Introduction to Phylogenetic Analysis

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Slide taken from Dr. Itai Yanai 2 1 Different kinds of trees can be used to depict different aspects of evolutionary history 3 3 1 1 1 1 1 1 3 7 2 1 1 5 3 1. Cladogram: simply shows relative recency of common ancestry 4 3 2. Additive trees: a cladogram with branch lengths, also called phylograms and metric trees 3. Ultrametric trees: (dendograms) special kind of additive tree in which the tips of the trees are all equidistant from the root Rooted Tree = Cladogram A phylogenetic tree that all the "objects" on it share a known common ancestor (the root). There exists a particular root node. The paths from the root to the nodes correspond to evolutionary time. Root A C B The Molecular Clock Hypothesis All the mutations occur in the same rate in all the tree branches. The rate of the mutations is the same for all positions along the sequence. The Molecular Clock Hypothesis is most suitable for closely related species. Unrooted Tree = Phenogram A phylogenetic tree where all the "objects" on it are related descendants - but there is not enough information to specify the common ancestor (root). The path between nodes of the tree do not specify an evolutionary time. B
Slide taken from Dr. Itai Yanai Rooted vs. Unrooted Rooted Unrooted Interior Total Interior Total Types of Trees Branches M – 2 2M – 2 M – 3 Nodes M – 1 2M – 1 M – 2 2M – 3 2M – 2 M is the number of OTU’s Slide taken from Dr. Itai Yanai The number of rooted and unrooted trees: Possible Number of Number of OTU’s Rooted trees Unrooted trees 2 1 1 3 3 1 4 15 3 5 105 15 6 945 105 7 10395 945 8 135135 10395 9 2027025 135135 10 34459425 2027025 OTU – Operational Taxonomical Unit Rooted versus Unrooted The number of tree topologies of rooted tree is much higher than that of the unrooted tree for the same number of OTUs. Therefore, the error of the unrooted tree topology is smaller than that of the rooted tree. Orthologs - genes related by speciation events. Meaning same genes in different species. Paralogs - genes related by duplication events. Meaning duplicated genes in the same species.
Page 1 and 2: Introduction to Phylogenetic Analys
Page 3 and 4: How we calculate the Degree of Dive
Page 5: I H Internal branches - are branche
Page 9 and 10: Known Problems of Multiple Alignmen
Page 11 and 12: Taken from Dr. Itai Yanai Estimatin
Page 13 and 14: Character Based Methods - Maximum P
Page 15 and 16: Distances Matrix Methods Distance
Page 17 and 18: Mutations - Substitutions Point mu
Page 19 and 20: Kimura two-parameter model This mod
Page 21: Known problems of Phylogenetic Anal

Introduction to Phylogenetic Analysis

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