Counterexample to a claim about the reconstruction of ancestral character states.

Since Pauling and Zuckerkandl first suggested it more than 40 years ago, the idea of reconstructing ancestral proteins and DNA sequences from the information contained in sequences of present day species has held considerable fascination (Pauling & Zuckerkandl, 1963). Such reconstructions can provide a unifying framework for understanding the molecular origins and evolution of key components in living organisms. However, only recently has it become relatively straightforward to perform such reconstructions and then test the reconstructed molecules functionally in the lab. Now there is a surge of activity in this area. Ancestral protein sequences for rhodopsin (Chang, et al., 2002), ultra-violet vision gene SWS1 (Shi & Yokoyama, 2003), ribonucleases (Jermann, et al., 1995; Zhang & Rosenberg, 2002), Tu elongation factors (Gaucher, et al., 2003), and steroid receptors (Thornton, et al., 2003) have been reconstructed and tested (see the reviews (Chang & Donoghue, 2000) and (Thornton, 2004)). In addition, DNA from the common ancestor of placental mammals has been reconstructed for a megabase-sized region containing the cystic fibrosis gene (Blanchette, et al., 2004), for several families of transposons (Adey, et al., 1994; Ivics, et al., 1997; Smit & Riggs, 1996; Jurka, 2002), and for some complete small genomes like HIV (Hillis, et al., 1994). In the latter case the predicted ancestral sequences were compared to the known ones, so the accuracy of the resonstruction could be measured directly. However, in other cases theoretical results (Yang, et al., 1995; Schultz, et al., 1996; Schultz & Churchill, 1999) and computer simulations (Zhang & Nei, 1997; Blanchette, et al., 2004; Cai, et al., 2004) are required to assess the accuracy of the reconstructed sequence. In these investigations it has been observed that the topology of the phylo-