Heterogeneity in sequence evolution: Simple models for a complex world?

Modern phylogenetics depends on models that describe how nucleotides and amino acids substitute each other during evolution. These models typically make many simplifying assumptions about the evolutionary process, including that evolution looks the same at each site in a sequence and on all the branches of a phylogenetic tree. Many studies have shown that in reality evolution is heterogeneous and that failure to account for this variability can introduce systematic errors into many forms of phylogenetic analysis, which can lead to misleading inferences about the phylogenetic tree and the evolutionary process. Current models struggle to account for this heterogeneity, with the complexity of the model often growing to an unacceptable degree as the amount of data grows. I describe some of the different types of heterogeneity that can occur in sequence evolution and introduce a model for investigating their prevalence in nucleotide sequence evolution. I conclude by discussing some of the potential causes of heterogeneity and what we can hope to do about it.