@ARTICLE{TreeBASE2Ref15990, author = {Robert K Jansen and Kent E. Holsinger and Helen J. Michaels and Jeffrey D. Palmer}, title = {Phylogenetic analysis of chloroplast DNA restriction site data at higher taxonomic levels: an example from the Asteraceae.}, year = {1990}, keywords = {}, doi = {}, url = {}, pmid = {}, journal = {Evolution}, volume = {44}, number = {}, pages = {2089--2105}, abstract = {Chloroplast DNA variation was examined among 57 genera of Asteraceae representing 15 currently recognized tribes. Complete cleavage maps were constructed for 11 six-base pair restriction enzymes, and a total of 927 cleavage site differences was detected, 328 of which are phylogenetically informative. The data were used to construct phylogenetic trees using both Wagner and Dollo parsimony and the resulting monophyletic groups were evaluated statistically using the bootstrap method. The level of homoplasy in the restriction site data is 54-56% (excluding autapomorphies), most of which is due to parallel site losses. The most parsimonious trees generated by both parsimony methods have nearly identical topologies at lower taxonomic levels, but differ in subfamilial circumscriptions and tribal groupings. Dollo parsimony provides support for the monophyly of two subfamilies, the Lactucoideae (excluding the Barnadesiinae) and Asteroideae, but Wagner parsimony supports the monophyly of the Asteroideae only. This incongruence is due to different assumptions of the two parsimony methods about relative rates of parallel site gains and losses. After eliminating the six most rapidly changing restriction sites or performing successive approximation, Wagner parsimony produces trees with the same subfamilial groupings as the Dollo trees. We conclude that the Dollo tree with two monophyletic subfamilies is the best estimate of phylogenetic relationships in the Asteraceae because this method more accurately reflects the evolution of restriction sites. We also demonstrate that in spite of high levels of homoplasy in chloroplast DNA restriction site data at these higher taxonomic levels, it is possible to make statistically supported estimates of phylogenetic relationships.} }

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