Conflict and resolution between phylogenies inferred from molecular and phenotypic data sets for hagfish, lampreys, and gnathostomes

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.

Assembly and Expression of Shark Ig Genes

“…Cartilaginous fish taxa are indicated in black. The scale shows divergence times according to molecular clock estimations [2–4]. The cyclostome (jawless fish) divergence is problematic [5], shown here by a balance of dating from fossil evidence and by gene sequence (www.timetree.org).…”

microRNAs revive old views about jawless vertebrate divergence and evolution

“…Morphologists who defended cylostome paraphyly argued that molecular sequence-based trees were inconclusive because of the uncertainty as to the outgroups of the vertebrates (i.e., their closest relatives and either tunicates of amphioxus) (Fig. 1) or because of biases in the methods of molecular tree reconstruction that were at odds with the original standard parsimony methods of cladistics (9). Clearly, a third independent source of characters was needed to resolve this conflict, and much hope was put in developmental data for deciding whether hagfishes were actually primitive and had lost many characteristics since their divergence from other vertebrates (10).…”

microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate

“…Indeed, an analysis of combined morphological and molecular datasets has suggested that the signal of cyclostome paraphyly in morphological datasets is stronger than the signal for monophyly from molecular data (39). The interrelationships of hagfish, lampreys, and gnathostomes thus remain uncertain, and this has become a classic example of phylogenetic conflict between morphological and molecular data (7,39). If morphological phylogenies are correct, hagfish provide an experimental model for investigating the evolutionary assembly of the vertebrate body plan shared by lampreys and gnathostomes.…”