Categorizing chicken Z gene M:F ratios by their degree of difference from zebra finch. (A) Genes were categorized into group 1 with M:F ratios greater in chicken than zebra finch (C>Z, blue), group 2 with M:F ratios similar in the two species (green, >85% of genes), and group 3 with M:F ratios lower in chicken than in zebra finch (C<Z, red). Genes higher in one species were those for which the log2 M:F ratio was ≥0.25 more in that species than the other. (B) Graph of the three classes of genes by gene order along the Z chromosome of chicken. The region 20–40 Mb was abundant in red spots (C<Z) but lacking in blue spots (C>Z). (C) The proportion of the three classes of genes in four major divisions of the chicken Z chromosomes. Along most of the chromosome regions, red genes (C<Z) were less abundant than blue genes (C>Z), except for the region 20–40 Mb. When gene order was randomized 1000 times, the large difference in proportion of red and blue genes in this interval was found to occur rarely by chance (P < 0.05), whereas the difference in other chromosome regions was not unlikely. The patterns shown here are common to all 12 chicken versus zebra finch comparisons for the three chicken tissues of Itoh et al. (2007) and the four zebra finch telencephalic samples measured here. (D) The ratio of the number of blue (C>Z) to red (C<Z) genes is plotted as a moving average across a window 20 Mb wide (step size 1 Mb) graphed by window center along the Z chromosome. The curve minimum is at 31–32 Mb, near the MHM locus. Thus, the MHM region is unusual because its genes tend to have lower M:F ratios in chicken than zebra finch.
