Discordance Between ITS and Chloroplast Topologies in the Boykinia Group (Saxifragaceae)

Abstract

To assess whether discord exists between nuclear- and chloroplast-based phylogenetic trees within the Boykinia group (Saxifragaceae), we compared topologies obtained from analyses of ITS sequences with those acquired earlier via analyses of cpDNA restriction sites and matK sequences. We found manual alignment of sequences in the Boykinia group to be extremely difficult; we therefore explored different alignment strategies using CLUSTAL W and assessed the impact of different gap-open and gap-extension weights. To accomodate the multiple alignments possible with our ITS data set, we also employed the elision approach. Both cpDNA and matK sequences provide essentially identical topologies for the Boykinia group and differ from the ITS trees only in the placement of Suksdorfia ranunculifolia. The chloroplast trees place S. ranunculifolia as sister to Boykinia; in the ITS trees, S. ranunculifolia appears in a clade with S. violacea and Bolandra, a placement in agreement with morphology. The chloroplast-based and nuclear-based positions for S. ranunculifolia are each strongly supported, having high bootstrap values. This discordance could be the result of ancient hybridization and chloroplast capture between S. ranunculifolia and a species of Boykinia, resulting in chloroplast-based topologies that do not accurately reflect organismal relationships.