Although the expanded BXD set increases the precision of the genetic map, there is concern as to whether one can simultaneously analyze the historical and new BXD RI lines, or whether systematic differences between the two sub-populations preclude this integration. In an analysis of the genetic architecture of these lines, Shifman et al. (2006) report 52 SNPs of 13 367 typed loci that only segregate among the new sub-populations (47 of which do not segregate in the oldest set, 5 of which do not segregate in the old lines or the first expansion). These are found on 17 chromosomes and are not tightly linked. It is especially important to note that Shifman et al. (2006) find these to be recent polymorphisms, not segregating among other inbred mouse strains, and therefore just an indicator of the potential recent mutation rate of 0.39% among polymorphic SNPs. It is predicted that some traits may be affected by these loci, underlying systematic differences may occur among the sub-populations. It would seem that if BXD sub-population effects are detected, the trait may be readily mapped
