One of several issues that I raise in my essay on DNA and the Book of Mormon is the tendency for scientists to ignore DNA evidence that might point to non-Asian origins for Native Americans. Non-Asian DNA types found in living Native Americans is almost universally assumed to be from European admixture (often a reasonable assumption, of course), and non-Asian DNA types found in ancient DNA (from, say, pre-Columbian remains) is often assumed to be due to modern contamination (again, this is a correct conclusion in many cases), even when there is no apparent source to explain the alleged contamination. Such discarding of non-Asian genetic links, in my opinion, may sometimes be made not so much because it is truly demanded by a sound scientific analysis of the data, but because it is demanded by the paradigm of the “established” Asia-only origin of Native Americans.
It is wrong to say that there has been no DNA evidence pointing to non-Asian (e.g., European or Middle East) origins of ancient Native Americans. But some of the possible evidence has routinely been discarded and ignored. Here is an excerpt from my essay on DNA and the Book of Mormon:
The problem in applying DNA analysis to the Book of Mormon goes beyond the likelihood of discarding the most relevant evidence. There is also the possibility of attributing evidence of pre-Columbian migrations to recent admixture. Worse, there is the possibility of missing the date of entry of the most relevant genes, and thus eliminating them from the scope of the Book of Mormon, as we shall discuss below.
All this is compounded by the fact that researchers are understandably interested in explaining the dominant genetic origins of Native Americans, which will likely correspond to the dominant population groups that were already on the continent when Lehi’s little boatload of people landed. There is typically little interest in understanding or even studying the origins of unusual haplotypes in Native Americans. For example, Bonatto and Salzano (1997), in concluding that the four major mtDNA haplotypes likely derived from a single Asian migration, felt that other less common haplotypes could be safely ignored:
We agree that some additional founding haplogroups (such as group X from Forster et al. 1996; also see Bailliet et al. 1994; Merriwether and Ferrell 1996) might exist, besides the four major ones studied here. However, they constitute only ~10% of the sequences now found in the Americas and, because of their very small sample size, could not be analyzed in the study. Since we analyzed each haplogroup separately, and since the number of haplogroups was not a relevant parameter, including these putatively additional founding haplogroups should not significantly change the results presented here.
Salzano (2002) lists 7 biallelic haplotypes for Y chromosomes in Native Americans in his Table 9. He states that haplotypes 5 through 7 “occur in low frequencies, and since they present high prevalences in European or African populations, may be due to interethnic gene flow.” But these haplotypes occur in Eskimos, Na-Denes, and Amerinds of North American, as well as in natives of Central America and South America. Can we safely ignore them because they are also characteristic of Old World peoples outside of Asia?
As a further characteristic example of the exclusion of “other” DNA types, Malhi et al. (2002) investigated the mtDNA haplogroup identities of 1,612 Native Americans. They state that:
Individuals whose mtDNAs did not belong to one of the five Native American haplogroups were not included in this analysis. Although it is possible that one or more of these individuals possess previously undocumented founding Native American mtDNA types, previous studies indicate that the frequency of “other” mtDNA types is very low and that most–or all–of these result from recent admixture (Torroni et al. 1993b, 1994; Huoponen et al. 1997; Smith et al. 1999).
An excellent discussion of the very real problem of contamination of ancient DNA samples is provided by Kolman and Tuross (2000), who also provide an interesting example in which pre-Columbian genetic material from a Native American appears to provide reproducible evidence of European origins. In spite of numerous efforts to exclude contamination, this result, identically reproduced in multiple careful trials, is presented as a case of “obvious” contamination because it was non-Asian:
The data presented here can be used to illustrate the dangers of imprudent inclusion of data. The DNA sequence identified in sample 5 had never been detected in our laboratory or in New World indigenous populations. All associated extraction and PCR controls were negative. Multiple extractions resulted in the same RFLP/deletion haplotype. Therefore, it could be proposed that this haplotype represents a new founding lineage for the New World. However, the fact that this haplotype is found at high frequency in European populations (17%, Richards et al., 1996) and is not found in presumably ancestral Asian populations argues against this interpretation and against the inclusion of this sequence in a NewWorld database.
In total, seven different non-New World sequences were identified in the current study. They are most likely all European in origin and may represent a minimum of seven independent sources of contamination. . . .
In sum, there is no easy, objective method of identifying contaminating sequences other than to painstakingly analyze them within the genetic framework of the ancient population under study.
The conclusion is understandable, if one is constrained by the paradigm that all ancient Native Americans must have DNA originating from Asia. But when an ancient human’s DNA comes up as European, in trial after trial with great precautions taken to prevent contamination, and then that data is simply excluded as a fine example of the dangers of contamination because it is not Asian, what chance do we have to find non-Asian genes in ancient human samples from the Americas? Ancient DNA that does not fit the out-of-Asia paradigm is repeatedly discarded from consideration because of “obvious” contamination.
There is no evidence in the paper by Kolman and Tuross that any of the other samples discarded for “contamination” had contamination from any of the researchers conducting the study. The approach appears to be that anything unexpected will be discarded as due to contamination. Is it any surprise that this approach – apparently a common approach – consistently suppresses surprises, surprises like the presence of non-Asian groups in ancient America?
Further work with the typically neglected outliers still needs to be done, and done without instantly assuming that modern contamination or admixture is the source of genes that appear to have a non-Asian origin. While contamination can be a serious problem, it is still possible to get good results with ancient DNA if proper procedures are followed, as shown by Gilbert et al. (2003). More recently, Matthew Spencer and Christopher J. Howe (Spencer and Rowe, 2004) have established statistical tools and recommended procedures to help researchers determine the probability that an amplified DNA sequence from an ancient sample actually corresponds to ancient DNA or modern contamination. Their discussion of the problem of contamination is also helpful.
References cited above:
Bailliet, G., et al., “Founder Mitochondrial Haplotypes in Amerindian Populations,” American Journal of Human Genetics, 55(1): 27-33 (July 1994). (Available online.)
Bonatto, S.L. and Salzano, F.M., “Diversity and Age of the Four Major mtDNA Haplogroups, and their Implications for the Peopling of the New World”, American Journal of Human Genetics, 61:1413-1423 (1997a). (Available online.)
Forster, P., Hardin, R., Torroni, A., and Bandelt, H.-J., “Origin and Evolution of Native American mtDNA Variation: A Reappraisal,” American Journal of Human Genetics, 59: 935-954 (1996).
Gilbert, M.T.P., Willerslev, E., Hansen, A.J., Barnes, I., Rudleck, L., Lynnerup, N., and Cooper, A., “Distribution Patterns of Postmortem Damage in Human Mitochondrial DNA,” American Journal of Human Genetics, 72:32-47 (2003). (Available online.)
Huoponen, K., Torroni, A., Wickman, P.R., Sellitto, D., Gurley, D.S., Scozzari, R., and Wallace, D.C., “Mitochondrial DNA and Y Chromosome-specific Polymorphisms in the Seminole of South Florida,” European Journal of Human Genetics, 5:25-34 (1997), as cited by Malhi et al., 2000.
Kolman, C.J., and Tuross, N., “Ancient DNA Analysis of Human Populations,” American Journal of Physical Anthropology, 111: 5-23 (2000). (Available online.)
Malhi, R.S., et al., “The Structure of Diversity within New World Mitochondrial DNA Haplogroups: Implications for the Prehistory of North America,” American Journal of Human Genetics, 70(4): 905-919 (April 2002). (Available online.)
Merriwether D.A., and Ferrell, R.E., “The Four Founding Lineage Hypothesis for the New World: A Critical Reevaluation. Mol. Phylogenet. Evol., 5:241-246 (1996), as cited by Bonatto and Salzano (1997a). (Abstract available online.)
Richards, M., Corte-Real, H., Forster, P., Macaulay, V., Wilkinson-Herbots, H., Demaine, A., Papiha, S., Hedges, R., Bandelt, H.-J., Sykes, B., “Paleolithic and Neolithic Lineages in the European Mitochondrial Gene Pool,” American Journal of Human Genetics, 59:185-203 (1996), as cited by Kolman and Tuross (2000).
Salzano, F.M., “Molecular Variability in Amerindians: Widespread but Uneven Information,” Anais de Academia Brasileira de Ciencias, 74(2): 223-263 (2002). (Available online.)
Smith, D.G., Malhi, R.S., Eshleman, J., Lorenz, J.G., Kaestle, F.A., “Distribution of mtDNA Haplogroup X among Native North Americans,” American Journal of Physical Anthropology, 110: 271-284 (1999).
Spencer, M. and Rowe, C.J., “Authenticity of Ancient-DNA Results: A Statistical Approach,” American Journal of Human Genetics, 75(2): 240-250 (Aug. 2004). (Available online.)
Torroni, A., et al. “Asian Affinities and Continental Radiation of the Four Founding Native American mtDNAs,” American Journal of Human Genetics, 53: 563-590 (1993b).
Torroni, A., Neel, J.V., Barrantes, R., Schurr, T.G., Wallace, D.C., “Mitochondrial DNA “Clock” for the Amerinds and Its Implications for Timing Their Entry into North America,” Proceedings of the National Academy of Science USA, 91: 1158-1162 (1994). (Available online.)