Chapter 4Distance–Based Methods of Phylogenetics.pptVIP

Chapter 4Distance–Based Methods of Phylogenetics 暨南大學資訊工程學系 黃光璿 (HUANG, Guan-Shieng) 2004/03/29 Motivation Evolution events on genomes: substitutions insertions deletions rearrangements We focus on cluster analysis in this chapter. 4.1 History of Molecular Phylogenetics taxonomists (分類學家)： naming (命名) grouping (分類) traditional approach based on anatomic difference (解剖) Linnaeu’s system 界 門 綱 目 科 屬 種 Darwing (達爾文) Nuttall (1902~1904) humans apes 最晚分化 (從免疫系統的角度) 1950s protein electrophoresis (size, charge) 1960s protein sequencing 1970s genomic information 先有 restriction enzyme 後有 DNA sequencing 比較解剖學 蟒蛇與人 Linnaeus 林奈 十八世紀博物學家 帶領未受訓練的學生到世界各地蒐集標本, 遠征過程中有三分之一的學生死亡. 創立「二名法」(binomial system of nomenclature) 屬名(genus)＋種名(species) 4.2 Advantages of Molecular Phylogenies fundamental evolution is defined as genetic changes molecular clock hypothesis (Chap. 3) In early days, taxonomists inferred genotypes from phenotypes. phenotypes(表現型): how organisms looks genotypes: the genes that gave rise to their physical appearance And then behavior (行為) ultrastructural (超顯微結構) biochemical characteristics were studied. 傳統研究方法有以下問題無法解決 convergent evolution 眼睛：humans, flies, mollusks (軟體動物) many organisms do not have easily studied phenotypic features bacteria (細菌) comparing distantly related organisms bacteria, worms, mammals few characteristics in common! 4.3 Phylogenetic Trees 4.3.1 Terminology of Tree Reconstruction phylogenetic tree, or dendrogram nodes: taxonomical units branches terminal nodes collected data (I, II, III, IV, V) internal nodes inferred ancestors (A, B, C, D) Newick format (((I, II), (III, IV)), V) bifurcate: 一變二 multifurcate: ≥3 scaled trees branch lengths are proportional to the differences between pairs of neighboring nodes additive in a scaled tree physical length of two nodes reflects their accumulated difference unscaled trees convey only their relative kinship 4.3.2 Rooted and Unrooted Trees NR=#(rooted binary trees) NU=#(unrooted binary trees)