These are just my reactions to the essay. I'm not being critical of the essay. I'm simply offering suggestions for improvement in the future. (The essay has already been edited at least once.)
First, I'll note some irony about the Book of Mormon geography. Then I'll comment on the science.
Here's the link to the essay: https://www.lds.org/topics/book-of-mormon-and-dna-studies?lang=eng
1. Repudiating the prophets. Apart from the conclusion, the essay quotes exactly one General Authority: President Anthony W. Ivins of the First Presidency, who said this in the April 1929 general conference: "We must be careful in the conclusions that we reach. The Book of Mormon … does not tell us that there was no one here before them [the peoples it describes]. It does not tell us that people did not come after.”
But the footnotes to the essay cite LDS scholars who have specifically repudiated what President Ivins taught just a year previously, when he spoke in General Conference about the Church's acquisition of the Hill Cumorah in New York.
President Ivins: "The passages which I have quoted from the Book of Mormon... definitely establish the following facts: That the Hill Cumorah, and the Hill Ramah are identical; that it was around this hill that the armies of both the Jaredites and Nephites, fought their great last battles; that it was in this hill that Mormon deposited all of the sacred records which had been entrusted to his care by Ammaron, except the abridgment which he had made from the plates of Nephi, which were delivered into the hands of his son, Moroni. We know positively that it was in this hill that Moroni deposited the abridgment made by his father, and his own abridgment of the record of the Jaredites, and that it was from this hill that Joseph Smith obtained possession of them."
Of course, President Ivins was simply repeating what Joseph Smith and Oliver Cowdery taught in Letter VII, which Joseph had republished multiple times while he was alive. This is what all of Joseph's contemporaries taught about the Hill Cumorah in New York, as well as all of his successors who have addressed the topic.
However, Footnote 6 of the DNA essay cites John L. Soreson's book Mormon's Codex: An Ancient American Book, in which brother Sorenson wrote, "There remain Latter-day Saints who insist that the final destruction of the Nephites took place in New York, but any such idea is manifestly absurd. Hundreds of thousands of Nephites traipsing across the Mississippi Valley to New York, pursued (why?) by hundreds of thousands of Lamanites, is a scenario worthy only of a witless sci-fi movie, not of history.”
The DNA essay is telling careful readers that President Ivins' teaching about Cumorah in General Conference is "manifestly absurd."
Footnote 8 cites the anonymous Times and Seasons article and attributes it to Joseph Smith, even though that same issue of the Times and Seasons contains a letter (D&C 127) that Joseph mailed to the editor because he was in hiding at the time; i.e., according to this theory, Joseph mailed a letter to himself. [The historical evidence shows that Joseph had little to no direct involvement with editing the paper, any more than he was directly involved with printing it. In fact, he resigned from the paper after another article about Central America was published as a headline.]
Footnote 9 cites an article that discusses the Wentworth letter, which Joseph apparently adapted in part from Orson Pratt's pamphlet, without pointing out that Joseph replaced Pratt's extended musings on a Central and South American setting with the correction that "The remnant are the Indians that now inhabit this country." The author of this article has consistently repudiated what President Ivins taught about the Hill Cumorah in New York.
The citation to these sources in the DNA essay convey an official endorsement of the Mesoamerican/two-Cumorahs theory, contrary to the widely understood policy of official neutrality on Book of Mormon geography.
I've pointed out that the Mesoamerican/two-Cumorahs theory has become the de facto official position of the Church, and this essay is another indication of that.
All I ask is, if we're going to repudiate Letter VII and all the other teachings of modern prophets and apostles about the Hill Cumorah in New York, why don't we do it overtly to eliminate the confusion?
2. Darwinian evolution. The theory of evolution by natural selection has come a long way since Charles Darwin, but colloquially, the term refers to evolution including natural selection, mutation, migration, and genetic drift. These concepts are explained in the DNA essay, including the footnotes.
3. Scientific Claims. In supporting its conclusion,* the essay relies on key scientific claims,including these:
a. The human species split from the chimpanzee species about 6.5 million years ago:
As I've said, I'm fine with this as an alternative working hypothesis, if people want to believe it, but I hope there is still room in the Church for those who interpret the scriptures more literally, as I mentioned in the original post.
*The purpose of the essay is to support this conclusion:
"Much as critics and defenders of the Book of Mormon would like to use DNA studies to support their views, the evidence is simply inconclusive. Nothing is known about the DNA of Book of Mormon peoples. Even if such information were known, processes such as population bottleneck, genetic drift, and post-Columbian immigration from West Eurasia make it unlikely that their DNA could be detected today. As Elder Dallin H. Oaks of the Quorum of the Twelve Apostles observed, “It is our position that secular evidence can neither prove nor disprove the authenticity of the Book of Mormon.”29
"Book of Mormon record keepers were primarily concerned with conveying religious truths and preserving the spiritual heritage of their people. They prayed that, in spite of the prophesied destruction of most of their people, their record would be preserved and one day help restore a knowledge of the fulness of the gospel of Jesus Christ. Their promise to all who study the book “with a sincere heart, with real intent, having faith in Christ,” is that God “will manifest the truth of it unto you, by the power of the Holy Ghost.”30 For countless individuals who have applied this test of the book’s authenticity, the Book of Mormon stands as a volume of sacred scripture with the power to bring them closer to Jesus Christ."
The question of evolution and the creation of Adam is a far more involved topic than I can address here, but the essay does not even acknowledge a literal interpretation of the scriptures as a possibility.
I leave it up to readers to decide whether the principles and time frame of Darwinian evolution, as established in this DNA essay, tend to prove or disprove the authenticity of the Book of Mormon.
For now, I'll just ask how the pre-Adamite human beings described in the DNA essay fit into the oft-repeated scriptural teaching that Adam and Eve were distinct individuals who were our first parents.
One purpose of the Book of Mormon is to corroborate the Bible. In Ether 1, Moroni explained:
3. And as I suppose that the first part of this record, which speaks concerning the creation of the world, and also of Adam, and an account from that time even to the great tower, and whatsoever things transpired among the children of men until that time, is had among the Jews—
4 Therefore I do not write those things which transpired from the days of Adam until that time; but they are had upon the plates; and whoso findeth them, the same will have power that he may get the full account.
Mosiah discussed this as well:
17 Now after Mosiah had finished translating these records, behold, it gave an account of the people who were destroyed, from the time that they were destroyed back to the building of the great tower, at the time the Lord confounded the language of the people and they were scattered abroad upon the face of all the earth, yea, and even from that time back until the creation of Adam." Mosiah 28:17
Aaron taught about this: "12 And it came to pass that when Aaron saw that the king would believe his words, he began from the creation of Adam, reading the scriptures unto the king—how God created man after his own image, and that God gave him commandments, and that because of transgression, man had fallen." Alma 22:12-13
As did Alma: "22 Now Alma said unto him: This is the thing which I was about to explain. Now we see that Adam did fall by the partaking of the forbidden fruit, according to the word of God; and thus we see, that by his fall, all mankind became a lost and fallen people." Alma 12:22-23
Moroni reiterated the importance of the creation of Adam in the verse every missionary teaches every investigator:
Moroni 10:3 "Behold, I would exhort you that when ye shall read these things, if it be wisdom in God that ye should read them, that ye would remember how merciful the Lord hath been unto the children of men, from the creation of Adam even down until the time that ye shall receive these things, and ponder it in your hearts."
Mormon taught about the family of Adam: Mormon 3:20 "And these things doth the Spirit manifest unto me; therefore I write unto you all. And for this cause I write unto you, that ye may know that ye must all stand before the judgment-seat of Christ, yea, every soul who belongs to the whole human family of Adam; and ye must stand to be judged of your works, whether they be good or evil..."
I raise this because everyone who reads this essay carefully will ask the same question. And the essay doesn't offer any alternatives to the current scientific understanding of Darwinian evolution with its associated time frames.