Bruce Bower of Science News enters an article covering the last year of application of phylogenetic methods to questions of language evolution: "Darwin's Tongues".
He gives a description of work by Quentin Atkinson and Russell Gray and colleagues, which have attempted to place the origination of modern human languages (in Africa, naturally), and separately have challenged the Chomskian assertion that human languages are constrained by deep structure. A number of linguists challenge these conclusions, and Bower describes the debates ably.
Others suspect Atkinson’s analytical approach could be fruitful if informed by more sophisticated assumptions about how languages change. “I think many linguists would praise Atkinson’s contribution if it weren’t for the fact that his conclusions are so outlandish and contrary to linguistic intuition,” says linguist Michael Cysouw of Ludwig Maximilians University Munich in Germany.
I think criticism of these approaches is in the "throw everything and see what sticks" phase. I've seen it before, in the modern human origins arena. In this phase, many of the criticisms lack force -- they emerge from skepticism about the conclusions, not necessarily an understanding of the method. That means the method has not yet been described in ways sufficient for linguists to understand its limitations, nor has it been applied in contexts where the answer is already well known from other approaches. Personally, I think the phylogenetic methods being applied to linguistic corpus data are statistically very useful and powerful, but that doesn't mean the alternative hypotheses have been differentiated cleanly from each other.