Kdr origins and diplotype clustering#
The Vgsc gene encodes a voltage-gated sodium channel which is the binding target of DDT and pyrethroid insecticides. Variants in this gene, referred to as Kdr (knockdown resistance) are associated with resistance to DDT and/or pyrethroids.
This notebook determines the origin of Kdr for each sample, and performs diplotype clustering to visualise the distribution of amino acids and haplotypes.
Knockdown resistance mutations have arisen independently multiple times in different mosquito populations, and genetic backgrounds can help trace the origin and spread of resistance (Martinez-Torres et al., 1998; Ranson et al., 2000).
Unexpected kdr 402 genotype. GH_04 ??
Unexpected kdr 402 genotype. GH_07 ??
Unexpected kdr F genotype. GH_16 ??
Unexpected kdr S genotype. GH_16 ??
Unexpected kdr F genotype. GH_17 ??
Unexpected kdr S genotype. GH_17 ??
Unexpected kdr F genotype. GH_18 ??
Unexpected kdr S genotype. GH_18 ??
Unexpected kdr F genotype. GH_20 ??
Unexpected kdr S genotype. GH_20 ??
Unexpected kdr 402 genotype. GH_20 ??
Unexpected kdr F genotype. GH_22 ??
Unexpected kdr S genotype. GH_22 ??
Unexpected kdr 402 genotype. GH_46 ??
Unexpected kdr F genotype. GH_58 ??
Unexpected kdr S genotype. GH_58 ??
Unexpected kdr F genotype. GH_77 ??
Unexpected kdr S genotype. GH_77 ??
Unexpected kdr F genotype. GM_01 ??
Unexpected kdr S genotype. GM_01 ??
Unexpected kdr 402 genotype. GM_01 ??
Unexpected kdr F genotype. GM_06 ??
Unexpected kdr S genotype. GM_06 ??
Unexpected kdr 402 genotype. GM_12 ??
Unexpected kdr F genotype. GM_17 ??
Unexpected kdr S genotype. GM_17 ??
Unexpected kdr F genotype. GM_18 ??
Unexpected kdr S genotype. GM_18 ??
Unexpected kdr F genotype. GM_23 ??
Unexpected kdr S genotype. GM_23 ??
Unexpected kdr 402 genotype. GM_33 ??
Unexpected kdr F genotype. GM_42 ??
Unexpected kdr S genotype. GM_42 ??
Unexpected kdr F genotype. GM_43 ??
Unexpected kdr S genotype. GM_43 ??
Unexpected kdr 402 genotype. GM_44 ??
Unexpected kdr F genotype. GM_54 ??
Unexpected kdr S genotype. GM_54 ??
Unexpected kdr F genotype. GM_56 ??
Unexpected kdr S genotype. GM_56 ??
Unexpected kdr F genotype. GM_59 ??
Unexpected kdr S genotype. GM_59 ??
Unexpected kdr F genotype. GM_60 ??
Unexpected kdr S genotype. GM_60 ??
Unexpected kdr 402 genotype. GM_66 ??
Unexpected kdr F genotype. VK7_alive_01 ??
Unexpected kdr S genotype. VK7_alive_01 ??
Unexpected kdr F genotype. VK7_dead_25 ??
Unexpected kdr S genotype. VK7_dead_25 ??
Unexpected kdr F genotype. VK7_dead_32 ??
Unexpected kdr S genotype. VK7_dead_32 ??
Unexpected kdr 402 genotype. Siaya_Delta_Dead_07 ??
Unexpected kdr 402 genotype. Siaya_Delta_Alive_97 ??
Too many different mutant haplotype backgrounds in sample GH_59
Counts of origins:
| kdr_origin | F | F1 | F2 | S | S1 | S3 | wt | |
|---|---|---|---|---|---|---|---|---|
| location | taxon | |||||||
| Gambia_URR | arabiensis | 0 | 0 | 0 | 8 | 0 | 0 | 58 |
| coluzzii | 1 | 1 | 0 | 0 | 0 | 0 | 24 | |
| gambiae | 1 | 5 | 0 | 0 | 0 | 0 | 0 | |
| unassigned | 0 | 0 | 0 | 4 | 0 | 0 | 4 | |
| Obuasi | gambiae | 6 | 126 | 0 | 0 | 0 | 0 | 0 |
| Siaya | gambiae | 0 | 0 | 19 | 0 | 1 | 0 | 0 |
| gcx3 | 3 | 0 | 217 | 6 | 127 | 7 | 0 | |
| unassigned | 1 | 0 | 78 | 2 | 19 | 0 | 0 | |
| VK7 | coluzzii | 0 | 142 | 0 | 0 | 0 | 0 | 0 |
Frequencies of known origins:
| kdr_origin | F | F1 | F2 | S | S1 | S3 | wt | |
|---|---|---|---|---|---|---|---|---|
| location | taxon | |||||||
| Gambia_URR | arabiensis | 0.0000 | 0.000 | 0.00 | 0.120 | 0.00 | 0.000 | 0.88 |
| coluzzii | 0.0380 | 0.038 | 0.00 | 0.000 | 0.00 | 0.000 | 0.92 | |
| gambiae | 0.1700 | 0.830 | 0.00 | 0.000 | 0.00 | 0.000 | 0.00 | |
| unassigned | 0.0000 | 0.000 | 0.00 | 0.500 | 0.00 | 0.000 | 0.50 | |
| Obuasi | gambiae | 0.0450 | 0.950 | 0.00 | 0.000 | 0.00 | 0.000 | 0.00 |
| Siaya | gambiae | 0.0000 | 0.000 | 0.95 | 0.000 | 0.05 | 0.000 | 0.00 |
| gcx3 | 0.0083 | 0.000 | 0.60 | 0.017 | 0.35 | 0.019 | 0.00 | |
| unassigned | 0.0100 | 0.000 | 0.78 | 0.020 | 0.19 | 0.000 | 0.00 | |
| VK7 | coluzzii | 0.0000 | 1.000 | 0.00 | 0.000 | 0.00 | 0.000 | 0.00 |
Diplotype clustering#
Diplotype clustering groups samples based on genetic similarity at the Vgsc locus, revealing evolutionary relationships between resistance haplotypes and helping identify potential selective sweeps (Miles et al., 2017).