title: Identifying Optimal Models of Evolution.
abstract: Most phylogenetic methods are model-based and depend on models of evolution designed to approximate the evolutionary processes. Several methods have been developed to identify suitable models of evolution for phylogenetic analysis of alignments of nucleotide or amino acid sequences and some of these methods are now firmly embedded in the phylogenetic protocol. However, in a disturbingly large number of cases, it appears that these models were used without acknowledgement of their inherent shortcomings. In this chapter, we discuss the problem of model selection and show how some of the inherent shortcomings may be identified and overcome.
authors.affiliation: CSIRO Land & Water, Canberra, ACT, Australia. lars.jermiin@csiro.au.
authors.forename: Lars S
authors.initials: LS
authors.lastname: Jermiin
authors.affiliation: School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.
authors.forename: Vivek
authors.initials: V
authors.lastname: Jayaswal
authors.affiliation: Department of Mathematics & Statistics, Al-Hussein Bin Talal University, Ma'an, Jordan.
authors.forename: Faisal M
authors.initials: FM
authors.lastname: Ababneh
authors.affiliation: School of Mathematics & Statistics, University of Sydney, Sydney, NSW, Australia.
authors.forename: John
authors.initials: J
authors.lastname: Robinson
mesh_terms: D000465:Algorithms; D019143:Evolution, Molecular; D008390:Markov Chains; D008957:Models, Genetic; D010802:Phylogeny
keywords: Evolutionary processes; Homogeneous conditions; Markov models; Model evaluation; Model selection; Phylogenetic assumptions; Rate-heterogeneity across sites; Reversible conditions; Stationary conditions