Elevation as a selective force on mitochondrial respiratory chain complexes of the Phrynocephalus lizards in the Tibetan plateau
#* # Yuanting JINa , Debora Y. C. BRANDTb , Jiasheng LIa, Yubin WOa, Haojie
TONGa, Vladimir SHCHURc aCollege of Life Science, China Jiliang University, Hangzhou, 310018, China; bDepartment of
Integrative Biology, University of California at Berkeley, Berkeley, CA 94720-3140,USA; cNational
Research University Higher School of Economics, Moscow, Russia.
*Address correspondence to Yuanting Jin. E-mail: [email protected]
#both authors contributed equally to this work
Handling editor: Maria Servedio
Received on 22 April, 2020; accepted on10 September, 2020
1
Online supplementary Table S1. The number of mtDNA and nDNA encoded proteins in each of the five respiratory chain complexes.
Five mitochondrial respiratory chain Sum.
compelxes
I II III IV V
mtDNA-encoded 7 0 1 3 2 13
proteins
nDNA-encoded 37 4 9 16 18 84
proteins
Total 44 4 10 19 20 97
2
Online supplementary Table S2. Sampling location and altitude of Phrynocephalus specimens.
No. Altitude Species Longitude Latitude Specimen Locality (m) 1 Geermu, located at Western Qinghai-Xizang (Tibetan) Phrynocephalus vlangalii 95.03E 36.39N 2826 1-VLA Plateau 2 Phrynocephalus theobaldi 90.83E 29.38N 3617 2-THE Qushui County, Tibet 3 Phrynocephalus guinanensis 100.63E 35.66N 3238 3-GUI Sand dunes, Guinan county, Qinghai Province 4 Phrynocephalus putjatia 101.44E 36.02N 2280 4-PUT Nanhai temple in Guide county, Qinghai provience 5 Phrynocephalus forsythii 86.17E 41.39N 886 5-FOR Yuli county, Xinjiang Uygur Autonomous Region 6 Phrynocephalus erythrurus 92.26E 34.93N 4541 6-ERY Tuotuo River region, Northern Qiangtang Plateau of Tibet 7 Phrynocephalus przewalskii 105.02E 37.47N 1301 7-PRZ Shapotou, Zhongwei city, Ningxia Hui Autonomous Region 8 Phrynocephalus versicolor 100.88E 41.98N 933 8-VER Ejin Banner, Inner Mongolia Autonomous Region 9 Phrynocephalus frontalis 108.72E 40.75N 1067 9-FRO Urad Front Banner, Inner Mongolia 10 Hoxtolgay town, Mongolian Autonomous County of Phrynocephalus helioscopus 86.06E 46.45N 723 10-HEL Hoboksar, Xinjiang Uygur Autonomous Region 11 Phrynocephalus mystaceus 80.79E 44.02N 602 11-MYS Tukai Desert, Huocheng County 12 Phrynocephalus axillaris 88.03E 38.98N 884 12-AXI Ruoqiang County, Xinjiang Uygur Autonomous Region 13 Phrynocephalus grumgrzimailoi 90.12E 44.34N 711 13-GRU Qitai county, Xinjiang Uygur Autonomous Region 14 Phrynocephalus guttatus 80.87E 43.98N 605 14-GAT Tukai Desert, Huocheng County 15 Phrynocephalus axillaris 94.33 39.96 1402 15-AXI2 Dunhuang, Gansu
3
4
Online supplementary Table S3. The list of 106 analysed genes and their likelihood ratios.
No. Gene Respiratory Chain Complexes Likelihood ratio
(I-V) or Complex assembling
factors (AF)
1 ACAD9 AF 1.442098
2 ATP5F1A V 2.716534
3 ATP5F1B V 9.179776
4 ATP5F1C V -1.4E-05
5 ATP5F1D V 4.431594
6 ATP5IF1 V -0.160622
7 ATP5MC1 V 0.897124
8 ATP5MC2 V 1.241316
9 ATP5MC3 V 4.772246
10 ATP5ME V 1.17804
11 ATP5PB V 0.91995
12 ATP5PD V 5.212764
13 ATP5PO V 20.95332
14 ATPAF1 AF 7.849014
15 ATPAF2 AF 1.871712
16 BCS1L AF 14.660634
17 COA4 AF 2.905368
5
18 COA5 AF 0.145192
19 COA6 AF -7.2E-05
20 COA7 AF 0.044768
21 COX10 AF 0
22 COX11 AF 7.801726
23 COX14 AF 0
24 COX15 AF 6.196
25 COX17 AF -0.000324
26 COX18 AF 1.352526
27 COX19 AF -4.2E-05
28 COX20 AF 0.513916
29 COX4I1 IV 1.494504
30 COX4I2 IV 1.340188
31 COX5A IV 4.21896
32 COX5B IV 23.73244
33 COX6A1 IV 1.458144
34 COX6B1 IV 0.67178
35 COX6C IV 26.370904
36 COX7A2 IV 3.62978
37 COX7C IV 13.38482
38 CYC1 III 8.569892
6
39 ECSIT AF 7.231438
40 FOXRED1 AF 3.842736
41 NDUFA10 I 1.719368
42 NDUFA11 I 5.854786
43 NDUFA12 I 1.455992
44 NDUFA13 I -0.000278
45 NDUFA1 I 5.92429
46 NDUFA2 I 0.122382
47 NDUFA3 I 2.522642
48 NDUFA5 I 4.878656
49 NDUFA6 I -7.8E-05
50 NDUFA7 I -4E-06
51 NDUFA8 I 4.797908
52 NDUFA9 I -0.05999
53 NDUFAB1 I 10.703812
54 NDUFAF1 AF 0.237084
55 NDUFAF2 AF -2E-06
56 NDUFAF3 AF -0.000136
57 NDUFAF4 AF 0.0111
58 NDUFAF5 AF 0.467726
59 NDUFAF6 AF 1.18736
7
60 NDUFAF7 AF 0.305608
61 NDUFB10 I 3.50866
62 NDUFB11 I 6.584112
63 NDUFB1 I 1.967564
64 NDUFB2 I 2E-06
65 NDUFB3 I -0.25933
66 NDUFB4 I 11.422632
67 NDUFB5 I 15.300464
68 NDUFB6 I 6.992398
69 NDUFB7 I -6.6E-05
70 NDUFB8 I -0.000226
71 NDUFB9 I 10.76486
72 NDUFC1 I 0.080454
73 NDUFC2 I 21.147992
74 NDUFS1 I 8.202896
75 NDUFS2 I 11.820604
76 NDUFS3 I 5.31607
77 NDUFS4 I 1.90855
78 NDUFS5 I -2.2E-05
79 NDUFS6 I 2.204102
80 NDUFS7 I 44.36556
8
81 NDUFS8 I 5.278342
82 NDUFV1 I -0.000948
83 NDUFV2 I 3.583606
84 NDUFV3 I 3.152976
85 NUBPL AF 10.423886
86 SCO1 AF 5.448692
87 SCO2 AF 1.573884
88 SDHAF1 AF -2E-05
89 SDHAF2 AF -0.00018
90 SDHAF3 AF 5.939028
91 SDHAF4 AF 0.051624
92 SDHA II 3.51566
93 SDHB II 1.56985
94 SDHC II -6E-05
95 SDHD II 1.56985
96 SURF1 AF 0
97 TIMMDC1 AF 4.217812
98 UQCC1 AF 1.930944
99 UQCC2 AF 1.387358
100 UQCR10 III -0.803674
101 UQCR11 III 8.631014
9
102 UQCRB III 1.413218
103 UQCRC1 III 13.919878
104 UQCRC2 III -2.6E-05
105 UQCRFS1 III 1.465978
106 UQCRQ III 12.483544
Online supplementary Table S4. Delta elevations, proportions of positive selection codons, likelihood ratio, mean branch lengths of 28 branches of phylogenetic trees corresponding to
Fig. 2 and 3.
Branches Delta proportions of SUM of likelihood Mean branch
elevations positive selection ration for 106 lengths
codons genes
1 394.738600 59.831270 138.279716 .010045
2 -394.738500 49.177200 275.94743 .012062
3 -1333.457300 153.233640 14.602588 .003600
4 479.314900 106.628800 63.433342 .049400
5 14.082200 84.000390 10.018996 .005344
6 238.735500 49.194040 52.85351 .051645
7 215.616700 250.363000 11.93875 .003037
8 1387.875600 194.931150 11.231316 .001980
9 327.124400 .000000 -32.375638 .006622
10
10 679.492300 155.824840 28.996762 .008028
11 525.145600 .000000 -2.609876 .010126
12 432.854400 .000000 -14.10 .007248
13 -827.980200 .680800 41.788676 .007940
14 -274.339100 73.679370 228.213102 .012780
15 -21.055500 10.087000 36.80641 .017097
16 -164.332700 15.200320 172.07988 .053713
17 36.258300 20.221540 75.363822 .010370
18 -250.585600 7.875780 7.494168 .014926
19 267.414400 .000000 -3.950744 .005004
20 54.965700 .000000 12.58288 .010583
21 -195.018700 1.989490 15.97940 .010227
22 -73.289700 9.054800 7.87334 .022844
23 -117.738600 14.201350 6.82464 .011587
24 -94.566700 68.991930 0.694614 .015837
25 -15.532400 .873600 5.42174 .008989
26 218.467600 .000000 -11.103472 .003089
27 32.448900 .000000 -5.60367 .005297
28 73.551100 .000000 -12.544792 .011263
11
12
Online supplementary Table S5. Binary matrix for site-branch permutation analyses.
- B1 B2 B3 B4 B5 B6 B7 B8 B10 B14 B15 B16 B17 B21 B22 B23 SUM
C3117 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1
C3152 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1
C3548 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1
C3574 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1
C3613 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1
C3700 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1
C3759 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1
C3767 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1
C3955 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1
C3956 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 2
C4180 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1
C4363 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1
C5098 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1
C6933 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1
C6938 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1
C6947 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 2
C6950 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 2
C6951 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 2
C6953 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1
13
C8151 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2
C10098 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1
C10100 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1
C10385 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1
C10394 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1
C11252 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1
C11253 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 2
C11254 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1
C11255 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 2
C11257 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 2
C11318 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 2
C13293 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
C13471 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2
C13487 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2
C13663 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
C13666 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 3
C13689 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1
C13693 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
C13702 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
C13724 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
C13725 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1
C13736 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
14
C13746 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1
C13768 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 2
C13962 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 2
C14046 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
C14077 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
C14536 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
C14542 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 2
C14555 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 2
C14557 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2
C14560 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
C14564 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
C14572 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
C14582 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2
C14589 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 2
C14595 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2
C14600 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2
C14608 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2
C14621 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 3
C16502 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 3
C16504 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1
C16507 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 4
C16511 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2
15
C16515 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1
C16518 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 3
C16521 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 2
C16533 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1
C16539 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 3
C16544 1 0 0 1 1 0 0 0 0 0 0 1 0 0 0 1 5
C16545 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2
C16546 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 4
C16548 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 3
C16551 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 4
C16558 1 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 4
C16573 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2
C16574 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 1 4
C16575 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 2
C16580 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 3
C16582 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 3
C16586 0 1 0 0 0 0 0 0 0 1 0 1 1 0 0 0 4
C16588 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2
C16589 1 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 4
C16596 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 3
C16605 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2
C16608 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 3
16
C16620 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 2
C16625 1 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 4
C16630 1 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 4
C16631 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1
C16632 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
C16636 1 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 4
C16642 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 5
C16643 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 3
C16645 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 4
C17991 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
C18303 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
C19093 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 2
C19191 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1
C20404 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1
C20408 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1
C20458 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1
C20491 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1
C20497 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1
C20543 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1
C20635 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1
C21438 1 0 0 1 0 1 1 1 0 0 0 0 0 0 0 0 5
C21441 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 3
17
C21443 1 0 0 1 0 1 1 1 0 0 0 0 0 0 0 0 5
C21454 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2
C21457 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 3
C21468 1 0 0 1 0 1 1 1 0 0 0 0 0 0 0 0 5
C21471 1 0 0 1 0 1 1 1 0 0 0 0 0 0 0 0 5
C21479 1 0 0 1 0 1 1 1 0 0 0 0 0 0 0 0 5
C21559 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1
C21565 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1
C21900 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 2
C21910 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1
C22795 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 2
C22799 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
C22823 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
SUM 45 29 6 35 16 22 18 5 5 22 1 21 4 2 2 7 -
18
Online supplementary Table S6. Binary matrix for gene-branch permutation analyses.
- B1 B2 B3 B4 B5 B6 B7 B8 B10 B13 B14 B15 B16 B17 B18 B21 B22 B23
B25 SUM
G1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
1
G2 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
2
G5 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
1
G8 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
2
G10 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
1
G11 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0
2
G12 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0
2
G13 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0
3
G14 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
1
G17 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
19
1
G20 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
1
G21 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
1
G22 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
1
G28 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1
G36 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
1
G38 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0
2
G41 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0
4
G45 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0
3
G46 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
1
G48 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0
3
G52 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
20
1
G53 0 0 0 1 0 1 0 0 0 0 1 0 1 0 0 0 0 0 0
4
G60 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
1
G61 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
1
G63 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
1
G64 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2
G66 0 1 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0
4
G68 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
2
G71 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1
G73 1 1 0 1 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0
5
G80 1 1 1 1 1 1 1 0 1 0 1 1 1 1 1 1 0 1 0
15
G84 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
21
2
G85 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2
G87 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
1
G90 0 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0
3
G96 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
1
G97 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
1
G100 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
0 1
G101 1 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0
0 4
G102 0 1 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0
0 4
G103 0 1 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0
0 4
G105 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 1
G106 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
22
0 2
SUM 7 10 2 8 3 5 3 1 5 3 17 4 13 8 1 2 2 2
1
23
Online supplementary Table S7. The amino acid codon state convergence among foreground branches.
1 Gene Codon B01 B02 B03 B04 B05 B06 B07 B08 B10 B13 B14 B15 B16 B17
B18 B21 B22 B23 B25
2 1 71 0 0 0 0 0 0 0 0 0 0 0 0 0 SS 0 0 0
0 0
3 1 85 0 0 0 0 0 0 0 0 0 0 0 0 0 II 0 0 0
0 0
4 1 284 0 0 0 0 0 0 0 0 0 0 0 0 0 GG 0 0 0
0 0
5 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 LF 0 0 0
0 0
6 2 65 0 0 0 0 0 0 0 0 0 0 0 0 0 RR 0 0 0
0 0
7 2 76 0 0 0 0 0 0 0 0 0 0 0 0 0 VV 0 0 0
0 0
8 2 80 0 0 0 0 0 0 0 0 0 0 0 0 0 KR 0 0 0
0 0
9 2 115 0 0 0 0 0 0 0 0 0 0 0 0 0 RR 0 0 0
0 0
10 2 126 0 0 0 0 0 0 0 0 0 0 0 0 0 TT 0 0 0
24
0 0
11 5 45 0 0 0 0 0 0 0 0 0 0 0 LL 0 0 0 0 0
0 0
12 5 87 0 0 0 0 0 0 0 0 0 0 0 RQ 0 0 0 0 0
0 0
13 8 16 0 0 0 0 0 0 0 0 AT 0 0 0 0 0 0 0 0
0 0
14 8 40 0 0 0 0 0 0 0 0 AF 0 0 0 0 0 0 0 0
0 0
15 8 75 0 0 0 0 0 0 0 0 AV 0 0 0 0 0 0 0 0
0 0
16 11 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 AA
17 11 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 AT
18 11 88 0 0 0 0 0 0 0 0 VL 0 0 0 0 0 0 0 0
0 0
19 11 114 0 0 0 0 0 0 0 0 IL 0 0 0 0 0 0 0 0
0 0
20 11 119 0 0 0 0 0 0 0 0 LV 0 0 0 0 0 0 0 0
0 0
21 11 153 0 0 0 0 0 0 0 0 IL 0 0 0 0 0 0 0 0
25
0 0
22 11 183 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 RR
0 0
23 11 240 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 TV
0 0
24 12 28 0 0 0 0 0 0 0 0 0 0 0 0 KR 0 0 0 0
0 0
25 12 58 0 0 0 0 0 0 0 0 0 0 0 0 GD 0 0 0 0
0 0
26 12 63 0 0 0 0 0 0 0 0 0 0 SL 0 0 0 0 0 0
0 0
27 12 139 0 0 0 0 0 0 0 0 0 0 YY 0 0 0 0 0 0
0 0
28 12 145 0 0 0 0 0 0 0 0 0 0 DE 0 0 0 0 0 0
0 0
29 12 150 0 0 0 0 0 0 0 0 0 0 LL 0 0 0 0 0 0
0 0
30 13 68 0 0 0 0 0 0 0 0 0 0 SP 0 0 0 0 0 0
0 0
31 13 90 0 0 0 0 0 0 0 0 0 0 KR 0 0 0 0 0 0
0 0
32 13 91 0 0 0 0 0 0 0 0 0 0 AI 0 0 0 0 0 0
26
IV 0
33 13 129 0 0 0 0 0 0 0 0 0 0 VI 0 0 0 0 0 0
0 0
34 13 152 0 0 0 0 0 0 0 0 0 0 RQ 0 0 0 0 0 0
0 0
35 13 170 0 0 0 0 0 0 0 0 0 0 LM 0 0 0 0 0 0
0 0
36 13 187 0 0 0 0 0 0 0 0 0 0 LM 0 0 0 0 0 0
0 0
37 14 82 0 0 0 FL 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0
38 17 15 0 0 0 0 0 0 0 0 0 0 PP 0 0 0 0 0 0
0 0
39 17 19 0 0 0 0 0 0 0 0 0 0 KK 0 0 0 0 0 0
0 0
40 17 20 0 0 0 0 0 0 0 0 0 0 KE 0 0 0 0 0 0
0 0
41 17 29 0 0 0 0 0 0 0 0 0 0 ED 0 0 0 0 0 0
0 0
42 17 41 0 0 0 0 0 0 0 0 0 0 CC 0 0 0 0 0 0
0 0
43 17 85 0 0 0 0 0 0 0 0 0 0 RK 0 0 0 0 0 0
27
0 0
44 17 92 0 0 0 0 0 0 0 0 0 0 AS 0 0 0 0 0 0
0 0
61 21 90 0 0 0 0 0 0 0 0 0 0 0 0 LL 0 0 0 0
0 0
62 21 91 0 0 0 0 0 0 0 0 0 0 0 0 LL 0 0 0 0
0 0
63 21 138 0 0 0 0 0 0 0 0 0 0 0 0 PP 0 0 0 0
0 0
64 21 159 0 0 0 0 0 0 0 0 0 0 0 0 AA 0 0 0 0
0 0
65 21 188 0 0 0 0 0 0 0 0 0 0 0 0 NN 0 0 0 0
0 0
66 21 225 0 0 0 0 0 0 0 0 0 0 0 0 IV 0 0 0 0
0 0
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