Problems regarding the "phylogenetic" analysis of language evolution

In my brief exposition, I will present (a) some of the reasons why historical-comparative linguists have been reluctant to adopt phylogenetic methods regularly used in other disciplines, and (b) some of the reasons why I think linguistics can benefit from considering such methods and perhaps even contribute to the refinement of such methods. One problem is the pervasiveness of "horizontal transmission", i.e. the effects of language contact, which can make it difficult or even impossible to arrive at a strictly cladistic account of language differentiation. Traditionally, linguists have used painstaking methods that give very accurate answers to certain questions (e.g. relative chronology of phonetic changes), but that leave many questions unanswered, and are (at least possibly) inapplicable beyond a relatively shallow time-depth (say, around 10,000 years). If historical linguistics is to break through this "time barrier", it is essential to consider methods that provide approximations at greater time-depths, even if the results of applying these methods are less solid than those linguists have been accustomed to considering.