These two locations do not correlate to a known boundary of the X chromosomal evolutionary strata, and the compositional differences between the sequences on either side of these boundaries might not be a result of a different evolutionary origin.
A wider comparison of noncoding DNA regions between the X and Y chromosomes, especially those near the PAR, will help delineate the boundaries of evolutionary strata and define differences in the degree of heteromorphy between these strata, which will be essential for gaining a broader understanding of the evolution of plant sex chromosomes.
Ross et al. (2005) presented a scenario of inversions between the human X and Y chromosomes consistent with the evolutionary strata 3, 4, and 5.
The question can be addressed by examine the X specific genes between the two evolutionary strata in the X chromosome.
In conclusion, we present a novel method for the unbiased detection of the presence of evolutionary strata on sex chromosomes and fine-scale delineation of their boundaries.
We show here Wilcoxon test p-values for comparing substitution rates between Z and autosomes or different evolutionary strata.
Similar to the case in mammals [ 42], avian sex chromosome evolution has been characterized by step-wise cessation of recombination between the Z and W chromosomes that have generated at least two evolutionary strata, roughly corresponding to the p and q arms [ 43].
Indeed, we find the Z-linked introns show a significantly higher substitution rate (P < 2.2e-16, Wilcoxon test) than autosomal introns, and older evolutionary strata (we named the oldest strata as S0, then S1, S2 etc).
The absence of segmental structure within chicken autosomal sequences homologous to human X-linked sequences demonstrates that stratum formation fundamentally alters sequence composition, thus allowing identification of compositional signals unique to evolutionary strata by the proposed segmentation and clustering method.
On the basis of sequence divergence between these genes, the authors predicted the existence of two evolutionary strata: one large pericentric region encompassing most of the chromosome and another much smaller region distal to the mat locus.
