Figure 1.

Null hypothesis for sequence evolution in allopolyploids. (A) Phylogenetic history of diploid (A- and D-genome) and allopolyploid cotton species, as inferred from multiple lines of evidence (32–34). Allopolyploid cottons formed 0.5–2 mya from hybridization between A-genome and D-genome diploids, which diverged from each other ca. 5–10 mya. (B) Phylogenetic expectations of independence and equal rates of sequence evolution following allopolyploid formation. Shown are phylogenetic relationships between sequences from diploid progenitor ge-nomes (A and D) and their orthologous counterparts (A_T and D_T) in derived allopolyploids. G. kirkii serves as the outgroup (32) for testing both rate equivalence and independence. (C) An accelerated rate of sequence evolution in allopolyploids will generate longer branches leading to A_T and/or D_T than to A and D. (D) Concerted evolutionary forces may lead to nonindependent sequence evolution after allopolyploidization. Illustrated is conversion of an A-subgenome homoeologue to a D-subgenomic form, as has been demonstrated for ribosomal genes in allotetraploid Gossypium (20).