Phylogeny and classification of the Digenea (Platyhelminthes ...

P.D. Olson et al. / International Journal for Parasitology 33 (2003) 733–755 741Fig. 2. Comparison of maximum parsimony and Bayesian inference on the combined data (ssrDNA þ lsrDNA) for the Trematoda. Nodal support based onbootstrapping (maximum parsimony) and posterior probabilities (Bayesian inference). Families shown together as terminal taxa contain one or moreparaphyletic groups.or when using a strict consensus topology of the equallyparsimonious trees resulting from prior MP analyses. Thusall Bayesian inference analyses used the following parameters:nst ¼ 6, rates ¼ invgamma, ncat ¼ 4, shape ¼estimate, inferrates ¼ yes and basefreq ¼ empirical, thatcorresponds to the model estimated (general-time-reversibleincluding estimates of invariant sites and gamma distributedamong-site rate variation). Posterior probabilities wereapproximated over 300,000 generations (ngen ¼ 300,000)via four simultaneous Markov Chain Monte Carlo (MCMC)chains (nchains ¼ 4) with every 100th tree saved(samplefreq ¼ 100). Default values were used for theMCMC parameters. Consensus trees with mean branchlengths were constructed using the ‘sumt’ command withthe ‘contype ¼ allcompat’ option and ignoring the initialtopologies saved during ‘burn in’; the initial n-generationsbefore log-likelihood values and substitution parametersplateau (see Huelsenbeck and Ronquist, 2001). Maximumparsimony nodal support was estimated by bootstrapanalysis (fast-heuristic, 10,000 replicates), and as posteriorprobabilities in the Bayesian inference analyses (Huelsenbecket al., 2001).3. Results3.1. Presentation of resultsFigs. 1–5 depict the results of the individual analyses andFig. 6 depicts a revised classification based on the results ofBayesian inference of lsrDNA and ssrDNA combined (Fig.3). Figs. 1, 2, 4 and 6 show reduced trees that depictinterrelationships of the trematode families as currentlydefined (Table 1). In cases of paraphyly, the families are