The two major approaches to studying macroevolution in deep time are the fossil record and reconstructed relationships among extant taxa from molecular data. Results based on one approach sometimes conflict with those based on the other, with inconsistencies often attributed to inherent flaws of one (or the other) data source. Any contradiction between the molecular and fossil records represents a failure of our ability to understand the imperfections of our data, as both are limited reflections of the same evolutionary history. We therefore need to develop conceptual and mathematical models that jointly explain our observations in both records. Fortunately, the different limitations of each record provide an opportunity to test or calibrate the other, and new methodological developments leverage both records simultaneously. However, we must reckon with the distinct relationships between sampling and time in the fossil record and molecular phylogenies. These differences impact our recognition of baselines and the analytical incorporation of age estimate uncertainty.