Chapter 8Molecular Phylogenetics:

Measuring Evolution

Figure 8.1: The Tree of Life shows relationships among major groups of organisms

Courtesy of Andrew J. Roger, Alastair B. Simpson, and Mitchell L. Sogin

Figure 8.2: Sequence alignments can provide clues to evolutionary change by examining the effect of mutations occurring over time in species with a

common ancestor

Figure 8.3: An example of a phylogenetic tree showing the evolutionary relationships among four modern species

Figure 8.4: Alignment of a portion of the casein gene from whales and related organisms, and a phylogenetic tree based on the differences among

these genes

Figure 8.5: DNA sequence changes in the cytochrome c gene reflect evolutionary distance

Figure 8.6: Calculating the substitution rate (r) for two sequences that have changed over time

Figure 8.7: Relative substitution rates for different regions of a chromosome, showing that functional constraints reduce the likelihood that

mutations will be preserved

Figure 8.8: Substitution mutations can be categorized as transitions or transversions

Figure 8.9: Example of a single FASTA file with two sequences to compare

Figure 8.10: Sample ClustalW output for a protein alignment

Figure 8.11: Phylogentic trees: (A) Rooted; (B) Unrooted

Figure 8.12: A phylogenetic tree showing the relationships among six example species

Figure 8.13: Three different linkage methods that could be used to compute the distance between two clusters

Figure 8.14: A partial phylogenetic tree after merging clusters A and B and calculating branch lengths

Figure 8.15: A partial phylogenetic tree after merging clusters (AB) with C and calculating branch lengths

Figure 8.16: A partial phylogenetic tree after merging clusters (ABC) with D and calculating branch lengths

Figure 8.17: A partial phylogenetic tree after merging clusters (ABCD) with E and calculating branch lengths