April 29, 2009

9-repeat allele at D9S1120 and a single founding population of Native Americans

The authors make a good case that this allele is not due to natural selection, but I don't really see how this demonstrates that Native Americans are primarily descended from a single founding population. Perhaps this allele occurred at a decent frequency due to genetic drift in an early group of colonists. This group later expanded in numbers, as they exploited the resources of the empty new continent, and later groups of arrivals incorporated (were incorporated by) the earlier colonists, resulting in a pervasive presence of the haplotype in question.

Related:

Molecular Biology and Evolution 2009 26(5):995-1016; doi:10.1093/molbev/msp024

Haplotypic Background of a Private Allele at High Frequency in the Americas

Kari B. Schroeder et al.

Abstract

Recently, the observation of a high-frequency private allele, the 9-repeat allele at microsatellite D9S1120, in all sampled Native American and Western Beringian populations has been interpreted as evidence that all modern Native Americans descend primarily from a single founding population. However, this inference assumed that all copies of the 9-repeat allele were identical by descent and that the geographic distribution of this allele had not been influenced by natural selection. To investigate whether these assumptions are satisfied, we genotyped 34 single nucleotide polymorphisms across ~500 kilobases (kb) around D9S1120 in 21 Native American and Western Beringian populations and 54 other worldwide populations. All chromosomes with the 9-repeat allele share the same haplotypic background in the vicinity of D9S1120, suggesting that all sampled copies of the 9-repeat allele are identical by descent. Ninety-one percent of these chromosomes share the same 76.26 kb haplotype, which we call the "American Modal Haplotype" (AMH). Three observations lead us to conclude that the high frequency and widespread distribution of the 9-repeat allele are unlikely to be the result of positive selection: 1) aside from its association with the 9-repeat allele, the AMH does not have a high frequency in the Americas, 2) the AMH is not unusually long for its frequency compared with other haplotypes in the Americas, and 3) in Latin American mestizo populations, the proportion of Native American ancestry at D9S1120 is not unusual compared with that observed at other genomewide microsatellites. Using a new method for estimating the time to the most recent common ancestor (MRCA) of all sampled copies of an allele on the basis of an estimate of the length of the genealogy descended from the MRCA, we calculate the mean time to the MRCA of the 9-repeat allele to be between 7,325 and 39,900 years, depending on the demographic model used. The results support the hypothesis that all modern Native Americans and Western Beringians trace a large portion of their ancestry to a single founding population that may have been isolated from other Asian populations prior to expanding into the Americas.

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4 comments:

AK said...

"Perhaps this allele occurred at a decent frequency due to genetic drift in an early group of colonists. This group later expanded in numbers, as they exploited the resources of the empty new continent, and later groups of arrivals incorporated (were incorporated by) the earlier colonists, resulting in a pervasive presence of the haplotype in question."

I don't see how this is much different from "the hypothesis that all modern Native Americans and Western Beringians trace a large portion of their ancestry to a single founding population that may have been isolated from other Asian populations prior to expanding into the Americas."

Basically both statements say that after the initial founding population expanded, further immigrations were quickly assimilated into the existing population.

Dienekes said...

Basically both statements say that after the initial founding population expanded, further immigrations were quickly assimilated into the existing population.The issue is the relative contributions of the various groups.

If selection was responsible, then the allele could have found itself established in diverse populations with very little interbreeding, because of its selective advantage.

If selection is not responsible, then the presence of the allele in diverse populations is due to the presence of a common population stratum; but there is no reason to think that this stratum was major or minor: if the allele was fixed in the population that bore it, then a heavy migration of latecomers would account for its frequency. Conversely, if the allele occurred at near the present-day frequency, then the contribution of any latecomers would be relatively minor.

In other words, I don't see how this supports anything in the single vs. multiple waves debate on Native American origins.

Doug said...

I don't think the authors make a good case against natural selection. They fail to overcome a big piece of evidence. This allele is found in more than 30% of the descendants of this ancient Beringian race in which they postulate the 9-repeat first arose. How did it get from one person to 30% of the whole descent group without being associated with some genetic advantage? The ancestor that passed on the 9-repeat must also have passed on other genes that helped them to survive. If only we knew how common the 9-repeat was before European diseases wiped out 90% of Native Americanss and West Beringians.

Doug said...

How does a genetic mutation go from a minority of one to majority status? There are only two ways.
(1) A series of migrations of small genetically atypical groups carries the gene to new lands were it is overrepresented in each successive migration until it becomes the majority. Such as the case of the M242 mutation in Kets, Selkups, and Native Americans.
(2) The mutation conferrs some advantage or arises in an individual with pre-existing advantages and is thus associated with genetic advantage. A possible example of this is blue eyes. The first blue-eyed person was supposedly born 10,000 years ago and comprised 0.001% of the global population. Now, 3%-4% of the global population has blue eyes. Blue eyes confer no objective advantage so the person in whom the mutation arose must have had some pre-existing advantage that was passed on to descendants along with the blue eyes.
...
This strikes me as a goodexplanation for the 9-repeat allele. It arose in a person with some advantage like resistance to diseases brought by Europeans to America and Eastern Siberia.