A comparison of global, gene-specific, and relaxed clock methods in a comparative genomics framework: dating the polyploid history of soybean (Glycine max).

A mixed model nested analysis of variance testing the effects of framework, method, and gene found that framework had a significant effect on the divergence date estimates but that most variation among dates is due to variation among genes, suggesting a need to further characterize and understand the evolutionary phenomena underlying rate variation within genomes, within genes, and across lineages.