I think many interesting tools developed by people in phylodynamics are largely underutilized in other branches of evolutionary biology. Indeed, many models might be useful in analyzing processes at macroevolutionary scales. Still, these tools were designed to study viral evolution: viral phylodynamic data typically contain high temporal and spatial information (well, we can track the process itself in a real-time process in many cases), enabling the use of parameter-rich models like complex diffusion models. Unfortunately for the long-term macroevolutionary processes, we often lack such informativeness, and thus the data might not have enough power for parameter inference, leading to nonsensical results.

However, I do think that these approaches might be effective, at least for some types of clades, if their dispersal dynamics are not so complicated and species are well sampled, although further simulation study and empirical validation might be needed to completely justify their uses.

I am not an expert on this topic and my suggestions might not be optimal but I think these studies might be useful to start your investigation on applying diffusion-type models in biogeography at a macroevolutionary scale:

Article Phylogenetic Biogeography Inference Using Dynamic Paleogeogr...

Article Phylogeographic Estimation and Simulation of Global Diffusiv...

I hope this helps.

@Wonseop Lim

Thanks for your opinion. Then I plan to make some horizontal comparisons of each methods to check if they can be applied to my area.