Extensive Linkage Disequilibrium in Small Human Populations in Eurasia

Henrik Kaessmann,1,* Sebastian Zöllner,1,* Anna C. Gustafsson,2 Victor Wiebe,1 Maris Laan,3 Joakim Lundeberg,2 Mathias Uhlén,2 and Svante Pääbo1

1Max Planck Institute for Evolutionary Anthropology, Leipzig; 2Royal Institute of Technology, Stockholms Center for Physics, Astronomy and Biotechnology, Department of Biotechnology, Stockholm; and 3University of Tartu Institute of Molecular and Cell Biology, Estonian Biocentre, Tartu, Estonia

Received October 8, 2001; accepted for publication December 10, 2001; electronically published January 28, 2002.

The extent of linkage disequilibrium (LD) was studied in two small food-gathering populationsEvenki and Saamiand two larger food-producing populationsFinns and Swedesin northern Eurasia. In total, 50 single-nucleotide polymorphisms (SNPs) from five genes were genotyped using real-time pyrophosphate DNA sequencing, whereas 14 microsatellites were genotyped in two X-chromosomal regions. In addition, hypervariable region I of the mtDNA was sequenced to shed light on the demographic history of the populations. The SNP data, as well as the microsatellite data, reveal extensive levels of LD in Evenki and Saami when compared to Finns and Swedes. mtDNA-sequence variation is compatible with constant population size over time in Evenki and Saami but indicates population expansion in Finns and Swedes. Furthermore, the similarity between Finns and Swedes in SNP allele- and haplotype-frequency distributions indicate that these two populations may share a recent common origin. These findings suggest that populations such as the Evenki and the Saami, rather than the Finns, may be particularly suited for the initial coarse mapping of common complex diseases.

* The first two authors contributed equally to this work.