Abstract
We present the first genome-wide study of recent evolution in Culex pipiens species complex focusing on the genomic extent, functional targets and likely causes of global and local adaptations. We resequenced pooled samples of six populations of C. pipiens and two populations of the outgroup Culex torrentium. We used principal component analysis to systematically study differential natural selection across populations and developed a phylogenetic scanning method to analyse admixture without haplotype data. We found evidence for the prominent role of geographical distribution in shaping population structure and specifying patterns of genomic selection. Multiple adaptive events, involving genes implicated with autogeny, diapause and insecticide resistance were limited to specific populations. We estimate that about 5–20% of the genes (including several histone genes) and almost half of the annotated pathways were undergoing selective sweeps in each population. The high occurrence of sweeps in non-genic regions and in chromatin remodelling genes indicated the adaptive importance of gene expression changes. We hypothesize that global adaptive processes in the C. pipiens complex are potentially associated with South to North range expansion, requiring adjustments in chromatin conformation. Strong local signature of adaptation and emergence of hybrid bridge vectors necessitate genomic assessment of populations before specifying control agents.
Highlights
Arms races between antagonistic species have been of longstanding interest to evolutionary biologists [1,2]
We present the results of the first genome-wide analysis of population structure and recent natural selection in the Culex pipiens complex, members of which are notorious vectors of West Nile Virus, St
Louise Encephalitis Virus and filariasis worms in the US and worldwide [3,4,5]. This complex consists of Culex quinquefasciatus and C. pipiens
Summary
Arms races between antagonistic species have been of longstanding interest to evolutionary biologists [1,2]. Molestus have been described within the C. pipiens species based on physiological and ecological differences including the choice of host species, seasonal activity, mating behaviour and preferred habitat [3,6,7] Hybridization between these two forms and with C. quinquefasciatus has been reported in certain areas, leading to the rise of bridge vectors transmitting pathogens between birds and humans [3,6,8,9,10]. PCA of Pool-hmm sweep scores was done to compare the broad patterns of genomic selection among the studied populations. The large number of polymorphic sites in H1 genes allowed statistical analysis of association of different types of amino acid changes with certain structural features of the protein. More details on the methods can be found in electronic supplementary material, S1
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