Character coding and phylogenetic methods

      General and theoretical issues in systematics arise frequently when one is involved in empirical projects.  Sometimes these are worth pursuing on their own, as they can provide a meaningful contribution to our field.

      With post-doc Mark Simmons, I have been working on a number of theoretical issues in character coding and methods used in systematics.  These projects have included a consideration of composite character coding vs. reductive coding, looking at the costs and benefits of the two approaches.  This was then focused into a comparison of coding amino acids and nucleotide characters, which built on a particular interest of Mark's (see Cladistics 16 (3): 274-282).  We have also investigated the behavior and claims of RASA, a method put forth to assess phylogenetic signal in data sets.  An analysis of how DNA alignment is affected by varying distance among taxa revealed that too few gaps are typically inserted in alignments of ITS sequences when the distance between taxa is great.  We expanded on Mark's idea of "Uninode Coding" (Molecular Biology and Evolution 17: 469-473) and compared it with the method of Rod Page for reconciling trees.

      I have also dealt with issues such as coding of insertions-deletions (Systematic Botany 26: 643-657) and the nature of monophyletic taxa (Taxon 47: 95-104).