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As in many clades of flowering plants, the Quamoclit clade of morning glories (Ipomoea subgenus Quamoclit) exhibits unequal proportions of different flower colors, with pigmented species outnumbering unpigmented species by nearly a factor of 7. We examined three possible macroevolutionary explanations for this pattern: (1) asymmetric transition rates between pigmented and unpigmented flowers; (2) low transition rates preventing the flower colors from reaching equilibrium; and (3) differential diversification. In order to discriminate among these explanations, we employ the newly-developed Binary-State Speciation and Extinction (BiSSE) model, which jointly estimates transition rates among states and the speciation and extinction rates in each state. Using maximum likelihood and Bayesian BiSSE estimation, we find no evidence for asymmetrical transition rates. Also, BiSSE simulations of character evolution demonstrate that there is sufficient time for the estimated transition rates to produce as many or even more white species than we observe in Quamoclit, suggesting that lowtransition rates do not fully account for the paucity of white species. In contrast, we find support for the differential diversification hypothesis with the rate of speciation in pigmented lineages estimated as three-fold greater than the rate in unpigmented lineages. Our analyses thus indicate the low frequency of white-flowered morning glory species is due largely to lineage selection. Our analysis also suggests that estimating character transition rates without simultaneously estimating speciation and extinction rates can lead to greatly biased estimates of transition rates.