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.