Nuclear intron regions are becoming a promising source of variation in studying closely related species for which ITS data are often inconclusive. We have shown the phylogenetic utility of two such introns, the third intron of Nitrate Reductase (NIA) and the second intron of Leafy (LFY), in seven closely related Hawaiian endemic Scaevola species (Goodeniaceae). The location of these introns is conserved across Angiosperms, and they are often large (>1kb). In Scaevola, these two introns contain considerably more parsimony informative variation (2.8% in NIA and 3.6% in LFY) than in either ITS (1.6%) or Glyceraldehyde 3-Phosphate Dehydrogenase (G3PDH) (0.4%). We compared multiple accessions of each of seven species of Scaevola (S. chamissoniana, S. coriacea, S. gaudichaudiana, S. gaudichaudii, S. kilaueae, S. mollis, and S. procera) for each of these four nuclear regions. The sequences from all four loci were congruent across five of the seven species (excluding S. kilaueae and S. procera). Importantly, the overall phylogenetic relationships of these five species only became apparent when all four regions were combined. This combined matrix demonstrates the effectiveness of utilizing multiple regions when attempting to elucidate closely related species relationships. Additionally, through comparing these data we show that two species, S. procera and S. kilaueae, are sharing alleles across taxa, resulting in incongruence between loci. We hypothesize that S. procera is the result of a homoploid hybridization event between S. gaudichaudii and S. mollis.

Key words: Hawaiian Islands, nuclear introns, Scaevola (Goodeniaceae)