Abstract
It is estimated that a large proportion of amino acid substitutions in Drosophila have been fixed by natural selection, and as organisms are faced with an ever-changing array of pathogens and parasites to which they must adapt, we have investigated the role of parasite-mediated selection as a likely cause. To quantify the effect, and to identify which genes and pathways are most likely to be involved in the host–parasite arms race, we have re-sequenced population samples of 136 immunity and 287 position-matched non-immunity genes in two species of Drosophila. Using these data, and a new extension of the McDonald-Kreitman approach, we estimate that natural selection fixes advantageous amino acid changes in immunity genes at nearly double the rate of other genes. We find the rate of adaptive evolution in immunity genes is also more variable than other genes, with a small subset of immune genes evolving under intense selection. These genes, which are likely to represent hotspots of host–parasite coevolution, tend to share similar functions or belong to the same pathways, such as the antiviral RNAi pathway and the IMD signalling pathway. These patterns appear to be general features of immune system evolution in both species, as rates of adaptive evolution are correlated between the D. melanogaster and D. simulans lineages. In summary, our data provide quantitative estimates of the elevated rate of adaptive evolution in immune system genes relative to the rest of the genome, and they suggest that adaptation to parasites is an important force driving molecular evolution.
Highlights
Hosts face an ever-changing array of parasites to which they must adapt, and parasites are widely believed to be one of the most important and universal selection pressures in natural populations
After excluding sites with less than 20-fold coverage (Figure S1) and genes represented by less than 100 bp of sequence, there remained a total of 462.7 kbp of protein coding sequence from D. melanogaster representing 415 genes, and 335.6 kbp from D. simulans representing 309 genes
In this coding sequence we identified 12,974 putative SNPs in D. melanogaster and 10,759 in D. simulans
Summary
Hosts face an ever-changing array of parasites to which they must adapt, and parasites are widely believed to be one of the most important and universal selection pressures in natural populations Consistent with this view, immune genes in several taxa are known to evolve faster than other genes, and sometimes significantly faster than the neutral rate – a signature of adaptive evolution [1,2,3]. The rate at which natural selection fixes new mutations can be estimated by comparing the amount of polymorphism within populations to divergence between species at synonymous and nonsynonymous sites [10,11,12,13,14] Approaches of this kind have been used to estimate the genome-wide rate of adaptive evolution, and found that it is often surprisingly high [10,13,15,16,17]. The nature of the selection pressures underlying this evolution remains unknown
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