Limitations of the phylogenetic method
Comparison with previous analyses
The accuracy of linguistic phylogenetic trees depends heavily on the properties of the data matrix (Pompei et al., 2011). The reliability of the data matrix in turn can be affected by rapidly mutating words, the varying rate of change of meanings and undetected borrowing. Words that mutate at a very rapid rates and meanings in a language that transform at differing rates can result in the disproportionality of language distance and evolutionary distance. Furthermore, undetected borrowing can look like shared ancestry but it is actually information flowing horizontally between languages. These factors may pose as confounds to language trees and researchers may fail to account for these factors if caution is not taken.
Use of Simulations
Even though the generation of data could provide us a correct simulated phylogenetic tree, it does, however, suffers from the fact that the true evolution remains unknown as it only provides us a probable scenario of how languages have evolved over the years. There is a limit to how far back in time we can trace the evolution of languages and this will pose as a striking limitation.
In addition, researchers tend to evaluate the methods on a language family that is most common to them, which may be a disadvantage for languages in other language families.