Chapter 7: Molecular Phylogeny
and Evolution
This page offers the web documents that are referred to in Chapter 7 of the book. In Chapter 6 we discussed multiple sequence alignments. These can be visualized as phylogenetic trees. We describe the main features of a tree (topology and branch lengths) and the stages of generating a tree. Approaches include maximum parsimony, distance-based methods, maximum likelihood, and Bayesian inference of phylogeny.
| Web documents | Description |
| Web Document 7-1 | 13 globin protein sequences |
| Web Document 7-2 | Globin evolution from Zuckerkandl and Pauling (1962) |
| Web Document 7-3 | 12 aligned myoglobin DNA coding sequences (plus cytoglobin) |
| Web Document 7-4 | vertebrate globins (used to make an HMM) |
| Web Document 7-5 | Test for positive or negative selection using MEGA software |
| Web Document 7-6 | Eleven randomly selected protein sequences used for phylogenetic analysis |
| Web Document 7-7 | Output file from the ModelTest program in which 56 models of nucleotide substitution were evaluated for a set of myoglobins |
| Web Document 7-8 | Phylogenetic analysis of 13 globins using TreePuzzle : maximum likelihood inference of phylogeny |
| Web Document 7-9 | TreePuzzle output |
| Web Document 7-10 | Bayesian inference of phylogeny: 13 globins using MrBayes |
| Web Document 7-11 | Bayesian inference of phylogeny: MrBayes output |
| Web Document 7-12 | Six primate mitochondrial DNA sequences (nexus format) |
| Web Document: Table 7.1 | Example of the UPGMA method of tree construction |
Chapter 7 Resources |
| Powerpoint of the phylogeny lecture (December 2008)(December 2009/January 2010) |
| PDF (black & white) of the handout for printing, 6 slides per page (December 2008) |
| Moodle site. This teaching site includes quizzes and readings; non-registered students can enter as guests |
| Computer lab (coming soon) |
| Audio file of a phylogeny lecture (December 2008)(January 2010) |
| Key URLs: Joseph Felsenstein's list of phylogeny links; MEGA website; LANL HIV sequence database with tutorial; MrBayes; PHYLIP; PAUP; TreePuzzle. |
Chapter 7 errata |
|
| Page 261, legend to Fig. 7.28 | Text should read: “However, columns having entirely conserved residues (filled arrowheads) are not informative. Columns in which there are at least two different residues that occur at least two times (open arrowheads) are informative.” |
This page updated 1-21-10