An apportionment of human DNA diversity

Abstract

It is often taken for granted that the human species is divided in rather homogeneous groups or races, among which biological differences are large. Studies of allele frequencies do not support this view, but they have not been sufficient to rule it out either. We analyzed human molecular diversity at 109 DNA markers, namely 30 microsatellite loci and 79 polymorphic restriction sites (restriction fragment length polymorphism loci) in 16 populations of the world. By partitioning genetic variances at three hierarchical levels of population subdivision, we found that differences between members of the same population account for 84.4% of the total, which is in excellent agreement with estimates based on allele frequencies of classic, protein polymorphisms. Genetic variation remains high even within small population groups. On the average, microsatellite and restriction fragment length polymorphism loci yield identical estimates. Differences among continents represent roughly 1͞10 of human molecular diversity, which does not suggest that the racial subdivision of our species ref lects any major discontinuity in our genome.In 1972, Richard Lewontin analyzed allele frequencies at 15 protein loci and concluded that 85% of the overall human genetic diversity is represented by individual diversity within populations (1). Differences among seven racial groups accounted for less than 7% of the total. Nei and Roychoudhury reached a similar apportionment of genetic diversity among populations from three continents (2). Although these results were repeatedly confirmed by studies of protein markers (3-5), the idea that the human species is deeply subdivided into races has not disappeared (6, 7). Reasons for this include some perceived discontinuity among populations, usually reported for quantitative traits (6), and the possibility that protein markers, including blood groups, may not exhaustively describe genetic variation, leaving open the possibility that the undetected variation might show a different pattern.In this study, we analyzed how DNA variation is distributed at 109 loci (Fig. 1). Based on the lengths and frequencies of the microsatellite alleles and on the frequencies of allelic variants at restriction fragment length polymorphism (RFLP) loci, we quantified the differences among members of the same population, among populations of the same continent, and among four or five geographical groups. Materials and MethodsThree largely independent sets of genetic data were used in this study. The microsatellite database comprises individual allele lengths for 29 repeats and one tetranucleotide repeat of chromosomes 13 and 15. This is the set of data used by Bowcock et al. (8) from which we excluded nonhuman primates. The map distances between adjacent loci, except eight of them, are such that linkage disequilibrium can hardly be considered a major disturbing factor. Fourteen populations are included, for an overall sample size of 148. However, for no marker was a complete set of 296 chromosomes available. The mi...

Extreme population differences across Neuregulin 1 gene, with implications for association studies

“…The average F ST for all 39 populations is B0.13, in agreement with previous studies of neutral markers. 47,[53][54][55][56] However, two SNPS, namely SNPnrg9 and SNPnrg10, were observed to show particularly high F ST values. It is the differences between continental groupings that is of note here; the frequencies remain homogenous across populations within continental groupings.…”

Divergent patterns of linkage disequilibrium and haplotype structure across global populations at the interleukin-13 (IL13) locus

“…The South Amerindian populations appear to be outliers, likely due to high levels of genetic drift in these small and isolated populations. The among-population component of genetic variance (F ST ¼ 0.24) is relatively high, nearly twice the mean global F ST value for human populations (0.10-0.12 33 ).…”

“…Signatures of natural selection can also be detected by analysis of F ST Figure 4), which are considerably higher than the average F CT value for individual SNPs at the IL13 gene (0.08), and higher than typical values of F ST observed for other loci (0.10-0.12 33 ). These SNPs are in LD with each other in non-African populations ( Figure 5), which could explain why they share high F CT values.…”

Haplotype tagging efficiency in worldwide populations in CTLA4 gene

“…The average F ST for all 44 populations is B0.10, in agreement with previous studies of neutral markers. [32][33][34] When instead of 44 independent populations the eight continental groups are considered, there is only a slight decrease in the F ST values. As expected, the highest continental F ST value is found in sub-Saharan Africa, with very low values and extreme homogeneity within Europe, North-Africa and Central/South Asia.…”