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CBMG 670 (PBIO 699K) - Molecular Systematics

Suppementary Reading

Books

*Felsenstein, J. 2004. Inferring Phylogenies. Sinauer Associates, Sunderland MA.

Freeman, S., and Herron, J.C. 2001. Evolutionary Analysis, 2nd Edition. Prentice Hall, Upper Saddle River, NJ.

Hillis, D.M., Moritz, C., and Mable, B.K. 1996. Molecular Systematics, 2nd Edition. Sinauer Associates, Sunderland MA.

Li, W.-H. 1997. Molecular Evolution. Sinauer Associates, Sunderland MA.

Page, R.D.M., and Holmes, E.C. 1998. Molecular Evolution, a Phylogenetic Approach. Blackwell Science, Oxford.


Supplementary books

Alberts et al. 1994. Molecular Biology of the Cell, 4th Edition. Garland Press, New York, NY. (The 3d edition is available on line at NCBI)

Crawford, D.J., 1990. Plant Molecular Systematics - Macromolecular Approaches. John Wiley & Sons, New York, NY.

Gibas, C., and Jambeck, P. 2001. Developing Bioinformatics Computer Skills. O'Reilly and Associates, Sebastopol, CA.

Harborne, J.B., and B.L. Turner, 1984. Plant Chemosystematics. Academic Press.

Harborne, J.B., 1984. Phytochemical methods (2nd ed.). Chapman and Hall

Miyamoto, M.M., and Cracraft, J. 1991. Phylogenetic Analysis of DNA Sequences. Oxford University Press, New York, NY.

Osawa, S. 1995. Evolution of the Genetic Code. Oxford University Press, New York, NY.

Soltis, D.E., Soltis, P.S., and Doyle, J.J. 1998. Molecular Systematics of Plants II: DNA Sequencing. Kluwer Academic Press, Boston MA.

Soltis, P.S., Soltis, D.E., and Doyle, J.J. 1992. Molecular Systematics of Plants. Chapman and Hall, London.


Required Reading from the Literature

Felsenstein, J. 1978. Cases in which parsimony or compatability methods will be positively misleading. Syst. Zool. 27:401-410.

Huelsenbeck, J.P., and B. Rannala. 1997. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276:227-232.

Huelsenbeck, J.P., and D.M. Hillis. 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42:247-264.

Hillis, D.M., and J.J. Bull. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182-192.

Posada, D., and K.A. Crandall. 2001. Selecting models of nucleotide substitution: an application to human immunodeficiency virus 1 (HIV-1). Mol. Biol. Evol. 18:897-906.

Reeck, G. R., et al. 1987. "Homology" in proteins and nucleic acids: a terminological muddle and a way out of it. Cell 50:667.

Riedl, R. 1978. Order in Living Organisms (Translated by R.P.S. Jefferies). John Wiley & Sons, Chichester. Pp. 32-40.

Zuckerkandl, E., and L. Pauling. 1965. Molecules as documents of evolutionary history. J. Theoret. Biol. 8:357-366.


Supplementary Reading from the Literature

Hillis, D.M., J.P. Huelsenbeck, and C.W. Cunningham. 1994. Application and accuracy of molecular phylogenies. Science 264:671-677.

Maddison, D.R., D.L. Swofford, and W.P. Maddison. 1997. Nexus: an extensible file format for systematic information. Syst. Biol. 46:590-621.

Bremer, K. 1994. Branch support and tree stability. Cladistics 10:295-304.

Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-378.

Kimura, M. 1983. The neutral theory of evolution. in M. Nei and R.K. Koehn, eds. Evolution of Genes and Proteins. Sinauer Associates, Inc. Sunderland, MA.

Hillis, D.M. 1996. Inferring complex phylogenies. Nature 383:130131.

Huelsenbeck, J.P., and D.M. Hillis. 1992. Signal, noise, and reliability in molecular phylogenetic analyses. J. Heredity 83:189-195.

Jin, L. and M. Nei. 1990. Limitations of the Evolutionary Parsimony Method of Phylogenetic Analysis. Mol. Biol. Evol. 7:82-102. [describes the gamma shape parameter to account for among-site rate variation]

Efron, B., and R. Tibshirani. 1991. Statistical data analysis in the computer age. Science 253:390-400.

Maddison, D.R. 1991. The discovery and importance of multiple islands of most-parsimonious trees. Syst. Zool. 40:315-328.

Olmstead, R.G., ad J.A. Sweere. 1994 Combining data in phylogenetic systematics: an empirical approach using three molecular data sets in the Solanaceae. Syst. Biol. 43:467-481.


Other Relevant Literature

Lecointre, G., et al. 1993. Species sampling has a major impact on phylogenetic inference. Mol. Phylog. Evol. 2:205-224.

Bandelt, H-J., and A.W.M. Dress. 1992. Split Decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol. Phylog. Evol. 1 (3):242-252.

Beanland, T.J., and C.J. Howe. 1992. The inference of evolutionary trees from molecular data. Comp. Biochem. Physiol. 102B(4):643-659.

Friday, A. 1993. The primacy of models in phylogenetic reconstruction: some indicators to future developments. BINARY 5:105-108.

Shoemaker, J.S., and W.M. Fitch. 1989. Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated. Mol. Biol. Evol. 6(3):270-289.

Rzhetsky, A., and T. Sitnikova. 1996. When is it safe to use an oversimplified model in tree-making? Mol. Biol. Evol. 13(9):1255-1265.

Kelchner, S.A., and J.F. Wendel. 1996. Hairpins create minute inversions in non-coding regions of chloroplast DNA. Curr. Genet. 30:259-262.

Lloyd, A.M., M. Schena, V. Walbot, and R.W. Davis. 1994. Epidermal cell fate determination in Arabidopsis: patterns defined by a steroid-inducible regulator. Science 266:436-439.

Sanderson, M.J., and M.J. Donoghue. 1994. Shifts in diversification rate with the origin of angiosperms. Science 264:1590-1593.

Chaw, S.-M., A. Zarkikh, H.-M. Sung, T.-C. Lau and W.-H. Li. 1997. Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences. Mol. Biol. Evol. 14:56-68.

Soltis, D.E. (et al.). 1997. Angiosperm phylogeny inferred from 18S ribosomal DNA sequences. Ann. Missouri Bot. Gard. 84:1-49.

Chase, M.W. (et al.). 1993. Phylogenetics of seed plants. Ann. Missouri Bot. Gard. 80:528-580. (See also entire issue of Ann. Missouri Bot. Gard.)

A.M. Dean. 1998. The molecular anatomy of an ancient adaptive event. Amer. Sci. 86:26-37.

Sytsma, K.J. 1990. DNA and Morphology: Inference of Plant Morphology. TREE 5:104-110.

Mishler, B.D. 1994. Cladistic analysis of molecular and morphological data. Amer. J. Physical Anthro. 94:143-156.

Stewart, C.-B. 1993. The powers and pitfalls of parsimony. Nature 361:603-607.

Sidow, A. 1994. Parsimony or statistics? Nature 367:26. & Stewart, C.-B. 1994. (Stewart replies) Nature 367:26-27.

Raubeson, L.A., and R.K. Jansen. 1992. Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science 255:1697-1699.

Levy, M., 1977. Minimum biosynthetic step indices as measures of comparative flavonoid affinity. Syst. Bot. 2:89-98.

 

Crawford, D.J., 1978. Flavonoid chemistry and angiosperm evolution. The Bot. Rev. 44:431-456.

McClure, J.W., and R.E. Alston, 1966. A chemosystematic study of Lemnaceae. Am. J. Bot 53:849-860.

Seaman, F.C., and V.A. Funk. 1983. Cladistic analysis of complex natural products: developing transformation series from sesquiterpene lactone data. Taxon 32:1-27.

Logsdon, J.M. Jr., and W.F. Doolittle. 1997. Origin of antifreeze protein genes: a cool tale in molecular evolution. Proc. Natl. Acad. Sci. USA 94:3485-3487.

Chen, L., A.L. DeVries, and C.-H. C. Cheng. 1997. Convergent evolution of antifreeze glycoproteins in Antarctic notothenioid fish and Arctic cod. Proc. Natl. Acad. Sci. USA 94:3817-3822.

Chen, L., A.L DeVries, and C.-H. C. Cheng. 1997. Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish. Proc. Natl. Acad. Sci. USA 94:3811-3816.

Yang, Z. 1996. Among-site rate variation and its impact on phylogenetic analyses. TREE 11: 367-373.

Dayhoff, M.O., R.M. Schwartz, and B.C. Orcutt. 1979. A model of evolutionary change in proteins. In Atlas of Protein Sequence and Structure 5 (supplement 3): 345-352.

Schwartz, R.M., and M.O. Dayhoff, 1979. Matrices for detecting distant relationships. In Atlas of Protein Sequence and Structure 5 (supplement 3): 353-358.

Jones, D.T., W.R. Taylor, and J.M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. CABIOS 3:275-282.

E.A. Kellogg, R. Appels, and R.J. Mason-Gamer. 1996. When genes tell different stories: the diploid genera of Triticeae (Gramineae). Systematic Botany 21:321-347.

Huelsenbeck, J.P., J.J. Bull, and C.W. Cunningham. 1996. Combining data in phylogenetic analysis. TREE 11:152-158.

N. Goldman and Z. Yang. 1994. A condon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11:725-736.

Rieseberg, L.H., B. Sinervo, C. R. Linder, M.C. Ungerer, and D.M. Arias. 1996. Role of gene interactions in hybrid speciation: evidence from ancient and experimental hybrids. Science 272:741-744.

Ayala, F.J. 1995. The myth of eve: molecular biology and human origins. Science 270:1930-1936.

Jarne, P., and P.J.L. Lagoda. 1996. Microsatellites, from molecules to populations and back. TREE 11:424-429.

L.B. Jorde, A.R. Rogers, M. Bamshad, W.S. Watkins, P. Krakowiak, S. Sung, J. Kere, and H.C. Harpending. 1997. Microsatellite diversity and the demographic history of modern humans. Proc. Natl. Acad. Sci. USA 94:3100-3103.

Woese, C.R. 1994. There must be a prokaryote somewhere: microbiology's search for itself. 58:1-9.

Rivera, M.C., and J.A. Lake. 1992. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257:74-76.

Cavalier-Smith, T. 1993. Kingdom Protozoa and its 18 phyla. Microbiol. Rev. 57: 953-994.

Keeling, P.J., and W.F. Doolittle. 1996. Alpha-tubulin from early-diverging eukaryotic lineages and the evolution of the tubulin family. Mol. Biol. Evol. 13:1297-1305.

DeSalle, R. J. Gatesy, W. Wheeler, and D. Grimaldi. 1992. DNA sequences from a fossil termite in Oligo-Miocene amber and their phylogenetic implications. Science 257:1933-1936.

Cano, R.J., and M.K. Borucki. 1995. Revival and identification of bacterial spores in 25- to 40- million-year-old Dominican amber. Science 268:1060-1062. (plus technical comments, Science 270:2015-2017).

Messier, W., and C.-B. Stewart. 1997. Episodic adaptive evolution of primate lysozymes. Nature 385:151-154.

Delwiche, C.F., and J.D. Palmer. 1996. Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids. Mol. Biol. Evol. 13:873-882.

Environmental Molecular Biology

Amann, R.I., W. Ludwig, and K-H Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.

Barns, S.M., C.F. Delwiche, J.D. Palmer, and N.R. Pace. 1996. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA 93:9188-9193.

Barns, S.M., R.E. Fundyga, M.W. Jeffries, and N.R. Pace. 1994. Remarkable archaeal diversity detected in a yellowstone national park hot spring environment. Proc. Natl. Acad. Sci. USA 91:1609-1613.

Burggraf, S., P. Heyder, and N. Eis. 1997. A pivotal Archaea group. Nature 385:780.

Ward, D.M., M.M. Bateson, R. Weller, and A.L. Ruff-Roberts. 1992. Ribosomal RNA analysis of microorganisms as they occur in nature. Adv. Microb. Ecol. 12:219-287.


PBIO699K webpage / www.wam.umd.edu/~delwiche/pbio699k.html/ last major revision 2/1/2006