DOI: 10.5061/dryad.m0cfxppbd
title: Genotypes of Aedes aegypti mosquitoes derived from SNP chip and low-coverage whole genome sequencing for platform cross-validation

description: 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. 
description: DNA from individual <em>Aedes aegypti </em>mosquitoes
 was extracted and used for genotyping at 50,000 loci distributed along the
 species genome, using the Axiom Aegypti1 SNP chip (Life Technologies
 Corporation CAT#550481).  Files
 "all_snps_G3Dryad" and "Replicas_SNPchip" contain all
 50,000 SNPs genotyped, prior to filtering.  File
 "50k_SNPs_30_samples_LD_MAF_miss_FINAL" contain the SNPs after
 applying filters in Plink 1.9 (https://www.cog-genomics.org/plink/) for
 linkage disequilibrium (LD: -indep-pairwise 50 10 0.3), minor allele
 frequency (MAF: -maf 0.1) and missing data (-geno 0.1).
description: # Genotypes of Aedes aegypti mosquitoes derived from SNP chip and
 low-coverage whole genome sequencing for platform cross-validation
 [https://doi.org/10.5061/dryad.m0cfxppbd](https://doi.org/10.5061/dryad.m0cfxppbd) Files: Replicas_SNPchip SNP chip data generated from 20 individual *Aedes aegypti* mosquitos from Sudan and Sri Lanka using the Axiom Aegypti1 array (Life Technologies Corporation CAT#550481) . Each mosquito was genotyped in triplicate independently in different chips. All 50,000 loci genotyped are included, prior to any filtering. Files: all_snps_G3Dryad SNP chip data generated from 13 individual *Aedes aegypti* mosquitos from populations worldwide using the Axiom Aegypti1 array (Life Technologies Corporation CAT#550481). All 50,000 loci genotyped are included, prior to any filtering. File: 50k_SNPs_30_samples_LD_MAF_miss_FINAL.vcf.gz Variant calling file (vcf) containing 30 individual *Aedes aegypti *genotypes used for population genetic analysis, with five individuals from each population. SNPs have been filtered for linkage disequilibrium, minor allele frequency, and missing data (-maf 0.1 -geno 0.1 -indep-pairwise 50 10 0.3). ## Description of the data and file structure Files: "Replicas_SNPchip" and "all_snps_G3Dryad" are in standard PLINK format ([https://www.cog-genomics.org/plink/](https://www.cog-genomics.org/plink/)), with .ped and .map files are included. File: 50k_SNPs_30_samples_LD_MAF_miss_FINAL.vcf.gz is a compressed variant calling file.