Syllabus

Date	Lecturer	Lecture Title	Readings Hall (H) Salemi and Vandamme (SV) Higgs and Attwood (HA)	Additional Readings

9/7	Cohan	The Tree of Life: A Graph of Life's Relationships is More Than a Story of Who Begat Whom	Chapter 1 (SV)	Larson et al, 2005 Mikkelsen et al, 2005 Westneat et al , 2005 Slides
9/12	Krizanc	Algorithms in Everyday Life and in Research	Section 6.1 (HA)	Harel, 2000 Skiena, 1998 Notes Figures
9/14	Cohan	Approaches to Phylogeny through Overall Similarity of Organisms (Phenetics)		Felsenstein, 2004 Mallet, 1995 Slides
9/19	Krizanc	Phenetic Algorithms	5.1-5.2 (SV) Pg 42, 74 (H) Section 8.3 (HA)	Notes Figures
9/21	Krizanc	Cladistic Algorithms-Maximum Parsimony	7.1-7.3 (SV) Pg 94 (H) Section 8.7 (HA)	Ridley, 1985 Ridley, 1996 Notes Figures
9/26	Krizanc	Search Algorithms for the Best Phylogeny	7.4 (SV) Pg 70 (H) Section 8.5 (HA)	Felsenstein, 1978 Notes Figures
9/28	Krizanc	Models of Molecular Evolution	Chapter 4, 10.7 (SV) Pg 110 (H) Chapter 4 (HA)	Kimura, 1983 Notes Figures
10/3	Cohan	The Importance of Using Evolutionary Trees in Testing Hypotheses about Natural Selection		Donoghue, 1989 Slides
10/5	Chernoff	Compatibility of Characters
10/10	Cohan	Algorithms for Using Evolutionary Trees in Testing Hypotheses about Natural Selection		Harvey & Pagel,part,1991 Harvey & Pagel,part2,1991 Pagel,1999 Slides
10/12	Krizanc	Alignment of DNA and Protein Sequences	Chapter 3 (SV) Chapter 6 (HA)	Notes
10/19	Krizanc	Cladistic Algorithms--Maximum Likelihood	Chapter 6 (SV) Pg 104 (H) Section 8.6 (HA)	Notes Comparison
10/24	Krizanc	Testing the Robustness of a Tree	5.3 (SV) Pg 52 (H) Section 8.4 (HA)	Notes
10/26	Cohan	A genomic approach toward obtaining the true organism phylogeny		Rokas et al, 2003 Zeigler, 2003 Slides
10/31	Cohan	Modes of Adaptation: Changes in Existing Genes Versus Horizontal Transfer Versus Losses of Genes Versus Hybridization		Ochman et al, 2000 Palmisano et al, 2001 Schiteritz-Ponten et al, 2001 Zeigler, 2003 Slides
11/2	Cohan	Modes of Adaptation (continued)		Feldgarden et al, 2003 Parkhill et al, 2003 Moran&Mira, 2002 Wernegreen,2002 Baar et al, 2003 Slides
11/7	Krizanc	Gene Trees Versus Organism Trees: Duplicated Genes	Chapter 12 (HA)	Lynch&Force, 2000 Gu et al, 2003 Zmasek&Eddy, 2001 Enright et al, 2002
11/9	Krizanc	Recombination and networks for representing phylogenetic relationships	Chapter 12 (SV)	Huson, 1998 Strimmer&Moulton, 2000 Posada&Crandall, 2001 Moret et al, 2004
11/14	Krizanc	Genome Rearrangement	Chapter 12 (HA)	Snel et al, 1999 Nadeau & Sankoff, 1998 Murphy et al, 2005 Bourque&Pevzner, 2002 Kellis et al, 2004
11/16	Cohan	Sequence-Based Genomic Approaches for Finding Genes under Recent Natural Selection: Finding the Genes Responsible for Our Humanity		Schlotterer, 2002 Schlotterer, 2003 Penny, 2004 Clark et al, 2003
11/21	Cohan	Genomics in Ecosystem Biology: How to Find out he Physiological Processes Occurring in an Ecosystem Even When We Don't Know Who the Organisms Are		Robertson et al, 2004 Rondon et al, 2000 Taroncher-Oldenburg et al, 2003
11/28	Cohan	Metagenomic Approaches for Characterizing Ecosystem-Wide Diversity		Tyson et al, 2004 Venter et al, 2004 Delong, 2004
11/30	Krizanc	Algorithms for Metagenomics		Green, 1997 Weber&Myers, 1997 Waterston et al, 2002 Myers et al, 2002 She et al, 2004
12/5	Cohan	Empirically Based Molecular approaches for Quantifying Microbial Diversity in Natural Communities		Rappe&Giovannoni, 2003 Dykhuizen,1998 Martin, 2002 Readings
12/7	Cohan	Theoretically Based Molecular approaches for Identifying Ecologically Distinct Populations of Bacteria		Feil et al, 2004 Cohan, 2002 Gevers et al, 2005 Readings
12/12	Cohan and Krizanc	Community Phylogeny Approach to Characterizing Diversity		Cohan, 2004 Papke et al, 2003 Lawrence, 2002 Cohan-Krizanc-pt1 Cohan-Krizanc-pt2 Cohan-Krizanc-pt3

References for Additional Readings

Block, B. A., Finnerty, J. R., Stewart, A. F. R. & Kidd, J. (1993). Evolution of endothermy in fish: mapping physiological traits on a molecular phylogeny. Science 260, 210-214.

Clark, A. G., Glanowski, S., Nielsen, R., Thomas, P. D., Kejariwal, A., Todd, M. A., Tanenbaum, D. M., Civello, D., Lu, F., Murphy, B., Ferriera, S., Wang, G., Zheng, X., White, T. J., Sninsky, J. J., Adams, M. D. & Cargill, M. (2003). Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302, 1960-1963.

Donoghue, M. J. (1989). Phylogenies and the analysis of evolutionary sequences, with examples from seed plants. Evolution 43, 1137-1156.

Feldgarden, M., Byrd, N. & Cohan, F. M. (2003). Gradual evolution in bacteria: evidence from Bacillus systematics. Microbiology 149, 3565-3573.

Felsenstein, J. (1978). The number of evolutionary trees. Syst. Zool. 27, 27-33.

Felsenstein, J. (2004). Ch. 10: A digression on history and philosophy. In Inferring Phylogenies, pp. 123-146. Sunderland, Mass.: Sinauer Associates.

Ferea, T. L., Botstein, D., Brown, P. O. & Rosenzweig, R. F. (1999). Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci U S A 96, 9721-9726.

Goto, S. G., Kitamura, H. W. & Kimura, M. T. (2000). Phylogenetic relationships and climatic adaptations in the Drosophila takahashii and montium species subgroups. Mol Phylogenet Evol 15, 147-156.

Gould, S. J. (2000). Linnaeus's luck? Natural History 109, 18.

Harel, D. (2000). In Computers Ltd.: What They Really Can't Do, pp. 91-117. Oxford: Oxford University Press.

Harvey, P. H. & Pagel, M. D. (1991). In The Comparativew Method in Evolutionary Biology, pp. 78-95, 114-121. Oxford: Oxford University Press.

Kimura, M. (1983). The neutral theory of molecular evolution. In Evolution of Genes and Proteins, pp. 208-233. Edited by M. Nei & R. K. Koehn. Sunderland, Mass.: Sinauer.

Lanyon, S. M. (1992). Interspecific brood parasitism in blackbirds (Icterinae): a phylogenetic perspective. Science 255, 77-79.

Lynch, M. & Conery, J. S. (2000). The evolutionary fate and consequences of duplicate genes. Science 290, 1151-1155.

Mallet, J. (1995). A species definition for the modern synthesis. Trends Ecol. Evol. 10, 294-299.

Ochman, H., Lawrence, J. G. & Groisman, E. A. (2000). Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299-304

Palmisano, M. M., Nakamura, L. K., Duncan, K. E., Istock, C. A. & Cohan, F. M. (2001). Bacillus sonorensis sp. nov., a close relative of Bacillus licheniformis, isolated from soil in the Sonoran Desert, Arizona. Int J Syst Evol Microbiol 51, 1671-1679.

Parkhill, J., Sebaihia, M., Preston, A., Murphy, L. D., Thomson, N., Harris, D. E., Holden, M. T., Churcher, C. M., Bentley, S. D., Mungall, K. L., Cerdeno-Tarraga, A. M., Temple, L., James, K., Harris, B., Quail, M. A., Achtman, M., Atkin, R., Baker, S., Basham, D., Bason, N., Cherevach, I., Chillingworth, T., Collins, M., Cronin, A., Davis, P., Doggett, J., Feltwell, T., Goble, A., Hamlin, N., Hauser, H., Holroyd, S., Jagels, K., Leather, S., Moule, S., Norberczak, H., O'Neil, S., Ormond, D., Price, C., Rabbinowitsch, E., Rutter, S., Sanders, M., Saunders, D., Seeger, K., Sharp, S., Simmonds, M., Skelton, J., Squares, R., Squares, S., Stevens, K., Unwin, L., Whitehead, S., Barrell, B. G. & Maskell, D. J. (2003). Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat Genet 35, 32-40.

Ridley, M. (1985). In The Problems of Evolution, pp. 75-76. Oxford: Oxford University Press.

Ridley, M. (1996). In Evolution, pp. 492-493, color plate 497. Cambridge, Mass.: Blackwell.

Rieseberg, L. H., Raymond, O., Rosenthal, D. M., Lai, Z., Livingstone, K., Nakazato, T., Durphy, J. L., Schwarzbach, A. E., Donovan, L. A. & Lexer, C. (2003). Major ecological transitions in wild sunflowers facilitated by hybridization. Science 301, 1211-1216.

Schlotterer, C. (2003). Hitchhiking mapping--functional genomics from the population genetics perspective. Trends Genet 19, 32-38.

Sicheritz-Ponten, T. & Andersson, S. G. (2001). A phylogenomic approach to microbial evolution. Nucleic Acids Res 29, 545-552.

Skiena, S. A. (1998). In The Algorithm Design Manual, pp. 275-278, 339-342. Santa Clara, Calif.: Springer/TELOS.

Woese, C. R. (1987). Bacterial evolution. Microbiol Rev 51, 221-271.

Zeigler, D. R. (2003). Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53, 1893-1900.