Museum specimens reveal the genomics of extinct populations of Aedes aegypti in the Mediterranean

The yellow fever mosquito, Aedes aegypti, has been a major driver of pandemics throughout centuries, due to its role as major vector of yellow fever, dengue, chikungunya, and Zika viruses. Ae. aegypti arrived to the Americas from Africa with the European colonization, circa 1500 A.D., and made its way to Europe and Asia in the 1800’s. Details of Ae. aegypti’s journey to Asia remain unknown. It is possible that the now extinct populations that thrived in the Mediterranean until 1950 acted as the bridge between American and Asian Ae. aegypti. In the absence of fresh material, we investigated this possibility by analyzing the DNA from ~120 year old museum specimens obtained from French and Portuguese Museums. Short-read next generation sequencing technology produced a 3X mean coverage across the three Ae. aegypti chromosomes, with 22% of the genome at 5X and 5.8% at 10X. The entire mitochondrial genome was recovered. Approximately 352,000 SNPs from modern and museum specimen samples were identified and used for subsequent analyses. Phylogenetic reconstruction indicates that museum specimens from Algeria, Tunisia, France, and Greece, group with Ae. aegypti from the Americas and Asia, clustering closely with modern samples from the Black Sea (Georgia). Thus, our results suggest that modern Black Sea populations are likely remnants of the now extinct Mediterranean populations rather than recent introductions. Moreover, we show that museum specimens can successfully yield good quality DNA for population genetic studies of ancient mosquito populations.