Analysis of the Amaranthaceae <i>rbcL</i> genes for positively selected sites.

a<p>M1a (nearly neutral), M2a (positive selection), M8a (beta & <i>ω = </i>1) and M8 (beta & <i>ω</i>) are PAML site models; A1 and A are PAML branch site models; SLR is “sitewise likelihood-ratio” method.</p>b<p><i>κ</i> is transition/transversion rate ratio; ω is <i>d</i>_N/<i>d</i>_S ratio; <i>ω</i>_s is <i>d</i>_N/<i>d</i>_S ratio in a class under putative positive selection; <i>p</i>₀ and <i>p</i>_s are proportion of codons with <i>ω</i><1 and <i>ω</i>>1, respectively; <i>p</i> and <i>q</i> are parameters of beta distribution in the range (0, 1); for the SLR test, the parameter values given are those optimal under M0.</p>c<p>The 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.</p>d<p>LRT is likelihood ratio test, 2<i>l</i> is twice the difference of model log-likelihoods.