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The handle http://hdl.handle.net/1887/35731 holds various files of this Leiden University dissertation

Author: Mennes, Constantijn Title: Antiquities of the rainforest : evolution of mycoheterotrophic angiosperms growing on Glomeromycota Issue Date: 2015-10-06 Appendix A: Supplementary Tables.

153 Antiquities of the rainforest

154 Appendix A.1. Taxon information, voucher information and GenBank accession numbers.

155 Antiquities of the rainforest nad1b-c — DQ786160 — KF258208 KF258207 KF197098 KF258211 KF258212 — KF258210 KF258209 GQ469502 DQ786157 KF298298 KF298299 KF298300 KF298301 KF298302 KF298303 KF197102 KF197103 — — KF258206 DQ786163.1 GQ469504 HM576829.1 KF298333 KF298334 KF298335 KF298336 KF298337 KF298338 KF298339 KF298332 KF298340 KF298341 KF298342 KF298343 matR — KF264492 KF197111 KF258579 KF258199 KF197105 KF258198 KF258204 AF197735.1 KF258205 KF258203 KF298370 KF264495 KF298292 KF298293 KF298294 KF298295 KF298296 KF298297 KF197113 KF197112 KF197110 — KF258202 KF264496 KF264497 AF197745.1 KF298319 KF298320 KF298321 KF298322 KF298323 KF298324 KF298325 KF298318 KF298326 KF298327 KF298328 KF298329 atpA AY299698.1 FJ215780.1 — KF258580 KF258578 KF197075 KF258577 KF258586 AF197708.1 KF258587 KF258588 AY277804.1 EU421029.1 KF298286 KF298287 KF298288 KF298289 KF298290 KF298291 KF197072 KF298373 KF298372 AY299794.1 KF258589 AY299809.1 EU421041.1 AY299816.1 KF298305 KF298306 KF298307 KF298308 KF298309 KF298310 KF298311 KF298304 KF298312 KF298313 KF298314 KF298315 18S rDNA AY952411.1 DQ786092.1 KF197094 KF264476 KF264477 KF197081 KF264478 KF264479 AF168835.1 KF264480 KF264481 EU186223.1 DQ786090.1 KF298366 KF298363 KF298381 KF298367 KF298365 KF298362 KF197095 KF197093 — — KF264482 AF309411.1 EU186219.1 AF293753.1 KF298360 KF298359 KF298358 KF298357 KF298356 KF298355 KF298354 KF298361 KF298364 KF298353 KF298352 KF298351 Voucher (only applies to new sequences) Voucher 2833, Papua New Wood Sands, Pattison, Guinea RBGB 19720037- RBGB 19790005- RBGB 19084359- HBL812119-22130 RBGB 19221361- RBGB 19510200- RBGB 19391773- HBL910022 RBGB 20080173-09 HBL950608 HBL981172 RBGB 20080172-08 RBGB 20080174-10 Cameroon YA, Sainge 1620, Cameroon Merckx et al. 102, LV, Cameroon YA, Sainge 1668, RBGB 19810835- RBGB 19610454- HBL910011 RBGB 10005462- RBGB 19381346- RBGB 2000134-92 RBGB 19630068- RBGB 19773283- HBL920709/ HBL920276 HBL990062 RBGB 19392017- RBGB 20031134-52 RBGB 19480610- Family Velloziaceae Nartheciaceae Triuridaceae Cyclanthaceae Cyclanthaceae Velloziaceae Cyclanthaceae Cyclanthaceae Stemonaceae Cyclanthaceae Cyclanthaceae Dioscoreaceae Dioscoreaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Cyclanthaceae Nartheciaceae Nartheciaceae Araceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Warb. Benth. P.C.Kao (H.Wendl.) Harling (H.Wendl.) Hemsl. Gaudich. 1 Gaudich. 2 E.Martínez & Ramos Thouars Kurz ex Miq. Kurz ex Miq.^ laevis (L.) Huds. Ruiz & Pav 2 Poit. ex A.Rich. Poit. ex Ruiz & Pav 1 (L.) Caddick & Wilkin (L.) Caddick & L. Steyerm. Spreng. Bory J.H.Veitch^ var. Cheek & S.A.Williams 1 Cheek & S.A.Williams 2 Cheek & S.A.Williams (Balf.) Pax (Nutt.) Torr. Misonne^ Parkinson ex Du Roi Brongn. Roxb. (Aubl.) Harling Prain & Burkill dubius venezuelensis Small sp. 1 sp. 2 sp. 3 cf. sp. 1 sp. 2 cf. sp. sp. Chapter 2 Chapter Species Acanthochlamys bracteata Aletris lutea Andruris Asplundia Asplundia rigida Barbacenia elegans Carludovica palmata Carludovica palmata pauciflora Croomia Cyclanthus bipartitus Dicranopygium atrovirens communis Dioscorea rockii Dioscorea cumingiana Freycinetia cumingiana Freycinetia philippinensis Freycinetia Freycinetia Freycinetia Freycinetia Kihansia Kupea martinetugei Kupea martinetugei Lacandonia schismatica Ludovia lancifolia Narthecium ossifragum Nietneria paniculata aquaticum Orontium Pandanus baptistii Pandanus Pandanus furcatus Pandanus labyrinthicus Pandanus montanus Pandanus pacificus Pandanus purpurascens Pandanus Pandanus Pandanus stenophyllus Pandanus tectorius Pandanus tectorius

156 nad1b-c KF298344 KF298345 KF258576 KF197100 — KF197099 — KF197101 KF298346 KF298347 — KF197096 — — — — — — KF258575 KF258574 DQ786153 KF264499 — — — KF197097 — matR KF298330 KF298331 KF298369 KF298375 KF298376 KF298377 KF298378 KF197109 KF197108 KF197107 KF197106 KF298379 KF298380 KF298371 KF258193 KF258194 KF258195 KF258196 KF258200 KF258201 KF264494 KF264493 KF258197 KF298374 — KF197104 — atpA KF298316 KF298317 KF264506 KF197069 KF197071 KF197073 — KF197070 KF197077 KF197076 KF298368 KF197079 — KF197078 KF258583 — KF258584 — KF264505 KF264504 EU421045.1 JN850565.1 KF258585 KF258582 KF258581 KF197074 AF039256.1 atpA AY299699.1 EU421002.1 EU421004.1 AY299706.1 FJ215780.1 AF197717.1 AY299710.1 AF039246.1 EU421007.1 EU421008.1 EU421016.1 EU421023.1 18S rDNA KF298350 KF298349 KF264490 KF197092 KF197091 KF197090 KF197089 KF197088 KF197086 KF197085 KF197084 KF197083 KF197087 KF197082 KF264483 KF264484 KF264485 KF264486 KF264491 KF298348 DQ786085.1 AF309395.1 KF264487 KF264488 KF264489 KF197080 L24078.1 18S rDNA AF197584.1 EU420988.1 EU420990.1 AF309390.1 DQ786092.1 AF197585.1 D29786.1 AF069214.1 DQ786034.1 DQ786074.1 DQ786078.1 DQ786069.1 Voucher (only applies to new sequences) Voucher RBGB 19074101 RBGB 19270660- HBL910375 O. Banki 108, Guiana Maas et al. 9650, U, French Guiana Jansen-Jacobs 6567, Suriname Maas et al.9667, Guiana Cameroon Merckx et al. 128, LV, Dessein 1850, BR, Gabon Vietnam Poncrt s.n., 298, Hammell 3105, Panama Alzatc 4151, 291, Colombia Venezuela Maas et al. 830, Papua New Guinea Polak 1118, Prieditis s.n. (NHN-U 0253669), Borneo Papua New Guinea Polak 1117, Tanzania Bridson 634 WAG, Madagascar WAG, Dorr 4592 HBL20081117 HBL910374 Renz 14120, Guiana Sano & Laessoe 52195, Brazil Marquez-Guzman s.n. (d.d. 1990), Mexico HBLA86167 (only applies to new sequences) Voucher Family Pandanaceae Pandanaceae Stemonaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Stemonaceae Stemonaceae Taccaceae Trichopodaceae Triuridaceae Triuridaceae Triuridaceae Velloziaceae Araceae Family Araceae Thismiaceae Thismiaceae Nartheciaceae Nartheciaceae Alismataceae Bromeliaceae Haemodoraceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae (J.J.Sm.) Duyfjes C.H.Wright L. Steenis T.Franke, Sainge & Agerer Sainge & T.Franke, J.J.Sm. (H.Perrier) Caddick & Wilkin (H.Perrier) Caddick & Engl. 1 Engl. 2 Vollesen ternatensis DC. Maas (Miers) Hook.f. Benth. 2 Benth. 3 Benth. 1 Benth. 2 Benth. 1 Benth. 4 Makino Sainge & T.Franke var. Ker Gawl. Aiton Mast.^ Blume (L.) Merr. L. Mart. Bory (Nutt.) Barnhart ex Small (Balf.) Talbot ex Hook.f.^ Talbot (Balf.) L. Miers 1 Miers Miers 2 Small sp. sp. Species Pandanus utilis Pandanus veitchii Pentastemona sumatrana Sciaphila albescens Sciaphila albescens Sciaphila albescens Sciaphila albescens Sciaphila ledermannii Sciaphila ledermannii Sciaphila nana Blume Sciaphila picta Sciaphila purpurea Sciaphila purpurea Sciaphila quadribullifera Sciaphila Sciaphila tenella Seychellaria africana Seychellaria madagascariensis Stemona Stemona tuberosa integrifolia Tacca sempervirens Trichopus hexophthalma Triuris hyalina Triuris hyalina Triuris elegans Vellozia Acorus calamus Species Acorus gramineus foertheriana Afrothismia hydra Afrothismia Aletris farinosa Aletris lutea Alisma plantago-aquatica Ananas comosus Anigozanthos flavidus Apteria aphylla Burmannia alba Burmannia itoana Burmannia wallichii

157 Antiquities of the rainforest atpA AY299733.1 AY299735.1 EU421024.1 AY299741.1 AY299745.1 AY299748.1 EU421025.1 DQ401297.1 AY299755.1 AY124503.1 EU421026.1 EU421027.1 AY277804.1 EU421028.1 EU421029.1 AF039248.1 EU421049.1 EU421031.1 AF039244.1 AY299775.1 EU421037.1 AY299778.1 EU421038.1 AY299788.1 AY299789.1 AY299790.1 AY124519.1 AY299797.1 EU421039.1 EU421040.1 AY299804.1 AY299809.1 AY299813.1 EU421041.1 U58833.1 AY299816.1 AY299821.1 AY299823.1 U58831.1 AY299825.1 AY299827.1 18S rDNA AH003489.1 AF069224.1 EU420996.1 D29785.1 AF206884.1 AF168833.1 DQ786038.1 AY952404.1 AF069208.1 AJ417898.1 DQ786056.1 EU420997.1 EU186223.1 DQ786089.1 DQ786090.1 AF206913.1 AF309405.1 EU420998.1 AF069200.1 AF387604.1 DQ786082.1 AF168850.1 DQ786057.1 AF135204.1 AF206940.1 AF206942.1 AF168855.1 AF206952.1 DQ786091.1 AF309410.1 AF168861.1 AF309411.1 AF168863.1 EU186219.1 AY012357.1 AF293753.1 AF206987.1 AF206990.1 AF206991.1 AY012398.1 AF206995.1 Voucher (only applies to new sequences) Voucher Family Butomaceae Maranthaceae Burmanniaceae Cannaceae Trichopodaceae Liliaceae Burmanniaceae Cyperaceae Orchidaceae Dasypogonaceae Burmanniaceae Dioscoreaceae Dioscoreaceae Dioscoreaceae Dioscoreaceae Flagellariaceae Thismiaceae Burmanniaceae Araceae Hanguanaceae Thismiaceae Heliconiaceae Burmanniaceae Orchidaceae Ixioliriaceae Petrosaviaceae Joinvilleaceae Liliaceae Nartheciaceae Nartheciaceae Costaceae Nartheciaceae Orchidaceae Nartheciaceae Arecaceae Araceae Petrosaviaceae Philydraceae Arecaceae Arecaceae Tofieldiaceae Benth. Maxim. (Hook.) Miers Urb. Spruce Airy Shaw (Miers) Benth. & Hook.f.^ (L.) Huds. L. R.Knuth Letouzey Blume (Poepp. ex Petersen) Maas R.Br. (L.) A.Gray L. (L.) Caddick & Wilkin (L.) Caddick & (Jack) Merr. L. (R.Br.) Caruel (R.Br.) Steyerm. Gaudich. ex Brongn. & Gris (Pall.) Schult. & Schult.f. L. Becc. Nakai Becc. Ruiz & Pav. J.F.Macbr. L. (Muhl. ex Willd.) Raf. Willd.) (Muhl. ex (Aiton) Raf. Prain & Burkill L. Prain & Burkill Michx. Ker Gawl. Wurmb L. sp. sp. Species Butomus umbellatus Calathea loeseneri Campylosiphon purpurascens Canna indica Chamaelirium luteum Clintonia borealis Gymnosiphon refractus Cyperus alternifolius Cypripedium calceolus Dasypogon Dictyostega orobanchoides althaeoides Dioscorea communis Dioscorea prazeri Dioscorea rockii Dioscorea Flagellaria indica Geomitra clavigera Gymnosiphon bekensis Gymnostachys anceps Hanguana malayana Haplothismia exannulata Heliconia rostrata gentianoides Hexapterella Isotria verticillata Ixiolirion tataricum Japonolirion osense Joinvillea ascendens Lilium superbum Lophiola aurea Metanarthecium luteo-viride Monocostus uniflorus Narthecium ossifragum Neuwiedia veratrifolia Nietneria paniculata Nypa fruticans aquaticum Orontium stellaris Petrosavia pygmaea Philydrella Phoenix Phytelephas aequatorialis Pleea tenuifolia

158 Plastid genome — NC_007407 — — — Givnish et al. (2010)* — — — JX088668 KC968976 NC_005086 — — — — nad5 — — — — — — — — — — KP420358 — — — — KP420359 cob — — — — — — — — — — KP420327 — — — — KP420328 matR — DQ007422 DQ007423 — — — — KF264492 AF197815 — KP420285 — — — KP420311 KP420286 atpA AY299828.1 AY299830.1 AY277803.1 AY124509.1 EU421042.1 AY299843.1 DQ859116.1 EU421043.1 EU421044.1 EU421045.1 EU421046.1 EU421047.1 AY299846.1 AY299848.1 EU421050.1 AY299849.1 AY299851.1 AY299724.1 AY277805.1 AF197716.1 AF039253.1 AY299857.1 DQ859121.1 atpA AY299698 AF039256 AY299699 EU421002 EU421004 — AY299706 FJ215780 AF197717 — KP420384 — AY299710 AF039246 EU421007 KP420385 18S rDNA AF206998.1 AF069228.1 AF069202.1 AF069220.1 DQ786087.1 AF069229.1 AF168876.1 AF309397.1 DQ786086.1 DQ786085.1 EU421000.1 U42063.1 AH003649.1 AF207036.1 DQ786081.1 AF309403.1 AF207043.1 AF309395.1 AF309394.1 AF197586.1 AF168879.1 AF207056.1 HQ445940.1 18S rDNA AY952411 L24078 AF197584 EU420988 EU420990 — AF309390 DQ786092 AF197585 — KP420428 — D29786 AF069214 DQ786034 KP420410 Voucher (only applies to new sequences) Voucher (only applies to new sequences) Voucher 19990 (K) Chase, M.W. Maas et al. 9662 (U) Bidartondo, M.I. et al., 2002, Nature 419 Family Pontederiaceae Strelitziaceae Scheuchzeriaceae Typhaceae Dioscoreaceae Strelitziaceae Cymodoceaceae Taccaceae Taccaceae Taccaceae Taccaceae Taccaceae Costaceae Tecophilaeaceae Thismiaceae Thismiaceae Tofieldiaceae Trichopodaceae Trichopodaceae Juncaginaceae Liliaceae Xeronemataceae Zosteraceae Family Velloziaceae Acoraceae Acoraceae Thismiaceae Thismiaceae Asparagaceae Nartheciaceae Nartheciaceae Alismataceae Zingiberaceae Alstroemeriaceae Amborellaceae Bromeliaceae Haemodoraceae Burmanniaceae Corsiaceae Sonn. P.C.Kao Planch. L. T.Franke, Sainge & Agerer Sainge & T.Franke, Leyb. Engelm. (H.Perrier) Caddick & Wilkin (H.Perrier) Caddick & L. Baill. W.R.B.Oliv. L. DC. (Michx.) Salisb. Kütz. Gaertn. Seem. (Standl.) Jonker L. (L.) Wahlenb. Graham Phil. (Hance) Drenth Aiton Sainge & T.Franke Sainge & Ker Gawl. F.Muell. (L.) Merr. (Pers.) B.L.Burtt & R.M. Sm. Regel & K.Koch L. L. (Nutt.) Barnhart ex Small André L. Blume sp. (Baker) Brenan Small Species Pontederia cordata Ravenala madagascariensis Scheuchzeria palustris eurycarpum Sparganium Stenomeris dioscoreifolia nicolai Strelitzia Syringodium filiforme artocarpifolia Tacca chantieri Tacca integrifolia Tacca palmata Tacca plantaginea Tacca Tapeinochilos cyanocrocus Tecophilaea Thismia panamensis Thismia rodwayi calyculata Tofieldia sempervirens Trichopus zeylanicus Trichopus maritimum Triglochin grandiflorum Trillium callistemon Xeronema Zostera marina 3 Chapter Species Acanthochlamys bracteata Acorus calamus Acorus gramineus foertheriana Afrothismia hydra Afrothismia Albuca kirkii Aletris farinosa Aletris lutea Alisma plantago-aquatica Alpinia zerumbet aurea Alstroemeria trichopoda Amborella Ananas comosus Anigozanthos flavidus Apteria aphylla Arachnitis uniflora

159 Antiquities of the rainforest Plastid genome KP462884 Givnish et al. (2010)* — — — JX088664 — Givnish et al. (2010)* — — — — NC_009599 JX088663 — JX088666 — NC_004993 — KP462881 — — — KP462882 JX088667 — Givnish et al. (2010)* — KP462885 — — — — — — — — — Givnish et al. (2010)* — nad5 — — — — — — KP420360 — — — — — — — — — KP420361 — — KP420362 KP420363 — KP420364 — — JX182960 — KP420365 KP420368 KP420366 KP420367 JX182944 — — — — — — — — cob — — — — — — KP420356 — — — — — — — — — KP420329 — — KP420330 KP420331 — KP420332 — — DQ916679 — KP420333 KP420336 KP420334 KP420335 DQ916676 — — — — — — — — matR — — KF258579 KF258199 KF197105 — KP420287 — — KP420323 KP420312 — — — — — KP420288 — KP420313 KP420289 KP420290 EU281101 KF258204 — — — — KP420291 KP420294 KP420292 KP420293 — AF197735 KF258205 KP420314 DQ401381 DQ110336 — — KF258203 atpA — — KF258580 KF258578 KF197075 — KP420386 — EU421008 EU421016 EU421023 AY299733 — — AY299735 — KP420387 — EU421024 KP420388 KP420389 AY299741 KF258586 — — AY299745 — KP420390 KP420392 KP420407 KP420391 AY299748 AF197708 KF258587 EU421025 DQ401297 AY299755 AY124503 — KF258588 18S rDNA — — KF264476 KF264477 KF197081 — KP420429 — DQ786074 DQ786078 DQ786069 AH003489 — — AF069224 — KP420411 — EU420996 KP420430 KP420436 D29785 KF264479 — — AF206884 — KP420412 KP420415 KP420413 KP420414 AF168833 AF168835 KF264480 DQ786038 AY952404 AF069208 AJ417898 — KF264481 - Voucher (only applies to new sequences) Voucher Neyland, R. 1928 (MCN) 520 (K) Chase, M.W. Kun-Ping Lo 821 (PPI) Zhang s.n. (K) HBL20130196 Banki 1257 (U) 1842 (K) Duretto, M.F. Pillon, Barrabé, Maudet, Richard & Du montet 24 (K) RBGB 19221361- 14836 (K) Chase, M.W. RBGB 19630413- S., SPL470-2, PNG (L) Lyon, S., SPL468, PNG (L) Lyon, S., SPL446, PNG (L) Lyon, Kress s.n. (US) Family Corsiaceae Asparagaceae Cyclanthaceae Cyclanthaceae Velloziaceae Arecaceae Alstroemeriaceae Bromeliaceae Burmanniaceae Burmanniaceae Burmanniaceae Butomaceae Buxaceae Arecaceae Maranthaceae Dasypogonaceae Liliaceae Calycanthaceae Burmanniaceae Campynemataceae Campynemataceae Cannaceae Cyclanthaceae Cyclanthaceae Arecaceae Melanthiaceae Asparagaceae Colchicaceae Corsiaceae Corsiaceae Corsiaceae Liliaceae Stemonaceae Cyclanthaceae Burmanniaceae Cyperaceae Orchidaceae Dasypogonaceae Dasypogonaceae Cyclanthaceae (Willd.) Torr. & A. Gray & Torr. (Willd.) Bjorå & Hemp Benth. Harling Baill. (H.Wendl.) Harling (H.Wendl.) R.Br. glaucus Miers) Benth. & Hook.f.^ L.Barrett & K.W.Dixon L. (Baker) Mez (L.) A.Gray Poit. ex A.Rich. Burret L. Ruiz & Pav. [plastid genome only] Ruiz & Pav. A. Cunn ex Mart. R. ‌ P.Royen Douglas ex Benth. Ruiz & Pav. (Miers) Hook.f. L. L. var. var. P.Royen (Balf.) Pax^ L. (Nutt.) Torr. Labill. J.F.Macbr. Hildebr. & H.Wendl. Hildebr. Phil. [plastid genome data only] Siebold & Zucc. Makino (Aiton) Raf. P.Royen Mart. (Aubl.) Harling (Tussac) Herb. (Tussac) L. sp. boridiensis huonensis brassii cf. cf. cf. Species Arachnitis uniflora Asparagus officinalis Asplundia cf. venezuelensis Asplundia rigida Barbacenia elegans nobilis Bismarckia edulis Bomarea micrantha Brocchinia Burmannia alba Burmannia itoana Burmannia wallichii Butomus umbellatus Buxus microphylla Calamus caryotoides Calathea loeseneri Calectasia narragara Calochortus venustus Calycanthus floridus Campylosiphon purpurascens Campynema lineare Campynemanthe viridiflora Canna indica Carludovica palmata Carludovica palmata seifrizii Chamaedorea Chamaelirium luteum rhizopendulum Chlorophytum Colchicum autumnale Corsia Corsia Corsia Clintonia borealis pauciflora Croomia Cyclanthus bipartitus ( Gymnosiphon refractus Cyperus alternifolius Cypripedium calceolus Dasypogon Dasypogon bromeliifolius Dicranopygium atrovirens

160 Plastid genome — — — NC_009601 — — — NC_008456 EU016883–EU016962 — — — — — NC_023247 — — — — — — — — JX088660 — Givnish et al. (2010)* — NC_008590 Givnish et al. (2010)* NC_009600 — — JQ068951–JQ069028 — — JX051651 — — NC_010109 — — nad5 — — — — — — DQ406959 — — — — — — — — — KP420374 KP420370 KP420369 — — — — — — — — — — — — — — — — — — KP420371 — KP420372 KP420373 cob — — DQ916732 — — — DQ916732 — — — — — — — — — KP420342 KP420338 KP420337 — — — — — — — — — — — — — — — — — — KP420339 — KP420340 KP420341 matR KP420315 KP420324 KF298370 — KP420316 KF264495 KF264495 — — — KF298292 KF298294 KF298295 KF298297 — — KP420300 KP420296 KP420295 KP420317 — — KP420318 — — — KP420325 — — — — — — — KF197113 — KF197112 KP420297 — KP420298 KP420299 atpA EU421026 EU421027 AY277804 — EU421028 EU421029 EU421029 — — AF039248 KF298286 KF298288 KF298289 KF298291 — EU421049 KP420397 KP420394 KP420393 EU421031 AF039244 AY299775 EU421037 — AY299778 — EU421038 — — — AY299788 AY299789 AY299790 AY124519 KF197072 — KF298373 KP420395 — KP420408 KP420396 18S rDNA DQ786056 EU420997 EU186223 — DQ786089 DQ786090 DQ786090 — — AF206913 KF298366 KF298381 KF298367 KF298362 — AF309405 KP420421 KP420417 KP420416 EU420998 AF069200 AF387604 DQ786082 — AF168850 — DQ786057 — — — AF135204 AF206940 AF206942 AF168855 KF197095 — KF197093 KP420418 — KP420419 KP420420 Voucher (only applies to new sequences) Voucher Maas et al. 9620 (U) RBGE 19940649 878 (K) Wilkin RBGB 20000067-25 HBL20140588 RBGB 19832234- (LV) Merckx et al. 117 Sasidharan & Sujanapal 30476 (KFRI) Maas et al. 9614 (U) HBL20110165 HBL20140587 RBGB 20120193-65 Family Burmanniaceae Dioscoreaceae Dioscoreaceae Dioscoreaceae Dioscoreaceae Dioscoreaceae Dioscoreaceae Winteraceae Arecaceae Flagellariaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Liliaceae Burmanniaceae Colchicaceae Colchicaceae Colchicaceae Burmanniaceae Araceae Hanguanaceae Thismiaceae Heliconiaceae Heliconiaceae Asparagaceae Burmanniaceae Poaceae Asparagaceae Schisandraceae Orchidaceae Ixioliriaceae Petrosaviaceae Joinvilleaceae Triuridaceae Dasypogonaceae Triuridaceae Philesiaceae Araceae Liliaceae Liliaceae (Hook.) Miers Urb. Hemsl. Airy Shaw Gaudich. Letouzey (L’Hér.) Engl. (L’Hér.) R.Knuth Griggs (Torr.) J.M.Coult. (Torr.) R.Br. (L.) Caddick & Wilkin (L.) Caddick & P.Y.Li (Jack) Merr. Gaudich. ex Brongn. & Gris Merr. & Chun Merr. L.f. Nakai Cheek & S.A.Williams (Pall.) Schult. & Schult.f. Becc. Ruiz & Pav. L. (Muhl. ex Willd.) Raf. Willd.) (Muhl. ex Prain & Burkill (Hook.) J.C.Manning & Vinn. (Hook.) J.C.Manning & L. 1 L. 2 L. Stearn Prain & Burkill Ruiz & Pav. Lindl. R.Br. (Kunth) Cortés Baker L. sp. 1 sp. 2 sp. sp. Species Dictyostega orobanchoides althaeoides Dioscorea communis Dioscorea elephantipes Dioscorea prazeri Dioscorea rockii Dioscorea Dioscorea Drimys granadensis Elaeis oleifera Flagellaria indica cumingiana Freycinetia philippinensis Freycinetia Freycinetia Freycinetia Fritillaria taipaiensis Geomitra clavigera Gloriosa modesta Gloriosa superba Gloriosa superba Gymnosiphon bekensis Gymnostachys anceps Hanguana malayana Haplothismia exannulata Heliconia collinsiana Heliconia rostrata Hesperaloe parviflora gentianoides Hexapterella vulgare Hordeum Hosta ventricosa Illicium oligandrum Isotria verticillata Ixiolirion tataricum Japonolirion osense Joinvillea ascendens Kihansia Kingia australis Kupea martinetugei Lapageria rosea Lemna minor Lilium auratum Lilium henryi

161 Antiquities of the rainforest Plastid genome KC968977 KP462883 NC_008326 — — — — — EU016983–EU017063 NC_008336 — Givnish et al. (2010)* — — Givnish et al. (2010)* NC_008788 — NC_014056 Henriquez et al. (2014) NC_001320 — — — — — — — — — — — — — — — — NC_007499 — — — — nad5 — — — — — KP420375 — — — — — — — — — — — — DQ406996 — — — — — — — — — — — — — KP420376 — JX182963 — — — KP420377 — — cob — DQ916677 — — — KP420343 — — — — DQ916670 — — — — — — — DQ916648 — — — — — — — — — — — — — KP420344 — KP420357 — — — KP420345 — — matR — — — — KF258202 KP420301 — — — — KF264496 — — KF264497 — — AY289674 — AF197745 — KF298319 KF298320 KF298321 KF298322 KF298323 KF298324 KF298325 KF298326 KF298318 KF298327 KF298328 KF298330 KF298331 KF298369 — — — — KP420302 — EU281116 atpA — AY299797 — EU421039 KF258589 KP420398 EU421040 AY299804 — — AY299809 — AY299813 EU421041 — — NFU58833 — AY299816 — KF298305 KF298306 KF298307 KF298308 KF298309 KF298310 KF298311 KF298312 KF298304 KF298313 KF298314 KF298316 KF298317 KF264506 KP420409 AY299821 — AY124524 KP420399 AY299823 PRU58831 18S rDNA — AF206952 — DQ786091 KF264482 KP420431 AF309410 AF168861 — — AF309411 — AF168863 EU186219 — — AY012357 — AF293753 — KF298360 KF298359 KF298358 KF298357 KF298356 KF298355 KF298354 KF298364 KF298361 KF298353 KF298352 KF298350 KF298349 KF264490 KP420422 AF206987 — AM774510 KP420423 AF206990 AF206991 Voucher (only applies to new sequences) Voucher (NCU) 112 Chase, M.W. 499 (K) Chase, M.W. RBGB 19270660- Briggs, B.G. 10025 (NSW) RBGB 19850151- Family Liliaceae Liliaceae Magnoliaceae Nartheciaceae Cyclanthaceae Alstroemeriaceae Nartheciaceae Costaceae Musaceae Berberidaceae Nartheciaceae Bromeliaceae Orchidaceae Nartheciaceae Asparagaceae Nymphaeaceae Araceaceae Orchidaceae Araceae Poaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Pandanaceae Stemonaceae Petermanniaceae Petrosaviaceae Orchidaceae Poaceae Philesiaceae Philydrellaceae Arecaceae Maxim. Steenis Thouars Kurz ex Miq. Rchb.f. (L.) Huds. L. Kurz ex Miq. Blume (Poepp. ex Petersen) Maas Steyerm. J.F.Gmel. (Beer) L.B.Sm. Bory L. (R.Br.) Caruel (R.Br.) F.Muell. Spreng. Thunb. Ruiz & Pav. Bartlett J.H.Veitch Misonne Becc. Parkinson ex Du Roi Thunb. Roxb. Brongn. Mast. L. Colla Bory (Aiton) W.T.Aiton Ker Gawl. Wurmb dubius L. cf. sp. 1 sp. 2 ‘Gower Ramsey’ sp. sp. Species Lilium longiflorum Lillium superbum tulipifera Liriodendron Lophiola aurea Ludovia lancifolia Luzuriaga radicans Metanarthecium luteo-viride Monocostus uniflorus Musa acuminata Nandina domestica Narthecium ossifragum carolinae Neoregelia Neuwiedia veratrifolia Nietneria paniculata Nolina atopocarpa Nuphar advena Nypa fruticans Oncidium aquaticum Orontium Oryza sativa Pandanus baptistii Pandanus Pandanus furcatus Pandanus labyrinthicus Pandanus montanus Pandanus pacificus Pandanus purpurascens Pandanus Pandanus Pandanus stenophyllus Pandanus tectorius Pandanus utilis Pandanus veitchii Pentastemona sumatrana Petermannia cirrosa stellaris Petrosavia Phalaenopsis aphrodite Pharus Philesia magellanica pygmaea Philydrella Phoenix

162 Plastid genome NC_013991 — NC_008457 NC_008335 — — JX088662 Givnish et al. (2010)* — — — NC_006084 — — — — — — — — — — HM536959 NC_008602 — — NC_015891 — — — — — — — — — — — — — — nad5 — — — — — — — — — JX182965 KP420378 — — — — — — — — — — KP420379 KP420380 — — — — — — — — — — — DQ406941 — — — — — — cob — — — — — — — — — JX182924 KP420346 — — — — — — — — — — KP420347 KP420348 — — — — — KP420349 — — — — — — — — — — — — matR — — — — AF197743 EU281117 — — — — KP420303 — — KF298377 KF197109 KF197107 KF197106 KF298379 KF298371 KF258193 KF258195 KP420304 KP420305 — — DQ401396 — KF258200 KF258201 — — AY453112 — KP420326 DQ401377 KF264494 KP420319 KP420322 — KP420320 KP420321 atpA — AY299825 — — AY299827 AY299828 — — AY299830 AY299831 KP420400 — AY277803 KF197073 KF197070 KF197076 KF298368 KF197079 KF197078 KF258583 KF258584 — KP420401 — AY124509 AY124509 — KF264505 KF264504 EU421042 AY299843 AY299843 DQ859116 EU421043 EU421044 EU421045 EU421046 EU421047 AY299846 EU421050 AY299849 18S rDNA — AY012398 — — AF206995 AF206998 — — AF069228 — KP420432 — AF069202 KF197090 KF197088 KF197085 KF197084 KF197083 KF197082 KF264483 KF264485 KP420433 KP420424 — AF069220 AF069220 — KF264491 KF298348 DQ786087 AF069229 AF069229 AF168876 AF309397 DQ786086 DQ786085 EU421000 TPU42063 AH003649 DQ786081 AF309403 Voucher (only applies to new sequences) Voucher 187 (K) Chase, M.W. HBLA00716-04649 RBGB 19991503- HBL910374 Caddick 305 (K) Chase 6201 (K) Leiden BG 920520 Aizprua 2946 (LV) Garnock-Jones 2218 (WELTU) P. Family Arecaceae Arecaceae Piperaceae Platanaceae Tofieldiaceae Pontederiaceae Arecaceae Bromeliaceae Strelitziaceae Ripogonaceae Ripogonaceae Poaceae Scheuchzeriaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Triuridaceae Smilacaceae Smilacaceae Poaceae Typhaceae Typhaceae Araceae Stemonaceae Stemonaceae Dioscoreaceae Strelitziaceae Strelitziaceae Cymodoceaceae Taccaceae Taccaceae Taccaceae Taccaceae Taccaceae Costaceae Thismiaceae Thismiaceae (J.J.Sm.) Duyfjes Sonn. Spruce J.J.Sm. Planch. Engelm. (Mart.) Becc. L. F.Muell. Engl. L. ternatensis Kütz. L. Vollesen Seem. (Standl.) Jonker Benth. F.Muell. Benth. (L.) Schleid. L. L. var. (Hance) Drenth C.DC. Ker Gawl. Regel & K.Koch F.Muell. (L.) Moench Michx. Miers André Blume L. Blume sp. L. sp. sp. L.B.Sm. sp. sp. Species Phoenix dactylifera Phytelephas aequatorialis Piper cenocladum Platanus occidentalis Pleea tenuifolia Pontederia cordata Pseudophoenix vinifera Puya laxa Ravenala madagascariensis Ripogonum discolor Ripogonum elseyanum Saccharum officinarum Scheuchzeria palustris Sciaphila albescens Sciaphila ledermannii Sciaphila nana Sciaphila picta Sciaphila purpurea Sciaphila quadribullifera Sciaphila Seychellaria africana Smilax aspera Smilax china bicolor Sorghum eurycarpum Sparganium Sparganium polyrhiza Spirodela Stemona Stemona tuberosa Stenomeris dioscoreifolia nicolai Strelitzia Strelitzia Syringodium filiforme artocarpifolia Tacca chantieri Tacca integrifolia Tacca palmata Tacca plantaginea Tacca Tapeinochilos Thismia panamensis Thismia rodwayi

163 Antiquities of the rainforest Plastid genome — — Givnish et al. (2010)* — — — — — — — NC_002762 — — NC_013823 — — — NC_022715 NC_007957 NC_015899 NC_015894 JX088669 — — DQ069337–DQ069702; EU016681–EU016700 NC_001666 JX088661 — nad5 — — — — — — — — KP420381 JX182961 — — — — KP420382 KP420383 — — — — — — — JX182958 — — — — cob — — — — — KP420350 KP420351 — KP420352 DQ916682 — — — — KP420353 KP420354 KP420355 — — — — — — JX182921 — — — — matR — AF197744 — KF264493 — KP420306 KP420307 AF197725 KP420308 DQ110364 — KF258197 KF298374 — KF197104 KP420309 KP420310 — — — — — — — — — — — atpA AY299848 AY299851 — JN850565 AY277805 KP420402 KP420403 AF197716 KP420404 AF039253 — KF258585 KF258582 — KF197074 KP420405 KP420406 — — — — — AY299857 JX182888 — — — DQ859121 matK HM850600 EU604049 EU596520 EU604053 EU596516 KR002164 KR002165 — 18S rDNA AF207036 AF207043 — AF309395 AF309394 KP420434 KP420435 AF197586 KP420425 AF168879 — KF264487 KF264489 — KF197080 KP420426 KP420427 — — — — — AF207056 AF207057 — — — HQ445940 ITS JF420111 GQ888877 GQ888883 GQ888885 GQ888889 KM982697 KM982698 KM982699 Voucher (only applies to new sequences) Voucher HBL20077020 HBL967484 HBL20107053 HBLA86167 A.15.02 (Clusius garden) HBL A.15.04 (Clusius garden) HBL (only applies to new sequences) Voucher CM030 (L) CM032 (L) Wilde-Duyfjes & BEE de Wilde WJJO de 18791 (L) Family Tecophilaeaceae Tofieldiaceae Commelinaceae Dioscoreaceae Dioscoreaceae Liliaceae Liliaceae Juncaginaceae Melanthiaceae Melanthiaceae Poaceae Triuridaceae Triuridaceae Typhaceae Velloziaceae Melanthiaceae Melanthiaceae Melanthiaceae Vitaceae Araceae Araceae Haemodoraceae Xeronemataceae Melanthiaceae Asparagaceae Poaceae Zingiberaceae Zosteraceae Family Fabaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Leyb. (Gand.) Prain Willd. (H.Perrier) Caddick & Wilkin (H.Perrier) Caddick & Blume 2 Blume 3 Raf. W.R.B.Oliv. Blume 1 L. (Michx.) Salisb. Maas Aubl. Gaertn. Baker (L.) Wahlenb. Griff. (Benth.) Hartog & Plas (Hegelm.) Hegelm. Raf. (Oliv. Ex Chodat) Stapf (Oliv. (Pursh) Nutt. O.Loes. L. (Andrews) Willd. L. Roezl ex Ortgies G.Don L. (Balf.) Talbot ex Hook.f. Talbot (Balf.) L. Miers L. (Thunb.) Hook. L. L. Species cyanocrocus Tecophilaea calyculata Tofieldia ohiensis Tradescantia sempervirens Trichopus zeylanicus Trichopus formosana Tricyrtis hirta Tricyrtis maritimum Triglochin cuneatum Trillium grandiflorum Trillium aestivum Triticum hexophthalma Triuris hyalina Triuris latifolia Typha elegans Vellozia album Veratrum nigrum Veratrum patulum Veratrum vinifera Vitis australiana Wolffia lingulata Wolffiella Xiphidium caeruleum callistemon Xeronema tenax Xerophyllum schidigera Yucca Zea mays Zingiber spectabile Zostera marina *This study reports the accession numbers for individual genes in the plastid genome data 4 Chapter Species Acacia longifolia afzeliana Atroxima floribunda Bredemeyera Carpolobia alba Comesperma esulifolium Epirixanthes elongata Epirixanthes elongata Epirixanthes elongata

164 trnL-F AF508509 FJ628602 rps4 X84109 JQ274289 rbcL HM640478 JQ273896 matK HM640592 JF972927 cob AY832076 JQ421522 matK KR002166 KR002167 KR002168 KR002169 KR002170 KR002171 KR002172 KR002173 KR002174 KR002175 KR002176 EU604051 AY386881 EU604047 KR002177 KR002178 EU604041 KR002179 AY386842 FR865062 EU362027 JQ588826 JQ588832 EU604043 EU596518 HQ593391 EU604034 EU604035 EU604046 KR002180 KR002181 JQ588835 JX517755 EU604029 EU604044 atpA AY299703 AY299707 ITS KM982700 KM982701 KM982702 KM982703 KM982704 KM982705 KM982706 KM982707 KM982708 KM982709 KM982710 GQ888891 AF053142 GQ888909 KM982711 KM982712 GQ888923 KM982713 GQ888937 GQ888939 GQ888941 GQ888943 GQ888981 GQ888988 GQ888995 GQ888996 AJ812649 GQ889040 GQ889042 KM982714 KM982715 GQ889047 GQ889049 GQ889051 GQ889055 18S rDNA AF206841 JN797262 Voucher (only applies to new sequences) Voucher CM013 (L) CM004 (L) CM006 (L) CM001-1 (L) CM001-2 (L) CM002-1 (L) CM002-2 (L) CM007-1 (L) CM007-2 (L) CM009 (L) (L) CM011 139 (K) Victor 281 (K) Chase, M.W. 614 (K) Tribsch Schönswetter & Wilde-Duyfjes & BEE de Wilde WJJO de 21409 (L) 78 6390 (L) K’tung (only applies to new sequences) Voucher Family Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Fabaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Polygalaceae Family Asparagaceae Amaryllidaceae Fresen. T.Wendt Lour. (L.) S.F.Blake L. Chodat ex T.Durand & Pittier T.Durand Chodat ex J.J.Sm. T.Wendt 3 T.Wendt 5 T.Wendt Kunth Nutt. Schltr. T.Wendt 1 T.Wendt 2 T.Wendt 4 T.Wendt 6 T.Wendt 7 T.Wendt 8 T.Wendt 9 T.Wendt L. Kunth Aubl. L. P.Royen & Steenis P.Royen (L.) Dumort. Levyns Benth. L. Rupr. (L.) DC. Schkuhr L. L. L. sp. sp. sp. Species Epirixanthes kinabaluensis Epirixanthes pallida Epirixanthes pallida Epirixanthes pallida Epirixanthes pallida Epirixanthes pallida Epirixanthes pallida Epirixanthes pallida Epirixanthes pallida Epirixanthes pallida Epirixanthes papuana Eriandra fragrans Medicago sativa Monnina xalapensis Muraltia karroica Nylandtia spinosa Polygala alpicola Polygala amara Polygala californica Polygala chamaebuxus Polygala comosa Polygala costaricensis Polygala longicaulis Polygala myrtifolia Polygala paniculata Polygala pauciflora Polygala senega Polygala violaceae Polygala vulgaris Salomonia cantoniensis Salomonia ciliata Securidaca diversifolia Securidaca longipedunculata Securidaca retusa Xanthophyllum 5 Chapter Species Agave Allium

165 Antiquities of the rainforest trnL-F AJ290255/ AJ290289 JX464334 AJ290285/ AJ290319 AF508514 AB933518 AB933516 HM459530 GQ982571 HM459535 — AJ290260/ AJ290294 AY430700/ AY430629 AF519913 AJ409572 KC428478 AJ409580 AY557224 EF397919 FJ707507 AJ232440/ AJ290315 AF117014/ AF117039 AJ409598 — AB933501 AJ247494/ AJ247495 AJ409616 AJ409574 AJ290265/ AJ290299 FJ707513 JQ670618 HM459501 EU939491 AJ290283/ AJ290317 AJ290280/ AJ290314 rps4 JQ274300 JQ274292 Z68232 JQ274297 JQ274301 — — Z68234 — — — — — AJ409022 JQ274312 Z68237 — — — AJ409053 JQ274284 JQ670293 — — JQ274316 AJ409045 Z68256 JQ274302 — AJ409042 — FM253430 Z68243 AJ409051 rbcL AJ512283 JQ273899 AF206736 HQ182417 JQ273908 AJ512314 AF307906 GQ381614 Z73694 AF206741 AJ512323 AF275986 AF074119 AJ309660 JQ273919 JX903214 EF370100 AB519785 FJ707498 HM640534 JQ273891 JQ670533 KF419090 AJ512324 JQ273923 Z77285 HM850030 AJ512318 L05036 JQ670541 HM640539 D28332 JX903219 HM640543 matK AY323724 JX903555 AJ579933 AB646503 JX903600 AJ511415 AY368372 GQ381376 JX903609 AY368373 AJ511414 JN417362 AF263635 AJ579938 JX903595 JX903624 AY557208 AB519772 AB088787 AB088785 JQ276386 AJ579950 KF419099 AJ511418 JQ276418 AJ579955 HQ394384 AY323714 JX903612 AJ580620 JX903619 HM574678 AJ579963 AJ579965 cob JQ421547 JQ421532 JQ421596 JQ421544 JQ421548 JQ421549 JQ421555 JQ421597 DQ916655 DQ916656 JQ421550 KP420329 DQ916664 JQ421598 JQ421613 JQ421599 DQ916665 DQ916658 DQ916657 DQ859087 JQ421601 DQ916666 JQ421551 JQ421565 JQ421602 JQ421603 JQ421552 DQ916659 JQ421595 DQ916661 JQ421604 JQ421605 DQ916731 atpA JQ421658 JQ421646 JQ421699 AF197713 JQ421659 AY299721 AY299722 JQ421700 AY299727 AY299728 JQ421660 KP420387 AY299738 JQ421701 JQ421715 JQ421702 AY299755 AY299756 AY299760 DQ859075 JQ421704 AY299766 JQ421661 JQ421672 JQ421705 JQ421706 JQ421662 AY299780 JQ421698 AY299784 DQ401300 JQ421708 AY299789 18S rDNA JQ283935 JQ283909 AF206854 GU217543 JQ283940 HM640760 HM640762 — AF206869 AF206872 AF206876 KP420411 — — JQ283903 AJ489273 AF069208 AB027309 GQ497575 HM640766 JQ283933 — — HM640759 JQ283932 EU816707 L54062 JQ283936 HM640769 — HM640771 JQ283937 L54063 HM640775 Voucher (only applies to new sequences) Voucher Family Xanthorrhoeaceae Amaryllidaceae Iridaceae Asparagaceae Xanthorrhoeaceae Xanthorrhoeaceae Asteliaceae Iridaceae Blandfordiaceae Boryaceae Xanthorrhoeaceae Liliaceae Orchidaceae Iridaceae Asparagaceae Iridaceae Orchidaceae Orchidaceae Xanthorrhoeaceae Doryanthaceae Asparagaceae Iridaceae Orchidaceae Xanthorrhoeaceae Asparagaceae Iridaceae Iridaceae Xanthorrhoeaceae Xanthorrhoeaceae Iridaceae Hypoxidaceae Iridaceae Iridaceae Ixioliriaceae (L.) N.E.Br. L. L. (Hook.) T.Moore (Pall.) Schult. & Schult.f. Corrêa sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. Species Aloe Amaryllis belladonna Aristea Asparagus Asphodeline Asphodelus Astelia Babiana Blandfordia Borya Bulbine Calochortus Calopogon Chasmanthe aethiopica Cordyline Crocus Cypripedium calceolus Dendrobium Dianella Doryanthes excelsa Echeandia Ennealophus Epipactis Eremurus Eriospermum Geosiris Gladiolus Haworthia Hemerocallis Herbertia Hypoxis Iris Isophysis tasmanica Ixiolirion tataricum

166 trnL-F AJ409617 AJ290267/ AJ290301 HM459536 GQ294041 AJ409593 AY557216 AJ290287/ AJ290321 JQ670631 AJ409432 AY014586 JX287016 EU939523 AY828229 DQ500904/ DQ500938 JQ670643 GU945057 AJ290276/ AJ290310 AJ409594 AY699229 AJ409577 AY557223 AJ290286/ AJ290320 AB933523 EU092602 rps4 AJ409047 JQ274303 — Z68258 JQ670313 — Z68266 JQ670317 — — HQ183091 Z68259 JQ274305 JQ274287 JQ670328 X84144 AJ409049 JQ670350 — AJ409023 — AJ409046 JQ274328 DQ069456 rbcL AJ309667 JQ273910 Z77313 GQ285140 AY298842 AF074200 Z77289 JQ670552 AJ542396 AF074203 HQ182443 AJ277879 HQ182444 JQ273894 JQ670565 KJ719883 HM640544 AJ309680 AY465711 AJ30965 AF074242 AJ277880 JQ273935 DQ069504 matK AJ579966 JX903605 AY368376 AJ579971 AJ579972 AY557209 AJ580622/ AJ580621 HQ606813 HE858506 JN895683 JX286875 AJ580624/ AJ580623 JX903615 JQ276389 KF577210 KF782882 HM640661 AJ579987 JN417361 AJ579990 FJ816098 AJ580628/ AJ580627 JX903650 AB088789 cob — JQ421553 JQ421610 JQ421606 DQ916662 JQ421619 JQ421607 JQ421608 — — JQ421635 — JQ421581 DQ859079 DQ916663 KP420305 JQ421625 JQ421609 KP420306 — — JQ421630 DQ859084 matR na — — — na — na na — atpA — AY299792 JQ421713 JQ421709 AY299812 AY299813 JQ421710 — — — KF298316 — JQ421685 DQ859068 AY299837 KP420401 AY299848 JQ421711 KP420403 — FJ425825 — AF039250 DQ859073 atpA na EU421002 na FJ215772 EU421003 EU421004 EU421005 na EU421006 18S rDNA — JQ283934 GQ497576 — — AF168863 — — — AF135194 KF298350 — JQ283929 JQ283922 — KP420433 AF207036 — KP420434 — FJ425762 — JQ283930 AF168882 18S rDNA na EU420988 na FJ215766 EU420989 DQ786083 EU420991 na EU420992 Voucher (only applies to new sequences) Voucher (only applies to new sequences) Voucher Family Iridaceae Xanthorrhoeaceae Lanariaceae Iridaceae Iridaceae Orchidaceae Iridaceae Iridaceae Orchidaceae Orchidaceae Pandanaceae Iridaceae Xanthorrhoeaceae Asparagaceae Iridaceae Smilacaceae Tecophilaeaceae Iridaceae Melanthiaceae Iridaceae Orchidaceae Iridaceae Xanthorrhoeaceae Asparagaceae Family Thismiaceae Thismiaceae Thismiaceae Thismiaceae Thismiaceae Thismiaceae Thismiaceae Thismiaceae Thismiaceae Mill. Leyb. H. Maas (Lam.) G.J.Lewis T.Franke, Sainge & Agerer Sainge & T.Franke, Sainge & T.Franke Dauby & Stévart Cheek (Engl.) Schltr. Sainge & Kenfack^ (Ker Gawl.) Baker (E.Mey. ex C.Presl) Goldblatt (E.Mey. Sainge & Franke (L.f.) DC. J.R.Forst. & G.Forst. (L.) Thunb. Bory (L.) T.Durand & Schinz T.Durand (L.) sp. (G.J.Lewis) Goldblatt sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. sp. Species Klattia flava Kniphofia Lanaria lanata Moraea Neomarica Neuwiedia Nivenia corymbosa Olsynium junceum Ophrys Orchis Pandanus utilis Patersonia Phormium tenax Polianthes Sisyrinchium angustifolium Smilax cyanocrocus Tecophilaea pavonia Tigridia Tricyrtis unguicularis Tritoniopsis Vanilla maura Witsenia Xanthorrhoea Yucca Species amiettii Afrothismia foertheriana Afrothismia fungiformis Afrothismia gabonensis Afrothismia gesnerioides Afrothismia hydra Afrothismia korupensis Afrothismia pusilla Afrothismia winkleri Afrothismia

167 Antiquities of the rainforest matR — KF264492 na — na na na — na na na na na na na na na na na na na na na na na na na na na na atpA AY299706 FJ215780 EU421007 EU421008 GQ469514 GQ469515 EU421009 EU421012 EU421013 — EU421014 EU421015 EU421016 GQ469518 — EU421017 — na AY299732 EU421019 EU421021 — EU421022 EU421023 EU421024 EU421025 EU421026 EU421027 FJ215775 FJ215779 18S rDNA EU186221 AB679359 DQ786034 DQ786074 DQ786072 AF168827 DQ786065 DQ786061 DQ786071 U59947 DQ786077 EU420994 DQ786078 DQ786063 na DQ786062 DQ786079 na AF309401 EU420995 GQ469513 DQ786075 DQ786068 DQ786069 EU420996 DQ786038 DQ786056 EU420997 AF069203 FJ215769 Voucher (only applies to new sequences) Voucher Family Nartheciaceae Nartheciaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Dioscoreaceae Dioscoreaceae Dioscoreaceae Baker Benth. (Hook.) Miers Jonker (Miers) Benth. & Hook.f.^ R.Knuth Oliv. Schltr. Becc. (C.H.Wright) Jonker (C.H.Wright) Becc. Pobég. Lipsky (Miers) Hook.f. L. Hieron. & Schltr. L. Ridl. (Walter ex J.F.Gmel.) Mart. ex J.F.Gmel.) (Walter Beauverd (Miers) Thwaites L. Sol. ex R.Br. Mart. Makino Mart. Mart. (Nutt.) Barnhart ex Small L. Small Species Aletris farinosa Aletris lutea Apteria aphylla Burmannia alba Burmannia bicolor Burmannia biflora Burmannia capitata Burmannia congesta Burmannia damazii Burmannia disticha Burmannia flava Burmannia hexaptera Burmannia itoana Burmannia juncea Burmannia kalbreyeri Burmannia latialata Burmannia ledermannii Burmannia longifolia Burmannia lutescens Burmannia madagascariensis Burmannia oblonga Burmannia pusilla Burmannia stuebelii Burmannia wallichii Campylosiphon purpurascens Gymnosiphon refractus Dictyostega orobanchoides althaeoides Dioscorea bulbifera Dioscorea caucasica Dioscorea

168 matR KF298370 na na KF264495 na na na na na na na na na na na na na na na — KF264496 KF264497 — na DQ401377 KF264494 na na na na na na na na na na na na na na atpA AY277804 FJ215777 EU421028 EU421029 FJ215778 FJ215776 EU421030 EU421031 na EU421032 EU421033 na EU421034 EU421035 EU421036 — — EU421037 EU421038 EU421039 AY299809 EU421041 EU421042 EU421043 EU421044 EU421045 JN850559 JN850560 JN850561 JN850563 EU421048 KF692539 EU421049 na KF692543 na EU421050 KF692542 EU421051 FJ215770 18S rDNA EU186223 FJ215767 DQ786089 DQ786090 FJ215768 DQ786088 AF309402 EU420998 na DQ786040 DQ786054 na DQ786045 DQ786051 DQ786047 DQ786050 U59942 DQ786082 DQ786057 DQ786091 AB679370 EU186219 DQ786087 AF309397 DQ786086 DQ786085 EU420999 EU421000 DQ786084 U42063 AF309404 KF692533 AF309405 na KF692534 na DQ786081 KF692536 DQ786080 FJ215764 Voucher (only applies to new sequences) Voucher Maas 10504 (L) Merlijn Jocqué (219) Family Dioscoreaceae Dioscoreaceae Dioscoreaceae Dioscoreaceae Dioscoreaceae Dioscoreaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Burmanniaceae Thismiaceae Burmanniaceae Nartheciaceae Nartheciaceae Nartheciaceae Dioscoreaceae Taccaceae Taccaceae Taccaceae Taccaceae Taccaceae Taccaceae Taccaceae Thismiaceae Thismiaceae Thismiaceae Thismiaceae Thismiaceae Thismiaceae Thismiaceae Thismiaceae Thismiaceae Thismiaceae ^ s Snelders & Maas Urb. (Benth.) Benth. & Hook.f. Planch. (H.Karst.) Urb. Airy Shaw (Benth.) Benth. & Hook.f. Snelders & Maas (Benth.) Hutch. Gleason C.Hunt, G.Steenbeeke & (Benth.) Urb. Blume (L’Hér.) Engl. (L’Hér.) (L.) Huds. Snelders & Maas (L.) Kuntze Letouzey K.R.Thiele (L.) Caddick & Wilkin (L.) Caddick & Steyerm. Seem. Sheng Z.Yang, R.M.K.Saunders & Sheng Z.Yang, (Standl.) Jonker Eckl. Becc.) F.Muell. Baker (Hance) Drenth Prain & Burkill Ker Gawl. cymosus F.Muell. Makino ex Miyabe P.E.Berry & C.L.Woodw. P.E.Berry P.Y.Jiang & T.H.Hsieh P.Y.Jiang Prain & Burkill André Ker Gawl. Blume Becc. cf. (Cheeseman) N. Pfeiff. Species communis Dioscorea elephantipes Dioscorea prazeri Dioscorea rockii Dioscorea sylvatica Dioscorea tokoro Dioscorea Gymnosiphon aphyllus Gymnosiphon bekensis Gymnosiphon brachycephalu Gymnosiphon breviflorus Gymnosiphon capitatus Gymnosiphon Gymnosiphon divaricatus Gymnosiphon longistylus Gymnosiphon minutus Gymnosiphon recurvatus Gymnosiphon suaveolens Haplothismia exannulata gentianoides Hexapterella Lophiola aurea Narthecium ossifragum Nietneria paniculata Stenomeris dioscoreifolia artocarpifolia Tacca chantieri Tacca integrifolia Tacca leontopetaloides Tacca palmata Tacca palmatifida Tacca plantaginea Tacca Thismia aseroe Thismia clavarioides Thismia clavigera ( Thismia hillii Thismia huangii Thismia megalongensis V.Merckx^ Thismia panamensis Thismia rodwayi Thismia taiwanensis C.J.Hsu foetida Tiputinia

169 Antiquities of the rainforest nad1b-c na na na na matR KF264493 na matR na na na na trnL AF102375 AJ490190 AF102377 KF501344 EU834128 AF102383 AJ512341 AF102388 AF102389 AF402247 AJ490194 — AF102398 AY251746 AJ315225 GQ244819 AJ315186 AY251745 AJ408000 AJ242606 AF152637 AF102415 — atpA JN850565 AY277805 atpA na na na na matK AJ388206/ AJ388137 JX518238 AJ388208/ AJ388139 KF496065 KF496071 AJ388210/ AJ388141 AJ512343/ AJ512342 AJ388211/ AJ388142 AJ388212/ AJ388143 JN894719 JQ587941 — AJ388215/ AJ388146 AJ011438/ AJ010509 KC861240 AJ388218/ AJ388149 KC861276 AJ388219/ AJ388150 AJ011441/ AJ010512 AJ388220/ AJ388151 FJ905360 AJ011443/ AJ010514 — 18S rDNA AF309395 AF309394 18S rDNA na na na na ITS DQ449914 DQ449916 DQ449915 EU812470 EU812473 EU812474 FJ232556 EU709787 AJ489867 KC535851 EU709790 AJ489869 EU709791 AJ489871 AF346008 AJ580552 DQ317493 EU709780 GU251021 AJ242613+ AJ242614 KC535853 AJ489875 AJ489874 Voucher (only applies to new sequences) Voucher (only applies to new sequences) Voucher Pillon 585 Vanuatu Maas 10507 Jourdan et al. 1 New Caledonia (228) 440 PNG (L) SPL (only applies to new sequences) Voucher Family Trichopodaceae Trichopodaceae Family Triuridaceae Triuridaceae Triuridaceae Triuridaceae Family Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Rubiaceae Gentianaceae Gentianaceae (Aubl.) Struwe, S.Nilsson & (Kunth) Gilg Baker (Turcz.) Toyok. (Turcz.) Schltr. Gilg (Forrest) Holub (C.B.Clarke) Klack. (H.Perrier) Caddick & Wilkin (H.Perrier) Caddick & Rafn Oliv. (Rottb.) Toyok. Gaertn. C.B.Clarke (Aubl.) Pulle (Michx.) Muhl. Planch. L. Aubl. Maas (L.) Britton, Sterns & Poggenb. (Vahl) R.Br. ex Roem. & Schult. R.Br. (Vahl) (Aubl.) Knobl. (Michx.) Raf. ex Barton dolichostyla cf. sp. 2 sp. 3 Species sempervirens Trichopus zeylanicus Trichopus Species Sciaphila Sciaphila polygyna Sciaphila Sciaphila Species Anthocleista amplexicaulis Anthocleista grandiflora Anthocleista vogelii Bartonia paniculata Bartonia verna Bartonia virginica Bisgoeppertia sp. Calolisianthus sp. Canscora diffusa Centaurium erythraea Chelonanthus alatus Chelonanthus angustifolius Chelonanthus purpurascens V.A.Albert baccifera Chironia Comastoma pulmonarium Comastoma tenellum Comastoma traillianum Coutoubea spicata speciosa Crawfurdia Curtia tenuifolia Emmenopterys henryi Eustoma sp. Exacum paucisquamum

170 trnL AF102418 FJ014155 AF102419 AF102420 AF102421 JX217774 AF102428 AB453085 KJ947654 AF102434 KM226748 X77882 KJ947678 KM226741 GQ864091 KM226747 AB453084 KJ947645 AB453094 AB453073 KM226749 AB453068 AB453103 KJ947675 GQ245001 X77872 AJ408006 AF102401 X77877 X77885 EU834123 AB453104 GQ245006 AJ408008 matK AJ388225/ AJ388156 — AJ388226/ AJ388157 AJ388227/ AJ388158 AB925025 AB925042 AJ429322 AJ388235/ AJ388165 KC861278 KJ746189 KC861280 KF536676 KJ947443 GQ434141 JN162098 KM226692 JN162100 KJ947408 JN162094 KM226689 KC861282 KJ947423 JN162095 KJ947440 JN896137 AJ295335/ AJ295334 KC935906 AJ388232/ AJ388162 JN895553 AJ406363/ AJ406335 AJ406341/ AJ406369 AJ406343/ AJ406371 KC861288 AJ388234/ AJ388164 ITS AJ489908 FJ666024 DQ449918 FJ232579 FJ232574 FJ232577 DQ358881 AJ580549 DQ398637 DQ398635 DQ398633 KC535854 DQ398629 DQ398653 GQ864018 DQ398639 GQ864022 DQ398643 GQ864016 DQ398642 FJ980363 DQ398641 GQ864020 DQ398627 AJ580573 AJ580560 AF346014 AY136498 AF346005 AJ580566 EU812469 AY136499 AF346007 AJ580551 Voucher (only applies to new sequences) Voucher Family Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gelsemiaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gilg) Kissling^ (L.) J.St.-Hil. (L.) Small ^ (L.) Börner (Willd.) Börner (Willd.) (Hook.f.) Holub Pall. Maxim. ex Kusn. Duthie ex Burkill L. (Froel.) Ma Kitag. (L.) Harry Sm. A.Gray ex Benth. (L.) Ma Roxb. Maxim. Harry Sm. Franch. ex Hemsl.^ (Hegetschw. & Heer) Dostál ex (Hegetschw. (G.Forst.) Holub (Bunge) Holub Fisch. Beck Jack Burkill Burkill Roxb. L. King ex Hook.f. Roxb. King ex Hook.f. Pall. Bunge Species Exacum tetragonum Exochaenium oliganthum ( Fagraea berteroana Fagraea elliptica Fagraea fragrans Fagraea racemosa Gelsemium sempervirens Gentiana asclepiadea Gentiana crassicaulis Gentiana cruciata Gentiana dahurica Gentiana dinarica Gentiana lhassica Gentiana macrophylla Gentiana manshurica Gentiana officinalis Gentiana rigescens Gentiana robusta Gentiana scabra Gentiana siphonantha Gentiana straminea Gentiana tibetica Gentiana triflora Gentiana waltonii Gentianella amarella Gentianella aspera Skalický, Chrtek & Gill Gentianella azurea Gentianella bellidifolia Gentianella campestris Gentianella germanica Gentianella quinquefolia Gentianella saxosa Gentianopsis barbata Gentianopsis ciliata

171 Antiquities of the rainforest trnL KJ947663 AF102448 AJ315228 GQ245087 AM117371 AF102454 AF102457 AF102458 GQ864096 AJ490241 AJ490242 FJ014163 AF152680 AF102470 AF102471 AF102473 AJ242608 AF102479 FJ014170 KC479277 AJ408013 AJ315212 KF564020 AJ408019 AJ315229 AJ315224 AF102498 FJ014193 AF102495 matK KC861243 AJ011451/ AJ010522 KC861247 KC935910 JF954409 AJ011452/ AJ010523 AJ388245/ AJ388175 KC861245 JN162102 AJ388248/ AJ388178 AJ388182 AJ011454/ AJ010525 JQ626556 AJ388253/ AJ388183 AJ388254/ AJ388184 AJ388255/ AJ388185 AJ388257/ AJ388187 AJ011456/ AJ010527 AJ388259/ AJ388189 JF270955 KC861264 JF956567 KC861267 KC861257 KC861270 JF956585 AJ388268/ AJ388198 AJ011460/ AJ011434 AJ388265/ AJ388195 ITS AF346012 EU709782 AF346011 AF346010 KC535861 EU709799 EU528139 AY858679 AY562174 AJ489916 AJ489917 FJ666017 KC535862 DQ449919 DQ449923 KC535863 AJ242612/ AJ242615 KC535864 FJ666000 JF938049 JF978820 JF978824 AF251122 JF978830 JF978834 JF978836 EU709802 AJ489923 FJ232583 Voucher (only applies to new sequences) Voucher Family Gentianaceae Gentianaceae Gentianaceae Gentianaceae Rubiaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Rubiaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Loganiaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae - (Diels & Gilg) Fernald (Baker) Klack. Urb. & Ekman (Baker) N.E.Br. (Franch.) T.N.Ho & S.W.Liu T.N.Ho (Franch.) C.B.Clarke (C.B. Clarke) Harry Sm. (L.) Fr. ex Fernald (L.) Fr. Gilg & Gilg-Ben. (Desr.) Griseb. (Desr.) Maguire & Pires (Sw.) Struwe & K.R. Gould (Sw.) (Schinz) Gilg Maxim. Burkill Malme (Rudge) Schult. (L.) E.Mey. (Siebold & Zucc.) Hook. f. & Thom (Siebold & Zucc.) Hook. f. A. Robyns & T.S. Elias T.S. A. Robyns & Maxim. (L.) Schinz Mart. D.Don Hook. Hemsl. Franch. Aubl. Species Halenia elliptica Lisianthius jefensis Lomatogonium macranthum Lomatogonium rotatum Luculia pinceana domingensis Macrocarpaea rubra Macrocarpaea Megacodon stylophorus Metagentiana rhodantha pubescens Microrphium Ornichia madagascariensis Orphium frutescens Posoqueria latifolia Potalia amara Potalia resinifera Pycnosphaera buchananii Saccifolium bandeirae Schinziella tetragona Sebaea exacoides Strychnos sp. Swertia bimaculata son ex C.B. Clarke Swertia decora Swertia erythrosticta Swertia punicea Swertia tetraptera Swertia yunnanensis Symbolanthus frigidus carinatus Tachiadenus ulugurensis Urogentias

172 trnL AF102497 — — — — — — — — — — — — AJ242607 matK KC861249 — — — — — — — — — — — — AJ388267/ AJ388197 ITS AF251123 KC535866 KC535867 KC535868 KC535869 KC535870 na KC535871 KC535873 KC535874 KC535875 KC535876 KC535878 KC535879 Voucher (only applies to new sequences) Voucher Maas 10469 (L) Family Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Gentianaceae Miq. Baker Franch. Splitg. Splitg. (Schltdl. & Cham.) Ruyters Maas Griseb. Griseb. Progel Aubl. (Jacq.) Pers. Splitg. Guiling ex Hook. Aubl. Species baillonii Veratrilla aphylla Voyria aurantiaca Voyria caerulea Voyria clavata Voyria corymbosa Voyria flavescens Voyria obconica Voyria parasitica Voyria primuloides Voyria rosea Voyria tenella Voyria tenuiflora Voyria parviflora Voyriella April 2015 The Plant List, 21 All names (except noted^) verified with

173 Antiquities of the rainforest

174 Appendix A.2. Protein-coding genes retained in plastomes of Arachnitis uniflora and Corsia cf. boridiensis (Ψ, interrupted reading frame, probable pseudogene) (Chapter 3). Arachnitis uniflora Corsia cf. boridiensis ATP synthase atpI (Ψ) Photosystem II psbC (Ψ) Photosystem I psaB (Ψ) Ribosomal proteins (small) rps2, rps3, rps4, rps7, rps8, rps2, rps3, rps4, rps7, rps8, rps11, rps12, rps14, rps18, rps11, rps12, rps14, rps15, rps19 rps18, rps19 Ribosomal proteins (large) rpl2, rpl14, rpl16, rpl20 rpl2, rpl14, rpl16, rpl20, rpl22, rpl32, rpl33, rpl36 (Ψ) Ribosomal RNAs 4.5S, 5S, 16S, 23S 4.5S, 5S, 16S, 23S Serine protease clpP clpP Fatty acid synthesis accD accD Group II intron maturase matK Misc. ycf1, ycf2, ccsA (Ψ)

175 Antiquities of the rainforest

Appendix A.3. Voucher information of Arbuscular Mycorrhizal Fungi obtained from plant taxa. For each fungal sequence, the host plant taxon, OTU assignment and collection number are given. Furthermore, sequences obtained from cloning and GenBank numbers are indicated (Chapter 4). Taxon OTU Collection number Cloning? (new 18s rDNA (new sequences sequences only) only) Epirixanthes elongata symbiont 1 3 CM032_4494-8G Yes KR002150 Epirixanthes elongata symbiont 2 3 CM030_4584- No KR002146 AM58 Epirixanthes elongata symbiont 3 3 CM032_4494-8F Yes KR002149 Epirixanthes elongata symbiont 4 3 CM030_4583- No KR002147 AM57 Epirixanthes elongata symbiont 5 3 CM032_4494- No KR002148 AM17 Epirixanthes elongata symbiont 6 7 CM032_4585-4E Yes KR002153 Epirixanthes elongata symbiont 7 7 CM032_4585-4C Yes KR002152 Epirixanthes elongata symbiont 8 8 CM032_4585-4A Yes KR002151 Epirixanthes elongata symbiont 9 9 CM032_4585- No KR002145 AM59/84 Epirixanthes kinabaluensis symbiont 1 1 CM013_4582-3D Yes KR002154 Epirixanthes kinabaluensis symbiont 2 14 CM013_4582- No KR002144 AM56/83 Epirixanthes pallida symbiont 1 2 CM001_4560-1C Yes KR002156 Epirixanthes pallida symbiont 10 10 CM001_4560- No KR002142 AM39/81 Epirixanthes pallida symbiont 11 10 CM001_4560-1F Yes KR002157 Epirixanthes pallida symbiont 12 10 CM001_4560-1H Yes KR002158 Epirixanthes pallida symbiont 13 11 CM001_4578- No KR002137 AM52 Epirixanthes pallida symbiont 14 12 CM004_4569- No KR002140 AM48 Epirixanthes pallida symbiont 15 13 CM004_4592- No KR002134 AM69/78 Epirixanthes pallida symbiont 2 5 CM009_4593- No KR002133 AM79 Epirixanthes pallida symbiont 3 5 CM004_4580- No KR002135 AM54 Epirixanthes pallida symbiont 4 5 CM004_4497- No KR002143 AM33 Epirixanthes pallida symbiont 5 5 CM001_4562- No KR002141 AM41 Epirixanthes pallida symbiont 6 5 CM001_4577- No KR002138 AM51 Epirixanthes pallida symbiont 7 5 CM001_4576- No KR002139 AM50 Epirixanthes pallida symbiont 8 7 CM002_4579- No KR002136 AM53/82 Epirixanthes pallida symbiont 9 10 CM001_4560-1A Yes KR002155

176 Epirixanthes papuana symbiont 1 4 CM011_4581- No KR002131 AM55/85 Epirixanthes papuana symbiont 2 4 CM011_4491- No KR002132 AM14 Epirixanthes papuana symbiont 3 5 CM011_4581-2E Yes KR002161 Epirixanthes papuana symbiont 4 6 CM011_4581-2A Yes KR002159 Epirixanthes papuana symbiont 5 6 CM011_4581-2G Yes KR002162 Epirixanthes papuana symbiont 6 6 CM011_4581-2H Yes KR002163 Epirixanthes papuana symbiont 7 6 CM011_4581-2C Yes KR002160 Polygala alpestris symbiont 1 15 HE615151 Polygala amara ssp. brachyptera symbiont 1 2 HE615152 Polygala amara ssp. brachyptera symbiont 2 2 HE614286 Polygala amara ssp. brachyptera symbiont 3 16 HE615140 Polygala amara ssp. brachyptera symbiont 4 C 2 HE614290 Polygala amarella symbiont 1 16 HE615143 Polygala amarella symbiont 2 16 HE615153 Polygala calcarea symbiont 1 2 HE615141 Polygala calcarea symbiont 2 2 HE615142 Polygala calcarea symbiont 3 13 HE614283 Polygala comosa symbiont 1 13 HE614289 Polygala myrtifolia symbiont 1 2 HE615149 Polygala myrtifolia symbiont 2 16 HE614284 Polygala myrtifolia symbiont 3 18 HE615150 Polygala rupestris symbiont 1 17 HE615147 Polygala serpyllifolia symbiont 1 15 HE614287 Polygala serpyllifolia symbiont 2 C 1 HE615144 Polygala vulgaris ssp. collina symbiont 1 13 HE614288 Polygala vulgaris ssp. vulgaris symbiont 1 17 HE614285 Polygala vulgaris ssp. vulgaris symbiont 2 17 HE615146 Polygala vulgaris ssp. vulgaris symbiont 3 17 HE615148 Salomonia cantoniensis symbiont 1 7 MR321/MR369-i2 Yes LN713534 Salomonia cantoniensis symbiont 2 7 MR372/MR373-i2 Yes LN713532 Salomonia cantoniensis symbiont 3 19 MR315-i1 No LN713535 Salomonia cantoniensis symbiont 4 21 MR322-i2 Yes LN713530 Salomonia longiciliata symbiont 1 20 MR324/MR390-i1 Yes LN713539 Salomonia longiciliata symbiont 2 20 MR323-i1 Yes LN713537 Salomonia longiciliata symbiont 3 20 MR388/MR389-i1 Yes LN713540 Salomonia longiciliata symbiont 4 20 MR325-i2 Yes LN713529 Salomonia longiciliata symbiont 5 20 MR375-i1 Yes LN713536 Salomonia longiciliata symbiont 6 22 MR320-i2 No LN713528

177 Antiquities of the rainforest

Appendix A.4. OTU assignments Chapter 4. OTU Taxon Sequence Percentage Target sequence length similarity to target sequence 1 Epirixanthes kinabaluensis sym- 505 100.0 Epirixanthes kinabaluensis biont 1 symbiont 1 2 Epirixanthes pallida symbiont 1 502 100.0 Epirixanthes pallida symbiont 1 2 Polygala amara spp. brachyptera 496 97.4 Epirixanthes pallida symbiont 1 symbiont 1 2 Polygala myrtifolia symbiont 1 496 97.8 Epirixanthes pallida symbiont 1 2 Polygala calcarea symbiont 2 495 97.4 Epirixanthes pallida symbiont 1 2 Polygala amara spp. brachyptera 495 97.2 Epirixanthes pallida symbiont 1 symbiont 2 2 Polygala calcarea symbiont 1 495 98.0 Epirixanthes pallida symbiont 1 3 Epirixanthes elongata symbiont 5 504 100.0 Epirixanthes elongata symbiont 5 3 Epirixanthes elongata symbiont 3 504 99.2 Epirixanthes elongata symbiont 5 3 Epirixanthes elongata symbiont 2 468 99.8 Epirixanthes elongata symbiont 5 3 Epirixanthes elongata symbiont 1 504 99.0 Epirixanthes elongata symbiont 5 3 Epirixanthes elongata symbiont 4 504 99.8 Epirixanthes elongata symbiont 5 4 Epirixanthes papuana symbiont 2 460 98.9 Epirixanthes papuana symbiont 1 4 Epirixanthes papuana symbiont 1 477 100.0 Epirixanthes papuana symbiont 1 5 Epirixanthes pallida symbiont 6 442 100.0 Epirixanthes pallida symbiont 6 5 Epirixanthes pallida symbiont 5 463 99.5 Epirixanthes pallida symbiont 6 5 Epirixanthes pallida symbiont 4 450 98.0 Epirixanthes pallida symbiont 6 5 Epirixanthes pallida symbiont 7 496 98.2 Epirixanthes pallida symbiont 6 5 Epirixanthes papuana symbiont 3 505 98.2 Epirixanthes pallida symbiont 6 5 Epirixanthes pallida symbiont 2 496 98.4 Epirixanthes pallida symbiont 6 5 Epirixanthes pallida symbiont 3 467 98.4 Epirixanthes pallida symbiont 6 6 Epirixanthes papuana symbiont 6 506 100.0 Epirixanthes papuana symbiont 6 6 Epirixanthes papuana symbiont 5 505 98.2 Epirixanthes papuana symbiont 6 6 Epirixanthes papuana symbiont 4 505 98.2 Epirixanthes papuana symbiont 6 6 Epirixanthes papuana symbiont 7 506 98.4 Epirixanthes papuana symbiont 6 7 Salomonia cantoniensis symbiont 2 435 98.2 Epirixanthes pallida symbiont 8 7 Epirixanthes pallida symbiont 8 502 100.0 Epirixanthes pallida symbiont 8 7 Epirixanthes elongata symbiont 6 503 97.4 Epirixanthes pallida symbiont 8 7 Epirixanthes elongata symbiont 7 504 97.2 Epirixanthes pallida symbiont 8 7 Salomonia cantoniensis symbiont 1 435 98.6 Epirixanthes pallida symbiont 8 8 Epirixanthes elongata symbiont 8 504 100.0 Epirixanthes elongata symbiont 8 9 Epirixanthes elongata symbiont 9 494 100.0 Epirixanthes elongata symbiont 9 10 Epirixanthes pallida symbiont 11 504 97.2 Epirixanthes pallida symbiont 12 10 Epirixanthes pallida symbiont 12 506 100.0 Epirixanthes pallida symbiont 12 10 Epirixanthes pallida symbiont 9 504 97.6 Epirixanthes pallida symbiont 12

178 10 Epirixanthes pallida symbiont 10 504 97.2 Epirixanthes pallida symbiont 12 11 Epirixanthes pallida symbiont 13 428 100.0 Epirixanthes pallida symbiont 13 12 Epirixanthes pallida symbiont 14 463 100.0 Epirixanthes pallida symbiont 14 13 Epirixanthes pallida symbiont 15 250 99.2 Polygala comosa symbiont 1 13 Polygala comosa symbiont 1 495 100.0 Polygala comosa symbiont 1 13 Polygala vulgaris ssp. collina 496 97.6 Polygala comosa symbiont 1 symbiont 1 13 Polygala calcarea symbiont 3 495 99.8 Polygala comosa symbiont 1 14 Epirixanthes kinabaluensis sym- 372 100.0 Epirixanthes kinabaluensis biont 2 symbiont 2 15 Polygala alpestris symbiont 1 497 100.0 Polygala alpestris symbiont 1 15 Polygala serpyllifolia symbiont 1 497 98.2 Polygala alpestris symbiont 1 16 Polygala amarella symbiont 1 496 100.0 Polygala amarella symbiont 1 16 Polygala amara ssp. brachyptera 496 98.8 Polygala amarella symbiont 1 symbiont 3 16 Polygala myrtifolia symbiont 2 496 99.0 Polygala amarella symbiont 1 16 Polygala amarella symbiont 2 497 99.0 Polygala amarella symbiont 1 17 Polygala rupestris symbiont 1 495 100.0 Polygala rupestris symbiont 1 17 Polygala vulgaris ssp. vulgaris 494 98.2 Polygala rupestris symbiont 1 symbiont 2 17 Polygala vulgaris ssp. vulgaris 494 98.2 Polygala rupestris symbiont 1 symbiont 3 17 Polygala vulgaris ssp. vulgaris 495 98.4 Polygala rupestris symbiont 1 symbiont 1 18 Polygala myrtifolia symbiont 3 498 100.0 Polygala myrtifolia symbiont 3 19 Salomonia cantoniensis symbiont 3 437 100.0 Salomonia cantoniensis symbiont 3 20 Salomonia longiciliata symbiont 3 436 100.0 Salomonia longiciliata symbiont 3 20 Salomonia longiciliata symbiont 2 436 99.8 Salomonia longiciliata symbiont 3 20 Salomonia longiciliata symbiont 4 436 99.8 Salomonia longiciliata symbiont 3 20 Salomonia longiciliata symbiont 5 436 97.5 Salomonia longiciliata symbiont 3 20 Salomonia longiciliata symbiont 1 436 99.8 Salomonia longiciliata symbiont 3 21 Salomonia cantoniensis symbiont 4 435 100.0 Salomonia cantoniensis symbiont 4 22 Salomonia longiciliata symbiont 6 417 100.0 Salomonia longiciliata symbiont 6 C 1 Polygala serpyllifolia symbiont 2 * * * C 2 Polygala amara ssp. brachyptera * * * symbiont 4 * For these chimeric sequences no measurements were carried out.

179 Antiquities of the rainforest

180