Proportionally more deleterious genetic variation in European than in African populations

Abstract

The analysis of genome-wide patterns of variation in human populations can provide genetic evidence of patterns of human migration and adaptation across the world. Two contrasting papers in this issue illustrate the power of the method. By combining a large number of datasets, Lohmueller et al. obtain precise estimates of the number of deleterious mutations carried by each of 15 African-Americans and 20 European-Americans, resequenced across 11,000 genes. They find that individuals with a European background have more potentially damaging mutations lurking in their genomes than those with an African background. This is interpreted as a genetic legacy from the 'out-of-Africa' bottleneck that accompanied the peopling of Europe. Jakobsson et al. take a broader snapshot of human variation by examining 29 populations in the Human Genome Diversity Project. They obtain genotype data for over 500,000 markers in the human genome. Echoing the study of Americans with African and European backgrounds, these data reveal increasing linkage disequilibrium with increasing geographic distance from Africa. Combining a number of large data sets has established that a sample of European Americans have more potentially damaging mutations lurking in their genomes than a comparable sample of African Americans, supporting the model of European Americans going through a more recent population bottleneck than African Americans. Quantifying the number of deleterious mutations per diploid human genome is of crucial concern to both evolutionary and medical geneticists1,2,3. Here we combine genome-wide polymorphism data from PCR-based exon resequencing, comparative genomic data across mammalian species, and protein structure predictions to estimate the number of functionally consequential single-nucleotide polymorphisms (SNPs) carried by each of 15 African American (AA) and 20 European American (EA) individuals. We find that AAs show significantly higher levels of nucleotide heterozygosity than do EAs for all categories of functional SNPs considered, including synonymous, non-synonymous, predicted ‘benign’, predicted ‘possibly damaging’ and predicted ‘probably damaging’ SNPs. This result is wholly consistent with previous work showing higher overall levels of nucleotide variation in African populations than in Europeans4. EA individuals, in contrast, have significantly more genotypes homozygous for the derived allele at synonymous and non-synonymous SNPs and for the damaging allele at ‘probably damaging’ SNPs than AAs do. For SNPs segregating only in one population or the other, the proportion of non-synonymous SNPs is significantly higher in the EA sample (55.4%) than in the AA sample (47.0%; P < 2.3 × 10-37). We observe a similar proportional excess of SNPs that are inferred to be ‘probably damaging’ (15.9% in EA; 12.1% in AA; P < 3.3 × 10-11). Using extensive simulations, we show that this excess proportion of segregating damaging alleles in Europeans is probably a consequence of a bottleneck that Europeans experienced at about the time of the migration out of Africa.