Molecular marker incongruence in plant hybrid zones and phylogenetic trees

One of the striking observations from the young field of molecular evolutionary biology has been the high frequency of cases where taxon-specific markers are found to differ widely in both phylogenetic and geographic distribution. This pattern has been observed most frequently when cytoplasmic markers are compared with those of nuclear origin (Rieseberg & Soltis 1991), but similar observations are often made for comparisons among markers of nuclear origin only (Rieseberg & Ellstrand 1993). These observations are important to phylogenists because they provide ‘footprints’ of past evolutionary events, information that may be critical to elucidating true organismal phylogeny. Marker incongruence also is significant to the evolutionist because it may provide insights into the differences in the evolutionary biology of organellar versus nuclear genes (as well as differences among nuclear genes), the role of selection, linkage and recombination in controlling the frequency and spatial distribution of introgressed genes, and the effects of introgression on the maintenance of species differences. In this paper, we list some of the best examples of molecular marker incongruence from both hybrid zones and phylogenetic trees in plants. General patterns emerging from this tabulation are discussed, and possible explanations are briefly summarized. In addition, recent studies of differential introgression and its mechanistic basis in wild sunflowers of the genus Helianthus are reviewed in detail. Results from these studies appear to explain patterns of marker discordance in Helianthus, and possibly many other groups of plants as well.