Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system

One of the most important aspects of mitochondrial (mt) genome evolution in Metazoa is constancy of size and gene content of mtDNA, whose plasticity i s maintained through a great variety of gene rearrangements probably mediat ed by tRNA genes. The trend of mtDNA to maintain the same genetic structure within a phylum (e.g., Chordata) is generally accepted, although more rece nt reports show that a considerable number of transpositions are observed a lso between closely related organisms. Base composition of mtDNA is extreme ly variable. Genome GC content is often low and, when it increases, the two complementary bases distribute asymmetrically, creating, particularly in v ertebrates, a negative GC-skew. In mammals, we have found coding strand bas e composition and average degree of gene conservation to be related to the asymmetric replication mechanism of mtDNA. A quantitative measurement of mt DNA evolutionary rate has revealed that each of the various components has a different evolutionary rate. Non-synonymous rates are gene specific and f all in a range comparable to that of nuclear genes, whereas synonymous rate s are about 22-fold higher in mt than in nuclear genes. tRNA genes are amon g the most conserved but, when compared to their nuclear counterparts, they evolve 100 times faster. Finally, we describe some molecular phylogenetic reconstructions which have produced unexpected outcomes, and might change o ur vision of the classification of living organisms. (C) 1999 Elsevier Scie nce B.V. All rights reserved.