The complete nucleotide sequence of the mitochondrial genome (mitogenome) of Geisha distinctissima (Hemiptera: Flatidae) has been determined in this study. The genome is a circular molecule of 15,971 bp with a total A+T content of 75.1%. The gene content, order, and structure are consistent with the Drosophila yakuba genome structure and the hypothesized ancestral arthropod genome arrangement. All 13 protein-coding genes are observed to have a putative, inframe ATR methionine or ATT isoleucine codons as start signals. Canonical TAA and TAG termination codons are found in nine protein-coding genes, and the remaining four (cox1, atp6, cox3, and nad4) have incomplete termination codons. The anticodons of all transfer RNA (tRNAs) are identical to those observed in D. yakuba and Philaenus spumarius, and can be folded in the form of a typical clover-leaf structure except for tRNA(Ser(AGN)). The major non-coding region (the A+T-rich region or putative control region) between the small ribosomal subunit and the tRNA(Ile) gene includes two sets of repeat regions. The first repeat region consists of a direct 152-bp repetitive unit located near the srRNA gene end, and the second repeat region is composed of a direct repeat unit of 19 bp located toward tRNA(Ile) gene. Comparisons of gene variability across the order suggest that the gene content and arrangement of G. distinctissima mitogenome are similar to other hemipteran insects.
Molecular surveys are leading to the discovery of many new cryptic species of marine algae. This is particularly true for red algal intertidal species, which exhibit a high degree of morphological convergence. DNA sequencing of recent collections of Gelidium along the coast of California, USA, identified two morphologically similar entities that differed in DNA sequence from existing species. To characterize the two new species of Gelidium and to determine their evolutionary relationships to other known taxa, phylogenomic, multigene analyses, and morphological observations were performed. Three complete mitogenomes and five plastid genomes were deciphered, including those from the new species candidates and the type materials of two closely related congeners. The mitogenomes contained 45 genes and had similar lengths (24,963-24,964 bp). The plastid genomes contained 232 genes and were roughly similar in size (175,499-177,099 bp). The organellar genomes showed a high level of gene synteny. The two Gelidium species are diminutive, turf-forming, and superficially resemble several long established species from the Pacific Ocean. The phylogenomic analysis, multigene phylogeny, and morphological evidence confirms the recognition and naming of two new species, describe herein as G. gabrielsonii and G. kathyanniae. On the basis of the monophyly of G. coulteri, G. gabrielsonii, G. galapagense, and G. kathyanniae, we suggest that this lineage likely evolved in California. Organellar genomes provide a powerful tool for discovering cryptic intertidal species and they continue to improve our understanding of the evolutionary biology of red algae and the systematics of the Gelidiales.
The complete mitochondrial genome is greatly important for studies on genetic structure and phylogenetic relationship at various taxonomic levels. To obtain information about the evolutionary trends of mtDNA in the Ulvophyceae and also to gain insights into the phylogenetic relationships between ulvophytes and other chlorophytes, we determined the mtDNA sequence of Caulerpa lentillifera (sea grape) using de novo mitochondrial genome sequencing. The complete genomic DNA of C. lentillifera was circular and 209,034 bp in length, and it was the largest green-algal mitochondrial genome sequenced to date, with a low gene density of 65.2%, which is reminiscent of the "expanded" pattern of evolution exhibited by embryophyte mtDNAs. The C. lentillifera mtDNA consisted of a typical set of 17 protein-coding genes (PCGs), 20 transfer RNA (tRNA) genes, three ribosomal RNA (rRNA) genes, 42 putative open reading frames (ORFs) and 29 introns, which had homologs in green-algal mtDNAs displaying an "ancestral" or a "reduced-derived" pattern of evolution. The overall base composition of its mitochondrial genome was 24.19% for A, 24.94% for T, 25.80% for G, 25.07% for C and 50.87% for GC. The mitochondrial genome of C. lentillifera was characterized by numerous small intergenic regions and introns, which was clearly different from other green algae. With the exception of the NADH dehydrogenase subunit 6 (ND6), ND1, ATP and three tRNA genes (tRNA-His, tRNA-Thr and tRNA-Ala), all other mitochondrial genes were encoded on the heavy strand. All of the PCGs had ATG as their start codon and employed TAA, TGA or TAG as their termination codon. To gain insights into the evolutionary trends of mtDNA in the Ulvophyceae, we inferred the complete mtDNA sequence of C. lentillifera, an ulvophyte belonging to a distinct, early-diverging lineage. Taken together, our data offered useful information for the studies on phylogenetic hypotheses and phylogenetic relationships of C. lentillifera within the Chlorophyta.
We sequenced and annotated the complete mitochondrial genome (mitogenome) of Bactrocera diaphora (Diptera: Tephtitidae), which is an economically important pest in the southwest area of China, India, Sri Lanka, Vietnam and Malaysia. This mitogenome is 15 890 bp in length with an A + T content of 74.103%, and contains 37 typical animal mitochondrial genes that are arranged in the same order as that of the inferred ancestral insects. All protein-coding genes (PCGs) start with a typical ATN codon, except cox1 that begins with TCG. Ten PCGs stop with termination codon TAA or TAG, whereas cox1, nad1 and nad5 have single T-- as the incomplete stop codon. All of the transfer RNA genes present the typical clover leaf secondary structure except trnS1 (AGN) with a looping D-arm. The A + T-rich region is located between rrnS and trnI with a length of 946 bp, and contains a 20 bp poly-T stretch and 22 bp poly-A stretch. Except the control region, the longest intergenic spacer is located between trnR and trnN that is 94 bp long with an excessive high A + T content (95.74%) and a microsatellite-like region (TA)13.
The complete nucleotide sequence of the mitochondrial genome of the white rhinoceros, Ceratotherium simum, was determined. The length of the reported sequence is 16,832 nucleotides. This length can vary, however, due to pronounced heteroplasmy caused by differing numbers of a repetitive motif (5'-CG-CATATACA-3') in the control region. The 16,832 nucleotide sequence presented here is the longest version of the molecule and contains 35 copies of this motif. Comparison between the complete mitochondrial sequences of the white and the Indian (Rhinoceros unicornis) rhinoceroses allowed an estimate of the date of the basal evolutionary divergence among extant rhinoceroses. The calculation suggested that this divergence took place approximately 27 million years before present.
The first complete mitochondrial genome sequence for a nemertean, Cephalothrix simula, was determined by conventional and long PCR and sequencing with primer walking methods. This circular genome is 16,296 bp in size and encodes 37 genes (13 protein-coding genes, 2 ribosomal RNAs, and 22 transfer RNAs) typically found in metazoans. All genes are encoded on H-strand except two tRNAs (trnT and trnP). It differs from those reported for other metazoans, but some gene junctions are shared with those of other protostomes. Structure of the mitochondrial genome of C. simula is mostly concordant with the partial mitochondrial genome known for Cephalothrix rufifrons, but notable differences include three large indel events and transposition of 2 tRNAs. Nucleotide composition of the mitochondrial genome of C. simula is highly A+T biased. The compositional skew is strongly reflected in the codon-usage patterns and the amino acid compositions of the mitochondrial proteins. An AT-rich noncoding region with potential to form stem-loop structures may be involved in the initiation of replication or transcription. Gene adjacencies and phylogenetic analysis based on the 12 concatenated amino acid sequences (except atp8) of mitochondrial protein-coding genes show that the nemertean is close to the coelomate lophotrochozoans, rather than the acoelomate platyhelminths.
Four new complete mitochondrial genomes (mitogenomes) from the two superfamilies Ocypodoidea and Grapsoidea were sequenced, which represented Uca (Gelasimus) borealis (Ocypodidae: Ucinae), Dotilla wichmani (Dotillidae), Metopograpsus quadridentatus (Grapsidae: Grapsinae), and Gaetice depressus (Varunidae: Gaeticinae). All of the mitogenomes shared the complete set of 37 mitochondrial genes. Mitogenome lengths were 15,659, 15,600, 15,517, and 16,288 bp, respectively, with A + T contents of 69.41%, 68.46%, 70.30%, and 72.96%, respectively. Comparative genomic analyses suggested that they exhibited different genomic rearrangements. In particular, G. depressus shared a major rearrangement pattern present in Eriocheir crabs, while the remainder shared the brachyuran ground genomic rearrangement patterns. Phylomitogenomic inferences provided new evidence for the strongly supported nesting of Thoracotremata within Heterotremata clades. A close phylogenetic relationship was observed between Varunidae and Macrophthalmidae crabs, and between Dotillidae and Grapsidae crabs, which was consistent with mitochondrial genomic rearrangement similarities. Altogether, these results suggest the presence of reciprocal paraphyly for Ocypodoidea and Grapsoidea.
Structural and functional observations are reviewed which provide evidence for a central role of redox Bohr effect linked to the low-spin heme a in the proton pump of bovine heart cytochrome c oxidase. Data on the membrane sidedness of Bohr protons linked to anaerobic oxido-reduction of the individual metal centers in the liposome reconstituted oxidase are analysed. Redox Bohr protons coupled to anaerobic oxido-reduction of heme a (and Cu(A)) and Cu(B) exhibit membrane vectoriality, i.e. protons are taken up from the inner space upon reduction of these centers and released in the outer space upon their oxidation. Redox Bohr protons coupled to anaerobic oxido-reduction of heme a(3) do not, on the contrary, exhibit vectorial nature: protons are exchanged only with the outer space. A model of the proton pump of the oxidase, in which redox Bohr protons linked to the low-spin heme a play a central role, is described. This article is part of a Special Issue entitled: Allosteric cooperativity in respiratory proteins.
Ceratitis fasciventris is a serious agricultural pest of the Tephritidae family that belongs to the African Ceratitis FAR species complex. Species limits within the FAR complex are obscure and multidisciplinary approaches have attempted to resolve phylogenetic relationships among its members. These studies support the existence of at least three additional species in the complex, C. anonnae, C. rosa and C. quilicii, while they indicate the presence of two structured populations (F1 and F2) within the C. fasciventris species. In the present study we present the mitotic karyotype, polytene chromosome maps, in situ hybridization data and the complete mitochondrial genome sequence of an F2 population of C. fasciventris. This is the first polytene chromosome map and complete mitogenome of a member of the FAR complex and only the second reported for the Ceratitis genus. Both polytene chromosomes and mitochondrial sequence could provide valuable information and be used as reference for comparative analysis among the members of the complex towards the clarification of their phylogenetic relationships.
We analyze mitochondrial genomes to reconstruct a robust phylogenetic framework for caecilian amphibians and use this to investigate life-history evolution within the group. Our study comprises 45 caecilian mitochondrial genomes (19 of them newly reported), representing all families and 27 of 32 currently recognized genera, including some for which molecular data had never been reported. Support for all relationships in the inferred phylogenetic tree is high to maximal, and topology tests reject all investigated alternatives, indicating an exceptionally robust molecular phylogenetic framework of caecilian evolution consistent with current morphology-based supraspecific classification. We used the mitogenomic phylogenetic framework to infer ancestral character states and to assess correlation among three life-history traits (free-living larvae, viviparity, specialized pre-adult or vernal teeth), each of which occurs only in some caecilian species. Our results provide evidence that an ancestor of the Seychelles caecilians abandoned direct development and re-evolved a free-living larval stage. This study yields insights into the concurrent evolution of direct development and of vernal teeth in an ancestor of Teresomata that likely gave rise to skin-feeding (maternal dermatophagy) behavior and subsequently enabled evolution of viviparity, with skin feeding possibly a homologous precursor of oviduct feeding in viviparous caecilians.
Little is known about the variations of nematode mitogenomes (mtDNA). Sequencing a complete mtDNA using a PCR approach remains a challenge due to frequent genome reorganizations and low sequence similarities between divergent nematode lineages. Here, a genome skimming approach based on HiSeq sequencing (shotgun) was used to assemble de novo the first complete mtDNA sequence of a root-knot nematode (Meloidogyne graminicola). An AT-rich genome (84.3%) of 20,030 bp was obtained with a mean sequencing depth superior to 300. Thirty-six genes were identified with a semi-automated approach. A comparison with a gene map of the M. javanica mitochondrial genome indicates that the gene order is conserved within this nematode lineage. However, deep genome rearrangements were observed when comparing with other species of the superfamily Hoplolaimoidea. Repeat elements of 111 bp and 94 bp were found in a long non-coding region of 7.5 kb, as similarly reported in M. javanica and M. hapla. This study points out the power of next generation sequencing to produce complete mitochondrial genomes, even without a reference sequence, and possibly opening new avenues for species/race identification, phylogenetics and population genetics of nematodes.
The complete sequence of mitochondrial DNA of a longnose skate, Raja rhina was determined for the first time. It is 16,910 bp in length containing 2 rRNA, 22 tRNA and 13 protein coding genes with the same gene order and structure as those of other Rajidae species. The nucleotide of L-strand is composed of 30.1% A, 27.2% C, 28.5% T and 14.2% G, showing a slight A + T bias. The G is the least used base and markedly lower at the third codon position (5.4%). Twelve of the 13 protein coding genes use ATG as their start codon while the COX1 starts with GTG. As for stop codon, only ND4 shows incomplete stop codon TA. This mitogenome is the first report for a species of the genus Raja, and providing a valuable resource of genetic information for understanding the phylogenetic relationship and the evolution of the genus Raja as well as the family, Rajidae.
Six complete and three partial actiniarian mitochondrial genomes were amplified in two semi-circles using long-range PCR and pyrosequenced in a single run on a 454 GS Junior, doubling the number of complete mitogenomes available within the order. Typical metazoan mtDNA features included circularity, 13 protein-coding genes, 2 ribosomal RNA genes, and length ranging from 17,498 to 19,727 bp. Several typical anthozoan mitochondrial genome features were also observed including the presence of only two transfer RNA genes, elevated A + T richness ranging from 54.9 to 62.4%, large intergenic regions, and group 1 introns interrupting NADH dehydrogenase subunit 5 and cytochrome c oxidase subunit I, the latter of which possesses a homing endonuclease gene. Within the sea anemone Alicia sansibarensis, we report the first mitochondrial gene order rearrangement within the Actiniaria, as well as putative novel non-canonical protein-coding genes. Phylogenetic analyses of all 13 protein-coding and 2 ribosomal genes largely corroborated current hypotheses of sea anemone interrelatedness, with a few lower-level differences.
The gypsy moth, Lymantria dispar L., is one of the most destructive forest pests in the world. While the subspecies established in North America is the European gypsy moth (L. dispar dispar), whose females are flightless, the two Asian subspecies, L. dispar asiatica and L. dispar japonica, have flight-capable females, enhancing their invasiveness and warranting precautionary measures to prevent their permanent establishment in North America. Various molecular tools have been developed to help distinguish European from Asian subspecies, several of which are based on the mitochondrial barcode region. In an effort to identify additional informative markers, we undertook the sequencing and analysis of the mitogenomes of 10 geographic variants of L. dispar, including two or more variants of each subspecies, plus the closely related L. umbrosa as outgroup. Several regions of the gypsy moth mitogenomes displayed nucleotide substitutions with potential usefulness for the identification of subspecies and/or geographic origins. Interestingly, the mitogenome of one geographic variant displayed significant divergence relative to the remaining variants, raising questions about its taxonomic status. Phylogenetic analyses placed this population from northern Iran as basal to the L. dispar clades. The present findings will help improve diagnostic tests aimed at limiting risks of AGM invasions.
The complete mitochondrial genome of the Epinephelus tukula was presented in this study. The mitochondrial genome is 16,503 bp long and consists of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region. The gene order and composition of Epinephelus tukula mitochondrial genome was similar to that of most other vertebrates. The nucleotide compositions of the light strand are 28.37% of A, 29.00% of C, 26.36% of T and 16.26% of G. With the exception of the NADH dehydrogenase subunit 6 (ND6) and seven tRNA genes, all other mitochondrial genes are encoded on the heavy strand.
Cox14p and Coa3p have been shown to regulate translation of the mitochondrial COX1 mRNA and to be required for assembly of cytochrome oxidase. We present evidence that Cox14p and Coa3p stabilize previously identified Cox1p intermediates and that in the absence of either protein, Cox1p aggregates with itself and other mitochondrial gene products, including cytochrome b, Var1p and Cox2p. Our evidence suggests that Cox1p assembly intermediates are in close proximity to other mitochondrially translated proteins and that an important function of Cox14p and Coa3p is to prevent Cox1 from entering into unproductive aggregation pathways.
We have determined the complete mitochondrial genome of the yellow-spotted long horned beetle, Psacothea hilaris (Coleoptera: Cerambycidae), an endangered insect species in Korea. The 15,856-bp long P. hilaris mitogenome harbors gene content typical of the animal mitogenome and a gene arrangement identical to the most common type found in insect mitogenomes. As with all other sequenced coleopteran species, the 5-bp long TAGTA motif was also detected in the intergenic space sequence located between tRNA(Ser)(UCN) and ND1 of P. hilaris. The 1,190-bp long non-coding A+T-rich region harbors an unusual series of seven identical repeat sequences of 57-bp in length and several stretches of sequences with the potential to form stem-and-loop structures. Furthermore, it contains one tRNA(Arg)-like sequence and one tRNA(Lys)-like sequence. Phylogenetic analysis among available coleopteran mitogenomes using the concatenated amino acid sequences of PCGs appear to support the sister group relationship of the suborder Polyphaga to all remaining suborders, including Adephaga, Myxophaga, and Archostemata. Among the two available infraorders in Polyphaga, a monophyletic Cucujiformia was confirmed, with the placement of Cleroidea as the basal lineage for Cucujiformia. On the other hand, the infraorder Elateriformia was not identified as monophyletic, thereby indicating that Scirtoidea and Buprestoidea are the basal lineages for Cucujiformia and the remaining Elateriformia.
The metazoan taxon Syndermata (Monogononta, Bdelloidea, Seisonidea, Acanthocephala) comprises species with vastly different lifestyles. The focus of this study is on the phylogeny within the syndermatan subtaxon Acanthocephala (thorny-headed worms, obligate endoparasites). In order to investigate the controversially discussed phylogenetic relationships of acanthocephalan subtaxa we have sequenced the mitochondrial (mt) genomes of Echinorhynchus truttae (Palaeacanthocephala), Paratenuisentis ambiguus (Eoacanthocephala), Macracanthorhynchus hirudinaceus (Archiacanthocephala), and Philodina citrina (Bdelloidea). In doing so, we present the largest molecular phylogenetic dataset so far for this question comprising all major subgroups of Acanthocephala. Alongside with publicly available mt genome data of four additional syndermatans as well as 18 other lophotrochozoan (spiralian) taxa and one outgroup representative, the derived protein-coding sequences were used for Maximum Likelihood as well as Bayesian phylogenetic analyses. We achieved entirely congruent results, whereupon monophyletic Archiacanthocephala represent the sister taxon of a clade comprising Eoacanthocephala and monophyletic Palaeacanthocephala (Echinorhynchida). This topology suggests the secondary loss of lateral sensory organs (sensory pores) within Palaeacanthocephala and is further in line with the emergence of apical sensory organs in the stem lineage of Archiacanthocephala.
The complete sequence mitochondrial genome of Takydromus sexlineatus was determined using long PCR and conserved primers walking approaches. The genome was 18,943 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region (CR). The gene composition and order of T. sexlineatus were similar to most other squamate reptiles. All protein-coding genes begin with ATG as initiation codon except COI using GTG. Seven genes (ATP8. ND4L. ND5. Cytb. ND1. COI and ND6) ended with TAA, TAG, AGGA and AGA stop codon, the remaining 6 genes had incomplete stop codons T/TA. The overall base composition of the genome in descending order was 31.48% A, 24.67% C, 30.79% T and 13.05% G, with a slight A + T bias of 62.27%. CR is located between the tRNA-Pro and tRNA-Phe genes and is 3562 bp in length, some tandem repeat sequences, conserved elements (CSB1-3) and termination associated sequences (TAS1-3) were found in the control region.
The complete mitochondrial genome (mitogenome) sequences of two primitive crabs, Umalia orientalis and Lyreidus brevifrons (Decapoda: Brachyura: Raninidae) were determined. The mitogenomes of the two species are 15,466 and 16,112bp in length with AT content of 68.0% and 70.6%, respectively. Each genome contains 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes. The gene arrangement of U. orientalis is the same with those reported for most brachyuran species. Nevertheless, the gene arrangement of L. brevifrons differs from that of U. orientalis in having an additional non-coding region. The newly found non-coding region is located between nad3 and trnA with 641bp in length. Its nucleotide composition and secondary structure are similar to the typical control region. In L. brevifrons, the secondary structures of trnS-AGN and trnI are significantly different from those in U. orientalis and other brachyuran species. The start codon for cox1 is ATG in all reported Eubrachyura mitogenomes, while a common start codon ACG is found in the Podotremata. Phylogenetic analyses for crustacean decapods based on the nucleotide and amino acid of 13 PCGs indicate that Homolidae is more primitive in Brachyura, and Raninidae is a sister group to Eubrachyura. This implies that Raninidae is closer to Eubrachyura than to Homolidae, and Podotremata may be a paraphyletic assemblage. The results also indicate that the subfamily Lyreidinae is closer to Notopodinae than to Ranininae within Raninidae. The novel mitogenome data provides useful information for refining the phylogenetic relationships within Brachyura.
Because hornworts occupy a pivotal position in early land colonization as sister to other bryophytes, sister to tracheophytes, or sister to all other land plants, a renewed interest has arisen in their phylogenetic diversity, morphology, and genomes. To date, only five organellar genome sequences are available for hornworts. We sequenced the plastome (155,956 bp) and mitogenome (212,153 bp) of the hornwort Leiosporoceros dussii, the sister taxon to all hornworts. The Leiosporoceros organellar genomes show conserved gene structure and order with respect to the other hornworts and other bryophytes. Additionally, using RNA-seq data we quantified the frequency of RNA-editing events (the canonical C-to-U and the reverse editing U-to-C) in both organellar genomes. In total, 109 sites were found in the plastome and 108 in the mitogenome, respectively. The proportion of edited sites corresponds to 0.06% of the plastome and 0.05% of the mitogenome (in reference to the total genome size), in contrast to 0.58% of edited sites in the plastome of Anthoceros angustus (161,162 bp). All edited sites in the plastome and 88 of 108 sites in the mitogenome are C-to-U conversions. Twenty reverse edited sites (U-to-C conversions) were found in the mitogenome (17.8%) and none in the plastome. The low frequency of RNA editing in Leiosporoceros, which is nearly 88% less than in the plastome of Anthoceros and the mitogenome of Nothoceros, indicates that the frequency of RNA editing has fluctuated during hornwort diversification. Hornworts are a pivotal land plant group to unravel the genomic implications of RNA editing and its maintenance despite the evident evolutionary disadvantages.
In this study, we determined the complete mitochondrial (mt) genome of Microphysogobio alticorpus (Cypriniformes, Cyprinidae). This mt genome, consisting of 16,568 base pairs (bp), encoded genes for 13 protein-coding genes, 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and a noncoding control region (CR) as those found in other vertebrates, with the gene order identical to that of typical vertebrates. The overall base composition of the heavy strand shows T: 26.03%, C: 26.73%, A: 30.20% and G: 17.04%, apparently with a slight AT bias. The two rRNA genes of 12S rRNA (958 bp) and 16S rRNA (1693 bp) are located between tRNA(Phe) and tRNA(Leu()(UUR)) and separated by the tRNA(Val) gene. CR, of 890 bp in length, is located between tRNA(Pro) and tRNA(Phe).
Recent development and advancement of next-generation sequencing (NGS) technologies have enabled the determination of mitochondrial genome (mitogenome) at extremely efficiency. In this study, complete or partial mitogenomes for 19 cicadomorphan species and six fulgoroid species were reconstructed by using the method of high-throughput sequencing from pooled DNA samples. Annotation analyses showed that the mitogenomes obtained have the typical insect mitogenomic content and structure. Combined with the existing hemipteran mitogenomes, a series of datasets with all 37 mitochondrial genes (up to 14,381 nt total) under different coding schemes were compiled to test previous hypotheses of deep-level phylogeny of Cicadomorpha. Thirty-seven species representing Cicadomorpha constituted the ingroup. A taxon sampling with nine species from Fulgoroidea and six from Heteroptera comprised the outgroup. The phylogenetic reconstructions congruently recovered the monophyly of each superfamily within Cicadomorpha. Furthermore, the hypothesis (Membracoidea + (Cicadoidea + Cercopoidea)) was strongly supported under the heterogeneous CAT model.
In this study, a comparative genomics approach is employed to investigate the forces that shape evolutionary change in the mitochondrial DNA (mtDNA) of members of the Drosophila melanogaster subgroup. This approach facilitates differentiation of the patterns of variation resulting from processes acting at a higher level from those acting on a single gene. The mitochondrial genomes of three isofemale lines of D. simulans (siI, -II, and -III), two of D. melanogaster (Oregon R and a line from Zimbabwe), and D. mauritiana (maI and -II), and one of D. sechellia were sequenced and compared with that derived from D. yakuba. Data presented here indicate that at least three broad mechanisms shape the evolutionary dynamics of mtDNA in these taxa. The first set of mechanisms is intrinsic to the molecule. Dominant processes may be interpreted as selection for an increased rate of replication of the mtDNA molecule, biases in DNA repair, and differences in the pattern of nucleotide substitution among strands. In the genes encoded on the major strand (62% of the coding DNA) changes to or from C predominate, whereas on the minor changes to or from G predominate. The second set of mechanisms affects distinct lineages. There are evolutionary rate differences among lineages, possibly owing to population demographic changes or changes in mutational biases. This is supported by the heterogeneity found in synonymous, nonsynonymous, and silent substitutions. The third set of mechanisms differentially affects distinct genes. A maximum-likelihood sliding-window analysis detected four disjunct regions that have a significantly different nucleotide substitution process from that derived from the complete sequence. These data show the potential for comparative genomics to tease apart subtle forces that shape the evolution of DNA.