Organismal biology, molecular systematics, and phylogenetic reconstruction

Abstract

DNA sequence data enjoys the singular position of being the arbiter of phylogenetic relationships; yet the justi fications for this endeavor-the notions of continual molecular change, and that the degree of overall similarity re flects recency of divergence from a common, constantly changing ancestral sequence-was based on studies of bacteria not multicellular organisms. This is important because ca. 98% of a bacterial genome codes for metabolically active proteins, while a similar proportion in the metazoan genome is dedicated to the regulation of development. Consequently, random mutation in the metazoan genome would likely lead to organismal failure, not survival, which suggests that sequence similarity in this region re flects primitive retention (= nonchange). Further, since metazoan mtDNA and the ca. 2% coding region are involved in metabolic processes, demonstration of taxic similarity in these nucleotide sequences is likely to re flect similar physiological adaptation, not evolutionary history.