The information content and degree of homoplasy for indels is investigated using four non-coding regions, two chloroplast (trnL-trnF, atpB-rbcL) and two nuclear DNA intergenic spacers (nrDNA: ITS1, ITS2). The evolution of indels is characterized for the family Rhizophoraceae. To produce a well supported phylogeny to test the various strategies, we constructed a tree using the combined information of seven data sets (rbcL, atpB-rbcL spacer, trnL-trnF sapcer, ITS1, 5.8S, ITS2 and morphology). A subset of 14 taxa for which the complete sequences were available include members of all three tribes (Rhizophoreae, Macarisieae, Gynotrocheae) as well as the sister family Erythroxylaceae. The evolution of indels is then interpreted in the context of this well-supported phylogeny. We distinguished two types of indels: duplications/insertions of sequences containing more than one type of nucleotide and runs of one type of nucleotide. We address the following questions. 1. What proportion do the different types contribute to the total number of indels? 2. Is the length of the indel correlated with the degree of homoplasy? 3. Do homoplastic indels more often occur on deeper branches or in the tips of trees? 4. Do chloroplast indels differ in their behavior from nuclear indels? We were also using different coding strategies to test which minimizes the amount of homoplasy and maximizes the phylogenetically informative information.

Key words: homoplasy, indels, Rhizophoraceae