Genetic variation, population structure, and implications for vector control

Evolutionary forces and genetic variation

Mutation increases genetic diversity in a population. These new alleles are then subject to natural selection whereby deleterious alleles are removed by purifying

selection and advantageous alleles increase through directional selection. For example, directional selection from insecticide application removes susceptible alleles and over time an insecticide resistance allele can become “fixed” in the population. Directional and purifying selection reduce genetic variability; however, heterozygote advantage and changes in selection (e.g., movement between environments selecting for different alleles) can increase genetic variation.

The variability of a region of the genome depends on the mutation rate and the degree of functional constraint by natural selection. Protein coding genes are usually quite conserved due to purifying selection, but often show more variability in third position codons. Because of the critical role that ribosomes play in protein synthesis, and the three-dimensional structure needed to carry out this role, most regions of ribosomal DNA are even more conserved than protein coding genes. Noncoding regions including the mitochondrial control region, and nuclear repetitive DNA (e.g., microsatellites) and intergenic regions (e.g., ribosomal Internal Transcribed Spacers, ITS), are usually the most variable regions of genomes.

In addition to the effects of mutation and selection, genetic variation can be reduced simply due to chance alone, a process known as genetic drift. Genetic drift is the change in allele frequencies that occur due to finite population size and is especially important in smaller populations. Migration is a counteracting force to genetic drift. By mixing alleles among populations, migration distributes and homogenizes genetic variation among populations. In the absence of mutation, selection, and migration, genetic drift leads to the random fixation and loss of alleles. The pattern of reduced variation from drift is distinct from that caused by selection because the whole genome is affected, not just a particular locus. Inbreeding is also more prevalent in smaller populations and, in the absence of selection on inbred genotypes, does not change allele frequencies but reduces the frequency of heterozygotes.

Microsatellites

The study of microsatellite loci has been instrumental in understanding fine scale population structure including estimating movement between ecotopes and identifying potential sources of reinfestation following insecticide application (Table 8.1). Microsatellites (2—5 tandemly repeated nucleotides, Fig. 8.2) have a relatively high mutation rate, are presumably not under selection and heterozygotes are easily distinguished from homozygotes.

DNA sequence

DNA sequences or haplotypes are favored because of their objectivity and resolution. The differences between the mitochondrial and nuclear genomes, and a wide range of variability due to different mutation rates and functional constraints among regions of DNA facilitate addressing many population genetics questions.²²

Table 8.1 Microsatellite estimates of population subdivision for major triatomine species

^aMay include a cryptic species.

b

”st.

Figure 8.2 Schematic representation of an AC microsatellite repeat. DNA polymerase slippage during replication results in alleles with different numbers of repeats that show different-sized bands after amplification using primers flanking the repeat region. Mutations in the primer binding sites can prevent primer annealing and amplification, resulting in a null allele and underestimates of heterozygosity.²¹

Figure 8.3 Schematic representation of the mitochondrial genome of T. dimidiat. Source: From Dotson EM, Beard CB. Sequence and organization of the mitochondrial genome of the Chagas disease vector, Triatoma dimidiata. Insect Mol Biol 2001;10:205-15.²³

Mitochondrial DNA (Fig. 8.3), especially cytochrome b (cyt b), cytochrome oxidase I (coI), and NADH ubiquinone oxidoreductase core subunit 4 (ND4), has been very important in understanding the geographic origin and movement of Triatominae.²⁴ It is highly variable, evolving approximately 10 times faster than the nuclear genome. This haploid genome eliminates complications due to crossing- over and heterozygosity. However, as mitochondria are maternally inherited, inferences about variation and gene flow are based on females only.

Ribosomal DNA (rDNA) sequences have also been useful in Chagas vector control studies and the more variable internal transcribed spacers, ITS-1 and ITS-2 (Fig. 8.4) and less variable 18S, 5.8S, and 28S (in that order) regions, are useful at different taxonomic scales. As a tandemly-repeated array, mutations within individual repeat units are usually homogenized by concerted evolution. The high copy number makes it an abundant PCR target, however, pseudogenes sometimes can confound the analysis. Although nuclear single copy genes (e.g., protein coding genes) have many advantages over ribosomal genes, to date, a sufficiently variable

Figure 8.4 Schematic representation of the tandemly repeated nuclear rDNA cistron unit (blue (black in print versions) boxes, above) and its primary transcript (below).

gene has not been identified. ITS-2 is the rDNA region most often used in population level studies in triatomines (Table 8.2), and has led to the discovery of hybridization,³⁶ and introgression. Recent multigene studies have revealed that several Chagas vector species actually are complexes including cryptic species, often with different epidemiological properties.^27,30’^36-39