Phylogenetic and Population Genetic

Methods in the Cunningham Lab

 

6-parameter Parsimony

This little-used but useful method allows each substitution type to be weighted differently in a dynamically weighted parsimony framework. It is most useful among closely related taxa, where maximum likelihood has very little information to work with. The method was pioneered by Walter Fitch, and further developed in the following papers (click for pdf's)

C. W. Cunningham, 1997a. Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods. Systematic Biology 46: 464-478

Stanger-Hall, K., and C. W. Cunningham. 1998. Support for a monophyletic Lemuriformes: Overcoming incongruence between data partitions. Molecular Biology and Evolution 15:1572-1577.

 

Click for instructions for making and using 6-P stepmatrices

 

To download Excel spreadsheet either right click here and download to disk (Windows),

or click and hold here until you get option to download to disk (Mac)

 

Ancestral State Reconstruction

This lab has produced a series of papers exploring the limitations of ancestral reconstruction methods (click for pdfs)

C.W. Cunningham, K. Omland , and T. Oakley 1998. Reconstructing ancestral states, a critical reappraisal. Trends in Ecology and Evolution 13: 361-368.

Cunningham, C. W. 1999. Some limitations of ancestral character state reconstruction when testing evolutionary hypotheses. Systematic Biology 48:665-674.

Oakley, T. and Cunningham, C. W. 2000. Ancestor state reconstruction fails where independent contrasts succeed in a known viral phylogeny. Evolution 54:397-405.

 

Experimental Phylogenetics

C. W. Cunningham, K. Jeng, J. Husti, M. Badgett, I. Molineux, D. M. Hillis, and J. J. Bull. 1997. Parallel molecular evolution of deletions and nonsense mutations. Molecular Biology and Evolution 14(1):113-11614

C.W. Cunningham, H. Zhu and D. M. Hillis 1998. Best-fit maximum likelihood models for phylogenetic inference: Empirical tests with known phylogenies. Evolution 52:978-987

Oakley, T. and Cunningham, C. W. 2000. Ancestor state reconstruction fails where independent contrasts succeed in a known viral phylogeny. Evolution 54:397-405.

Buckley, T. R., and C. W. Cunningham 2002. The Effects of Nucleotide Substitution Model Assumptions on Estimates of Nonparametric Bootstrap Support. Molecular Biology and Evolution 39:394-405

Experimental Population Genetics

Hahn, M. W., M. D. Rausher, and C. W. Cunningham. 2002. Distinguishing Between Selection and Population Expansion in an Experimental Lineage of Bacteriophage T7. Genetics 161:11-20