Using first-principles modeling, we investigate how phonon transport evolves in layered/van der Waals materials when going from 3D to 2D, or vice versa, by gradually pulling apart the atomic layers in graphite to form graphene. Focus is placed on identifying the features impacting thermal conductivity that are likely shared with other layered materials. The thermal conductivity κ of graphite is found to be lower than that of graphene mainly due to changes in the phonon dispersion driven by van der Waals coupling. Specifically, as the atomic layers are brought closer together, the acoustic flexural phonons in graphene form low-energy optical flexural phonons in graphite that possess lower in-plane velocities, density-of-states and phonon occupation, thus reducing κ. Similar dispersion changes, and impact on thermal conductivity, can be expected in other van der Waals materials when transitioning from 2D to 3D. Our findings also indicate that the selection rules in graphene, which reduce phonon-phonon scattering and contribute to its large κ, effectively hold as the atomic layers are brought together to form graphite. While the selection rules do not strictly apply to graphite, in practice similar scattering behavior is displayed due in part to the weak inter-layer coupling. This suggests that van der Waals materials, in bulk 3D form, may have lower phonon-phonon scattering rates than other non-layered bulk materials.