![]() This assumption may be justifiable if the sites can be assumed to be evolving neutrally. They are often used for analyzing the evolution of an entire locus by making the simplifying assumption that different sites evolve independently and are identically distributed. The models described on this page describe the evolution of a single site within a set of sequences. By expressing models in terms of the instantaneous rates of change we can avoid estimating a large numbers of parameters for each branch on a phylogenetic tree (or each comparison if the analysis involves many pairwise sequence comparisons). The mathematical details of this transformation from rate-matrix to probability matrix are described in the mathematics of substitution models section of the substitution model page. If we are given a starting (ancestral) state at one position, the model's Q matrix and a branch length expressing the expected number of changes to have occurred since the ancestor, then we can derive the probability of the descendant sequence having each of the four states. Thus, it is convenient to express these models in terms of the instantaneous rates of change between different states (the Q matrices below). However, the Kimura (K80) model described below only attempts to capture the effect of both forces in a parameter that reflects the relative rate of transitions to transversions.Įvolutionary analyses of sequences are conducted on a wide variety of time scales. For example, mutational biases and purifying selection favoring conservative changes are probably both responsible for the relatively high rate of transitions compared to transversions in evolving sequences. Rather they describe the relative rates of different changes. These Markov models do not explicitly depict the mechanism of mutation nor the action of natural selection. These models are phenomenological descriptions of the evolution of DNA as a string of four discrete states. HKY85 model (Hasegawa, Kishino and Yano 1985).DNA evolution as a continuous-time Markov chain.In particular, they are used during the calculation of likelihood of a tree (in Bayesian and maximum likelihood approaches to tree estimation) and they are used to estimate the evolutionary distance between sequences from the observed differences between the sequences. These models are frequently used in molecular phylogenetic analyses. These substitution models differ in terms of the parameters used to describe the rates at which one nucleotide replaces another during evolution. ( November 2010) ( Learn how and when to remove this template message)Ī number of different Markov models of DNA sequence evolution have been proposed. Please help to improve this article by introducing more precise citations. This article includes a list of general references, but it lacks sufficient corresponding inline citations.
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