ABSTRACT
Our current knowledge about phylogeny and classification of " fishes" is in a state of flux. Most classification schemes which proposed to organize the vast fish biodiversity (Helfman et al. 1997; Nelson 2006) have been based on loosely formulated syntheses of many, largely disconnected phylogenetic studies among some of its components. An explicit cladistic analysis including representatives of all major taxonomic groups across the diversity of fishes has never been accomplished. As a consequence, phylogenetic relationships among the major groups of fishes are still controversial and unresolved, as are many of the proposed higher-level taxa (Greenwood et al. 1973; Lauder and Liem 1983; Jamieson 1991; Stiassny et al. 1996; Kocher and Stepien 1997; Chen et al. 2003; Meyer and Zardoya 2003; Miya et al. 2003; Chen et al. 2004; Cloutier and Arratia 2004; Stiassny et al. 2004). We expect this situation to change soon, as ongoing efforts by morphologists and molecular systematists are seeking to converge on a synthesis. While DNA sequence data are being collected rapidly and cost effectively, and provide a useful way to reconstruct phylogeny, the promise of a data-rich supermatrix approach to explicitly analyze phylogenetic relationships among representatives of all major groups of "fishes" still is unaccomplished. These are, therefore, exciting times for molecular systematics in general, and fish phylogenetics in particular. Molecular data sets are proliferating and rapidly transitioning towards phylogenomic proportions (Miya and Nishida 2000; Rokas et al. 2003; 2005; McMahon and Sanderson 2006; Comas et al. 2007) and a more thorough interpretation of morphological and paleontological material is also underway (Diogo 2007; Mabee et al. 2007). For example, a recent analysis of higher-level relationships among the major early-branching lineages of sarcopterygians and actinopterygians (Diogo 2007), based on osteological and
myological characters, could pave the way for an expanded effort that may include the most diverse euteleostean taxa. We anticipate that in just a few years, efforts along these two fronts will converge to produce a well-supported phylogenetic classification based on genealogical analyses of large numbers of genes and a better understanding of morphological homologies based on detailed analysis of genetic and developmental pathways. In this chapter, we summarize some of the most recent results, with major emphasis on hypotheses for actinopterygian fishes derived from our own molecular studies.
