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Figure 2 in The first genomic resource for the 'near threatened' Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae
Figure 2. Codon usage analysis of PCGs in the mitochondrial genome of Lontra longicaudis. All 20 amino acids [adenine (A), cysteine (C), aspartic acid (D), glutamic acid (E), phenylalanine (F), glycine (G), histidine (H), isoleucine (I), lysine (K), leucine (L), methionine (M), asparagine (N), proline (P), glutamine (Q), arginine (R), serine (S), threonine (T), valine (V), tryptophan (W), tyrosine (Y)] are listed by their one-letter abbreviations along the horizontal axis. Each amino acid comprises several codons that are listed and colour coded below their respective amino acid. The length of the coloured regions indicates the frequency of the respective codon within that amino acid. The vertical axis represents the RSCU values for the amino acids.
Figure 5 in The first genomic resource for the 'near threatened' Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae
Figure 5. Characteristics of the domains found in the D-Loop/CR of the Lontra longicaudis mitochondrial genome. Top: Features observed in all three well-conserved domains. Centre: Secondary structure of long tandem repeat observed in the CSB region, between CSB1 and CSB2. Bottom: D-Loop/CR sequence in which the different features have been highlighted with different colours.
Figure 1 in The first genomic resource for the 'near threatened' Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae
Figure 1. Circular DNA mitochondrial genome map of Lontra longicaudis. The annotated map depicts 13 protein-coding genes (PCGs), two ribosomal RNA genes (rrnS: 12S ribosomal RNA and rrnL: 16S ribosomal RNA), 22 transfer RNA (tRNA) genes, and the putative control region. Photo credit: John Tomsett.
Figure 4 in The first genomic resource for the 'near threatened' Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae
Figure 4. tRNAs in the mitochondrial genome of Lontra longicaudis usually display 'cloverleaf̍ secondary structures; however, in Serine 1 (tRNA-Ser(AGY) or trnS1), the DHU loop (3–4bp) was absent. The truncation of this tRNA is a conserved trait in metazoans.
Fig. 2.—Bayesian maximum clade credibility tree showing 37 mitochondrial genome haplotypes from 60 in Phylogeography of moose in western North America
Fig. 2.—Bayesian maximum clade credibility tree showing 37 mitochondrial genome haplotypes from 60 moose and an inset of sample locations according to haplotype number, sampled in western North America, 2004–2016, and including a Eurasian moose mitogenome from Kazakhstan (Hassanin et al. 2012—GenBank accession NC_020677). In the tree, each haplotype is followed by a sequence of highlighted (by subspecies) and labeled (by state or provincial abbreviation) squares signifying the location where each sample was collected. In the inset, haplotypes unique to a single individual are colored white, while the seven haplotypes found in multiple moose are colored by haplotype number.
Figure 3 in Higher-level phylogeny and evolutionary history of nonditrysians (Lepidoptera) inferred from mitochondrial genome sequences
Figure 3. Heterogeneity of mitogenome composition for different datasets: 13PCG, 13PCG + 2RNA, 13PCG_ codon12 + 2RNA, 13PCG_AA and 13PCG_codon3. The pairwise Aliscore values range from −1 indicating full random similarity, to +1 indicating nonrandom similarity. Species names are listed on top and on the right side of the matrix and are colour-coded to match their member superfamilies (lower right corner).
Figure 4 in Higher-level phylogeny and evolutionary history of nonditrysians (Lepidoptera) inferred from mitochondrial genome sequences
Figure 4. Mitochondrial gene rearrangements in nonditrysia. Gene sizes are not drawn to scale. Abbreviations of gene names are as follows: ATP6 and ATP8, ATP synthase subunits 6 and 8; COI–COIII, cytochrome c oxidase subunits 1–3; Cytb, cytochrome b; ND1–6 and ND4L, NADH dehydrogenase subunits 1–6 and 4L; 16S and 12S, large and small rRNA subunits. tRNA genes are indicated by their one-letter corresponding amino acids. CR, control region/A + T-rich region. Genes are transcribed from left to right except for those that are underlined, which have the opposite transcriptional orientation. Rearrangements of tRNA genes are highlighted by colours (green: gene inversion; blue and orange: gene rearrangements).
Figure 2 in Higher-level phylogeny and evolutionary history of nonditrysians (Lepidoptera) inferred from mitochondrial genome sequences
Figure 2. Scatter plot of AT- and GC-skews in the nonditrysian mitogenomes. Values were calculated for the majority strand of the entire mitogenome sequences. All the species are listed in the Supporting Information, Table S2. The legend indicates nonditrysian families and their corresponding taxa numbers. AT-skew = (A-T)/(A + T); GC-skew = (G-C)/(G + C).
Figure 6 in Higher-level phylogeny and evolutionary history of nonditrysians (Lepidoptera) inferred from mitochondrial genome sequences
Figure 6. Chronogram showing nonditrysian phylogeny, divergence time estimation and ancestral state reconstruction of the tRNA gene arrangement. Phylogenetic tree presenting divergence dates produced by the Bayesian method of the 13PCG dataset using three fossil calibration points (grey star targets). Blue bars indicate the 95% mean confidence interval (CI) of each node. A geological timescale is shown at the top. Branch lengths are measured in Myr. The colour of pie and block charts represent different tRNA gene arrangements in the gene clusters MIQ and TP, respectively.
Figure 5 in Higher-level phylogeny and evolutionary history of nonditrysians (Lepidoptera) inferred from mitochondrial genome sequences
Figure 5. Bayesian inference and the maximum likelihood estimate of phylogenetic relationships among nonditrysian Lepidoptera inferred from the combined molecular dataset (PCGRNA, 64 taxa). Numbers on each node from left to right correspond to the Bayesian posterior probability values and the bootstrap percentage values of ML analysis, respectively. '-' indicates support values <0.5/50 or missing. All habitus photographs are taken by CQ Liao, except photographs of c and g taken by S Yagi, with scientific names as follows: a, Vietomartyria aeuyunjiena Liao, Hirowatari & Huang, 2020 (Micropterigidae); b, Neopseustis fanjingshana Yang, 1988 (Neopseustidae); c, Eriocrania komaii Mizukawa, Hirowatari & Hashimoto, 2006 (Eriocraniidae); d, Ogygioses maoershana Liao, Hirowatari & Huang, 2021 (Palaeosetidae); e, Stigmella sp. (Nepticulidae); f, Nemophora fluorites (Meyrick, 1907) (Adelidae); g, Tischeria decidua Wocke, 1876 (Tischeriidae); h, GibboƲalƲa kobusi Kumata & Kuroko, 1988 (Gracillariidae); i, Lethe helle Leech, 1891 (Nymphalidae)
Figure 1 in Higher-level phylogeny and evolutionary history of nonditrysians (Lepidoptera) inferred from mitochondrial genome sequences
Figure 1. Previous hypotheses on relationships among nonditrysian lineages. A, most parsimonious tree for combined 18S rDNA plus morphological characters from Wiegmann et al. (2002). B, synopsis of relationships inferred from morphology by Kristensen et al. (2007). C, maximum likelihood tree of the nonditrysian portion based on eight genes and 350 taxa from Mutanen et al. (2010). D, relationships among nonditrysian superfamilies inferred from 19 genes and 86 taxa by Regier et al. (2015). E, maximum likelihood tree of over 500 morphological characters and eight molecular genes of 473 taxa combined by Heikkilä et al. (2015). F, maximum likelihood tree of phylogenetic relationships among nonditrysian lineages estimated on phylotranscriptomics data of 28 taxa by Bazinet et al. (2017). G, estimated phylogeny of nonditrysian superfamilies of Lepidoptera synthesized from multiple previous studies by Mitter et al. (2017). H, evolutionary tree derived from a maximum-likelihood analysis of 749 791 amino acid sites from transcriptomes of 186 species by Kawahara et al. (2019). I, phylogenetic tree inferred using 1835 CDS nucleotides of 172 taxa by Mayer et al. (2021). Thicker lines indicate better supported groupings.
Fig. 1 in The mitochondrial genomes of ladybird beetles and implications for evolution and phylogeny
Fig. 1. Organizational maps of the 13 new mitogenomes sequenced in this study. Genes labelled above the line are transcribed in the same direction from left to right, while genes labelled below the line are transcribed in the same direction from right to left. The genes and intergenic spacers are scaled to their length in the mitogenome. Abbreviations: I, transfer RNA specifying Isoleucine; Q, transfer RNA specifying Glutamine; M, transfer RNA specifying Methionine; W, transfer RNA specifying Tryptophan; C, transfer RNA specifying Cysteine; Y, transfer RNA specifying Tyrosine; K, transfer RNA specifying Lysine; D, transfer RNA specifying Aspartic acid; L2, transfer RNA specifying Leucine, codon recognized by UUR; G, transfer RNA specifying Glycine; A, transfer RNA specifying Alanine; R, transfer RNA specifying Arginine; N, transfer RNA specifying Asparagine; S1, transfer RNA specifying Serine, codon recognized by AGN; E, transfer RNA specifying Glutamic acid; F, transfer RNA specifying Phenylalanine; H, transfer RNA specifying Histidine; T, transfer RNA specifying Threonine; P, transfer RNA specifying Proline; S2, transfer RNA specifying Serine, codon recognized by UCN; L1, transfer RNA specifying Leucine, codon recognized by CUN; V, transfer RNA specifying Valine; cox1, cox2, cox3, cytochrome oxidase subunits I, II, III; cob, cytochrome b apoenzyme; nad 1–6, 4L, NADH dehydrogenase subunits 1–6, 4L; atp6, atp8, ATP synthase subunits 6, 8; rrnL, large ribosomal subunit; rrnS, small ribosomal subunit; CR, the putative control region.
Fig. 5 in The mitochondrial genomes of ladybird beetles and implications for evolution and phylogeny
Fig. 5. Ancestral state reconstructions of food preferences based on the PCGRNA-ML tree performed under Mesquite using parsimony method. Probabilities of character states are presented at nodes with pie diagrams.
FIGURE 4 in A new subgenus, Australixodes n. subgen. (Acari: Ixodidae), for the kiwi tick, Ixodes anatis Chilton, 1904, and validation of the subgenus Coxixodes Schulze, 1941 with a phylogeny of 16 of the 22 subgenera of Ixodes Latreille, 1795 from entire mitochondrial genome sequences
FIGURE 4. Ventral view of the gnathosoma of Ixodes (Endopalpiger) barkeri to illustrate the strongly salient (ss) palpal article 1 (I) of the subgenus Endopalpiger (I, palpal article 1). Scale-bar 0.2 mm.
FIGURE 1 in A new subgenus, Australixodes n. subgen. (Acari: Ixodidae), for the kiwi tick, Ixodes anatis Chilton, 1904, and validation of the subgenus Coxixodes Schulze, 1941 with a phylogeny of 16 of the 22 subgenera of Ixodes Latreille, 1795 from entire mitochondrial genome sequences
FIGURE 1. Mitochondrial genomes of Ixodes (Australixodes) anatis Chilton, 1904 (kiwi tick); Ixodes (Coxixodes) ornithorhynchi Lucas, 1846 (platypus tick); Ixodes (Amerixodes) loricatus Neumann, 1899 (no common name); Ixodes (Ixodes) pacificus Cooley & Kohls, 1943 (no common name); Ixodes (Multidentatus) kohlsi Arthur, 1955 (little penguin Ixodes) and I. (Eschatocephalus) vespertilionis (long-legged bat tick). Protein-coding genes are in green, tRNAs are in yellow, rRNAs are in red whereas the two control regions are in blue. Protein-coding genes are labelled with their four-character abbreviations, tRNAs are labelled with their one-letter amino-acid abbreviations whereas the control regions are labelled as CR1 and CR2. The sizes of the mt genomes are indicated in brackets.
thus and genetic % 1 than less indicates Green . ) kb 15 . ca ( Ixodes of ) individuals 40 ( species bold 34 in of are genomes study present mitochondrial the in entire sequenced the Species among. differences reference for genetic, species ) % ( same Pairwise the. 3 from FIGURE sequences in A new subgenus, Australixodes n. subgen. (Acari: Ixodidae), for the kiwi tick, Ixodes anatis Chilton, 1904, and validation of the subgenus Coxixodes Schulze, 1941 with a phylogeny of 16 of the 22 subgenera of Ixodes Latreille, 1795 from entire mitochondrial genome sequences
thus and genetic % 1 than less indicates Green . ) kb 15 . ca ( Ixodes of ) individuals 40 ( species bold 34 in of are genomes study present mitochondrial the in entire sequenced the Species among. differences reference for genetic, species ) % ( same Pairwise the. 3 from FIGURE sequences
indicate branches. above MrBayes numbers by inferred The . supports Ixodes of probability subgenera 22 posterior the of Inference 16 from Bayesian ticks of indicate genomes mitochondrial branches below 40 numbers of The sequences. RAxML nucleotide by the inferred from support inferred bootstrap Phylogenies Likelihood . 2 FIGURE Maximum in A new subgenus, Australixodes n. subgen. (Acari: Ixodidae), for the kiwi tick, Ixodes anatis Chilton, 1904, and validation of the subgenus Coxixodes Schulze, 1941 with a phylogeny of 16 of the 22 subgenera of Ixodes Latreille, 1795 from entire mitochondrial genome sequences
indicate branches. above MrBayes numbers by inferred The . supports Ixodes of probability subgenera 22 posterior the of Inference 16 from Bayesian ticks of indicate genomes mitochondrial branches below 40 numbers of The sequences. RAxML nucleotide by the inferred from support inferred bootstrap Phylogenies Likelihood . 2 FIGURE Maximum
Figure 4 in The mitochondrial genome of the endemic and endangered trumpet-nosed bat Musonycteris harrisoni (Chiroptera: Phyllostomidae)
Figure 4. Selective pressure in protein-coding genes of Musonycteris harrisoni vs Ectophylla alba and vs Anoura caudifer.
Figure 1 in The mitochondrial genome of the endemic and endangered trumpet-nosed bat Musonycteris harrisoni (Chiroptera: Phyllostomidae)
Figure 1. Circular map of the mitochondrial genome in Musonycteris harrisoni (Photo credit: Lorena Orozco-Lugo).
Figure 3 in Whole and nearly complete mitochondrial genomes of an endemic and endangered neotropical rabbit (Romerolagus diazi) assembled using non-invasive eDNA metagenomics (field droppings)
Figure 3. Phylogenetic analysis of Romerolagus diazi and related species in the family Leporidae. Totalevidence phylogenetic tree obtained from ML analysis based on a concatenated alignment of amino acids of the 13 protein-coding genes present in the mitochondrial genome of representatives of the family Leporidae. In the analysis, two species of the family Ochotonidae were used as the outgroup. Numbers above or below the branches represent bootstrap values. Photo credit: J.A. Guerrero.
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