1. env 1 st + 2 nd cdp3 rd cdp gag pol tax 1 st + 2 nd cdp3 rd cdp 1 st + 2 nd cdp3 rd cdp 1 st + 2 nd cdp3 rd cdp Fig. S1

2. HTLV-1(ATK) HTLV-1(Boi) HTLV-1(ATL-YS) HTLV-1(Mel5) STLV-5(MarB43) STLV-1(Tan90) STLV-1(TE4) HTLV-3(Pyl43) HTLV-3(2026ND) STLV-3(NG409) STLV-3(Ph969) STLV-3(CTO604) STLV-3(TGE2117) STLV-3(Ppaf3) STLV-2(Pan-p) HTLV-2b(G12) STLV-2(pp1664) HTLV-2a(Kay96) HTLV-4(1863LE) HTLV-2b(Gab) HTLV-2b(G2) HTLV-2a(MoT) HTLV-2d(Efe) HTLV-2a(SP-WV) 75 97 78 96 100 99 68 100 99 93 94 100 74 NJ gag (1041-bp) 0.01 Fig. S2a

3. HTLV-1(ATK) HTLV-1(Boi) HTLV-1(ATL-YS) HTLV-1(Mel5) STLV-5(MarB43) STLV-1(Tan90) STLV-1(TE4) HTLV-3(Pyl43) HTLV-3(2026ND) STLV-3(NG409) STLV-3(Ph969) STLV-3(CTO604) STLV-3(TGE2117) STLV-3(Ppaf3) STLV-2(Pan-p) HTLV-2b(G12) STLV-2(pp1664) HTLV-2a(Kay96) HTLV-4(1863LE) HTLV-2b(Gab) HTLV-2b(G2) HTLV-2a(MoT) HTLV-2d(Efe) HTLV-2a(SP-WV) 100 95 100 85 82 100 99 100 75 82 100 NJ pol (2418-bp) 0.05 Fig. S2b

4. HTLV-1(ATK) HTLV-1(Boi) HTLV-1(ATL-YS) HTLV-1(Mel5) STLV-5(MarB43) STLV-1(Tan90) STLV-1(TE4) HTLV-3(Pyl43) HTLV-3(2026ND) STLV-3(NG409) STLV-3(Ph969) STLV-3(CTO604) STLV-3(TGE2117) STLV-3(Ppaf3) STLV-2(Pan-p) HTLV-2b(G12) STLV-2(pp1664) HTLV-2a(Kay96) HTLV-4(1863LE) HTLV-2b(Gab) HTLV-2b(G2) HTLV-2a(MoT) HTLV-2d(Efe) HTLV-2a(SP-WV) 81 100 94 100 90 84 100 98 99 100 70 82 85 88 NJ env (1299-bp) 0.02 Fig. S2c

5. HTLV-1(ATK) HTLV-1(Boi) HTLV-1(ATL-YS) HTLV-1(Mel5) STLV-5(MarB43) STLV-1(Tan90) STLV-1(TE4) HTLV-3(Pyl43) HTLV-3(2026ND) STLV-3(NG409) STLV-3(Ph969) STLV-3(CTO604) STLV-3(TGE2117) STLV-3(Ppaf3) STLV-2(Pan-p) HTLV-2b(G12) STLV-2(pp1664) HTLV-2a(Kay96) HTLV-4(1863LE) HTLV-2b(Gab) HTLV-2b(G2) HTLV-2a(MoT) HTLV-2d(Efe) HTLV-2a(SP-WV) 100 90 100 90 80 96 74 98 99 100 99 92 100 71 75 96 NJ tax (960-bp) 0.01 Fig. S2d

6. HTLV-1(ATK) HTLV-1(Boi) HTLV-1(ATL-YS) HTLV-1(Mel5) STLV-5(MarB43) STLV-1(Tan90) STLV-1(TE4) HTLV-3(Pyl43) HTLV-3(2026ND) STLV-3(NG409) STLV-3(Ph969) STLV-3(CTO604) STLV-3(TGE2117) STLV-3(Ppaf3) STLV-2(Pan-p) HTLV-2b(G12) STLV-2(pp1664) HTLV-2a(Kay96) HTLV-4(1863LE) HTLV-2b(Gab) HTLV-2b(G2) HTLV-2a(MoT) HTLV-2d(Efe) HTLV-2a(SP-WV) 100 97 100 97 100 99 100 94 100 NJ entire genome sans LTR (6934-bp) 0.05 Fig. S2e

7. HTLV-1(ATK) HTLV-1(Boi) HTLV-1(ATL-YS) HTLV-1(Mel5) STLV-5(MarB43) STLV-1(Tan90) STLV-1(TE4) HTLV-3(Pyl43) HTLV-3(2026ND) STLV-3(NG409) STLV-3(Ph969) STLV-3(CTO604) STLV-3(TGE2117) STLV-3(Ppaf3) STLV-2(Pan-p) HTLV-2b(G12) STLV-2(pp1664) HTLV-2a(Kay96) HTLV-4(1863LE) HTLV-2b(Gab) HTLV-2b(G2) HTLV-2a(MoT) HTLV-2d(Efe) HTLV-2a(SP-WV) 0.2 97 92 81 99 95 99 100 99 92 100 79 100 97 96 85 99 100 ML gag (1041-bp) Fig. S2f

8. Fig. S2g HTLV-1(ATK) HTLV-1(Boi) HTLV-1(ATL-YS) HTLV-1(Mel5) STLV-5(MarB43) STLV-1(Tan90) STLV-1(TE4) HTLV-3(Pyl43) HTLV-3(2026ND) STLV-3(NG409) STLV-3(Ph969) STLV-3(CTO604) STLV-3(TGE2117) STLV-3(Ppaf3) STLV-2(Pan-p) HTLV-2b(G12) STLV-2(pp1664) HTLV-2a(Kay96) HTLV-4(1863LE) HTLV-2b(Gab) HTLV-2b(G2) HTLV-2a(MoT) HTLV-2d(Efe) HTLV-2a(SP-WV) ML pol (2418-bp) 0.3 100 90 99 92 100 99 100 97 87 90 74

9. Fig. S2h HTLV-1(ATK) HTLV-1(Boi) HTLV-1(ATL-YS) HTLV-1(Mel5) STLV-5(MarB43) STLV-1(Tan90) STLV-1(TE4) HTLV-3(Pyl43) HTLV-3(2026ND) STLV-3(NG409) STLV-3(Ph969) STLV-3(CTO604) STLV-3(TGE2117) STLV-3(Ppaf3) STLV-2(Pan-p) HTLV-2b(G12) STLV-2(pp1664) HTLV-2a(Kay96) HTLV-4(1863LE) HTLV-2b(Gab) HTLV-2b(G2) HTLV-2a(MoT) HTLV-2d(Efe) HTLV-2a(SP-WV) ML env (1299-bp) 0.3 79 98 99 76 99 95 94 100 93 99 98 100

10. HTLV-1(ATK) HTLV-1(Boi) HTLV-1(ATL-YS) HTLV-1(Mel5) STLV-5(MarB43) STLV-1(Tan90) STLV-1(TE4) HTLV-3(Pyl43) HTLV-3(2026ND) STLV-3(NG409) STLV-3(Ph969) STLV-3(CTO604) STLV-3(TGE2117) STLV-3(Ppaf3) STLV-2(Pan-p) HTLV-2b(G12) STLV-2(pp1664) HTLV-2a(Kay96) HTLV-4(1863LE) HTLV-2b(Gab) HTLV-2b(G2) HTLV-2a(MoT) HTLV-2d(Efe) HTLV-2a(SP-WV) ML tax (960-bp) 0.08 99 95 99 97 98 75 99 100 90 100 99 96 99 Fig. S2i

11. Fig. S2j HTLV-1(ATK) HTLV-1(Boi) HTLV-1(ATL-YS) HTLV-1(Mel5) STLV-5(MarB43) STLV-1(Tan90) STLV-1(TE4) HTLV-3(Pyl43) HTLV-3(2026ND) STLV-3(NG409) STLV-3(Ph969) STLV-3(CTO604) STLV-3(TGE2117) STLV-3(Ppaf3) STLV-2(Pan-p) HTLV-2b(G12) STLV-2(pp1664) HTLV-2a(Kay96) HTLV-4(1863LE) HTLV-2b(Gab) HTLV-2b(G2) HTLV-2a(MoT) HTLV-2d(Efe) HTLV-2a(SP-WV) ML entire genome sans LTR (6934-bp) 0.2 100 96 100 99 100 86 100 99 100 99 100 99