Nyssorhynchus darlingi population genetic structure across forest cover levels in Amazonian Brazil

The relationship between deforestation and malaria in Amazonian Brazil is complex, and a deeper understanding of this relationship is required to inform effective control measures in this region. Here, we are particularly interested in characterizing the impact of land use and land cover change on the genetics of the major regional vector of malaria, Nyssorhynchus darlingi. We used nextera-tagmented, Reductively Amplified DNA (nextRAD) genotyping-by-sequencing to genotype 164 Ny. darlingi collected from 16 collection sites with divergent forest cover levels in four municipality groups in Amazonian Brazil. Using a dataset of 5,561 single nucleotide polymorphisms (SNPs), we investigated the genetic structure of these Ny. darlingi populations with a combination of model- and non-model-based analyses. We identified weak to moderate genetic differentiation among the four municipality groups. There was no evidence for microgeographic structure of Ny. darlingi among forest cover levels within the municipality groups, indicating that there is gene flow across areas of these municipalities with different degrees of deforestation . We identified 14 SNPs associated with forest cover by two outlier detection methods, and investigated functions associated with their proximal genes, which could be further characterized in future studies.