Arbitrarily primed DNA fingerprinting for phylogenetic reconstruction in vertebrates: the Xiphophorus model

Arbitrarily primed PCR (AP-PCR or RAPD) is a technique for producing species-specific DNA fingerprints. We tested the utility of AP-PCR as a source of phylogenetically informative characters in three separate experiments, using fishes of the genus Xiphophorus. We chose Xiphophorus as a standard of comparison, because evolutionary relationships within the genus have been studied repeatedly using a variety of techniques. We compared our results to a "classical" phylogenetic hypothesis synthesized from studies using morphological, pigmentation, and allozyme characters, and to a recent conflicting hypothesis constructed from DNA sequence data. The sequence-based hypothesis places the southern swordtail Xiphophorus clemenciae squarely within the platyfish, whereas the classical hypothesis separates the two groups. In addition, the two hypotheses differ in their clustering of species of northern swordtails. Our findings are in close accord with the classical hypothesis. Our results allow the strongest phylogenetic hypothesis yet for Xiphophorus and demonstrate the utility of AP-PCR for studying species relationships within vertebrate genera.