Exceptional diversity, maintenance of polymorphism, and recent directional selection on the APL1 malaria resistance genes of Anopheles gambiae

Abstract

The three-gene APL1 locus encodes essential components of the mosquito immune defense against malaria parasites. APL1 was originally identified because it lies within a mapped QTL conferring the vector mosquito Anopheles gambiae natural resistance to the human malaria parasite, Plasmodium falciparum, and APL1 genes have subsequently been shown to be involved in defense against several species of Plasmodium. Here, we examine molecular population genetic variation at the APL1 gene cluster in spatially and temporally diverse West African collections of A. gambiae. The locus is extremely polymorphic, showing evidence of adaptive evolutionary maintenance of genetic variation. We hypothesize that this variability aids in defense against genetically diverse pathogens, including Plasmodium. Variation at APL1 is highly structured across geographic and temporal subpopulations. In particular, diversity is exceptionally high during the rainy season, when malaria transmission rates are at their peak. Much less allelic diversity is observed during the dry season when mosquito population sizes and malaria transmission rates are low. APL1 diversity is weakly stratified by the polymorphic 2La chromosomal inversion but is very strongly subdivided between the M and S "molecular forms." We find evidence that a recent selective sweep has occurred at the APL1 locus in M form mosquitoes only. The independently reported observation of a similar M-form restricted sweep at the Tep1 locus, whose product physically interacts with APL1C, suggests that epistatic selection may act on these two loci causing them to sweep coordinately.

Figure 1. Schematic representation of proteins encoded by APL1A, APL1B, and APL1C genes.

The two major structural variants of APL1A are shown separately. APL1A¹ alleles are characterized by the deletion of the PANGGL region. APL1A² alleles carry an early stop codon that eliminates the coiled-coil domain.

Figure 2. Population differentiation among A. gambiae collections at the APL1 locus as estimated by K_ST*.

Statistical significance determined by permutation of alleles among subpopulation pairs . Mosquitoes sampled during the 2005 rainy season from the humid Toumani-Oulena (TM) and Makouchetoum (MK) regions are undifferentiated. These populations are mildly differentiated from a collection drawn from Bancoumana in the 2005 rainy season (BC rainy). All collections are highly differentiated from a collection drawn from Bancoumana in the 2003 dry season (BC dry). The analysis presented in this figure pools all mosquitoes by site and date of collection and does not take into account 2La karyotype or M/S molecular form.

Figure 3. Number of observations of mosquitoes with each 2La inversion karyotype in each molecular form (M and S) over each sample collection.

Population frequencies (in percentages) are given in the margins of each table. “Unk.” indicates that 2La karyotype was not determined.

Figure 4. Plot of nucleotide diversity and skew in the site frequency spectrum as a function of physical distance from the APL1 locus.

M form mosquitoes exhibit a sharp drop in polymorphism at the APL1 locus relative to S form mosquitoes, plotted as the ratio of nucleotide diversity (π) in the M form to diversity in the S form. The M form mosquitoes also exhibit an enhanced skew toward rare variants, indicated by negative values of Fu and Li's F* . The data are consistent with a recent selective sweep at APL1 in the M form only.