Lee & Hasegawa (2011) use phylogenetic methods to trace the origins of Japonic languages and dialects. Two hypotheses are considered: First, the farming/language dispersal hypothesis posits that the main factor for the divergence of genetic and linguistic diversity was agricultural expansion. Second, the diffusion/transformation hypothesis posits that cultural innovations such as farming can diffuse between societies, and so genetic and linguistic diversity should not be linked. The estimate of the common linguistic ancestor was in accordance with the farming/language dispersal hypothesis, again suggesting that that linguistic diversity followed genetic diversity.
The study is notable in considering dialects as well as languages and using etymology dictionaries to reconstruct forms from Middle and Old Japanese. The analysis is also done with their own reconstructions and another, unrelated set. The technique is similar to that used by Russel Gray et al. (2009) to study Pacific settlement patterns.
Lee S, & Hasegawa T (2011). Bayesian phylogenetic analysis supports an agricultural origin of Japonic languages. Proceedings. Biological sciences / The Royal Society PMID: 21543358
Gray, R., Drummond, A., & Greenhill, S. (2009). Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement Science, 323 (5913), 479-483 DOI: 10.1126/science.1166858