The distribution of human genetic diversity: A comparison of mitochondrial, autosomal, and Y-chromosome data

We report a comparison of worldwide genetic variation among 255 individuals by using autosomal, mitochondrial, and Y-chromosome polymorphisms. Variati on is assessed by use of 30 autosomal restriction-site polymorphisms (RSPs) , 60 autosomal short-tandem-repeat polymorphisms (STRPs), 13 Alu-insertion polymorphisms and one LINE-1: element, 611 bp of mitochondrial control-regi on sequence, and 10 Y-chromosome polymorphisms. Analysis of these data reve als substantial congruity among this diverse array of genetic systems. With the exception of the autosomal RSPs, in which an ascertainment bias exists , all systems show greater gene diversity in Africans than in either Europe ans or Asians. Africans also have the largest total number of alleles, as w ell as the largest number of unique alleles, for most systems. G(ST) values are 11%-18% for the autosomal systems and are two to three times higher fo r the mtDNA sequence and Y-chromosome RSPs. This difference is expected bec ause of the lower effective population size of mtDNA and Y chromosomes. A l ower value is seen for Y-chromosome STRs, reflecting a relative lack of con tinental population structure, as a result of rapid mutation and genetic dr ift. Africa has higher G(ST) values than does either Europe or Asia for all systems except the Y-chromosome STRs and Alus. All systems except the Y-ch romosome STRs show less variation between populations within continents tha n between continents. These results are reassuring in their consistency and offer broad support for an African origin of modern human populations.