Ancient HLA genes from 7,500-year-old archaeological remains

In the past decade there has been increasing interest in cloning DNA from ancient and preserved tissues. Most studies, however, have focused on mitochondrial or chloroplast genes, present at hundreds to thousands of copies per cell compared with one or two for each nuclear gene. With a probe containing Alu repeat sequences, Pääbo isolated a 3.4-kilobase DNA fragment from a 2,400-year-old Egyptian mummy which was subsequently shown to contain an intron of the nuclear gene HLA-DQA (ref. 11). Here we report a more targeted approach to the characterization of nuclear genes from archaeological specimens. The Windover pond of central Florida has provided skeletal and soft tissue remains from 165 humans, radiocarbon-dated to be 6,990-8,130 years old. Using DNA obtained from one individual we have characterized segments from six nuclear genes: that for beta 2-microglobulin and five members of the class I HLA heavy chain gene family. Distinctive patterns of nucleotide substitution in the cloned heavy chain gene segments permit tentative assignment of the HLA-A,B type of the ancient individual.