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Supplementary Figure 1. G1PDH full tree, 111 sequences, 190 positions, inferred under LG+C60 model. Root position inferred using relaxed uncorrelated lognormal clock model with a Yule prior and LG substitution model. MAD root indicated with asterisk. \
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Supplementary Figure 2. GGGPS full tree, 133 sequences, 129 positions, inferred under LG+C40 model. Root position inferred using relaxed uncorrelated lognormal clock model with a Yule prior and LG substitution model. MAD root indicated with asterisk. \
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Supplementary Figure 3. GGGPS large subclade, 98 sequences, 166 positions, inferred under LG+C40 model. Root position inferred using relaxed uncorrelated lognormal clock model with a Yule prior and LG substitution model. MAD root indicated with asterisk. \
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Supplementary Figure 4. DGGGPS full tree, 97 sequences, 119 positions, inferred under LG+C60 model. Root position inferred using relaxed uncorrelated lognormal clock model with a Yule prior and LG substitution model. MAD root indicated with asterisk. \
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Supplementary Figure 5. GpsA full tree, 84 sequences, 169 positions, inferred under LG+C60 model. Root position inferred using relaxed uncorrelated lognormal clock model with a Yule prior and LG substitution model. MAD root indicated with asterisk. \
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Supplementary Figure 6. Glp full tree, 51 sequences, 199 positions, inferred under LG+C40 model. Root position inferred using relaxed uncorrelated lognormal clock model with a Yule prior and LG substitution model. MAD root indicated with asterisk. \
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Supplementary Figure 7. GlpK full tree, 77 sequences, 363 positions, inferred under LG+C60 model. Root position inferred using relaxed uncorrelated lognormal clock model with a Yule prior and LG substitution model. MAD root indicated with asterisk. \
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Supplementary Figure 8. PlsC full tree, 74 sequences, 57 positions, inferred under LG+C60 model. Root position inferred using relaxed uncorrelated lognormal clock model with a Yule prior and LG substitution model. MAD root between clade comprising of sequences in red and other sequences. \
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Supplementary Figure 9. PlsY full tree, 60 sequences, 104 positions, inferred under LG+C50 model. Root position inferred using relaxed uncorrelated lognormal clock model with a Yule prior and LG substitution model. MAD root indicated with asterisk. \
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Supplementary Figure 10. G1PDH full tree, 123 sequences, 173 positions, inferred under LG+C60 model. Root position inferred using 3-dehydroquinate synthase\cf2 (DHQS), five glucerol dehydrogenase (GDH) and five alcohol dehydrogenase (ALDH) sequences as an outgroup \
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\cf0 Supplementary Figure 11. Glp full tree, 63 sequences, 183 positions, inferred under LG+C60 model. Root position inferred using \cf2 12 \cf0 FAD-dependent oxidoreductase sequences \cf2 as an outgroup \
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\cf0 Supplementary Figure 12. Gpsa full tree, 96 sequences, 148 positions, inferred under LG+C60 model. Root position inferred using \cf2 six \cf0 hydroxyacyl-CoA dehydrogenase\cf2 (HACDH) and 6\cf0 UDP-glucose 6-dehydrogenase\cf2 (UDPGDH) sequences as an outgroup \
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Supplementary Figure 13. Gpsa full tree with eukaryotic sequences, 113 sequences, 159 positions, inferred under LG+C50 model.\
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Supplementary Figure 14. Glp full tree with eukaryotic sequences, 80 sequences, 190 positions, inferred under LG+C50 model.\
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Supplementary Figure 15. PlsC full tree with eukaryotic sequences, 96 sequences, 54 positions, inferred under LG+C60 model.\
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\cf0 Supplementary Figure 16. Unrooted G1PDH full tree, 111 sequences, 190 positions, inferred under LG+C60 model. \
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Supplementary Figure 17. Unrooted GGGPS full tree, 133 sequences, 129 positions, inferred under LG+C40 model. \
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Supplementary Figure 18. Unrooted DGGGPS full tree, 97 sequences, 119 positions, inferred under LG+C60 model. \
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Supplementary Figure 19. Unrooted GpsA full tree, 84 sequences, 169 positions, inferred under LG+C60 model. \
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Supplementary Figure 20. Unrooted Glp full tree, 51 sequences, 199 positions, inferred under LG+C40 model. \
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Supplementary Figure 21. Unrooted GlpK full tree, 77 sequences, 363 positions, inferred under LG+C60 model. \
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Supplementary Figure 22. Unrooted PlsC full tree, 74 sequences, 57 positions, inferred under LG+C60 model. \
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Supplementary Figure 23. Unrooted PlsY full tree, 60 sequences, 104 positions, inferred under LG+C50 model \
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Supplementary Figure 24. Gpsa full tree, 96 sequences, 148 positions, inferred under LG+C50 model. Root position inferred using \cf2 six \cf0 hydroxyacyl-CoA dehydrogenase\cf2 (HACDH) and 6\cf0 UDP-glucose 6-dehydrogenase\cf2 (UDPGDH) sequences as an outgroup \
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\cf0 Supplementary Figure 25. UbiA full tree, 227 sequences, 69 positions, inferred under LG+C60 model. DGGGP sequences in blue, chlorophyll a synthase in green, protoheme IX farnesyltransferase in red, and 4-hydroxybenzoate octaprenyltransferase in black. \
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Supplementary Figure 26. Unrooted GGGPS full tree, 133 sequences, 129 positions, inferred under LG+C60 model. \
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Supplementary Figure 27. Unrooted PlsY full tree, 60 sequences, 104 positions, inferred under LG+C60 model\
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Supplementary Figure 28. \cf2 Glp full tree with eukaryotic sequences, 80 sequences, 190 positions, inferred under LG+C60 model\cf0 \
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Supplementary Figure 29. \cf2 Gpsa full tree with eukaryotic sequences, 113 sequences, 159 positions, inferred under LG+C60 model\
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\cf2 Supplementary Table 1. Highest marginal posterior probabilities for each gene tree for both the molecular clock and MAD rooting methods.\
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Supplementary Table 2. Comparison of Bayesian Information Criterion (BIC) scores for the models selected by IQTree compared to the model used by Yokobori et al. (LG+gamma) for the outgrip rooting analyses. Lower BIC scores indicate better fit of model to data. \
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Supplementary Table 3. Accession numbers for sequences used in phylogenetic analyses. \
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