The Stochastic Mode of Molecular Evolution: What Consequences for Systematic Investigations?

-Biochemical characters have been proposed as ideal sources of phylogenetic information. The homologous characters are easily identified, the relationships between such characters and the underlying genetic code is well understood, and, most importantly, biochemical characters are thought to evolve in a stochastic, clock-like manner. I present a modified version of the Zuckerkandl and Pauling (1965) model of stochastic evolution which is used to explore the consequences of a stochastic mode of evolution. The probability of observing shared character states is determined as a function of the evolutionary rate of a character, the time of independent ancestry for two sister taxa, the time of shared ancestry for the sister taxa independent of their next closest relative, and the number of functionally equivalent, equally probable character states. I found that, while many branching patterns can be reliably reconstructed using stochastically evolving characters, a large subset of theoretically possible phylogenies (as defined by the duration of shared and independent ancestry) would not be derived correctly. The model simulates a "best-case scenario" in which the rate of character evolution is constant over time. Violation of this assumption complicates phylogeny reconstruction and further limits the types of phylogenies that can be addressed with stochastically evolving characters. I discuss the implications of these findings for data analysis and experimental design. Received 14 October 1987, accepted 14 March 1988. SYSTEMATICS has undergone a period of revitalization as a result of innovations in data analysis (Hennig 1966, Sneath and Sokal 1973, Felsenstein 1982) and availability of new sets of characters obtained with biochemical techniques (e.g. amino acid sequencing [Goodman et al. 1979], mtDNA sequencing [Brown 1983], DNA x DNA hybridization [Sibley and Ahlquist 1983], electrophoresis [Brush 1976, Matson 1984]). Although the use of biochemical characters has not met with complete acceptance, the impact of biochemical approaches on systematics has been profound (for reviews see Thorpe 1982, Buth 1984). Gould (1985) stated, for example, that DNA x DNA hybridization solves the problem of how and why organisms are related. One reason that biochemical characters evoke such enthusiasm is that they are thought to evolve in an essentially time-dependent manner, as a result of stochastic processes (Wilson et al. 1977, Kimura 1983, Gillespie 1986). To understand why stochastically evolving characters are considered such promising sources of phylogenetic information, it is instructive to examine why traditional morphological characters have often proved unreliable for phylogeny reconstruction. Under natural selection, morphological characters may evolve at different rates in different lineages (e.g. bill morphology in the Galapagos finches compared with other assemblages of similar age). Furthermore, the direction of morphological change may not be strictly divergent because direct selection may result in reversal, convergence, and parallelism, all of which confound phylogenetic inference. Recognition of these limitations has lead to development of techniques to minimize the problem (Hennig 1966). The derivation of transformation series is a difficult task (Stuessy and Crisci 1984), and it is likely that the phylogenies produced from analysis of traditional characters will contain some misinformation. In contrast, if the evolution of biochemical characters can be characterized as time-dependent divergence as a result of stochastic processes, systematic studies that employ such characters would not be plagued by convergence and parallelism. The expected magnitude of change in sister lineages would be the same, and would depend solely on time of independent evolution and on rate of change for the characters involved. Sister taxa would theoretically have more character states in common 565 The Auk 105: 565-573. July 1988 This content downloaded from 157.55.39.215 on Wed, 31 Aug 2016 05:01:00 UTC All use subject to http://about.jstor.org/terms 566 ScoTT M. LANYON [Auk, Vol. 105 ------------------------