The discovery of recently occurring Alu insertions that are polymorphic across human populations has provided a very valuable tool to understand human population genetics and in particular our evolutionary history. Alu elements, as well as other SINEs and LINEs, have particular advantages for such studies over other forms of genetic variation such as microsatellites or SNPs. Notably, the ancestral state is known - the absence of the insertion -such that the root of a particular population tree can be determined (Batzer et al. 1994). With these markers it is also possible to infer identity by descent. If people share a particular Alu insertion, they have inherited it from a common ancestor, as the chances of a second Alu insertion having occurred independently at the same genomic location are extremely remote. The number of potential sites of insertion is huge and the rate of insertion low, moreover loss or reversion of an element is extremely rare (Ho et al. 2005a). For the study of human population genetics, Alu markers are considered to be 'homoplasy free': every observed insertion at a particular genomic locus being identical by descent to the insertion created by the original transposition event (Salem et al. 2003c; Witherspoon et al. 2006; Xing et al. 2007). A number of studies have investigated the diversity of recent Alu and L1 insertions in a range of different populations (Box 8.4).
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