ABSTRACT
The strategies of gene sequencing and gene characterization in phylogenetic studies are frequently determined by a balance between cost and benefit, where benefit is measured in terms of the amount of phylogenetic signal resolved for a given problem at a specific taxonomie level. Generally, cost is far easier to predict than benefit. Building upon existing databases is a cost-effective means by which molecular data may rapidly contribute to addressing systematic problems. As technology advances and gene sequencing becomes more affordable and accessible to many researchers, it may be surprising that certain genes and gene products remain favoured targets for systematic and phylogenetic studies. In particular, ribosomal DNA (rDNA), and the various RNA products transcribed from it continue to find utility in wide-ranging groups of organisms. The small (SSU) and large subunit (LSU) rDNA fragments especially lend themselves to study as they provide an attractive mix of constant sites that enable multiple alignments between homologues, and variable sites that provide phylogenetic signal (Hillis and Dixon 1991; Dixon and Hillis 1993). Ribosomal RNA (rRNA) is also the commonest nucleic acid in any cell, and thus was the prime target for sequencing in both eukaryotes and prokaryotes during the early history of SSU nucleotide based molecular systematics (Olsen and Woese 1993). In particular, the SSU gene (rDNA) and gene product (SSU rRNA1) have become such established sources of taxonomie and systematic markers among some taxa that databanks dedicated to the topic have been developed and maintained with international and governmental funding (e.g., The Ribosomal Database Project II, Maidak et al. 1999; the rRNA WWW Server, van de Peer et al. 2000). One or more species from all metazoan phyla, except the Loricifera, have had their SSU genes characterized in part or fully, and if SSU rDNA appears to be a suitable target at the outset of a phylogenetic study then these databases (including EMBL and GenBank) often provide a head start. In addition to raw sequences, many of the databases include sequences aligned against models of secondary structure and/or against other sequences in the database. Addresses of the WWW pages for all these databases are given below2. In addition, the development of our knowledge of molecular evolution as it relates to phylogeny reconstruction has been influenced greatly by the genes chosen, and SSU rRNA has certainly played its part such that features of the gene have been characterized for many phyla (e.g., Abouheif et al. 1998; Zrzavý et al. 1998).
