Active Alu elements are passed primarily through paternal germlines.

Repetitive elements are distributed non-randomly in the human genome but, as reviewed in this paper, biological processes underlying the observed patterns appear to be complex and remain relatively obscure. Recent findings indicate that chromosomal distribution of Alu retroelements deposited in the past is different from the distribution of Alu elements that continue to be inserted in human population. These active elements from AluY sub(sub)families are the major focus of this paper. In particular, we analyzed chromosomal proportions of 19 AluY subfamilies, of which nine are reported for the first time in this paper. These 19 subfamilies contain over 80% of Alu elements that are polymorphic in the human genome. The chromosomal density of these most recent Alu insertions is around three times higher on chromosome Y than on chromosome X and over two times higher than the average density for all human autosomes. Based on this observation and other data we propose that active Alu elements are passed through paternal germlines. There is also some evidence that a small fraction of active Alu elements from less abundant subfamilies can be retroposed in female germlines or in the early embryos. Finally, we propose that the origin of Alu subfamilies in human populations may be related to evolution of chromosome Y.