Figure 6. The 2La inversion has a monophyletic origin throughout Africa.
Phylogenetic trees were constructed for genomic windows of 5 megabases (Mb) each extracted from whole-genome sequences of 103 2La/2La and 107 2L+a/2L+a wild A. gambiae mosquitoes, obtained with permission from the Anopheles gambiae 1000 (Ag1000) Genomes Consortium (Miles et al., 2016), and whole-genome sequences of 1 2La/2La and 11 2L+a/2L+a wild Burkina Faso A. gambiae Goundry form mosquitoes (Crawford et al., 2016). Branch color indicates the country origin of the sample (see country key). The terminal label at the end of each branch indicates genotype of the 2La inversion (black ‘a’ for 2La/2La, and red ‘+' for 2L+a/2L+a). The 2La inversion genotypes of Ag1000 samples were determined informatically (Figure 6—figure supplement 1), and Goundry form samples were genotyped by molecular diagnostic assay. The chromosome map depicts the left arm of chromosome 2 (Chr2L), with the centromere to the left, and the dashed line indicates the extent of the 2La inversion. Brackets indicate the genomic windows at three distinct positions relative to the 2La inversion: (i) Spanning the proximal and distal inversion breakpoints (respectively, 2L:18–23 Mb and 2L:39–44 Mb), (ii) in the central region of the inversion (2L: 29–34 Mb), and controls outside the 2La inversion on the same chromosome (2L:8–13 Mb) or on Chromosome 3 (3L:15–20 Mb and 3L:15–20 Mb). Breakpoint and inversion-central trees display a subdivision between 2La inversion genotypes, regardless of the geographic origin of the samples, while trees outside the inversion cluster by geography and not inversion genotype. Branch length scale under the key indicates nucleotide substitutions per site and applies to all six trees.
Figure 6—figure supplement 1. Principal components analysis (PCA) for 2La genotype assignment of whole-genome sequenced samples.
