Evolution of alcohol dehydrogenase genes in peonies (Paeonia): phylogenetic relationships of putative nonhybrid species

Alcohol dehydrogenase genes were amplified by PCR, cloned, and sequencedfrom 11 putative nonhybrid species of the angiosperm genus Paeonia.Sequences of five exons and six intron regions of the Adh gene were used toreconstruct the phylogeny of these species. Two paralogous genes, Adh1A,and Adh2, were found; an additional gene, Adh1B, is also present in sectionMoutan. Phylogenetic analyses of exon sequences of the Adh genes of Paeoniaand a variety of other angiosperms imply that duplication of Adh1 and Adh2occurred prior to the divergence of Paeonia species and was followed by aduplication resulting in Adh1A and Adh1B. Concerted evolution appears to beabsent between these paralogous loci. Phylogenetic analysis of only thePaeonia Adh exon sequences, positioning the root of the tree between theparalogous genes Adh1 and Adh2, suggests that the first evolutionary splitwithin the genus occurred between the shrubby section Moutan and the othertwo herbaceous sections Oneapia and Paeonia. Restriction of Adh1B genes tosection Moutan may have resulted from deletion of Adh1B from the commonancestor of sections Oneapia and Paeonia. A relative-rate test was designedto compare rates of molecular change among lineages based on the divergenceof paralogous genes, and the results indicate a slower rate of evolutionwithin the shrubby section Moutan than in section Oneapia. This may beresponsible for the relatively long branch length of section Oneapia andthe short branch length between section Moutan and the other two sectionsfound on the Adh, ITS (nrDNA), and matK (cpDNA) phylogenies of the genus.Adh1 and Adh2 intron sequences cannot be aligned, and we therefore carriedout separate analyses of Adh1A and Adh2 genes using exon and intronsequences together. The Templeton test suggested that there is notsignificant incongruence among Adh1A, ITS, and matK data sets, but thatthese three data sets conflict significantly with Adh2 sequence data. Acombined analysis of Adh1A, ITS, and matK sequences produced a tree that isbetter resolved than that of any individual gene, and congruent withmorphology and the results of artificial hybridization. It is thereforeconsidered to be the current best estimate of the species phylogeny.Paraphyly of section Paeonia in the Adh2 gene tree may be caused by longercoalescence times and random sorting of ancestral alleles.