Molecular Phylogenetics of Perciform Fishes Using the Nuclear Recombination Activating Gene 1
The order Perciformes contains one-third of all extant fishes in twenty different suborders and over 10,000 species. Few systematic investigations have been performed on this large group of fishes at the suborder level and their evolutionary history is widely recognized as problematic. This dissertation presents three studies: a molecular phylogenetic analysis of the putative suborders of the order Perciformes, an analysis of interrelationships of the families of the perciform suborder Percoidei, and a multi-gene investigation of the percoid superfamily Sparoidea. The taxa sampled in this dissertation represent one of the most inclusive molecular datasets, to date, testing the monophyly of the Perciformes and relationships of its suborders, including the Percoidei. Analyses are performed using a 1425-1431 base fragment of exon three of the single copy, nuclear recombination activating gene 1 (RAG1). Results of these tests reject the monophyly of the Perciformes and of its largest suborder, the Percoidei. However, this study does support some previous relationships at the suborder and family level for these groups and also presents novel interpretations of many groups. A lack of nodal support is seen for mid-level clades in these analyses. Genetic bias, such as high GC content and low effective number of codons, in some taxa, is hypothesized to be one of the causes for some of the unexpected relationships found in this work. A multi-gene approach was taken to test the monophyly of the superfamily Sparoidea and its families. Analyses of RAG1, cytochrome b (cytB), and combined RAG1 + cytB datasets reject a monophyletic Sparoidea but find the Nemipteridae, Sparidae plus Centracanthidae, and Lethrinidae to be individually monophyletic. The one exception to this is in the cytB maximum likelihood phylogeny, which fails to resolve a monophyletic Lethrinidae. The phylogenetic hypotheses discussed in this dissertation are an important step toward an understanding of perciform, percoid, and sparoid relationships and deserve further testing. The high level of taxon sampling presented here should be replicated and expanded using other molecular markers to help resolve the bush at the top of the teleostean tree.
Fishes, Molecular phylogenetics;, Nuclear recombination activating gene 1, Perciform, Aquaculture and Fisheries, Ecology and Evolutionary Biology, Molecular Biology
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