XPEHH/AOM.GWA/2/1

This page describes a signal of selection found in the Angola An. coluzzii 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 3,054,895 and 3,394,895. 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 26 genes overlap the focal region: 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, AGAP004768 (periodic tryptophan protein 1), AGAP004769 (Ras-related protein Rap-1b precursor), AGAP004770 (female reproductive tract protease GLEANR_896), AGAP004771, AGAP004772 (SLIT-ROBO Rho GTPase activating protein), AGAP004773 (pyruvate dehydrogenase E1 component subunit alpha, mitochondrial), AGAP004774 (host cell factor).

The following 12 genes are within 50 kbp of the focal region: 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), AGAP004775 (Xaa-Pro dipeptidase), AGAP004776 (pre-mRNA-processing factor SLU7), AGAP004777.

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/UGS/2/2 H12 Uganda An. gambiae 2L:1,814,895-3,094,895 1,377 100.0% Vgsc
XPEHH/BFS.GWA/2/1 XPEHH Burkina Faso An. gambiae 2L:2,234,895-3,274,895 938 99.6% Vgsc
H12/CMS/2/2 H12 Cameroon An. gambiae 2L:3,054,895-3,614,895 725 99.7% nan
H12/GAS/2/2 H12 Gabon An. gambiae 2L:2,734,895-3,094,895 325 99.8% nan
XPEHH/GAS.GWA/2/2 XPEHH Gabon An. gambiae 2L:3,354,895-3,714,895 274 99.9% 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_exponential_peak)
[[Fit Statistics]]
    # function evals   = 52
    # data points      = 424
    # variables        = 4
    chi-square         = 118.029
    reduced chi-square = 0.281
    Akaike info crit   = -534.212
    Bayesian info crit = -518.013
[[Variables]]
    center:      0 (fixed)
    amplitude:   3.25255305 +/- 0.102693 (3.16%) (init= 3)
    decay:       2.99999948 +/- 0.375860 (12.53%) (init= 0.5)
    skew:        0.86174784 +/- 0.045384 (5.27%) (init= 0)
    baseline:    2.58358772 +/- 0.068185 (2.64%) (init= 1)
    ceiling:     100 (fixed)
    floor:       0 (fixed)
[[Correlations]] (unreported correlations are <  0.100)
    C(decay, baseline)           =  0.798
    C(skew, baseline)            =  0.333
    C(amplitude, baseline)       = -0.330
    C(decay, skew)               =  0.301
    C(amplitude, skew)           = -0.196
    C(amplitude, decay)          =  0.167

Null model:

[[Model]]
    Model(constant)
[[Fit Statistics]]
    # function evals   = 12
    # data points      = 423
    # variables        = 1
    chi-square         = 419.972
    reduced chi-square = 0.995
    Akaike info crit   = -1.039
    Bayesian info crit = 3.008
[[Variables]]
    c:   3.61942187 +/- 0.048504 (1.34%) (init= 1)

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