Y chromosome STR testing

Another way of getting information on a male contributor is to use PCR to target STRs on the Y chromosome.  Since females have two X chromosomes, instead of an X and a Y, the male DNA can sometimes be distinguished even if there is more female than male DNA present.  Such Y-chromosome STR tests are in use, but they tend to be used only after the other tests have failed to give clear results.  There are several reasons:  First, the Y-chromosome is a small chromosome with no pairing partner.  Pairing of the other chromosomes promotes exchange of DNA, effectively a scrambling event, known as recombination.  An effect of this is that various loci, when far enough apart, can become independent markers (they are said to be in equilibrium).  This means having allele type 1, at locus A on the chromosome doesn't imply an increased or decreased probability of having a particular allele at locus B on the same chromosome.  This is idealized and requires the locus be far apart on the chromosome, and also that functional products in the two regions don't interact.  The Y chromosome, on the other hand, only recombines (with the X chromosome) at a small region of the short end of the chromosome.  As far as we know, it doesn't recombine in other regions of its length.  One probable result of this is that loci on the Y-chromosome may be more dependent on one another than loci on other chromosomes.  Y-chromosome STR testing is an active area of research, since despite the limitations, there may eventually prove to be some advantages.