Length polymorphisms, restriction site variation, and maternal inheritance of mitochondrial DNA of Drosophila melanogaster

Frequent Paternal Mitochondrial Inheritance and Rapid Haplotype Frequency Shifts in Copepod Hybrids

Mitochondria are assumed to be maternally inherited in most animal species, and this foundational concept has fostered advances in phylogenetics, conservation, and population genetics. Like other animals, mitochondria were thought to be solely maternally inherited in the marine copepod Tigriopus californicus, which has served as a useful model for studying mitonuclear interactions, hybrid breakdown, and environmental tolerance. However, we present PCR, Sanger sequencing, and Illumina Nextera sequencing evidence that extensive paternal mitochondrial DNA (mtDNA) transmission is occurring in inter-population hybrids of T. californicus. PCR on four types of crosses between three populations (total sample size of 376 F1 individuals) with 20% genome-wide mitochondrial divergence showed 2% to 59% of F1 hybrids with both paternal and maternal mtDNA, where low and high paternal leakage values were found in different cross directions of the same population pairs. Sequencing methods further verified nucleotide similarities between F1 mtDNA and paternal mtDNA sequences. Interestingly, the paternal mtDNA in F1s from some crosses inherited haplotypes that were uncommon in the paternal population. Compared to some previous research on paternal leakage, we employed more rigorous methods to rule out contamination and false detection of paternal mtDNA due to non-functional nuclear mitochondrial DNA fragments. Our results raise the potential that other animal systems thought to only inherit maternal mitochondria may also have paternal leakage, which would then affect the interpretation of past and future population genetics or phylogenetic studies that rely on mitochondria as uniparental markers.

Clarifying the phylogenetic relationships and taxonomy of Stenonema, Stenacron and Maccaffertium, three common eastern North American mayfly genera

Stenonema, Stenacron, and Maccaffertium are three closely related genera of mayflies (Ephemeroptera:Heptageniidae) commonly found across North America. Due to their primarily aquatic life history and sensitivity to aquatic pollutants, these mayflies are often used as water quality indicators. However, there is little morphological variation within these genera, leading to difficulties in identification and rampant taxonomic confusion, limiting their utility as bioindicators. In an attempt to resolve the phylogenetic relationships of Stenonema, Stenacron, and Maccaffertium, and to clarify their higher-level classifications, we sequenced regions of two mitochondrial genes (cytochrome oxidase subunit 1 (cox1) and 16S ribosomal RNA (rrnl)) and two nuclear genes (Wingless (Wg) and histone H3) from 60 individuals representing most of the described species in these genera and included data from representatives of three heptageniid genera (Kageronia, Macdunnoa and Pseudiron) proposed in previous studies to be closely related to our focal taxa as well as two more distantly related heptageniid genera (Epeorus and Heptagenia) to root the phylogenies. Maximum likelihood and Bayesian analysis were conducted on single-gene and concatenated multi-gene data sets and species tree methods were utilized to resolve relationships. These analyses resolved Stenacron as a monophyletic group sister to a clade comprising Macdunnoa, Maccaffertium and Stenonema. Maccaffertium was found to be paraphyletic, with Stenonema femoratum resolved within Maccaffertium as sister to M. mexicanum. Many relationships remained unresolved or varied across analyses, making revision of the classification based on phylogenetic considerations challenging. To minimize confusion while naming clades and acknowledging uncertainty in our phylogenetic conclusions, we redefine Stenonema to include Maccaffertium and propose three subgenera-Stenonema, Maccaffertium and Lewisa- for key well-supported clades.

Complete Anopheles funestus mitogenomes reveal an ancient history of mitochondrial lineages and their distribution in southern and central Africa

Anopheles funestus s.s. is a primary vector of malaria in sub-Saharan Africa. Despite its important role in human Plasmodium transmission, evolutionary history, genetic diversity, and population structure of An. funestus in southern and central Africa remains understudied. We deep sequenced, assembled, and annotated the complete mitochondrial genome of An. funestus s.s. for the first time, providing a foundation for further genetic research of this important malaria vector species. We further analyzed the complete mitochondrial genomes of 43 An. funestus s.s. from three sites in Zambia, Democratic Republic of the Congo, and Tanzania. From these 43 mitogenomes we identified 41 unique haplotypes that comprised 567 polymorphic sites. Bayesian phylogenetic reconstruction confirmed the co-existence of two highly divergent An. funestus maternal lineages, herein defined as lineages I and II, in Zambia and Tanzania. The estimated coalescence time of these two mitochondrial lineages is ~500,000 years ago (95% HPD 426,000–594,000 years ago) with subsequent independent diversification. Haplotype network and phylogenetic analysis revealed two major clusters within lineage I, and genetic relatedness of samples with deep branching in lineage II. At this time, data suggest that the lineages are partially sympatric. This study illustrates that accurate retrieval of full mitogenomes of Anopheles vectors enables fine-resolution studies of intraspecies genetic relationships, population differentiation, and demographic history. Further investigations on whether An. funestus mitochondrial lineages represent biologically meaningful populations and their potential implications for malaria vector control are warranted.

The Mitochondrial DNA Polymerase Promotes Elimination of Paternal Mitochondrial Genomes

Mitochondrial DNA (mtDNA) is typically inherited from only one parent [1-3]. In animals, this is usually the mother. Maternal inheritance is often presented as the passive outcome of the difference in cytoplasmic content of egg and sperm; however, active programs enforce uniparental inheritance at two levels, eliminating paternal mitochondrial genomes or destroying mitochondria delivered to the zygote by the sperm [4-13]. Both levels operate in Drosophila [8, 12, 13]. As sperm formation begins, hundreds of doomed mitochondrial genomes are visualized within the two huge mitochondria of each spermatid. These genomes abruptly disappear during spermatogenesis. Genome elimination, which is not in the interests of the restricted genomes, is directed by nuclear genes. Mutation of EndoG, which encodes a mitochondria-targeted endonuclease, retarded elimination [8]. Here, we show that knockdown of the nuclear-encoded mtDNA polymerase (Pol γ-α), Tamas, produces a more complete block of mtDNA elimination. Tamas is found in large particles that localize to mtDNA during genome elimination. We discount a simple possible mechanism by showing that the 3'-exonuclease function of the polymerase is not needed. While DNA elimination is a surprising function for DNA polymerase, it could provide a robust nexus for nuclear control of mitochondrial genome copy number, since use of common interactions for elimination and replication might limit options for the mitochondrial genome to escape restriction. We suggest that the DNA polymerase may play this role more widely and that inappropriate activation of its elimination ability might underlie association of DNA loss syndromes with mutations of the human mtDNA polymerase [14-16].

Maternal inheritance of mitochondrial DNA by diverse mechanisms to eliminate paternal mitochondrial DNA

The mitochondrion is an organelle that has its own DNA (mtDNA). Mitochondria play essential roles in energy production and in various cellular processes such as metabolism and signal transduction. In most animals, including humans, although the sperm-derived paternal mitochondria enter the oocyte cytoplasm after fertilization, their mtDNA is never transmitted to the offspring. This pattern of mtDNA inheritance is well known as "maternal inheritance." However, how the paternal mitochondria and mtDNA are eliminated from the cytoplasm of gametes or zygotes remains an enigma. Recently, a variety of mechanisms, including specific nuclease-dependent systems, ubiquitin-proteasome system, and autophagy have been shown to degrade the paternal mtDNA or the paternal mitochondria themselves in order to prevent paternal mtDNA transmission. In this review, we will address the current state of knowledge of the molecular mechanisms underlying the elimination of paternal mtDNA or mitochondrial structures for ensuring the maternal transmission of mtDNA.

Barriers to male transmission of mitochondrial DNA in sperm development

Across the eukaryotic phylogeny, offspring usually inherit their mitochondrial genome from only one of two parents: in animals, the female. Although mechanisms that eliminate paternally derived mitochondria from the zygote have been sought, the developmental stage at which paternal transmission of mitochondrial DNA is restricted is unknown in most animals. Here, we show that the mitochondria of mature Drosophila sperm lack DNA, and we uncover two processes that eliminate mitochondrial DNA during spermatogenesis. Visualization of mitochondrial DNA nucleoids revealed their abrupt disappearance from developing spermatids in a process requiring the mitochondrial nuclease, Endonuclease G. In Endonuclease G mutants, persisting nucleoids are swept out of spermatids by a cellular remodeling process that trims and shapes spermatid tails. Our results show that mitochondrial DNA is eliminated during spermatogenesis, thereby removing the capacity of sperm to transmit the mitochondrial genome to the next generation.

Chloroplast and mitochondrial DNA are paternally inherited in Sequoia sempervirens D. Don Endl

Restriction fragment length polymorphisms in controlled crosses were used to infer the mode of inheritance of chloroplast DNA and mitochondrial DNA in coast redwood (Sequoia sempervirens D. Don Endl.). Chloroplast DNA was paternally inherited, as is true for all other conifers studied thus far. Surprisingly, a restriction fragment length polymorphism detected by a mitochondrial probe was paternally inherited as well. This polymorphism could not be detected in hybridizations with chloroplast probes covering the entire chloroplast genome, thus providing evidence that the mitochondrial probe had not hybridized to chloroplast DNA on the blot. We conclude that mitochondrial DNA is paternally inherited in coast redwood. To our knowledge, paternal inheritance of mitochondrial DNA in sexual crosses of a multicellular eukaryotic organism has not been previously reported.

Extensive variation and heteroplasmy in size of mitochondrial DNA among geographic populations of Drosophila melanogaster

Size variation and heteroplasmy in mitochondrial DNA (mtDNA) are relatively common in natural populations of Drosophila melanogaster. Of 92 isofemale lines of flies obtained from various geographic regions throughout the world, 75 lines were homoplasmic and showed a total of 12 different mtDNA size classes. The remaining 17 lines were heteroplasmic, each line carrying two different mtDNAs, and, in all but one case, the mtDNAs in these heteroplasmic lines differed in size; a total of nine size classes was represented among them. In cases where one type was predominant within an individual, it was usually the smaller mtDNA. This finding parallels what was observed in homoplasmic lines, in that the smaller mtDNAs were much more common than the larger variants in most populations. The data suggest a high rate of mutational occurrence of mtDNA size variants and some natural selection against them.

Inheritance of chloroplast DNA in Chlamydomonas reinhardtii

Two symmetrically located deletions of approximately 100 base pairs each have been identified in chloroplast DNA of Chlamydomonas reinhardtii. Although present in a mutant strain that requires acetate for growth, both deletions have been shown to be distinct from the nonphotosynthetic phenotype of this strain. These physical markers in the chloroplast genome and maternally inherited genetic markers showed strict cotransmission in reciprocal crosses. Thus, our results are consistent with the location of the well-characterized maternally inherited genetic markers in chloroplast DNA of C. reinhardtii.

Review of cytological studies on cellular and molecular mechanisms of uniparental (maternal or paternal) inheritance of plastid and mitochondrial genomes induced by active digestion of organelle nuclei (nucleoids)

In most sexual organisms, including isogamous, anisogamous and oogamous organisms, uniparental transmission is a striking and universal characteristic of the transmission of organelle (plastid and mitochondrial) genomes (DNA). Using genetic, biochemical and molecular biological techniques, mechanisms of uniparental (maternal and parental) and biparental transmission of organelle genomes have been studied and reviewed. Although to date there has been no cytological review of the transmission of organelle genomes, cytology offers advantages in terms of direct evidence and can enhance global studies of the transmission of organelle genomes. In this review, I focus on the cytological mechanism of uniparental inheritance by "active digestion of male or female organelle nuclei (nucleoids, DNA)" which is universal among isogamous, anisogamous, and oogamous organisms. The global existence of uniparental transmission since the evolution of sexual eukaryotes may imply that the cell nuclear genome continues to inhibit quantitative evolution of organelles by organelle recombination.

Maternal inheritance of mitochondria: multipolarity, multiallelism and hierarchical transmission of mitochondrial DNA in the true slime mold Physarum polycephalum

Direct evidence of digestion of paternal mitochondrial DNA (mtDNA) has been found in the true slime mold Physarum polycephalum. This is the first report on the selective digestion of mtDNA inside the zygote, and is striking evidence for the mechanism of maternal inheritance of mitochondria. Moreover, two mitochondrial nuclease activities were detected in this organism as-candidates for the nucleases responsible for selective digestion of mtDNA. In the true slime mold, there is an additional-feature of the uniparental inheritance of mitochondria.Although mitochondria are believed to be inherited from the maternal lineage in nearly all eukaryotes, the mating types of the true slime mold P. polycephalum is not restricted to two: there are three mating loci--matA, matB,and matC--and these loci have 16, 15, and 3 alleles,-respectively. Interestingly, the transmission patterns of mtDNA are determined by the matA locus, in a hierarchical-fashion (matA hierarchy) as follows: matA7[matA2[matA11[matA12[matA15/matA16[matA1[matA6.The strain possessing the higher status of matA would be the mtDNA donor in crosses. Furthermore, we have found that some crosses showed biparental inheritance of mitochondria.This review describes the phenomenon of hierarchical transmission of mtDNA in true slime molds, and discusses the presumed molecular mechanism of maternal and biparental inheritance.

Population genetics of extranuclear genomes under the neutral mutation hypothesis

Population genetics of extranuclear genomes is further developed under the neutral-mutation random-drift hypothesis, and the characteristic evolutionary aspects are summarized. Several formulae derived here are concerned with the variances of genetic variability (gene identity) at a single extranuclear locus and the evolutionary distance between two isolated populations which is estimated from a comparison of homologous linked nucleotide sites. Two types of variance are considered; one is the variance in the entire population (VQ) and the other is the variance within a single germ cell (VH). When compared with a Mendelian genetic system in a panmictic population, an extranuclear genetic system has the following equilibrium properties: (1) the mean genetic variability is low if, despite the high multiplicity of the genome in a cell, the proportion of the cytoplasmic contribution from the male's gamete is small, (2) the effect of recombination is small and a large amount of variance of linkage disequilibrium tends to be maintained, (3) the overall relationship between the mean and variance of genetic variability does not much differ butVQ(VH) is expected to be small if the paternal contribution is small, and (4) the evolutionary distance estimated depends on the extent of intrapopulational variation in a common ancestor population which in turn depends on within-cell variation. I argue that there is an analogy between the model of extranuclear genomes in a finite population and that of nuclear genes in a subdivided population. The analogy helps our understanding of some properties in an extranuclear genetic system.

Evolutionary dynamics of extranuclear genes

We studied the evolutionary dynamics of extranuclear genes taking into account simple kinds of selection, two modes of inheritance and the multiplicity of genomes within a cell. Particular attention was paid to the accumulation of advantageous or deleterious mutations in an extranuclear genome. Within-generation drift due to multiplicity of genome and non-Mendelian segregation promotes the fixation of advantageous mutations and prevents deleterious mutations from accumulating. We show also that the extent of paternal contribution makes little difference in the rate, but, in contrast, the configuration of the genome and the mode of transmission both makes a large difference. These results are compatible with what is known about extranuclear genomes.

Revealing the hidden complexities of mtDNA inheritance

Mitochondrial DNA (mtDNA) is a pivotal tool in molecular ecology, evolutionary and population genetics. The power of mtDNA analyses derives from a relatively high mutation rate and the apparent simplicity of mitochondrial inheritance (maternal, without recombination), which has simplified modelling population history compared to the analysis of nuclear DNA. However, in biology things are seldom simple, and advances in DNA sequencing and polymorphism detection technology have documented a growing list of exceptions to the central tenets of mitochondrial inheritance, with paternal leakage, heteroplasmy and recombination now all documented in multiple systems. The presence of paternal leakage, recombination and heteroplasmy can have substantial impact on analyses based on mtDNA, affecting phylogenetic and population genetic analyses, estimates of the coalescent and the myriad of other parameters that are dependent on such estimates. Here, we review our understanding of mtDNA inheritance, discuss how recent findings mean that established ideas may need to be re-evaluated, and we assess the implications of these new-found complications for molecular ecologists who have relied for decades on the assumption of a simpler mode of inheritance. We show how it is possible to account for recombination and heteroplasmy in evolutionary and population analyses, but that accurate estimates of the frequencies of biparental inheritance and recombination are needed. We also suggest how nonclonal inheritance of mtDNA could be exploited, to increase the ways in which mtDNA can be used in analyses.

Rapid, selective digestion of mitochondrial DNA in accordance with the matA hierarchy of multiallelic mating types in the mitochondrial inheritance of Physarum polycephalum

Although mitochondria are inherited uniparentally in nearly all eukaryotes, the mechanism for this is unclear. When zygotes of the isogamous protist Physarum polycephalum were stained with DAPI, the fluorescence of mtDNA in half of the mitochondria decreased simultaneously to give small spots and then disappeared completely approximately 1.5 hr after nuclear fusion, while the other mitochondrial nucleoids and all of the mitochondrial sheaths remained unchanged. PCR analysis of single zygote cells confirmed that the loss was limited to mtDNA from one parent. The vacant mitochondrial sheaths were gradually eliminated by 60 hr after mating. Using six mating types, the transmission patterns of mtDNA were examined in all possible crosses. In 39 of 60 crosses, strict uniparental inheritance was confirmed in accordance with a hierarchy of relative sexuality. In the other crosses, however, mtDNA from both parents was transmitted to plasmodia. The ratio of parental mtDNA was estimated to be from 1:1 to 1:10(-4). Nevertheless, the matA hierarchy was followed. In these crosses, the mtDNA was incompletely digested, and mtDNA replicated during subsequent plasmodial development. We conclude that the rapid, selective digestion of mtDNA promotes the uniparental inheritance of mitochondria; when this fails, biparental inheritance occurs.

Mitochondrial DNA differentiation in the Japanese brown frog Rana japonica as revealed by restriction endonuclease analysis

To elucidate mtDNA differentiation in the Japanese brown frog Rana japonica, and compare it with results from allozyme analysis and crossing experiments, RFLP analysis was conducted on 78 frogs from 16 populations in Honshu. Purified mtDNA was digested with eight six-base recognizing restriction enzymes and analyzed by 1% agarose-slab gel electrophoresis. Cleavage patterns of the mtDNA showed three distinct genome size classes: small (18.5 kb), middle (20.0 kb) and large (21.5 kb). Ten haplotypes (I approximately X) were observed among the 16 populations. The expected nucleotide divergences within populations ranged from 0 to 0.47% with a mean of 0.08%. The net nucleotide divergences among 16 populations ranged from 0 to 7.74% with a mean of 3.49%. The UPGMA dendrogram and NJ tree, which were constructed based on the net nucleotide divergences, showed that R. japonica diverged first into the eastern and western groups. The eastern group subsequently differentiated into a subgroup containing six populations and the Akita population, and the western group divided into several subgroups. These results, as well as the results of allozyme analysis and crossing experiments, suggest the the eastern and western groups have experienced secondary contact, and introgression has occurred in the Akita population.

Selective transmission of mitochondrial DNA in heteroplasmic lines for intra- and interspecific combinations in Drosophila melanogaster

The transmission of mitochondrial DNA (mtDNA) was investigated in the heteroplasmic lines of Drosophila melanogaster at 19 degrees C and at 25 degrees C. The selective transmission of one type of mtDNA was dependent on the temperature at which the lines were maintained. In heteroplasmic lines for an intraspecific combination induced by germ-plasm transplantation using D. melanogaster as a germ-plasm donor, the proportion of donor mtDNA decreased in four out of five lines examined, the decreasing rate of which being greater at 25 degrees C than at 19 degrees C. Donor mtDNA was lost by the 20th generation at 25 degrees C. For an interspecific combination using D. mauritiana as a germ-plasm donor, the proportion of donor mtDNA increased and endogenous mtDNA was replaced with donor mtDNA at 25 degrees C. But donor mtDNA was almost lost at 19 degrees C by the 14th generation in all four lines examined. Possible mechanisms involved in the temperature-dependent modes of mtDNA transmission are discussed.

Restriction site variation, length polymorphism and changes in gene order in the mitochondrial DNA of the yeast Kluyveromyces lactics

The purpose of this work was to compare mitochondrial DNA restriction endonuclease patterns in strains of the yeast Kluyveromyces lactis, from different sources, to see how conserved is the organization of this organellar genome. The mitochondrial DNA of five independently-isolated strains and one of unknown origin were compared. Strains NRRL Y-1205, NRRL Y-8279 and NRRL Y-1140 gave identical patterns. Strain NRRL Y-1564 showed an insertion, with respect to the other three, of approximately 1250 bp. Strain W600B had also an insertion with extra restriction sites for EcoRI, HpaI, HaeIII, HincII and XbaI. On the other hand, strain Y-123 showed a restriction pattern quite different from the others. Sequences putatively encoding apocytochrome b, ATPase subunit 9 and ribosomal RNA large subunit, were localized on the physical maps of three strains. Results demonstrated that the order of these three genes shows a common feature in strains W600B and WM37 (auxotroph of Y-1140) but a different distribution in WM27 (auxotroph derived from Y-123). All these facts explain the extensive intraspecific polymorphism observed in the mtDNA of this yeast.

Maternal transmission of mitochondrial DNA in ducks

Maternal transmission of mitochondrial DNA (mtDNA) has been studied in amphibians, insects and mammals, but little is known about mtDNA inheritance in the ovaripirous avian species. In this study, we have constructed the physical maps of mitochondrial genomes from two different genera of ducks (Cairina and Anas) and taken advantage of the availability of their hybrids to demonstrate that mtDNA is maternally inherited.

The generation of transplasmic Drosophila simulans by cytoplasmic injection: effects of segregation and selection on the perpetuation of mitochondrial DNA heteroplasmy

Experimental transplasmic Drosophila simulans were obtained through cytoplasm microinjection between eggs carrying different mitochondrial genomes. These genomes (siII and siIII) show a 1.5% difference in their sequences. They produced a large number of heteroplasmic flies in their F1 progeny and several flies were still heteroplasmic at the eighth generation. The distribution of frequencies of mitochondrial genotypes in the offspring of heteroplasmic females suggests that the stochastic processes involved in the evolution of experimental heteroplasmy of multiple nucleotide sites are very similar to those previously described for spontaneous length heteroplasmy. In addition, the siII genome has a noticeable advantage over the siIII genome in both directions of injection. This advantage is estimated at 58% per fly generation and 5% per cell generation.

Heterosis × nutrition interaction in Drosophila melanogaster

The relationship between heterozygosity and the expression of heterosis at two different nutrition levels was investigated using Drosophila melanogaster. Average daily egg production and egg hatchability were measured in two parental strains and in F1, F2 and reciprocal backcross generations. Heterosis was more pronounced in the poor nutritional conditions. Two electrophoretic markers used to estimate the level of heterozygosity in F2 and backcrosses revealed an excess of heterozygous genotypes. Quantitative genetic effects (an additive line effect and individual and maternal heterosis) were estimated for both traits in the two environments. Although this model gave a reasonable fit in most cases, some epistatic interaction would have to be invoked in order to explain fully the results.

Polymorphisms in mitochondrial DNA of European and Africanized honeybees (Apis mellifera)

This study demonstrates polymorphisms in both the length and in the restriction enzyme cleavage sites of honeybee mitochondrial DNA (mtDNA). The levels of variation are typical of those found in other metazoan species. These polymorphisms are potentially useful for the identification of Africanized bees in the western hemisphere and for study of honeybee phylogenetics.

Mitochondrial DNA insertion polymorphism and germ line heteroplasmy in the Triturus cristatus complex

Restriction enzyme analysis of mitochondrial (mt) DNA isolated from oocytes of 185 individuals of the T. cristatus complex collected from 10 European countries has demonstrated that large length variation (greater than 40 bp) is a common feature of the group. Insertion polymorphism was found both within and among populations, and in all cases maps to the control region of the molecule. In addition, 2 individuals from Pisa, (Italy) were each found to be heteroplasmic for 2 large insertions comprising tandem repeats of 1100 bp of the control region. Large-scale length variation has been described in a few other lower vertebrates, but some of the insertion variants within populations described here are of unprecedented size (up to 8500 bp). This is in dramatic contrast to mammalian mtDNA in which size variation is largely restricted to small (less than 15 bp) insertions and deletions.

Mitochondrial DNA evolution in the melanogaster species subgroup of Drosophila

Detailed restriction maps (40 cleavage sites on average) of mitochondrial DNAs (mtDNAs) from the eight species of the melanogaster species subgroup of Drosophila were established. Comparison of the cleavage sites allowed us to build a phylogenetic tree based on the matrix of nucleotide distances and to select the most parsimonious network. The two methods led to similar results, which were compared with those in the literature obtained from nuclear characters. The three chromosomally homosequential species D. simulans, D. mauritiana, and D. sechellia are mitochondrially very related, but exhibit complex phylogenetic relationships. D. melanogaster is their closest relative, and the four species form a monophyletic group (the D. melanogaster complex), which is confirmed by the shared unusual length of their mt genomes (18-19 kb). The other four species of the subgroup (D. yakuba, D. teissieri, D. erecta, and D. orena) are characterized by a much shorter mt genome (16-16.5 kb). The monophyletic character of the D. yakuba complex, however, is questionable. Two species of this complex, D. yakuba and D. teissieri, are mitochondrially indistinguishable (at the level of our investigation) in spite of their noticeable allozymic and chromosomal divergence. Finally, mtDNA distances were compared with the nuclear-DNA distances thus far established. These sequences seem to evolve at rather similar rates, the mtDNA rate being barely double that of nuclear DNA.

Mitochondrial DNA heteroplasmy in Drosophila mauritiana

Mitochondrial DNA extracted from an isofemale strain of Drosophila mauritiana (subgroup melanogaster) appeared to be heterogeneous in size. A short genome [S; 18,500 base pairs (bp)] and a longer one (L; 19,000 bp) coexist in the preparation. The additional 500 bp have been located within the A+T-rich region. Hpa I digest patterns suggest that the S genome may carry a duplication of a 500-bp sequence including an Hpa I site and that the L genome may carry a triplication of the same sequence. At the 30th generation of the isofemale strain, 60 female genotypes were examined individually. Half of the files were pure either for the S or the L DNA. The remaining 50% exhibited various degrees of heteroplasmy for the two DNA types. Among metazoan animals, this D. mauritiana strain offers an exceptional situation with regard to the number of individuals heterogeneous for mtDNA and the relative stability of heteroplasmy through generations.

Structural variations and optional introns in the mitochondrial DNAs of Neurospora strains isolated from nature

Mitochondrial DNAs from ten wild-type Neurospora crassa, Neurospora intermedia, and Neurospora sitophila strains collected from different geographical areas were screened for structural variations by restriction enzyme analysis. The different mtDNAs show much greater structural diversity, both within and among species, than had been apparent from previous studies of mtDNA from laboratory N. crassa strains. The mtDNAs range in size from 60 to 73 kb, and both the smallest and largest mtDNAs are found in N. crassa strains. In addition, four strains contain intramitochondrial plasmid DNAs that do not hybridize with the standard mtDNA. All of the mtDNA species have a basically similar organization. A 25-kb region that includes the rRNA genes and most tRNA genes shows very strong conservation of restriction sites in all strains. The 2.3-kb intron found in the large rRNA gene in standard N. crassa mtDNAs is present in all strains examined, including N. intermedia and N. sitophila strains. The size differences between the different mtDNAs are due to insertions or deletions that occur outside of the rRNA-tRNA region. Restriction enzyme and heteroduplex mapping suggest that four of these insertions are optional introns in the gene encoding cytochrome oxidase subunit I. Mitochondrial DNAs from different wild-type strains contain zero, one, three, or four of these introns.

Interspecific cytoplasmic gene flow in the absence of nuclear gene flow: evidence from Drosophila

mtDNA polymorphism has been studied by restriction endonuclease site variation in Drosophila pseudoobscura and its sibling species D. persimilis. Eight enzymes have been used to study 54 isofemale strains from areas where the two species are sympatric and D. pseudoobscura is allopatric. Where sympatric, 75-80% of the strains have mitochondrial genomes found in both species. Where allopatric, D. pseudoobscura has diverged to the point where none of the strains have mtDNA in common with D. persimilis. The most likely explanation for this observation is that where sympatric the two species hybridize frequently enough to keep their mtDNA from diverging. However, hybridization has not prevented their nuclear genomes from diverging, perhaps due to selection against nuclear gene introgression contrasted with little or no selection against mtDNA introgression. These observations suggest that nuclear and cytoplasmic genomes have different evolutionary dynamics.

Propagation of two species of mitochondrial DNA in chinese hamster-mouse somatic cell hybrids

Mouse-hamster hybrid cells were analyzed for the species of mitochondrial DNA (mtDNA) retained using Southern blotting and hybridization with highly labeled mitochondrial DNA probes. Initial analyses were performed as soon as there were 10(7) cells, which took between five and eight weeks from the time the fusion was performed (approximately 23 cell doublings). The majority of clones tested had detectable levels of both mouse and hamster mtDNA at first testing.

DNA methylation in mouse cells in culture as measured by restriction enzymes

Methylation of DNA in normal mouse cultured 3T3 cells and in their virally or chemically transformed derivatives was studied. DNA methylation was studied by restriction with HpaII, MspI, or HpaII plus MspI. DNA from the chemically transformed cells was cleaved about twice as often with HpaII than was the DNA of normal and virally transformed cells. Digests with MspI and HpaII plus MspI were identical in all cell lines studied. Densitometry of the restriction patterns allowed an estimate of total DNA methylation from the weight average lengths. The chemically transformed cell line showed 25% reduction in methylation compared to the other cell lines. Southern blot hybridization using satellite DNA showed that these sequences followed a pattern of modification similar to that of total DNA.

Polymorphisms of mitochondrial DNAs in Norway rats (Rattus norvegicus): cleavage site variations and length polymorphism of restriction fragments

Extensive polymorphism was found in mitochondrial DNAs (mtDNAs) of Norway rats (Rattus norvegicus). The restriction endonuclease cleavage patterns of mtDNAs of laboratory rats, wild rats, tumor cells, and culture cells were compared. The polymorphism is defined by two criteria; one is cleavage site variation and the other is length polymorphism of restriction fragments. The cleavage site variation may be caused by point mutation, and the length polymorphism by sequence deletions or insertions. At least five types, types A-E, were identified by cleavage site variations, and two groups, a and b, were identified by length polymorphism of one HpaII fragment, Hpa5. All types except type C belonged to either group-a or group-b, whereas both groups were found in type C. Differentiation of polymorphic Norway rat mtDNA types and the experimental use of the polymorphism are discussed.

Maternal inheritance of mitochondrial DNA polymorphisms in cultured human fibroblasts

We have isolated the total cellular DNA from the cultured diploid fibroblasts of a six-member, three-generation human family. Using a specific radioactive probe for mitochondrial (mt) sequences we have identified new polymorphic variants in this family for the Hhal restriction endonuclease cleavage pattern of the mtDNA. The inheritance of these cleavage patterns verifies the maternal inheritance of mtDNA through all three generations.

Intraspecific diversity of nucleotide sequences within the adenine + thymine-rich region of mitochondrial DNA molecules of Drosophila mauritiana, Drosophila melanogaster and Drosophila simulans

Mitochondrial DNA (mtDNA) molecules from Drosophila mauritiana, D. melanogaster, and D. simulans contain a single adenine + thymine (A+T)-rich region, which is similarly located in all molecules, but varies in size among these species. Using agarose gel electrophoresis and electron microscopy, a difference in occurrence of one EcoRI site, and a difference in size (approximately 0.7 kb) of the A+T-rich regions was found between mtDNA molecules of flies of two female lines of D. mauritiana. In heteroduplexes constructed between these two kinds of mtDNA molecules, two or three regions of strand separation, each comprising single strands of unequal length, were apparent near the center of the A+T-rich region. Using the structural differences between D. mauritiana mtDNA molecules it was demonstrated the mtDNA of this species is maternally inherited. Differences in length of A+T-rich regions were also found between mtDNA molecules of two geographically separated strains of D. melanogaster, and between mtDNA molecules of two geographically separated strains of D. simulans. However, in both cases, in heteroduplexes constructed between mtDNA molecules of different strains of one species, the A+T-rich regions appeared completely paired.

Maternal inheritance of human mitochondrial DNA

Human mitochondrial DNA was obtained from peripheral blood platelets donated by the members of several independent families. The samples were screened for nucleotide sequence polymorphisms between individuals within these families. In each family in which we were able to detect a distinctly different restriction endonuclease cleavage pattern between the parents, the progeny exhibited the maternal cleavage pattern. Informative polymorphisms were detected for Hae II (PuGCGCPy) in a three-generation family composed of 33 members, for HincII (GTPyPuAC) in a two-generation family composed of four members, and for Hae III(GGCC) in a two-generation family composed of four members. The Hae II polymorphism was analyzed through all three generations in both the maternal and paternal lines. The results of this study demonstrate that human mitochondrial DNA is maternally inherited. The techniques described for using peripheral blood platelets as a source of human mitochondrial DNA represent a convenient way to obtain data on mitochondrial DNA variation in both individuals and populations.