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A final analysis to detect diversifying selection was performed using Clade model C [ 34].
Site models permit differing dN/dS ratios at each codon, and because selective pressures are expected to vary across amino acids, this approach has high power to detect diversifying selection in genes [ 11].
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Site-specific models [ 26] account for rate variation among sites and are powerful tools for detecting diversifying selection.
For example, Manier et al. [ 42] detected diversifying selection of different ecotypes of garter snake Thamnophis elegans (in terms of coloration and scalation).
MEME [ 57], which is designed to overcome the drawbacks of site-specific assessments, was used to detect episodic diversifying selection.
Ka/ Ks ratios were estimated to detect the diversifying selection pressures on TNL and non-TNL genes.
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.
The discrepancy with our IL4 analysis [that failed to detect significant evidence of diversifying selection when restricted to primates alone (Table 1)] may be due to different species analyzed in each study.
To detect functional sequence diversity and diversifying selection, putative exon sequences were compared between sspp.
Based upon the failure to detect a similar signature of diversifying selection in γc itself, the authors proposed that cytokine selection was driven by mutual competition for γc, a common receptor subunit for each cytokine [ 25].
They removed human DNA from the samples and used highly diversified libraries of primers to detect and grow anything other than a known microbe.
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