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Table 3 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
<p><b>Table 3.</b> Characteristic (AT content, repeat, number of predicted secondary structure, range of <i>ΔG</i> value (kcal/mol)) of control region of <i>Cubaris murina</i> by RNAstructure.</p><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><i>ΔG</i> value (kcal/mol)</td></tr><tr><th><i>Cubaris murina</i></th><td>NCR1</td><td>5219</td><td>5360</td><td>142</td><td>Between <i>nad1</i> and <i>trnN</i></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 <i>trnS1</i> and <i>trnL1</i></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 <i>rrnL</i> and <i>trnE</i></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 <i>trnE</i> and <i>trnV</i></td><td>71.70%</td><td>AG-rich</td><td>5</td><td>−13.4 to −12.3</td></tr><tr><th><i>Panulirus argus</i> [Baeza, 2018]</th><td>NCR</td><td>13,525</td><td>14,326</td><td>801</td><td>Between <i>rrnS</i> and <i>trnI</i></td><td>69.60%</td><td>AT-rich</td><td>7</td><td>−99.20 to −94.52</td></tr><tr><th><i>Synalpheus microneptunus</i> [Chak <i>et al.</i>, 2020]</th><td>NCR</td><td>13,365</td><td>14,198</td><td>834</td><td>Between <i>rrnS</i> and <i>trnI</i></td><td>79.50%</td><td>AT-rich</td><td>20</td><td>− 104 (lowest)</td></tr></tbody></table>
FIGURE 1 in Phylogenetic relationships among the genera of the Penaeidae (Crustacea: Decapoda) revealed by mitochondrial 16S rRNA gene sequences
FIGURE 1. Morphological phylogeny of the penaeid genera proposed by (a) Kubo 1949, reconstructed from text (genera in brackets were not fully analyzed and '?' refers to uncertain relationship) and (b) Burkenroad 1983, reconstructed from key (mentioned by the author as "...a natural key down to the level of genus"), with Penaeini as Peneini, Parapenaeini as Parapeneini, Trachypenaeini as Trachypeneini, and Metapenaeus as Mangalura. *Considered to be the most primitive genus in the family.
FIGURE 2 in Phylogenetic relationships among the genera of the Penaeidae (Crustacea: Decapoda) revealed by mitochondrial 16S rRNA gene sequences
FIGURE 2. BIO-neighbor-joining (BIO-NJ) tree of Penaeidae based on partial mitochondrial 16S rRNA gene sequences. Numbers on branches indicate bootstrap values from BIO-NJ (normal text), maximum parsimony (in italics), maximum likelihood (in bold) analyses and posterior probability values from Bayesian (in italics bold) analyses. Bootstrap values below 50% are not shown. A, B, C refer to the three main clades in the tree. Parapenaeini, Trachypenaeini and Penaeini are the three groups as defined by Burkenroad (1983).
Figure 7. Mitochondrial DNA gene tree estimated for Acanthocercus atricollis using a in Lifting the blue-headed veil - integrative taxonomy of the Acanthocercus atricollis species complex (Squamata: Agamidae)
Figure 7. Mitochondrial DNA gene tree estimated for Acanthocercus atricollis using a portion of the 16S gene. The support for branches from BI and ML are shown on each branch, respectively. The *BEAST species tree is shown in the top left with posterior probability values on branches.
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.
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).
Figure 6 in A new species of Cistopus Gray, 1849 (Cephalopoda: Octopodidae) from the East and South China Seas and phylogenetic analysis based on the mitochondrial COI gene
Figure 6. The phylogenetic tree based on cytochrome c oxidase type I (COI) gene data. Numbers in bold face above branches are maximum likelihood/neighbour joining/maximum parsimony bootstrap support values (1000 replicates). Asterisk indicates bootstrap values less than 50%. Sepioteuthis lessoniana was used as distant outgroup species.
Figure 2 in A new species of Cistopus Gray, 1849 (Cephalopoda: Octopodidae) from the East and South China Seas and phylogenetic analysis based on the mitochondrial COI gene
Figure 2. Cistopus chinensis sp. nov. (A) Funnel organ, OUC-XKS021, male, 57.3 mm DML, scale bar 1 mm; (B) radula, OUC-XKS013, male, 75.6 mm DML, scale bar 100 µm; (C) distal end of hectocotylized arm, lateral view, OUC-XKS024, male, 43.2 mm DML, scale bar 1 mm; (D) stylet, OUC-XKS016, female, 56.3 mm DML, scale bar 5 mm; (E) digestive system, OUC-XKS021, male, 57.3 mm DML, scale bar 50 mm. Abbreviations: a, anus; asg, anterior salivary gland; bm, buccal mass; c, caecum; cd, crop diverticulum; cr, crop; dg, digestive gland; i, intestine; is, ink sac; o, oesophagus; psg, posterior salivary gland; s, stomach.
Figure 5 in A new species of Cistopus Gray, 1849 (Cephalopoda: Octopodidae) from the East and South China Seas and phylogenetic analysis based on the mitochondrial COI gene
Figure 5. Cistopus chinensis sp. nov.. (A,C) OUC-XKS-WH001, 71.8 mm DML male; (B) OUC-XKS015, 59.2 mm DML female. (D,E) obtained from hatching pond indoors. (A) Male reproductive tract, scale bar 10 mm; (B) reproductive system of female, scale bar 10 mm; (C) spermatophore, scale bar 5 mm; (D) egg cluster; (E) single laid egg (length = 13.0 mm). Abbreviations: ag, accessory gland; do, distal oviduct; ea, ejaculatory apparatus; f, filament; mg, mucilaginous gland; o, ovary; og, oviducal gland; sr, sperm reservoir; ss, spermatophore storage sac; t, testis; to, terminal organ; vd, vas deferens.
Figure 1 in A new species of Cistopus Gray, 1849 (Cephalopoda: Octopodidae) from the East and South China Seas and phylogenetic analysis based on the mitochondrial COI gene
Figure 1. Cistopus chinensis sp. nov. Dorsal (left) and ventral view (right) of whole animal, holotype (CMRC-XKS-0908026, male, 96 mm DML).
Figure 4 in A new species of Cistopus Gray, 1849 (Cephalopoda: Octopodidae) from the East and South China Seas and phylogenetic analysis based on the mitochondrial COI gene
Figure 4. Cistopus chinensis sp. nov. (A–C) OUC-XKS-WH002, male (mature), 83.0 mm DML, scale bar 5 mm: (A) upper beak, lateral view; (B) lower beak, top view; (C) lower beak, lateral view. (D,E) Scanning electron micrographs of the radula, scale bar 100 µm: (D) OUC-XKS014, female, 63.2 mm DML; (E) OUC-XKS013, male, 76.5 mm DML.
Figure 3 in A new species of Cistopus Gray, 1849 (Cephalopoda: Octopodidae) from the East and South China Seas and phylogenetic analysis based on the mitochondrial COI gene
Figure 3. Cistopus chinensis sp. nov. (A) Hectocotylus, lateral view, OUC-XKS024, male, 43.2 mm DML, scale bar 1 mm; (B) enlarged suckers (see arrows), OUC-XKS007, male, 56.5 mm DML, scale bar 10 mm, (C) mucous pouch (see arrows), OUC-XS020, female, 49.8 mm DML, scale bar 10 mm; (D) mucous pouch (see arrows), OUC-XKS021, male, 57.3 mm DML, scale bar 10 mm; (E) live animal just caught from Putian, Fujian Province.
Figure 5 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)
Figure 5. Phylogenetic informativeness of three mtDNA gene fragments (16S, 12S, and COI) in peppermint, cleaner, and semi-terrestrial shrimps. (A) Phylogenetic informativeness (PI) profiles of the three different mtDNA gene fragments studied through relative time in shrimps from the genera Lysmata, Exhippolysmata, and Merguia. The sum of the instantaneous asymptotic informativeness of all sites in each gene is plotted. The arrows and numbers above or below them indicate the relative time (arrow) and magnitude (numbers) at which PI reaches its maximum value. (B) Tree topology resulting from the maximum-likelihood analysis of the sequences studied with a relative time-enforced branch length. This phylogeny was used to calculate the PI profiles in panel (A). Species pertaining to the different monophyletic clades previously revealed by the combined analyses of the three mtDNA gene fragments are highlighted with different colours, as in Figure 3.
Figure 7. Neighbour-nets generated using SplitsTree4 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)
Figure 7. Neighbour-nets generated using SplitsTree4 from the three mtDNA gene fragments studied (16S, 12S, and COI) in shrimps from the genera Lysmata, Exhippolysmata, and Merguia. Species pertaining to the different monophyletic clades previously revealed by the combined analyses of the three mtDNA gene fragments are highlighted with different colours, as in Figure 3. Abbreviations: LA, Lysmata ankeri; LABP, Lysmata cf. vittata; LAM, Lysmata amboinensis; LARG, Lysmata argentopuctata; LBA, Lysmata bahia; LBO, Lysmata boggessi; LCA, Lysmata californica; LD, Lysmata debelius; LGA, Lysmata galapagensis; LGB, Lysmata grabhami; LGR, Lysmata gracilirostris; LH, Lysmata hochi; LHO, Lysmata holthuisi; LI, Lysmata intermedia; LIM2, Lysmata cf. intermedia; LK, Lysmata kuekenthali; LM, Lysmata moorei; LN, Lysmata nayaritensis; LNI, Lysmata nilita; LO, Lysmata olavoi; LP, Lysmata pederseni; LRA, Lysmata rafa; LSET, Lysmata seticaudata; LT, Lysmata cf. ternatensis; LV, Lysmata vittata; LU, Lysmata udoi; LWEF, Lysmata wurdemanni EFL; LWG, Lysmata wurdemanni TX; LWWF, Lysmata wurdemanni WFL; EXO, Exhippolysmata oplophoroides; EXE, Exhippolysmata ensirostris; MO, Merguia oligodon; MR, Merguia rhizophorae; and NSP, Nikoides sp.
Figure 3 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)
Figure 3. Tree topology resulting from the combined analysis of the three mtDNA gene fragments studied (16S, 12S, and COI) for shrimps from the genus Lysmata (29 taxa), Exhippolysmata (two taxa), Merguia (two taxa), and one out-group (Nikoides sp.), under maximum likelihood (ML). Numbers above or below the branches represent the bootstrap values obtained from the maximum likelihood (ML) analysis in TREEFINDER and posterior probabilities from the Bayesian inference (BI) analysis in MrBayes (ML/BI). The general topology of the trees obtained from ML and BI analyses was the same.
Figure 1 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)
Figure 1. Amino acid usage analysis (mean amino acid count per sequence) for COI reference sequences (from selected species of crustaceans: Macrobrachium rosenbergii, Exopalaemon caricaudinata, Halocaridina rubra, and Cherax destructor), for COI orthologous sequences obtained from shrimps from the genus Lysmata, and for COI-like cloned sequences from Lysmata seticaudata. The error bars in each graph represent the highest and lowest amino acid counts per sequence in the three data sets. Amino acid determination and naming follows the invertebrate mitochondrial translation code, and was performed in MEGA 5.
Figure 2 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)
Figure 2. Tree topologies resulting from the analysis of COI-like cloned sequences from Lysmata seticaudata and mtDNA COI gene fragments for shrimps from the genus Lysmata (29 taxa), Exhippolysmata (two taxa), Merguia (two taxa), and one out-group (Nikoides sp.), under maximum likelihood (ML) and Bayesian inference (BI). Numbers above or below the branches represent the bootstrap values obtained from the ML analysis in TREEFINDER, and posterior probabilities from the BI analysis in MrBayes.
FIGURE 2. The tree represents a 50 in A molecular phylogeny of the Grunts (Perciformes: Haemulidae) inferred using mitochondrial and nuclear genes
FIGURE 2. The tree represents a 50% majority rule consensus of the Bayesian topology (numbers represent the posterior probability of the clades), with bootstrap values from MP and ML mapped onto the topology. MP, ML, and Bayesian analyses produced similar topologies (MP: TL = 12,869, consistency index CI = 0.2372, retention index RI = 0.4450; ML: Ln Likelihood = -54309.4503) with differences mostly on nodes with low bootstrap support. The numbers on branches are MP and ML bootstrap values and posterior probabilities from Bayesian analysis, respectively. Asterisks indicate a bootstrap value of 100% for MP and ML and 1.0 for Bayesian analysis. Nodes with less than 50% bootstrap value are marked with an X if the clade had less than 50% support in any of the MP, ML, or Bayesian analyses.
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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