Haplotypic background of a private allele at high frequency in the Americas

Kari B. Schroeder, Mattias Jakobsson, Michael H. Crawford, Theodore G. Schurr, Simina M. Boca, Don Conrad, Raul Y. Tito, Ludmilla P. Osipova, Larissa A. Tarskaia, Sergey I. Zhadanov, Jeffrey D. Wall, Jonathan K. Pritchard, Ripan S. Malhi, David G. Smith, Noah A. Rosenberg

Research output: Contribution to journalArticle

52 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)995-1016
Number of pages22
JournalMolecular Biology and Evolution
Volume26
Issue number5
DOIs
StatePublished - May 1 2009
Externally publishedYes

Fingerprint

allele
Alleles
alleles
North American Indians
American Indians
Haplotypes
haplotypes
ancestry
Population
common ancestry
Microsatellite Repeats
chromosome
Genealogy and Heraldry
Americas
microsatellite repeats
Chromosomes, Human, Pair 9
chromosomes
Genetic Selection
genealogy
Gene Frequency

Keywords

  • D9S1120
  • Homo sapiens
  • Migration
  • Native American
  • Private allele

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

Schroeder, K. B., Jakobsson, M., Crawford, M. H., Schurr, T. G., Boca, S. M., Conrad, D., ... Rosenberg, N. A. (2009). Haplotypic background of a private allele at high frequency in the Americas. Molecular Biology and Evolution, 26(5), 995-1016. https://doi.org/10.1093/molbev/msp024

Haplotypic background of a private allele at high frequency in the Americas. / Schroeder, Kari B.; Jakobsson, Mattias; Crawford, Michael H.; Schurr, Theodore G.; Boca, Simina M.; Conrad, Don; Tito, Raul Y.; Osipova, Ludmilla P.; Tarskaia, Larissa A.; Zhadanov, Sergey I.; Wall, Jeffrey D.; Pritchard, Jonathan K.; Malhi, Ripan S.; Smith, David G.; Rosenberg, Noah A.

In: Molecular Biology and Evolution, Vol. 26, No. 5, 01.05.2009, p. 995-1016.

Research output: Contribution to journalArticle

Schroeder, KB, Jakobsson, M, Crawford, MH, Schurr, TG, Boca, SM, Conrad, D, Tito, RY, Osipova, LP, Tarskaia, LA, Zhadanov, SI, Wall, JD, Pritchard, JK, Malhi, RS, Smith, DG & Rosenberg, NA 2009, 'Haplotypic background of a private allele at high frequency in the Americas', Molecular Biology and Evolution, vol. 26, no. 5, pp. 995-1016. https://doi.org/10.1093/molbev/msp024
Schroeder, Kari B. ; Jakobsson, Mattias ; Crawford, Michael H. ; Schurr, Theodore G. ; Boca, Simina M. ; Conrad, Don ; Tito, Raul Y. ; Osipova, Ludmilla P. ; Tarskaia, Larissa A. ; Zhadanov, Sergey I. ; Wall, Jeffrey D. ; Pritchard, Jonathan K. ; Malhi, Ripan S. ; Smith, David G. ; Rosenberg, Noah A. / Haplotypic background of a private allele at high frequency in the Americas. In: Molecular Biology and Evolution. 2009 ; Vol. 26, No. 5. pp. 995-1016.
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AU - Conrad, Don

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