Molecular arms-races and the evolution of immune genes

pathways We are interested in understanding how gene function determines the rate of adaptive evolution, and particularly whether molecular 'arms-races' might drive a disproportionate amount of adaptive substitution. Because the immune system coevolves with pathogens (and other parasites), it is expected to evolve rapidly relative to the rest of the genome, and we have used population genetics approaches in Drosophila to look for differences in the rate of adaptive evolution between immunity and non-immunity genes, and between different types of immunity gene. In Drosophila it is striking that RNAi genes (including those that defend against viruses) show very strong evidence of adaptive evolution, suggesting that they are engaged in a host-parasite arms race with viruses. To understand whether this is peculiar to Drosophila, we are now asking similar questions using a population-genomic study of Daphnia magna, in collaboration with Tom Little.

Drosophila viruses

Twelve different species of Drosophila Although Drosophila is one of our best models for innate immunity, until recently we have known surprisingly little about Drosophila's natural pathogens. Viruses are common in Drosophila and may be a major driver of evolution in its immune system. However, so far only a handful have been studied in the lab, and apart from the Sigma rhabdovirus (see The Jiggins Lab) none have been widely studied in the wild. We have used metagenomic sequencing to identify nearly 100 new RNA viruses and around 10 DNA virus in wild Drosophila of many different species, and we maintain a comprehensive list of published Drosophila viruses, and provide a broad sample of different virus and isolate sequences. RT-PCR surveys of flies in the wild, and of publicly available RNAseq data from lab stocks and cell culture, show that many of these viruses are common (and that cell culture infections are almost ubiquitous. We have isolated one DNA virus for further study (just email for an aliquot), and we would like to isolate more.

The evolution of RNAi

RNAi Pathways in the metazoa RNA interference has an essential role in mediating defence against viruses and transposable elements. This is well-studied in plants, fungi, nematodes and insects, and so appears to be phylogenetically ancient. However, in the absence of experimental data from basal eukaryotes (and most animal phyla), the origins and homology between antiviral RNAi mechanisms remains unclear. We are therefore using a metagenomic approach to study viruses and virus-derived siRNAs in a range of non-model lineages. We also have a broad interest in the way that RNAi pathway genes evolve. This includes both the origins and duplication history of major RNAi gene families, and the role that selection mediated by viruses and/or transposable elements might have played in shaping their sequences.

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