Abstract.---Accuracy of phylogenetic methods may be assessed in terms of consistency, efficiency, and robustness. Four principal methods have been used for assessing phylogenetic accuracy: simulation, known phylogenies, statistical analyses, and congruence studies. Simulation studies are useful for studying accuracy of methods under idealized conditions, and can be used to make general predictions about the behavior of methods if the limitations of the models are taken into account. Studies of known phylogenies can be used to test predictions from simulation studies, which provides a check on the robustness of the models (and may suggest refinements for future simulations). Statistical analyses allow general predictions to be applied to specific results, facilitate assessments as to whether or not sufficient data have been collected to formulate a robust conclusion, and ask whether a given data set is any more structured than random noise. Finally, congruence studies of multiple data sets assess the degree to which independent results agree, and thus the minimum proportion of the findings that can be attributed to an underlying phylogeny. These different methods of assessing phylogenetic accuracy are largely complementary, and the results are consistent in identifying a large class of problems that are amenable to phylogenetic reconstruction. [Phylogeny; accuracy; simulations; experimental evolution; statistics; congruence; consistency; efficiency; robustness]
"The major problem in studying the relative efficiencies [of phylogenetic methods] is that the true tree is usually unknown for any set of real organisms or any set of real DNA sequences, so that it is difficult to judge which tree is the correct one. However, this problem can be avoided if we use computer simulation" (Nei, 1991:90).
"The evolutionary models used in many simulation studies are exceedingly simple, and even though they will surely become more sophisticated (e.g., more ´realistic═) in the future, such studies will still face a credibility gap" (Miyamoto and Cracraft, 1991:11).
"[T]here are some fundamental philosophical and empirical differences between simulations of fictitious taxa and their DNA sequences, on the one hand; and real-world taxa and their sequence characteristics, on the other" (Miyamoto and Cracraft, 1991:11).
"Although I am skeptical that the results of [experimental phylogenies] ´directly support the legitimacy of methods for phylogenetic estimation,═ it remains to be seen what experimental phylogenetics can teach us about the problem of phylogenetic inference" (Sober, 1993:89).
"As DNA sequences accumulate, there will be an increasing demand for statistical methods to estimate evolutionary trees from them, and to test hypotheses about the evolutionary process" (Felsenstein, 1981:368).
"It is remarkable that, in a century which has seen such a large growth in the application of statistics to the natural sciences, the fundamental issues of statistical inference have not been resolved. There are not many more statisticians than opinions as to how to assess rival hypotheses in the light of data" (Edwards, 1969:1233).
"[E]xtensive congruence among branching patterns derived from independent data sets and by different methods of analysis is unlikely to occur for any reason other than phylogeny" (Sheldon and Bledsoe, 1993:256-257).
"[T]here may indeed be substantial congruence between the two data sets, but that ´congruence═ is not quite what we had hoped it would be" (Swofford, 1991:326).
"On that happy day when molecular systematists achieve the goal of adequate sampling in terms of both taxa and sequence length..., and when the computer and the program capable of analysing the alignment of life exist, there are two possible extremes: 'one tree,' or '10999 equally parsimonious trees'" (Patterson et al., 1993:180).
"'I checked it quite thoroughly,' said the computer, "and that quite definitely is the answer. I think the problem, to be quite honest with you, is that you═ve never actually known what the question is'" (Adams, 1979:181).
Jim Bull, Mike Charleston, Paul Chippindale, Keith Crandall, Tim Crowe, Cliff Cunningham, A. W. F. Edwards, Jotun Hein, John Huelsenbeck, Mike Miyamoto, Barbara Mable and an anonymous reviewer read this manuscript and offered useful suggestions. I thank Mike Miyamoto for inviting me to prepare an introduction to this series of papers on phylogenetic accuracy. My studies on phylogenetic accuracy have been supported by grants from the National Science Foundation.
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Received 11 August 1994; accepted 5 October 1994.