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Figure 3. Bayesian 50 in Molecular systematics and evolution of the subgenus Mesocarabus Thomson, 1875 (Coleoptera: Carabidae: Carabus), based on mitochondrial and nuclear DNA
Figure 3. Bayesian 50% majority rule consensus trees from (a) nuclear (NUC) and (b) mitochondrial (MIT) data sets. The numbers beside nodes represent posterior probabilities and bootstrap values for maximum-likelihood and maximumparsimony analyses, respectively. Labels A–D indicate cladogenetic events referred to in the text for Mesocarabus (in blue) and Iberian Oreocarabus (in red). Asterisks indicate incongruent nodes between MIT and NUC data sets. The species colour codes are as described in Figure 1. Voucher numbers are indicated in brackets. Specimens illustrated: 1, Carabus (Mesocarabus) lusitanicus from Salamanca, Spain; 2, Carabus (Oreocarabus) ghiliani from Segovia, Spain.
Figure 6 in Molecular systematics and evolution of the subgenus Mesocarabus Thomson, 1875 (Coleoptera: Carabidae: Carabus), based on mitochondrial and nuclear DNA
Figure 6. Ultrametric time-calibrated tree for combined DNA markers (ALL-B data set) in Carabus showing ancestral area inferences (A, Iberian Peninsula; B, Eurasia; C, North Africa and Canary Islands). Pie charts represent the probability for each area reconstruction. The grey bars on nodes represent the 95% confidence intervals for node ages (Myr), with mean ages indicated inside bars. The palaeogeographic reconstructions are taken from Andeweg (2002).
Figure 5 in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 5. Phylogenetic relationships of control regions inferred by the maximum likelihood (ML) method. Statistical support is shown on the branches: bootstrap values (above) and posterior probability (below). BI, Bayesian inference; CR, control region.
Figure 1 in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 1. Evolution of mitochondrial genomes in Antarctic notothenioids modified from Zhuang & Cheng (2010). Abbreviations: 12S, 12S ribosomal RNA; CR, control region; Cyt b, cytochrome b; E, tRNAGlu; F, tRNAPhe; ND, nicotinamide adenine dinucleotide (reduced form) dehydrogenase; P, tRNAPro; T, tRNAThr.
Figure 4. A in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 4. A, linear representation of three types of gene content from the partial cytochrome b (Cyt b) to 12S rRNA in the mitochondrial (mt) genome of the mackerel icefish. Black and dark grey arrows respectively represent the first and the second duplicates. The first duplicate of the type-1 genome contains full-length nicotinamide adenine dinucleotide (reduced form) dehydrogenase subunit 6 (ND6) and tRNAGlu. Type-2 contains a half-sized ND6 only. Type-3 does not contain ND6 or tRNAGlu. B, PCR amplifications for detecting ND6 and tRNAGlu in the three types of mt genome of the mackerel icefish. PCR fragments between Cyt b and control region (CR) 2 (Cyt b-CR2) and between CR2 and CR3 (CR2-CR3) contain the first and second copies of ND6, respectively. The PCR fragment between ND5 and Cyt b (ND5-Cyt b) did not contain ND6 or tRNAGlu. M, size marker. Lanes 1, 2, 7, and 10 are type-1 individuals. Lanes 3, 4, 8 and 11 are type-2 individuals. Lanes 5, 6, 9, and 12 are type-3 individuals. Abbreviations: E, tRNAGlu; F, tRNAPhe; P, tRNAPro; T, tRNAThr.
Figure 3 in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 3. Map of the mackerel icefish mitochondrial (mt) genome as a circular diagram. The map represents the mt genome of a type-1 individual in which ND6 and tRNAGlu were transposed to a position between tRNAThr and tRNAPro flanked by intergenic spacers (UN3 and UN4), and the ND6- to -CR segment was duplicated once. Fourteen protein-coding genes, two rRNA genes, and noncoding regions are labelled with abbreviations. Twenty-four tRNA genes are shown by a one-letter amino acid code. Different codons used by each of tRNALeu and tRNASer are shown in parentheses. Genes transcribed from the heavy strand and light strand are respectively presented outside and inside the circle. Heavy- and light-strand replication origins are represented by OH and OL, respectively. Abbreviations: 12S, 12S ribosomal RNA; 16S, 16S ribosomal RNA; A, tRNAAla; ATP, ATP synthase; C, tRNACys; CO, cytochrome oxidase; Cyt b, cytochrome b; D, tRNAAsp; E, tRNAGlu; F, tRNAPhe; G, tRNAGly; H, tRNAHis; I, tRNAIle; K, tRNALys; L, tRNALeu; M, tRNAMet; N, tRNAAsn; ND, nicotiamide adenine dinucleotide (reduced form) dehydrogenase; P, tRNAPro; Q, tRNAGln; R, tRNAArg; S, tRNASer; T, tRNAThr; V, tRNAVal; W, tRNATrp; Y, tRNATyr.
Bioenergetic consequences of sex-specific mitochondrial DNA evolution
<p>Doubly uniparental inheritance (DUI) represents a notable exception to the general rule of strict maternal inheritance (SMI) of mitochondria in metazoans. This system entails the coexistence of two mitochondrial lineages (F- and M-type) transmitted separately through oocytes and sperm, thence providing an unprecedented opportunity for the mitochondrial genome to evolve adaptively for male functions. In this study, we explored the impact of a sex-specific mitochondrial evolution upon gamete bioenergetics of DUI and SMI bivalve species, comparing the activity of key-enzymes of glycolysis, fermentation, fatty acid metabolism, tricarboxylic acid cycle, oxidative phosphorylation and antioxidant metabolism. Our findings suggest reorganized bioenergetic pathways in DUI gametes compared to SMI gametes. This generally results in a decreased enzymatic capacity in DUI sperm with respect to DUI oocytes, a limitation especially prominent at the terminus of the electron transport system. This bioenergetic remodelling fits a reproductive strategy that does not require a high energy input and could potentially link with the preservation of the paternally-transmitted mitochondrial genome in DUI species. Whether this phenotype may derive from positive or relaxed selection acting on DUI sperm is still uncertain.</p>
Figure 6 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements
Figure 6. Hypothetical radiation schemes for Uromastyx and possibly relevant geological events. Approximate distribution range for each taxon (Wilms, 2001) is shown with its abbreviated name: Hard (Uromastyx hardwickii), Aca (U. acanthinura), Mali (U. d. maliensis), Gey (U. geyri), Dis (U. d. dispar), Oce (U. ocellata), Mac (U. macfadyeni), Aeg (U. a. aegyptia), Mic (U. a. microlepis), Orn (U. ornata) and Ben (U. benti).
Figure 5 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements
Figure 5. Neighbour-joining tree constructed based on maximum likelihood distances from 1503 alignable nucleotide sites (the HKY model and transition/transversion ratio of 3.48). The tree was rooted with Chamaeleo africanus as an outgroup. Bootstrap probabilities are shown for neighbour joining, maximum likelihood and maximum parsimony analyses (from left to right). Underlined values mean that the branch was not reconstructed in the best tree topology by the corresponding analyses. Note that two distinct sequence haplotypes are included for Uromastyx acanthinura and U. ocellata. See Material and methods for more details on the analytical conditions. The nucleotide sequences taken from the database are: Chamaeleo africanus (accession No., AF448743), Chlamydosaurus kingii (AF128469), Physignathus lesueurii (AF128463), Acanthosoura capra (AF128498), Salea horsfieldii (AF128490), Trapelus savignii (AF128512), Leiolepis guentherpetersi (AF128461), Leiolepis belliana (U82689), Laudakia caucasia (AF028681) and Laudakia lehmanni (AF028677).
Figure 4 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements
Figure 4. Secondary structures of the inserted sequences found between tRNAGln and tRNAIle genes. The 128 bp insert for Uromastyx ornata can assume alternative secondary structures either with an extremely stable and long stem region (A) or with a clover-leaf structure for the second tRNAGln gene (or pseudogene) and a stable stem-and-loop structure (B). The 59 bp inserted for U. ocellata may also assume a somewhat less stable stem-and-loop structure (C). Heavy-strand sequences are shown and numbers refer to the corresponding positions in their light-strand sequences shown in Fig. 3A. Bars in stems represent Watson–Crick base pairs and dots stand for wobble G–U pairs for RNA.
Figure 2 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements
Figure 2. Evolution of mitochondrial gene organization in Uromastyx. A, typical vertebrate organization plesiomorphic to lizards. B, typical organization for acrodont lizards including Leiolepis and likely the direct common ancestor of Leiolepis and Uromastyx. C, typical Uromastyx organization in which the putative origin of light-strand replication (black box) disappeared from the WANCY tRNA gene cluster. D, organization for U. ornata and likely for the direct common ancestor of U. ornata and U. ocellata, which has an insertion containing a stem-and-loop structure (hatched box) and the second tRNAGln gene or pseudogene (Q*). E, organization for U. ocellata in which Q* disappeared. See Figs 3 and 4 for sequences and secondary structures of the inserted region in U. ornata and U. ocellata.
Figure 3 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements
Figure 3. Nucleotide sequences of the inserted region between the tRNA Gln and tRNAIle genes. A, alignment between the 128 bp insertion in Uromastyx ornata and the 59 bp insertion in U. ocellata (65% identity). B, alignment between the original tRNAGln gene and its second copy within the inserted region for U. ornata (49% identity). Light-strand and heavystrand sequences are shown for A and B, respectively. Dots indicate identity with the first sequence and dashes denote a gap.
Figure 1 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements
Figure 1. Position of primers used for amplification and/or sequencing. See Table 1 for the primer sequences; numbers of primers correspond to those in Table 1.
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.
Data from: Biogeography and evolution of body size and life history of African frogs: phylogeny of squeakers (Arthroleptis) and long-fingered frogs (Cardioglossa) estimated from mitochondrial data
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Mother’s curse and indirect genetic effects: do males matter to mitochondrial genome evolution?
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Bioenergetic consequences of sex-specific mitochondrial DNA evolution
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Accelerated mitochondrial genome evolution in parasitic barnacles driven by adaptive and non-adaptive responses
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Data from: Ancient mitochondrial DNA reveals convergent evolution of giant short-faced bears (Tremarctinae) in North and South America
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