Larger Genetic Differences Within Africans Than Between Africans and Eurasians

TLDR

Worldwide SNP variation remains incompletely understood, and noncoding regions—less affected by selection—are used to trace human evolutionary history, requiring careful specification of sample geographic origins. The study aimed to characterize SNP patterns in noncoding DNA, which better reflect human evolutionary history. Researchers sequenced 50 ~500‑bp noncoding segments from 10 individuals each of African, European, and Asian ancestry, and estimated nucleotide diversity (π) for autosomal and X‑linked regions. African populations exhibit roughly twice the nucleotide diversity of Asians and Europeans, with African diversity exceeding that between Africans and Eurasians, confirming that Eurasian diversity is a subset of African diversity and supporting the out‑of‑Africa model.

Abstract

Abstract The worldwide pattern of single nucleotide polymorphism (SNP) variation is of great interest to human geneticists, population geneticists, and evolutionists, but remains incompletely understood. We studied the pattern in noncoding regions, because they are less affected by natural selection than are coding regions. Thus, it can reflect better the history of human evolution and can serve as a baseline for understanding the maintenance of SNPs in human populations. We sequenced 50 noncoding DNA segments each ∼500 bp long in 10 Africans, 10 Europeans, and 10 Asians. An analysis of the data suggests that the sampling scheme is adequate for our purpose. The average nucleotide diversity (π) for the 50 segments is only 0.061% ± 0.010% among Asians and 0.064% ± 0.011% among Europeans but almost twice as high (0.115% ± 0.016%) among Africans. The African diversity estimate is even higher than that between Africans and Eurasians (0.096% ± 0.012%). From available data for noncoding autosomal regions (total length = 47,038 bp) and X-linked regions (47,421 bp), we estimated the π-values for autosomal regions to be 0.105, 0.070, 0.069, and 0.097% for Africans, Asians, Europeans, and between Africans and Eurasians, and the corresponding values for X-linked regions to be 0.088, 0.042, 0.053, and 0.082%. Thus, Africans differ from one another slightly more than from Eurasians, and the genetic diversity in Eurasians is largely a subset of that in Africans, supporting the out of Africa model of human evolution. Clearly, one must specify the geographic origins of the individuals sampled when studying π or SNP density.