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These eQTL had peak likelihood ratio statistics (LRS) over 40.
When migration was capped at more realistic values (m1 = m2 ≤ 4 ≈ 2 migrants per generation), divergence times were often multimodal, but had peak likelihood post-dating the LGM.
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Thus a minimisation routine, such as amoeba, need not be used in this discrete framework as an exhaustive search of the grid to locate the peak posterior likelihood can be performed quickly.
This requires computation at each iteration of the posterior probabilities (τ i ) that the sire transmits allele Q, conditional on its phenotype, At the peak log-likelihood position (i.e. estimated QTL location), these τ i values can be used to classify backcross animals with high probability of having received the Q (or q) allele.
This is because the "numerical error" (here, error measures the deviation of the approximated AFS from the exact AFS) can be very different from the "propagated numerical error" (here, error measures the deviation of the numerically approximated likelihood peak from the exact likelihood peak), even if both decay as the truncation parameter increases.
The confidence interval in centimorgans of each QTL corresponded to a LOD score drop of 1 and 2 on either side of the likelihood peak, i.e. at -1LOD and -2LOD below the QTL-LOD peak, providing at least 95% confidence [ 61].
In that case, the likelihood peak would also provide an estimate for the target location.
A target would be considered present then if the weighted likelihood peak exceeded a certain threshold.
When we decoded the summed population response (consisting of the linear superposition of elevated baseline activity and 4-kHz-evoked activity [5]), the peak of the likelihood function was shifted towards 7kHz for the 7kHz-over-represented model (Fig. 2c, right).
a Position of likelihood peak (highest LOD score).
Markers flanking the likelihood peak for a putative QTL. 5 a = additive effect.
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