THE TORTOISE AND THE HARE - CHOOSING BETWEEN NONCODING PLASTOME AND NUCLEAR ADH SEQUENCES FOR PHYLOGENY RECONSTRUCTION IN A RECENTLY DIVERGED PLANT GROUP

Phylogenetic resolution is often low within groups of recently diverge d taxa due to a paucity of phylogenetically informative characters. We tested the relative utility of seven noncoding cpDNA regions and a pa ir of homoeologous nuclear genes for resolving recent divergences, usi ng tetraploid cottons (Gossypium) as a model system. The five tetraplo id species of Gossypium are a monophyletic assemblage derived from an allopolyploidization event that probably occurred within the last 0.5- 2 million years. Previous analysis of cpDNA restriction site data prov ided only partial resolution within this clade despite a large number of enzymes employed. We sequenced three cpDNA introns (rpl16, rpoC1, n dhA) and four cpDNA spacers (accD-psaI, trnL-trnF, trnT-trnL, atpB-rbc L) for a total of over 7 kb of sequence per taxon, yet obtained only f our informative nucleotide substitutions (0.05%) resulting in incomple te phylogenetic resolution. In addition, we sequenced a 1.65-kb region of a homoeologous pair of nuclear-encoded alcohol dehydrogenase (Adh) genes. In contrast with the cpDNA sequence data, the Adh homoeologues yielded 25 informative characters (0.76%) and provided a robust and c ompletely resolved topology that is concordant with previous cladistic and phenetic analyses. The enhanced resolution obtained using the nuc lear genes reflects an approximately three- to sixfold increase in nuc leotide substitution rate relative to the plastome spacers and introns .