Table 1.
Composition of the clades of interest from the cladogram of figure 1 and their synapomorphies
| Clade 1 |
| 19 Specimens: all from HNTDI |
| GSM512558, GSM512561, GSM512562, GSM512564, GSM512565, GSM512566, GSM512567, GSM512568, GSM512569, GSM512570, GSM512571, GSM512572, GSM512574, GSM512575, GSM512576, GSM512577, GSM512578, GSM512579, GSM512580 |
| 45 Synapomorphies |
| ATP5E, ATP5SL, BLCAP, C19orf10, CALD1, CAPN7, FAM65A, FLOT1, FNDC3B, GANAB, H2AFX, HNRNPA1, HSPD1, IFI35, JUN, KIAA1033, LARP4B, LONP2, LPAL2, MKNK1, MSH6, MYCBP2, NGLY1, ORC2L, PLSCR3, PPCDC, PRDX2, PSMB2, R02172, RAB7A, RARS, RBM16, RBX1, RPIA, SLC25A14, SLC35D2, SNRPB, SWAP70, TARDBP, TEAD4, TIMP1, TRADD, TUBA1C, UBXN7, UQCRC2 |
| Subclade 1a, 43 synapomorphies |
| AKR1C3, ANXA4, ARPC3, BBS9, BLZF1, C3, CTSB, DDR2, EIF3G, ESPL1, FRMD1, GM2A, GPX1, GPX7, HLA-DQA1, IER3, IGF1, LARS2, LGALS3BP, LPAR1, LPCAT1, MED28, MIR936, MSLN, MXRA8, NF1, NLRP1, NPM3, NR4A2, NUDT1, PLTP, PSKH1, QPRT, RPL10P10, RPL28, RPRM, SERTAD2, SRSF1, SSR4, TFAP2A, YTHDF1, ZFP64, ZNF451 |
| Subclades 1b–e, 49 synapom orphies |
| ADAM8, AP2A2, ATP5C1, ATP5C1, AU146983, BAZ1B, BCL7B, CAPZB, CBX6, COMMD4, CSNK1D, CSTB, DDX3X, DNMT1, DUSP8, EDNRB, EPHB4, FRAT2, FYCO1, KLF11, KPNB1, LPPR2, LSM6, MAGEF1, MED27, MRPS31, MTIF2, NAA35, NAP1L1, P4HB, PBXIP1, PDLIM4, PLA2G4B, RAB3GAP1, RARA, RCN3, RNF13, SERINC3, SNRK, SNRNP200, SON, SPTLC2, TMCO6, TMEM159, TMEM2, TMSL3, TNS4, UBR5, ZMYM4 |
| Subclades 1c–e, 110 synapomorphies |
| SEPTIN5, AA719797, ACTB, ADD1, AL109716, ALG6, AMACR, ARFGEF1, ARHGAP11A, ARHGEF7, ARL4A, ARL6IP5, ARNT, ASH1L, ATP6V1B2, BAALC, BAT2, BBS9, BST2, C11orf21, C1orf144, CACNA1A, CBWD7, CD84, CDV3, COL16A1, COMMD3, CSNK1G2, CXCL9, DAZAP1, DECR1, DFNB31, EFNA2, EIF3G, ERP44, F12, FAM125B, FLJ11292, FSHB, FTL, GMEB2, GNAI2, GOLGA1, H49077, HAO1, HIRA, HNRNPL, HNRNPM, ILF3, ITFG1, JMJD6, KCNMB4, KDM5B, KIAA1009, KLHL2, KLRG1, LOC100132247, LOC441899, MACROD1, MAT2A, MON1B, MRAS, MRPL39, MYST2, NDUFS4, NGRN, NLRP1, NSA2, NXT1, PIGC, PPP2R3A, PPP4C, PRDM2, PRUNE, PSMF1, RAD1, RAD23A, RGS5, RHOD, RIOK3, RNF25, RPL28, RPL3, RPLP0, RPLP1, RPP30, RPS16, RPS2, RPS21, RPS3A, RUSC1, SFI1, SFT2D2, SIGLEC6, SIPA1L1, SLC11A2, SNURF, SPTBN1, SRI, STX6, TAF1, THBS1, TRIM32, TRPC1, UBE2Q1, UNC50, WDR1, WDR55, ZNF287, ZNF350 |
| Clade 2 |
| 14 Specimens: all from HNTDI |
| GSM242014, GSM242015, GSM242017, GSM242018, GSM242022, GSM242023, GSM242024, GSM242025, GSM242026, GSM242027, GSM512557, GSM512559, GSM512563, GSM512573 |
| 5 Synapomorphies: |
| CYR61, DUSP1↓, EIF1↓, FOSB, TACSTD2 |
| Subclade 2a, 54 synapomorphies |
| AHNAK, AK000834, AK025360, AKAP13, AL109696, ANKFY1, AP1M2, ARID3B, C1orf116, CCDC88C, CHRNA1, CLCN6, COL4A3, CROCC, DUSP12, DZIP3, EPS8L1, ERLIN2, ERO1LB, FER, FOXO4, GATC, GUSBP3, HOXA5, LHB, MAGEA3, MCOLN1, MXD4, MZF1, PAIP2B, PLGLB1, PRPF39, PRSS22, RB1CC1, RERGL, ROR2, SKAP2, SLC33A1, SLC35A3, SLC6A13, SPATA6, SPRED2, SPTLC1, STK17B, SULF1, TMEM90B, TRMT11, ULK2, WNT2B, ZAK, ZBTB17, ZNF224, ZNF350, ZNF665 |
| Subclade 2b, 124 synapomorphies |
| ADAMTS7, ADRA1B, AGAP2, AK022254, AK024568, AMACR, AP2S1, ARHGDIG, ARHGEF16, ARSJ, ASAH1, ATF4, ATP5H, ATP5L, ATXN7L1, ATXN8OS, AV720803, BAT2, BAX, BGN, BID, BRD2, C7orf28B, CABIN1, CAPZB, CASS4, CCDC88C, CCK, CD58, CDCA4, CDKN2A, CHIT1, CKAP4, COG8, CRCP, CRELD2, CTNNBL1, CYP27B1, CYP2R1, D25272, DGCR8, DRD1, DYSF, EDN2, EHMT2, FGD1, FRS2, FSHB, GALK1, GALNT2, GGCX, GIPR, GLRX3, GNAS, GOLGA2, GPR135, GRHPR, HDLBP, HLA-DOB, HSDL2, HSP90B1, IDH2, IL17B, IL1A, IRAK1, KCNG2, KIAA0319, KIAA1045, KIF1C, KLC1, KLHL20, LANCL2, LMNA, LOC440792, LRCH4, LYZL6, MAP4, MARCO, MDK, MECR, MFNG, NCOR2, NCRNA00260, NFU1, NPHS1, NRIP2, NUP50, OVOL1, P2RY2, PDCD5, PECR, PFDN2, PFN1, PLAUR, PLK3, POLD1, POLR1E, POM121C, PTGIR, PTPLAD1, PUM1, RARG, RFC2, RNF126, RPL22P22, RRP7B, SH3BP2, SLC7A5, SNRPB2, SPIN2A, TGM5, TM9SF1, TMEM132A, TMEM134, TPM4, TSSC1, TUBG1, TXN, UBE2V1P2, UBR4, VEGFA, VENTX, WDR18, Z21967 |
| Subclade 2c–e, 48 synapomorphies |
| AA427737, ADORA1, AF257099, AL137403, BCLAF1, CA3, CCL2, CFLAR, CXCL2, CXCR4, CYLD, DKFZp686O1327, EIF4A1, FKBP8, FRMD1, FUT6, GPR183, GTF2F1, HEY2, IFNGR1, IGHV4-31, KIAA0020, MCL1, MLF1, MYH14, NCLN, NDRG2, NUP88, PDE4B, PNLIPRP2, PPP1R15A, PRNP, PTMA, PTMAP7, PTPN21, RGS1, RNF114, SEC24A, SFRP1, SRF, SRGN, TNFAIP2, TRIM2, UPF3A, WASF3, WSB1, YWHAH, ZFP36 |
| Clade 3 |
| 5 Specimens: all from HNTDI |
| GSM242016, GSM242019, GSM242020, GSM242021, GSM512560 |
| 44 Synapomorphies: |
| ACTR10, ALDH1A3, C14orf147, CAPZA1, CD59, CHMP1B, COPS8, CPD, CSDE1, DCUN1D4, GALNT1, GCOM1, GMFB, HSPH1, KRT10, LEPROTL1, LOC440366, LYST, MCL1, NCRNA00081, NCRNA00120, NUDT4P1, NUPL1, PDS5A, PTP4A1, RAP1A, RBBP7, RBM16, RRAS2, RRP15, SCARB2, SCML1, SET, SLC25A14, SMEK2, SNRNP27, SNRPE, SNX27, SOCS5, YRDC, YWHAZ, ZFP36L1, ZMPSTE24, ZSCAN18 |
| Clade 4 |
| 11 Specimens: all from RM |
| GSM242009, GSM242013, GSM512540, GSM512543, GSM512547, GSM512549, GSM512550, GSM512551, GSM512552, GSM512554, GSM512556 |
| 6 Synapomorphies: |
| DSCAM, DUSP1↑, EIF1↑, HIST1H2BC, JUN, SIK1 |
| Subclades 4a, b, 17 synapomorphies |
| ACAT2, ACBD3, ADAR, ARL4C, BRD7, CAPZB, KATNA1, MRPL39, NEDD8, NSMCE4A, PBX1, PEX19, PTP4A2, SF3A3, SSBP1, TDRD7, WBP4 |
| Subclades 4c, 17 synapomorphies |
| AF198444, AK021633, CITED2, DCUN1D4, DUSP7, FILIP1L, GATM, HIST2H2AA4, HIST2H2AA4, HSPC157, KLF6, NEAT1, PNRC1, REG1A, RHOB, SLC38A2, TOP3A |