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Background Although whole-genome sequencing (WGS) is the preferred genotyping method for most genomic analyses, limitations are often experienced when studying genomes characterized by a high percentage of repetitive elements, high linkage, and recombination deserts. The Asian tiger mosquito ( Aedes albopictus ), for example, has a genome comprising up to 72% repetitive elements, and therefore we set out to develop a single-nucleotide polymorphism (SNP) chip to be more cost-effective. Aedes albopictus is an invasive species originating from Southeast Asia that has recently spread around the world and is a vector for many human diseases. Developing an accessible genotyping platform is essential in advancing biological control methods and understanding the population dynamics of this pest species, with significant implications for public health. Methods We designed a SNP chip for  Ae. albopictus (Aealbo chip) based on approximately 2.7 million SNPs identified using WGS data from 819 worldwide samples. We validated the chip using laboratory single-pair crosses, comparing technical replicates, and comparing genotypes of samples genotyped by WGS and the SNP chip. We then used the chip for a population genomic analysis of 237 samples from 28 sites in the native range to evaluate its usefulness in describing patterns of genomic variation and tracing the origins of invasions. Results Probes on the Aealbo chip targeted 175,396 SNPs in coding and non-coding regions across all three chromosomes, with a density of 102 SNPs per 1 Mb window, and at least one SNP in each of the 17,461 protein-coding genes. Overall, 70% of the probes captured the genetic variation. Segregation analysis found that 98% of the SNPs followed expectations of single-copy Mendelian genes. Comparisons with WGS indicated that sites with genotype disagreements were mostly heterozygotes at loci with WGS read depth < 20, while there was near complete agreement with WGS read depths > 20, indicating that the chip more accurately detects heterozygotes than low-coverage WGS. Sample sizes did not affect the accuracy of the SNP chip genotype calls. Ancestry analyses identified four to five genetic clusters in the native range with various levels of admixture. Conclusions The Aealbo chip is highly accurate, is concordant with genotypes from WGS with high sequence coverage, and may be more accurate than low-coverage WGS. Graphical Abstract

The Asian tiger mosquito, Aedes albopictus, is currently the most widespread invasive mosquito species in the world. It poses a significant threat to human health, as it is a vector for several arboviruses. We used a SNP chip to genotype 748 Ae. albopictus mosquitoes from 41 localities across Europe, 28 localities in the native range in Asia, and 4 in the Americas. Using multiple algorithms, we examined population genetic structure and differentiation within Europe and across our global dataset to gain insight into the origin of the invasive European populations. We also compared results from our SNP data to those obtained using genotypes from 11 microsatellite loci (N = 637 mosquitoes from 25 European localities) to explore how sampling effort and the type of genetic marker used may influence conclusions about Ae. albopictus population structure. While some analyses detected more than 20 clusters worldwide, we found mosquitoes could be grouped into 7 distinct genetic clusters, with most European populations originating in East Asia (Japan or China). Interestingly, some populations in Eastern Europe did not share genetic ancestry with any populations from the native range or Americas, indicating that these populations originated from areas not sampled in this study. The SNP and microsatellite datasets found similar patterns of genetic differentiation in Europe, but the microsatellite dataset could not detect the more subtle genetic structure revealed using SNPs. Overall, data from the SNP chip offered a higher resolution for detecting the genetic structure and the potential origins of invasions. The Asian tiger mosquito, Aedes albopictus, is currently the most widespread invasive mosquito species in the world and poses a significant threat to human health. We genotyped 748 Ae. albopictus mosquitoes from locations across Europe and Asia (the native range) to examine population genetic structure and found evidence for multiple independent invasions into Europe from both the native region and other areas of the invasive range. SNP and microsatellite datasets found similar patterns of genetic differentiation in Europe, but the microsatellite dataset could not detect the more subtle genetic structure revealed using SNPs.