PCR assays of variable nucleotide sites for identification of conservation units

A number of authors have recently suggested that the best approach for identifying units of conservation is to follow a systematics model of character analysis (Amato, 1991; Cracraft, 1991; Vogler and DeSalle, 1994). This approach necessitates the use of an operational, typological, evolutionary species concept. The use of the phylogenetic species concept has the utility and philosophical logic appropriate for this task. Additionally, there is a large body of literature that uses this framework, along with a parsimony based character analysis to identify patterns of phylogeny (Cracraft, 1983; Nelson and Platnick, 1981; Nixon and Wheeler, 1990). While we advocate this approach, we recognize that one of its limiting factors is sample size. We propose that by selective direct sequencing plus rapid sampling of variable target characters by polymerase chain reaction (PCR) assays of specific sites, sufficiently large numbers of individuals can be accurately, inexpensively, and quickly surveyed for diagnostic characters. This procedure is demonstrated by a survey of variable nucleotide sites in the Caiman crocodilus complex.