XPEHH/BFS.GWA/2/1

This page describes a signal of selection found in the Burkina Faso An. gambiae population when compared with the Guinea Bissau population using the XPEHH (Cite et al. 20XX) statistic.The focus of this signal is on chromosome arm 2L between positions 2,234,895 and 3,274,895. The evidence supporting this signal is strong (\Delta_{i} >= 100 on both flanks).

This signal overlaps the Vgsc locus, a genome region with prior evidence of an association with insecticide resistance and/or recent positive selection in Anopheles mosquitoes.

Signal location. Blue markers show the values of the selection statistic. The dashed black line shows the fitted peak model. The shaded red area shows the focus of the selection signal. The shaded blue area shows the genomic region in linkage with the selection event. Use the mouse wheel or the controls at the top right of the plot to zoom in, and hover over genes to see gene names and descriptions.

Genes

The following 66 genes overlap the focal region: AGAP004703 (DNA-directed RNA polymerase III subunit RPC1), AGAP004704 (COMPASS component SPP1), AGAP028437, AGAP004706, AGAP0047072 (para - voltage-gated sodium channel), AGAP004708 (arginyl-tRNA synthetase), AGAP004709 (mRpL18 - 39S ribosomal protein L18, mitochondrial), AGAP0047101 (ubiquinol-cytochrome c reductase subunit 9), AGAP004711 (ATP-dependent RNA helicase DDX41), AGAP004712, AGAP004713, AGAP004714, AGAP0047151 (Pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial), AGAP0047163 (Gr57 - gustatory receptor 57), AGAP004717, AGAP004718, AGAP004719 (CLIPC9 - CLIP-domain serine protease), AGAP004720, AGAP004721 (N-acetylglucosamine-6-sulfatase), AGAP004722, AGAP004723 (chromobox protein homolog 1), AGAP004724 (Intraflagellar transport 74 homolog), AGAP004725 (eIF3c - Eukaryotic translation initiation factor 3 subunit C), AGAP004726 (Uncharacterized protein CG3556), AGAP0047273 (Gr25 - gustatory receptor 25), AGAP004728, AGAP004729, AGAP004730 (phospholipase A2, venom), AGAP004731 (secretory phospholipase A2), AGAP029113, AGAP004733, AGAP004735, AGAP004736 (mitochondrial GTPase 1 homolog), AGAP004737 (Rhomboid-4, isoform B), AGAP004738 (IK cytokine), AGAP004739 (H/ACA ribonucleoprotein complex subunit 4), AGAP004740, AGAP004741 (serine proteinase), AGAP004742 (Pyruvate carboxylase), AGAP004743 (Transmembrane emp24 domain-containing protein), AGAP004744 (skap - succinyl-CoA ligase beta subunit), AGAP004745 (transcription elongation regulator 1), AGAP004746 (Thoc5 - THO complex subunit 5), AGAP004747 (Uncharacterized protein C05D11.1), AGAP004748, AGAP0047491 (coproporphyrinogen III oxidase), AGAP004750 (translation initiation factor 4G), AGAP004751 (condensin-2 complex subunit D3), AGAP004752 (tRNA (guanine-N(7)-)-methyltransferase), AGAP004753, AGAP004754 (CASPL2 - long caspase (CASPL2)), AGAP004755, AGAP004756, AGAP013546 (Vacuolar ATPase assembly integral membrane protein VMA21 homolog), AGAP004757, AGAP004758, AGAP004759 (oligoribonuclease), AGAP004760, AGAP004761, AGAP004762 (alpha-tocopherol transfer protein-like protein), AGAP004763, AGAP004764, AGAP004765 (ATP-dependent RNA helicase DDX1), AGAP028129, AGAP004766 (endophilin-A), AGAP004767.

The following 3 genes are within 50 kbp of the focal region: AGAP004768 (periodic tryptophan protein 1), AGAP004769 (Ras-related protein Rap-1b precursor), AGAP004770 (female reproductive tract protease GLEANR_896).

Key to insecticide resistance candidate gene types: 1 metabolic; 2 target-site; 3 behavioural; 4 cuticular.

Overlapping selection signals

The following selection signals have a focus which overlaps with the focus of this signal.

Signal Statistic Population Focus Peak model \Delta_{i} Max. percentile Known locus
H12/BFM/2/1 H12 Burkina Faso An. coluzzii 2L:2,474,895-2,894,895 1,800 99.9% Vgsc
H12/BFS/2/1 H12 Burkina Faso An. gambiae 2L:1,454,895-2,694,895 1,776 100.0% Vgsc
H12/GNS/2/1 H12 Guinea An. gambiae 2L:1,294,895-2,474,895 1,685 100.0% Vgsc
H12/UGS/2/2 H12 Uganda An. gambiae 2L:1,814,895-3,094,895 1,377 100.0% Vgsc
XPEHH/BFM.GWA/2/1 XPEHH Burkina Faso An. coluzzii 2L:2,334,895-2,974,895 917 99.8% Vgsc
H12/CMS/2/2 H12 Cameroon An. gambiae 2L:3,054,895-3,614,895 725 99.7% nan
XPEHH/AOM.GWA/2/1 XPEHH Angola An. coluzzii 2L:3,054,895-3,394,895 533 100.0% nan
H12/GAS/2/2 H12 Gabon An. gambiae 2L:2,734,895-3,094,895 325 99.8% nan

Diagnostics

The information below provides some diagnostics from the Peak modelling algorithm.

Selection signal in context. @@TODO

Peak targetting. @@TODO

Peak fitting diagnostics. @@TODO

Model fit reports

Peak model:

[[Model]]
    Model(skewed_gaussian)
[[Fit Statistics]]
    # function evals   = 43
    # data points      = 430
    # variables        = 4
    chi-square         = 238.833
    reduced chi-square = 0.561
    Akaike info crit   = -244.849
    Bayesian info crit = -228.594
[[Variables]]
    center:      0 (fixed)
    amplitude:   6.39309161 +/- 0.112594 (1.76%) (init= 3)
    sigma:       1.89548239 +/- 0.041105 (2.17%) (init= 0.5)
    skew:        0.86431697 +/- 0.020128 (2.33%) (init= 0)
    baseline:    1.44777481 +/- 0.061273 (4.23%) (init= 1)
    ceiling:     100 (fixed)
    floor:       0 (fixed)
[[Correlations]] (unreported correlations are <  0.100)
    C(sigma, baseline)           = -0.565
    C(amplitude, baseline)       = -0.385
    C(sigma, skew)               = -0.290
    C(amplitude, sigma)          = -0.260

Null model:

[[Model]]
    Model(constant)
[[Fit Statistics]]
    # function evals   = 11
    # data points      = 429
    # variables        = 1
    chi-square         = 2148.706
    reduced chi-square = 5.020
    Akaike info crit   = 693.189
    Bayesian info crit = 697.251
[[Variables]]
    c:   3.43966846 +/- 0.108167 (3.14%) (init= 1)

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