Anopheles immune genes and amino acid sites evolving under the effect of positive selection

Abstract

Background: It has long been the goal of vector biology to generate genetic knowledge that can be used to "manipulate" natural populations of vectors to eliminate or lessen disease burden. While long in coming, progress towards reaching this goal has been made. Aiming to increase our understanding regarding the interactions between Plasmodium and the Anopheles immune genes, we investigated the patterns of genetic diversity of four anti-Plasmodium genes in the Anopheles gambiae complex of species.

Methodology/principal findings: Within a comparative phylogenetic and population genetics framework, the evolutionary history of four innate immunity genes within the An. gambiae complex (including the two most important human malaria vectors, An. gambiae and An. arabiensis) is reconstructed. The effect of natural selection in shaping the genes' diversity is examined. Introgression and retention of ancestral polymorphisms are relatively rare at all loci. Despite the potential confounding effects of these processes, we could identify sites that exhibited dN/dS ratios greater than 1.

Conclusions/significance: In two of the studied genes, CLIPB14 and FBN8, several sites indicated evolution under positive selection, with CLIPB14 exhibiting the most consistent evidence. Considering only the sites that were consistently identified by all methods, two sites in CLIPB14 are adaptively driven. However, the analysis inferring the lineage -specific evolution of each gene was not in favor of any of the Anopheles lineages evolving under the constraints imposed by positive selection. Nevertheless, the loci and the specific amino acids that were identified as evolving under strong evolutionary pressure merit further investigation for their involvement in the Anopheles defense against microbes in general.

Figure 1. 50% majority-rule consensus Bayesian (unrooted) tree of MDL1.

Numbers on branches are the posterior probabilities of clades, only values above 0.5 are presented. Species names have been abbreviated as follows: ARA: An. arabiensis, BWA: An. bwambae, GAM: An. gambiae, MEL: An. melas, MER: An. merus, and KNP905: An. quadriannulatus. The number following the species abbreviation refers to the individual specimen code, whereas the letters A and B differentiate between the two alleles of a single individual specimen.

Figure 2. 50% majority-rule consensus Bayesian (unrooted) tree of MDL2.

Numbers on branches are the posterior probabilities of clades, only values above 0.5 are presented. Species names have been abbreviated as follows: ARA: An. arabiensis, BWA: An. bwambae, GAM: An. gambiae, MEL: An. melas, MER: An. merus, and KNP905: An. quadriannulatus. The number following the species abbreviation refers to the individual specimen code, whereas the letters A and B differentiate between the two alleles of a single individual specimen.

Figure 3. 50% majority-rule consensus Bayesian (unrooted) tree of CLIPB14.

Numbers on branches are the posterior probabilities of clades, only values above 0.5 are presented. Species names have been abbreviated as follows: ARA: An. arabiensis, BWA: An. bwambae, GAM: An. gambiae, MEL: An. melas, MER: An. merus, and KNP905/SQUA: An. quadriannulatus. The number following the species abbreviation refers to the individual specimen code, whereas the letters A and B differentiate between the two alleles of a single individual specimen.

Figure 4. 50% majority-rule consensus Bayesian (unrooted) tree of FBN8.

Numbers on branches are the posterior probabilities of clades, only values above 0.5 are presented. Species names have been abbreviated as follows: ARA: An. arabiensis, BWA: An. bwambae, GAM: An. gambiae, MEL: An. melas, MER: An. merus, and QUA: An. quadriannulatus. The number following the species abbreviation refers to the individual specimen code, whereas the letters A and B differentiate between the two alleles of a single individual specimen.