Supplementary Table S2
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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