CONCLUSIONS

StrataPhy is still in development, and we are still adding functionality. Improvements for future releases will focus on three major themes. First, performance increases will come in the form of published "shortcuts" (e.g., Goloboff 1996, 1998, 1999; Ronquist 1998) that are not currently implemented in StrataPhy. This will also include the exploration of alternative tree search strategies besides TBR. The second main focus of future development will be the incorporation of probabilistic optimality criteria (Bayesian and likelihood; Huelsenbeck and Crandall 1997; Wagner 1998; Huelsenbeck and Rannala 2000; Wagner 2000). Finally, StrataPhy, which is currently written in C++, is being converted to a Java-based program to make it truly cross-platform and allow the development of a simple graphical user interface (GUI) with tree visualization that will be independent of MacClade.

Stratocladistics has not been explored as fully as warranted due to want of an automated application. Thus some of the issues raised by critics that are not purely philosophical objections (e.g., Smith 2000; Sumrall and Brochu 2003; but see replies by Fisher et al. 2002; Fisher and Bodenbender 2003), and some aspects of the behavior of the method have not yet been explored in sufficient detail. We hope that StrataPhy will allow these issues to be addressed more fully and foster continued exploration of the use of stratigraphic data in phylogenetic inference.

Because not all clades have fossil records that are well suited to stratocladistic analysis, StrataPhy should be viewed as an additional tool for phylogenetic analysis to complement currently available methods, and not a replacement. Taken together, these methods will continue to help us understand the evolutionary histories of lineages and to determine the patterns that result from the diverse processes that have controlled the evolution of life as recorded in the fossil record and the extant biota.