Analysis of the Amaranthaceae rbcL genes for positively selected sites.

aM1a (nearly neutral), M2a (positive selection), M8a (beta & ω = 1) and M8 (beta & ω) are PAML site models; A1 and A are PAML branch site models; SLR is “sitewise likelihood-ratio” method.bκ is transition/transversion rate ratio; ω is dN/dS ratio; ωs is dN/dS ratio in a class under putative positive selection; p0 and ps are proportion of codons with ωω>1, respectively; p and q are parameters of beta distribution in the range (0, 1); for the SLR test, the parameter values given are those optimal under M0.cThe sites listed are those at which positive selection is detected with a cutoff (significance level or posterior probability, as appropriate to the method used) >95%; those >99% are in italics. For the SLR test, the italic underlined sites are those at which there is still evidence for positive selection after correcting for multiple comparisons.dLRT is likelihood ratio test, 2l is twice the difference of model log-likelihoods.a. aM1a（近中性模型）、M2a（正选择模型）、M8a（β分布且ω=1模型）以及M8（β分布与ω模型）均属于PAML位点模型；A1与A属于PAML支位点模型；SLR即“逐位点似然比（sitewise likelihood-ratio, SLR）”方法。 b. κ为转换/颠换速率比；ω为dN/dS比值（非同义替换速率与同义替换速率之比）；ωs为推定正选择下某一类位点的dN/dS比值；p₀与pₛ分别为ω>1的密码子占比；p和q为(0,1)区间内β分布的参数；针对SLR检验，所给出的参数值为M0模型下的最优参数值。 c. 本次列出的位点为通过检验阈值（根据所用方法选取显著性水平或后验概率）大于95%时检测到正选择的位点；其中阈值大于99%的位点以斜体标注。针对SLR检验，带有下划线的斜体位点为经过多重比较校正后仍存在正选择证据的位点。 d. LRT为似然比检验（likelihood ratio test, LRT）；2ℓ为模型对数似然值之差的两倍。