FIGURE 2.2. The configuration of the major continental landmasses at the close of the Paleozoic (250 mya) as Pangea approached its maximum extent. Based on Torsvik and Van der Voo (2002) and Torsvik and Cocks (2004).

      Ages can also be determined indirectly from a well-developed phylogeny if there are fossils or geologic events available for calibration of molecular divergence times (Box 2.3; Lieberman 2003). For example, based on a calibrated molecular clock analysis, species’ divergence times within logperches (a group of darters in the genus Percina) ranged from 4.20 to 0.42 mya, with most speciation events taking place in the Pleistocene (Near and Benard 2004). The divergence times were based on the assumption that there is a constant rate of gene substitutions over time, and that by comparing the degree of genetic divergence among darter lineages, it is possible to convert the degree of divergence to a time estimate—the “molecular clock.” Because it is known that rates of gene substitution vary among taxonomic groups (Britten 1986; Avise 2004) and, consequently, that molecular clocks need to be calibrated using related taxa, Near and Benard (2004) used rates of gene substitution from the family Centrarchidae (in the same order, Perciformes, as the darters) and applied this to their analysis of logperches to generate their divergence time estimates.

      BOX 2.3 • Phylogenies and Cladistic Methodology

      The study of evolutionary relationships of species or higher taxa is the field of systematic biology. The concepts and methodologies underlying how evolutionary relationships are studied, and how best to portray the resultant phylogenies, have been areas of considerable debate and advancement over the last several decades. (For an overview, see Mayden and Wiley [1992] and Mayden and Wood [1995].) Concurrent with the development of principles and procedures of systematic biology, molecular data, first as protein analyses and then broadened to include mitochondrial and genomic DNA information, have complemented morphological, ecological, and behavioral data that are used in developing phylogenies. Phylogenetic (i.e., evolutionary) relationships are shown hierarchically in branching diagrams referred to as dendrograms or cladograms, depending on the methodology used to construct them. For the most part, especially among ichthyologists, phylogenies follow methods proposed by the German biologist Willi Hennig (English translation, 1966)—the method of phylogenetic systematics. This approach has been further developed by Niles Eldredge and Joel Cracraft (1980), Gareth Nelson and Norman Platnick (1981), Edward Wiley (1981), and many others.

      Basic principles of the cladistic method are that (1) relationships among groups are based primarily on branching points in evolution and not on degrees of divergence; (2) recognized groups should be derived from a single ancestral group (the principle of monophyly); and (3) taxa should be recognized on the basis of possessing shared, derived characters (synapomorphies) (Mayr and Ashlock 1991; Brooks and McLennan 1991). Sister groups are derived from the same common ancestor. A major goal of cladistic analysis is the recognition of synapomorphies, the derived (homologous) characters. Convergent evolution can result in organisms possessing structurally analogous but not evolutionarily related characters (termed homoplasies). Cladograms should be considered as hypotheses of evolutionary relationships. Support for cladistic hypotheses increases with the number of synapomorphies used in a study (i.e., studies based on few characters can be misleading), and by the number of studies, based on different characters, that come to the same or similar conclusions.

      Age information from fossils or calibrated molecular phylogenies is available for 27 families of North American freshwater fishes (Figure 2.3). One family, the lampreys (Petromyzontidae), likely dates to the Paleozoic, and 5 groups (bowfins, Amiidae; pikes, Esocidae; sturgeons, Acipenseridae; paddlefishes, Polyodontidae; and gars, Lepisosteidae) have been present since the Cretaceous Period of the late Mesozoic. The remaining 21 families all date within the Cenozoic. Although 6 of the 27 families (22%) were represented prior to the Cenozoic, considering the current number of species per family, the ancestors of only 1.8% of the North American fish fauna occurred earlier than the Cenozoic. Within the Tertiary Period of the Cenozoic, 11 families are represented in the Paleogene Period (Paleocene to Oligocene epochs), and the remaining 10 families are represented in the Neogene Period (Miocene to Pliocene epochs).

      Paleogene families include the ictalurids, percopsids, clupeids, salmonids, moronids, hiodontids, catostomids, centrarchids, aphredoderids, umbrids, and cyprinids. Neogene families are represented by the goodeids, poeciliids, percids, cichlids, fundulids, cyprinodontids, cottids, gasterosteids, atherinopsids, and sciaenids. Although the second most speciose family of North American freshwater fishes, the Percidae, is known from fossils only from the Pleistocene, calibrated molecular phylogenies suggest a much earlier occurrence. The separation of darters from nondarter percids dates to 19.8 mya (Carlson et al. 2009) and within the darter genus Nothonotus, the age of the most recent common ancestor dates to 18.5 mya (Near and Keck 2005). Consequently, percids likely occurred in North America at least by the early Miocene (approximately 23 mya). Seventy-eight percent of the 27 major families were present in North America by the early Miocene (23–16 mya) and were thus affected by numerous geologic and climatic events of the late Tertiary.