Reconstructing hybrid speciation using sequences of low copy nuclear genes:: Hybrid origins of five Paeonia species based on Adh gene phylogenies

Alcohol dehydrogenase (Adh) genes were amplified with PCR, cloned, and sequenced for five putative hybrid species of the genus Paeonia (Paeoniaceae): P. sinjiangensis, P. arietina, P. humilis, P. officinalis, and P. parnassica. Two to three diverged types of sequences were found at each of the Adh1A and Adh2 loci for each species. Parsimony analyses of these sequences together with previously obtained Bih sequences of non-hybrid species of Paeonia indicated that two major types of Adh sequences of each of the five species were phylogenetically separated on the Adh1A and Adh2 trees. Along with nrDNA and cpDNA phylogenies, it is most parsimonious to hypothesize that these diverged sequences represent alleles derived from different parents through hybrid speciation. The approach of separating parental alleles of a nuclear gene in a hybrid genome and reconstructing phylogenies of these alleles offers a solution to the long standing methodological difficulty of reconstructing reticulate evolution. Phylogenies of plant nuclear genes, however, may be confounded by dynamic evolutionary processes of the gene families, such as gene duplication/deletion, gene conversion, and recombination. Thus, a strong hypothesis of hybrid speciation should rely on the congruence of multiple gene phylogenies as well as the congruence between gene phylogenics and other lines of evidence.