Ribosomal DNA: Intraspecific Polymorphism, Concerted Evolution, and Phylogeny Reconstruction

Williams et al. (1988) commented on the use of ribosomal DNA (rDNA) in systematic studies. Although we share their desire for greater rigor in systematic studies of rDNA, many of their points are inaccurate or misleading. Specifically, Williams et al. inaccurately report and interpret data presented by us (Hillis and Davis, 1986), and misrepresent both the effects of concerted evolution on phylogenetic analyses and the use of heterologous molecular probes. Williams et al. (1988) note that the nontranscribed spacer (NTS) of rDNA evolves in concert within a species. They fail to note that the entire rDNA repeat evolves in such a fashion (Coen et al., 1982a, b; Dover, 1982; Arnheim, 1983). Among concerted gene families, such as rDNA, new variants are rapidly homogenized and fixed within reproductive groups. Clearly, during the process of homogenization, intraspecific polymorphisms must occur. Williams et al. state that it is ". . . improbable that closely related species can become differentially fixed for NTS restriction site patterns without exhibiting both within and between individual polymorphism during at least some stage of the divergence process." Although these periods of polymorphism clearly exist, they appear to be short-lived compared to speciation rates. As a result, polymorphisms of concerted sequences are found mostly within, rather than shared among, species. When polymorphisms exist within populations, these polymorphisms are also found within the repeated arrays of individuals. More germane to the problem of phylogeny reconstruction is that shared interspecific polymorphisms will be common only if the speciation rate exceeds the homogenization rate. The observed homogenization rate in studied species is very rapid (Coen et al., 1982a, b); the low intraindividual and intraspecific polymorphism observed in the rDNA arrays of most other species suggests that rapid rates of homogenization are widespread, if not universal. Therefore, abundant shared interspecific polymorphisms are expected only in cases of explosive radiation. Except under unusual circumstances, only intraspecific polymorphisms of concerted gene families are to be expected; restriction sites shared among species are usually fixed, unless the variation arises as the result of a convergent event or hybridization. Even if species were sampled during polymorphic phases, undetected autapomorphic polymorphisms would not affect phylogenetic reconstruction (Wiley, 1981). Williams et al. (1988) cite a number of studies of rDNA that record intraspecific variation, but none that record shared interspecific polymorphisms. They note that some variable rDNA restriction sites are shared among subspecies of Mus (Suzuki et al., 1986), which is expected in cases of rapid evolution and/or hybridization. The lack of reported interspecific rDNA polymorphisms supports our contention that interspecific polymorphisms must be comparatively rare with respect to interspecific fixed synapomorphies (as well as autapomorphies) in rDNA. Although single individuals theoretically are sufficient to examine phylogeny using concerted sequences, we sampled more extensively in geographically widespread taxa to verify that rDNA evolves in a concerted fashion in frogs (Hillis and Davis, 1986). As we reported, we examined specimens from geographically separated parts of the ranges of three species, without find-