28S and 18S rDNA sequences support the monophyly of lampreys and hagfishes

Resolving the interrelationships of three major extant lineages of vertebra tes (hagfishes, lampreys, and gnathostomes) is a particularly important iss ue in evolution because the basal resolution critically influences our unde rstanding of primitive vertebrate characters. A consensus has emerged over the last 20 years that lampreys are the sister group to the gnathostomes an si the hagfishes represent an ancient, basal lineage. This hypothesis has e ssentially displaced the classical hypothesis of monophyly of the cyclostom es (lampreys plus hagfishes). To test these hypotheses, we compared nearly complete ribosomal DNA sequences from each of these major lineages, as well as those from a cephalochordate and a urochordate, which represent a parap hyletic outgroup for assessing the basal vertebrate relationships. For this comparison, 92%-99% complete 28S rDNA sequences were obtained from the lan celet Branchiostoma floridae, the hagfish Eptatretus stouti, the lamprey Pe tromyzon marinus, and cartilaginous fishes Hydrolagus colliei and Squalus a canthias and were then analyzed with previously reported 28S and 18S rDNA s equences from other chordates. We conducted conventional (nonparametric) bo otstrap analyses, under maximum-likelihood, parsimony, and minimum-evolutio n (using LogDet distances) criteria, of both 28S and 18S rDNA sequences con sidered separately and combined. All these analyses provide moderate to ver y strong support for the monophyly of the cyclostomes. Furthermore, the cur rently accepted hypothesis of a lamprey-gnathostome clade is moderately rej ected by the Kishino-Hasegawa test (P = 0.099) and resoundingly rejected by parametric bootstrap tests (P < 0.01) in favor of monophyly of living cycl ostomes. Another significant finding is that the hagfish E. stouti has the longest 28S rDNA gene known in any organism (>5,200 nt).