The discussions about DNA and the Limited Geographic Theory (LGT) or Model (LGM) have focused, to some degree, on the terms used in the Introduction to the Book of Mormon. Specifically, these have focused on the phrase "they [the Lamanites] are the principal ancestors of the American Indians."
The phrase "principal ancestors" is subject to multiple interpretations. I think it refers to the primary or most prominent ancestors, not the most numerous.
The term "American Indians" I think refers to the Indians of the U.S. and Canada, which is the normal use of the term.
I'm interested to read alternative points of view. For example, John Clark, a prominent ("principal") BYU apologist, has said this:
[John Clark:] If a general authority—I don't care who it is—says something that contradicts the Book of Mormon, I do not accept it. ... So nothing that they can say on the matter, other than the prophet saying "Thus saith the Lord," matters to me at all.
[Question from Richard Jensen, BYU associate professor of church history:] What if the general authority is Joseph Smith? How about then? The statements he's made placing [...] [Jensen is cutoff by Clark's response.]
[John Clark:] He was all over the map. ... The Book of Mormon is truer than Joseph Smith ever realized. What that means is Joseph Smith didn't understand the book that he translated.
as quoted on http://www.tungate.com/John-E-Clark_BYU-Q&A-excerpts_25May04.doc
I find Clark's approach bizarre. It sounds precisely like the Christian response to additional revelation after the Bible had been canonized.
For example, I don't know that Joseph Smith ever said "Thus saith the Lord" when he was revising the Bible; according to Clark's approach, we should disregard the JST.
Beyond that, how can someone say whether a statement "contradicts" the Book of Mormon other than by private interpretation of both the statement and the BoM?
A good example is this debate about the Introduction. Sure, it is possible to interpret the term "principal ancestors" to mean the "most numerous ancestors," and then to conclude that the term cannot be accurate in light of the DNA evidence. On top of that, if one interprets the BoM to describe people living in Central America (LGT), despite the DNA and cultural evidence, one can conclude the Introduction contradicts the BoM because it refers to the American Indians and is therefore wrong.
On the other hand, if one interprets the term "principal ancestors" to mean "most prominent ancestors" or "best known ancestors," then the DNA evidence is irrelevant. If one rejects the LGT in favor of a North American civilization in the central U.S., as I think one must, then the Introduction is consistent with the BoM.
Beyond that, why would Clark and so many others prefer the BoM to the modern prophets? The only reason I can think of is a preference for an ancient text, where anyone's interpretation is as valid as anyone else's (an approach favored by intellectuals who are invested in their own interpretations), over a modern speaker who can explain what he or she means and leave less room for the intellectuals to debate.
I prefer to believe that revelation continues and can expand and clarify the ancient texts, including the Book of Mormon. I wish it happened more than it does, of course; but I wouldn't want to reject it when it does happen.
