Genetic diversity on the human X chromosome suggests there is no single pseudoautosomal boundary.
Unlike the autosomes, recombination between the X chromosome and Y chromosome is thought be constrained to two small pseudoautosomal regions (PARs) at the tips of each sex chromosome. The PAR1 spans the first 2.6 Mb of the proximal arm of the human sex chromosomes and is conserved across most eutherian mammals. The PAR1 is separated from the nonPAR region on the Y chromosome by a Y-specific inversion that is hypothesized to suppress X-Y recombination. The much smaller PAR2, spanning the distal 320 kb of the long arm of each chromosome, was duplicated from the terminal end of the X to the terminal end of the Y in the common ancestor of humans. In addition to the PAR1 and PAR2, there is a human-specific X-transposed region (XTR) that is suspected to behave as a third pseudoautosomal region. Genetic diversity is expected to be higher in recombining regions than in nonrecombining regions. In this study we investigate patterns of genetic diversity across unrelated individuals and divergence between primates across all regions of the human X chromosome. We observe that genetic diversity in PAR1 is significantly greater than the non-PARs. However, we observe a gradual shift from higher to lower diversity across this region, not an abrupt shift at the proposed pseudoautosomal boundary, suggesting that non-homologous recombination is common on the human sex chromosomes and spans the pseudoautosomal boundary. In contrast, diversity in the PAR2 is not significantly elevated compared to the nonPAR, suggesting that recombination is not obligatory in the PAR2. Finally, diversity in the XTR is higher than both the surrounding nonPARs, and the PAR2, providing evidence that recombination may occur with some frequency between the X and Y in the XTR. Although they comprise only a small percentage of the genome, the PARs and the XTR house essential genes for both sexes