Chromosomal location effects on gene sequence evolution in mammals

Background: Nucleotide substitution rates and G+C content vary considerably among mammalian genes. it has been proposed that the mammalian genome comprises a mosaic of regions - termed isochores - with differing G+C content. The regional variation in gene G+C content might therefore be a reflection of the isochore structure of chromosomes, but the factors influencing the variation of nucleotide substitution rate are still open to question. Results: To examine whether nucleotide substitution rates and gene G+C content are influenced by the chromosomal location of genes, we compared human and murid (mouse or rat) orthologues known to belong to one of the chromosomal (autosomal) segments conserved between these species. Multiple members of gene families were excluded from the dataset. Sets of neighbouring genes were defined as those lying within 1 centiMorgan (cM) of each other on the mouse genetic map. For both synonymous substitution rates and G+C content at silent sites, neighbouring genes were found to be significantly more similar to each other than sets of genes randomly drawn from the dataset. Moreover, we demonstrated that the regional similarities in G+C content (isochores) and synonymous substitution rate were independent of each other. Conclusions: Our results provide the first substantial statistical evidence for the existence of a regional variation in the synonymous substitution rate within the mammalian genome, indicating that different chromosomal regions evolve at different rates. This regional phenomenon which shapes gene evolution could reflect the existence of 'evolutionary rate units' along the chromosome.