Evidence of the adaptive evolution of immune genes in chicken

Abstract

The basis for understanding the characteristics of gene functional categories in chicken has been enhanced by the ongoing sequencing of the zebra finch genome, the second bird species to be extensively sequenced. This sequence provides an avian context for examining how variation in chicken has evolved since its divergence from its common ancestor with zebra finch as well as well as a calibrating point for studying intraspecific diversity within chicken. Immune genes have been subject to many selective processes during their evolutionary history: this gene class was investigated here in a set of orthologous chicken and zebra finch genes with functions assigned from the human ortholog. Tests demonstrated that nonsynonymous sites at immune genes were highly conserved both in chicken and on the avian lineage. McDonald-Kreitman tests provided evidence of adaptive evolution and a higher rate of selection on fixation of nonsynonymous substitutions at immune genes compared to that at non-immune genes. Further analyses showed that GC content was much higher in chicken than in zebra finch genes, and was significantly elevated in both species' immune genes. Pathogen challenges are likely to have driven the selective forces that have shaped variation at chicken immune genes, and continue to restrict diversity in this functional class.

Figure 1

Correlation of chicken chromosome length with chromosomal GC3 content for chicken genes and their zebra finch orthologs. The best fitting linear correlations of GC content at the third codon position (GC3) for chicken (red, r² = 0.435, p = 0.010) and zebra finch (blue, r² = 0.358, p = 0.030) with chicken chromosome size (on a log scale) are shown by the dashed lines.