Introduction to Phylogenetics Part I: Evolutionary Model

Series Contents

1. Introduction to Phylogenetics: Preface
2. Introduction to Phylogenetics Part I: Evolutionary Model
3. Introduction to Phylogenetics Part II: Stationary Probabilities of Mutation
   
4. Introduction to Phylogenetics Part III: Phylogenetic Construction by Maximum Likelihood
5. Introduction to Phylogenetics Part IV: Multiple Sequence Alignments
   
6. Introduction to Phylogenetics Appendix A: Entrez SOAPing
7. Introduction to Phylogenetics Appendix B: CUDA in C#
   
8. Introduction to Phylogenetics Appendix C: CUDA Optimisation

Introduction

For constructing a phylogenetic tree based on DNA data, we need to have an idea of the evolutionary trends or how specific bases mutated over time. It is likeley that with high evolutionary rates result a tree with short branches will be produced, low evolutionary rates would result in a tree with long branches. Evolutionary models which don't impose an equal probability of mutation on all bases (not unlike the Jukes-Cantor model), require some parameters on the likelihood of such a mutation.


Scope of Article

Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Proin in ante in sapien placerat accumsan. Sed non turpis nec ipsum dapibus molestie. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Donec sem neque, gravida sed, dapibus a, laoreet quis, justo. Ut semper neque vel ligula. In placerat consequat dui. Praesent consectetuer feugiat metus. Phasellus consequat semper diam. Suspendisse massa. Praesent vel risus. Donec sodales posuere risus. Donec scelerisque ante sagittis erat. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Morbi vitae lectus sit amet nisi ultricies ullamcorper. Duis lobortis. Aenean dignissim risus sit amet sem. Donec mollis diam id est. Vestibulum pulvinar leo id diam.

Predicting Evolution

We construct a Markov Chain representing all possible changes of state DNA can undergo (a generalized model is shown below). The assumption of a constant rate of change is heavily tied to the concept of a molecular clock and is highly contraversial. The idea that evolution occurs at a constant rate is a gross oversimplification of the process but to ease computation and also generate a sense of direction, it is often inherant in phylogenetic reconstruction.

Figure I -Markov Chain representing the change of states for all bases of DNA

Jukes-Cantor Model

Developed in 1969, is the simplest evolutionary model, available in descrete and continuous time flavours. The model assumes a constant rate of evolution which remain equal for all bases.


Kimura Model

Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Proin in ante in sapien placerat accumsan. Sed non turpis nec ipsum dapibus molestie. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Donec sem neque, gravida sed, dapibus a, laoreet quis, justo. Ut semper neque vel ligula. In placerat consequat dui. Praesent consectetuer feugiat metus. Phasellus consequat semper diam. Suspendisse massa. Praesent vel risus. Donec sodales posuere risus. Donec scelerisque ante sagittis erat. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Morbi vitae lectus sit amet nisi ultricies ullamcorper. Duis lobortis. Aenean dignissim risus sit amet sem. Donec mollis diam id est. Vestibulum pulvinar leo id diam.


HKY Model
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Proin in ante in sapien placerat accumsan. Sed non turpis nec ipsum dapibus molestie. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Donec sem neque, gravida sed, dapibus a, laoreet quis, justo. Ut semper neque vel ligula. In placerat consequat dui. Praesent consectetuer feugiat metus. Phasellus consequat semper diam. Suspendisse massa. Praesent vel risus. Donec sodales posuere risus. Donec scelerisque ante sagittis erat. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Morbi vitae lectus sit amet nisi ultricies ullamcorper. Duis lobortis. Aenean dignissim risus sit amet sem. Donec mollis diam id est. Vestibulum pulvinar leo id diam.


Felsenstein Model

Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Proin in ante in sapien placerat accumsan. Sed non turpis nec ipsum dapibus molestie. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Donec sem neque, gravida sed, dapibus a, laoreet quis, justo. Ut semper neque vel ligula. In placerat consequat dui. Praesent consectetuer feugiat metus. Phasellus consequat semper diam. Suspendisse massa. Praesent vel risus. Donec sodales posuere risus. Donec scelerisque ante sagittis erat. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Morbi vitae lectus sit amet nisi ultricies ullamcorper. Duis lobortis. Aenean dignissim risus sit amet sem. Donec mollis diam id est. Vestibulum pulvinar leo id diam.

---

References

1. Ewens W. J., Grant G. R., Statistical Methods in Bioinformatics, Springer 2005