The entire mitochondrial genome was sequenced in a prostriate tick, Ixodes hexagonus, and a metastriate tick, Rhipicephalus sanguineus. Both genomes encode 22 tRNAs, 13 proteins, and two ribosomal RNAs. Prostriate ticks are basal members of Ixodidae and have the same gene order as Limulus polyphemus. In contrast, in R. sanguineus, a block of genes encoding NADH dehydrogenase subunit 1 (ND1), tRNA(Leu)(UUR), tRNA(Leu)(CUN), 16S rDNA, tRNA(Val), 12S rDNA, the control region, and the tRNA(Ile) and tRNA(Gln) have translocated to a position between the tRNA(Glu) and tRNA(Phe) genes. The tRNA(Cys) gene has translocated between the control region and the tRNA(Met) gene, and the tRNA(Leu)(CUN) gene has translocated between the tRNA(Ser)(UCN) gene and the control region. Furthermore, the control region is duplicated, and both copies undergo concerted evolution. Primers that flank these rearrangements confirm that this gene order is conserved in all metastriate ticks examined. Correspondence analysis of amino acid and codon use in the two ticks and in nine other arthropod mitochondrial genomes indicate a strong bias in R. sanguineus towards amino acids encoded by AT-rich codons.

Quantitative trait loci (QTL) affecting the ability of the mosquito Aedes aegypti to become infected with dengue-2 virus were mapped in an F₁ intercross. Dengue-susceptible A. aegypti aegypti were crossed with dengue refractory A. aegypti formosus. F₂ offspring were analyzed for midgut infection and escape barriers. In P₁ and F₁ parents and in 207 F₂ individuals, regions of 14 cDNA loci were analyzed with single-strand conformation polymorphism analysis to identify and orient linkage groups with respect to chromosomes I–III. Genotypes were also scored at 57 RAPD-SSCP loci, 5 (TAG)_n microsatellite loci, and 6 sequence-tagged RAPD loci. Dengue infection phenotypes were scored in 86 F₂ females. Two QTL for a midgut infection barrier were detected with standard and composite interval mapping on chromosomes II and III that accounted for ∼30% of the phenotypic variance (⁠ $σp2$⁠) in dengue infection and these accounted for 44 and 56%, respectively, of the overall genetic variance (⁠ $σg2$⁠). QTL of minor effect were detected on chromosomes I and III, but these were not detected with composite interval mapping. Evidence for a QTL for midgut escape barrier was detected with standard interval mapping but not with composite interval mapping on chromosome III.

▪ Abstract Modern population genetics underwent a major paradigm shift during the last decade of the 20th century with the discovery that thousands of genes of known function and position in a genome can be analyzed simultaneously in a single individual. The impact of this technology on insect population genetics is potentially profound. Sampling distributions of genetic statistics can now be derived from many individual loci or among many segregating sites within a gene. Inferences regarding random mating, gene flow, effective population sizes, disequilibrium, and relatedness among populations can now be based on patterns of variation at many loci. More importantly, genome-wide sampling enables population geneticists to distinguish effects that act on the whole genome from those that act on individual loci or nucleotides. We introduce the term “population genomics” to describe the process of simultaneous sampling of numerous variable loci within a genome and the inference of locus-specific effects from the sample distributions. The four critical assumptions implicit in the population genomics approach are explained in detail. Studies adopting this paradigm are reviewed, and the steps necessary to complete a population genomics study are outlined.

Worldwide the mosquito Aedes aegypti (L.) is the principal urban vector of dengue viruses. Currently 2.5 billion people are at risk for infection and reduction of Ae. aegypti populations is the most effective means to reduce the risk of transmission. Pyrethroids are used extensively for adult mosquito control, especially during dengue outbreaks. Pyrethroids promote activation and prolong the activation of the voltage gated sodium channel protein (VGSC) by interacting with two distinct pyrethroid receptor sites [1], formed by the interfaces of the transmembrane helix subunit 6 (S6) of domains II and III. Mutations of S6 in domains II and III synergize so that double mutants have higher pyrethroid resistance than mutants in either domain alone. Computer models predict an allosteric interaction between mutations in the two domains. In Ae. aegypti, a Ile1,016 mutation in the S6 of domain II was discovered in 2006 and found to be associated with pyrethroid resistance in field populations in Mexico. In 2010 a second mutation, Cys1,534 in the S6 of domain III was discovered and also found to be associated with pyrethroid resistance and correlated with the frequency of Ile1,016. A linkage disequilibrium analysis was performed on Ile1,016 and Cys1,534 in Ae. aegypti collected in Mexico from 2000–2012 to test for statistical associations between S6 in domains II and III in natural populations. We estimated the frequency of the four dilocus haplotypes in 1,016 and 1,534: Val1,016/Phe1,534 (susceptible), Val1,016/Cys1,534, Ile1,016/Phe1,534, and Ile1,016/Cys1,534 (resistant). The susceptible Val1,016/Phe1,534 haplotype went from near fixation to extinction and the resistant Ile1,016/Cys1,534 haplotype increased in all collections from a frequency close to zero to frequencies ranging from 0.5–0.9. The Val1,016/Cys1,534 haplotype increased in all collections until 2008 after which it began to decline as Ile1,016/Cys1,534 increased. However, the Ile1,016/Phe1,534 haplotype was rarely detected; it reached a frequency of only 0.09 in one collection and subsequently declined. Pyrethroid resistance in the vgsc gene requires the sequential evolution of two mutations. The Ile1,016/Phe1,534 haplotype appears to have low fitness suggesting that Ile1,016 was unlikely to have evolved independently. Instead the Cys1,534 mutation evolved first but conferred only a low level of resistance. Ile1,016 in S6 of domain II then arose from the Val1,016/Cys1,534 haplotype and was rapidly selected because double mutants confer higher pyrethroid resistance. This pattern suggests that knowledge of the frequencies of mutations in both S6 in domains II and III are important to predict the potential of a population to evolve kdr. Susceptible populations with high Val1,016/Cys1,534 frequencies are at high risk for kdr evolution, whereas susceptible populations without either mutation are less likely to evolve high levels of kdr, at least over a 10 year period. Constant use of pyrethroid insecticides has driven mosquito populations to develop resistance. In Aedes aegypti, the primary mosquito vector of dengue, yellow Fever, and chikungunya viruses, pyrethroid resistance is primarily associated with mutations in the voltage-gated sodium channel protein. One mutation occurs in codon 1,016 and involves a replacement of valine with isoleucine (Ile1, 016), and a second located in subunit 6 of domain III in codon 1,534, replaces phenylalanine with cysteine (Cys1,534). In Mexico, we found that Cys1,534 was present in the same mosquito collections that were previously analyzed for Ile1,016. In this study, we performed a linkage disequilibrium analysis on both Ile1,016 and Cys1,534 in Mexican collections from 2000–2012. Our analysis suggests that pyrethroid resistance requires the sequential evolution of the two mutations and that Cys1,534 must occur first and appears to enable the Ile1,016 mutation to survive.