Phylogenetics in Clarkia (Onagraceae): Restriction Site Mapping of Chloroplast DNA

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Abstract
Restriction site maps of chloroplast DNA (cpDNA), maternally inherited in Clarkia, were obtained in representative species of all seven diploid sections, the allotetraploid sect. Clarkia, and the outgroup Epilobium brachycarpum. CpDNA restriction site variation was analyzed by Wagner and Dollo parsimony, bootstrapping, and genetic distance methods. Four shortest Wagner trees, one of which was also the shortest Dollo and Bootstrap majority-rule tree, were examined along with 21 one-step longer trees. Section Myxocarpa was placed as basal in Clarkia followed by a trichotomy of the Rhodanthos lineage, the Eucharidium/Clarkia lineage, and the lineage including sects. Sympherica, Phaeostoma, Fibula, and Godetia. However, when trees only one step longer are considered, many of these ectional alignments are lost. Early and rapid divergence of most sectional lineages, coupled with higher rates of cpDNA restriction site homoplasy, is proposed to account for the lack of many synapomorphic restriction site characters at the sectional level in Clarkia. A comparison of the cpDNA results to morphology, cytology, and biogeography with respect to intersectional relationships is presented. Diploid sect. Fibula, previously believed to have originated through intersectional crossing between sects. Phaeostoma and Sympherica, has a chloroplast genome similar to one species of sect. Phaeostoma. Monophyletic lineages as previously described on the basis of the distribution of duplicated PGI genes are supported, but not fully so. The origin of the allotetraploid C. pulchella involved sect. Eucharidium as the maternal diploid parent and sect. Myxocarpa as the paternal diploid parent. The origin of C. pulchella was ancient, predating the divergence of the two extant species of sect. Eucharidium.