JEFFERY, J.E.*; BININDA-EMONDS, O.R.P.; COATES, M.I.; RICHARDSON, M.K.: Using Heterochrony to Reconstruct Phylogeny

Numerous studies have shown that change in the sequence of development is a widespread phenomenon in vertebrate evolution. However, these heterochronies are usually examined on pre-existing phylogenies, rather than used as data for phylogenetic reconstruction. Before such data can be used in reconstruction, some serious methodological difficulties must be overcome: heterochrony can alter sequences to such an extent that simple timing comparisons are impossible. Practical difficulties in observing development means that there are likely to be missing data. Also, vertebrate development seldom produces fully resolved sequences – two or more developmental events may occur simultaneously. This simultaneity may be real (‘hard’) or may be an artefact caused by insufficient observations (‘soft’). Most existing methods of sequence comparison cannot be applied in these circumstances. Therefore, we have adapted a method orignally used for phylogenetic analysis of mitochondrial gene-order. ‘Breakpoint’ analysis produces a distance metric for two sequences (A and B), based on the minimum number of changes (breaks) needed to make A match B. By calculating the distances between all the sequences under study, a distance matrix can be built up. This can be subjected to a phylogenetic analysis using standard techniques. If data are missing from one or more sequences, comparisons can be ‘rescaled’ to account for the reduced number of events. Hard simultaneities may be included using a similar process. Soft simultaneities are more difficult to include, but we are currently researching possible techniques.