Geography and Genetics

The Nephites occupied a limited geography of not more than 300 miles square. The Sea south and the sea north are not referring to the Arctic and Antarctic Oceans. Seas can be lakes, or gulfs (part of larger bodies of water).

Hel. 3:8 And it came to pass that they did multiply and spread, and did go forth from the land southward to the land northward, and did spread insomuch that they began to cover the face of the whole earth, from the sea south to the sea north, from the sea west to the sea east.

The Book of Mormon never claimed that they would be the major genetic ancestor to the modern Native Americans The Book of Mormon continually refers to the Book of Mormon coming forth to a "remnant of their seed." This is of course specifically referring to genetics. The Nephites were the victims of genocide and the Lamanites had continually been mixing with the indigenous people from the beginning. The Nephites in the Introduction were only considered "principal ancestors" in terms of the covenants of the Lord and not genetics. Because of continual genetic mixing of Lamanites with indigious Americans, there is a significantly different connotation to saying someone is a direct descendant of the Lamanites verses a direct descendant of the Nephites. While the former is often heard, I have never heard the later sentiment expressed.

1 Ne. 15: 3-1413 And now, the thing which our father meaneth concerning the grafting in of the natural branches through the fulness of the Gentiles, is, that in the latter days, when our seed shall have dwindled in unbelief, yea, for the space of many years, and many generations after the Messiah shall be manifested in body unto the children of men, then shall the fulness of the gospel of the Messiah come unto the Gentiles, and from the Gentiles unto the remnant of our seed— 14 And at that day shall the remnant of our seed know that they are of the house of Israel, and that they are the covenant people of the Lord; and then shall they know and come to the knowledge of their forefathers, and also to the knowledge of the gospel of their Redeemer, which was ministered unto their fathers by him; wherefore, they shall come to the knowledge of their Redeemer and the very points of his doctrine, that they may know how to come unto him and be saved. (see also 1 Ne. 13:34,38-39, 2 Ne. 30:3-4)

While the majority of Native American DNA is Asian, Siberian and Mongolian, by mtDNA haplogroup migration genetics studies. Researcher have discovered haplogroup X2a which is not found in Siberia or Mongolia but is considered a founding haplogroup in America because it is found in pre-Columbian remains. However, the highest concentration of X2 haplogroup is found in the Druze of Galilee. Researchers do not believe the Druze to be the source of the Haplogroup X but that they have preserved the mtDNA through intermarriage which represents the genotype of the people living in Galilee at the time the Druze settled in Northern Israel.

The Druze: A Population Genetic Refugium of the Near East. PLoS ONE. 2008 May 7;3(5)
http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0002105

There is a small trace of X in Altai Republic in Central Asia. However according to the study: it shows that the X2a clave in America is in not a decendant variation of the X2e in Altai or anywhere else in Asia. But that X2a must have undergone an early split in the phylogenetic tree from the Middle East. In other words, the X2a in America came directly from the Middle East and not via Asia. They also say the the Altians only have a very low rate of haplogroup X, and that it got there through recent migration. The highest rates of haplogroup X are found in the Druze and the Orkney of Scotland.

Origin and Diffusion of mtDNA Haplogroup X, Am J Hum Genet. 2003 November; 73(5): 1178–1190. http://www.pubmedcentral.nih.gov/art...?artid=1180497
http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1180497&blobtype=pdf