Just so you know, I am not blowing off your recommendation to read Rexová. In fact, I’m looking into the flurry of work of which Rexová is an example in some detail. I’ll probably write a post about the issues raised by this body of work in the not-too-distant future.

I look forward to reading your post on MMLC and subgroupings.

Just to be clear, I have no complaints about the genetic analysis in GVPSNA. I am far too ignorant about the issues to have any opinion one way or another about the suitability of neighbor-joining and the like. I am also clear on the fact that the population trees presented in the paper are not based on linguistic classifications. After all, the point is to treat genetic relatedness and linguistic relatedness as independent variables and see how the two measures coincide or not.

My point is a much more narrow one: that the method by which that the authors of GVPSNA arrive at their measure of linguistic relatedness would not accepted by most Americanist historical linguists.

Right. I think that the point that was not clear to the authors [...]

Agreed.

There is no restriction, in principle, on the number of languages for which one can construct cognate sets and correspondence sets.

Indeed there isn’t any in theory, but there is one in practice. In biology, the method was made so explicit in 1950 that it can be used in computers. Lying next to me I have a paper that did a phylogenetic analysis with 3297 nucleotides of a gene of 88 species. The simplest method they used produced the two shortest trees ( = the ones that require the smallest number of assumptions) that explain the enormous dataset and contain, as part of the tree-building process, complete reconstructions of every single node; the authors don’t mention how long the calculation took, but based on my experience with much smaller datasets, I suppose it took a few hours to at most a day. Imagine comparing 88 languages within that time, including a complete reconstruction of their phylogeny and a complete reconstruction of each node.

Now, of course, this was a molecular dataset; from sequencing to analysis, it may have taken six weeks (apart from the fact that the authors downloaded most sequences from GenBank rather than sequencing the genes themselves). Compiling morphological (anatomical) dataset of, say, 150 taxa and 400 characters is a Ph.D. thesis. The analysis itself, however, is a matter of hours.

perhaps historical linguists could learn something from their biological colleagues, as you suggest.

Would be the first time, though! :o)

Have you read the paper by Rexová et al. (2004) in Cladistics? (It’s a cladistic analysis of Indo-European.) If not, I can send you the pdf.

Comments on your comments:

No method can do that a priori, apart from recognizing the most obvious cases of onomatopoeia and the most obvious loans. You have to reconstruct the tree and then look at the distribution of the a-priori similarities on the tree to see whether they are cognate or not.

Right. I think that the point that was not clear to the authors of the original article is that mass/multilateral comparison has no analytical means for distinguishing true cognates from false ones, whereas the comparative method does (even if it is not, in your terms, an a priori method).

It can only compare very few languages at once and lacks a clear optimality criterion (which is parsimony in the case of cladistics).

I’m not sure I agree with your claim that the comparative method can only compare a few languages at a time. There is no restriction, in principle, on the number of languages for which one can construct cognate sets and correspondence sets. But maybe I am misunderstanding you…

But I am intrigued by the possibility of developing computational tools to aid reconstruction and classification — perhaps historical linguists could learn something from their biological colleagues, as you suggest.

Probably the best work to consult would be Lyle Campbell’s book, which I include in the references at the end of my post. Not only is the classification in that book the most widely accepted by Americanists, but Campbell also provides extensive discussion of other classificatory proposals (including Greenberg’s) and the methodological and theoretical issues involved. (A rough measure of linguists’ opinion of the volume is given by the fact that it won the Linguistic Society of America’s annual book prize.)