A phylogenetic model for the detection of epistatic interactions.

Paired epistatic interactions, such as those in the stem regions of RNA, play an important role in many biological processes. However, unlike protein-coding regions, paired epistatic interactions have lacked the appropriate statistical tools for the detection of departures from selective neutrality. Here, a model is presented for the analysis of paired epistatic regions that draws upon the population genetics of the compensatory substitution process to detect the relative strength of natural selection acting against deleterious combinations of alleles. The method is based upon the relative rates of double and single substitution, and can differentiate between nonindependent interactions and negatively epistatic ones. The model is implemented in a fully Bayesian framework for parameter estimation and is demonstrated using a 5S rRNA data set. In addition to the detection of selection, modeling the double and single substitution processes in this manner inherently accounts for a substantial proportion of rate variation among stem positions.

The dynamics of alternative pathways to compensatory substitution.

The role of epistatic interactions among loci is a central question in evolutionary biology and is increasingly relevant in the genomic age. While the population genetics of compensatory substitution have received considerable attention, most studies have focused on the case when natural selection is very strong against deleterious intermediates. In the biologically-plausible scenario of weak to moderate selection there exist two alternate pathways for compensatory substitution. In one pathway, a deleterious mutation becomes fixed prior to occurrence of the compensatory mutation. In the other, the two loci are simultaneously polymorphic. The rates of compensatory substitution along these two pathways and their relative probabilities are functions of the population size, selection strength, mutation rate, and recombination rate. In this paper these rates and path probabilities are derived analytically and verified using population genetic simulations. The expected time durations of these two paths are similar when selection is moderate, but not when selection is weak. The effect of recombination on the dynamics of the substitution process are explored using simulation. Using the derived rates, a phylogenetic substitution model of the compensatory evolution process is presented that could be used for inference of population genetic parameters from interspecific data.

Quantifying the impact of dependent evolution among sites in phylogenetic inference.

Nearly all commonly used methods of phylogenetic inference assume that characters in an alignment evolve independently of one another. This assumption is attractive for simplicity and computational tractability but is not biologically reasonable for RNAs and proteins that have secondary and tertiary structures. Here, we simulate RNA and protein-coding DNA sequence data under a general model of dependence in order to assess the robustness of traditional methods of phylogenetic inference to violation of the assumption of independence among sites. We find that the accuracy of independence-assuming methods is reduced by the dependence among sites; for proteins this reduction is relatively mild, but for RNA this reduction may be substantial. We introduce the concept of effective sequence length and its utility for considering information content in phylogenetics.

Stathmin prevents the transition from a normal to an endomitotic cell cycle during megakaryocytic differentiation.

Physiological polyploidy is a characteristic of several cell types including the megakaryocytes (MK) that give rise to circulating blood platelets. MK achieve polyploidy by switching from a normal to an endomitotic cell cycle characterized by the absence of late mitotic stages. During an endomitotic cycle, the cells enter into mitosis and proceed normally through metaphase and early anaphase. However, late anaphase, telophase and cytokinesis are aborted. This abortive mitosis is associated with atypical multipolar mitotic spindles and limited chromosome segregation. Stathmin is a microtubule-depolymerizing protein that is important for the regulation of the mitotic spindle and interfering with its expression disrupts the normal mitotic spindle and leads to aberrant mitotic exit. As cells enter mitosis, the microtubule depolymerizing-activity of stathmin is switched-off, allowing microtubules to polymerize and assemble into a mitotic spindle. Reactivation of stathmin in the later stages of mitosis is necessary for the disassembly of the mitotic spindle and the exit from mitosis. Previous studies had shown that stathmin expression is downregulated as MK become polyploid and inhibition of its expression in K562 cells increases their propensity to become polyploid. In this report, we describe our studies of the mechanism by which stathmin plays its role in MK polyploidization. We show that stathmin overexpression prevents the transition from a mitotic cycle to an endomitotic cycle as determined by a decrease in the number of multipolar mitotic spindles. These observations support a model in which downregulation of stathmin expression in megakaryocytes and other polyploid cells may be a critically important factor in endomitosis and polyploidy.