In addition to being used for identifying taxa and detecting rare cytotypes, FCM may be useful for reconstructing relationships and developing phylogenetic hypotheses in taxonomic groups with polyploids. The direction of polyploid evolution is, with few exceptions (e.g. haploid parthenogenesis), unidirectional, leading from diploidy to higher ploidies. Based on this assumption (aneuploid changes notwithstanding), it could be predicted that polyploid genomes have arisen more recently in mixed-ploidy clades. Therefore, ploidy estimates may be used to establish relationships within taxonomic groups. It should, however, be noted that the value of ploidy alone as a phylogenetic marker should be used cautiously and ideally in concert with independent sources of phylogenetic data, as there are numerous reports of polyploidy having multiple origins, even within species (Soltis and Soltis 1993, 1999).
Although little explored as yet, FCM can also be useful for tracing progenitors of polyploid taxa through genome size analysis (Leitch and Bennett 1997). For example, in allopolyploid, triploid banana cultivars, Lysak et al. (1999) demonstrated about 12% difference in DNA amount between their component genomes A (donated from Musa acuminata; Musaceae) and B (donated from M. balbisiana), and proposed that comparative analysis of genome size may be helpful in identifying putative diploid progenitors of cultivated triploid Musa clones. Similarly, hexaploid wheat comprises three different diploid genomes: the D genome (2C = 5.05 pg) seems to contain less DNA than both A (2C = 6.15 pg) and B (2C = 6.09 pg) genomes (Lee et al. 1997). In addition, differences in genome size within Hieracium subg. Pilosella (Asteraceae; Brautigam and Brautigam 1996) can be used as a clue for clarification of species relationships, identification of putative parents and genomic constitution in hybridogenous taxa (J. Suda et al., unpublished data). However, the general efficacy of this application will depend on the extent of homoeologous crossing over and genome restructuring, which may cause the component genomes in the allopolyploid to diverge quantitatively from the ancestral diploids.
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