The evolution of the ZZB-TE, Cyp6p4-236M andCyp6aap-Dup1 haplotypes
Based upon Ag1000g data and a time series of collections from Central
and East Africa, we were able to trace the sequence of mutational events
(ZZB-TE, Cyp6p4-236M and Cyp6aap-Dup1 ) and reconstruct the
evolutionary history of the swept haplotype. Among the Ag1000g data
[19], the Cyp6p4-236M mutation was only observed in
collections from eastern Uganda (collected in 2012) suggesting that this
mutation originated in the eastern Ugandan/western Kenyan region. In a
screen of collections from Uganda and Kenya predating the Ag1000g
collections by eight years (2004) (Fig 3) only the ZZB-TE insertion was
detected, although the sample size was too small (n=4) to conclude that
the Cyp6p4-236M allele was absent. The Cyp6p4-236Mmutation was first observed in this region in 2005 (frequencyCyp6p4-236M =0.10) in individuals carrying the ZZB-TE mutation,
whilst the Cyp6aap-Dup1 CNV was first recorded in 2008
(proportion of individuals with Dup1=0.8%). This inferred sequence of
events may explain why ZZB-TE and Cyp6p4-236M mutations are in
tighter statistical linkage with each other than withCyp6aap-Dup1 (Figure 2), despite the closer proximity of ZZB-TE
and Cyp6aap-Dup1 (Figure 1). Given the very tight association
between the ZZB-TE insertion and the Cyp6p4-236M SNP, we will
henceforth refer to the Cyp6p4-236M (double mutant) haplotype and
the Cyp6aap-Dup1 (triple mutant). The double mutant haplotype
shows a steady increase in frequency between 2004 and 2011 in Kenya
(Figure 3); possibly in response to the introduction and subsequent
intensification of bednet distribution programmes [29, 33,
34].
Following its appearance in 2008, the triple mutant haplotype, rapidly
increased towards fixation in both collections from Uganda and Kenya,
replacing the double mutant. This haplotype replacement and the
observation that the triple mutant is the only non-wildtype haplotype
observed outside Kenya/Uganda (such as in Tanzania and DRC, Figure 1 and
3) strongly implies an additional selective advantage to the triple
mutant. The time series data from across DRC are particularly striking
both in terms of the speed of increase of the triple mutant but also the
north-south heterogeneity, with very low frequencies in the more
southerly provinces (Figure 3).