Conflict and Resolution Between Phylogenies Inferred From Molecular and Phenotypic Data sets for Hagfish, Lampreys, and Gnathostomes THOMAS J. NEAR Ã Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, Connecticut ABSTRACT One of the most problematic issues in vertebrate phylogenetics is the disagreement between phenotypic and molecular inferences regarding the relationships among hagfishes, lampreys, and gnathostomes. Phenotypic characters support monophyly of lampreys and gnathostomes, whereas nearly all published analyses of molecular data sets support monophyly of hagfishes and lampreys. In this study I present results of phylogenetic analyses of combined phenotypic and molecular data sets that focus on relationships among hagfishes, lampreys, and gnathostomes. Maximum parsimony analyses of 115 phenotypic characters combined with 4,638 rRNA sites and more than 10,000 amino acids each result in monophyly of lampreys and gnathostomes, demonstrating that the addition of relatively few phenotypic characters can alter phylogenetic inferences from large molecular data sets. On the other hand, Bayesian analyses of the combined data sets support monophyly of hagfish and lampreys, indicating that model-based analyses may be prone to data ‘‘swamping,’’ where the phylogenetic signal of the larger molecular data sets overwhelm the signal present in the much smaller phenotypic data set. Nodes that relate hagfish and lampreys were recovered at a low frequency in parametric bootstrapping analyses, indicating that the timing of diversification among hagfishes, lampreys, and gnathostomes has created a difficult phylogenetic problem for molecular data. The fact that addition of relatively few phenotypic characters can alter phylogenetic inferences of cyclostome monophyly obtained from molecular data sets, and the inability of simulated data sets to recover key nodes in the craniate phylogeny provide reasons to view the strong support for cyclostome monophyly inferred from molecular data sets with a measured degree of skepticism. J. Exp. Zool. (Mol. Dev. Evol.) 312B:749– 761, 2009. r 2009 Wiley-Liss, Inc. How to cite this article: Near TJ. 2009. Conflict and resolution between phylogenies inferred from molecular and phenotypic data sets for hagfish, lampreys, and gnathos- tomes. J. Exp. Zool. (Mol. Dev. Evol.) 312B:749–761. The conflict between molecular and phenotypic data sets regarding the relationships of hagfish and lampreys remains one of the most vexing problems in vertebrate phylogenetics (Forey and Janvier, ’93; Patterson et al., ’93; Forey, ’95; Janvier, ’96b; Donoghue et al., 2000; Meyer and Zardoya, 2003; Janvier, 2007a,b). Extant craniates are repre- sented by three major clades, the hagfishes (Myxinioidea), lampreys (Petromyzontiformes), and the gnathostomes, or jawed vertebrates. Huxley (1876) and Parker (1883) hypothesized that the similar appearance of hagfish and lam- preys was the result of degenerative changes associated with parasitism. Cope (1889) classified hagfish and lampreys in the class Agnatha, and this classification was used in Hubbs and Potter’s (’71) comprehensive and influential review of lamprey species diversity. Noting the absence of jaws, paired fins, and exoskeletons, later investi- gators hypothesized that hagfish and lampreys Published online 28 April 2009 in Wiley InterScience (www. interscience.wiley.com). DOI: 10.1002/jez.b.21293 Received 12 January 2009; Revised 21 March 2009; Accepted 1 April 2009 Grant sponsor: National Science Foundation; Grant number: DEB-0716155. Ã Correspondence to: Thomas J. Near, Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520. E-mail: thomas.near@yale.edu r 2009 WILEY-LISS, INC. JOURNAL OF EXPERIMENTAL ZOOLOGY (MOL DEV EVOL) 312B:749–761 (2009)