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. 2021 Jan 16;9(1):coaa136. doi: 10.1093/conphys/coaa136

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© The Author(s) 2021. Published by Oxford University Press and the Society for Experimental Biology.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Ratios of non-synonymous versus synonymous nucleotide substitution rates (dN:dS ratios; ω) in 532 genes estimated from codon evolution models in PAML. (A) baseline estimates for whole alignments from null models (ω₀), estimates for foreground (cetacea; ω_f) and background (all others; ω_b) branches from branch models, and estimates for codons under purifying (ω₀) and positive (ω₂) selection in foreground branch (cetacea) from branch-site models. (B) Foreground dN:dS ratio (ω_f) and statistical significance (P value) from likelihood-ratio tests between free-ratio branch models and neutral branch models. Significant tests after FDR correction (q ≤ 0.05) are highlighted in blue. (C) Foreground dN:dS ratio of positively selected codons (ω₂) and statistical significance (P value) from likelihood-ratio tests between positive-selection branch-site models and neutral branch-site models. Significant tests after FDR correction (q ≤ 0.05) are highlighted in orange. The red solid lines in all plots represent neutral evolution (ω = 1).