§5MolecularPhylogeny生物信息学国外教程2010版课件(2962KB).ppt

* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * A to B: known distance A to outgroup: known distance A to X: unknown (and solvable) B to X: unknown (and solvable) Question: is X-to-A the same length as X-to-B? X An often-held view of evolution is that just as organisms propagate through natural selection, so also DNA and protein molecules are selected for. According to Motoo Kimura’s 1968 neutral theory of molecular evolution, the vast majority of DNA changes are not selected for in a Darwinian sense. The main cause of evolutionary change is random drift of mutant alleles that are selectively neutral (or nearly neutral). Positive Darwinian selection does occur, but it has a limited role. As an example, the divergent C peptide of insulin changes according to the neutral mutation rate. Neutral theory of evolution Page 230 Molecular evolutionary studies can be complicated by the fact that both species and genes evolve. speciation usually occurs when a species becomes reproductively isolated. In a species tree, each internal node represents a speciation event. Genes (and proteins) may duplicate or otherwise evolve before or after any given speciation event. The topology of a gene (or protein) based tree may differ from the topology of a species tree. Species trees versus gene/protein trees Page 238 species 1 species 2 speciation event Species trees versus gene/protein trees Fig. 7.14 Page 238 past present species 1 species 2 speciation event Species trees versus gene/protein trees Gene duplication events Fig. 7.14 Page 238 species 1 species 2 speciation event Species trees versus gene/protein trees Gene duplication events OTUs Fig. 7.14 Page 238 * * Tree-building methods: UPGMA Step 4: Keep going. Cluster. 1 2 3 4 5 1 2 6 4 5 7 3 8 Fig. 7.26 Page 257 Tree-building methods: UPGMA Step 4: Last cluster! This is your tree. 1 2 3 4 5 1 2 6 4 5 7 3 8 9 Fig. 7.26 Page 257 UPGMA is a simple approach for making tree