Evolutionary patterns in the antimicrobial immune response

Immune genes tend to evolve more quickly and adaptively than non-immune genes in vertebrates and insects (Murphy, 1991; Schlenke and Begun, 2003; Nielsen et al., 2005; Sackton et al, 2007; Waterhouse et al., 2007). This adaptive evolution is shown by elevated rates of amino acid substitution between species and by elevated rates of duplication within gene families. The availability of whole-genome sequences allows for quantitative contrasts to be made between immune and non-immune genes, as well as for comparisons between functional classes of immune response genes. The recent complete genome sequencing of 12 species of fruit flies in the genus Drosophila has allowed particularly fine measurement of rates of substitution and genomic rearrangements between closely related species. More distant comparative genomic analyses can be achieved by comparing genome sequences of Drosophila, the mosquitoes Anopheles gambiae and Aedes aegypti, the honey bee Apis mellifera, and the red flour beetle Tribolium castaneum (Figure 13.1).

Genome comparisons between species reveal the distinct selective pressures acting on each species through its unique life history. For example, the honey bee A. mellifera has apparently reduced copy number in immune-related gene families, perhaps reflecting decreased emphasis on immuno-logical defence due to hygienic behaviour in the hive (Evans et al., 2006). Mosquitoes have expansions in gene families thought to play defensive roles against pathogens borne in vertebrate blood (Christophides et al., 2002; Waterhouse et al, 2007). Interpretation of these comparisons is often limited, however, because identification of most immune genes in insects stems from functional characterization in only a few species, and primarily in D. melanogaster. Novel defence mechanisms in functionally uncharacterized organisms will not be detected through homology searching of genome sequences if they are too divergent to be detected by similarity at the DNA sequence level. Additionally, genes that are evolving extremely rapidly may diverge too quickly to be identified in comparisons between distantly related species. Genomic comparisons will gain power with melanogaster group melanogaster subgroup y

Apis mellifera Tribolium castaneum Anopheles gambiae Aedes aegypti Drosophila grimshawi Drosophila virilis Drosophila mojavensis Drosophila willistoni Drosophila persimilis Drosophila pseudoobscura Drosophila ananassae Drosophila erecta Drosophila yakuba Drosophila sechellia Drosophila simulans Drosophila melanogaster

Approximate ^ divergence time 0 (millions of years)

Figure 13.1 Phylogeny of select insect species with sequenced genomes. The melanogaster species group and melanogaster species subgroup are indicated. Gene-family expansions and contractions were evaluated among Drosophila (fruit flies), Anopheles gambiae (African malaria mosquito), Aedes aegypti (yellow fever mosquito), Apis mellifera (honey bee), and Tribolium castaneum (red flour beetle) and within the genus Drosophila. Adaptive amino acid evolution measurement, which requires shorter phylogenetic distances, was performed primarily in the melanogaster species group of Drosophila (Tamura et al., 2004; Savard et al., 2006; Drosophila 12 Genomes Consortium, 2007; Waterhouse et al., 2007).

increasing functional characterization of nonmodel systems and the accumulation of whole-genome sequences for phylogenetically dispersed organisms.

Comparative genomic and molecular evolutionary analyses have revealed that not all genes in the immune system evolve along the same trajectories. Genes in broadly defined functional categories differ in evolutionary mode, suggesting contrasting selective pressures based on gene function. The supporting data and potential selective pressures that drive these evolutionary patterns will be considered in detail.

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