Why do a phylogenetic analysis? Important for deciphering relationships in gene function and protein structure and function in different organIsms Helps to utilize genetic information of a model organism to analyze a second organism Helps to sort out gene family relationships Valuable tool for tracing the evolutionary history of genes
Why do a phylogenetic analysis? • Important for deciphering relationships in gene function and protein structure and function in different organisms • Helps to utilize genetic information of a model organism to analyze a second organism • Helps to sort out gene family relationships • Valuable tool for tracing the evolutionary history of genes
Evaluating sequence relationships sequence A ERKSIQDLFQSFTLFERRLLIEF sequence B ERLSISELIGSLRLYERRLIIEY sequence C DRKSISDLIGSLRLALLIEF sequence D DRKDLISSLRKALLIEW 1. Account for all column variations A, B and C, D form similar groups based on col. 1 A, C, D based on col. 3 2. Count differences between sequences A B 17 23 similar, 6/23 different C D 21/23 similar. 2/23 different
Evaluating sequence relationships sequence A ERKSIQDLFQSFTLFERRLLIEF sequence B ERLSISELIGSLRLYERRLIIEY sequence C DRKSISDLIGSLRLALLIEF sequence D DRKDLISSLRKALLIEW 1. Account for all column variations |A,B and C,D form similar groups based on col. 1 |A,C,D based on col. 3 2. Count differences between sequences A,B 17/23 similar, 6/23 different C,D 21/23 similar, 2/23 different
What is a tree? A graphical representation of the sequence similarities among a group of nucleic acid or protein sequences For example: number of differences between 3 sequences may be represented by AB C 7 A B AB
What is a tree? • A graphical representation of the sequence similarities among a group of nucleic acid or protein sequences • For example: number of differences between 3 sequences may be represented by .. A B C A 9 7 B 12 7 A B C 5 2
Tree of life Gram Bacteria positives see Proteobacteria lower Chlamydia Archaea (purple bacteria) right chlamydia Korarchaeota see above Euryarchaeota- see above β, Spirochetes see below Crenarchaeota Cyanobacteria Sulfolobus soMfataricus Aquifex Synechocystis sp Aquilex aeolicus Bacteroides Flavobacteria Eukarya Porphyromonas Thermotogales gingivalis Thermotoga Green non maritima sulfur bacteria Deinococcus radiodurans Cenancestor
Tree of life
Phylogenetic tree (dendrogram) Nodes: branching points Branches: lines Topology: branching pattern Terminal (leaf) Internal node (hypothetical ancestor) Branch (edge Root Fig 2.1 A simple tree and associated terms
Phylogenetic tree (dendrogram) Nodes: branching points Branches: lines Topology: branching pattern