Ancestral numbers of digits for the forelimb (manus) and hind limb (pes) were inferred independently using BayesTraits v. 1.0 (available at www.evolution.rdg.ac.uk; see Pagel et al. 2004), assuming five different models of character evolution (table 1). All analyses involved running a single Markov chain for 10 million generations, sampling every 1000 generations. Uniform priors (with default upper and lower bounds of 0 and 100) were assumed for all estimated model parameters. The s.d. of successive alterations to proposed model parameter values (specified by the ratedev command) was adjusted so as to produce acceptance rates of 20–30%. Phylogenies were drawn from the sample of 5000 trees generated in the BEAST analysis described above; where a phylogeny did not include an internal node represented in the maximum clade credibility tree, posterior probabilities for alternative character states were calculated for the most recent shared ancestor of the taxa defined by that node (see Pagel et al. 2004). Posterior probability distributions for alternative states were estimated for all internal nodes in the maximum clade credibility tree from posterior probabilities sampled after one million generations (the first 10% of the Markov chain was discarded as burn-in in all analyses).

The consistency of reconstructed numbers of manual and pedal digits for each combination of the five models examined is presented in figure 1. Ancestral states inferred assuming the two models that provide the best fit to the data (model E for the manus and model B for the pes) are the least consistent, implying ancestral digit configurations represented among known species of Lerista for only 62 of 76 internal nodes; inconsistent ancestral states are generally associated with basal nodes and entail digit configurations of either four or five digits for the manus and two or three digits for the pes (figure 2). The most consistent ancestral state estimates are obtained where the best-fitting model for the manus (model E) is assumed for both the manus and pes. Ancestral state reconstructions for this combination of models invariably imply ancestral digit configurations observed among known species of Lerista.

The substantial proportion of implausible digit configurations implied by ancestral state reconstructions for the two best-fitting models (model E for the manus and model B for the pes) indicate that one or both reconstructions are inaccurate. Several considerations suggest that the inconsistent ancestral states are attributable to the reconstructions for the pes. As indicated in figure 1 and above, when the reconstructions for the manus (i.e. for the best-fitting model) are considered in combination with ancestral states for the pes inferred assuming a suboptimal model (model E), they imply digit configurations represented among known species of Lerista for all internal nodes. The reconstructions for the pes (i.e. for the best-fitting model), conversely, are inconsistent with one or more ancestral states for the manus in all instances (figure 1). As well as yielding ancestral states that consistently entail implausible digit configurations for internal nodes, the model that best fits the data for the pes may be regarded as inappropriate for inferring patterns of limb reduction or potential re-elaboration, as it assumes identical rates for all transitions; Brandley et al. (2008) recently presented evidence for significantly different rates of digit acquisition and loss across squamates, so that models assuming a single transition rate may inadequately represent the process of limb evolution. Significantly, the model producing ancestral state estimates consistent with those for the manus (model E) has a marginal likelihood differing negligibly from that for similar models (model C; table 1), and conforms well with current understanding of squamate limb evolution (which indicates a low frequency of digit acquisition).

An objective means of assessing the plausibility of implied ancestral phenotypes is essential if the criterion of consistency among ancestral states for multiple characters is to be useful. Ancestral phenotypes were evaluated here according to whether they occur among observed states for the terminal nodes of the phylogeny (i.e. known species). This convenient criterion for assessing combinations of inferred ancestral states is only appropriate, however, if the distribution of phenotypes exhibited by known species adequately represents the range of attainable phenotypes; where this is not the case, the absence of particular phenotypes may be attributable to either anagenesis or extinction. All inconsistent ancestral states for the two models that best fit the data entail ancestors possessing well-developed forelimbs and moderately reduced hind limbs (see figure 2 and above). Although similar phenotypes are observed in the closely related clade Anomalopus (see Wiens 2009), known species of Lerista never exhibit fewer digits for the pes than the manus (indeed, the combination of well-developed forelimbs and substantially reduced hind limbs is exceedingly rare in squamates generally). The phylogenetic distribution of particular (observed) digit configurations indicates that nearly all configurations have evolved independently multiple times (figure 2). Moreover, observed digit configurations represent a continuous, relatively limited region of the possible morphospace (the shaded cells in the inset of figure 2). Accordingly, it may be assumed that the potential morphospace available to the immediate ancestor of Lerista is completely occupied (or nearly so). Insofar as this assumption is valid, our analyses indicate that the two-rate model with unordered character state transitions and a specified rate of digit acquisition of zero (model E) yields accurate ancestral character state reconstructions for both the manus and pes.