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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.

FIGURE 1 in The complete mitochondrial genome of the flat bug Aradacanthia heissi (Hemiptera: Aradidae)

FIGURE 1. Map of the mitochondrial genome of A. heissi. The tRNAs are denoted by the color blocks and are labeled according to the IUPACIUB single-letter amino acid codes. Gene name without underline indicates the direction of transcription from left to right, and with underline indicates right to left. Overlapping lines within the circle denote PCR fragments amplified used for cloning and sequencing.

FIGURE 5 in The complete mitochondrial genome of a tessaratomid bug, Eusthenes cupreus (Hemiptera: Heteroptera: Pentatomomorpha: Tessaratomidae)

FIGURE 5. Control region of the E. cupreus mitogenome. (A) Structure elements found in the control region of E. cupreus. The red, yellow and green box represent three different repetitive sequences found in the control region and tRNAIle -tRNAGln - tRNAMet -ND2 gene cluste. (B) The putative stem-loops structure was found in the control region. The light green and pink indicates highly conserved flanking sequence. (C) Predicted secondary clover-leaf structure of one extra tRNAGln-like sequences in the control region (gray indicates the sequences are identical to the typical tRNAGln; the light green indicates the different sequences). Alignments with the corresponding regular tRNAGln sequences also provided. The boxed nucleotides indicate the anticodon, which designates the corresponding tRNA.

FIGURE 2 in The complete mitochondrial genome of a tessaratomid bug, Eusthenes cupreus (Hemiptera: Heteroptera: Pentatomomorpha: Tessaratomidae)

FIGURE 2. Inferred secondary structure of 22 tRNAs of the E. cupreus mitogenome. The tRNAs are labeled with the abbreviations of their corresponding amino acids (gray indicates the mismatches). Dashed (-) indicate Watson-Crick base pairing and () indicate G-U base pairing.

FIGURE 3 in The complete mitochondrial genome of a tessaratomid bug, Eusthenes cupreus (Hemiptera: Heteroptera: Pentatomomorpha: Tessaratomidae)

FIGURE 3. Predicted secondary structure of the rrnL gene in E. cupreus. Roman numerals denote the conserved domain structure. The numbering system follows Gillespie et al. (2006) (established at the Comparative RNA Website). Dashed (–) indicate Watson-Crick base pairing and dot () indicate G-U base pairing.

FIGURE 1 in The complete mitochondrial genome of a tessaratomid bug, Eusthenes cupreus (Hemiptera: Heteroptera: Pentatomomorpha: Tessaratomidae)

FIGURE 1. Map of the mitogenome of E. cupreus. The tRNAs are denoted by the color blocks and are labeled according to the IUPAC-IUB single-letter amino acid codes. Gene name without underline indicates the direction of transcription from left to right, and with underline indicates right to left. Overlapping lines within the circle denote PCR fragments amplified used for cloning and sequencing.

FIGURE 6 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs

FIGURE 6. Phylogenetic tree of four sequenced assassin bugs. Bayesian inference and Maximum likelihood analysis inferred from all genes recovered the same topological structure. Bootstrap values and Bayesian posterior probabilities are indicated at each node.

FIGURE 3 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs

FIGURE 3. Predicted secondary structure of the rrnL in S. flavipes. Regions in red indicate the high variability in the four assassin bugs. Roman numerals denote the conserved domain structure. Dashed (-) indicate Watson-Crick base pairing and dot () indicate G-U base pairing.

FIGURE 2 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs

FIGURE 2. Inferred secondary structures of 22 tRNAs of S. flavipes. The tRNAs are labeled with the abbreviations of their corresponding amino acids. Dashed (-) indicate Watson-Crick base pairing and dot () indicate G-U base pairing.

FIGURE 4 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs

FIGURE 4. Predicted secondary structure of the rrnS in S. flavipes. Regions in red indicate the high variability in the four assassin bugs. Roman numerals denote the conserved domain structure. Dashed (-) indicate Watson-Crick base pairing and dot () indicate G-U base pairing.

FIGURE 5 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs

FIGURE 5. (A) The conserved region of the mitochondrial control region of S. flavipes, A. dohrni, T. dimidiata and V. hoffmanni. (B) The structural organization of the mitochondrial control region of S. flavipes. The control region flanking genes rrnS, trnI (I), trnQ (Q), and trnM (M) are represented in purple and green boxes. The light blue boxes with roman numerals indicate the tandem repeat region. "G+C" indicates high G+C content region. "A+T" indicates high A+T content region. The black box indicates G element.

FIGURE 1 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs

FIGURE 1. Map of the mtochondrial genome of S. flavipes. Direction of gene transcription is indicated by the arrows. PCGs are shown as blue arrows, rRNA genes as purple arrows, tRNA genes as red arrows and large non-coding regions (>100 bp) as cyan rectangles. tRNA genes are labeled according to single-letter IUPAC-IUB abbreviations (L1: UUR; L2:CUN; S1:AGN; S2:UCN). The GC content is plotted using a black sliding window, as the deviation from the average GC content of the entire sequence. GC Skew is plotted as the deviation from the average GC skew of the entire sequence. Ticks in the inner cycle indicate the sequence length.

Figure 5 in Complete phylogeny and historical biogeography of true rosefinches (Aves: Carpodacus)

Figure 5. Localities of individually checked museum specimens () and genotyped samples (.) of the Carpodacus eos/pulcherrimus complex, encircled by breeding distributions of C. eos (green) and C. pulcherrimus (red), according to BirdLife International and NatureServe (2011).

Figure 1 in Complete phylogeny and historical biogeography of true rosefinches (Aves: Carpodacus)

Figure 1. Breeding distribution of extant rosefinch (Carpodacus) species according to BirdLife International and NatureServe (2011), subdivided into nine areas (A–I), with number of rosefinch species per area and connectivity among areas (Table 4).

Figure 4 in Complete phylogeny and historical biogeography of true rosefinches (Aves: Carpodacus)

Figure 4. Minimum spanning network for the Carpodacus eos/pulcherrimus complex based on cytochrome b alone.

Figure 3 in Complete phylogeny and historical biogeography of true rosefinches (Aves: Carpodacus)

Figure 3. Molecular phylogeny of true rosefinches (Carpodacus) based on cytochrome b sequences reconstructed in BEAST (codon positions partitioned, 10 000 000 generations; for details, see Table 3). At the nodes are posterior probabilities. The sample IDs refer to Table 2.

Figure 2 in Complete phylogeny and historical biogeography of true rosefinches (Aves: Carpodacus)

Figure 2. Molecular phylogeny of true rosefinches (Carpodacus) based on a 3212-bp alignment of up to four genes (for details see Table 3) reconstructed in BEAST (genes and codon positions partitioned, GTR/HKY models, 100 000 000 generations). At the nodes are posterior probabilities (left) and bootstrap values from a RAxML analysis with 1000 bootstrap replicates (right).