (n = 1) and East Azerbaijan (n = 1) Provinces in northern Iran. Bases identical to the lead sequence are denoted by dots (·); dashes (–) indicate bases missing because of differently sized fragments available in GenBank.
Figure 3. Haplotype networks for cytochrome oxidase I in Bythinella Moquin-Tandon, 1856 (Gastropoda: Rissooidea: Bythinellidae) in Romania: species richness in a glacial refugium
Figure 3. Haplotype networks for cytochrome oxidase I (COI), computed with TCS 1.21; square and ellipse size reflects haplotype frequency; connection limit excluding homoplastic changes was set to 95% (hence excluding some haplotypes from network); haplotypes in squares have biggest outgroup weights.
Figure 2. Bayesian phylogram computed for cytochrome oxidase I in Bythinella Moquin-Tandon, 1856 (Gastropoda: Rissooidea: Bythinellidae) in Romania: species richness in a glacial refugium
Figure 2. Bayesian phylogram computed for cytochrome oxidase I (COI) sequences with MRBAYES, Bayesian probabilities for branches are given.
Figure 5. Maximum likelihood trees constructed from mitochondrial cytochrome c oxidase subunit I in Cryptic diversity in coastal Australasia: a morphological and mitonuclear genetic analysis of habitat-forming sibling species
Figure 5. Maximum likelihood trees constructed from mitochondrial cytochrome c oxidase subunit I (left; log likelihood: -399.5730) and nuclear adenine nucleotide transporter intron (right; log likelihood: -12170.8682) sequences of Pyura praeputialis and Pyura doppelgangera sp. nov. Nodal support from 1000 bootstrap replications (> 75%) is indicated next to some branches. Circles indicate regions in which a particular allele was present. For simplicity, allele frequencies are not indicated.
FIGURE 2. The Neighbor-Joining tree for the cytochrome oxidase c subunit 1 in Mitochondrial diversity of the white-toothed shrews (Mammalia, Eulipotyphla, Crocidura) in Vietnam
FIGURE 2. The Neighbor-Joining tree for the cytochrome oxidase c subunit 1 (COI) gene fragment. The bootstrap values (≥ 50 %) obtained from 1000 pseudoreplications are presented above the branches. Crocidura olivieri is used as outgroup.
FIGURE 1 in Phylogenetic relationships among Unionicola (Acari: Unionicolidae) mussel-mites of North America based on mitochondrial cytochrome oxidase I sequences
FIGURE 1. Maximum-parsimony (MP; PAUP*4.0b10, Swofford 2002) tree showing phylogenetic relationships among subgenera of Unionicola spp. from North American that occur in association with freshwater mussels based on morphological and life history characters, excluding those related to sites of egg deposition. The analysis revealed 17 parsimony informative characters. Heuristic searches yielded 8 equally parsimonious trees with a length of 39 steps (CI=0.72). Bootstrap (100 pseudoreplicates) support values>50% from MP analysis are reported above the branches.
FIGURE 3 in Phylogenetic relationships among Unionicola (Acari: Unionicolidae) mussel-mites of North America based on mitochondrial cytochrome oxidase I sequences
FIGURE 3. Maximum-likelihood tree showing phylogenetic relationships among representative species of North American Unionicola from subgenera that occur in association with mussels based on partial sequence data of the cox1 gene. Bootstrap support values>50% from MP and ML analysis are reported above the branches. The outgroup species, Unionicola crassipes, is a sponge-associated mite.
FIGURE 2 in Phylogenetic relationships among Unionicola (Acari: Unionicolidae) mussel-mites of North America based on mitochondrial cytochrome oxidase I sequences
FIGURE 2. Maximum-parsimony tree showing phylogenetic relationships among representative species of North American Unionicola from subgenera that occur in association with mussels based on partial sequence data of the cox1 gene. Bootstrap support values>50% from MP and ML analysis are reported above the branches. The outgroup species, Unionicola crassipes, is a sponge-associated mite.
FIGURE 6 in Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene
FIGURE 6. Phylogeny of the Chinese Prionini based on combined sequences of 12S rRNA and 16S rRNA. A: Bootstrap 50% majority-rule consensus tree of distance method by PAUP* with bootstrap values (%), Wtd. S.S. = 0.0496, APSD = 3.764, 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 = 4527.5195, 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 = 792, CI = 0.7109, RI = 0.3639, 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 4 in Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene
FIGURE 4. Phylogeny of the Chinese Prionini based on partial sequences of 16S rRNA (excluding Priotyrannus closteroides)
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