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Recently published rRNA sequences (Hedges et al. 1990) provide important new information on tetrapod relationships. Specifically Hedges et al’s ( 1990) data support a monophyletic Lissamphibia, Amniota, Squamata, Mammalia, and Aves. It is surprising that the 18s rRNA sequences also support a close relationship between the two birds and the four mammals sequenced. Paleontological data provide considerable evidence for a close bird-crocodile relationship (e.g., see Gauthier et al. 1988; Donoghue et al. 1989), and the strength of these data suggested the possibility that the support for a bird-mammal relationship shown by the 1% rRNA sequences may be an artifact created by substitution biases. Table 1 shows that there are indeed pronounced substitution biases in the amniote 18s rRNA sequences. In particular, there is both a significant overrepresentation of T-to-C substitutions and a significant underrepresentation of A-to-T and T-to-A substitutions. It is interesting that a disproportionately large number of sites that support a bird-mammal relationship are T-to-C substitutions (table 1). The only site that involves T-to-A and/or A-to-T substitutions is site 13 17 in Hedges et al.% ( 1990) figure A 1 (note that there are 140 nucleotides/line in their fig. A 1, not 150 as indicated), and on the most parsimonious tree this site is homoplasious, requiring both a T-toA substitution in the branch leading to the four mammals and either a T-to-A substitution in the Coelacanth or an A-to-T substitution at the base of the amniotes. However, when viewed in isolation, site 13 17 supports a clade including birds and crocodiles, to the exclusion of mammals. Note that the substitution biases are quite complex. The T/C transitions are vastly overrepresented, yet A/G transitions are not. Similarly, A/T transversions are underrepresented, but C/G transversions are not (table I).

Substitution bias, weighted parsimony, and amniote phylogeny as inferred from 18S rRNA sequences.