Overall, this is a quality study. The incorporation of extinct lineages into phylogenetic models of historical biogeography is essential, and the LEMAD method seems appropriate for investigating the evolution of clades in many-region systems like Southeast Asia. I have only a few comments to improve the clarity of the manuscript.

1. Because the LEMAD method is essential to the study’s findings, it is important to explain how the model parameterizes rates (compared to GeoSSE). In particular, [Line 339] mentions that LEMAD makes several simplifying assumptions. It would be helpful to list these assumptions, and to clarify that LEMAD allows for instantaneous extinction of widespread lineages.

2. Because of the simplifying assumptions of LEMAD, it is unclear why the maximum range size needs to be limited to 3 regions. If it is computationally feasible, it would be worth increasing the maximum range size, especially since the ancestral state reconstructions under moderate extinction rates all include the maximum allowed number of regions. An unconstrained model may support even larger ancestral ranges.

3. A complicated and fluctuating system like Southeast Asia is likely to violate many of the assumptions of LEMAD (eg. equal rates, time constancy). To be clear, I do not think that these model violations invalidate the results. However, it is essential to explore some of these caveats in the discussion section.

Minor Comments:

1. Because the introduction focuses heavily on the updated paleogeography of Southeast Asia, readers may expect a biogeographic model that incorporates this paleogeographic information, which LEMAD does not do. It would be helpful to clarify this point early on.

2. Both between-region and within-region speciation events could be “geographically mediated” at different scales. It may be helpful to define the term “in-situ speciation” and clarify that a within-region speciation event does not necessarily imply a non-geographic mechanism.

3. It is logical that high extinction rates would lead to fewer widespread ranges, but it is unclear why this should also be accompanied by low rates of range expansion for extant lineages. [Line 270]

4. It is unclear why an island becoming devoid of all species is significant. [Line 275]