As in all aspects of historical inquiry, the study of character evolution is exceptionally sensitive to the amount of information that has actually survived up to the present. The reality of neural evolution was in most cases almost certainly very complex, and may be reliably regarded to have included vastly more numbers of independent transformations than has been recorded in the distribution of phenotypes preserved among living species. The signature of many historical events has been overwritten by reversals and convergences, or eliminated altogether by extinctions. Paleontologists estimate that more than 99% of all species that have ever lived are now extinct (Rosenzweig, 1995). This figure, of course, includes higher taxa (e.g., trilobites, placo-derms, plesiosaurs) that are now entirely extinct, bringing up the aggregate percentage of extinction for all taxa. The proportion of living species that persists within certain targeted taxa may be much higher (e.g., Lake Victoria cichlid fishes). Nevertheless, in comparative studies of neural, physiological, or behavioral phenotypes, it is rare to have information on all extant species. Whether it is from extinction or incomplete surveys, taxon sampling remains one of the greatest sources of error in phylogenetic estimates of character evolution (Sullivan et al., 1999; Zwickl and Hillis, 2002).

Despite all these reservations, we must continue to estimate ancestral traits in order to study pheno-typic evolution. None of the methods reviewed in this article should be regarded as a magic bullet, but rather there are advantages and disadvantages of each method as they are applied under different circumstances. All the methods reviewed here have proved to be useful tools in the phylogenetic toolbox. As in other aspects of science, it is important to make our assumptions explicit, and to use reasonable assumptions. Further, as in other aspects of evolutionary biology, critical insights into the evolution of neural characters will come from a better understanding of the biology of the phenotypes themselves, and the organisms in which they have evolved.

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