Mitochondrial DNA was purified from four species of higher primates (Guinea baboon, rhesus macaque, guenon, and human) and digested with 11 restriction endonucleases. A cleavage map was constructed for the mitochondrial DNA of each species. Comparison of the maps, aligned with respect to the origin and direction of DNA replication, revealed that the species differ from one another at most of the cleavage sites. The degree of divergence in nucleotide sequence at these sites was calculated from the fraction of cleavage sites shared by each pair of species. By plotting the degree of divergence in mitochondrial DNA against time of divergence, the rate of base substitution could be calculated from the initial slope of the curve. The value obtained, 0.02 substitutions per base pair per million years, was compared with the value for single-copy nuclear DNA. The rate of evolution of the mitochondrial MAnome appears to exceed that of the single-copy fraction of the nuclear genome by a factor of about 10. This high rate may be due, in part, to an elevated rate of mutation in mitochondrial DNA. Because of the high rate of evolution, mitochondrial DNA is likely to be an extremely useful molecule to employ for high-resolution analysis of the evolutionary process.

This essay reviews comparative studies of animal mitochondria1 DNA (mtDNA), with emphasis on findings made and ideas developed at Berkeley. It argues that such studies are bringing together two previous paths of progress in evolutionary biology. One path is that of those who worked far above the species level and were concerned with genealogical trees, time scales and the accumulation of new mutations on surviving molecular lineages. The other path is that of those who worked at and below the species level and were concerned mainly with population structure, migration and the frequencies of alleles that existed in an ancestral population. This fusion of paths is made possible by the high rate at which mutations accumulate on mtDNA lineages and by this molecule's uniparental and apparently haploid mode of inheritance. These properties make mtDNA a superb tool for building trees and time scales relating molecular lineages at and below the species level. In addition, owing to its mode of inheritance, mtDNA is more sensitive to bottlenecks in population size and to population subdivision than are nuclear genes. Joint comparative studies of both mtDNA and nuclear DNA variability give us valuable insights into how effective population size has varied through time. Such studies also give insight into the conditions under which mtDNA from one species can colonize another species.

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We report the complete genome sequence of enterobacteriophage SP6, which infects Salmonella enterica serovar Typhimurium. The genome contains 43,769 bp, including a 174-bp direct terminal repeat. The gene content and organization clearly place SP6 in the coliphage T7 group of phages, but there is ϳ5 kb at the right end of the genome that is not present in other members of the group, and the homologues of T7 genes 1.3 through 3 appear to have undergone an unusual reorganization. Sequence analysis identified 10 putative promoters for the SP6-encoded RNA polymerase and seven putative rho-independent terminators. The terminator following the gene encoding the major capsid subunit has a termination efficiency of about 50% with the SP6-encoded RNA polymerase. Phylogenetic analysis of phages related to SP6 provided clear evidence for horizontal exchange of sequences in the ancestry of these phages and clearly demarcated exchange boundaries; one of the recombination joints lies within the coding region for a phage exonuclease. Bioinformatic analysis of the SP6 sequence strongly suggested that DNA replication occurs in large part through a bidirectional mechanism, possibly with circular intermediates.Bacteriophage SP6 is a small double-stranded DNA tailed phage that infects Salmonella enterica serovar Typhimurium LT2. It shares many features with coliphage T7; however, no significant DNA sequence homology was detected between these phages by DNA hybridization (26). Previous studies of SP6 have elucidated its virion structure and the function and regulation of its early genes. Many of these previous studies examined the phage-encoded SP6 RNA polymerase (SP6RP) (7,9,26,27,30,41). SP6RP has been used to produce synthetic RNA for a wide variety of applications (29,30,33,37,43).As with phage T7, the SP6 genome is transcribed in a temporally ordered manner (26); transcription by SP6RP gives rise to 10 discrete RNA species (26). This finding suggests that discrete sites present in the SP6 genome serve as specific initiation and termination signals. One terminator sequence for the SP6 species IX RNA transcript has been identified, cloned, and sequenced (5). This sequence appears to be analogous to the stem-loop structure found at a comparable position in the T7 genome and to other rho-independent terminators (14). Preliminary studies have provided evidence for the presence of this termination sequence in the SP6 genome (5), but the termination efficiency has not been fully characterized.Bacteriophage SP6 has been reported to be closely related to phages K1-5, K5, and K1E (51). In addition, Scholl et al. reported that SP6 encodes a tail protein that is in the same family as the tail spike protein of the otherwise apparently unrelated phage P22 (51). However, information about SP6 phage genetics, SP6 molecular biology, and the relationship of the sequence of this phage to other phage and prophage sequences is still limited. We completed the 43,769-bp sequence of the phage SP6 genome, identified the positions of individual genes an...