New World tetraploid cottons contain Old World cytoplasm

New World tetraploid cottons (Gossypium spp.) originated through hybridization of ancestral diploid species that presently have allopatric ranges in Asia-Africa (the A genome) and the New World tropics and subtropics (the D genome). Despite intensive study, the identity of the parental diploids and the antiquity of polyploidization remain unresolved. In this study, variation in the maternally inherited chloroplast genome was assessed among species representing both of the parental genomes and the tetraploids. Approximately 560 restriction sites were assayed in each accession, representing sequence information for about 3200 nucleotides. The resulting maternal phylogeny has no convergent restriction site mutations and demonstrates that the cytoplasm donor for all tetraploid species was an A genome diploid with a chloroplast genome that is similar to Gossypium arboreum and Gossypium herbaceum. No mutational differences were detected between these two species, and few mutations distinguish the chloroplast genomes of A genome diploids from those of tetraploid taxa. In contrast to expectations based on extensive taxonomic, geographic, and genetic diversity, a surprisingly low level of sequence divergence has accumulated subsequent to polyploidization. Chloroplast genomes of tetraploid species are distinguished from each other by between one and six apparent point mutations. The data suggest that tetraploid cotton originated relatively recently, perhaps within the last 1-2 million years, with subsequent rapid evolution and diversification throughout the New World tropics.