Genetic variation among world populations: Inferences from 100 Alu insertion polymorphisms

W. Scott Watkins, Alan R. Rogers, Christopher T. Ostler, Steve Wooding, Michael J. Bamshad, Anna Marie E Brassington, Marion L. Carroll, Son V. Nguyen, Jerilyn A. Walker, B. V Ravi Prasad, P. Govinda Reddy, Pradipta K. Das, Mark A. Batzer, Lynn B. Jorde

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Abstract

We examine the distribution and structure of human genetic diversity for 710 individuals representing 31 populations from Africa, East Asia, Europe, and India using 100 Alu insertion polymorphisms from all 22 autosomes. Alu diversity is highest in Africans (0.349) and lowest in Europeans (0.297). Alu insertion frequency is lowest in Africans (0.463) and higher in Indians (0.544), E. Asians (0.557), and Europeans (0.559). Large genetic distances are observed among African populations and between African and non-African populations. The root of a neighbor-joining network is located closest to the African populations. These findings are consistent with an African origin of modern humans and with a bottleneck effect in the human populations that left Africa to colonize the rest of the world. Genetic distances among all pairs of populations show a significant product-moment correlation with geographic distances (r = 0.69, P < 0.00001). FST, the proportion of genetic diversity attributable to population subdivision is 0.141 for Africans/E. Asians/Europeans, 0.047 for E. Asians/Indians/Europeans, and 0.090 for all 31 populations. Resampling analyses show that ∼50 Alu polymorphisms are sufficient to obtain accurate and reliable genetic distance estimates. These analyses also demonstrate that markers with higher FST values have greater resolving power and produce more consistent genetic distance estimates.

Original languageEnglish (US)
Pages (from-to)1607-1618
Number of pages12
JournalGenome Research
Volume13
Issue number7
DOIs
StatePublished - Jul 1 2003

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Population
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Medical Genetics
India

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  • Genetics

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Watkins, W. S., Rogers, A. R., Ostler, C. T., Wooding, S., Bamshad, M. J., Brassington, A. M. E., ... Jorde, L. B. (2003). Genetic variation among world populations: Inferences from 100 Alu insertion polymorphisms. Genome Research, 13(7), 1607-1618. https://doi.org/10.1101/gr.894603

Genetic variation among world populations : Inferences from 100 Alu insertion polymorphisms. / Watkins, W. Scott; Rogers, Alan R.; Ostler, Christopher T.; Wooding, Steve; Bamshad, Michael J.; Brassington, Anna Marie E; Carroll, Marion L.; Nguyen, Son V.; Walker, Jerilyn A.; Prasad, B. V Ravi; Reddy, P. Govinda; Das, Pradipta K.; Batzer, Mark A.; Jorde, Lynn B.

In: Genome Research, Vol. 13, No. 7, 01.07.2003, p. 1607-1618.

Research output: Contribution to journalArticle

Watkins, WS, Rogers, AR, Ostler, CT, Wooding, S, Bamshad, MJ, Brassington, AME, Carroll, ML, Nguyen, SV, Walker, JA, Prasad, BVR, Reddy, PG, Das, PK, Batzer, MA & Jorde, LB 2003, 'Genetic variation among world populations: Inferences from 100 Alu insertion polymorphisms', Genome Research, vol. 13, no. 7, pp. 1607-1618. https://doi.org/10.1101/gr.894603
Watkins WS, Rogers AR, Ostler CT, Wooding S, Bamshad MJ, Brassington AME et al. Genetic variation among world populations: Inferences from 100 Alu insertion polymorphisms. Genome Research. 2003 Jul 1;13(7):1607-1618. https://doi.org/10.1101/gr.894603
Watkins, W. Scott ; Rogers, Alan R. ; Ostler, Christopher T. ; Wooding, Steve ; Bamshad, Michael J. ; Brassington, Anna Marie E ; Carroll, Marion L. ; Nguyen, Son V. ; Walker, Jerilyn A. ; Prasad, B. V Ravi ; Reddy, P. Govinda ; Das, Pradipta K. ; Batzer, Mark A. ; Jorde, Lynn B. / Genetic variation among world populations : Inferences from 100 Alu insertion polymorphisms. In: Genome Research. 2003 ; Vol. 13, No. 7. pp. 1607-1618.
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