Searching for convergence in phylogenetic Markov chain Monte Carlo

Markov chain Monte Carlo (MCMC) is a methodology that is gaining widespread use in the phylogenetics community and is central to phylogenetic software packages such as MrBayes. An important issue for users of MCMC methods is how to select appropriate values for adjustable parameters such as the length of the Markov chain or chains, the sampling density, the proposal mechanism, and, if Metropolis-coupled MCMC is being used, the number of heated chains and their temperatures. Although some parameter settings have been examined in detail in the literature, others are frequently chosen with more regard to computational time or personal experience with other data sets. Such choices may lead to inadequate sampling of tree space or an inefficient use of computational resources. We performed a detailed study of convergence and mixing for 70 randomly selected, putatively orthologous protein sets with different sizes and taxonomic compositions. Replicated runs from multiple random starting points permit a more rigorous assessment of convergence, and we developed two novel statistics, delta and epsilon, for this purpose. Although likelihood values invariably stabilized quickly, adequate sampling of the posterior distribution of tree topologies took considerably longer. Our results suggest that multimodality is common for data sets with 30 or more taxa and that this results in slow convergence and mixing. However, we also found that the pragmatic approach of combining data from several short, replicated runs into a metachain to estimate bipartition posterior probabilities provided good approximations, and that such estimates were no worse in approximating a reference posterior distribution than those obtained using a single long run of the same length as the metachain. Precision appears to be best when heated Markov chains have low temperatures, whereas chains with high temperatures appear to sample trees with high posterior probabilities only rarely. [Bayesian phylogenetic inference; heating parameter; Markov chain Monte Carlo; replicated chains.]

A generalized Markov sampler

A recent development of the Markov chain Monte Carlo (MCMC) technique is the emergence of MCMC samplers that allow transitions between different models. Such samplers make possible a range of computational tasks involving models, including model selection, model evaluation, model averaging and hypothesis testing. An example of this type of sampler is the reversible jump MCMC sampler, which is a generalization of the Metropolis-Hastings algorithm. Here, we present a new MCMC sampler of this type. The new sampler is a generalization of the Gibbs sampler, but somewhat surprisingly, it also turns out to encompass as particular cases all of the well-known MCMC samplers, including those of Metropolis, Barker, and Hastings. Moreover, the new sampler generalizes the reversible jump MCMC. It therefore appears to be a very general framework for MCMC sampling. This paper describes the new sampler and illustrates its use in three applications in Computational Biology, specifically determination of consensus sequences, phylogenetic inference and delineation of isochores via multiple change-point analysis.

Phylogenetic position and ultrastructure of two Dermocystidium species (Ichthyosporea) from the common perch (Perca fluviatilis)

Sequences of small-subunit rRNA genes were determined for Dermocystidium percae and a new Dermocystidium species established as D. fennicum sp. n. from perch in Finland. On the basis of alignment and phylogenetic analysis both species were placed in the Dermocystidium-Rhinosporidium clade within Ichthyosporea, D. fennicum as a specific sister taxon to D. salmonis, and D. percae in a clade different from D. fennicum. The ultrastructures of both species well agree with the characteristics approved within Ichthyosporea: walled spores produce uniflagellate zoospores lacking a collar or cortical alveoli. The two Dermocystidium species resemble Rhinosporidium seeberi (as described by light microscope), a member of the nearest relative genus, but differ in that in R. seeberi plasmodia have thousands of nuclei discernible, endospores are discharged through a pore in the wall of the sporangium, and zoospores have not been revealed. The plasmodial stages of both Dermocystidium species have a most unusual behaviour of nuclei, although we do not actually know how the nuclei transform during the development. Early stages have an ordinary nucleus with double, fenestrated envelope. In middle-aged plasmodia ordinary nuclei seem to be totally absent or are only seldom discernible until prior to sporogony, when rather numerous nuclei again reappear. Meanwhile single-membrane vacuoles with coarsely granular content, or complicated membranous systems were discernible. Ordinary nuclei may be re-formed within these vacuoles or systems. In D. percae small canaliculi and in D. fennicum minute vesicles may aid the nucleus-cytoplasm interchange of matter before formation of double-membrane-enveloped nuclei. Dermocystidium represents a unique case when a stage of the life cycle of an eukaryote lacks a typical nucleus.

Multiple origins of parasitism in lice: phylogenetic analysis of SSU rDNA indicates that the Phthiraptera and Psocoptera are not monophyletic

The Paraneoptera (Hemipteroid Assemblage) comprises the orders Thysanoptera (thrips), Hemiptera (bugs), Phthiraptera (lice) and Psocoptera (booklice and barklice). The phylogenetic relationships among the Psocodea (Phthiraptera and Psocoptera), Thysanoptera and Hemiptera are unresolved, as are some relationships within the Psocodea. Here, we present phylogenetic hypotheses inferred from SSU rDNA sequences; the most controversial of which is the apparent paraphyly of the Phthiraptera, which are parasites of birds and mammals, with respect to one family of Psocoptera, the Liposcelididae. The order Psocoptera and the suborder that contains the Liposcelididae, the Troctomorpha, are also paraphyletic. The two remaining psocopteran suborders, the Psocomorpha and the Trogiomorpha, are apparently monophyletic. The Liposcelididae is most closely related to lice from the suborder Amblycera. These results suggest that the taxonomy of the Psocodea needs revision. In addition, there are implications for the evolution of parasitism in insects; parasitism may have evolved twice in lice or have evolved once and been subsequently lost in the Liposcelididae.