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In the former gene, the branch-site models detected episodic selection on lineages that were not detected by branch-models, as expected if positive selection occurs at a few sites in an overall purifying selection background.
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In AGAP005196, the branch model detected episodic selection along the branch separating the A. melas-like from the A. gambiae-like alleles, and along the branch leading to A. melas.
In AGAP005196 the branch model detected episodic selection along the branch separating the A. melas-like from the A. gambiae-like groups (ω = 2.22, p < 0.05, see Figure 2c).
Finally, branch-site models can detect episodic events of adaptive evolution on specific sites in different branches of a phylogeny [34].
The branch model performed using a gene-tree reconstructed after excluding A. arabiensis and A. quadriannulatus from the dataset also detected episodic selection for the branch separating A. gambiae from the other two species (ω = 2.14; p < 0.05).
More specifically, this study detected episodic deformation related to two of these three events in the GNSS time series (Figure 2) but failed to estimate a reasonable fault model.
The researchers calculated the difference in responses to familiar versus novel words, and detected episodic memory coding.
Screening for diversifying selection over alignment positions was implemented with mixed effects model of evolution with default parameters, due to its ability of detecting episodic selection (Murrell et al. 2012).
To address the shortcomings of the aforementioned approaches, we employed the advanced Mixed Effects Model Evolution (MEME) [ 57], which uses fixed effects likelihood (FEL) along the sites and random effects likelihood (REL) across the branches to detect episodic diversifying selection.
MEME [ 57], which is designed to overcome the drawbacks of site-specific assessments, was used to detect episodic diversifying selection.
For instance, detecting episodic selection at a handful of residues may require a particularly large number of sufficiently diverged sequences.
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