Endotherms, ectotherms, and mitochondrial genome-size variation

A description of the complete mitochondrial genomes of Amphiporus formidabilis, Prosadenoporus spectaculum and Nipponnemertes punctatula (Nemertea: Hoplonemertea: Monostilifera)

We sequenced the complete mitochondrial genomes (mitogenomes) of three Hoplonemertea species, Amphiporus formidabilis, Prosadenoporus spectaculum and Nipponnemertes punctatula, which are 14,616, 14,655 and 15,354 bp in length, respectively. Each of the three circular mitogenomes consists of 37 typical genes and some non-coding regions. The nucleotide composition of the coding strand is biased toward T, almost a half of total nucleotides in these mitogenomes. There are many poly-T tracts across these mitogenomes, which exhibit T-number variation within different clones of protein-coding genes, mainly resulting from false PCR amplification. The major non-coding regions have tandem repeat motifs and hairpin-like structures that may be associated with the initiation of replication or transcription. Data published to date for nemerteans show that Palaeonemertea species usually bear the largest mitogenomes, while representatives in the more recently derived Distromatonemertea clade bear the smallest ones; and that the gene arrangement of mitogenomes seems to be variable within the phylum Nemertea, but stable within either of Heteronemertea and Hoplonemertea.

Evolution along the mutation gradient in the dynamic mitochondrial genome of salamanders

Mitochondria are intracellular organelles where oxidative phosphorylation is carried out to complete ATP synthesis. Mitochondria have their own genome; in metazoans, this is a small, circular molecule encoding 13 electron transport proteins, 22 tRNAs, and 2 rRNAs. In invertebrates, mitochondrial gene rearrangement is common, and it is correlated with increased substitution rates. In vertebrates, mitochondrial gene rearrangement is rare, and its relationship to substitution rate remains unexplored. Mitochondrial genes can also show spatial variation in substitution rates around the genome due to the mechanism of mtDNA replication, which produces a mutation gradient. To date, however, the strength of the mutation gradient and whether movement along the gradient in rearranged (or otherwise modified) genomes impacts genic substitution rates remain unexplored in the majority of vertebrates. Salamanders include both normal mitochondrial genomes and independently derived rearrangements and expansions, providing a rare opportunity to test the effects of large-scale changes to genome architecture on vertebrate mitochondrial gene sequence evolution. We show that: 1) rearranged/expanded genomes have higher substitution rates; 2) most genes in rearranged/expanded genomes maintain their position along the mutation gradient, substitution rates of the genes that do move are unaffected by their new position, and the gradient in salamanders is weak; and 3) genomic rearrangements/expansions occur independent of levels of selective constraint on genes. Together, our results demonstrate that large-scale changes to genome architecture impact mitochondrial gene evolution in predictable ways; however, despite these impacts, the same functional constraints act on mitochondrial protein-coding genes in both modified and normal genomes.

Geographic variation within a tandemly repeated mitochondrial DNA D-loop region of a North American freshwater fish, Pylodictis olivaris

The present study reports the distribution of a 35-bp mitochondrial DNA (mtDNA) D-loop tandemly repeated sequence in the populations of a North American freshwater catfish, Pylodictis olivaris, and the important role of a past geological event in the phylogeographic pattern of this species. A total of 330 individuals of flathead catfish, representing 34 drainages throughout the species' native range in the United States, were collected. While more than 70% of individuals sampled from the Southeastern Gulf Coast drainages were characterized by the presence of a 35-bp mtDNA D-loop tandem repeat proximal to the 5' end, more than 95% of samples from the Mississippi River and its tributaries, as well as from the drainages of the Southwest Gulf Coast region, lack this tandem repeat. Concomitantly, phylogenetic analyses revealed the existence of two distinct matrilineal lineages (lineage I and II) of P. olivaris, which were estimated to have diverged from a common ancestor sometime between 0.70 and 2.05myr ago. While one lineage is comprised of samples from the Mississippi River and its tributaries and rivers draining to the Southwest Gulf Coast, the other lineage is comprised of samples from the Southeastern Gulf Coast drainages. Each lineage also has two sub-lineages, which also showed geographic specificity.

An examination of the origin and evolution of additional tandem repeats in the mitochondrial DNA control region of Japanese sika deer (Cervus Nippon)

Tandem repeat units are only detected in the left domain of the mitochondrial DNA control region in sika deer. Previous studies showed that Japanese sika deer have more tandem repeat units than its cousins from the Asian continent and Taiwan, which often have only three repeat units. To determine the origin and evolution of these additional repeat units in Japanese sika deer, we obtained the sequence of repeat units from an expanded dataset of the control region from all sika deer lineages. The functional constraint is inferred to act on the first repeat unit because this repeat has the least sequence divergence in comparison to the other units. Based on slipped-strand mispairing mechanisms, the illegitimate elongation model could account for the addition or deletion of these additional repeat units in the Japanese sika deer population. We also report that these additional repeat units could be occurring in the internal positions of tandem repeat regions, possibly via coupling with a homogenization mechanism within and among these lineages. Moreover, the increased number of repeat units in the Japanese sika deer population could reflect a balance between mutation and selection, as well as genetic drift.

Structure and evolution of the Phasianidae mitochondrial DNA control region

The mitochondrial DNA control region is an area of the mitochondrial genome which is non-coding DNA. To infer the structural and evolutionary characteristics of Phasianidae mitochondrial DNA control region, the entire control region sequences of 34 species were analyzed. The length of the control region sequences ranged from 1144 bp (Phasianus colchicus) to 1555 bp (Coturnix japonica) and can be separated into three domains. The average genetic distances among the species within the genera varied from 1.96% (Chrysolophus) to 12.05% (Coturnix). The average genetic distances showed significantly negative correlation with ts/tv. In most genera (except Coturnix), domain I is the most variable among the three domains. However, the first 150 nucleotides apparently evolved at unusually low rates. Four conserved sequence boxes in the domain II of Phasianidae sequences were identified. The alignment of the Phasianidae four boxes and CSB-1 sequences showed considerable sequence variation.

Intraspecific rearrangement of duplicated mitochondrial control regions in the Luzon Tarictic Hornbill Penelopides manillae (Aves: Bucerotidae)

Philippine hornbills of the genera Aceros and Penelopides (Bucerotidae) are known to possess a large tandemly duplicated fragment in their mitochondrial genome, whose paralogous parts largely evolve in concert. In the present study, we surveyed the two distinguishable duplicated control regions in several individuals of the Luzon Tarictic Hornbill Penelopides manillae, compare their characteristics within and across individuals, and report on an intraspecific mitochondrial gene rearrangement found in one single specimen, i.e., an interchange between the two control regions. To our knowledge, this is the first observation of two distinct mitochondrial genome rearrangements within a bird species. We briefly discuss a possible evolutionary mechanism responsible for this pattern, and highlight potential implications for the application of control region sequences as a marker in population genetics and phylogeography.

Ancestral gene organization in the mitochondrial genome of Thyridosmylus langii (McLachlan, 1870) (Neuroptera: Osmylidae) and implications for lacewing evolution

The first complete mitochondrial genome of the lacewing family Osmylidae (Thyridosmylus langii (McLachlan, 1870)) (Neuroptera) was sequenced in this study. The genome is a circular molecule of 16,221 bp containing the typical 37 genes but is arranged in the same order as that of the putative ancestor of hexapod and lacks translocation of trnC as shared by all previously sequenced neuropteran mtDNAs. This reveals that trnC translocation does not represent an organizational synapomorphy in the mitochondrion for the entire Neuroptera clade. Comparative analysis of neuropteran tRNA genes reveals a relatively slow and conserved evolution of the mitochondrion throughout the order. Secondary structure models of the ribosomal RNA genes of T. langii largely agree with those proposed for other insect orders. Nevertheless, domain I of T. langii rrnL is consisted of nine helices rather than eight helices which is typical for neuropteran rrnL. Protein-coding genes have typical mitochondrial start codons, with the exception of COI, which uses the TCG start codon also found in Ithonidae and Chrysopidae. Like other neuropteran insects, the control region is the most AT-rich region and comparatively simple, with little evidence of conserved blocks or long tandem repeats. Considering the issues of base-compositional and branch length heterogeneity, we used a range of phylogenetic approaches to recover neuropteridan relationships and explored the effect of method choice on recovery of monophyly of Neuropterida: ((Neuroptera + Megaloptera) + Raphidioptera). The monophyly of Neuroptera and the more basal position of Osmylidae were also recovered by different datasets and phylogenetic methods.

The complete mitochondrial genomes of three grasshoppers, Asiotmethis zacharjini, Filchnerella helanshanensis and Pseudotmethis rubimarginis (Orthoptera: Pamphagidae)

The complete mitogenomes of Asiotmethis zacharjini, Filchnerella helanshanensis and Pseudotmethis rubimarginis are 15,660 bp, 15,657 bp and 15,661 bp in size, respectively. All three mitogenomes contain a standard set of 13 protein - coding genes, 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and an A+T-rich region in the same order as those of the other analysed caeliferan species, including the rearrangement of trnAsp and trnLys. The putative initiation codon for the cox1 gene in the three species is CCG. The long polythymine stretch (T-stretch) in the A+T-rich region of the three species is not adjacent to the trnIle but inside the stem-loop sequence in the majority strand. The mitogenomes of F. helanshanensis and P. rubimarginis have higher overall similarities. The characterization of the three mitogenomes will enrich our knowledge on the Pamphagidae mitogenome. The phylogenetic analyses indicated that within the Caelifera, Pyrgomorphoidea is a sister group to Acridoidea. The species from the Pamphagidae form a monophyletic group, as is the case for Acrididae. Furthermore, the two families cluster as sister groups, supporting the monophyly of Acridoidea. The relationships among eight acridid subfamilies were (Cyrtacanthacridinae+(Calliptaminae+(Catantopinae+(Oxyinae+(Melanopline+(Acridinae+(Oedipodinae+Gomphocerinae).

Low metabolic rates in salamanders are correlated with weak selective constraints on mitochondrial genes

Mitochondria are the site for the citric acid cycle and oxidative phosphorylation (OXPHOS), the final steps of ATP synthesis via cellular respiration. Each mitochondrion contains its own genome; in vertebrates, this is a small, circular DNA molecule that encodes 13 subunits of the multiprotein OXPHOS electron transport complexes. Vertebrate lineages vary dramatically in metabolic rates; thus, functional constraints on mitochondrial-encoded proteins likely differ, potentially impacting mitochondrial genome evolution. Here, we examine mitochondrial genome evolution in salamanders, which have the lowest metabolic requirements among tetrapods. We show that salamanders experience weaker purifying selection on protein-coding sequences than do frogs, a comparable amphibian clade with higher metabolic rates. In contrast, we find no evidence for weaker selection against mitochondrial genome expansion in salamanders. Together, these results suggest that different aspects of mitochondrial genome evolution (i.e., nucleotide substitution, accumulation of noncoding sequences) are differently affected by metabolic variation across tetrapod lineages.

Thermal habit, metabolic rate and the evolution of mitochondrial DNA

The hallmarks of animal mitochondrial DNA (mtDNA) are a rapid rate of sequence evolution, a small genome carrying the same set of homologous genes, maternal inheritance and lack of recombination. Over the past few years, a variety of different observations has challenged these accepted notions of mitochondrial biology. Notable examples include evidence for variable rates of mtDNA sequence evolution among taxa, evidence for large and variable mitochondrial genome sizes in certain groups, and a growing number of cases in metazoans of 'paternal leakage' in the inheritance of mtDNA. Several recent studies have uncovered different lines of evidence suggesting that an organism's thermal habit, or metabolic rate, can influence the evolution of mtDNA.

Multiple independent origins of mitochondrial control region duplications in the order Psittaciformes

Mitochondrial genomes are generally thought to be under selection for compactness, due to their small size, consistent gene content, and a lack of introns or intergenic spacers. As more animal mitochondrial genomes are fully sequenced, rearrangements and partial duplications are being identified with increasing frequency, particularly in birds (Class Aves). In this study, we investigate the evolutionary history of mitochondrial control region states within the avian order Psittaciformes (parrots and cockatoos). To this aim, we reconstructed a comprehensive multi-locus phylogeny of parrots, used PCR of three diagnostic fragments to classify the mitochondrial control region state as single or duplicated, and mapped these states onto the phylogeny. We further sequenced 44 selected species to validate these inferences of control region state. Ancestral state reconstruction using a range of weighting schemes identified six independent origins of mitochondrial control region duplications within Psittaciformes. Analysis of sequence data showed that varying levels of mitochondrial gene and tRNA homology and degradation were present within a given clade exhibiting duplications. Levels of divergence between control regions within an individual varied from 0-10.9% with the differences occurring mainly between 51 and 225 nucleotides 3' of the goose hairpin in domain I. Further investigations into the fates of duplicated mitochondrial genes, the potential costs and benefits of having a second control region, and the complex relationship between evolutionary rates, selection, and time since duplication are needed to fully explain these patterns in the mitochondrial genome.

Complete mitochondrial genome of Locusta migratoria migratoria (Orthoptera: Oedipodidae): three tRNA-like sequences on the N-strand

The complete 16053 bp mitochondrial genome (mitogenome) sequence of Locusta migratoria migratoria has been determined. This mitogenome contains the base compositional biases and codon usage typical of metazoans, and the RSCU values indicate a negative correlation with the C and G contents in codon. The orientation and gene order of the L. migratoria migratoria is identical to Locusta migratoria migratoiodes. An unusual feature of the L. migratoria migratoria mitogenome is the presence of three tRNA-like structures on the N-strand: one tRNA(Ile)-like and two tRNA(Leu(CUN))-like sequences. The tRNA-like sequences have proper folding structures and anticodons sequences. Two repeated DNA sequences, Rpt I and Rpt II, were found in the A+T-rich region of the L. migratoria migratoria mitogenome. Both repeated sequences have various features. In the 5' region of Rpt I, a 51 bp fragment is localized in the srRNA gene; and there are two tandemly sub-repeated DNA sequences (sub-Rpts), Rpt 1-4, within Rpt I and Rpt II. One stem-loop structure on the N-strand that may be involved in the N-strand replication initiation was found in the A+T-rich region.

Variation in repeat length and heteroplasmy of the mitochondrial DNA control region along a core-edge gradient in the eastern spadefoot toad (Pelobates syriacus)

Peripheral populations are those situated at the distribution margins of a species and are often subjected to more extreme abiotic and biotic conditions than those at the core. Here, we hypothesized that shorter repeat length and fewer heteroplasmic mitochondrial DNA (mtDNA) copies, which are associated with more efficient mitochondrial function, may be related to improved survival under extreme environmental conditions. We sampled eastern spadefoot toads (mostly as tadpoles) from 43 rain pools distributed along a 300-km gradient from core to edge of the species' distribution. We show that mean pool tandem repeat length and heteroplasmy increase from edge to core, even after controlling for body size. We evaluate several alternative hypotheses and propose the Fisher hypothesis as the most likely explanation. However, additional sequential sampling and experimental studies are required to determine whether selection under extreme conditions, or alternative mechanisms, could account for the gradient in heteroplasmy and repeat length in the mtDNA control region.

Polymorphic minisatellites in the mitochondrial DNAs of Oryza and Brassica

Polymorphic analyses of angiosperm mitochondrial DNA are rare in comparison with chloroplast DNA, because few target sequences in angiosperm mitochondrial DNA are known. Minisatellites, a tandem array of repeated sequences with a repeat unit of 10 to ~100 bp, are popular target sequences of animal mitochondria, but Beta vulgaris is the only known angiosperm species for which such an analysis has been conducted. From this lack of information, it was uncertain as to whether polymorphic minisatellites existed in other angiosperm species. Ten plant mitochondrial DNAs were found to contain minisatellite-like repeated sequences, most of which were located in intergenic regions but a few occurred in gene coding and intronic regions. Oryza and Brassica accessions were selected as models for the investigation of minisatellite polymorphism because substantial systematic information existed. PCR analysis of 42 Oryza accessions revealed length polymorphisms in four of the five minisatellites. The mitochondrial haplotypes of the 16 Oryza accessions with chromosomal complement (genome) types of CC, BBCC and CCDD were identical but were clearly distinguished from BB-genome accessions, a result consistent with the notion that the cytoplasmic donor parent of the amphidiploid species might be the CC-genome species. Twenty-nine accessions of six major cultivated species of Brassica were classified into five mitochondrial haplotypes based on two polymorphic minisatellites out of six loci. The haplotypes of Brassica juncea and Brassica carinata accessions were identical to Brassica rapa and Brassica nigra accessions, respectively. The haplotypes of Brassica napus accessions were heterogeneous and unique, results that were consistent with previous studies.

Population genetics of the cytoplasm and the units of selection on mitochondrial DNA in Drosophila melanogaster

Biological variation exists across a nested set of hierarchical levels from nucleotides within genes to populations within species to lineages within the tree of life. How selection acts across this hierarchy is a long-standing question in evolutionary biology. Recent studies have suggested that genome size is influenced largely by the balance of selection, mutation and drift in lineages with different population sizes. Here we use population cage and maternal transmission experiments to identify the relative strength of selection at an individual and cytoplasmic level. No significant trends were observed in the frequency of large (L) and small (S) mtDNAs across 14 generations in population cages. In all replicate cages, new length variants were observed in heteroplasmic states indicating that spontaneous length mutations occurred in these experimental populations. Heteroplasmic flies carrying L genomes were more frequent than those carrying S genomes suggesting an asymmetric mutation dynamic from larger to smaller mtDNAs. Mother-offspring transmission of heteroplasmy showed that the L mtDNA increased in frequency within flies both between and within generations despite sampling drift of the same intensity as occurred in population cages. These results suggest that selection for mtDNA size is stronger at the cytoplasmic than at the organismal level. The fixation of novel mtDNAs within and between species requires a transient intracellular heteroplasmic stage. The balance of population genetic forces at the cytoplasmic and individual levels governs the units of selection on mtDNA, and has implications for evolutionary inference as well as for the effects of mtDNA mutations on fitness, disease and aging.

A comparative analysis of mitochondrial genomes in Orthoptera (Arthropoda: Insecta) and genome descriptions of three grasshopper species

The complete sequences of mitochondrial DNA (mtDNA) from the three new grasshopper species, Euchorthippus fusigeniculatus, Mekongiana xiangchengensis and Mekongiella xizangensis, consisting of 15772 bp, 15567 bp, and 15885 bp, respectively, were analyzed and compared to mtDNAs from other 19 Orthoptera species obtained from GenBank. The three mitochondrial genomes contain a standard set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes. and an A+T-rich region in the same order as those of the other analyzed caeliferan species, but different from those of the ensiferan species by the rearrangement of trnD and trnK. The putative initiation codon for the cox1 gene is ATC in E. fusigeniculatus, CTG in M. xiangchengensis and CCG in M. xizangensis. All secondary structures of tRNA-Ser((AGN)) in the three species lack a DHU arm. In this study, we stressed the comparative analysis of the stem-loop secondary structure in A+T-rich region of all Orthoptera species available to date, and report new findings which may facilitate further investigation and better understanding of this secondary structure. Finally, we undertook a phylogenetic study of all Orthoptera species available from GenBank to date based on three different datasets using parsimony, maximum likelihood, and Bayesian inference. Our result showed that protein-coding genes (PCG) and amino acid sequences (PCG_PROT) provided good resolution of higher-level relationships within the Orthoptera, whereas ribosomal RNA genes (RIBO) perform poorly under different optimality criteria.

A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles

Coleoptera is the most diverse group of insects with over 360,000 described species divided into four suborders: Adephaga, Archostemata, Myxophaga, and Polyphaga. In this study, we present six new complete mitochondrial genome (mtgenome) descriptions, including a representative of each suborder, and analyze the evolution of mtgenomes from a comparative framework using all available coleopteran mtgenomes. We propose a modification of atypical cox1 start codons based on sequence alignment to better reflect the conservation observed across species as well as findings of TTG start codons in other genes. We also analyze tRNA-Ser(AGN) anticodons, usually GCU in arthropods, and report a conserved UCU anticodon as a possible synapomorphy across Polyphaga. We further analyze the secondary structure of tRNA-Ser(AGN) and present a consensus structure and an updated covariance model that allows tRNAscan-SE (via the COVE software package) to locate and fold these atypical tRNAs with much greater consistency. We also report secondary structure predictions for both rRNA genes based on conserved stems. All six species of beetle have the same gene order as the ancestral insect. We report noncoding DNA regions, including a small gap region of about 20 bp between tRNA-Ser(UCN) and nad1 that is present in all six genomes, and present results of a base composition analysis.

The mitochondrial genome of Protohermes concolorus Yang et Yang 1988 (Insecta: Megaloptera: Corydalidae)

The first complete mitochondrial genome of dobsonfly Protohermes concolorus Yang et Yang, 1988 (Megaloptera: Corydalidae) was sequenced in this study. The genome was a circular molecule of 15,851 bp containing the typical 37 genes that arranged in the same order as that of the putative ancestor of hexapods. Sequences overlaps were observed between several neighbor genes, which made the genome relatively compact. The tRNA-Ser (GCT) could not be folded into typical secondary structure because its DHU arm was replaced with a simple loop. Six of the 13 protein genes were terminated with a single T adjacent to a downstream tRNA gene in the same strand. The variation of GC content caused the different nucleotide substitution patterns of the protein genes. The genome was AT-biased with a total A + T content of 75.83% which was also demonstrated by the codon usage. The control region was the most AT-rich region with a sub-region of even higher A + T content. Protein genes of two strands presented opposite CG-skew trends which was also reflected by the codon usage. For most of the amino acids, the protein coding sequences did not prefer to use the cognate codons of corresponding tRNAs and the codon usage of the protein genes was not random. The variation of nucleotide substitution patterns of protein genes was significantly correlated with the GC content. The phylogenetic analyses based on all the 13 protein genes showed that Megaloptera was the sister group of other holometabolous insects except Coleoptera.

Complete mitochondrial DNA sequence of the scallop Placopecten magellanicus: evidence of transposition leading to an uncharacteristically large mitochondrial genome

Complete sequence determination of the mitochondrial (mt) genome of the sea scallop Placopecten magellanicus reveals a molecule radically different from that of the standard metazoan. With a minimum length of 30,680 nucleotides (nt; with one copy of a 1.4 kilobase (kb) repeat) and a maximum of 40,725 nt, it is the longest reported metazoan mitochondrial DNA (mtDNA). More than 50% of the genome is noncoding (NC), consisting of dispersed, imperfectly repeated sequences that are associated with tRNAs or tRNA-like structures. Although the genes for atp8 and two tRNAs were not discovered, the genome still has the potential for encoding 46 genes (the additional genes are all tRNAs), 9 of which encode tRNAs for methionine. The coding portions appear to be evolving at a rate consistent with other members of the pectinid clade. When the NC regions containing "dispersed repeat families" are examined in detail, we reach the conclusion that transposition involving tRNAs or tRNA-like structures is occurring and is responsible for the large size and abundance of noncoding DNA in the molecule. The rarity of enlarged mt genomes in the face of a demonstration that they can exist suggests that a small, compact organization is an actively maintained feature of metazoan mtDNA.

Mitochondrial genome haplotype hypervariation within the isopod parasitic nematode Thaumamermis cosgrovei

Characterization of mitochondrial genomes from individual Thaumamermis cosgrovei nematodes, obligate parasites of the isopod Armadillidium vulgare, revealed that numerous mtDNA haplotypes, ranging in size from 19 to 34 kb, are maintained in several spatially separated isopod populations. The magnitude and frequency of conspecific mtDNA size variation is unprecedented among all studied size-polymorphic metazoan mitochondrial genomes. To understand the molecular basis of this hypervariation, complete nucleotide sequences of two T. cosgrovei mtDNA haplotypes were determined. A hypervariable segment, residing between the atp6 and rrnL genes, contributes exclusively to T. cosgrovei mtDNA size variation. Within this region, mtDNA coding genes and putative nonfunctional sequences have accumulated substitutions and are duplicated and rearranged to varying extents. Hypervariation at this level has enabled a first insight into the life history of T. cosgrovei. In five A. vulgare hosts infected with multiple nematodes, four carried nematodes with identical mtDNA haplotypes, suggesting that hosts may become infected by ingesting a recently hatched egg clutch or become parasitized by individuals from the same brood prior to dispersal of siblings within the soil.

Structure and evolution of the mitochondrial control region and flanking sequences in the European cave salamander Proteus anguinus

The European cave salamander Proteus anguinus Laurenti 1768 is one of the best-known subterranean animals, yet its evolutionary history and systematic relationships remain enigmatic. This is the first comprehensive study on molecular evolution within the taxon, using an mtDNA segment containing the control region (CR) and adjacent sequences. Two to seven tandem repeats of 24-32 bp were found in the intergenic spacer region (VNTR1), and three, four or six repeats, 59-77 bp each, in the 3' end of the CR (VNTR2). Different molecular mechanisms account for VNTR2 formation in different lineages of Proteus. The overall CR variation was lower than that of the spacer region, the 3' end of the cytb gene, or the tRNA genes. Individual genes and the concatenated non-repetitive sequences produced similar, well resolved maximum likelihood, Bayesian inference and parsimony trees. The numbers of repeat elements as well as the genealogy of the VNTR2 repeat units were mostly inconsistent with the groupings of the non-repetitive sequences. Different degrees of repeat array homogenization were detected in all major groups. Orthology was established for the first and the second VNTR2 elements of some populations. These two copies may therefore be used for analyses at the population level. The pattern of CR sequence variation points to strong genetic isolation of hydrographically separated populations. Genetic separation of the major groups of populations is incongruent with the current division into subspecies.

Origin and evolution of tandem repeats in the mitochondrial DNA control region of shrikes (Lanius spp.)

The origin and evolution of a 128-bp tandem repeat in the mtDNA control region of shrikes (Lanius: Aves) were investigated. The tandem repeat is present in only two species, L. excubitor and L. ludovicianus. In contrast to the variation in repeat number in L. ludovicianus, all individuals of three subspecies of L. excubitor had three repeats. Comparative analysis suggests that a short direct repeat, and a secondary structure including the tandem repeat and a downstream inverted repeat, may be important in the origin of the tandem repeat by slipped-strand mispairing and its subsequent turnover. Homogenization of repeat sequences is most simply explained by expansion and contraction of the repeat array. Surprisingly, mtDNA sequences from L. excubitor were found to be paraphyletic with respect to L. ludovicianus. These results show the utility of a comparative analysis for insights into the evolutionary dynamics of mtDNA tandem repeats.

Gene rearrangements and evolution of tRNA pseudogenes in the mitochondrial genome of the parrotfish (Teleostei: Perciformes: Scaridae)

Genomic size of animal mitochondrial DNA is usually minimized over time. Thus, when regional duplications occur, they are followed by a rapid elimination of redundant material. In contrast to this general view, we report here long-sustained tRNA pseudogenes in the mitochondrial genome (mitogenome) of teleost fishes of the family Scaridae (parrotfishes). During the course of a molecular phylogenetic study of the suborder Labroidei, we determined the complete nucleotide sequence of the mitogenome for a parrotfish, Chlorurus sordidus, and found a gene rearrangement accompanied by a tRNA pseudogene. In the typical gene order of vertebrates, a tRNA-gene cluster between ND1 and ND2 genes includes tRNA(Ile) (I), tRNA(Gln) (Q), and tRNA(Met) (M) genes in this order (IQM). However, in the mitogenome of the parrotfish, the tRNA(Met) gene was inserted between the tRNA(Ile) and the tRNA(Gln) genes, and the tRNA(Gln) gene was followed by a putative tRNA(Met) pseudogene (psiM). Such a tRNA gene rearrangement including a pseudogene (IMQpsiM) was found in all of the 10 examined species, representing 7 of the 10 currently recognized scarid genera. All sister groups examined (20 species of Labridae and a single species of Odacidae) had the typical gene order of vertebrate mitogenomes. Phylogenetic analysis of the tRNA(Met) genes and the resulting pseudogenes demonstrated that the ancestral tRNA(Met) gene was duplicated in a common ancestor of the parrotfish. Based on the fossil record, these results indicate that the pseudogenes have survived at least 14 million years. Most of the vertebrate mitochondrial gene rearrangements involving the IQM region have held the tRNA(Met) gene just upstream of the ND2 gene, and even in a few exceptional cases, including the present ones, the tRNA pseudogenes have been found in that position. In addition, most of these tRNA(Met) pseudogenes maintained clover-leaf secondary structures, with the remainder sustaining the clover-leaf structure in the "top half (TpsiC and acceptor arms). Considering their potential secondary structures (holding "top halves" of the clover-leaf structures), locations within mitogenomes (flanking the 5' ends of the ND2 genes) and stabilities over time (survived at least 14 Myr), it is likely that the tRNA pseudogenes retain function as punctuation marks for mitochondrial ND2 mRNA processing.

Molecular phylogenetic relationships based on mitochondrial and nuclear gene sequences for the Todies (Todus, Todidae) of the Caribbean

We used mitochondrial/nuclear gene sequence analyses to determine the historical relationships of the endemic species of Todus (Aves: Todidae) from the Caribbean. We collected 1920-bp of nucleotide sequence data from the mitochondrial genes cytochrome b, ATPase 6, ATPase 8, and 591-bp of the single-copy nuclear gene c-mos for all Todus species and representatives of their outgroup taxa (Hylomanes, Barypthengus, Chloroceryle, Ceryle, and Galbula) to reconstruct the evolutionary history (via parsimony and maximum likelihood) of the five Todus species. The substitution rates among the mitochondrial genes were found to be much higher than the substitution rate for the c-mos gene, consequently resulting in higher substitutional saturation for the mitochondrial genes. When we applied weighting schemes to account for the variance in substitutional heterogeneity among the genes then parsimony and likelihood analyses both demonstrate that the genus Todus is monophyletic and closer to the Hylomanes and Barypthengus genera than the Chloroceryle and Ceryle genera. The mitochondrial-gene trees and nuclear-gene trees both show similar results, thus providing support for the relationships among the taxa from loci within two independently evolving genomes. The nuclear gene c-mos was found, therefore, to be a viable nuclear gene candidate for resolving intermediate and deep divergences.

Mitochondrial genome size variation in New World and Old World populations of Drosophila melanogaster

Drosophila melanogaster originated in Africa, spread to Europe and Asia, and is believed to have colonized the New World in the past few hundred years. Levels of genetic variation are typically reduced in New World populations, consistent with a founder event following range expansion out of Africa and the Old World. We describe the patterns of mtDNA length variation within and among several populations of Drosophila melanogaster from the Old and New World. MtDNA length variation is due to insertion and deletion of tandem repeats in the control region (D-loop) of D. melanogaster mitochondrial genome. The distinct mutational dynamics of this system provide an opportunity to compare the patterns of variation in this marker to those of other markers with different mutational pressures and linkage relationships. The data show significantly more length variation in African and Asian samples than in New World samples. New World samples also show more pronounced skew of the length distribution. Our results are distinct from an earlier study that showed significantly higher levels of length variation and heteroplasmy. The level of heteroplasmy is highly correlated with the number of years that samples have been maintained in laboratory culture, suggesting that relaxed selection in small populations permits the accumulation of mtDNA length variation and heteroplasmy. Together, the data indicate that mtDNA length variants retain a signature of founder events and selection, and suggest that further investigation into the mutation-selection dynamics of the D-loop region of mtDNA would provide a distinct and informative marker for analysis of the recent history of populations.

Evolution of heteroplasmy at a mitochondrial tandem repeat locus in cultured rabbit cells

Surveys of animal mitochondrial DNA (mtDNA) polymorphism reveal that mtDNA length variation is common. Much of this variation involves non-coding tandem repeat arrays in the main control region of the molecule. Despite a high mutation rate, generating systematic individual mtDNA length heteroplasmy, the number of repeats in a tandem array is maintained within a narrow range in lagomorphs. To investigate the basis for this apparent paradox, we studied the evolution of mtDNA length polymorphism in several rabbit cell clones containing different proportions of mtDNA, with four or five 153-bp repeats. Our data show that equivalent amounts of two mtDNA molecular types are not stable (evolution towards a predominant type being the rule) and that other types remain represented, maintaining the length polymorphism. The data suggest that mtDNA molecules with a longer array of repeats have a replicative advantage that could depend on the nuclear background.

History of infection with different male-killing bacteria in the two-spot ladybird beetle Adalia bipunctata revealed through mitochondrial DNA sequence analysis

The two-spot ladybird beetle Adalia bipunctata (Coleoptera: Coccinellidae) is host to four different intracellular maternally inherited bacteria that kill male hosts during embryogenesis: one each of the genus Rickettsia (alpha-Proteobacteria) and Spiroplasma (Mollicutes) and two distinct strains of Wolbachia (alpha-Proteobacteria). The history of infection with these male-killers was explored using host mitochondrial DNA, which is linked with the bacteria due to joint maternal inheritance. Two variable regions, 610 bp of cytochrome oxidase subunit I and 563 bp of NADH dehydrogenase subunit 5, were isolated from 52 A. bipunctata with known infection status and different geographic origin from across Eurasia. Two outgroup taxa were also considered. DNA sequence analysis revealed that the distribution of mitochondrial haplotypes is not associated with geography. Rather, it correlates with infection status, confirming linkage disequilibrium between mitochondria and bacteria. The data strongly suggest that the Rickettsia male-killer invaded the host earlier than the other taxa. Further, the male-killing Spiroplasma is indicated to have undergone a recent and extensive spread through host populations. In general, male-killing in A. bipunctata seems to represent a highly dynamic system, which should prove useful in future studies on the evolutionary dynamics of this peculiar type of symbiont-host association.

Heteroplasmy in the mtDNA control region of sturgeon (Acipenser, Huso and Scaphirhynchus)

Data from 1238 fishes from 19 sturgeon species and 1 paddlefish were used to analyze heteroplasmy in sturgeon. Lengths of central repeat units ranged from 74 to 83 bp among sturgeon species. No repeat sequence was found in the paddlefish, Polyodon spathula. A general feature of the repeat units was the presence of termination associated sequence (TAS) motifs. About 50% of 138 interspecific mutations observed among the D-loop sequences are located 10 bp down- and upstream from these TAS motifs. Interestingly, most homoplasmic species showed deletions upstream to the TAS motifs, whereas deletions downstream to the TAS motifs observed in two species do not seem to preclude heteroplasmy. Calculations of secondary structures and thermal stabilities of repeat units showed DeltaG values for all heteroplasmic species to be <-8 and for most homoplasmic species DeltaG value to be >-8. Most heteroplasmic fishes had two and/or three repeat units. No homoplasmic sturgeon with >2 repeat units were observed. Molecular phylogeny based on the entire cytochrome b showed that heteroplasmy probably resulted from a single evolutionary event. Our data demonstrate that heteroplasmy is present in most sturgeon species and suggest that the thermal stability of the secondary structure of the repeat unit in combination with mutations downstream of the TAS sequences influences heteroplasmy.

Tandemly repeated sequences in mtDNA control region of whitefish, Coregonus lavaretus

Length variation of the mitochondrial DNA control region was observed with PCR amplification of a sample of 138 whitefish (Coregonus lavaretus). Nucleotide sequences of representative PCR products showed that the variation was due to the presence of an approximately 100-bp motif tandemly repeated two, three, or five times in the region between the conserved sequence block-3 (CSB-3) and the gene for phenylalanine tRNA. This is the first report on the tandem array composed of long repeat units in mitochondrial DNA of salmonids.

Organization of the large mitochondrial genome in the isopod Armadillidium vulgare

The mitochondrial DNA (mtDNA) in animals is generally a circular molecule of approximately 15 kb, but there are many exceptions such as linear molecules and larger ones. RFLP studies indicated that the mtDNA in the terrestrial isopod Armadillidium vulgare varied from 20 to 42 kb. This variation depended on the restriction enzyme used, and on the restriction profile generated by a given enzyme. The DNA fragments had characteristic electrophoretic behaviors. Digestions with two endonucleases always generated fewer fragments than expected; denaturation of restriction profiles reduced the size of two bands by half; densitometry indicated that a number of small fragments were present in stoichiometry, which has approximately twice the expected concentration. Finally, hybridization to a 550-bp 16S rDNA probe often revealed two copies of this gene. These results cannot be due to the genetic rearrangements generally invoked to explain large mtDNA. We propose that the large A. vulgare mtDNA is produced by the tripling of a 14-kb monomer with a singular rearrangement: one monomer is linear and the other two form a circular dimer. Densitometry suggested that these two molecular structures were present in different proportions within a single individual. The absence of mutations within the dimers also suggests that replication occurs during the monomer phase.

Heteroplasmy, length and sequence variation in the mtDNA control regions of three percid fish species (Perca fluviatilis, Acerina cernua, Stizostedion lucioperca)

The nucleotide sequence of the control region and flanking tRNA genes of perch (Perca fluviatilis) mtDNA was determined. The organization of this region is similar to that of other vertebrates. A tandem array of 10-bp repeats, associated with length variation and heteroplasmy was observed in the 5' end. While the location of the array corresponds to that reported in other species, the length of the repeated unit is shorter than previously observed for tandem repeats in this region. The repeated sequence was highly similar to the Mt5 element which has been shown to specifically bind a putative D-loop DNA termination protein. Of 149 perch analyzed, 74% showed length variation heteroplasmy. Single-cell PCR on oocytes suggested that the high level of heteroplasmy is passively maintained by maternal transmission. The array was also observed in the two other percid species, ruffe (Acerina cernua) and zander (Stizostedion lucioperca). The array and the associated length variation heteroplasmy are therefore likely to be general features of percid mtDNAs. Among the perch repeats, the mutation pattern is consistent with unidirectional slippage, and statistical analyses supported the notion that the various haplotypes are associated with different levels of heteroplasmy. The variation in array length among and within species is ascribed to differences in predicted stability of secondary structures made between repeat units.

Aging, mating, and the evolution of mtDNA heteroplasmy in Drosophila melanogaster

Heteroplasmy, the presence of more than one type of mtDNA within cells, is common in animals and has been associated with aging and disease in humans. Changes in the frequencies of mtDNA variants between cell and animal generations thus bears on the evolution of mtDNA and the progression of diverse pathologies. We have used densitometry of Southern blots of individual heteroplasmic Drosophila melanogaster to study the effects of age, increased egg production after mating, and temperature on evolution of heteroplasmy within and between generations. The frequency of the longer mtDNA variant consistently increased between early and late cohorts of F1 offspring derived from 18 independent heteroplasmic mothers as they aged. Neither temperature (flies maintained at 25 degrees C and 18 degrees C) nor the holding of flies as virgins for 10 days before mating had significant effects on transmission patterns. However, at the ends of their lives, flies that had laid eggs at 25 degrees C had a greater frequency of the long mtDNA than did their siblings who had laid eggs at 18 degrees C. The evolution of heteroplasmy within a generation was studied in samples of siblings that either were mated or held as virgins, and then scored for mtDNA haplotype frequencies at two different ages (day 2 and day 14). Mated flies showed a significantly greater increase in the frequency of the long mtDNA variant with age than did the unmated flies. This system provides a model for the joint analysis of generational and chronological age in the transmission dynamics of a molecular polymorphism.

Highly conserved nuclear copies of the mitochondrial control region in the desert locust Schistocerca gregaria: some implications for population studies

Animal mitochondrial DNA has proved a valuable marker in intraspecific systematic studies. However, if nucleotide sequence heterogeneity exists at the individual level, its usefulness will be much reduced. The study demonstrates that the presence of highly conserved non-coding mitochondrial sequences in the nuclear genome of Schistocerca gregaria greatly impairs the use of mtDNA in population genetic studies. Caution is called for in other organisms; and it seems necessary to check for conserved nuclear copies of mitochondrial sequences before launching into a large scale analysis of populations using mtDNA as a genetic marker. Experimental procedures are suggested for this purpose.

Molecular cloning and complete nucleotide sequence of the repeated unit and flanking gene of the scallop Pecten maximus mitochondrial DNA: putative replication origin features

In the bivalve mollusc Pecten maximus, the size of the mitochondrial DNA molecules ranges from 20 to 25.8 kbp. This variability is mainly correlated with the occurrence of a variable domain composed with two to five 1.6-kbp repeated units tandemly arrayed in the genome. DNA fragments spanning the 1,586-base-pair-long repeated element and the nearest flanking gene have been cloned and sequenced. This sequence was analyzed regarding its base composition and potential secondary structures. The repeated unit domain was positioned and oriented with regard to the known flanking gene. It ends 2 base pairs upstream relative to the beginning of the tRNAgly gene. The peculiar properties of the repeated unit were compared with those of the 1,442-bp repeated element found in the mitochondrial genome of the deep sea scallop Placopecten magellanicus. This comparison provided evidence for the absence of nucleotide conservation, except for a small sequence engaged in a secondary structure, but argued for a strong pressure maintaining domains with specific nucleotide content. A possible role for the conserved sequence is discussed.

Variable numbers of simple tandem repeats make birds of the order ciconiiformes heteroplasmic in their mitochondrial genomes

We have analyzed a variable domain of the mitochondrial DNA control region of 18 avian species. Intra-individual length variation was identified and characterized in 15 species. The occurrence of heteroplasmy among species is phylogenetically consistent with a current classification of birds. Polymerase chain reaction amplifications, direct sequencing, and Southern analysis of mitochondrial DNA showed that the heteroplasmy is due to variable numbers of direct repeats in a tandem organization, located in the control region close to the tRNAPhe gene. The tandem repeats consist of short sequence motifs that vary in size from 4 to 32 base pairs between species. Sequence complexity of the repeat motifs was low, with almost exclusively Ts and Gs in the heavy-strand. Extensive variation in the copy number of the repeats was seen both intra-specifically and within individuals. This is the first report of mitochondrial heteroplasmy characterized at the sequence level in birds.