XPEHH/CMS.GWA/3/1

This page describes a signal of selection found in the Cameroon 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 3R between positions 28,600,000 and 28,700,000. The evidence supporting this signal is strong (\Delta_{i} >= 100 on both flanks).

This signal overlaps the Gste 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 13 genes overlap the focal region: AGAP0091961 (GSTE7 - glutathione S-transferase epsilon class 7), AGAP0091971 (GSTE3 - glutathione S-transferase epsilon class 3), AGAP009198, AGAP009199 (palmitoyltransferase ZDHHC24), AGAP009200 (collagen type IV alpha), AGAP009201 (collagen type IV alpha), AGAP009202 (selenoprotein T), AGAP028058, AGAP009203 (SPRY domain-containing SOCS box protein 3), AGAP009204 (eIF3h - Eukaryotic translation initiation factor 3 subunit H), AGAP009205 (ankyrin repeat domain 39), AGAP009206, AGAP009207 (extracellular signal-regulated kinase 1/2).

The following 13 genes are within 50 kbp of the focal region: AGAP009185, AGAP0091871 (Indanol dehydrogenase), AGAP009188 (solute carrier family 39 (zinc transporter), member 9), AGAP009189, AGAP0091901 (GSTE8 - glutathione S-transferase epsilon class 8), AGAP0091911 (GSTE6 - glutathione S-transferase epsilon class 6), AGAP0091921 (GSTE5 - glutathione S-transferase epsilon class 5), AGAP0091931 (GSTE4 - glutathione S-transferase epsilon class 4), AGAP0091941 (GSTE2 - glutathione S-transferase epsilon class 2), AGAP0091951 (GSTE1 - glutathione S-transferase epsilon class 1), AGAP009208, AGAP009209 (Rpb11 - DNA-directed RNA polymerase II subunit RPB11), AGAP009210 (CAP-Gly domain-containing linker protein 1).

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/CMS/3/1 H12 Cameroon An. gambiae 3R:28,580,000-28,620,000 1,410 100.0% Gste
XPEHH/BFS.GWA/3/1 XPEHH Burkina Faso An. gambiae 3R:28,500,000-28,620,000 1,181 100.0% Gste
IHS/CMS/3/1 IHS Cameroon An. gambiae 3R:28,320,000-28,700,000 1,106 100.0% Gste
IHS/BFM/3/1 IHS Burkina Faso An. coluzzii 3R:28,260,000-28,620,000 1,058 100.0% Gste
H12/UGS/3/1 H12 Uganda An. gambiae 3R:28,560,000-28,600,000 876 97.3% Gste
XPEHH/BFM.GWA/3/1 XPEHH Burkina Faso An. coluzzii 3R:28,600,000-28,660,000 767 100.0% Gste
H12/BFM/3/1 H12 Burkina Faso An. coluzzii 3R:28,560,000-28,620,000 747 98.0% Gste
XPEHH/UGS.GWA/3/1 XPEHH Uganda An. gambiae 3R:28,540,000-28,600,000 662 100.0% Gste
XPEHH/BFM.AOM/3/1 XPEHH Burkina Faso An. coluzzii 3R:28,600,000-28,640,000 569 100.0% Gste
IHS/UGS/3/1 IHS Uganda An. gambiae 3R:28,440,000-28,640,000 493 99.7% Gste
XPEHH/GAS.GWA/3/1 XPEHH Gabon An. gambiae 3R:28,540,000-28,620,000 129 100.0% Gste

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   = 45
    # data points      = 438
    # variables        = 4
    chi-square         = 198.067
    reduced chi-square = 0.456
    Akaike info crit   = -339.603
    Bayesian info crit = -323.274
[[Variables]]
    center:      0 (fixed)
    amplitude:   9.92761432 +/- 0.125624 (1.27%) (init= 3)
    sigma:       0.41285055 +/- 0.006657 (1.61%) (init= 0.5)
    skew:        0.51071026 +/- 0.018069 (3.54%) (init= 0)
    baseline:    1.60907336 +/- 0.038647 (2.40%) (init= 1)
    ceiling:     100 (fixed)
    floor:       0 (fixed)
[[Correlations]] (unreported correlations are <  0.100)
    C(amplitude, sigma)          = -0.451
    C(sigma, baseline)           = -0.329
    C(sigma, skew)               = -0.274
    C(amplitude, baseline)       = -0.222

Null model:

[[Model]]
    Model(constant)
[[Fit Statistics]]
    # function evals   = 11
    # data points      = 437
    # variables        = 1
    chi-square         = 3706.493
    reduced chi-square = 8.501
    Akaike info crit   = 936.266
    Bayesian info crit = 940.346
[[Variables]]
    c:   3.06291167 +/- 0.139468 (4.55%) (init= 1)

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