Lecture_7_phylogenetics

Distance a tree that recursively combines two nodes of

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Unformatted text preview: mp?ons are violated, etc., can the true, correct tree be found and proven to be scien<fically valid? •  Unfortunately, it is impossible to ever conclusively state what is the "true" tree for a group of sequences (or a group of organisms); taxonomy is constantly under revision as new data is gathered. Types of trees Unrooted tree represents the same phylogeny without the root node Common Ancestor 23 Depending on the model, data from current day species does not dis?nguish between different placements of the 24 root. 4 9/16/13 Rooted Versus Unrooted trees Tree A Tree B Posi?oning Roots in Unrooted Trees We can es?mate the posi?on of the root by introducing an outgroup: a set of species that are definitely distant from all the species of interest Proposed root Tree C b a Falcon c Represents the three rooted trees Aardvark Bison Chimp 25 Dog Elephant 26 Scaled vs Unscaled Type of Data A B C D E F Scaled trees: Branch lengths are propor?onal to the number of nucleo?de/ amino acid changes that occurred on that branch (usually a scale is included). Distance- based –  Input is a matrix of distances between species –  Can be frac?on of residue they disagree on, or alignment score between them, or … Character- based –  Examine each character (e.g., residue) separately Unscaled trees: Branch lengths are not propor?onal to the number...
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