Pilot HGDP: Contribution of Alu repeats to Human Genomic Diversity

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The insertion of mobile elements into the genome represents a new class of nuclear markers for the study of human genomic diversity. The Alu family of mobile elements comprise 5% of the human genome. Most members of the recently integrated Alu subfamilies are restricted to the human genome and absent from nonhuman primates. Many of these repeat units have inserted so recently within the human genome that they are polymorphic for the presence or absence of an Alu element at a particular chromosomal location. Alu insertion polymorphisms offer two important advantages over other nuclear based polymorphisms for human evolution studies. First, the presence of an Alu element represents identity by descent, since the probability that two different young Alu repeats would integrate independently in the same chromosomal location is negligible. Second, the ancestral state of each Alu insertion polymorphism is known to be the absence of the element, which can be used to root trees of population relationships. In this project we will determine the human genomic diversity associated with several polymorphic Alu elements and develop haplotyping systems composed of polymorphic Alu insertions and adjacent microsatellite loci. Using both Alu repeats and microsatellites in each haplotype results in the combination of an identical by descent (Alu insertion) marker, with a class of marker that has a high mutation rate (microsatellites) providing a genomic memory for both early radiations of humans as well as recent evolutionary history.