Intraspecific phylogeny analysis using ITS sequences: insights from studies of the Streptanthus glandulosus complex (Cruciferae)

Within many lineages diversity of the internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes has proven comparable to that of restriction sites of chloroplast DNA (cpDNA). Although cpDNA polymorphism has proven useful in many phylogenetic studies at the intraspecific level, the utility of ITS sequences in this application has been subjected only to limited testing. The Streptanthus glandulosus complex is an ideal candidate for this evaluation, given the substantial variation in cpDNA restriction site and enzyme electrophoretic markers present among populations. ITS sequences were obtained for 31 populations within the complex; phylogenetic patterns derived from these data were compared to a cpDNA phylogeny based on restriction site data from a previous study. No population exhibited the same ITS sequence, and average divergence among populations was 2.57%. The ITS strict consensus tree bears clades that are geographically distinct, but lacking in internal resolution; we suspect that some combination of gene flow, lineage sorting, and recombination has led to low resolution within these major clades. The ITS tree shares many features with the cpDNA tree, but the two also display substantial incongruities, including one that may have arisen via cytoplasmic introgression. Greater consistency is exhibited by the cpDNA tree most likely due to the haploid and non-recombining nature of the chloroplast genome. Combining the ITS and cpDNA data results in a more highly resolved tree than those from either of the separate analyses. Despite the pitfalls of using a diploid, recombining data source like ITS at the intraspecific level, potential benefits include tracking of maternal and paternal lineages as well as insight into patterns and levels of gene flow among populations. Furthermore, the joint use of ITS and cpDNA markers facilitates independent assessment of intraspecific phylogenetic hypotheses and can expose cases in which introgression or phylogenetic sorting has caused incongruencies among haplotype trees.