Genotypes of Aedes aegypti mosquitoes derived from SNP chip and low-coverage whole genome sequencing for platform cross-validation

The mosquito Aedes aegypti is the primary vector of many human arboviruses
such as dengue, yellow fever, chikungunya, and Zika, which affect millions
of people world-wide. Population genetics studies on this mosquito have
been important in understanding its invasion pathways and success as a
vector of human disease. The Axiom aegypti1 SNP chip was developed from a
sample of geographically diverse Ae. aegypti populations to facilitate
genomic studies on this species. Here we evaluate the utility of the Axiom
aegypti1 SNP chip for population genetics and compare it with a low-depth
shot-gun sequencing approach using mosquitoes from the species’ native
(Africa) and invasive range (outside Africa). These analyses indicate that
the results from the SNP chip are highly reproducible and have a higher
sensitivity to capture alternative alleles than a low-coverage
whole-genome sequencing approach. Although the SNP chip suffers from
ascertainment bias, results from population structure, ancestry,
demographic, and phylogenetic analyses using the SNP chip were congruent
with those derived from low coverage whole genome sequencing, and
consistent with previous reports on Africa and outside Africa populations
using microsatellites. More importantly, we identified a subset of SNPs
that can be reliably used to generate merged databases, opening the door
to combined analyses. We conclude that the Axiom aegypti1 SNP chip is a
convenient, more accurate, low-cost alternative to low-depth whole genome
sequencing for population genetic studies of Ae. aegypti that do not rely
on full allelic frequency spectra. Whole genome sequencing and SNP chip
data can be easily merged, extending the usefulness of both
approaches.