# Investigating genetic differentiation between brackish and fresh water collections of the arboviral vector Aedes aegypti

## TL;DR

This study explores genetic differences in Aedes aegypti mosquitoes from brackish and freshwater habitats in Sri Lanka, suggesting adaptation to salty environments.

## Contribution

The study identifies subtle genetic differentiation and candidate genes linked to salinity tolerance in Aedes aegypti populations.

## Key findings

- Brackish water Ae. aegypti populations show higher linkage disequilibrium and lower genetic diversity compared to freshwater populations.
- Genetic analyses highlight fatty acid metabolism and signaling pathways as potentially important for salinity tolerance in Ae. aegypti.

## Abstract

Aedes aegypti is typically regarded as a freshwater mosquito; however, recent studies have documented its development in brackish water habitats in coastal regions, including Sri Lanka’s Jaffna Peninsula. Compared with freshwater populations, brackish water samples in Jaffna display enhanced salt tolerance throughout larval-to-adult development, along with differences in gene expression, cuticle morphology and composition, and insecticide susceptibility.

To explore the genetic basis of these differences, we performed a comparative genomic analysis using 5135 genome-wide single nucleotide polymorphisms (SNPs) from Ae. aegypti inhabiting freshwater and brackish water sites in the Jaffna Peninsula. Genetic diversity, population structure, and demographic parameters were evaluated using publicly available software. Candidate genomic regions potentially involved in salinity tolerance were identified through tests for environmental associations and genetic outlier detection.

After performing genotype quality control and first-degree relative removal on the initial 121 mosquitoes genotyped, the final dataset comprised 13 freshwater and 21 brackish water individuals. Ae. aegypti populations from the Jaffna Peninsula showed limited evidence of genetic structuring by collection site, with a subtle pattern associated with larval water salinity (distance-based redundancy analysis [dbRDA] P = 0.002, adjusted R2 = 0.01). Brackish-water populations displayed higher linkage disequilibrium, reduced effective population size, and lower nucleotide diversity relative to freshwater populations. Genetic outlier and environmental association analyses identified loci associated with fatty acid metabolism and other cellular pathways (e.g. Toll and Imd signaling pathways) as differentiated among the groups.

We found subtle genetic differentiation between freshwater and brackish-water Ae. aegypti populations from the Jaffna Peninsula, suggesting that brackish-water populations may experience distinct evolutionary pressures potentially linked to adaptation to saline environments. Analyses point to fatty acid metabolism as one of the biological processes that could contribute to salinity tolerance in Ae. aegypti, possibly influencing cuticle modifications as a physiological response. Additional studies incorporating more collection sites and larger sample sizes for each salinity group are needed to further elucidate the mechanisms driving this differentiation. The ability of Ae. aegypti to adapt to brackish water substantially expands the range of potential larval sites it can occupy, particularly in coastal areas, and emphasizes the need to adjust vector control strategies accordingly.

The online version contains supplementary material available at 10.1186/s13071-025-07239-3.