More Taxa Are Not Necessarily Better for the Reconstruction of Ancestral Character States

Abstract

Ancestral state reconstruction is an important approach to understanding the origins and evolution of key features of different living organisms (Liberles, 2007). For example, ancestral proteins and genomic sequences have been reconstructed for investigating the origins of genes and proteins (Hillis et al., 1994; Jermann et al., 1995; Zhang and Rosenberg, 2002; Gaucher et al., 2003; Thornton et al., 2003; Blanchette et al., 2004; Cai et al., 2004; Felsenstein, 2004; Taubenberger et al., 2005). A variety of reconstruction methods, including parsimony and maximum likelihood, exist for biomolecular sequencing (Yang et al., 1995; Koshi and Goldstein, 1996; Elias and Tuller, 2007), multistate discrete data (Schultz et al., 1996; Mooers and Schluter, 1999; Pagel, 1999), and continuous data (Martins, 1999). These different reconstruction methods have been assessed by both theoretical analyses (Maddison, 1995; Yang et al., 1995) and computer simulation (Schultz et al., 1996; Zhang and Nei, 1997; Salisbury and Kim, 2001; Blanchette et al., 2004; Mooers, 2004; Williams et al., 2006). One important observation in these investigations is that the topology of the phylogenetic tree relating the extant taxa to the target ancestor has a significant influence on reconstruction accuracy. For instance, a star-like phylogeny allows the ancestral character states to be inferred more accurately than other topologies given the same number of terminal taxa under the two-state symmetric model (Schultz et al., 1996; Evans et al., 2000). For more complex models (e.g., on four-states such as DNA), the influence of topology on reconstruction accuracy is more complicated (Lucena and Haussler, 2005).

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