"Interesting that [Ugo Perego] uses DNA evidence to conclude that these children were not fathered by Joseph Smith, but when the same DNA evidence says that Native Americans did not descend from anyone of middle eastern origins, he goes through all sorts of mental gymnastics to suggest that the evidence is inconclusive. He fancies himself a scientist yet tries to manipulate the results of his research in order to reach the desired conclusion. Science indeed."
It is quite obvious that whoever wrote this statement either has not read the actual publications I wrote, or he might simply not understand them. A couple of years ago, at the conclusion of my presentation at the annual FAIR conference, a similar question was posed, this time by someone that could not understand why I felt so strongly about my conclusions regarding Joseph Smith alleged offspring and yet, I rejected the so-called genetic evidence of a Great Lakes geographical setting for the people described in the Book of Mormon. I am sure that others that are not familiar with the details and properties of genetic inheritance might be wondering the same thing.
The answer to these questions/criticisms is quite simple and I have addressed multiple times, including in some of my writings. DNA is not evidence only when it is convenient, but it is evidence when it is evidence. In the case of testing Joseph Smith purported children born to polygamous relationships, the genetic method employed was the uniparental marker Y chromosome, which is a section of DNA that is inherited exclusively from father to son, along an unbroken paternal line. Because of lack of recombination, Y chromosome testing can be ascertained to exact people in a person's pedigree chart. If the genealogy is known and the Y chromosome signature (called haplotype) of a number of male descendants of a specific ancestor can be collected and tested, then the Y chromosome profile of that ancestor can be inferred quite accurately, just as if a DNA sample could have been obtained from the ancestor himself. This process can be repeated over and over for any male ancestor (including Joseph Smith and his alleged biological sons) as long as living male descendants can be identified and a DNA sample collected from them. Then the game is quite easy. All you have to do is to line up and compare the inferred (or reconstructed) Y chromosome haplotypes for the two individuals you are trying to establish a connection along the paternal line. If the values match, then you probably have a biological relationship. If they don't, then you can be 100% confident that you are looking at two non-related individuals.
So, how could science be accurate in this instance, but it cannot be used to bring forth similar conclusions when it comes to the historicity of the Book of Mormon? The difference lays within the expectations from the genetic approach. In the case of Joseph Smith and his alleged posterity, the Y chromosome profiles that were reconstructed and used for that analysis were accurate genetic fingerprints that belonged to specific individuals that lived in the past. The known relationships obtained through the genealogical data were key to line up the proper candidates for the genetic testing necessary in the study. With regard to the Book of Mormon, I explained already and in great detail that you cannot exclude the historical presence of an Israelite family arriving in the Americas 2600 years ago based on the genetic sampling of modern-day Native American populations. This is simple and plain population genetics at work. Any population geneticist would agree that when a small group of people become part of a large population, their genetic signature is destined to disappear quite rapidly within a handful of generations. Moreover, we now know with great accuracy the Y chromosome haplotype of Joseph Smith and how it can be used as a standard for comparison against anyone who was claimed to be his biological child; however, we know nothing about the DNA profiles of the people of the Book of Mormon. The "mental gymnastic" I have been accused of is the very piece of truth that those criticizing the historicity of the Book of Mormon from a DNA standpoint are unwilling to accept: WE DON'T KNOW WHAT LEHI'S DNA IS and therefore this is the main reason why it cannot be identified in the Americas. Everything else is pretty much irrelevant. Show me Lehi's DNA and then let's go about looking for it among past and present indigenous populations of the Western Hemisphere. Without it, you are missing the very piece of genetic evidence that anyone interested in a genetic perspective on the Book of Mormon (both in favor or against it) would need.