Functional divergence of the duplicate genes has been recognized as an important source of evolutionary novelty (Yang et al., 2012). To evaluate potential functional divergence, type I and type II functional divergence between groups of the TPS family were estimated by posterior analysis (Gu and Velden, 2002). For this analysis, the collected plant TPS proteins were used and estimation was based on multiple alignments of proteins for any two groups (Table 2). Previous work proposed several possible evolutionary fates of duplicate genes (Hughes, 1994; Force et al., 1999). Our results showed that most type I coefficients (θI) of functional divergence were significantly greater than zero (P < 0.01), while few of the type II coefficients (θII) was statistically greater than zero. These results suggested that type I functional divergence was the dominant pattern for evolution of TPS family in these plants, and significantly site-specific altered selective constraints should contribute to most of the TPS members which would, after the diversification, cause a group-specific functional evolution.