Figure 16.5 The Accuracy of Phylogenetic Analysis

In 1992, David Hillis and colleagues published what is considered to be a landmark experiment in the field of experimental phylogenetics. Their experimental approach had two goals. The first was to determine the feasibility of inferring a phylogeny for an organism that displays considerable molecular variation. The second was to use the inferred phylogenies to test current methods of phylogenetic estimation. To achieve these goals, the investigators developed a system to grow bacteriophage T7 in a serial manner in the presence of a mutagen to increase the mutation rate. Specifically, a single viral plaque was selected at random to be the common ancestor for the experimental lineage. A sample of the common ancestor was saved for later molecular analysis and tree rooting, while the remaining viruses were allowed to propagate. After every 400 generations, each ingroup was split into two, and a sample of the ancestral lineage was saved. The viruses were taken through two more sets of 400 generations until a total of eight experimental lineages were obtained in addition to the one original common ancestor. The researchers then isolated and sequenced viruses from the end point of each lineage, and these data were used to reconstruct a phylogeny of the viral lineages. After the analysis, the researchers confirmed the accuracy of the phylogenetic tree by comparing the final sequence data to sequences obtained from samples taken after each branching point. Based on their results, Hillis and colleagues found that phylogenetic analysis of DNA sequences can accurately reconstruct evolutionary history and ancestral sequences. The authors noted that this test of phylogenetic analysis has an advantage over computer simulations in that the molecular evolution of T7 is biological, rather than based on human-designed computer algorithms. Computers use simple models of evolution and do not usually take into account variations in parameters over time and effects of selection in addition to other more complex factors. In the experiment described above, the researchers allowed the viruses to evolve for three sets of 400 generations and in the end had eight lineages (plus one outgroup) to analyze. One way to make the phylogeny more challenging to infer would be to modify the experimental conditions. To do so, one could vary the number of generations between each ingroup split, as well as increase the number of times that each ingroup lineage is split. These and many other variations of this experiment have helped demonstrate the effectiveness of phylogenetic analysis under a wide diversity of conditions (for example, see Cunningham et al., 1997, 1998, in the original papers list below). This research has since been applied to reconstruct many extinct gene sequences from naturally occurring organisms (such as the visual pigment protein genes from extinct archosaurs; see Chang et al., 2002 in the original papers list).

Original Papers

Hillis, D. M., J. J. Bull, M. E. White, M. R. Badgett, and I. J. Molineux. 1992. Experimental phylogenetics: generation of a known phylogeny. Science 255: 589–592.
http://www.jstor.org/stable/2876826

Bull, J. J., C. W. Cunningham, I. J. Molineux, M. R. Badgett, and D. M. Hillis. 1993. Experimental molecular evolution of bacteriophage T7. Evolution 47: 993–1007.
http://www.jstor.org/stable/2409971

Chang, B. S. W., K. Jönsson, M. A. Kazmi, M. J. Donoghue, and T. P. Sakmar. 2002. Recreating a Functional Ancestral Archosaur Visual Pigment. Molecular Biology and Evolution 19: 1483–1489.
http://mbe.oxfordjournals.org/cgi/reprint/19/9/1483

Cunningham, C. W., K. Jeng, J. Husti, M. Badgett, I. J. Molineux, D. M. Hillis, and J. J. Bull. 1997. Parallel Molecular Evolution of Deletions and Nonsense Mutations in Bacteriophage T7. Molecular Biology and Evolution 14: 113–116.
http://mbe.oxfordjournals.org/cgi/reprint/14/1/113.pdf

Cunningham, C. W., H. Zhu, and D. M. Hillis. 1998. Best-fit maximum-likelihood models for phylogenetic inference: Empirical tests with known phylogenies. Evolution 52: 978–987.
http://www.jstor.org/stable/2411230

Links

University of Texas: Hillis/Bull Lab
http://www.zo.utexas.edu/faculty/antisense/index.html

Hillis, D. M., J. J. Bull, M. E. White, M. R. Badgett, and I. J. Molineux. 1993. Experimental Approaches to Phylogenetic Analysis. Systematic Biology 42: 90–92.
http://www.jstor.org/stable/2992559
http://sysbio.oxfordjournals.org/cgi/reprint/42/1/90

Sanson, G. F. O., S. Y. Kawashita, A. Brunstein, and M. R. S. Briones. 2002. Experimental Phylogeny of Neutrally Evolving DNA Sequences Generated by a Bifurcate Series of Nested Polymerase Chain Reactions. Molecular Biology and Evolution 19: 170–178.
http://mbe.oxfordjournals.org/cgi/content/full/19/2/170

Baum, D. 2008. Trait Evolution on a Phylogenetic Tree: Relatedness, Similarity, and the Myth of Evolutionary Advancement. Nature Education 1(1)
http://www.nature.com/scitable/topicpage/trait-evolution-on-a-phylogenetic-tree-relatedness-41936

Baum, D. 2008. Reading a phylogenetic tree: The meaning of monophyletic groups. Nature Education 1(1)
http://www.nature.com/scitable/topicpage/reading-a-phylogenetic-tree-the-meaning-of-41956

American Museum of Natural History: M. Siddall: Phylogenetics: just methods
http://research.amnh.org/~siddall/methods/