XPEHH/UGS.BFS/2/1

This page describes a signal of selection found in the Uganda An. gambiae population when compared with the Burkina Faso An. gambiae population using the XPEHH (Cite et al. 20XX) statistic.The focus of this signal is on chromosome arm 2R between positions 27,980,000 and 28,280,000. The evidence supporting this signal is strong (\Delta_{i} >= 100 on both flanks).

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 23 genes overlap the focal region: AGAP002822, AGAP002823 (Med7 - Mediator of RNA polymerase II transcription subunit 7), AGAP002824 (GPRTAK1 - putative tachykinin receptor 1), AGAP0028251 (PPO1 - prophenoloxidase 1), AGAP002826, AGAP002828, AGAP002829 (SPN-E - ATP-dependent RNA helicase spindle-E), AGAP0028301 (C-1-tetrahydrofolate synthase, mitochondrial precursor), AGAP002831 (ribosomal RNA small subunit methyltransferase H), AGAP013130, AGAP002832 (protein-tyrosine phosphatase), AGAP002835 (alpha-tocopherol transfer protein-like protein), AGAP002836 (endoribonuclease Dicer), AGAP002837, AGAP013054, AGAP002838, AGAP013404, AGAP002839 (WD repeat-containing protein 85), AGAP002840, AGAP013351, AGAP002841 (pyridoxal phosphate phosphatase PHOSPHO2), AGAP002842 (CLIPD1 protein), AGAP002845.

The following 23 genes are within 50 kbp of the focal region: AGAP002815 (CLIPA15 - CLIP-domain serine protease), AGAP0028161 (ERO1-like protein alpha), AGAP002817, AGAP002818, AGAP002819, AGAP002820, AGAP002821, AGAP002846 (Trunk), AGAP013388 (Niemann-Pick Type C-2), AGAP002847 (Niemann-Pick Type C-2), AGAP002848 (Niemann-Pick Type C-2), AGAP002849 (Niemann-Pick Type C-2), AGAP002850 (Niemann-Pick Type C-2), AGAP002851 (Niemann-Pick C2 protein), AGAP002852, AGAP002853, AGAP002854, AGAP002855, AGAP002856, AGAP013529, AGAP013314, AGAP002857, AGAP002858 (Sodium/potassium-transporting ATPase subunit alpha).

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
IHS/UGS/2/1 IHS Uganda An. gambiae 2R:28,280,000-28,700,000 1,661 100.0% Cyp6p
IHS/CMS/2/1 IHS Cameroon An. gambiae 2R:28,240,000-28,560,000 1,249 100.0% Cyp6p
IHS/BFS/2/1 IHS Burkina Faso An. gambiae 2R:28,260,000-28,540,000 1,164 99.1% Cyp6p
H12/AOM/2/2 H12 Angola An. coluzzii 2R:28,040,000-28,080,000 478 100.0% nan
IHS/AOM/2/1 IHS Angola An. coluzzii 2R:27,980,000-28,040,000 324 100.0% nan
XPEHH/AOM.BFM/2/3 XPEHH Angola An. coluzzii 2R:28,000,000-28,060,000 295 99.4% nan
XPEHH/BFM.BFS/2/5 XPEHH Burkina Faso An. coluzzii 2R:28,200,000-28,240,000 139 98.7% nan
XPEHH/AOM.GWA/2/5 XPEHH Angola An. coluzzii 2R:27,980,000-28,040,000 96 95.2% 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   = 68
    # data points      = 614
    # variables        = 4
    chi-square         = 748.346
    reduced chi-square = 1.227
    Akaike info crit   = 129.493
    Bayesian info crit = 147.173
[[Variables]]
    center:      0 (fixed)
    amplitude:   5.18804876 +/- 0.146087 (2.82%) (init= 3)
    sigma:       0.88015851 +/- 0.031963 (3.63%) (init= 0.5)
    skew:       -0.72121420 +/- 0.039651 (5.50%) (init= 0)
    baseline:    1.89012149 +/- 0.059297 (3.14%) (init= 1)
    ceiling:     100 (fixed)
    floor:       0 (fixed)
[[Correlations]] (unreported correlations are <  0.100)
    C(amplitude, sigma)          = -0.397
    C(sigma, baseline)           = -0.364
    C(sigma, skew)               =  0.325
    C(amplitude, baseline)       = -0.322

Null model:

[[Model]]
    Model(constant)
[[Fit Statistics]]
    # function evals   = 11
    # data points      = 613
    # variables        = 1
    chi-square         = 2579.222
    reduced chi-square = 4.214
    Akaike info crit   = 882.806
    Bayesian info crit = 887.225
[[Variables]]
    c:   3.10791631 +/- 0.082911 (2.67%) (init= 1)

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