The truth of the matter is that the idea that the Lamanites are not the "principal" ancestors of the Amerindians has been around for a long time; much longer than DNA studies. Although the word change might be upsetting to some Mormons who take Lamanites as Amerindians literally, not every Mormon is upset. That is because those who are not as challenged by the change of a word read the Book of Mormon differently than the traditional simplistic descriptions. The text continually challenges the traditional explanation of Lamanites and Nephites as blood and relation designations. They end up (even before the utopia period) as political, cultural, and philosophical descriptions.
Probably the best two reads on the subject are the groundbreaking When Lehi's Party Arrived in the Land, Did They Find Others There? by John L. Sorenson and Blake Ostler's DNA Strands in the Book of Mormon, with a sidbar by the always questionable D. Michael Quinn. The first article doesn't present a new idea, but it explores it more than it ever had been before. The second article includes that the simplistic idea of Lamanite and Nephite as Amerindian ancestors has been challenged by faithful Mormons almost from the start. Blake Ostler makes the point that many Book of Mormon scholars have been saying for years:
In teaching our investigators that the Book of Mormon is a history of all Amerindians and its descriptions of lands northword and southword correspond to the North and South American continents, my companion had presented a view that he and many Latter-day Saints have been taught about the Book of Mormon peoples and lands. It was a good-faith belief, just as it is of most who teach it today. But a good-faith belief, even when taught by someone we revere as an inspired spiritual leader, is not necessaryily true. "straw man" versions of the Book of Mormon are much easier to disembowel than is the book as it actually reads. The Book of Mormon must be assessed based on what it says and not on what others say about it.
Of course, those who take issue with prophets not always correct even over generations will reject this as sophistry. However, the critics and those Mormons who agree with them reject the Mormon beliefs about prophets. They are inspired, but not perfect. They are as prone to human falibility of opinion and acceptance of tradition as any other person.
Tied to this discussion is what is known as the limited geography theory. It states that the events of the Book of Mormon didn't happen on the whole North and South American continent, but a small region. The history of where the Lamanites and Nephites lived has been a source of conflict and consideration since Joseph Smith himself. At first it seemed clear that the whole continent was considered part of the story. Other statements in journals and newspapers bring that uniformity to question. A survey of early opinions about Book of Mormon geography seems to show an increased focus on Central America since at least the 1840s, if not earlier.
Over the years scientific explanations of Amerindian origins did do damage to the traditional story of the Book of Mormon. Ironically it opened up the Book of Mormon text to closer scrutiny. That scrutiny has present a picture far more complicated than a simple Lamanite/Nephite population present in North and South America. As Sorenson points out:
It is true that the name "Nephites" sometimes connotes those who shared culture, religion, and ethnicity or biology. But every rule-of-thumb we construct that treats the Nephites as a thoroughly homogeneous unit ends up violated by details in the text. Variety shows through the common label, culturally (e.g., Mosiah 7:15; Alma 8:11–12), religiously (e.g., Mosiah 26:4–5 and 27:1; Alma 8:11), linguistically (e.g., Omni 1:17–18), and biologically (e.g., Alma 3:17, note the statement concerning Nephi's seed "and whomsoever shall be called thy seed"; Alma 55:4). "Nephites" should then be read as the generic name designating the nation (see Alma 9:20) ideally unified in a political structure headed by one direct descendant of Nephi at a time.
He says of the Lamanites:
What view of the Lamanites did the Nephites have that sheds light on the question of "others"? We may see a clarifying parallel to the Nephite-Lamanite relationship in how Mormons viewed "the Indians" in western America during the nineteenth century. Pioneer historical materials mention "Indians" about the same proportion of the time as the Nephite record mentions the "Mulekites," that is, rarely. This was not because the natives were a mystery. On the contrary, Latter-day Saint pioneers had an explanation for "the Indians" which they considered adequate—they were generic "Lamanites." With a few exceptions at a local level, no more detailed labelling or description was ever considered needed. Overall, "Indians"/"Lamanites" were of only occasional concern, as long as they did not make trouble. When they were a problem, the attention they received was, again, normally local. Periodic attempts to convert the Indians rarely had much practical effect, and this positive concern for them tended to be overwhelmed by the "practical" aim to put the natives in their (dominated) place. Wouldn't the Nephites have dealt with their "Lamanites" about like the Latter-day Saints with theirs? (Notice the mixed message—hope for converting the benighted ones but tough military measures, too—familiar in early Utah history, found in Enos 1:14, 20, and 24.) Thus Nephites in a particular area might have noted differences between one group or subtribe of "Lamanites" and another, while people who talked about the situation only from what they heard in the capital city would have generalized, with little interest in details. For example, it is only in the detailed account of Ammon's missionary travels that we learn that Lamoni and his people were not simply "Lamanites" in general but tribally distinct Ishmaelites inhabiting a region of their own (see Alma 17:19, 21). At the level of concern of the keepers of the overall Nephite account, nevertheless, one "Lamanite" must have seemed pretty much equivalent to any other "Lamanite," as Jacob 1:14 assumes. The Nephites' generic category of "Lamanite" could have lumped together a variety of groups differing in culture, ethnicity, language, and physical appearance without any useful purpose being served, in Nephite eyes, by distinguishing among them. (Of course the original records may have gone into more detail, but all we have is Mormon's edited version of those, plus the small plates of Nephi.)
The idea that there were "others" who were in the Americas prior to, during, and after the Book of Mormon has even had official approval before the word change. Again, a study of what was said about Nehi's Neighbors reveals a long history behind the notion of more than two leading groups of Amerindians. In 1938, the LDS Church's Department of Education stated, "Indian ancestry, at least in part, is attributed by the Nephite record to the Lamanites. However, the Book of Mormon deals only with the history and expansion of three small colonies which came to America and it does not deny or disprove the possibility of other immigrations, which probably would be unknown to its writers. Jewish origin may represent only a part of the total ancestry of the American Indian today." This was more than 60 years ago, when DNA was not an issue and yet seems closer to the idea expressed by a simple word change in the Book of Mormon introduction.
To repeat what was said several months back about Lehi ancestory, the discussion doesn't change more than long held misinformation. There is no doubt that the names Nephite and Lamanite still hold very specific family meaning. When you speak of Lamanite, it can very well be understood as having a relation to Lehi. However, the relationship is thin. It is more like saying Latter-day Saints are of the House of Israel. True enough from a spiritual standpoint. If we are to believe the Scriptures that is true from actual fact; as long as we understand the dilution of the original Israelite blood in our Gentile genes. So, from that perspective the Lamanites are the main progenators of Native Americans. Problem is, that isn't saying much. The original gene pool was mixed up, changed, scattered, and redefined long before Columbus. That means the story told about the Book of Mormon doesn't need to be changed, but better explained. All Amerindians have been spiritually adopted into the House of Lehi as LDS Gentiles are said to be adopted into the House of Israel.