Some Limitations of Ancestral Character-State Reconstruction When Testing Evolutionary Hypotheses

Abstract

The recent explosion of phylogenetic information has had an impact far beyond the Želd of systematic biology. Workers in a variety of disciplines are now interested in generating and using phylogenies for their groups (or genes) of interest (e.g., Brooks and McLennan, 1991; Harvey et al., 1995; Martins, 1996). In large part, this new interest has been driven by the promise of using phylogenies to reconstruct ancestral character states, usually by parsimony. The simplicity of testing evolutionary hypotheses by mapping characters ontoaphylogenyhas an appeal that has not been lost on the biological community. Despite its appeal, ancestral state reconstruction is an ambitious exercise. Although we are very familiar with the difŽculty of accurately inferring phylogenies with thousands of characters (reviewed by Swofford et al., 1996), the challenges associated with reconstructing ancestral character states of individual characters are correspondingly more difŽcult (Swofford and Maddison, 1987, 1992; Maddison and Maddison, 1992; Collins et al., 1994a; Frumhoff and Reeve, 1994; Pagel, 1994; Maddison, 1995; Schluter, 1995; Schultz et al., 1996; Omland, 1997; Schluter et al., 1997; Cunningham et al., 1998). Whereas we generally assume that data used for phylogenetic reconstruction are selectively neutral, many—if not most—of the characters we reconstruct to test evolutionary hypotheses are thought to be under selection (Brooks and McLennan, 1991; Harvey and Pagel, 1991). In fact, their presumed selective importance is often why we are interested in them in the Žrst place. Therefore, the problems of convergence and parallel evolution that plague phylogenetic inference should be that much more serious when we test evolutionary hypotheses with ancestral state reconstructions. In this paper, I discuss the limitations of using reconstructed ancestral character states to test evolutionary hypotheses. In particular, I argue that hypotheses of irreversible evolution (e.g., Dollo’s law; Dollo, 1893) are particularly difŽcult to test by using ancestral character state reconstruction. I illustrate this point with two case studies of life history evolution in echinoderms.