Appendix 4.3.4: PAML-BEB selected site analysis

To validate our findings from aBSREL and MEME using a different method, we applied Phylogenetic Analysis by Maximum Likelihood (PAML) branch by site analysis to the luciferase sequences. We tested the alternative hypothesis, that there is a class of sites under selection (ω &gt; 1) on the EAncLuc ancestral branch identified as under selection in the aBSREL analysis, against the null hypotheses, that all classes of sites on all branches are evolving either under constraint (ω &lt; 1) or neutrality (ω = 1). A likelihood ratio test supported the alternative hypothesis, that 13% of sites in luciferase were in a positively selected class (ω = 3.25). Subsequent Bayes Empirical Bayes (BEB) estimation identified 31 sites with evidence of selection on these branches, 5 of which were significant. <br>

为了通过不同方法验证我们从自适应分支位点随机效应似然法（aBSREL）和混合效应进化模型（MEME）得到的研究结果，我们将最大似然系统发育分析（PAML）的分支位点分析方法应用于荧光素酶序列。我们设置备择假设为：在aBSREL分析中被鉴定为受选择的EAncLuc祖先分支上，存在一类处于选择压力下的位点（ω>1）；并以所有分支上的各类位点均处于约束进化（ω<1）或中性进化（ω=1）状态作为零假设。似然比检验结果支持该备择假设，即荧光素酶序列中有13%的位点处于正选择类别（ω=3.25）。后续的贝叶斯经验贝叶斯（BEB）估计鉴定出31个在这些分支上存在选择证据的位点，其中5个位点具有统计学显著性。