This elevated rate of recombination in AR is likely because of the AR arrangement's demographic history and frequency distribution.
The breakpoint regions within the other gene arrangements also show significant LD, except for the AR arrangement.
The greatest chromosome-wide average recombination rate is detected in the AR arrangement (ρ Avg=0.061/bp), whereas the lowest is observed in the CH arrangement (ρ Avg = 0.018/bp).
It was shown that the PP arrangement had the highest levels of LD and the AR arrangement had the lowest levels of LD.
In addition, levels of variation are expected to be lower in the youngest arrangements and this is not true in the case of the AR arrangement.
There is increasing evidence that D. pseudoobscura has undergone a recent population expansion, which may be more pronounced in the AR arrangement due to recent selection (Schaeffer 2002; Schaeffer et al. 2003; Haddrill et al. 2011; Wallace et al. 2011).
Transposition of trnR on the α-strand, generating the RA versus AR arrangement, differentiates the Culicidae mosquitos from other species of Diptera (Beard et al. 1993; Mitchell et al. 1993; Behura et al. 2011).
The likely explanation is that ST to PP inversion is twice the size of the AR arrangement, which will likely result in more genetic exchange among chromosomes leading to more independence in the genetic information.
The proximal, distal, and inverted regions, however, failed to show the derived AR arrangement with consistently lower levels of variation compared to the ancestral ST chromosome (Table 1 and Figure 4).
The derived AR arrangement has lower heterozygosity levels at its two breakpoint regions compared with the ancestral ST arrangement or randomly chosen AR or ST chromosomes, but in the majority of other regions AR has greater levels of heterozygosity than ST.
GATK (McKenna et al. 2010) software was used to remove duplicate sequence reads, recalibrate base quality scores, and locally realign regions around indels for BWA alignments (Depristo et al. 2011).The reference strain carries the AR arrangement (Richards et al. 2005).
