Accurate Estimations of Evolutionary Times in the Context of Strong CpG Hypermutability
We consider the substitution model T92 + CpG of DNA sequence evolution which takes into account the hypermutability of CpG dinucleotides, an effect that can be especially observed in vertebrate genomes. We provide an exact method to simulate the evolution of finite DNA sequences under this model and numerical procedures to infer evolutionary times in two cases: between an ancestral and a present sequence and between two homologous sequences. We show on simulated data that our new numerical method yields very accurate estimations of divergence times. In a context of strong CpG hypermutability, it clearly outperforms the classical estimation procedure that is solely based on the model T92 without CpG influence. Supplementary Material is available at www.liebertonline.com/cmb.
cpg hypermutability dna sequence evolution markov model neighbor-dependent substitution process phylogenetic distances