Combined-method phylogenetic analysis of Hox and paraHox genes of the metazoa

The clustered Hox genes show a conserved role in patterning the body axis o f bilaterian metazoans. Increasingly, a broader phylogenetic sampling of no n-model system organisms is being examined to detect a correlation, if any, between Hox gene evolution, and body plan innovations. To assess how Hox g ene expression and function evolve with changing cluster arrangements, we m ust be able to reliably assign gene orthologies between Hox genes. Recent e vidence suggests that a four-gene proto-Hox cluster duplicated to form the precursor of the present cluster and an additional sister-cluster, the Para Hox group. Here, phylogenetic methods are used to determine Hox-gene orthol ogies and to infer probable clustering events leading to the current bilate rian Hox complement. This analysis supports the ParaHox hypothesis and give s first confirmation that ind (intermediate neuroblasts defective) is an an terior ParaHox ortholog from protostomes. This analysis supports a proto-Ho x cluster of four genes in which the central-class member of the ParaHox cl uster may have been lost. It is also proposed here that ancestral diploblas ts had central-class members of both Hox and ParaHox clusters. Primitive Ho x gene ancestors are estimated by phylogenetic methods and found to have no strong affinity to any particular class of extant Hox members. (C) 2000 Wi ley-Liss, Inc.