4. Temporal monitoring of the 4.3kb SV allele frequency
suggests it has evolved under strong positive selection
The high frequencies of this structural variant observed in Central
(Cameroon) and Eastern Africa (Uganda) suggested that it is under a
strong positive selection. To investigate this possibility, we measured
the frequencies of this SV in An. funestus s.s. populations of
Cameroon collected in 2014, 2016, 2017, 2018, 2020 and 2021. Samples
were available for 3 locations: Tibati and Mibellon, both from the
Adamawa region and Gounougou
(Northern region).
In Tibati, a temporal comparison of the frequency of the 4.3kb
structural variant in samples collected in 2018 revealed a 76% SV+
allele frequency and complete fixation of SV+ in 2021 Figure 2B. In
addition, all three genotypes (SV+/SV+, SV+/SV- and SV-/SV-) were
detected in 2018 at frequencies of 79%, 9% and 19%, respectively,
while in 2021, only the SV+/SV+ genotype was detected (Figure 2C),
indicating positive selection on the 4.3kb structural variant in this
location.
A similar pattern was observed in Mibellon, with the structural variant
present at a low allelic frequency (26%) in 2016, increasing to 98% in
less than 2 years (2018) and then to 100% in 2020 (Figure 2D). In 2016,
mosquitoes without the 4.3kb SV (SV-/SV) were more common (59%) than
those with the structural variant in either the homozygous or
heterozygous state (39% SV+/SV+; 11% SV+/SV-) (Figure 2E). By 2018 and
2020, the SV-/SV- homozygote was no longer detected, indicating that
this 4.3kb structural variant was also driven to fixation under positive
selection in this region.
Genotyping of this SV in samples collected in Gounougou in 2014, 2017,
2020 and 2021 revealed a similar selection pattern to those observed in
Tibati and Mibellon, with 3% in 2014, 31% SV+ in 2017, 63% in 2020
and 98% in 2021 (Figure S3A). The SV+/SV+ homozygous genotype was at a
very low frequency of 3% in 2014, reached a frequency of 26% in 2017
which doubled to 54% by 2020 in about 3 years and then almost got to
fixation in 2021 (Figure 2F).
The rapid increases in allele frequency of the 4.3kb SV in these 3
regions indicate strong selection acting on this structural variant (or
a tightly linked allele) in these mosquito populations.
Analysis of recent samples collected in Ghana and Benin (West Africa) in
2022 showed that this insertion is now present in these localities. In
Ghana, this SV was identified at a frequency of 5% with only 3
heterozygotes (Figure S3B & S3C), while in the Benin 2022 samples, a
higher frequency of 33% was observed (SV+). The genotypes were present
at frequencies of 16% (SV+/SV+), 34% (SV+/SV-) and 50% (SV-/SV-)
(Figure S3D & S3E).