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Thursday, 19 June 2014

updated post on asian dna

For almost 180 years most Mormons have believed that native people in the Americas and Polynesia are largely descended from Israelites. These views are primarily based on the Book of Mormon and they have been sustained over many decades by numerous statements by church leaders, including all of its prophets. Many Mormons think the large civilisations described in the Book of Mormon were located in a region now known as Mesoamerica. As recently as 2013 Mesoamerican Latter Day Saints were reassured by an apostle they are descended from Lehi, an Israelite who sailed to the Americas in 600BC.

Mormons believe ancient Jews sailed to the Americas

A Scientific Consensus

Scientists studying Native American populations see no cultural or genetic connection between them and Old World populations. There is a broad consensus view among archaeologists, geologists, anthropologists and biologists, based on more than a century of excavating thousands of archaeological sites, that the New World was first populated at least 15 thousand years ago, and possibly as early as 20 thousand years ago, by migrants from Asia. These people entered the Americas via a wide expanse of land—called Beringia—which connected northeastern Asia with northwestern North America during ice ages when sea levels are lowered. These small groups of migrants soon exploited the richness of this “new world,” and their populations grew quickly and expanded across the North and South American continents over a few thousand years. There is widespread agreement among archaeologists that there is no evidence that the cultural developments unveiled in the archaeological record in the New World were in any way inspired by more recent visitors or migrants from the Old World.

The ancestors of Native Americans walked to the Americas

During the last two decades, molecular studies have confirmed the Asian origin of Native Americans, the timing of migrations into the Americas and the routes these people took as they entered North and South America.

DNA studies

DNA is a long chain-like polymer comprised of four repeating units called bases, represented by the letters A, C, G, and T. Hereditary information is stored in coded form in the order of these lettered bases. There are roughly 3,000 million bases in the human genome, and every cell in our body contains an identical copy. The molecular library with the complete set of instructions for constructing the human body comes in forty-six volumes called chromosomes—twenty-three inherited from our mothers and twenty-three from our fathers.

Over 99.9 percent of our DNA is found within the nucleus of our cells (nuclear DNA), which is where our chromosomes are located (see figure below). A tiny fraction of our DNA is contained within structures called mitochondria (mitochondrial DNA), which are specialized compartments for synthesizing energy for the cell. Our nuclear DNA is passed from generation to generation as complex rearrangements of parental DNA. Mitochondrial DNA (mtDNA) is passed along maternal lines from mothers to their offspring, while Y chromosome DNA (YDNA) is passed from father to son.  These uni-parentally inherited DNAs have been used extensively to build maternal or paternal links between related populations and to study the movement of human populations throughout the world.

For the most part, the order of the letters contained within our DNA remains fixed as they are passed from generation to generation. However, in practice they gradually accumulate small errors that slightly alter the sequence of letters. The result is the development of branching maternal and paternal pedigrees that descend from earlier common lineages. Closely related DNA lineages share the same mutations.

Native American mitochondrial DNA

The first studies of Native American DNA were published in the 1990s. Back then, methods for analysing DNA were not well developed, making it difficult to study the large amounts of nuclear DNA. Consequently, the early research was largely focussed on mitochondrial DNA. An excellent summary of the distribution of global mtDNA and YDNA lineages can be found here.

Mitochondrial DNA variation in the Americas indicates unambiguously that the ancestors of Native Americans originated in Asia. Virtually all contemporary Native Americans possess a mtDNA lineage that belongs to one of five founding lineage families (called haplogroups), which are all present among native populations of Siberia. These maternal lineages have now been designated A, B, C, D and X (Table below; Brown et al. 1998; Schurr et al. 1990). Of these haplogroups, only X is present in both central Asian and European populations; however, the X haplogroup is large and diverse, and the particular X lineage (X2a) found in Native American populations represents a distinct branch on the Eurasian X lineage tree (Reidla et al. 2003).

A small proportion of mtDNA lineages found in indigenous peoples (<1%) are derived from recent non-native (European or African) admixture (Gonzales et al. 2003; Richards et al. 1996). The majority of these mtDNAs belong to lineage H, the most common mtDNA lineage family in European populations such as Spain and the United Kingdom (Table below). The most common mtDNA lineage among Ashkenazi Jews is lineage K (Behar et al. 2004) while lineage L is the most common lineage in African populations.

In the years since the publication of Losing a Lost Tribe (Southerton 2004) much more research has been published specifically on Mesoamerican populations, which are a subset of Central American populations. We now know the mtDNA lineages of over 1700 Mesoamericans (see table below). The mtDNA evidence suggests that Native Mesoamericans, like all other Native Americans, are largely descended from Asian ancestors. The very small number of non-Asian lineages that are found are almost certainly the result of post-Columbus admixture as they belong to lineage families that are most common in Europe or Africa. 

Only sixteen out of 1727 Mesoamericans (about 0.9%) possess a mtDNA lineage that didn’t originate in Asia. Of the non-Asian lineages, three have been found to be African L lineages, and two match mtDNA lineages found in Spain and Portugal. The remaining 11 lineages are either insufficiently characterised or most likely European lineages as the lineage family they belong to is found at high frequencies in Western European populations. 

Native American Nuclear DNA studies

Tremendous advances in DNA technology in the last two decades are now making it feasible for scientists to study the 3 billion base pairs of DNA carried in our nuclear DNA. Most scientists studying the human genome focus their attention on what's different between genomes rather than what's the same. That reduces the information they have to deal with by roughly a thousand-fold. By far the most common difference observed when the entire genome sequence of two different people are compared, are single base pair substitutions known as Single Nucleotide Polymorphisms (SNPs, pronounced SNiPs). The word "polymorphism" simply means different forms. The figure below illustrates a G/T SNP.    

SNPs are random variations that have arisen in a single human genome in the past and then subsequently passed on to future generations (we typically pass on about 50 or so new mutations to our children). Since mutations are arising all the time human populations that became separated soon begin to accumulate large numbers of SNPs that are unique to their population. As a result, global populations can be clearly distinguished on the basis of variation at hundreds of thousands of SNPs. This is graphically illustrated in the figure below which is drawn from a paper by Jun Li et al. (2008) who studied the nuclear DNA of 938 unrelated individuals from 51 global populations at 650,000 common SNPs.

Behar, D. M., Hammer, M. F. Garrigan, D., et al. (2004) MtDNA evidence for a genetic bottleneck in the early history of the Ashkenazi Jewish population. European Journal of Human Genetics. 12, 355-364.

Brown, M. D., Hosseini, S. H., Torroni, A. et al. (1998) MtDNA haplogroup X: An ancient link between Europe western Asia and North America? American Journal of Human Genetics 63, 1852–1861.

Gonzales, A. M., Brehm, A., Perez, J. A., et al. (2003) Mitochondrial DNA affinities at the Atlantic fringe of Europe. American Journal of Physical Anthropology. 120, 391-404.

Reidla, M., Kivisild, T. Metspalu, E. et al. (2003) Origin and diffusion of mtDNA haplogroup X. American Journal of Human Genetics 73, 1178–1190.

Richards, M., CĂ´rte-Real, M. Forster, P. et al. (1996). "Paleolithic and Neolithic lineages in the European mitochondrial gene pool," American Journal of Human Genetics 59, 185-203.

Schurr, T. G., Ballinger, S. W. Gan, Y. Y. et al. (1990) Amerindian mitochondrial DNAs have rare Asian mutations at high frequencies, suggesting they are derived from 4 primary maternal lineages. American Journal of Human Genetics 46, 613–623.

Southerton, S. G. (2004) Losing a Lost Tribe: Native Americans, DNA and the Mormon Church. Salt Lake City, Signature Books.