ABSTRACT
This study expands on a previous molecular-phylogenetic study of the interrelationships of hagfishes, lampreys and gnathostomes based on nearly complete ribosomal RNA gene sequences (Mallatt and Sullivan 1998). That study used several analytical techniques, including maximum likelihood, and provided support for the monophyly of hagfishes and lampreys as cyclostomes. In this study, we increased the number of relevant chordate outgroups by obtaining large-subunit rRNA sequences (26S [=28S] and 5.8S) from three urochordates, Styela plicata. Thalia democratica, and Oikopleura sp. These new sequences were then incorporated into the combined, 18S-28S-5.8S rRNA, data set used previously, which contains sequences from Branchiostoma and seven jawed and jawless vertebrate taxa. The new urochordate sequences had high frequencies of A and T nucleotides, which led to a nonstationarity of nucleotide composition among taxa and required us to use LogDet-based distance methods, which account for such nonstationarity. These distances were used for (1) minimum-evolution (ME) tree estimation, and (2) spectral analysis of support and conflict for various bipartitions in the data set. When the most reasonable estimates of the proportion of invariable sites were assumed (0.6-0.7), cyclostome monophyly was strongly supported over a lamprey-gnathostome group by the ME bootstrap analyses (>97 per cent bootstrap support) and by spectral analysis. The lampreygnathostome group received less than 55 per cent as much support and over twice as much conflict as the lamprey-hagfish group. Thus, the expanded rRNA data set continues to support cyclostome monophyly.
