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75 results for “cytochrome c oxidase”
Figure 3. Tetractinellida cytochrome c oxidase subunit I in An unprecedented new genus and family of Tetractinellida (Porifera, Demospongiae) from New Zealand's Colville Ridge, with a new type of mitochondrial group I intron
Figure 3. Tetractinellida cytochrome c oxidase subunit I (COI) maximum likelihood (ML) trees reconstructed with RAxML under the generalized time-reversible Gamma – GTRGAMMA – model: 140 sequences At each key node, ML bootstrap supports (100 bootstrap replicates) and Bayesian posterior probabilities are given. There are two bootstrap supports: nucleotide analyses/amino-acid analyses (only bootstrap supports above 50 are shown). GenBank accession numbers are given after each taxon name. Presence of mitochondrial introns are given in the COI tree (the number given to each intron indicates its position with respect to the Amphimedon queenslandica complete COI as reference).
Figure 4. Bootstrap consensus neigbor-joining tree deduced from the cytochrome c oxidase subunit I in A revision of the Monopis monachella species complex (Lepidoptera: Tineidae) from China
Figure 4. Bootstrap consensus neigbor-joining tree deduced from the cytochrome c oxidase subunit I gene sequences. Numbers indicate bootstrap proportions (%).
Figure 5. Bootstrap consensus minimum evolution tree deduced from the cytochrome c oxidase subunit I in A revision of the Monopis monachella species complex (Lepidoptera: Tineidae) from China
Figure 5. Bootstrap consensus minimum evolution tree deduced from the cytochrome c oxidase subunit I gene sequences. Numbers indicate bootstrap proportions (%).
Figure 4 in Cytochrome c oxidase subunit I barcode species delineation methods imply critically underestimated diversity in 'common' Hermeuptychia butterflies (Lepidoptera: Nymphalidae: Satyrinae)
Figure 4. Percentage of pairwise comparisons within each class of genetic distances (p-distance) for Hermeuptychia sequences calculated between (black bars) and within (grey bars) species. Species delimitation was based on the recursive partitioning ABGD analysis.
Figure 3. A in Cytochrome c oxidase subunit I barcode species delineation methods imply critically underestimated diversity in 'common' Hermeuptychia butterflies (Lepidoptera: Nymphalidae: Satyrinae)
Figure 3. A, relationships from our phylogenetic analyses based on Bayesian inference. Support values> 50 are indicated with posterior probability values indicated above the branch and bootstrap values indicated below the branch. Names and morphology group symbols are as presented in Seraphim et al. (2014), 'ns' indicates new sequences, and numbers in parentheses indicate the number of species within clades as indicated by the ABGD (recursive partitioning) approach. B, relationships among Hermeuptychia species redrawn from the phylogeny presented in Seraphim et al. (2014), for comparison.
Figure 2 in Cytochrome c oxidase subunit I barcode species delineation methods imply critically underestimated diversity in 'common' Hermeuptychia butterflies (Lepidoptera: Nymphalidae: Satyrinae)
Figure 2. Bayesian inference (BEAST2) tree for Hermeuptychia COI barcode sequences with posterior probabilities (top)> 0.5 and bootstrap values (bottom)> 50 indicated. Sequences generated in this study have voucher numbers beginning 'LEP' or 'IN' and are highlighted in blue. Species boundaries as indicated by the three most plausible implementations of each approach, bPTP (ML) (black), ABGD (recursive partitioning) (green) and GMYC (multiple thresholds) (grey), are illustrated as coloured bars on the side. * indicates groups that were recovered as one putative species but appear separated owing to the underlying phylogeny. Red vertical bars denote putative species that do not include an previously published sequences. Horizontal coloured bars and symbols beside sample voucher names denote morphology groupings identified in Seraphim et al. (2014).
FIGURE 1. Neighbor-joining tree for cytochrome c oxidase subunit I in Description of a new Kempnyia Klapálek from Brazil (Plecoptera: Perlidae) with life stages associated using DNA barcodes
FIGURE 1. Neighbor-joining tree for cytochrome c oxidase subunit I (COI) sequences (450 bp) from Kempnyia KlapÁlek and related stoneflies from Rio de Janeiro, Brazil modeled by Kimura-2-parameter (K2P).
FIGURE 1. Neighbor-joining tree for cytochrome c oxidase subunit I in Anacroneuria flintorum Froehlich 2002 (Plecoptera: Perlidae): Notes, distribution, and life stages association using molecular tools
FIGURE 1. Neighbor-joining tree for cytochrome c oxidase subunit I (COI) sequences (433 bp) from Anacroneuria flintorum Froehlich and related stoneflies from Espírito Santo and São Paulo States, Brazil, modeled by Kimura-2-parameter (K2P).
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 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 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 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 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 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.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
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