Bayesian phylogenetic analysis of Philippine languages supports a rapid migration of Malayo-Polynesian languages and complex patterns of post-migration contact and migration.

The Philippines are central to understanding the expansion of the Austronesian language family from
its homeland in Taiwan. It remains unknown to what extent the distribution of Malayo‑Polynesian
languages has been shaped by back migrations and language leveling events following the initial
Out‑of‑Taiwan expansion. Other aspects of language history, including the effect of language
switching from non‑Austronesian languages, also remain poorly understood. Here we apply Bayesian
phylogenetic methods to a core‑vocabulary dataset of Philippine languages. Our analysis strongly
supports a sister group relationship between the Sangiric and Minahasan groups of northern Sulawesi
on one hand, and the rest of the Philippine languages on the other, which is incompatible with a
simple North‑to‑South dispersal from Taiwan. We find a pervasive geographical signal in our results,
suggesting a dominant role for cultural diffusion in the evolution of Philippine languages. However, we
do find some support for a later migration of Gorontalo‑Mongondow languages to northern Sulawesi
from the Philippines. Subsequent diffusion processes between languages in Sulawesi appear to have
led to conflicting data and a highly unstable phylogenetic position for Gorontalo‑Mongondow. In
the Philippines, language switching to Austronesian in ‘Negrito’ groups appears to have occurred at
different time‑points throughout the Philippines, and based on our analysis, there is no discernible
effect of language switching on the basic vocabulary