IHS/BFS/2/5

This page describes a signal of selection found in the Burkina Faso An. gambiae populationusing the IHS (Cite et al. 20XX) statistic.The focus of this signal is on chromosome arm 2L between positions 25,434,895 and 25,614,895. The evidence supporting this signal is moderate (\Delta_{i} >= 50 on both flanks).

This signal occurs within 50 kbp of the Rdl 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 17 genes overlap the focal region: AGAP006029, AGAP006030 (mfrn - mitoferrin), AGAP006031 (nuclear pore complex protein Nup54), AGAP006032, AGAP006033, AGAP006034, AGAP006035 (Ras-related protein Rab-36), AGAP006036 (axonemal dynein intermediate chain inner arm i1), AGAP006037 (RpL24 - 60S ribosomal protein L24), AGAP006038 (serine/arginine repetitive matrix protein 2), AGAP006039, AGAP006040 (peroxisomal membrane protein 2), AGAP006041 (E3 ubiquitin-protein ligase RNF5), AGAP006042, AGAP029130, AGAP029102, AGAP006045 (protein yorkie).

The following 10 genes are within 50 kbp of the focal region: AGAP0060282 (Rdl - GABA-gated chloride channel subunit), AGAP006046 (Med23 - mediator of RNA polymerase II transcription subunit 23), AGAP0060471 (CYP4J9 - cytochrome P450), AGAP0060481 (CYP4J5 - cytochrome P450), AGAP0060491 (CYP4J10 - cytochrome P450), AGAP006050 (AarF domain containing kinase 5), AGAP006051 (pentatricopeptide repeat domain 1), AGAP006052 (protein phosphatase 1, regulatory (inhibitor) subunit 3), AGAP006053, AGAP006054.

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/2/2 H12 Burkina Faso An. coluzzii 2L:25,434,895-25,494,895 1,172 98.4% Rdl
XPEHH/BFM.GWA/2/2 XPEHH Burkina Faso An. coluzzii 2L:25,474,895-25,514,895 625 99.4% Rdl
H12/GAS/2/1 H12 Gabon An. gambiae 2L:25,454,895-25,514,895 529 100.0% Rdl
XPEHH/BFM.BFS/2/1 XPEHH Burkina Faso An. coluzzii 2L:25,454,895-25,554,895 468 99.3% Rdl
XPEHH/GAS.GWA/2/1 XPEHH Gabon An. gambiae 2L:25,474,895-25,634,895 423 100.0% Rdl
XPEHH/BFS.UGS/2/4 XPEHH Burkina Faso An. gambiae 2L:25,434,895-25,474,895 388 98.3% Rdl
H12/BFS/2/5 H12 Burkina Faso An. gambiae 2L:25,454,895-25,534,895 375 96.1% Rdl
H12/GNS/2/4 H12 Guinea An. gambiae 2L:25,534,895-25,814,895 332 97.8% nan
IHS/BFM/2/3 IHS Burkina Faso An. coluzzii 2L:24,754,895-25,434,895 304 99.9% Rdl
XPEHH/CMS.UGS/2/2 XPEHH Cameroon An. gambiae 2L:25,414,895-25,454,895 291 90.3% Rdl
XPEHH/GAS.BFS/2/2 XPEHH Gabon An. gambiae 2L:25,614,895-25,894,895 284 99.9% nan
XPEHH/BFS.GWA/2/6 XPEHH Burkina Faso An. gambiae 2L:25,434,895-25,474,895 138 95.3% Rdl

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_exponential_peak)
[[Fit Statistics]]
    # function evals   = 60
    # data points      = 369
    # variables        = 4
    chi-square         = 140.833
    reduced chi-square = 0.386
    Akaike info crit   = -347.429
    Bayesian info crit = -331.786
[[Variables]]
    center:      0 (fixed)
    amplitude:   3.39663112 +/- 0.206251 (6.07%) (init= 3)
    decay:       0.81291739 +/- 0.081672 (10.05%) (init= 0.5)
    skew:        0.99999999 +/- 0.007305 (0.73%) (init= 0)
    baseline:    1.72049089 +/- 0.043463 (2.53%) (init= 1)
    ceiling:     100 (fixed)
    floor:       0 (fixed)
[[Correlations]] (unreported correlations are <  0.100)
    C(amplitude, decay)          = -0.566
    C(decay, baseline)           = -0.486
    C(decay, skew)               =  0.433

Null model:

[[Model]]
    Model(constant)
[[Fit Statistics]]
    # function evals   = 11
    # data points      = 368
    # variables        = 1
    chi-square         = 286.167
    reduced chi-square = 0.780
    Akaike info crit   = -90.554
    Bayesian info crit = -86.646
[[Variables]]
    c:   2.07462138 +/- 0.046031 (2.22%) (init= 1)

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