Robustness in population-structure and demographic-inference results derived from the Aedes aegypti genotyping chip and whole-genome sequencing data.

Autor: Gómez-Palacio A; Department of Entomology, Center for Vector Biology & Zoonotic Diseases, The Connecticut Agricultural Experiment Station, 123 Huntington St., New Haven, CT 06511, USA.; Laboratorio de Investigación en Genética Evolutiva, Universidad Pedagógica y Tecnológica de Colombia, Avenida Central del Norte 39-115, Boyacá 150003, Colombia., Morinaga G; Faculty of Veterinary Medicine, University of Calgary, 2500 University Drive NW., Calgary, AB 2TN 1N4, Canada., Turner PE; Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St., New Haven, CT 06511, USA.; Quantitative Biology Institute, Yale University, 260 Whitney Ave., New Haven, CT 06511, USA., Micieli MV; Centro de Estudios Parasitológicos y de Vectores (CEPAVE), CONICET, Universidad Nacional de la Plata, Boulevard 120 s/n between Av. 60 and Calle 64, La Plata 1900, Argentina., Elnour MB; Department of Parasitology and Medical Entomology, Tropical Medicine Research Institute, National Center for Research, Khartoum 11111, Sudan., Salim B; Faculty of Veterinary Medicine, Department of Parasitology, University of Khartoum, Khartoum North 11111, Sudan.; Camel Research Center, King Faisal University, P.O. Box. 400, Al-Ahsa 31982, Saudi Arabia., Surendran SN; Department of Zoology, University of Jaffna, Jaffna 40000, Sri Lanka., Ramasamy R; Department of Zoology, University of Jaffna, Jaffna 40000, Sri Lanka., Powell JR; Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St., New Haven, CT 06511, USA., Soghigian J; Faculty of Veterinary Medicine, University of Calgary, 2500 University Drive NW., Calgary, AB 2TN 1N4, Canada., Gloria-Soria A; Department of Entomology, Center for Vector Biology & Zoonotic Diseases, The Connecticut Agricultural Experiment Station, 123 Huntington St., New Haven, CT 06511, USA.; Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St., New Haven, CT 06511, USA.
Jazyk: angličtina
Zdroj: G3 (Bethesda, Md.) [G3 (Bethesda)] 2024 Jun 05; Vol. 14 (6).
DOI: 10.1093/g3journal/jkae082
Abstrakt: 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 worldwide. Population genetic 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 A. aegypti populations to facilitate genomic studies on this species. We evaluate the utility of the Axiom aegypti1 SNP chip for population genetics and compare it with a low-depth shotgun sequencing approach using mosquitoes from the native (Africa) and invasive ranges (outside Africa). These analyses indicate that 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 A. 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.
Competing Interests: Conflicts of interest The author(s) declare no conflicts of interest.
(© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)
Databáze: MEDLINE
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