Mr. Gordon has some information to add on the issue of human language affinities. I cannot vouch for its accuracy, but it seems a reasonable example of the kinds of issues and points that are involved. Anyone with other information is welcome to respond to him.
I have to commend you on your article "Genetic Distance and Language Affinities Between Autochthonous Human Populations". It probably is the only decent source of information out on the net so far pertaining to long-range linguistic comparison since much of the net is usually populated by pages full of odd, misinformed theories that are shallowly paradoxical and dare I say schizophrenic. Your article is a good read and I hope to see more sobre talk on the net on this subject soon.
I'm personally an amateur in the field of comparative linguistics but have a vested interest in Nostratic and the illusive Dene-Caucasian (or Sino-Caucasian or Sino-Dene or...). I tend to be conservative in my approach and I never trust what people say at face value until I've logically picked at it and reassembled it again.
As much as I loved your article, there were some curious problems that I noticed concerning your linguistic relationships that you had drawn out. Certain languages seem to be severely misplaced.
The first more obvious one to me is Etruscan. You place it under "Basque-Caucasian" which simply cannot be correct. As far as I have researched, there is a sufficient amount of evidence and support for a close but seperate relationship with Indo-European. That is to say, that Etruscan is most probably a sister language to Proto-Indo-European (cf. the s-genitive (IE *-es), accusative "-n" (IE *-m), "-c" "and" (IE *kwe) etc). Some researchers find the similarities so close that they classify Etruscan as being Anatolian. At the very least, such distinctively Nostratic markers such as "mi" for "I" make it severely unlikely in my view for it to be SinoCaucasian. Allan Bomhard for one classifies Etruscan as Nostratic and he's not the only one.
Another problem is Ainu and the "Siberians" classified under Altaic. Ainu is very distinct from any Altaic language and will never be classified as such. Ainu is often considered to be Sino-Caucasian although I have no information concerning the evidence for this. Secondly, a title like "Siberian" is very vague in meaning. The Ket of C.Siberia for instance are most probably Sino-Caucasian. Since you have the ChuckKam grouping elsewhere under Nostratic, what "Siberians" are you refering to? Tungus?
The placement of Amerind as a Nostratic is completely unsupportable linguistically and there is no theory that I am aware that deals with a relationship of the two. Amerind itself is far too contraversial as of yet to consider relationships with other contraversial groupings.
Your placement of Eskaleut and ChuckKam is probably also a contraversial one to most Nostraticists. Allan Bomhard seems to classify it closer to Altaic, Uralic, etc under his Nostratic subbranch labeled "Eurasiatic" and I note at least certain connections with Eskaleut and Uralic (Uralic *ken "who" but Aleut "ki^n")
Thus we come to the last issue, Eurasiatic as a parent rather than child of Nostratic. I don't think Eurasiatic has ever been viewed as being greater in scope than Nostratic and most consider it as a subgrouping instead. Besides, if Eskaleut and ChuckKam are in fact closer to Altaic, Uralic, IE, etc. then there is no need for this higher node in the tree.
Well, I guess I'm done with the linguistic critique. I hope what I said is useful at all. Have you read anything regarding Allan Bomhard's "Indo-European and the Nostratic Hypothesis"? He mentions his views on migrational patterns based partly on Nostratic linguistics. He also alludes to there being native Caucasian speakers before the arrival of IE to the Pontic-Caspian region. It might be of some interest. Certainly if things like Eskaleut and ChuckKam are correct, we are presented with problems of how to distinguish between linguistical migration and physical (or genetic) migration. Food for thought.