Cuvier meets Watson and Crick: the utility of molecules as classical homologies

Abstract

Much phylogenetic information has been derived from the analysis of sequence similarity in genes and proteins. These data are generally considered to be more reliable than an examination of the phylogenetic distribution of similar biologically active molecules. However, molecules can provide significant phylogenetic information when accompanied by a careful analysis of their structure, synthesis, genetics and function. Molecules may be highly structurally and functionally constrained. Thus, similar or even chemically identical molecules may be unrelated, and this may be discernible only by examination of information beyond the simple structure of the molecule. Phylogenetic variation in the synthesis of tyrosine and lysine demonstrates that chemical identity of molecules may be brought about by unrelated synthetic pathways. The widespread distribution of collagen triple helices is shown to result from convergence under structural and functional constraints. This is demonstrated by an examination of the steric constraints upon collagens and the presence of several independent families of collagen genes. Lysyl oxidase crosslinking occurs in several unrelated proteins, indicating that similarity in the post-translational modification of proteins is not evidence of homology.

The Origin of the Crustacea*

“…Similar or identical end points can indeed be achieved via different routes. As Morris & Cobabe (1991) have recently pointed out, molecules such as tyrosine may be chemically (structurally) identical in different organisms but may be synthesized by different pathways and are therefore not homologous. Even more striking, they emphasize that, despite their complexity and the peculiarities of their synthesis, collagens, which occur in both vertebrates and invertebrates, have multiple independent evolutionary origins as is shown by differences in the structure of collagen genes.…”

Multiple sequence alignment for phylogenetic purposes

“…β-heamoglobin and cellulase E2). Thus, similarity of topology and shared functional constraints represent evidence on which to base hypotheses of homology, but they may still actually represent homoplasy rather than homology (for further examples see Morris and Cobabe 1991;Graham et al 2000;Pearson and Sierk 2005).…”

The Developmental Role of the Extracellular Matrix Suggests a Monophyletic Origin of the Kingdom Animalia

“…Such convergences are not readily identified in surveys of a few "representative" taxa. However, molecules may be effectively used to test phylogenetic hypotheses, ifthe same care is taken in their analysis as has traditionally been taken in the assessment of morphological homologies (Morris and CoBabe, 1991). Homology of anatomical similarities is more certain if numerous complex correspondences exist.…”

“…They are easier to demonstrate in complex anatomical structures than in simple ones. Complex molecular systems may likewise be more reliably compared than single molecules, since functional or structural constraints upon individual molecules may mask convergence (Morris and CoBabe, 1991). I argue that the developmental role of the extracellular matrix (ECM), a complex set of molecules including collagens, is a primitive feature of multicellularity in animals, and that it provides evidence that animals are monophyletic and derived from a common multicellular ancestor ( Fig.…”