Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa - PubMed (original) (raw)

Comparative Study

Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa

M Stoneking et al. Genome Res. 1997 Nov.

Abstract

Alu insertion polymorphisms (polymorphisms consisting of the presence/absence of an Alu element at a particular chromosomal location) offer several advantages over other nuclear DNA polymorphisms for human evolution studies. First, they are typed by rapid, simple, PCR-based assays; second, they are stable polymorphisms-newly inserted Alu elements rarely undergo deletion; third, the presence of an Alu element represents identity by descent-the probability that different Alu elements would independently insert into the exact same chromosomal location is negligible; and fourth, the ancestral state is known with certainty to be the absence of an Alu element. We report here a study of 8 loci in 1500 individuals from 34 worldwide populations. African populations exhibit the most between-population differentiation, and the population tree is rooted in Africa; moreover, the estimated effective time of separation of African versus non-African populations is 137,000 +/- 15,000 years ago, in accordance with other genetic data. However, a principal coordinates analysis indicates that populations from Sahul (Australia and New Guinea) are nearly as close to the hypothetical ancestor as are African populations, suggesting that there was an early expansion of tropical populations of our species. An analysis of heterozygosity versus genetic distance suggests that African populations have had a larger effective population size than non-African populations. Overall, these results support the African origin of modern humans in that an earlier expansion of the ancestors of African populations is indicated.

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Figures

Figure 1

Figure 1

Map of sample localities.

Figure 2

Figure 2

Neighbor-joining tree of population relationships. This tree is rooted where a hypothetical ancestral population—in which the frequency of the Alu element at each of the eight loci is set to 0.0—attaches to the unrooted network. Numbers indicate (in per cent) the fraction of 500 bootstrap replicates that supported a particular grouping.

Figure 3

Figure 3

Plot of the first two principal coordinates of the allele frequencies at the eight polymorphic Alu insertion loci. The same relative population relationships were observed when the hypothetical ancestral population (consisting of allele frequencies of zero for the presence of the Alu element at each locus) was removed from the analysis (data not shown), indicating that the inclusion of the ancestral population is not distorting the population relationships.

Figure 4

Figure 4

Plot of heterozygosity vs. distance from the centroid. The broken line is the expected relationship predicted by the model of Harpending and Ward (1982), according to the formula _h_i = H(1 − _r_i), where _r_i is the distance from the centroid and _h_i and H are the heterozygosities of population i and the total population, respectively.

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