Restriction fragment length polymorphisms reveal considerable nuclear divergence within a well-supported maternal clade in Allium section Cepa (Alliaceae)

Maternal phylogenies estimated by restriction fragment length polymorphisms (RFLPs) in the chloroplast DNA (cpDNA) delineated a well-supported clade containing Allium altaicum, A. cepa (bulb onion), A. fistulosum (Japanese bunching onion), A. galanthum, and A. vavilovii. Few polymorphic restriction-enzyme sites were detected among the wild and cultivated species within this clade, and relationships could not be confidently estimated. Random nuclear RFLPs revealed considerable variation among these species and three distinct groups were identified (Altaicum, Cepa, and Galanthum). Relationships were estimated using principal components and cluster analyses of the Jaccard's similarity matrix. For five out of six analyses, nuclear phylogenies estimated by UPGMA and neighbor joining of the Jaccard's similarity matrix produced a weakly supported monophyletic lineage for A. altaicum, A. fistulosum, and A. galanthum, disagreeing with maternal phylogenies that produced a weakly supported monophyletic lineage for A. altaicum, A. fistulosum, A. cepa, and A. vavilovii. Allium oschaninii was closely related to A. galanthum and these two species may represent the progenitor types. Overall, restriction-enzyme analyses of the nuclear and cpDNA produced few synapomorphies among closely related species in Allium section Cepa