Unequal synonymous substitution rates within and between two protein-coding mitochondrial genes.

Genes encoded by mitochondrial DNA display considerable heterogeneity of sequence change. Among protein-coding genes, rates and patterns of nonsynonymous nucleotide substitutions are influenced by differential selective constraints relative to amino acid composition and function of the gene product. Synonymous substitutions are presumably free of functional constraints on amino acid sequence. However, patterns of synonymous substitutions are not uniform. Observations of transition bias at synonymous sites across many groups of closely related taxa have led to general agreement that transitional substitutions, as a class, evolve more rapidly than transversional substitutions. Furthermore, strong nucleotide compositional bias present at largely synonymous third codon positions suggests that even within transitions or transversions the pattern of nucleotide substitution may not be uniform (Perna and Kocher 1995). Substitutional processes of mitochondrial genes are complex and additionally can vary with taxonomic group. In this study, we examined nucleotide sequence evolution of two protein-coding mtDNA genes (cytochrome b and ND4L) among closely related species of the North American cyprinid genus Notropis. Cytochrome b (cyt b) is a well-characterized gene whose predicted amino acid sequence appears to be conserved (Irwin, Kocher, and Wilson 1991; Martin and Palumbi 1993; Cantatore et al. 1994). ND4L is a smaller and less well-characterized gene whose predicted amino acid sequence is thought to be much less conserved than that of cyt b (Johansen, Guddal, and Johansen 1993; Meyer 1993). A 533-base-pair (bp) fragment of the cyt b gene and the entire ND4L gene (297 bp) were sequenced from representatives of eight species of the cyprinid genus Notropis. These included six species of the subgenus Notropis (N. amabilis, N. atherinoides, N. oxyrhynthus, N. shumardi, N. stilbius, and N. telescopus), N. rubellus (placed in the subgenus Notropis by Mayden and Matson [ 1988]), and N. girardi (placed in the subgenus Notropis by Coburn and Cavender [ 19921). Species were sampled from wild populations by seining. Genomic DNA was prepared using phenol : chloroform extraction and selected genes were amplified using the polymerase chain reaction (PCR). The PCR thermal profile consisted of 35 cycles of 95°C denaturation