lec1和0-11_MolEvo-2.ppt

* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * The Biological Story: Alu Evolution Alu Evolution Alu Evolution: The Master Alu Theory Alu Evolution: Alu Master Theory Proven Wrong Minimum Spanning Tree As An Evolutionary Tree Alu Evolution: Minimum Spanning Tree vs. Phylogenetic Tree A timeline of Alu subfamily evolution would give useful information Problem - building a traditional phylogenetic tree with Alu subfamilies will not describe Alu evolution accurately Why can’t a meaningful typical phylogenetic tree of Alu subfamilies be constructed? When constructing a typical phylogenetic tree, the input is made up of leaf nodes, but no internal nodes Alu subfamilies may be either internal or external nodes of the evolutionary tree because Alu subfamilies that created new Alu subfamilies are themselves still present in the genome. Traditional phylogenetic tree reconstruction methods are not applicable since they don’t allow for the inclusion of such internal nodes Constructing MST for Alu Evolution Building an evolutionary tree using an MST will allow for the inclusion of internal nodes Define the length between two subfamilies as the Hamming distance between their sequences Root the subfamily with highest average divergence from its consensus sequence (the oldest subfamily), as the root It takes ~4 million years for 1% of sequence divergence between subfamilies to emerge, this allows for the creation of a timeline of Alu evolution to be created Why an MST is useful as an evolutionary tree in this case The less the Hamming distance (edge weight) between two subfamilies, the more likely that they are directly related An MST represents a way for Alu subfamilies to have evolved minimizing the sum of all the edge weights (total Hamming distance between all Alu subfamilies) which makes it the most parsimonious way and thus the most likely way for the evolution