1. Identification of 4.3kb structural variant in Anopheles funestus populations.
Inspection of the PoolSeq IGV alignments revealed a prominent coverage increase in the intergenic region in Uganda in 2014 (Figure 1A), corresponding to a transposon insertion position of 8,556,411-8,556,420 on Chromosome 2 with an insertion sequence of “CAAATGTACA”. There was weak visual evidence for the insertion in Cameroon, and it was not present in other PoolSeq populations. TranSurVeyor detected an insertion at the same positions in Uganda but not in Cameroon or any other population. The Inserted fragment is present in the reference strain FUMOZ at positions 24,765,013-24,760,696 on Chromosome 3 within the intron of an uncharacterised gene (AFUN019979). Due to the mixed-template PoolSeq approach, it was not possible to accurately determine the frequency of the SV in Uganda and Cameroon in 2014, although it appears to have been of intermediate to high frequency in Uganda and very low frequency in Cameroon.
Nucleotide diversity was reduced in Uganda for the intergenic region (Figure S1) compared to Cameroon and FANG datasets and other regions . This was accompanied by low Tajima’s D values in the intergenic region between CYP6P5 and CYP6P9b genes (Table S2). There are multiple peaks of low diversity in Uganda across the rp1 locus versus other populations, suggestive of complex regional patterns of evolution not restricted to the 4.3 kb insertion. When the ratio of nucleotide diversity was inverted between Uganda and the other populations, a flat profile indicating little reduced diversity at otherrp1 loci versus Uganda was observed (Figure S2).