Abstract
BackgroundThe patterns of mutation vary both within and across genomes. It has been shown for a few mammals that mutation rates vary within the genome, while for unknown reasons, the sensu stricto yeasts have uniform rates instead. The generality of these observations has been unknown. Here we examine silent site substitutions in a more expansive set (20 mammals, 27 fungi, 4 insects) to determine why some genomes demonstrate this mosaic distribution and why others are uniform.ResultsWe applied several intragene and intergene correlation tests to measure regional substitution patterns. Assuming that silent sites are a reasonable approximation to neutrally mutating sequence, our results show that all multicellular eukaryotes exhibit mutational heterogeneity. In striking contrast, all fungi are mutationally uniform – with the exception of three Candida species: C. albicans, C. dubliniensis, and C. tropicalis. We speculate that aspects of replication timing may be responsible for distinguishing these species. Our analysis also reveals classes of genes whose silent sites behave anomalously with respect to the mutational background in many species, indicating prevalent selective pressures. Genes associated with nucleotide binding or gene regulation have consistently low silent substitution rates in every mammalian species, as well as multiple fungi. On the other hand, receptor genes repeatedly exhibit high silent substitution rates, suggesting they have been influenced by diversifying selection.ConclusionOur findings provide a framework for understanding the regional mutational properties of eukaryotes, revealing a sharp difference between fungi and multicellular species. They also elucidate common selective pressures acting on eukaryotic silent sites, with frequent evidence for both purifying and diversifying selection.
Highlights
The patterns of mutation vary both within and across genomes
Our results indicate that codon usage selection is a more widespread effect in N. crassa than in the sensu stricto yeasts (Figure 4)
Insects have heterogeneous mutation rates The fungal species we have studied are at phylogenetic distances generally larger than those for the mammalian species
Summary
The patterns of mutation vary both within and across genomes. It has been shown for a few mammals that mutation rates vary within the genome, while for unknown reasons, the sensu stricto yeasts have uniform rates instead. Uniform mutation rates have been observed only in the phylogeny of the sensu stricto yeasts S. cerevisiae, S. paradoxus, S. bayanus, and S. mikatae [9] The reason for this differing mutational behavior is not understood, and little is known about regional biases in other species. BMC Evolutionary Biology 2008, 8:186 http://www.biomedcentral.com/1471-2148/8/186 zation of regional biases in a broader range of species would improve our understanding of genomic mutational properties. It would aid in the calibration of phylogenetic footprinting methods, which are important for identifying sequences under purifying selection [10]
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