TABLE 5.

Comparison of amino acids in the C₄ PEP carboxylases of the Allionia and Okenia/Boerhavia C₄ clades with PEP carboxylase sites under positive selection in C₄ grasses.

	Sites with posterior probability > 0.999												Prob > 0.99			Prob > 0.95
Clade	466	517	531	560	577	579	625	637	761	780	794	807	572	599	813	665	733	863	866
Boerhavia/Okenia	Met	Thr	Ala	Arg	Ser	Ala	Leu	Met	Ala	Ala	Phe	Lys	Gln	Ile	Arg, Gln*	His	Met	Lys	Glu
Allionia	Met	Thr	Ala	Arg	Ser	Ala	Val	Met	Ala	Ala	Phe	Lys	Gln	Ile	Gln	His	Phe	Asn	Glu
C3 Nyctag	Met	Thr	Ala	Arg	Ser	Ala	Val	Met	Ser	Ala	Phe	Arg	Glu	Ile	Arg	His	Phe	Asn	Glu
C4 grasses (Christin et al. (2007)	Ile, Val	Ala, Cys	Pro	Pro	Ser	Glu	Ala	Leu, Phe	Ala	Ser	Val	Lys	Gln	Val	Gln	Asn	Met, Val	Lys	Glu

Site numbers correspond to the maize PEP carboxylase gene (PEPC). Sites under positive selection were identified by a screen of grass lineages examined by Christin et al. (2007). Posterior probabilities noted with blue headers are from that study. Sites showing an identical amino acid substitution in either or both C₄ Nyctaginaceae lineages are highlighted in yellow. We list the most frequent positively selected amino acid(s) at each site in C₄ grasses. The species in the C₃ Nyctag clade are the North American Xerophytic C₃ species in the PEPC1 gene tree in Supplementary Figure 2, which exhibited identical amino acids at the sites shown. *Gln is only present in B. burbidgeana; the other Boerhavia and Okenia have Arg at position 813.