Phylogenetics of Taxus Using the Internal Transcribed Spacers of Nuclear Ribosomal DNA and Plastid Trnl-F Regions

Supplementary Materials: Phylogenetics of Taxus Using the Internal Transcribed Spacers of Nuclear Ribosomal DNA and Plastid trnL-F Regions

Patricia Coughlan, James C. Carolan, Ingrid L. I. Hook, Lisa Kilmartin and Trevor R. Hodkinson

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r in ir a a i PP 1 3 _ T rn l_ a u d n 6 x na va __ e e ta 1 P 4 _ n T x a a s_ E 60 us _v r_ m n i P 11 5 _T r l_ Ta an _C nsi F6 637 _x_ ar _m a si PP 1 6 _T rn l_ C us de EF6 606 Tax me __ a ires P 1 7 _T rn T_ ax ana ea_ E 606 16T us dia ma ire i PP118 _Tnl_l_T F _C Aur F017 09T axu _cu _ irei P19 Tr rn C_ xus _F_ ata_ 314T axus s_c spid i P 2_ _Trnl _Ta cata fastig is D axus _sumuspi ata P200_T rnl Bac ata_ grand Q885 _x_hu atra d0ata PP2 1_Trnl_ acc ata_ 568Tax nnew na .76 P27_t rnl_B_bacc pidata_ 27_Tax us_x_m ellian P28_Trnl_T s_Cus _fastigata __cuspAs edia a PP29_Tnl_Taxu s_baccata 10 sembly_2 P3_Tr rnl_Taxu nsis_ HM591133Taxus_wa 8_TaxbacAme P30_Trnl_T_Canade etae_ llichiana_var__chinensis P5_Trnl_Taxus_Cuspidata_f_thay EU052214Taxus_wallichiana_var__chinensis0.99 P9_T EF660608Cephalotaxus_mannii torta b_JX680642_1__Taxus_con gi_409725585_g xus_conto0rt.a78 680635_1__Ta s_fuana 0.8 25578_gb_JX 1__Taxu a gi_4097 591150_ conto0rt.91 64_gb_HM Taxus_ fuana a_ 3169537 40_1__ axus_ chianna gi_21321287_dbj_AB gi_ X6806 260T walli chia a 083234_1__Cephalotaxus_ 3_gb_J F680 ar__ walli hian sinensis 2558 E a_v r__ allic a 9 i_4097 hian va w ian na.6 g wallic ana_ ar__ llich hia0 xus_ llichi a_v wa allic na 0.65 _Ta _wa ian r__ _w a hia na 6_1_ xus llich va r_ ian llic ia na 7 864 Ta wa na_ va ich a lich ia 5a_Cep_oli X18 122 us_ ia a_ all _w al ch J 91 ax lich an w _ w lli 6 i 5 T al hi _ r _ a a a9 e HM 21 w llic r_ va s w n n. a ir a 11 s_ a a _ u _ a ia0 a n a i 9 u w v a x s i n a i 4 5 ax _ _ n a u h h ia ia n re M s a a n m i e a 5 H T u n i T x lic lic h h ia ir s 17 x ia h 1 a l l c ia _ a n .i 1 a h lic 7 T a a li h _ ic h a s 1 T c l 2 l r ll ia 0 9 6 lli a 0 0 w w a ic ic M n P 5 1 a w 8 2 _ _ ll a ll _ m h 8_T 1 6 s w va e rnl_C M w _ 6 s a 2 e H 1 _ s 0 u w a _ _ ic 1 pha 9 s F u _ _ r ll in a lota 5 u 1 9 2 x 6 x x w _ w _ 2 us _ L E L u x a a r n a _h 6 a r . a M x a _ _ a h 4 rr 5 i a _ s n n r s g v i 2 1 t H a F a a n o T s a i r T T c _ ia i 0 _ _ T _ a _ fa 8 E _ v u ia a _ v s s 6 i 4 t r s _ a a ig 2 l s ia _ h 1 _ _ v i T ta 2 _ x s _ _w T _ a i n s 2 5 2 1 n d _ a _ o c E a s 2 1 ch _ i i a 2 i v s s _ f a _ l i r i l e n r o 6 l e _ 5 5 _ T l a r T 8 n _ 9 F x C 0 0 a _ n s a v x e i a n o b p 5 8 4 n a a i n T _ h i l U U a e e _ _ n v 6 _ s 6 5 h 7 a v e f in E w o E i r h c n r h l c 6 c w d 0 2 n e _ h i 6 l i _ n l _ h _ c 0 a a 8 a b _ c g 0 a i n a u s h i 0 a c l 6 8 T i _ _ 8 _ n n l h c s _ _ 6 l n n n X w h na 6 6 _ c s _ a xu s J a i _ c a u _ l a X a _ l a i r 3 F a l i r _ s u x s J u s w _ n d b a h a 6 _ r E T x a C u h s u s a x g b _ v e x c T 9 x c i v e w a T _ E _ s u i l T a g n F a 3 ll l _ 6 a _ 2 s _ a 6 u x m _ T _ 0 7 T T a s 6 0 1 1 s T a a 1 x a a u x 1 2 8 4 2 C 6 6 3 0 1 i 0 e b a u 1 w n s . p 5 1 9 T w 0 n x u 6 h 6 5 6 a x 1 T lo 2 1 T 0 _ a l a s t 2 _ i y a 5 5 6 a x 7 a 5 i 1 1 4 1 s 6 u 2 r s 4 _ _ 9 0 h T la 9 M T 8 h L n 0 7 2 1 u 0 nc 2 us c c e 5 6 i _ o 9 1 3 c 8 l 4 l l 4 H x l 6 a i 3 x l _ a t 0 l a i_ M 1 2 4 6 l a 6 n 4 a a 8 Q a n g 9 1 J r E i_ H T F a F F 0 s 5 1 T a 1 6

T 6 g A D w 0 4 E w 2 s 6 9 B d E 1 M _ _ 7 2 e C 5 2 _ A e e s 6 p H 2 s 7 m h n a M u lo 3 2 u P ta s x x

b u H 1 5 x s i _ a s d l r 0 0 a u y pa T c Y U T g ea 8 i_ A E 3 1 2 80 2 2 1 52 2 5 1 6_ 2 g 9 b_ 5 A 5 Y0 0 137 M 4 U A gi_ 2_1 H Y E 0 0 21 __C .6 0 13 321 ep 9 .8 72 28 halo 3Am 9_d taxu en bj_A s_s AJ tota B0 inen 1 1 441 xu 83 sis 09 s_a 236 8A rgo _1_ me tae _C g nt nia eph i_1 ota alot 80 xus axu 0. 25 _y s_f 61 25 un ortu 7_ na nei L gb nen 66 _A sis _T Y0 rn 13 l_A 74 m 3_ en 1_ to _A tax m us en _f tot P orm ax 24 o us_ 1 _T sa fo 1 n rm 0 g rn a o . i l _ g g _ _ s 9 T T a i 2 P r n i_ _ 3 o n a 1 1 4 2 r l 1 5 r 1 3 _ e 5 T _ y 8 2 T a 1 o r _ 0 2 r_ n C 2 3 l_ 7 7 n 7 a 5 0 2 3 u 5 lif 1 _ c 9 o 2 9 T 9 rn 3 9 _ o _ ic 3 r ia 8 e 1 _ _ _ 0 m E ja g _ F c b b g 6 _ _ b 6 _ A 1 0 A 6 E J Y 2 F 4 E 4 0 4 T 6 F 1 1 o 6 6 r 3 1 6 r 0 e 7 0 g 0 6 y 2 0 i_ 6 a 1 4 4 _ 1 _ 5 8 2 j _ 1 a _ 0 T c 1 _ A o 1 2 k _ _ Y r ii _ g 5 r _ P 0 i 2 e _ _ y P s 1 4 P 2 a e 3 1 6 s _ _ s u 7 3 t e g a e d 3 2 u b x u o 1 2 i d _ fo d t T 7 A o a o 3 li o 1 Y a t t x r a a u re _ 0 x x s y e 1 u m 3 u _ a 7 s s c _ b 3 _ _ h f _ 2 c a c ie r A _ h g h n J 1 ie i e 4 _ e ii s 4 _ n n ii T i _ 1 i ii 1 o v 0 r a 2 re r_ _ ya _ 1 y _ _ u _ ja n T cki n o a r i n re e y n a s _ i y s u n n a n e E n F s 6 is 6 1A 0 6 Y 0 0 6 1 A L 3 u 1 7 s 6 4 t 4_ 6 ro A ta T u x r s nl u tr s _ o _ A ta s u x p s u ic a tr s o _ ta t s a p 2 x ic u a s _s ta

p ic a ta

0.5 Figure S1. Bayesian inference phylogenetic reconstruction of Taxaceae based on trnL and trnL–F plastid DNA. Bayesian posterior probability values shown above branches. Summary Bayesian inference tree of same data is shown in Figure 2.

P3 Trnl Taxus Cuspidata P30 Trnl Taxus baccata fastigata

P29 Trnl T.baccata grandis

P28 Trnl Baccata fastigata P27 trnl Baccata F.Aurea

P21 Trnl Taxus Canadensis

P20 TrnlC-F

P20 Trnl Taxus Canadensis Aurea P2 Trnl T.Canadensis

P19 Trnl Taxus Cuspidata

P18 Trnl Taxus Cuspidata f.thayetae

P17 Trnl Taxus Cuspidata P16 Trnl Taxus x media hicksii

P15 Trnl Taxus Cuspidata

P14 Trnl Taxus Brevifolia P13TrnlC-F

P13 Trnl Taxus Aurea

P12 Trnl Taxus Cuspidata Luteobaccata P11 Trnl Taxus Canadensis

P10 Trnl Taxus Canadensis Aurea 52 P1 TrnlC-F P1 Trnl T.Canadensis aurea L94 Trnl T.baccata

L93 Trnl T.baccata

L33 Trnl Taxus canadensis L149 T.brevifolia

gi|316953769|gb|HM591155.1| Taxus baccata

gi|316953768|gb|HM591154.1| Taxus baccata

EF680264Taxus baccata EF660635Taxus baccata

51.Tax.bac

44.Tax.bac

42.Tx.bac 3 36.Tax.can.au

32.Tax.cus.fl 31.Tax.brev

26.Tax.med

112a.TaxbacFru

10.Tax.bac P5 Trnl T.Canadensis

L95 Trnl T.baccata

P9 Trnl Taxus Cuspidata f.thayetae 65 EU052214Taxus wallichiana var. chinensis HM591133Taxus wallichiana var. chinensis

gi|316953764|gb|HM591150.1| Taxus fuana 50 EF680260Taxus fuana gi|409725583|gb|JX680640.1| Taxus contorta

51 gi|409725578|gb|JX680635.1| Taxus contorta

gi|409725585|gb|JX680642.1| Taxus contorta

EF660639.Taxus x media AY013729Taxus wallichiana var. mairei

DQ885568Taxus x media

EF660609Taxus sumatrana

P22 Trnl Taxus Xmedia 5 108.TaxbacAme 27.Tax. cuspAssembly 2 EF017314Taxus x hunnewelliana

EF660616Taxus cuspidata

EF660637Taxus cuspidata

EU052226Taxus wallichiana var. mairei EU052228Taxus wallichiana var. mairei

EU052229Taxus wallichiana var. mairei

AY013720Taxus wallichiana var. chinensis

gi|18025258|gb|AY013744.1| Taxus baccata gi|30269924|gb|AF506838.1| Taxus cuspidata

HM591137Taxus wallichiana var. mairei

gi|316953758|gb|HM591144.1| Taxus sumatrana gi|316953759|gb|HM591145.1| Taxus sumatrana

gi|316953761|gb|HM591147.1| Taxus cuspidata

gi|316953762|gb|HM591148.1| Taxus cuspidata

EU052222Taxus wallichiana var. wallichiana EF680274Taxus wallichiana 58 HM591118Taxus wallichiana var. wallichiana gi|409725601|gb|JX680658.1| Taxus wallichiana

gi|409725602|gb|JX680659.1| Taxus wallichiana JX188646.1| Taxus wallichiana var. wallichiana

HM591117Taxus wallichiana var. wallichiana 3729 EF660620Taxus wallichiana

EF680271Taxus wallichiana

EU052218Taxus wallichiana var. wallichiana

HM591116Taxus wallichiana var. wallichiana HM591121Taxus wallichiana var. wallichiana

HM591122Taxus wallichiana var. wallichiana 92 EF660613Taxus globosa L162 Trnl T.floridana HM591139Taxus wallichiana var. mairei

AJ441101Taxus chinensis var. Mairei

HM591123Taxus wallichiana var. wallichiana AB083242Taxus chinensis var. mairei 96 AY013722Taxus wallichiana var. wallichiana

EU052224Taxus wallichiana var. chinensis

HM591124Taxus wallichiana var. wallichiana 24.Tax.can

EF660636Taxus canadensis

25.Tax.hun 84 89 L165 Trnl assembly L24 T.canadensisTrnl assembly

P6 Trnl Taxus Canadensis EU052223Taxus wallichiana var. chinensis 82 HM591128Taxus wallichiana var. chinensis DQ885567Taxus wallichiana

EF660604Taxus brevifolia gi|18025238|gb|AY013724.1| Pseudotaxus chienii 98 gi|21322729|emb|AJ441100.1| Pseudotaxus chienii 53 gi|151301930|gb|EF660615.1| Pseudotaxus chienii L164 Trnl Austrotaxus spicata EF660606Austrotaxus spicata2

100 AY013746Austrotaxus spicata gi|18025256|gb|AY013742.1| Cephalotaxus sinensis 69 gi|21321289|dbj|AB083236.1| Cephalotaxus fortunei EF660617Cephalotaxus drupacea

EF660612Cephalotaxus lanceolata 44 68.Ceph.sin P8 Trnl Cephalotaxus harringtoria fastigiata

98 EF660608Cephalotaxus mannii

gi|21321287|dbj|AB083234.1| Cephalotaxus sinensis 75a.Cep.oli 84 AY013723Amentotaxus argotaenia 53 98 AJ441098Amentotaxus yunnanensis gi|18025257|gb|AY013743.1| Amentotaxus formosana

L66 Trnl Amentotaxus formosana Trnl

AY013731Torreya fargesii var. yunnanensis 38 88 P24 Trnl Torreya Californicia P25 Trnl 7599 90 gi|21322731|emb|AJ441102.1| Torreya yunnanensis 34.Tor.nuc 69 gi|18025246|gb|AY013732.1| Torreya jackii 73.Tor.jac

EF660624Torreya jackii EF660642Torreya taxifolia 0.020 Figure S2. Maximum likelihood phylogenetic reconstruction of Taxaceae based on trnL and trnL–F plastid DNA. Maximum likelihood bootstrap values shown above branches.

1 1 EF680274_T_wallichiana 0.9467 1HM591118_T_wallichiana_var__wallichiana 1 JX680659_T_wallichiana_var__mairei 1 JX680658_T_wallichiana 1 HM591121_T_wallichiana_var__wallichiana 1 EF680271_T_wallichiana HM591122_T_sumatrana 0.6584 1 1 JX188646_T_wallichiana_var__wallichiana EF660620_T_wallichiana1 1 EU052222_T_wallichiana_var__wallichiana 1 HM591117_T_wallichiana_var__wallichiana 1 EU052218_T_wallichiana_var__wallichiana 1 HM591116_T_wallichiana_var__wallichiana 1 EF660604_T_brevifolia 1 EF680264_T_baccata 1 HM591154_T_baccata 1 EF660635_T_baccata 1 HM591155_T_baccata 1 P1_T_canadensis 1 L32_T_cuspidata_fructo_luteo 1 L44_T_baccata_rushmoor 1 P19_T_cuspidata 1 P30_T_baccata_fastigata 1 L31_T_brevifolia 1 L93_T_baccata 1 P14_T_brevifolia 1 L149_T_brevifolia 1 L26_T_x_media_Hicksii 1 L36_T_canadensis_aurea 1 P13_T__aurea 1 P11_T_canadensis 0.5365 1 P21_T_canadensis 1 P12_T_cuspidata_luteobaccata 1 P29_T_baccata_grandis 1 P20_T_canadensis_aurea 1 P17_T_cuspidata 1 P27_T_baccata_f_aurea 1 L51_T_baccata 1 P18_T_cuspidata_f_thayetae 1 P15_T_cuspidata 1 L42__T_baccata_fastigata 1 P5_T_canadensis 1 P1_T_canadensis_aurea 1 P10_T_canadensis_aurea 1 L33_T_canadensis 1 P28_T_baccata_fastigata 1 L95_T_baccata 1 L94_T_baccata 1 P16_T_x_media_hicksii 1 L112a_T_baccata_fructo_luteo 1AY013720_T_wallichiana_var__chinensis 1 DQ885568_T_x_media 1 EF660639_T_x_media 1 EF017314_T_x_hunnewelliana 1 HM591145_T_sumatrana 1 HM591144_T_sumatrana EU052228_T_wallichiana_var__mairei 1 1 HM591147_T_cuspidata1 0.9565 1 JX680640_T_contorta EF680260_T_fuana 0.8668 1 1 JX680642_T_contorta 1 JX680635_T_contorta 1 HM591150_T_fuana 1 HM591148_T_cuspidata 1 EF660609_T_sumatrana EF660616_T_cuspidata1 0.9749 1 EU052214_T_wallichiana_var__chinensis 1 HM591133_T_wallichiana_var__chinensis 1 AF506838_T_cuspidata 1 EU052226_T_wallichiana_var__mairei 1 HM591137_T_wallichiana_var__mairei 1 EF660637_T_cuspidata 1 P22_T_x_media 1 L27_T_cuspidata L108_T_baccata_amersfort1 1 DQ885567_T_wallichiana_var__mairei 1 HM591124_T_wallichiana_var__wallichiana 1 AY013722_T_wallichiana_var__wallichiana 1 AB083242_T_chinensis_var__mairei 1 HM591139_T_wallichiana_var__mairei 0.8424 1 AJ441101_T_chinensis_var__mairei 1 EU052224_T_wallichiana_var__chinensis HM591123_T_wallichiana_var__wallichiana1 1 1 HM591128_T_wallichiana_var__chinensis EU052223_T_wallichiana_var__chinensis1 1 EF660636_T_canadensis 1 L24_T_canadensis 1 1 L25_T_x_hunnewelliana 1 P6_T_canadensis 1 L165_T_canadensis L24_T_canadensis_2_1 0.7711 1 EF660613_T_globosa 1 L162_T_floridana 0.9309 1 1 AJ441100_Pseudotaxus_chienii 1 EF660615_Pseudotaxus_chienii AY013724_1__Pseudotaxus_chienii

0.4

Figure S3. Bayesian analysis of trnL+trnL-F data including Taxus and Pseudotaxus only. Bayesian posterior probability values shown above the branches.

Figure S4. Maximum likelihood bootstrap consensus tree of nrITS sequences including Taxus and Pseudotaxus only. The relationship between T. baccata, T. canadensis and T. cuspidata are not well resolved. T. brevifolia is sister to T. globosa and T. flordiana. Taxus fauna groups with T. contorta. Taxus wallichiana is monophyletic but its varieties are not.

Figure S5. Bayesian analysis of nrITS sequence data for Taxus and Pseudotaxus only. Bayesian posterior probability values shown above the branches.

Figure S6. TrnL intron and trnL-F haplotype TCS analysis. Bac=T. baccata; brev= T. brevifolia; can= T. canadensis; cus= T. cuspidata; fua= T. fuana; sum= T. sumatrana; wal (C, M, W) =T. wallichiana var. chinensis, var. mairei and var. wallichiana; xhun= T. xhunnewelliana; xmed= T. xmedia. Seq. numbers on pie charts are haplotype numbers 1=10.

Stomata

Papillae present

7 rows of stomata

Papillae d

Smooth midrib

Figure S7. Leaf anatomy of Taxus. a-e. Representative slides shown. Full data summarised in supplementary Table A1. a P16 T. xmedia ‘Hicksii’ at 20x magnification showing stomata; b P14 Taxus brevifolia at 10x magnification. Papillae present on middle of mid rib; c P16 Taxus x media ‘Hicksii’ at 10x magnification showing 7 rows of stomata; d P29 Taxus baccata "Grandis" at 10x magnification. Some papillae present on the midrib; e P29 Taxus baccata ‘Grandis’ 10x papillae absent.

Table S1a. Sequences used from GenBank for nrITS analysis in addition to the newly sequenced samples. Name GenBank Code ITS Amentotaxus argotaenia gi|641453453|gb|KJ588939.1 Amentotaxus formosana gi|6174774|dbj|AB023976.1 Amentotaxus formosana gi|343404279|gb|JF975884.1 Amentotaxus formosana gi|343404278|gb|JF975883.1 Amentotaxus formosana gi|343404277|gb|JF975882.1 Amentotaxus yunnanensis gi|6174780|dbj|AB023980.1 Amentotaxus yunnanensis gi|641453452|gb|KJ588938.1 Austrotaxus spicata gi|6174777|dbj|AB023978.1 Austrotaxus spicata gi|151301884|gb|EF660569.1 Cephalotaxus drupacea gi|151301890|gb|EF660575.1 Cephalotaxus hainanensis gi|151301907|gb|EF660592.1 Cephalotaxus harringtonia gi|151301896|gb|EF660581.1 Cephalotaxus koreana gi|151301889|gb|EF660574.1 Cephalotaxus lanceolata gi|343404500|gb|JF976105.1 Cephalotaxus mannii gi|6174788|dbj|AB023985.1 Cephalotaxus mannii gi|343404507|gb|JF976112.1 Cephalotaxus mannii gi|343404504|gb|JF976109.1 Cephalotaxus oliver gi|343404509|gb|JF976114.1 Cephalotaxus oliver gi|343404508|gb|JF976113.1 Cephalotaxus sinensis gi|6174843|dbj|AB023987.1 Cephalotaxus sinensis gi|343404514|gb|JF976119.1 Cephalotaxus sinensis gi|343404511|gb|JF976116.1 Taxus baccata gi|6174855|dbj|AB023995.1 Taxus baccata gi|359466028|gb|JN255686.1 Taxus baccata gi|403240040|gb|JX188555.1 Taxus baccata gi|403240042|gb|JX188557.1 Taxus baccata gi|403240043|gb|JX188558.1 Taxus baccata gi|13897861|gb|AF259294.1 Taxus baccata gi|13897854|gb|AF259287.1 Taxus baccata gi|151301914|gb|EF660599.1 Taxus brevifolia gi|13897862|gb|AF259295.1 Taxus canadensis gi|13897863|gb|AF259296.1 Taxus canadensis gi|13897865|gb|AF259298.1 Taxus canadensis gi|151301916|gb|EF660601.1 Taxus chinensis gi|13897859|gb|AF259292.1 Taxus chinensis gi|13897858|gb|AF259291.1 Taxus contorta gi|751372675|gb|KM886874.1 Taxus contorta gi|409725547|gb|JX680607.1 Taxus contorta gi|409725545|gb|JX680605.1 Taxus contorta gi|409725546|gb|JX680606.1 Taxus cuspidata gi|403240052|gb|JX188567.1 Taxus cuspidata gi|403240053|gb|JX188568.1 Taxus cuspidata gi|13897856|gb|AF259289.1 Taxus cuspidata gi|13897857|gb|AF259290.1 Taxus cuspidata gi|151301891|gb|EF660576.1 Taxus cuspidata gi|151301917|gb|EF660602.1 Taxus floridana gi|13897853|gb|AF259286.1 Taxus floridana gi|151301918|gb|EF660603.1 Taxus fauna gi|403240055|gb|JX188570.1 Taxus fauna gi|158132328|gb|EF680237.1 Taxus fauna gi|158132331|gb|EF680240.1 Taxus fauna gi|158132334|gb|EF680243.1 Taxus fauna gi|158132327|gb|EF680236.1 Taxus fauna gi|151301897|gb|EF660582.1 Taxus globosa gi|13897866|gb|AF259299.1 Taxus globosa gi|151301885|gb|EF660570.1 Taxus mairei gi|751372676|gb|KM886875.1 Taxus mairei gi|409725559|gb|JX680619.1 Taxus mairei gi|403240061|gb|JX188576.1 Taxus mairei gi|403240062|gb|JX188577.1 Taxus mairei gi|403240063|gb|JX188578.1 Taxus mairei gi|403240064|gb|JX188579.1 Taxus mairei gi|403240034|gb|JX188549.1 Taxus mairei gi|409725555|gb|JX680615.1 Taxus mairei gi|403240065|gb|JX188580.1 Taxus mairei gi|403240067|gb|JX188582.1 Taxus mairei gi|409725562|gb|JX680622.1 Taxus mairei gi|409725560|gb|JX680620.1 Taxus sumatrana gi|151301887|gb|EF660572.1 Taxus sumatrana gi|316953979|gb|HM590967.1 Taxus sumatrana gi|316953976|gb|HM590964.1 Taxus wallichiana gi|409725563|gb|JX680623.1 Taxus wallichiana gi|409725571|gb|JX680631.1 Taxus wallichiana gi|409725564|gb|JX680624.1 Taxus wallichiana gi|409725570|gb|JX680630.1 Taxus wallichiana gi|409725573|gb|JX680633.1 Taxus wallichiana gi|13897860|gb|AF259293.1 Taxus wallichiana var. chinensis gi|403240081|gb|JX188596.1 Taxus wallichiana var. chinensis gi|403240082|gb|JX188597.1 Taxus wallichiana var. chinensis gi|403240046|gb|JX188561.1 Taxus wallichiana var. chinensis gi|403240047|gb|JX188562.1 Taxus wallichiana var. chinensis gi|403240083|gb|JX188598.1 Taxus wallichiana var. chinensis gi|403240050|gb|JX188565.1 Taxus wallichiana var. chinensis gi|403240051|gb|JX188566.1 Taxus wallichiana var. chinensis gi|316953964|gb|HM590952.1 Taxus wallichiana var. chinensis gi|316953965|gb|HM590953.1 Taxus wallichiana var. chinensis gi|316953962|gb|HM590950.1 Taxus wallichiana var. chinensis gi|316953959|gb|HM590947.1 Taxus wallichiana var. chinensis gi|316953963|gb|HM590951.1 Taxus wallichiana var. chinensis gi|151301912|gb|EF660597.1 Taxus wallichiana var. mairei gi|316953968|gb|HM590956.1 Taxus wallichiana var. mairei gi|151301911|gb|EF660596.1 Taxus wallichiana var. mairei gi|316953973|gb|HM590961.1 Taxus wallichiana var. mairei gi|238695909|gb|FJ980299.1 Taxus wallichiana var. mairei gi|316953972|gb|HM590960.1 Taxus wallichiana var. mairei gi|316953971|gb|HM590959.1 Taxus wallichiana var. wallichiana gi|403240027|gb|JX188542.1 Taxus wallichiana var. wallichiana gi|403240069|gb|JX188584.1 Taxus wallichiana var. wallichiana gi|403240068|gb|JX188583.1 Taxus wallichiana var. wallichiana gi|403240070|gb|JX188585.1 Taxus wallichiana var. wallichiana gi|403240072|gb|JX188587.1 Taxus wallichiana var. wallichiana gi|403240028|gb|JX188543.1 Taxus wallichiana var. wallichiana gi|403240079|gb|JX188594.1 Taxus wallichiana var. wallichiana gi|403240080|gb|JX188595.1 Taxus wallichiana var. wallichiana gi|151301892|gb|EF660577.1 Taxus wallichiana var. wallichiana gi|151301883|gb|EF660568.1 Taxus wallichiana var. wallichiana gi|316953955|gb|HM590943.1 Taxus wallichiana gi|158132342|gb|EF680251.1 Taxus wallichiana gi|151301888|gb|EF660573.1 Taxus wallichiana gi|158132341|gb|EF680250.1 Taxus x hunnewelliana gi|13897855|gb|AF259288.1 Taxus x hunnewelliana gi|151301894|gb|EF660579.1 Taxus x media gi|13897864|gb|AF259297.1 Taxus x media gi|151301913|gb|EF660598.1 Taxus x media gi|151301895|gb|EF660580.1 Torreya californica gi|20339345|gb|AF259274.1 Torreya californica gi|6174858|dbj|AB023997.1 Torreya californica gi|641453440|gb|KJ588926.1 Torreya californica gi|641453441|gb|KJ588927.1 Torreya fargesii gi|641453432|gb|KJ588918.1 Torreya fargesii gi|641453433|gb|KJ588919.1 Torreya fargesii gi|641453435|gb|KJ588921.1 Torreya fargesii gi|641453436|gb|KJ588922.1 Torreya nucifera gi|641453426|gb|KJ588912.1 Torreya nucifera gi|641453427|gb|KJ588913.1 Torreya taxifolia gi|641453437|gb|KJ588923.1 Torreya taxifolia gi|641453438|gb|KJ588924.1 Torreya taxifolia gi|641453439|gb|KJ588925.1

Table S2b. Sequences used from GenBank for TrnL-F analysis in addition to the newly sequenced samples. Name GenBank Code TrnL-F Cephalotaxus drupacea gi|151301932|gb|EF660617.1 Cephalotaxus fortunei gi|21321289|dbj|AB083236.1 Cephalotaxus lanceolata gi|151301927|gb|EF660612.1 Cephalotaxus mannii gi|151301923|gb|EF660608.1 Cephalotaxus sinensis gi|21321287|dbj|AB083234.1 Cephalotaxus sinensis gi|18025256|gb|AY013742.1 Pseudotaxus chienii gi|21322729|emb|AJ441100.1 Pseudotaxus chienii gi|18025238|gb|AY013724.1 Taxus baccata gi|157381297|gb|EF680264.1 Taxus baccata gi|18025258|gb|AY013744.1 Taxus baccata gi|151301950|gb|EF660635.1 Taxus baccata gi|316953769|gb|HM591155.1 Taxus baccata gi|316953768|gb|HM591154.1 Taxus brevifolia gi|151301919|gb|EF660604.1 Taxus canadensis gi|151301951|gb|EF660636.1 Taxus chinensis var. mairei gi|21321295|dbj|AB083242.1 Taxus chinensis var. mairei gi|21322730|emb|AJ441101.1 Taxus contorta gi|409725583|gb|JX680640.1 Taxus contorta gi|409725578|gb|JX680635.1 Taxus contorta gi|409725585|gb|JX680642.1 Taxus cuspidata gi|30269924|gb|AF506838.1 Taxus cuspidata gi|151301931|gb|EF660616.1 Taxus cuspidata gi|151301952|gb|EF660637.1 Taxus cuspidata gi|316953761|gb|HM591147.1 Taxus cuspidata gi|316953762|gb|HM591148.1 Taxus fauna gi|157381293|gb|EF680260.1 Taxus fauna gi|316953764|gb|HM591150.1 Taxus globosa gi|151301928|gb|EF660613.1 Taxus sumatrana gi|151301924|gb|EF660609.1 Taxus sumatrana gi|316953758|gb|HM591144.1 Taxus sumatrana gi|316953759|gb|HM591145.1 Taxus wallichiana gi|157381304|gb|EF680271.1 Taxus wallichiana gi|409725602|gb|JX680659.1 Taxus wallichiana gi|409725601|gb|JX680658.1 Taxus wallichiana gi|157381307|gb|EF680274.1 Taxus wallichiana var. chinensis gi|18025234|gb|AY013720.1 Taxus wallichiana var. chinensis gi|158139179|gb|EU052214.1 Taxus wallichiana var. chinensis gi|316953747|gb|HM591133.1 Taxus wallichiana var. chinensis gi|316953742|gb|HM591128.1 Taxus wallichiana var. chinensis gi|158139188|gb|EU052223.1 Taxus wallichiana var. chinensis gi|158139189|gb|EU052224.1 Taxus wallichiana var. mairei gi|18025243|gb|AY013729.1 Taxus wallichiana var. mairei gi|114152646|gb|DQ885567.1 Taxus wallichiana var. mairei gi|158139191|gb|EU052226.1 Taxus wallichiana var. mairei gi|158139194|gb|EU052229.1 Taxus wallichiana var. mairei gi|316953751|gb|HM591137.1 Taxus wallichiana var. mairei gi|158139193|gb|EU052228.1 Taxus wallichiana var. mairei gi|316953753|gb|HM591139.1 Taxus wallichiana var. wallichiana gi|403240131|gb|JX188646.1 Taxus wallichiana var. wallichiana gi|18025236|gb|AY013722.1 Taxus wallichiana var. wallichiana gi|158139187|gb|EU052222.1 Taxus wallichiana var. wallichiana gi|316953730|gb|HM591116.1 Taxus wallichiana var. wallichiana gi|316953731|gb|HM591117.1 Taxus wallichiana var. wallichiana gi|316953735|gb|HM591121.1 Taxus wallichiana var. wallichiana gi|316953737|gb|HM591123.1 Taxus wallichiana var. wallichiana gi|316953738|gb|HM591124.1 Taxus wallichiana var. wallichiana gi|316953732|gb|HM591118.1 Taxus wallichiana var. wallichiana gi|158139183|gb|EU052218.1 Taxus wallichiana var. wallichiana gi|316953736|gb|HM591122.1 Taxus wallichiana gi|151301935|gb|EF660620.1 Taxus x hunnewelliana gi|119114806|gb|EF017314.1 Taxus x media gi|114152647|gb|DQ885568.1 Taxus x media gi|151301954|gb|EF660639.1 Torreya fargesii var. yunnanensis gi|18025245|gb|AY013731.1 Torreya jackii gi|18025246|gb|AY013732.1 Torreya jackii gi|151301939|gb|EF660624.1 Torreya taxifolia gi|151301957|gb|EF660642.1 Torreya yunnanensis gi|21322731|emb|AJ441102.1

Table S2. Leaf anatomy data for Taxus species. Sample name Sample no. Rows of stomata Midrib T. baccata T1 8 Papillae present T. baccata S.n. St. Doolaghs 7 to 8 Papillae absent T. baccata 'Grandis' 6603 7 Papillae present near tip of leaf only T. brevifolia P14 5 to 7 Papillae present near tip of leaf only T. canadensis P11 5 to 6 Papillae present at tip T. canadensis 'Aurea' P13 4 Papillae present near tip of leaf only T. cuspidata P15 8 to 9 Papillae present. Papillae absent at base of leaf T. cuspidata P17 6 Papillae present at tip of leaf only T. cuspidata P19 6 Papillae present near base of leaf only T. ×media 'Hicksii' P16 7 Papillae absent T. cuspidata f. thayerae P9 9 Papillae absent T. cuspidata 'Luteobaccata' P12 6 Papillae present near base of leaf only