Systematic relationships of Elopiformes and Albuliformes using multiplemtDNA gene sequences

Tarpon (Megalops), ladyfish (Flops ), and bonefish (Albula) are ecologically and economically important, but their systematics and population structures are poorly characterized and/or controversial. The current taxonomy is based mainly on morphology, but some species in these clades are difficult to distinguish based on ecological and morphological characters (cryptic species). The population structure of tarpon is also important to fisheries managers since the species supports a multi-billion dollar recreational fishery North and Central America and the Caribbean Islands. Molecular phylogenetics and population genetics techniques can be used to examine taxonomy and population structure of fishes, but care must be taken to select and apply the most informative analytical techniques.; In the studies reported here, mitochondrial DNA (mtDNA) sequences were used to examine the relationships among and between tarpon, ladyfish, and bonefish. Sequence data from I5 mitochondrial genes were combined to create a data set that was about 4.6 kb long and had 577 phylogenetically informative characters for 86 specimens. Thirteen consensus sequences were examined for relationships among species, and additional sequences were used to test for potential variations in the genetics of M. atlanticus collected from 12 geographic regions. The phylogenetic analyses were performed using weighted parsimony and likelihood methods to determine which genes and methods were best suited to exploring relationships among the genera. These analyses showed that methods that either accounted for differences in evolutionary rate and base pair composition between genes (e.g., maximum likelihood General Time Reversible method) or statistical resampling techniques (e.g., heuristic search algorithms with bootstrapping) using weighted parsimony while excluding characters with low signal to noise ratios (e.g., tRNA), produced phylogenies that were the most statistically robust and consistent with known biology. These methods produced phylogenies that were more completely resolved and had better statistical support when compared to methods that were less complex, and demonstrate the importance of carefully testing the assumptions of various phylogenetic methods against the actual data that are being analyzed. (Abstract shortened by UMI.)...