The immune system that we can observe and measure today is but a snapshot of a dynamic and evolving process, a moment in an ongoing genetic battle between hosts and their pathogens. Indications of this conflict are etched in the genome as signatures of adaptive evolution in the host immune system. These evolutionary signatures can also be read experimentally to give insight into the nature of host-pathogen interactions. This chapter will examine the evolutionary genetics of insect immune systems over both short and long timescales. In several instances, comparisons and contrasts will be drawn between species with distinct ecologies to elucidate commonalities and idiosyncrasies of insect immune evolution.

Adaptive evolution can manifest in evolutionar-ily favoured amino acid substitutions within genes as well as in genomic diversification of gene families. Both processes can be measured by comparing homologous genes and gene families across related species. Adaptive amino acid evolution is generally detected as a significantly elevated rate of amino acid substitution relative to an expectation based on the evolutionary rate at genetically silent positions (Box 13.1; Anisimova and Liberles, 2007). Adaptive gene family expansion can be inferred from an increased rate of duplication relative to that of other gene families in the genome (Hahn et al, 2005). The recent availability of whole-genome sequences from several insect species allows such comparisons to be made on a wide scale.

Innate immunity, which is shared by homology between vertebrates and insects, is hardwired within the genome and lacks the antibody production that characterizes the adaptive immune response of higher vertebrates. The insect innate immune system is capable of recognition and subsequent eradication of microbes and multicellular parasites through humoral and cellular defence mechanisms (reviewed in Lemaitre and Hoffmann, 2007). Humoral immunity is mediated by production of microbicidal peptides, enzymes, oxidative free radicals, and other compounds that are secreted directly into the insect haemolymph (blood). The humoral defence against microbial infection is genetically well understood in Drosophila melanogaster. Invading microbes are detected by recognition molecules performing surveillance, signal is transduced through two primary signalling pathways, and defence is effected in part by abundantly produced antimicrobial peptides (AMPs). The two signalling pathways, termed the Toll and Imd pathways, are conserved between invertebrates and vertebrates. Cellular immunity is defined by encapsulation or engulfment of infective agents by circulating haemocytes. It has been less well characterized at the genetic level, although some genes that mediate cellular recognition and trigger phagocytic engulf-ment of microbes have been identified. A distinct process, RNA silencing (RNA interference, RNAi), allows specific detection and eradication of RNA viruses (Wang et al, 2006). It is expected that functional diversity within the immune response will translate into variation in the selective pressures on different components of the defence response. This chapter will examine the evolutionary genetics of immune defence, interpreting molecular evolutionary patterns in light of protein function to

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