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Figure 2 in Characterisation of the complete mitochondrial genome of the imperiled Pearl darter Percina aurora (Perciformes: Percidae)

Figure 2. Codon usage in 13 protein coding genes of Percina aurora. Columns indicate the relative frequency of synonymous codons separated by amino acid.

Figure 3 in The mitochondrial genome of the Yellowtail Snapper Ocyurus chrysurus (Bloch, 1791) (Perciformes: Lutjanidae)

Figure 3. Secondary structure of the tRNA genes in the mitochondrial genome of yellowtail snapper Ocyurus chrysurus.

Figure 1 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures

Figure 1. Mitochondrial genome synteny in Cubaris murina and closely related species. A dash (-) before the gene name means that the gene is encoded on the light strand. NCR means a non-coding region that is longer than 100 bp. Cubaris murina is marked in bold black and shades of grey.

Figure 2 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures

Figure 2. Secondary structure of each transfer RNA (tRNA) visualised in Forna (http://rna.tbi.univie.ac. at/forna).

Figure 4 in Discordance between mitochondrial, nuclear, and svmbiont genomes in aphid phvlogenetics: who is telling the truth?

Figure 4. Buchnera tree obtained from the analvsis of 146 orthologous shared single-copv genes. Ŋe topologv corresponds to the consensus tree found under Bavesian analvses with the CAT model of PHYLOBAYES: values at nodes indicate posterior probabilities in Bavesian analvses/ultrafast bootstrap values under ML analvsis with the C20 model/ultrafast bootstrap values under ML analvsis with the the cpºEV*F*I*º8 model. * at nodes indicate bifurcations that were not observed in the ML analvsis. following species names indicate species for which dual-obligate svmbiosis has been demonstrated, * following species names indicate species for which the svmbiotic status (monosvmbiotic Buchnera or disvmbiotic svstem) is unknown. Names in bold are species for which new Buchnera data has been acquired for this studv.

Figure 5 in Discordance between mitochondrial, nuclear, and svmbiont genomes in aphid phvlogenetics: who is telling the truth?

Figure 5. Coplot of the combined analvsis of mitochondrial and nuclear data vs. Buchnera ML tree under C50 mode,l for species that have data from all three sources, ultrafast bootstrap values are given for subfamilv relationships and PP values obtained in PHYLOBAYES analvses of the same dataset. Branches with support below 50 have been collapsed.

Figure 2 in Discordance between mitochondrial, nuclear, and svmbiont genomes in aphid phvlogenetics: who is telling the truth?

Figure 2. Trees obtained from the analvsis of whole mitogenomes. Best tree found with ML analvses of the AA matrix under the best-fitting model (mMet*F*I*R6), values at nodes indicate bootstrap values obtained with best-fitting model/the C50 model/partitioned analvses/ and posterior probabilities under the CAT model of PhvloBaves; when a '*' is indicated instead of a support values it means that the nodes was not retrieved in the corresponding analvsis or that support was below 50. Alternative support values are onlv given for deep nodes that were inconsistent across analvses.

Figure 1 in Discordance between mitochondrial, nuclear, and svmbiont genomes in aphid phvlogenetics: who is telling the truth?

Figure 1. Alternative topologies found in previous phvlogenetic investigations of aphids: A, sketch of the Bavesian topologv on fig. 1 of Chen et al. 2017; B, sketch of the Bavesian topologv on fig. 2 fig. 2of Novakova et al. 2013; C, sketch of the ML topologv on fig. 1 of Owen et al. 2022; D, sketch of the phvlogenv obtained bv Hardv et al. 2022.

Figure 3 in Discordance between mitochondrial, nuclear, and svmbiont genomes in aphid phvlogenetics: who is telling the truth?

Figure 3. Trees obtained from the analvsis of 42 nuclear loci. Best tree found with ML analvses of the AA matrix under partitioned analvsis. Alternative support values are given for deep nodes: values at nodes indicate ultra-fast bootstrap values obtained under the partitioned analvsis/the non-partitioned analvsis under the best-fiưing model (Q.plant*F*I*º4)/the C50 model/posterior probabilities under the CAT model of PHYLOBAYES. When a '*' is indicated instead of a support value it means that the nodes was not retrieved in the corresponding analvsis or that support was below 50.

Table 3 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures

Table 3. Characteristic (AT content, repeat, number of predicted secondary structure, range of ΔG value (kcal/mol)) of control region of Cubaris murina by RNAstructure.<table><tbody><tr><th></th><th></th><th></th><th></th><th>Length</th><th></th><th></th><th></th><th>Number of predicted</th><th></th></tr></tbody><tbody><tr><th>Species [reference]</th><td>Name</td><td>Start</td><td>Stop</td><td>(bp)</td><td>Location</td><td>%AT</td><td>Repeat</td><td>secondary structures</td><td>ΔG value (kcal/mol)</td></tr><tr><th>Cubaris murina</th><td>NCR1</td><td>5219</td><td>5360</td><td>142</td><td>Between nad1 and trnN</td><td>52.80%</td><td></td><td>7</td><td>−16.9 to −15.4</td></tr><tr><th>[present study]</th><td>NCR2</td><td>6297</td><td>6666</td><td>370</td><td>Between trnS1 and trnL1</td><td>59.70%</td><td>CT-rich & AT-loop</td><td>20</td><td>−103.7 to −101.0</td></tr><tr><th></th><td>NCR3</td><td>12,550</td><td>12,753</td><td>204</td><td>Between rrnL and trnE</td><td>71.10%</td><td>poly-A</td><td>7</td><td>−17.5 to −17.1</td></tr><tr><th></th><td>NCR4</td><td>12,813</td><td>12,950</td><td>138</td><td>Between trnE and trnV</td><td>71.70%</td><td>AG-rich</td><td>5</td><td>−13.4 to −12.3</td></tr><tr><th>Panulirus argus [Baeza, 2018]</th><td>NCR</td><td>13,525</td><td>14,326</td><td>801</td><td>Between rrnS and trnI</td><td>69.60%</td><td>AT-rich</td><td>7</td><td>−99.20 to −94.52</td></tr><tr><th>Synalpheus microneptunus [Chak et al., 2020]</th><td>NCR</td><td>13,365</td><td>14,198</td><td>834</td><td>Between rrnS and trnI</td><td>79.50%</td><td>AT-rich</td><td>20</td><td>− 104 (lowest)</td></tr></tbody></table>

opennotspecifiedOct 2014View details →

Figure 2 in Molecular phylogeny of Acanthochitonina (Mollusca: Polyplacophora: Chitonida): three new mitochondrial genomes, rearranged gene orders and systematics

Figure 2. Molecular phylogeny of Acanthochitonina. Majority-rule consensus tree from the Bayesian analysis of the multilocus nucleotide data set, which includes three mitochondrial and two nuclear markers. Additional phylogenetic results are available in the Supplemental File 2. Note the proposed taxonomic arrangements shown by vertical lines. Numbers at nodes are support values from posterior probabilities and maximum likelihood bootstrap proportions, respectively. Scale bar is in substitutions per site.

opennotspecifiedOct 2014View details →

Figure 1 in Molecular phylogeny of Acanthochitonina (Mollusca: Polyplacophora: Chitonida): three new mitochondrial genomes, rearranged gene orders and systematics

Figure 1. Phylogenetic relationships and gene arrangements of available chiton mitochondrial genomes. Majority-rule consensus tree from the Bayesian analysis of the mitochondrial genome nucleotide data set (outgroup taxa is omitted for simplicity). Identical topologies were recovered from all other analyses of mitochondrial genome data sets (see main text). Numbers at nodes are posterior probabilities and maximum likelihood bootstrap proportions, respectively. Scale bar is in substitutions per site. Mitochondrial gene orders of Haliotis rubra (Gastropoda), Octopus vulgaris (Cephalopoda) and Solemya velum (Bivalvia) are shown for comparison. Genes encoded by the minus strand are underlined; rearranged genes are highlighted in red (translocations) and green (changes of coding strands).

opennotspecifiedJul 2012View details →

Figure 1 in The complete mitochondrial genome of the Chinese Sika deer (Cervus nippon Temminck, 1838), and phylogenetic analysis among Cervidae, Moschidae and Bovidae

Figure 1. Molecular phylogenetic tree derived from complete DNA sequence of 12 mitochondrial protein-coding genes using Bayesian inference and maximum parsimony analysis. The numbers beside the nodes are Bayesian posterior probabilities and bootstrap proportions. Equus asinus and Equus caballus were set as out-groups.

Figure 1 in Molecular phylogeny of major lineages of the avian family Phasianidae inferred from complete mitochondrial genome sequences

Figure 1. Molecular phylogenetic tree derived from complete DNA sequences of the 12 mitochondrial protein-coding genes using Bayesian inference, maximum parsimony and maximum likelihood analysis. The numbers beside the nodes are Bayesian posterior probabilities (≥ 0.95 retained) and bootstrap proportions (≥ 50% retained). Anas platyrhynchos was set as outgroup. ∗demonstrates that MP analysis does not support this branch.

opennotspecifiedNov 2010View details →

Figure 2 in Complete mitochondrial genome of Tetraophasis szechenyii Madarász, 1885 (Aves: Galliformes: Phasianidae), and its genetic variation as inferred from the mitochondrial DNA Control Region

Figure 2. Median-joining network of all the control region haplotypes found in Tetraophasis szechenyii. Notes: Missing haplotypes in the network are represented by black dots; circle sizes are proportional to the number of individuals sharing the same haplotypes (n); each mutation step is shown as a short line connecting neighbouring haplotypes; numbers of mutations between haplotypes are indicated near branches if greater than 1.

opennotspecifiedNov 2010View details →

Figure 1 in Complete mitochondrial genome of Tetraophasis szechenyii Madarász, 1885 (Aves: Galliformes: Phasianidae), and its genetic variation as inferred from the mitochondrial DNA Control Region

Figure 1. Molecular phylogenetic tree derived from the complete DNA sequences of 12 mitochondrial protein-coding genes using Bayesian inference and maximum likelihood analyses. Notes:The numbers beside the nodes are Bayesian posterior probabilities (≥ 0.9 retained) and bootstrap proportions of maximum likelihood analyses calculated with 100 replicates (≥ 50% retained); Anas platyrhynchos and Alectura lathami were set as outgroups; *clades not supported by Bayesian inference.

opennotspecifiedMay 2009View details →

Figure 1 in The complete mitochondrial genome and phylogenetic analysis of forest musk deer (Moschus berezovskii)

Figure 1. Phylogenetic relationships by partitioned Bayesian and maximum parsimony (MP) methods of selected Cetartiodactyla taxa as inferred from 12 heavy-strand protein-coding genes (A), RNA genes (B), and their combination (C). Values above branches represent the posterior probabilities of Bayesian analysis and bootstrap values with 1000 replicates for the MP method. No numbers above a branch indicate that Bayesian posterior probability,0.95 and MP bootstrap values are,50.

FIGURE 4 in The complete mitochondrial genome of the flat bug Aradacanthia heissi (Hemiptera: Aradidae)

FIGURE 4. Predicted secondary structure of the srRNA in A. heissi. The annotation is the same as in Fig. 3.

FIGURE 6 in The complete mitochondrial genome of the flat bug Aradacanthia heissi (Hemiptera: Aradidae)

FIGURE 6. Phylogenetic tree of 15 Pentatomomorpha insects. Bayesian analyses and ML show the same topology. Bayesian posterior probabilities and bootstrap values of ML were indicated at each node.

FIGURE 2 in The complete mitochondrial genome of the flat bug Aradacanthia heissi (Hemiptera: Aradidae)

FIGURE 2. Inferred secondary structure of 22 tRNAs of A. heissi. The tRNAs are labeled with the abbreviations of their corresponding amino acids. Dashed (–) indicate Watson-Crick base pairing and (+) indicate G-U base pairing.