UPDATE: Must read papers for graduate students

Following up on my previous post, here is the list of ‘Must Read’ papers in phylogenetics that were suggested on Twitter. I think that this is a great start, even though it is missing some classics and some important topics (divergence time estimation, for example). Thanks to everyone for chipping in with their thoughts and thanks again to Matt Hahn and Matt Pennell for getting the conversation started.

I apologize if I missed anyone’s contributions. Feel free to suggest additions, either here in the comments or on twitter with the hashtag #mustreadphylo.

Bull, J. J., Huelsenbeck, J. P., Cunningham, C. W., Swofford, D. L., & Waddel, P. J. (1993). Partitioning and combining data in phylogenetic analysis. Systematic Biology, 42(3), 384–397.

Cavalli-Sforza, L. L., & Edwards, a W. F. (1967). Phylogenetic analysis. Models and estimation procedures. The American Journal of Human Genetics, 19, 233–257.

Edwards, S. V. (2009). Is a new and general theory of molecular systematics emerging? Evolution, 63, 1–19.

Felsenstein, J. (1973). Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Systematic Biology, 22, 240–249.

Felsenstein, J. (1978). Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology, 27, 401–410.

Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17, 368–376.

Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783–791.

Felsenstein, J. (1985). Phylogenies and the comparative method. American Naturalist, 125, 1–15.

Goldman, N. (1993). Statistical tests of models of DNA substitution. Journal of Molecular Evolution, 36, 182–198.

Hillis, D. M., & Bull, J. J. (1993). An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis. Systematic Biology, 42, 182–192.

Holder, M., & Lewis, P. O. (2003). Phylogeny estimation: traditional and Bayesian approaches. Nature Reviews. Genetics, 4, 275–284.

Kumar, S., Filipski, A. J., Battistuzzi, F. U., Kosakovsky Pond, S. L., & Tamura, K. (2012). Statistics and truth in phylogenomics. Molecular Biology and Evolution, 29, 457–472.

Maddison, W. P. (1997). Gene Trees in Species Trees. Systematic Biology, 46, 523–536.

Pauling, L., & Zuckerkandl, E. (1963). Chemical paleogenetics. Acta Chem. Scand, 17, S9 – S16.

Sullivan, J., & Swofford, D. (1997). Are Guinea Pigs Rodents?? The Importance of Adequate Models in Molecular Phylogenetics. Journal of Mammalian Evolution, 4, 77–86.

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