Conflict and complementarity of paleontological and molecular chronologies?

Evolutionary history studies depend on having reliable chronologies of macroevolutionary processes. Construction of such chronologies often yields discrepancies between paleontological and molecular dates, which are sometimes viewed as conflicting. Nevertheless, each macroevolutionary process is composed of two main phases: emergence of a trait or clade and success of that trait or clade, which differ in mechanisms, drivers, and types of evidence. Moreover, emergence may be observed as gene divergence (which may be trait-coding or trait-unrelated genes), trait emergence, and clade emergence; whereas success can be observed as increase in abundance, diffusion, and/or diversity or as overall persistence over geologic time. Therefore, to fully and correctly understand any macroevolutionary process, it is of paramount importance to understand what event each date refers to, and how dates of various events and their integration reveal the complexity of macroevolutionary processes. I demonstrate this through three examples: the chronological gap between oxygenic photosynthesis emergence and the Great Oxidation Event, the chronological gap between paleontological and molecular dates of angiosperm emergence, and the evolution of plant silicon accumulation.