At Gambler's House, blogger teofilo provides a very nice walk through of a couple of studies that use linguistics to study the spread of agriculture into the Southwest Unites States from Mexico. The methodology hinges on 1) tracking loanwords and 2) the assumption that Proto-Northern-Uto-Aztecan (PNUA) is a valid genetic unit. I'm not qualified to comment, but I felt the post was thorough and raised some fair objections as well as noting strengths. Money quote:
"...the fact that the loans seem to have gone both ways shows that whatever contact took place involved both groups continuing to exist as social entities of some sort. This is not evidence for assimilation, in other words, but for peaceful contact between agricultural and hunter-gatherer groups involving the exchange of information that enhanced the subsistence options of both parties."