Drosophila Mitochondrial Genetics: Evolution of Heteroplasmy through Germ Line Cell Divisions.

The mitochondrial genotype of all F(1) female offspring (426 individuals) of a single Drosophila mauritiana female, heteroplasmic for two types of mtDNA (a short and a long genome), was established. All descendants were heteroplasmic. The earliest eggs laid by this female show the cytoplasmic genetic structure of ovariole stem cells at the end of development. Cohorts of females from the eggs laid day after day by this female, throughout the 31 days of its life, provide information on the evolution of the mitochondrial genotypes in the course of successive divisions of stem cells. An increase of the percentage of long DNA in offspring was observed as the female aged. Moreover, the variance of the genotypes increases as rounds of stem cell division progress. These results are supported by observations based on the adults issued from the early and late eggs, for three additional heteroplasmic females.

Genetic analysis of systematic mitochondrial heteroplasmy in rabbits.

One unusual property of rabbit mitochondrial DNA (mtDNA) is the existence of repeated 153-bp motifs in the vicinity of the replication origin of its H strand. Furthermore, every individual is heteroplasmic: it carries mtDNA molecules with a variable number of repeats. A systematic study of 8 females and their progeny has been devised to analyze mtDNA transmission through generations. The results suggest that three mechanisms are acting simultaneously. (1) Genetic drift in the germ line is revealed by the evolution of heteroplasmy when two major molecular forms are present in a female. (2) A high mutation rate (around 10(-2) per animal generation) generating molecular diversity, by deletion and addition of repeated units, is required to explain the observation of heteroplasmy in every individual. Moreover, the rates of mutation from the most frequent type to the other types are unequal. The deletion of one unit is more frequent than a deletion of two units, which is in turn more frequent than a deletion of three. (3) Selection for shorter molecules in somatic cells is probable. The frequency distribution of mtDNA types depends on the organ analyzed (kidney-spleen and liver vs. gonads).

Molecular characterization of mitochondrial DNA provides evidence for the recent introduction of Schistosoma mansoni into America.

Mitochondrial DNA was analyzed from 6 strains of Schistosoma mansoni with 12 restriction enzymes, corresponding to 40 restriction sites or about 1.5% of the coding region. An extensive length polymorphism among strains of S. mansoni was found, with size ranging from 16,500 bp to 24,900 bp. Five restriction sites among 40 were polymorphic; phylogenetic analysis using parsimony criteria supports the idea that American strains were introduced very recently from Africa. Two large fragments (2800 and 5400 bp), representing half of the coding region were cloned. The location of some genes was determined using heterospecific multigenes probes and suggests that this platyhelminth genome differs from all other known mtDNA gene organization.

Rate matrices for analyzing large families of protein sequences.

We propose and study a new approach for the analysis of families of protein sequences. This method is related to the LogDet distances used in phylogenetic reconstructions; it can be viewed as an attempt to embed these distances into a multidimensional framework. The proposed method starts by associating a Markov matrix to each pairwise alignment deduced from a given multiple alignment. The central objects under consideration here are matrix-valued logarithms L of these Markov matrices, which exist under conditions that are compatible with fairly large divergence between the sequences. These logarithms allow us to compare data from a family of aligned proteins with simple models (in particular, continuous reversible Markov models) and to test the adequacy of such models. If one neglects fluctuations arising from the finite length of sequences, any continuous reversible Markov model with a single rate matrix Q over an arbitrary tree predicts that all the observed matrices L are multiples of Q. Our method exploits this fact, without relying on any tree estimation. We test this prediction on a family of proteins encoded by the mitochondrial genome of 26 multicellular animals, which include vertebrates, arthropods, echinoderms, molluscs, and nematodes. A principal component analysis of the observed matrices L shows that a single rate model can be used as a rough approximation to the data, but that systematic deviations from any such model are unmistakable and related to the evolutionary history of the species under consideration.

MboI, ThaI and HinfI endonuclease cleavage maps of the yeast mitochondrial DNA : Localization of transfer RNA genes.

MboI, HinfI and ThaI cleavage maps have been constructed for the region of the mitochondrial DNA from S. cerevisiae where transfer RNA genes are principally located. About 40 cleavage sites have been localized between the C and P genetic markers. The MboI map covers about 50% of the total mitochondrial genome. For constructing maps we have used a series of rho(-) deletion mutants whose mitochondrial DNAs have a typical single deletion structure as judged by previous genetic and physical analyses. The mutant DNAs carry known transfer RNA genes and genetic markers and, therefore, the comparison between genetic and restriction maps has allowed us to localize individual transfer RNA genes within defined physical segments.

Phylogeography of the European rabbit (Oryctolagus cuniculus) in the Iberian Peninsula inferred from RFLP analysis of the cytochrome b gene.

We studied mitochondrial DNA variation in the European rabbit through the examination of restriction fragment length polymorphism in 526 individuals from 20 locations spread across the Iberian Peninsula. Digestion with eight enzymes of a 1120-bp fragment comprising most of the cytochrome b gene resolved 38 different haplotypes. These haplotypes were distributed in two highly divergent clades, with different but overlapping geographical distributions, and with comparable levels of within-clade variation. The overall phylogeographical pattern suggests a history of long-term regional isolation of two groups of rabbit populations, compatible with the recognition of two subspecies within the Iberian Peninsula, followed by recent contact and admixture. The underlying cause is sought in the alternation of glacial and interglacial periods in the late Pleistocene.

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.

[History of the rabbit and ancient DNA]. / Histoire des lapins et ADN ancien.

Present populations of Rabbits (Oryctolagus cuniculus) are organized into two well defined groups A and B according to their mitochondrial DNA sequences. Group A is restricted to the South Western part of the Iberian Peninsula while group B is found everywhere else. Domestic breeds belong to the latter. As evidenced from data on ancient bones (up to 12,000 years BP) the mitochondrial type B1, predominant in domestic animals, originated from Spain. B1 animals were introduced in France by man between late Roman times and Middle Ages.

Phylogeny of cephalopods inferred from mitochondrial DNA sequences.

Sequences of partial mitochondrial cytochrome oxidase III gene (533 bp) were obtained for 17 species of cephalopods, 14 decapods, 2 octopods, and 1 vampyromorph. This study aimed to: (1) compare partial COII and COIII amino acid sequences of three species of cephalopods with other invertebrates in terms of base composition and phylogenetic relationships. Cephalopod sequences are closer to Katharina tunicata sequences than to Mytilus edulis (marine bivalve) and Albinaria turrita (terrestrial gastropod); (2) investigate the phylogenetic relationships among cephalopods. Nucleotides as well as amino acid sequence variations of a COIII fragment were examined with parsimony and distance methods. Our data confirm the monophyly of the Decapoda and of each family. A high hierarchical rank for sepiolids, already suggested by other authors, appears justified. The order Sepioidea comprising five families should be abandoned, with Spirula being excluded. The surprising position of Idiosepius as the sister group of some oegopsids and not of sepioids or sepiolids is confirmed. Vampyroteuthis is the sister group of octopods. However, the data do not allow resolution of the phylogenetic relationships between the orders of Decapoda; consequently we suspect a rapid radiation.

Mapping of mutation tsm-8 with respect to transfer RNA genes on the mitochondrial DNA of Saccharomyces cerevisiae.

A precise localization of the tsm-8 mutation in relation to the transfer RNA genes has been attempted by rho- deletion analysis. The data show that the tsm-8 mutation is in close proximity to the isoleucyl transfer RNA gene. However, it is not yet possible to decide whether the tsm-8 mutation is within this transfer RNA gene.

Intrageneric phylogeny of Acomys (rodentia, muridae) using mitochondrial gene cytochrome b.

This paper investigates interspecies relationships within the genus Acomys (spiny mice) by analyzing entire mitochondrial cytochrome b gene (1141 bp). This gene provides strong phylogenetic signal, as shown by high support of the topology obtained (bootstrap value and RNA support number). The phylogeny is congruent with inferences from allozymes for the species considered. Controversial taxonomy of Acomys cahirinus, dimidiatus, airensis, and ignitus is clarified, with their specific ranks confirmed on the basis of tree topology and nucleotide distances. Phylogenetic relationship between the undescribed species Acomys sp. from west Africa and A. airensis argue in favor of two distinct colonization events in this zone.

Discrepancy in divergence of the mitochondrial and nuclear genomes of Drosophila teissieri and Drosophila yakuba.

Restriction sites were compared in the mitochondrial DNA (mtDNA) molecules from representatives of two closely related species of fruit flies: nine strains of Drosophila teissieri and eight strains of Drosophila yakuba. Nucleotide diversities among D. teissieri strains and among D. yakuba strains were 0.07% and 0.03%, respectively, and the nucleotide distance between the species was 0.22%. Also determined was the nucleotide sequence of a 2305-nucleotide pair (ntp) segment of the mtDNA molecule of D. teissieri that contains the noncoding adenine + thymine (A + T)-rich region (1091 ntp) as well as the genes for the mitochondrial small-subunit rRNA, tRNA(f-met), tRNA(gln), and tRNA(ile), and portions of the ND2 and tRNA(Val) genes. This sequence differs from the corresponding segment of the D. yakuba mtDNA by base substitutions at 0.1% and 0.8% of the positions in the coding and noncoding regions, respectively. The higher divergence due to base substitutions in the A + T-rich region is accompanied by a greater number of insertions/deletions than in the coding regions. From alignment of the D. teissieri A + T-rich sequence with those of D. yakuba and Drosophila virilis, it appears that the 40% of this sequence that lies adjacent to the tRNA(ile) gene has been highly conserved. Divergence between the entire D. teissieri and D. yakuba mtDNA molecules, estimated from the sequences, was 0.3%; this value is close to the value (0.22%) obtained from the restriction analysis, but 10 times lower than the value estimated from published DNA hybridization results.(ABSTRACT TRUNCATED AT 250 WORDS)

Taxonomic status and phylogenetic relationships of some species of the genus Gammarus (Crustacea, Amphipoda) deduced from mitochondrial DNA sequences.

Mitochondrial DNA nucleotide sequence analysis was used to determine the extent of genetic differentiation among six species of the genus Gammarus (Crustacea, Amphipoda) common in France (G. fossarum, G. pulex, G. lacustris, G. wautieri, G. roeseli, G. marinus). From 23 different populations, 104 specimens were compared to examine their taxonomic status and their phylogenetic relationships. Nucleotide sequences for a 376-base segment of the cytochrome c oxidase subunit I (COI) gene were obtained through direct sequencing of amplified DNA. The strong sequence variability found at the interspecific level, generally masked by morphological or ecological similarities, is consistent with that observed for other crustaceans and supports existing species classifications. A high level of genetic variation was observed at the intraspecific level, suggesting that the COI gene will be a powerful marker for amphipod population biology. Based on the mitochondrial population biology. Based on the mitochondrial DNA results, we propose a phylogenetic hypothesis of the relationships among the six studied species, which is discussed in biogeographic and evolutionary terms.

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.

Intra-individual length heterogeneity of Rana esculenta mitochondrial DNA.

Mitochondrial DNA extracted from Rana esculenta oocytes appears heterogeneous in size. The length of these molecules varies continuously from 18,700 bp to 19,700 bp. Each animal is heteroplasmic and can be characterized by the range of the variation (400-700 bp) and the extreme sizes of the various molecules it carries. The variable region of the genome has been localized between the coding region and the replication origin area.

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.

Phylogeny of decapod cephalopods based on partial 16S rDNA nucleotide sequences.

Various systematic and phylogenetic relationships have been proposed for extent decapod Cephalopods, based mainly on morphology and on the rare paleontological remains. Nucleotide sequence data from the 3' end of 16S rDNA gene were used as an alternative approach to morphology; this gene portion having proved to be appropriate to test divergences in other groups of assumed equivalent age. The results from 27 Decapoda species allowed us to calculate phylogenetic trees by the neighbor joining and parsimony methods (Paup and Hennig86). The trees were submitted to bootstrapping. The order Sepioidea, including the sepiids, sepiolids and spirulids, is not supported by molecular evidence. Sepiolids are clearly excluded from the order, and the position of the Spirulidae needs further clarification. In oegopsids, the intrafamilial groupings obtained by the molecular approach is in agreement with morphological data. The unresolved phylogeny at the suprafamilial level might be the result of two different events: earlier divergence than the Cenozoic, or unequal evolutionary rates among taxa having appeared either by successive emergence or by fast radiation. The 3' end of 16S rDNA gene of cephalopods is a precious tool to analyze taxonomic relationships at the infrafamilial level. A gene with a lower evolutionary rate, is necessary to establish higher taxa phylogeny.

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.

Low allozyme and mtDNA variability in the island endemic species Drosophila sechellia (D. melanogaster complex).

Genetic variability of D. sechellia is investigated at both mitochondrial and nuclear levels. The results reveal the existence of a single main type of mtDNA with very few variants and a very low enzyme polymorphism. This situation is consistent with the small population size of this specialized species.