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Chapter 8
Molecular 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