Phylogeny, Duplication, and Intraspecific Variation of Adh Sequences in New World Diploid Cottons (Gossypium L., Malvaceae)

The 13 “D-genome”cotton species are a monophyletic assemblage of morphologically diverse diploids that inhabit arid to semiarid regions in Mexico, with 1 disjunct species each in Peru and the Galapagos Islands and 1 species whose range extends northward into Arizona. While these species lack commercially significant fiber (i.e., cotton), they are important in that they represent one of the parental genomes of the cultivated tetraploid cottons. To assess phylogenetic relationships among these species, we sequenced and analyzed a region of a nuclear-encoded alcohol dehydrogenase gene (AdhA). Phylogenetic analysis resulted in a topology that is generally consistent with current taxonomic alignment of the species, although the phylogeny based on AdhA sequences conflicts with those inferred from cpDNA and ITS data sets, most notably in the position of the anomalous species Gossypium gossypioides. In one lineage, we detected both gene duplication and sequence polymorphisms that transcend species boundaries; sequences in this lineage formed a monophyletic clade, yet no taxon within the clade contained a monophyletic collection of sequences. Potential explanations for this latter phenomenon, including gene duplication, gene flow, and lineage sorting, are discussed.