Table 1.
Open in new tab

Summary of results of the SM test. BEB and FUBAR were applied to identify the codons targeted by positive selection. PSG = positively selected genes; ω = ratio of non-synonymous (Ka) to synonymous substitution rate (Ks); L = likelihood; M8 vs. M7 and M8a are the models tested as described in the Materials and Methods. Positive selection results were reported if the estimated ω was >1 and the likelihood ratio test was significant (P < 0.05). Positive selection of each codon estimated by BEB and FUBAR analysis is reported if P > 0.9. Position in the alignment, letter of amino acid residue and probability are reported for each codon selected

PSGLn L(M8)ω(M8)Ln L(M7)P  (M7–M8)BEB P > 0.9FUBAR P > 0.9
Ln L(M8a)P  (M8a–M8)
accD−4465.18204.144−4480.71121.8 × 10−771 Q 0.99, 94 D 0.90, 104 V 0.96, 197 H 0.94, 208 G 0.96, 217 L 0.96, 323 P 0.92, 490 K 0.9771 Q 0.98, 94 D 0.96, 283 L 96, 490 K 0.95
−4478.11023.7 × 10−7
atpA−3964.918851.867−4035.7022<10−10488 T 0.99, 500 R 0.98,459 A 0.97, 465 L 0.97, 488 T 0.98, 500 R 0.95
−4024.0715<10−10
matK−5187.29533.723−5193.95241.2 × 10−3118 A 0.91, 349 A 0.9188 Y 0.91, 168 A 0.92, 349 A 0.95, 482 L 0.91
−5174.25543.3 × 10−3
ndhH−2876.03025.393−2886.92801.8 × 10−5269 V 1.00269 V 1.00
−2879.53678.3 × 10−3
psaA−4841.18052.513−4865.7854<10−1019 I 0.94,152 N 0.98, 209 S 0.94, 626 L 0.9619 I 0.93, 152 N 0.98, 209 S 0.98, 626 L 0.98
−4844.58739.0 × 10−3
psaB−4551.2542 1.365−4561.05525.5 × 10−5273 I 0.92273 I 0.93, 245 G 0.93
−4547.33405.1 × 10−3
psaI−363.811511.351−375.70806.8 × 10−63 T 0.90, 4 L 0.96, 7 P 0.99, 8 S 1.00, 10 L 1.00, 15 G 0.994 L 0.96
−331.8516<10−9
psbA−2111.55892.004−2128.11536.5 × 10−8155 A 0.98, 351 I 0.92155 A 0.99, 235 A 0.92
−2105.37224.3 × 10−4
psbD−1983.77303.569−1997.12521.6 × 10−6146 A 0.97146 A 0.97
−1985.90453.9 × 10−2
psbK−461.93392.725−466.23671.4 × 10−247 L 1.0022 N 0.93
−455.82774.7 × 10−4
rbcL−4018.55964.215−4063.6618<10−1028 E 0.98, 30 E 0.97, 33 P 1.00, 86 H 1.00, 91 A 0.99, 97 F 0.99, 140 I 0.95, 142 P 1.00, 145 S 1.00, 219 L 0.99, 225 I 0.99, 251 I 1.00, 255 V 1.00, 256 F 0.91, 279 S 1.00, 309 M 1.00, 353 F 0.92, 461 V 0.95, 470 P 1.0010 S 0.98, 30 E 0.92, 33 P 0.93, 86 H 1.00, 91 A 0.99, 95 S 0.94, 140 I 0.94, 142 P 1.00, 143 A 0.97, 145 S 1.00, 219 L 0.99, 225 I 0.99, 251 I 0.95, 255 V 0.99, 256 F 0.95, 309 M 0.95, 320 L 0.91, 354 V 0.94, 461 V 0.98, 470 P 0.99
−4089.8081<10−10
rpoA−2567.08705.590−2572.43744.7 × 10−3155 R 0.91, 249 S 0.97, 316 R 0.907 T 0.93, 105 G 0.94, 249 S 0.90, 272 L 0.91, 316 R 0.94
−2556.25763.2 × 10−6
rpoC2−1521.34023.675−11529.28293.5 × 10−4434 F 0.96, 507 L 0.93, 508 S 0.96, 509 V 0.93, 1008 A 0.91, 1370 M 0.91434 F 0.99, 509 V 0.95, 758 K 0.91,766 L 0.91
−11217.1235< 10−10
rps19−812.094311.835−817.22845.9 × 10−329 W 0.9224 W 0.92, 29 W 0.95
-806.78121.1 × 10−3
PSGLn L(M8)ω(M8)Ln L(M7)P  (M7–M8)BEB P > 0.9FUBAR P > 0.9
Ln L(M8a)P  (M8a–M8)
accD−4465.18204.144−4480.71121.8 × 10−771 Q 0.99, 94 D 0.90, 104 V 0.96, 197 H 0.94, 208 G 0.96, 217 L 0.96, 323 P 0.92, 490 K 0.9771 Q 0.98, 94 D 0.96, 283 L 96, 490 K 0.95
−4478.11023.7 × 10−7
atpA−3964.918851.867−4035.7022<10−10488 T 0.99, 500 R 0.98,459 A 0.97, 465 L 0.97, 488 T 0.98, 500 R 0.95
−4024.0715<10−10
matK−5187.29533.723−5193.95241.2 × 10−3118 A 0.91, 349 A 0.9188 Y 0.91, 168 A 0.92, 349 A 0.95, 482 L 0.91
−5174.25543.3 × 10−3
ndhH−2876.03025.393−2886.92801.8 × 10−5269 V 1.00269 V 1.00
−2879.53678.3 × 10−3
psaA−4841.18052.513−4865.7854<10−1019 I 0.94,152 N 0.98, 209 S 0.94, 626 L 0.9619 I 0.93, 152 N 0.98, 209 S 0.98, 626 L 0.98
−4844.58739.0 × 10−3
psaB−4551.2542 1.365−4561.05525.5 × 10−5273 I 0.92273 I 0.93, 245 G 0.93
−4547.33405.1 × 10−3
psaI−363.811511.351−375.70806.8 × 10−63 T 0.90, 4 L 0.96, 7 P 0.99, 8 S 1.00, 10 L 1.00, 15 G 0.994 L 0.96
−331.8516<10−9
psbA−2111.55892.004−2128.11536.5 × 10−8155 A 0.98, 351 I 0.92155 A 0.99, 235 A 0.92
−2105.37224.3 × 10−4
psbD−1983.77303.569−1997.12521.6 × 10−6146 A 0.97146 A 0.97
−1985.90453.9 × 10−2
psbK−461.93392.725−466.23671.4 × 10−247 L 1.0022 N 0.93
−455.82774.7 × 10−4
rbcL−4018.55964.215−4063.6618<10−1028 E 0.98, 30 E 0.97, 33 P 1.00, 86 H 1.00, 91 A 0.99, 97 F 0.99, 140 I 0.95, 142 P 1.00, 145 S 1.00, 219 L 0.99, 225 I 0.99, 251 I 1.00, 255 V 1.00, 256 F 0.91, 279 S 1.00, 309 M 1.00, 353 F 0.92, 461 V 0.95, 470 P 1.0010 S 0.98, 30 E 0.92, 33 P 0.93, 86 H 1.00, 91 A 0.99, 95 S 0.94, 140 I 0.94, 142 P 1.00, 143 A 0.97, 145 S 1.00, 219 L 0.99, 225 I 0.99, 251 I 0.95, 255 V 0.99, 256 F 0.95, 309 M 0.95, 320 L 0.91, 354 V 0.94, 461 V 0.98, 470 P 0.99
−4089.8081<10−10
rpoA−2567.08705.590−2572.43744.7 × 10−3155 R 0.91, 249 S 0.97, 316 R 0.907 T 0.93, 105 G 0.94, 249 S 0.90, 272 L 0.91, 316 R 0.94
−2556.25763.2 × 10−6
rpoC2−1521.34023.675−11529.28293.5 × 10−4434 F 0.96, 507 L 0.93, 508 S 0.96, 509 V 0.93, 1008 A 0.91, 1370 M 0.91434 F 0.99, 509 V 0.95, 758 K 0.91,766 L 0.91
−11217.1235< 10−10
rps19−812.094311.835−817.22845.9 × 10−329 W 0.9224 W 0.92, 29 W 0.95
-806.78121.1 × 10−3
Table 1.
Open in new tab

Summary of results of the SM test. BEB and FUBAR were applied to identify the codons targeted by positive selection. PSG = positively selected genes; ω = ratio of non-synonymous (Ka) to synonymous substitution rate (Ks); L = likelihood; M8 vs. M7 and M8a are the models tested as described in the Materials and Methods. Positive selection results were reported if the estimated ω was >1 and the likelihood ratio test was significant (P < 0.05). Positive selection of each codon estimated by BEB and FUBAR analysis is reported if P > 0.9. Position in the alignment, letter of amino acid residue and probability are reported for each codon selected

PSGLn L(M8)ω(M8)Ln L(M7)P  (M7–M8)BEB P > 0.9FUBAR P > 0.9
Ln L(M8a)P  (M8a–M8)
accD−4465.18204.144−4480.71121.8 × 10−771 Q 0.99, 94 D 0.90, 104 V 0.96, 197 H 0.94, 208 G 0.96, 217 L 0.96, 323 P 0.92, 490 K 0.9771 Q 0.98, 94 D 0.96, 283 L 96, 490 K 0.95
−4478.11023.7 × 10−7
atpA−3964.918851.867−4035.7022<10−10488 T 0.99, 500 R 0.98,459 A 0.97, 465 L 0.97, 488 T 0.98, 500 R 0.95
−4024.0715<10−10
matK−5187.29533.723−5193.95241.2 × 10−3118 A 0.91, 349 A 0.9188 Y 0.91, 168 A 0.92, 349 A 0.95, 482 L 0.91
−5174.25543.3 × 10−3
ndhH−2876.03025.393−2886.92801.8 × 10−5269 V 1.00269 V 1.00
−2879.53678.3 × 10−3
psaA−4841.18052.513−4865.7854<10−1019 I 0.94,152 N 0.98, 209 S 0.94, 626 L 0.9619 I 0.93, 152 N 0.98, 209 S 0.98, 626 L 0.98
−4844.58739.0 × 10−3
psaB−4551.2542 1.365−4561.05525.5 × 10−5273 I 0.92273 I 0.93, 245 G 0.93
−4547.33405.1 × 10−3
psaI−363.811511.351−375.70806.8 × 10−63 T 0.90, 4 L 0.96, 7 P 0.99, 8 S 1.00, 10 L 1.00, 15 G 0.994 L 0.96
−331.8516<10−9
psbA−2111.55892.004−2128.11536.5 × 10−8155 A 0.98, 351 I 0.92155 A 0.99, 235 A 0.92
−2105.37224.3 × 10−4
psbD−1983.77303.569−1997.12521.6 × 10−6146 A 0.97146 A 0.97
−1985.90453.9 × 10−2
psbK−461.93392.725−466.23671.4 × 10−247 L 1.0022 N 0.93
−455.82774.7 × 10−4
rbcL−4018.55964.215−4063.6618<10−1028 E 0.98, 30 E 0.97, 33 P 1.00, 86 H 1.00, 91 A 0.99, 97 F 0.99, 140 I 0.95, 142 P 1.00, 145 S 1.00, 219 L 0.99, 225 I 0.99, 251 I 1.00, 255 V 1.00, 256 F 0.91, 279 S 1.00, 309 M 1.00, 353 F 0.92, 461 V 0.95, 470 P 1.0010 S 0.98, 30 E 0.92, 33 P 0.93, 86 H 1.00, 91 A 0.99, 95 S 0.94, 140 I 0.94, 142 P 1.00, 143 A 0.97, 145 S 1.00, 219 L 0.99, 225 I 0.99, 251 I 0.95, 255 V 0.99, 256 F 0.95, 309 M 0.95, 320 L 0.91, 354 V 0.94, 461 V 0.98, 470 P 0.99
−4089.8081<10−10
rpoA−2567.08705.590−2572.43744.7 × 10−3155 R 0.91, 249 S 0.97, 316 R 0.907 T 0.93, 105 G 0.94, 249 S 0.90, 272 L 0.91, 316 R 0.94
−2556.25763.2 × 10−6
rpoC2−1521.34023.675−11529.28293.5 × 10−4434 F 0.96, 507 L 0.93, 508 S 0.96, 509 V 0.93, 1008 A 0.91, 1370 M 0.91434 F 0.99, 509 V 0.95, 758 K 0.91,766 L 0.91
−11217.1235< 10−10
rps19−812.094311.835−817.22845.9 × 10−329 W 0.9224 W 0.92, 29 W 0.95
-806.78121.1 × 10−3
PSGLn L(M8)ω(M8)Ln L(M7)P  (M7–M8)BEB P > 0.9FUBAR P > 0.9
Ln L(M8a)P  (M8a–M8)
accD−4465.18204.144−4480.71121.8 × 10−771 Q 0.99, 94 D 0.90, 104 V 0.96, 197 H 0.94, 208 G 0.96, 217 L 0.96, 323 P 0.92, 490 K 0.9771 Q 0.98, 94 D 0.96, 283 L 96, 490 K 0.95
−4478.11023.7 × 10−7
atpA−3964.918851.867−4035.7022<10−10488 T 0.99, 500 R 0.98,459 A 0.97, 465 L 0.97, 488 T 0.98, 500 R 0.95
−4024.0715<10−10
matK−5187.29533.723−5193.95241.2 × 10−3118 A 0.91, 349 A 0.9188 Y 0.91, 168 A 0.92, 349 A 0.95, 482 L 0.91
−5174.25543.3 × 10−3
ndhH−2876.03025.393−2886.92801.8 × 10−5269 V 1.00269 V 1.00
−2879.53678.3 × 10−3
psaA−4841.18052.513−4865.7854<10−1019 I 0.94,152 N 0.98, 209 S 0.94, 626 L 0.9619 I 0.93, 152 N 0.98, 209 S 0.98, 626 L 0.98
−4844.58739.0 × 10−3
psaB−4551.2542 1.365−4561.05525.5 × 10−5273 I 0.92273 I 0.93, 245 G 0.93
−4547.33405.1 × 10−3
psaI−363.811511.351−375.70806.8 × 10−63 T 0.90, 4 L 0.96, 7 P 0.99, 8 S 1.00, 10 L 1.00, 15 G 0.994 L 0.96
−331.8516<10−9
psbA−2111.55892.004−2128.11536.5 × 10−8155 A 0.98, 351 I 0.92155 A 0.99, 235 A 0.92
−2105.37224.3 × 10−4
psbD−1983.77303.569−1997.12521.6 × 10−6146 A 0.97146 A 0.97
−1985.90453.9 × 10−2
psbK−461.93392.725−466.23671.4 × 10−247 L 1.0022 N 0.93
−455.82774.7 × 10−4
rbcL−4018.55964.215−4063.6618<10−1028 E 0.98, 30 E 0.97, 33 P 1.00, 86 H 1.00, 91 A 0.99, 97 F 0.99, 140 I 0.95, 142 P 1.00, 145 S 1.00, 219 L 0.99, 225 I 0.99, 251 I 1.00, 255 V 1.00, 256 F 0.91, 279 S 1.00, 309 M 1.00, 353 F 0.92, 461 V 0.95, 470 P 1.0010 S 0.98, 30 E 0.92, 33 P 0.93, 86 H 1.00, 91 A 0.99, 95 S 0.94, 140 I 0.94, 142 P 1.00, 143 A 0.97, 145 S 1.00, 219 L 0.99, 225 I 0.99, 251 I 0.95, 255 V 0.99, 256 F 0.95, 309 M 0.95, 320 L 0.91, 354 V 0.94, 461 V 0.98, 470 P 0.99
−4089.8081<10−10
rpoA−2567.08705.590−2572.43744.7 × 10−3155 R 0.91, 249 S 0.97, 316 R 0.907 T 0.93, 105 G 0.94, 249 S 0.90, 272 L 0.91, 316 R 0.94
−2556.25763.2 × 10−6
rpoC2−1521.34023.675−11529.28293.5 × 10−4434 F 0.96, 507 L 0.93, 508 S 0.96, 509 V 0.93, 1008 A 0.91, 1370 M 0.91434 F 0.99, 509 V 0.95, 758 K 0.91,766 L 0.91
−11217.1235< 10−10
rps19−812.094311.835−817.22845.9 × 10−329 W 0.9224 W 0.92, 29 W 0.95
-806.78121.1 × 10−3
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