New Phytologist Supporting Information Article title: Recently evolved diversity and convergent radiations of rainforest mahoganies (Meliaceae) shed new light on the origins of rainforest hyperdiversity Authors: Erik J.M. Koenen, James J. Clarkson, Terence D. Pennington, Lars W. Chatrou Article acceptance date: 15 April 2015. The following Supporting Information is available for this article: Fig. S1 Majority-rule consensus tree of BayesPhylogenies analysis with support values indicated next to nodes in posterior probability (pp). Figs S2-4 MCC trees for the three different root calibration scenarios. Width of branches is proportional to posterior probabilities and the blue bars show the 95% HPD interval of the age estimates. Time-scale in millions of years ago (Mya). Fig. S5 BiSSE profile plots of 100,000 MCMC generations for a) speciation and b) extinction rates. Green represents rainforest taxa (state 0) and yellow taxa in seasonal or montane tropical vegetation. Taxon sampling fractions for both states were nearly identical (0.35 and 0.34, respectively). Fig. S6 Credible shift set (CSS) of BAMM output, with sampling frequency for each shift configuration indicated above panels. The most sampled shift configuration is the MAP configuration, shown in the top left. Shifts are indicated by black circles, with the width of the circle relative to the marginal probability that a shift occurs along that branch. Branch colours indicate speciation rates across the phylogeny, with blue representing low rates and red high rates as in Fig. 2. These plots are derived from the BAMM analysis that was conducted on the MCC tree of scenario 2. Fig. S7 Phylorate plots for a) estimated extinction rates (μ), b) net diversification rate (r) when μ is estimated from the phylogeny, c) r when μ is fixed to 0.05 lineages/My and d) r when μ is fixed to 0.2 lineages/My. Fig. S8 Lineage-though-time plot, derived from the MCC tree of scenario 2. Y-axis is log- transformed. Table S1 Meliaceae diversity by genus and assigned sampling fractions for BAMM analyses. Table S2 GenBank accession numbers. Methods S1 Molecular laboratory methods. Figure S1. Majority-rule consensus tree of BayesPhylogenies analyses 1 Commiphora_africana Canarium_album Dacryodes_cuspidata_NH200660 1 1 Spondias_mombin 1 Rhus_thouarsii 1 1 Mangifera_foetida Trichoscypha_acuminata 0,99 Xanthoceras_sorbifolium Koelreuteria_paniculata 0,94 Allophylus_arboreus_Rakotovao3131 1 Allophylus_cobbe Acer_pseudoplatanus 0,85 Harpullia_arborea 1 Dodonaea_viscosa_Merello_1077 Cneorum_tricoccon 0,99 Harrisonia_abyssinica Melicope_paniculata 1 Acronychia_oblongifolia 0,84 Zanthoxylum_armatum 0,69 Flindersia_australis 1 Dictamnus_sp_cdK74 0,77 Ruta_graveolens 0,79 Aegle_marmelos 1 Atalantia_ceylanica 0,81 Citrus_sinensis Ailanthus_altissima 1 Brucea_mollis_PS0752MT01 0,91 Quassia_amara 1 Simarouba_amara 1 Simarouba_glauca Lovoa_trichilioides 1 Capuronianthus_mahafalensis Schmardaea_microphylla 0,95 Chukrasia_tabularis Entandrophragma_angolense 1 0,62 Entandrophragma_utile Toona_ciliata 0,96 Toona_sinensis 0,92 0,95 Cedrela_monroensis_Monro_Alexander_3081 Cedrela_tonduzii_Styles_82 1 0,87 Cedrela_salvadorensis_Formoso_2 0,86Cedrela_dugesii_German_450 1 Cedrela_oaxacensis_Mendoza_291 0,87 Cedrela_angustifolia_RT_Pennington_1150 0,98 Cedrela_montana_Palacios_Iguago_3046 0,53 Cedrela_balansae_Soria_2114 0,93 0,79Cedrela_molinensis_Daza_1551 Cedrela_fissilis 0,85 1 Cedrela_weberbaueri_Daza_4012 Cedrela_odorata 0,66 Cedrela_kualepensis_TD_Pennington_17583 0,88 Cedrela_nebulosa_AN_Muellner_2056 0,98 Cedrela_saltensis_Zapater_2348 Soymida_febrifuga Neobeguea_mahafalensis 0,52 Pseudocedrela_kotschyi 0,87 Xylocarpus_moluccensis 0,89 Swietenia_macrophylla 0,91 Swietenia_mahagoni 0,77 Khaya_anthotheca 1 Khaya_ivorensis 0,87 Khaya_senegalensis Carapa_grandiflora 0,66 Carapa_macrantha Carapa_parviflora Carapa_guianensis 1 1 0,56 Carapa_batesii Carapa_angustifolia 0,99 Carapa_zemagoana_sp27_DK_2009 Carapa_akuri_sp10_DK_2009 0,94 Carapa_surinamensis 0,94 0,54Carapa_vasquezii_sp3_DK_2009 0,66 Carapa_megistocarpa 0,93Carapa_alticola_sp5_DK_2009 0,99 Carapa_llanocarti_sp2_DK_2009 0,97 Carapa_longipetala_sp6_DK_2009 0,67 1 Carapa_nicaraguensis Carapa_littoralis_sp22_DK_2009 1 Carapa_oreophila_sp20_DK_2009 Carapa_mangaravensis_sp24_DK_2009 0,99 1 Carapa_hygrophila 0,97 Carapa_palustre_sp26_DK_2009 0,55 Carapa_dinklagei 0,98Carapa_microcarpa 1Carapa_procera 0,88 Carapa_velutina Owenia_vernicosa 1 Owenia_acidula 0,61 Azadirachta_indica 0,71 Melia_azedarach Sandoricum_koetjape 0,87 Ekebergia_capensis 1 Quivisianthe_papinae Heynea_trijuga 0,99 1 Walsura_tubulata Vavaea_amicorum 1 Vavaea_papuana Lepidotrichilia_volkensii 1 Astrotrichilia_aff_parvifolia_Birkin286 1 Astrotrichilia_asterotricha 1 Munronia_humilis 0,83 Munronia_breviflora 0,65 0,56 Munronia_pinnata Cipadessa_baccifera_MWC1310 0,89 Pseudoclausena_chrysogyne 0,7 Lepidotrichilia_ambrensis_Schatz1499 0,99 Malleastrum_mandenense 1 Malleastrum_rakotozafyi 0,85 Nymania_capensis_Chase270 1 Naregamia_alata_Kanodia89603 1 Calodecaryia_crassifolia 0,74 1 Turraea_obtusifolia 0,59 Turraea_thouarsiana 0,9 1 Humbertioturraea_labatii_BardotVaucoulon_160 0,54 Turraea_heterophylla 0,92 Turraea_nilotica 0,54 Turraea_sericea Trichilia_trifolia Trichilia_monadelpha 0,98 Trichilia_dregeana 0,79 Trichilia_emetica Pterorhachis_zenkeri 0,81 Trichilia_prieureana 1 0,86 0,75 Trichilia_capitata 0,9 Trichilia_rubescens 0,52 Pseudobersama_mossambicensis Trichilia_elegans25275 Trichilia_lepidota25289 Trichilia_multifoliola30533 Trichilia_pallida_NL110315 Trichilia_pleeana25303 0,86 Trichilia_euneura25279 0,98 Trichilia_sp4_25327 Trichilia_hirta25432 Trichilia_pallens25301 0,78 Trichilia_fasciculata255280 0,82 Trichilia_glabra25282 Trichilia_aquifolia25269 Trichilia_quadrijuga25309 Trichilia_singularis25316 0,64 Trichilia_bullata25271 Trichilia_catigua25272 Trichilia_lecointei25287 Trichilia_schomburgkii25313 Trichilia_sp3_25323 Trichilia_cipo_NL110021 1 0,72 Trichilia_surinamensis Trichilia_sp1_24267 0,73 Trichilia_breviflora25270 1 Trichilia_minutiflora25295 0,92 Trichilia_acuminata25266 Trichilia_primogenita25306 0,51 Trichilia_poeppigii25305 0,66Trichilia_silvatica25314 Trichilia_ulei25330 Trichilia_sp2_25274 Trichilia_magnifoliola25291 Trichilia_pseudostip25307 0,55 Trichilia_stellatotomen25319 Trichilia_ramalhoi25310 0,98 Trichilia_triacantha25326 Dysoxylum_alliaceum Dysoxylum_arborescens Anthocarapa_nitidula 0,52 Synoum_glandulosum Dysoxylum_gaudichaudianum 0,58 Chisocheton_patens 0,58 1 Chisocheton_polyandrus 1 Chisocheton_cumingianus 1 Chisocheton_macrophyllus Dysoxylum_binectariferum 1 Dysoxylum_cyrtobotryum Cabralea_canjerana 1 Dysoxylum_spectabile 0,97 Dysoxylum_bijugum 1 0,65 Dysoxylum_rufescens Aphanamixis_polystachya 1 Sphaerosacme_decandra 0,81 Aphanamixis_borneensis 0,74 Aglaia_lawii_HG488 1 Aglaia_teysmanniana_HG526 Lansium_cf_membranaceum_Pannell1934 1 Lansium_domesticum 1 0,8 Reinwardtiodendron_humile 1 Reinwardtiodendron_cinereum 0,79 0,67 Reinwardtiodendron_kinabaluense 1 0,84 Reinwardtiodendron_kostermansii Aglaia_spectabilis_HG660 1 Aglaia_macrocarpa_MWC16250 0,96 Aglaia_rugulosa_MWC15283 1 Aglaia_cucullata 0,79 Aglaia_australiensis_HG662 1 Aglaia_meridionalis_HG_MEL22 1 Aglaia_forbesii_HG538 0,99Aglaia_perviridis_HG13 1 Aglaia_silvestris_HG679 0,64 Aglaia_grandis_HG571 1 Aglaia_pachyphylla_HG812 1 Aglaia_argentea 1 1 Aglaia_eximia_HG540 Aglaia_exstipulata_HG717 0,57 Aglaia_tenuicaulis_HG901 1 Aglaia_tomentosa_HG543 1 0,89 Aglaia_crassinervia_HG523 1 Aglaia_sexipetala_HG524 1 Aglaia_samoensis_HG752 1 Aglaia_sapindina 1 Aglaia_basiphylla_HG692 1 Aglaia_archboldiana_HG696 0,7 1 Aglaia_vitiensis_HG691 Aglaia_coriacea_Muellner_2032 1 Aglaia_odorata 1 Aglaia_oligophylla_HG706 0,83 Aglaia_simplicifolia_HG484 0,87 Aglaia_elaeagnoidea Aglaia_glabrata_MWC15262 0,67 Aglaia_chittagonga_HG756 0,96 0,98 Aglaia_edulis_HG626 Aglaia_leucophylla_HG561 0,63 Aglaia_elliptica Aglaia_korthalsii 0,97 Aglaia_odoratissima Turraeanthus_africanus 1 Turraeanthus_longipes Turraeanthus_mannii Leplaea_mayombensis Leplaea_adenopunctata 1 1 Leplaea_mangenotiana 1 Leplaea_laurentii 0,63 Leplaea_thompsonii 0,84 Leplaea_cauliflora 0,99 Leplaea_cedrata 0,94 Heckeldora_leonensis 0,71 Heckeldora_jongkindii 1 Heckeldora_ledermannii 1 Heckeldora_staudtii Heckeldora_trifoliolata Heckeldora_leptotricha 0,99 Heckeldora_zenkeri Neoguarea_glomerulata Ruagea_insignis 1 Ruagea_pubescens 1 Ruagea_tomentosa 0,61 Guarea_jamaicensis25866 1 Guarea_kunthiana_25967 Guarea_anomala30514 1 Guarea_silvatica 0,63 Guarea_grandifolia Guarea_bullata 1 Guarea_chiricana_25922 0,95 0,97 Guarea_gentryi_30518 Guarea_tonduzii_25949 Guarea_bijuga_29879 1 Guarea_luxii_25943 Guarea_pterorhachis Guarea_ecuadoriensis_30522 Guarea_costata_25860 0,98 Guarea_velutina_25882 1 Guarea_caulobotrys_30527 0,71 Guarea_guentheri_25864 1 Guarea_macrophylla Guarea_fistulosa25871 1 0,84 Guarea_riparia_30529 Guarea_persistens_25872 0,98 Guarea_gomma_25862 0,67 Guarea_purusana25876 0,57 Guarea_pyriformis_25877 0,71 Guarea_guidonia 0,94 Guarea_fissicalyx_25861 0,98 Guarea_glabra Guarea_cinnamomea25859 Guarea_pendula_30528 Guarea_pubescens_25875 Guarea_sprucei_25881 Guarea_subandina_30530 Guarea_zepivae_33287 0,75 Guarea_macrocalyx_33283 1 Guarea_tafae_malekui_33285 Guarea_blanchetii_30515 1 Guarea_gracilia_30523 Guarea_carapoides_25856 1 Guarea_michel_moddei_30526 Guarea_carinata_25857 1 Guarea_cristata_30520 0,99 1 1 1 0,93 0.03 Fig. S2. MCC tree for root calibrated with normal prior (Scenario 1) Commiphora_africana Canarium_album Dacryodes_cuspidata_NH200660 Spondias_mombin Rhus_thouarsii Trichoscypha_acuminata Mangifera_foetida Xanthoceras_sorbifolium Acer_pseudoplatanus Harpullia_arborea Dodonaea_viscosa_Merello_1077 Koelreuteria_paniculata Allophylus_arboreus_Rakotovao3131 Allophylus_cobbe Cneorum_tricoccon Harrisonia_abyssinica Ruta_graveolens Aegle_marmelos Citrus_sinensis Atalantia_ceylanica Melicope_paniculata Acronychia_oblongifolia Dictamnus_sp_cdK74 Zanthoxylum_armatum Flindersia_australis Brucea_mollis_PS0752MT01 Ailanthus_altissima Quassia_amara Simarouba_glauca Simarouba_amara Soymida_febrifuga Schmardaea_microphylla Chukrasia_tabularis Lovoa_trichilioides Capuronianthus_mahafalensis Entandrophragma_angolense Entandrophragma_utile Toona_ciliata Toona_sinensis Cedrela_tonduzii_Styles_82 Cedrela_monroensis_Monro_Alexander_3081 Cedrela_salvadorensis_Formoso_2 Cedrela_dugesii_German_450 Cedrela_oaxacensis_Mendoza_291 Cedrela_angustifolia_RT_Pennington_1150 Cedrela_montana_Palacios_Iguago_3046 Cedrela_molinensis_Daza_1551 Cedrela_weberbaueri_Daza_4012 Cedrela_balansae_Soria_2114 Cedrela_odorata Cedrela_fissilis Cedrela_kualepensis_TD_Pennington_17583 Cedrela_nebulosa_AN_Muellner_2056 Cedrela_saltensis_Zapater_2348 Neobeguea_mahafalensis Pseudocedrela_kotschyi Xylocarpus_moluccensis Swietenia_macrophylla Swietenia_mahagoni Khaya_anthotheca Khaya_ivorensis Khaya_senegalensis Carapa_oreophila_sp20_DK_2009 Carapa_littoralis_sp22_DK_2009 Carapa_mangaravensis_sp24_DK_2009 Carapa_palustre_sp26_DK_2009 Carapa_hygrophila Carapa_dinklagei Carapa_microcarpa Carapa_velutina Carapa_procera Carapa_angustifolia Carapa_zemagoana_sp27_DK_2009 Carapa_macrantha Carapa_grandiflora Carapa_parviflora Carapa_guianensis Carapa_batesii Carapa_akuri_sp10_DK_2009 Carapa_vasquezii_sp3_DK_2009 Carapa_surinamensis Carapa_megistocarpa Carapa_alticola_sp5_DK_2009 Carapa_llanocarti_sp2_DK_2009 Carapa_longipetala_sp6_DK_2009 Carapa_nicaraguensis Owenia_vernicosa Melia_azedarach Owenia_acidula Azadirachta_indica Sandoricum_koetjape Ekebergia_capensis Quivisianthe_papinae Heynea_trijuga Walsura_tubulata Vavaea_amicorum Vavaea_papuana Lepidotrichilia_volkensii Astrotrichilia_aff_parvifolia_Birkin286 Astrotrichilia_asterotricha Munronia_humilis Munronia_pinnata Munronia_breviflora Cipadessa_baccifera_MWC1310 Pseudoclausena_chrysogyne Nymania_capensis_Chase270 Naregamia_alata_Kanodia89603 Turraea_thouarsiana Calodecaryia_crassifolia Turraea_obtusifolia Turraea_sericea Turraea_nilotica Turraea_heterophylla Humbertioturraea_labatii_BardotVaucoulon_160 Lepidotrichilia_ambrensis_Schatz1499 Malleastrum_mandenense Malleastrum_rakotozafyi Trichilia_trifolia Trichilia_monadelpha Trichilia_dregeana Trichilia_emetica Pterorhachis_zenkeri Trichilia_prieureana Trichilia_rubescens Trichilia_capitata Pseudobersama_mossambicensis Trichilia_elegans25275 Trichilia_pallens25301 Trichilia_hirta25432 Trichilia_glabra25282 Trichilia_fasciculata255280 Trichilia_multifoliola30533 Trichilia_lepidota25289 Trichilia_pallida_NL110315 Trichilia_pleeana25303 Trichilia_poeppigii25305 Trichilia_euneura25279 Trichilia_sp4_25327 Trichilia_singularis25316 Trichilia_aquifolia25269 Trichilia_quadrijuga25309 Trichilia_ulei25330 Trichilia_sp1_24267 Trichilia_breviflora25270 Trichilia_minutiflora25295 Trichilia_sp3_25323 Trichilia_schomburgkii25313 Trichilia_surinamensis Trichilia_cipo_NL110021 Trichilia_lecointei25287 Trichilia_bullata25271 Trichilia_primogenita25306 Trichilia_silvatica25314 Trichilia_acuminata25266 Trichilia_catigua25272 Trichilia_sp2_25274 Trichilia_ramalhoi25310 Trichilia_triacantha25326 Trichilia_magnifoliola25291 Trichilia_stellatotomen25319 Trichilia_pseudostip25307 Dysoxylum_alliaceum Dysoxylum_gaudichaudianum Chisocheton_macrophyllus Chisocheton_cumingianus Chisocheton_patens Chisocheton_polyandrus Dysoxylum_cyrtobotryum Dysoxylum_binectariferum Cabralea_canjerana Dysoxylum_spectabile Dysoxylum_bijugum Dysoxylum_rufescens Dysoxylum_arborescens Aphanamixis_polystachya Sphaerosacme_decandra Aphanamixis_borneensis Aglaia_teysmanniana_HG526 Aglaia_lawii_HG488 Aglaia_cucullata Aglaia_australiensis_HG662 Aglaia_meridionalis_HG_MEL22 Aglaia_spectabilis_HG660 Aglaia_macrocarpa_MWC16250 Aglaia_rugulosa_MWC15283 Lansium_domesticum Lansium_cf_membranaceum_Pannell1934 Reinwardtiodendron_cinereum Reinwardtiodendron_humile Reinwardtiodendron_kostermansii Reinwardtiodendron_kinabaluense Aglaia_forbesii_HG538 Aglaia_perviridis_HG13 Aglaia_silvestris_HG679 Aglaia_eximia_HG540 Aglaia_argentea Aglaia_pachyphylla_HG812 Aglaia_grandis_HG571 Aglaia_exstipulata_HG717 Aglaia_tenuicaulis_HG901 Aglaia_tomentosa_HG543 Aglaia_sexipetala_HG524 Aglaia_crassinervia_HG523 Aglaia_samoensis_HG752 Aglaia_sapindina Aglaia_basiphylla_HG692 Aglaia_archboldiana_HG696 Aglaia_vitiensis_HG691 Aglaia_coriacea_Muellner_2032 Aglaia_odorata Aglaia_oligophylla_HG706 Aglaia_simplicifolia_HG484 Aglaia_elaeagnoidea Aglaia_glabrata_MWC15262 Aglaia_chittagonga_HG756 Aglaia_edulis_HG626 Aglaia_leucophylla_HG561 Aglaia_elliptica Aglaia_korthalsii Aglaia_odoratissima Synoum_glandulosum Anthocarapa_nitidula Heckeldora_leonensis Heckeldora_jongkindii Heckeldora_trifoliolata Heckeldora_ledermannii Heckeldora_staudtii Heckeldora_leptotricha Heckeldora_zenkeri Turraeanthus_mannii Turraeanthus_africanus Turraeanthus_longipes Leplaea_cauliflora Leplaea_cedrata Leplaea_mayombensis Leplaea_adenopunctata Leplaea_mangenotiana Leplaea_thompsonii Leplaea_laurentii Neoguarea_glomerulata Ruagea_insignis Ruagea_pubescens Ruagea_tomentosa Guarea_jamaicensis25866 Guarea_kunthiana_25967 Guarea_silvatica Guarea_grandifolia Guarea_luxii_25943 Guarea_bijuga_29879 Guarea_gentryi_30518 Guarea_tonduzii_25949 Guarea_bullata Guarea_chiricana_25922 Guarea_anomala30514 Guarea_pterorhachis Guarea_costata_25860 Guarea_velutina_25882 Guarea_caulobotrys_30527 Guarea_macrophylla Guarea_guentheri_25864 Guarea_ecuadoriensis_30522 Guarea_fistulosa25871 Guarea_riparia_30529 Guarea_gomma_25862 Guarea_persistens_25872 Guarea_pyriformis_25877 Guarea_purusana25876 Guarea_guidonia Guarea_glabra Guarea_fissicalyx_25861 Guarea_zepivae_33287 Guarea_sprucei_25881 Guarea_cinnamomea25859 Guarea_tafae_malekui_33285 Guarea_macrocalyx_33283 Guarea_subandina_30530 Guarea_pubescens_25875 Guarea_carapoides_25856 Guarea_michel_moddei_30526 Guarea_gracilia_30523 Guarea_blanchetii_30515 Guarea_pendula_30528 Guarea_cristata_30520 Guarea_carinata_25857 80,0 70,0 60,0 50,0 40,0 30,0 20,0 10,0 0,0 0,0 Fig. S3. MCC tree for root calibrated with maximum age from the literature (Scenario 2) Commiphora_africana Canarium_album Dacryodes_cuspidata_NH200660 Spondias_mombin Rhus_thouarsii Mangifera_foetida Trichoscypha_acuminata Xanthoceras_sorbifolium Acer_pseudoplatanus Harpullia_arborea Dodonaea_viscosa_Merello_1077 Koelreuteria_paniculata Allophylus_arboreus_Rakotovao3131 Allophylus_cobbe Cneorum_tricoccon Harrisonia_abyssinica Ruta_graveolens Aegle_marmelos Atalantia_ceylanica Citrus_sinensis Dictamnus_sp_cdK74 Flindersia_australis Zanthoxylum_armatum Melicope_paniculata Acronychia_oblongifolia Brucea_mollis_PS0752MT01 Ailanthus_altissima Quassia_amara Simarouba_glauca Simarouba_amara Schmardaea_microphylla Chukrasia_tabularis Lovoa_trichilioides Capuronianthus_mahafalensis Entandrophragma_angolense Entandrophragma_utile Toona_ciliata Toona_sinensis Cedrela_tonduzii_Styles_82 Cedrela_monroensis_Monro_Alexander_3081 Cedrela_salvadorensis_Formoso_2 Cedrela_dugesii_German_450 Cedrela_oaxacensis_Mendoza_291 Cedrela_angustifolia_RT_Pennington_1150 Cedrela_montana_Palacios_Iguago_3046 Cedrela_odorata Cedrela_kualepensis_TD_Pennington_17583 Cedrela_nebulosa_AN_Muellner_2056 Cedrela_saltensis_Zapater_2348 Cedrela_balansae_Soria_2114 Cedrela_molinensis_Daza_1551 Cedrela_fissilis Cedrela_weberbaueri_Daza_4012 Soymida_febrifuga Neobeguea_mahafalensis Pseudocedrela_kotschyi Swietenia_macrophylla Swietenia_mahagoni Xylocarpus_moluccensis Khaya_anthotheca Khaya_senegalensis Khaya_ivorensis Carapa_angustifolia Carapa_zemagoana_sp27_DK_2009 Carapa_batesii Carapa_guianensis Carapa_grandiflora Carapa_parviflora Carapa_macrantha Carapa_akuri_sp10_DK_2009 Carapa_vasquezii_sp3_DK_2009 Carapa_surinamensis Carapa_megistocarpa Carapa_alticola_sp5_DK_2009 Carapa_llanocarti_sp2_DK_2009 Carapa_longipetala_sp6_DK_2009 Carapa_nicaraguensis Carapa_mangaravensis_sp24_DK_2009 Carapa_hygrophila Carapa_palustre_sp26_DK_2009 Carapa_oreophila_sp20_DK_2009 Carapa_littoralis_sp22_DK_2009 Carapa_dinklagei Carapa_microcarpa Carapa_velutina Carapa_procera Owenia_vernicosa Melia_azedarach Azadirachta_indica Owenia_acidula Sandoricum_koetjape Ekebergia_capensis Quivisianthe_papinae Heynea_trijuga Walsura_tubulata Vavaea_amicorum Vavaea_papuana Lepidotrichilia_volkensii Astrotrichilia_aff_parvifolia_Birkin286 Astrotrichilia_asterotricha Munronia_pinnata Munronia_humilis Munronia_breviflora Pseudoclausena_chrysogyne Cipadessa_baccifera_MWC1310 Nymania_capensis_Chase270 Naregamia_alata_Kanodia89603 Calodecaryia_crassifolia Turraea_obtusifolia Turraea_thouarsiana Turraea_sericea Humbertioturraea_labatii_BardotVaucoulon_160 Turraea_nilotica Turraea_heterophylla Lepidotrichilia_ambrensis_Schatz1499 Malleastrum_rakotozafyi Malleastrum_mandenense Trichilia_trifolia Trichilia_monadelpha Trichilia_dregeana Trichilia_emetica Pterorhachis_zenkeri Trichilia_prieureana Trichilia_capitata Pseudobersama_mossambicensis Trichilia_rubescens Trichilia_elegans25275 Trichilia_multifoliola30533 Trichilia_lepidota25289 Trichilia_pallida_NL110315 Trichilia_hirta25432 Trichilia_pallens25301 Trichilia_fasciculata255280 Trichilia_glabra25282 Trichilia_poeppigii25305 Trichilia_pleeana25303 Trichilia_euneura25279 Trichilia_sp4_25327 Trichilia_quadrijuga25309 Trichilia_singularis25316 Trichilia_aquifolia25269 Trichilia_ulei25330 Trichilia_sp3_25323 Trichilia_sp1_24267 Trichilia_breviflora25270 Trichilia_minutiflora25295 Trichilia_acuminata25266 Trichilia_silvatica25314 Trichilia_primogenita25306 Trichilia_bullata25271 Trichilia_lecointei25287 Trichilia_surinamensis Trichilia_cipo_NL110021 Trichilia_schomburgkii25313 Trichilia_catigua25272 Trichilia_magnifoliola25291 Trichilia_sp2_25274 Trichilia_pseudostip25307 Trichilia_stellatotomen25319 Trichilia_ramalhoi25310 Trichilia_triacantha25326 Dysoxylum_alliaceum Dysoxylum_gaudichaudianum Chisocheton_macrophyllus Chisocheton_cumingianus Chisocheton_patens Chisocheton_polyandrus Dysoxylum_cyrtobotryum Dysoxylum_binectariferum Cabralea_canjerana Dysoxylum_spectabile Dysoxylum_bijugum Dysoxylum_rufescens Dysoxylum_arborescens Aphanamixis_borneensis Sphaerosacme_decandra Aphanamixis_polystachya Aglaia_cucullata Aglaia_australiensis_HG662 Aglaia_meridionalis_HG_MEL22 Aglaia_spectabilis_HG660 Aglaia_macrocarpa_MWC16250 Aglaia_rugulosa_MWC15283 Lansium_domesticum Lansium_cf_membranaceum_Pannell1934 Reinwardtiodendron_cinereum Reinwardtiodendron_humile Reinwardtiodendron_kostermansii Reinwardtiodendron_kinabaluense Aglaia_teysmanniana_HG526 Aglaia_lawii_HG488 Aglaia_forbesii_HG538 Aglaia_perviridis_HG13 Aglaia_silvestris_HG679 Aglaia_pachyphylla_HG812 Aglaia_grandis_HG571 Aglaia_eximia_HG540 Aglaia_argentea Aglaia_tenuicaulis_HG901 Aglaia_exstipulata_HG717 Aglaia_tomentosa_HG543 Aglaia_sexipetala_HG524 Aglaia_crassinervia_HG523 Aglaia_samoensis_HG752 Aglaia_sapindina Aglaia_basiphylla_HG692 Aglaia_archboldiana_HG696 Aglaia_vitiensis_HG691 Aglaia_coriacea_Muellner_2032 Aglaia_odorata Aglaia_simplicifolia_HG484 Aglaia_oligophylla_HG706 Aglaia_glabrata_MWC15262 Aglaia_elaeagnoidea Aglaia_edulis_HG626 Aglaia_leucophylla_HG561 Aglaia_chittagonga_HG756 Aglaia_elliptica Aglaia_odoratissima Aglaia_korthalsii Anthocarapa_nitidula Synoum_glandulosum Neoguarea_glomerulata Turraeanthus_mannii Turraeanthus_longipes Turraeanthus_africanus Heckeldora_leonensis Heckeldora_jongkindii Heckeldora_staudtii Heckeldora_ledermannii Heckeldora_trifoliolata Heckeldora_leptotricha Heckeldora_zenkeri Leplaea_cauliflora Leplaea_cedrata Leplaea_mayombensis Leplaea_mangenotiana Leplaea_adenopunctata Leplaea_laurentii Leplaea_thompsonii Ruagea_insignis Ruagea_tomentosa Ruagea_pubescens Guarea_kunthiana_25967 Guarea_jamaicensis25866 Guarea_silvatica Guarea_grandifolia Guarea_bijuga_29879 Guarea_luxii_25943 Guarea_gentryi_30518 Guarea_chiricana_25922 Guarea_bullata Guarea_tonduzii_25949 Guarea_anomala30514 Guarea_pterorhachis Guarea_caulobotrys_30527 Guarea_guentheri_25864 Guarea_macrophylla Guarea_velutina_25882 Guarea_costata_25860 Guarea_sprucei_25881 Guarea_ecuadoriensis_30522 Guarea_fistulosa25871 Guarea_riparia_30529 Guarea_gomma_25862 Guarea_persistens_25872 Guarea_purusana25876 Guarea_pyriformis_25877 Guarea_guidonia Guarea_glabra Guarea_fissicalyx_25861 Guarea_zepivae_33287 Guarea_pendula_30528 Guarea_cinnamomea25859 Guarea_subandina_30530 Guarea_tafae_malekui_33285 Guarea_macrocalyx_33283 Guarea_carapoides_25856 Guarea_michel_moddei_30526 Guarea_pubescens_25875 Guarea_cristata_30520 Guarea_carinata_25857 Guarea_blanchetii_30515 Guarea_gracilia_30523 90,0 80,0 70,0 60,0 50,0 40,0 30,0 20,0 10,0 0,0 Fig. S4. MCC tree for root calibrated with maximum age as first tricolpate pollen (Scenario 3) Commiphora_africana Canarium_album Dacryodes_cuspidata_NH200660 Spondias_mombin Rhus_thouarsii Trichoscypha_acuminata Mangifera_foetida Xanthoceras_sorbifolium Koelreuteria_paniculata Allophylus_arboreus_Rakotovao3131 Allophylus_cobbe Acer_pseudoplatanus Harpullia_arborea Dodonaea_viscosa_Merello_1077 Cneorum_tricoccon Harrisonia_abyssinica Ruta_graveolens Aegle_marmelos Citrus_sinensis Atalantia_ceylanica Melicope_paniculata Acronychia_oblongifolia Dictamnus_sp_cdK74 Zanthoxylum_armatum Flindersia_australis Brucea_mollis_PS0752MT01 Ailanthus_altissima Quassia_amara Simarouba_glauca Simarouba_amara Chukrasia_tabularis Schmardaea_microphylla Entandrophragma_angolense Entandrophragma_utile Toona_ciliata Toona_sinensis Cedrela_monroensis_Monro_Alexander_3081 Cedrela_tonduzii_Styles_82 Cedrela_salvadorensis_Formoso_2 Cedrela_dugesii_German_450 Cedrela_oaxacensis_Mendoza_291 Cedrela_angustifolia_RT_Pennington_1150 Cedrela_montana_Palacios_Iguago_3046 Cedrela_weberbaueri_Daza_4012 Cedrela_molinensis_Daza_1551 Cedrela_balansae_Soria_2114 Cedrela_fissilis Cedrela_odorata Cedrela_kualepensis_TD_Pennington_17583 Cedrela_nebulosa_AN_Muellner_2056 Cedrela_saltensis_Zapater_2348 Lovoa_trichilioides Capuronianthus_mahafalensis Soymida_febrifuga Neobeguea_mahafalensis Pseudocedrela_kotschyi Swietenia_macrophylla Swietenia_mahagoni Xylocarpus_moluccensis Khaya_anthotheca Khaya_senegalensis Khaya_ivorensis Carapa_mangaravensis_sp24_DK_2009 Carapa_hygrophila Carapa_palustre_sp26_DK_2009 Carapa_oreophila_sp20_DK_2009 Carapa_littoralis_sp22_DK_2009 Carapa_dinklagei Carapa_microcarpa Carapa_velutina Carapa_procera Carapa_angustifolia Carapa_zemagoana_sp27_DK_2009 Carapa_batesii Carapa_guianensis Carapa_grandiflora Carapa_macrantha Carapa_parviflora Carapa_akuri_sp10_DK_2009 Carapa_surinamensis Carapa_vasquezii_sp3_DK_2009 Carapa_megistocarpa Carapa_alticola_sp5_DK_2009 Carapa_llanocarti_sp2_DK_2009 Carapa_nicaraguensis Carapa_longipetala_sp6_DK_2009 Owenia_vernicosa Melia_azedarach Azadirachta_indica Owenia_acidula Sandoricum_koetjape Ekebergia_capensis Quivisianthe_papinae Vavaea_papuana Vavaea_amicorum Heynea_trijuga Walsura_tubulata Lepidotrichilia_volkensii Astrotrichilia_aff_parvifolia_Birkin286 Astrotrichilia_asterotricha Munronia_humilis Munronia_pinnata Munronia_breviflora Pseudoclausena_chrysogyne Cipadessa_baccifera_MWC1310 Nymania_capensis_Chase270 Naregamia_alata_Kanodia89603 Calodecaryia_crassifolia Turraea_obtusifolia Turraea_thouarsiana Turraea_sericea Turraea_nilotica Humbertioturraea_labatii_BardotVaucoulon_160 Turraea_heterophylla Lepidotrichilia_ambrensis_Schatz1499 Malleastrum_mandenense Malleastrum_rakotozafyi Trichilia_trifolia Trichilia_monadelpha Trichilia_dregeana Trichilia_emetica Pterorhachis_zenkeri Trichilia_prieureana Trichilia_capitata Pseudobersama_mossambicensis Trichilia_rubescens Trichilia_elegans25275 Trichilia_pleeana25303 Trichilia_poeppigii25305 Trichilia_hirta25432 Trichilia_pallens25301 Trichilia_glabra25282 Trichilia_fasciculata255280 Trichilia_pallida_NL110315 Trichilia_lepidota25289 Trichilia_multifoliola30533 Trichilia_euneura25279 Trichilia_sp4_25327 Trichilia_aquifolia25269 Trichilia_singularis25316 Trichilia_quadrijuga25309 Trichilia_sp3_25323 Trichilia_ulei25330 Trichilia_sp1_24267 Trichilia_breviflora25270 Trichilia_minutiflora25295 Trichilia_catigua25272 Trichilia_magnifoliola25291 Trichilia_sp2_25274 Trichilia_triacantha25326 Trichilia_ramalhoi25310 Trichilia_stellatotomen25319 Trichilia_pseudostip25307 Trichilia_schomburgkii25313 Trichilia_surinamensis Trichilia_cipo_NL110021 Trichilia_bullata25271 Trichilia_primogenita25306 Trichilia_lecointei25287 Trichilia_silvatica25314 Trichilia_acuminata25266 Synoum_glandulosum Dysoxylum_alliaceum Dysoxylum_gaudichaudianum Chisocheton_macrophyllus Chisocheton_cumingianus Chisocheton_patens Chisocheton_polyandrus Dysoxylum_cyrtobotryum Dysoxylum_binectariferum Cabralea_canjerana Dysoxylum_spectabile Dysoxylum_bijugum Dysoxylum_rufescens Dysoxylum_arborescens Aphanamixis_borneensis Aphanamixis_polystachya Sphaerosacme_decandra Aglaia_teysmanniana_HG526 Aglaia_lawii_HG488 Lansium_domesticum Lansium_cf_membranaceum_Pannell1934 Reinwardtiodendron_humile Reinwardtiodendron_cinereum Reinwardtiodendron_kostermansii Reinwardtiodendron_kinabaluense Aglaia_cucullata Aglaia_australiensis_HG662 Aglaia_meridionalis_HG_MEL22 Aglaia_spectabilis_HG660 Aglaia_rugulosa_MWC15283 Aglaia_macrocarpa_MWC16250 Aglaia_forbesii_HG538 Aglaia_perviridis_HG13 Aglaia_silvestris_HG679 Aglaia_pachyphylla_HG812 Aglaia_grandis_HG571 Aglaia_eximia_HG540 Aglaia_argentea Aglaia_exstipulata_HG717 Aglaia_tenuicaulis_HG901 Aglaia_tomentosa_HG543 Aglaia_sexipetala_HG524 Aglaia_crassinervia_HG523 Aglaia_samoensis_HG752 Aglaia_sapindina Aglaia_basiphylla_HG692 Aglaia_archboldiana_HG696 Aglaia_vitiensis_HG691 Aglaia_coriacea_Muellner_2032 Aglaia_odorata Aglaia_simplicifolia_HG484 Aglaia_oligophylla_HG706 Aglaia_elaeagnoidea Aglaia_glabrata_MWC15262 Aglaia_leucophylla_HG561 Aglaia_edulis_HG626 Aglaia_chittagonga_HG756 Aglaia_elliptica Aglaia_odoratissima Aglaia_korthalsii Anthocarapa_nitidula Turraeanthus_mannii Turraeanthus_longipes Turraeanthus_africanus Leplaea_cauliflora Leplaea_cedrata Leplaea_mayombensis Leplaea_laurentii Leplaea_thompsonii Leplaea_mangenotiana Leplaea_adenopunctata Heckeldora_leonensis Heckeldora_jongkindii Heckeldora_ledermannii Heckeldora_staudtii Heckeldora_trifoliolata Heckeldora_zenkeri Heckeldora_leptotricha Neoguarea_glomerulata Ruagea_insignis Ruagea_tomentosa Ruagea_pubescens Guarea_jamaicensis25866 Guarea_kunthiana_25967 Guarea_silvatica Guarea_grandifolia Guarea_gentryi_30518 Guarea_bijuga_29879 Guarea_luxii_25943 Guarea_bullata Guarea_tonduzii_25949 Guarea_chiricana_25922 Guarea_anomala30514 Guarea_pterorhachis Guarea_costata_25860 Guarea_velutina_25882 Guarea_caulobotrys_30527 Guarea_guentheri_25864 Guarea_macrophylla Guarea_zepivae_33287 Guarea_sprucei_25881 Guarea_fistulosa25871 Guarea_ecuadoriensis_30522 Guarea_riparia_30529 Guarea_persistens_25872 Guarea_gomma_25862 Guarea_pyriformis_25877 Guarea_purusana25876 Guarea_guidonia Guarea_fissicalyx_25861 Guarea_glabra Guarea_subandina_30530 Guarea_cinnamomea25859 Guarea_tafae_malekui_33285 Guarea_macrocalyx_33283 Guarea_pendula_30528 Guarea_pubescens_25875 Guarea_carapoides_25856 Guarea_michel_moddei_30526 Guarea_carinata_25857 Guarea_cristata_30520 Guarea_blanchetii_30515 Guarea_gracilia_30523 120,0 110,0 100,0 90,0 80,0 70,0 60,0 50,0 40,0 30,0 20,0 10,0 0,0 Fig. S5. BiSSE MCMC profile plots a 12 lambda0 lambda1 Probability density 10 8 6 4 2 0 0.1 0.2 0.3 0.4 0.5 Speciation rates b mu0 mu1 Probability density 8 6 4 2 0 0.0 0.1 0.2 Extinction rates 0.3 0.4 Fig. S6. Credible shift set f = 0.34 f = 0.091 f = 0.09 f = 0.063 f = 0.06 f = 0.049 f = 0.034 f = 0.027 f = 0.021 1 2 5 10 N 20 50 100 200 Fig. S8. Lineage-through-time plot −60 −50 −40 −30 Time −20 −10 0 Table S1. Meliaceae diversity by genus and assigned sampling fractions for BAMM analyses Subfamily Cedreloideae: Chukrasia Schmardaea Capuronianthus Lovoa Entandrophragma Toona Cedrela Neobeguea Soymida febrifuga Xylocarpus Pseudocedrela Swietenia Khaya Carapa* Cedreloideae total: Subfamily Melioideae: Melia (2 spp.), Azadirachta (2) & Owenia (5) Sandoricum Quivisianthe Ekebergia Vavaea Walsura Heynea Astrotrichilia (16) & Lepidotrichilia volkensii Munronia Pseudoclauseana Cipadessa Nymania Naregamia Turraea (c. 66), Calodecaryia (2) & Humbertioturraea (11) Lepidotrichilia p.p. (3) & Malleastrum (24) African Trichilia (18), Pterorhachis (2) & Pseudobersama (1) New World Trichilia Anthocarapa Synoum Dysoxylum Chisocheton Cabralea Aglaia (114), Lansium (3) & Reinwardtiodendron (7) Aphanamixis (3) & Sphaerosacme (1) species sampled estimated total spp. sampling fraction 1 1 1 1 2 2 15 1 1 1 1 2 3 12 44 1 1 2 2 6 2 17 3 1 3 1 3 5 12 59 1 1 0,5 0,5 0,333333333 1 0,882352941 0,333333333 1 0,333333333 1 0,666666667 0,6 1 0,745762712 4 1 1 1 2 1 1 3 3 1 1 1 1 7 3 8 36 1 1 8 4 1 43 3 9 5 2 3 4 16 2 17 4 1 1 1 1 79 27 21 81 1 1 80 50 1 124 4 0,444444444 0,2 0,5 0,333333333 0,5 0,0625 0,5 0,176470588 0,75 1 1 1 1 0,088607595 0,111111111 0,380952381 0,444444444 1 1 0,1 0,08 1 0,346774194 0,75 African Guareeae (Leplaea (7), Heckeldora (7), Turraeanthus (3), Neoguarea (1)) Ruagea Guarea (unplaced) Malagasy Trichilia Melioideae total: 18 3 41 0 198 18 1 15 0,2 69 0,594202899 6 NA 643 0,307931571 family total: 242 702 0,344729345 genera: 53 (16 monospecific) * The phylogeny includes 24 accessions of Carapa, see methods for a discussion on why these were pruned for BAMM analyses Table S2. GenBank accession numbers matK taxon Acer pseudoplatanus Aegle marmelos Aglaia elliptica Aglaia korthalsii Aglaia odoratissima Ailanthus altissima Allophylus arboreus Aphanamixis polystachya Azadirachta indica Brucea mollis Canarium album Carapa guianensis Carapa procera Cedrela odorata Chisocheton cumingianus Chisocheton macrophyllus Cipadessa baccifera Commiphora africana Dacryodes cuspidata Dodonaea viscosa Dysoxylum binectariferum Dysoxylum gaudichaudianum Ekebergia capensis Guarea bullata Guarea glabra Guarea grandifolia Guarea guidonia Guarea pterorhachis Guarea silvatica Harpullia arborea Heckeldora staudtii Khaya anthotheca Koelreuteria paniculata Lansium domesticum Leplaea thompsonii Malleastrum mandenense Melia azedarach Munronia pinnata Naregamia alata Neobeguea mahafalensis Nymania capensis accession HM850604.1 HM163957.1 AY128177.1 GQ248073.1 GQ248074.1 FM179922.1 EU720681.1 AY128178.1 AY128180.1 GQ434125.1 HQ415266.1 AY128181.1 FJ514608.1 AY128182.1 GQ248096.1 AY128183.1 EF489116.1 JF270710.1 FJ514671.1 EU720567.1 JX982143.1 AY128187.1 JF270756.1 JQ588338.1 AY128188.1 GQ982002.1 HM446695.2 JQ588347.1 FJ514658.1 GQ248130.1 AY128189.1 AY128190.1 EU720695.1 AY128191.1 KC627594.1 AY128192.1 EF489117.1 AY128195.1 JF922888.1 AY128196.1 AY128197.1 notes in genbank as Neobeguea sp. Pseudobersama mossambicensisJX517407.1 Quassia amara AY128207.1 AY594484.1 Rhus thouarsii Ruagea pubescens AY128198.1 EF489055.1 Ruta graveolens Schmardaea microphylla AY128199.1 EU042898.1 Simarouba amara Simarouba glauca EF489113.1 AY594480.1 Spondias mombin Swietenia macrophylla EF489114.1 Swietenia mahagoni EU042835.1 Toona ciliata JX518246.1 Toona sinensis JN680328.1 JX518085.1 Trichilia capitata Trichilia dregeana JF270976.1 AY128202.1 Trichilia emetica Trichilia glabra JQ588355.1 FJ514739.1 Trichilia pallida Trichilia prieureana KC627568.1 Trichilia trifolia JQ588368.1 Turraea nilotica JF270981.1 Turraea obtusifolia JF270982.1 AY128203.1 Turraea sericea Turraeanthus mannii KC627513.1 AY128204.1 Walsura tubulata Xanthoceras sorbifolium AY724339.1 Table S2. GenBank accession numbers matK taxon Acer pseudoplatanus Aegle marmelos Aglaia elliptica Aglaia korthalsii Aglaia odoratissima Ailanthus altissima Allophylus arboreus Aphanamixis polystachya Azadirachta indica Brucea mollis Canarium album Carapa guianensis Carapa procera Cedrela odorata Chisocheton cumingianus Chisocheton macrophyllus Cipadessa baccifera Commiphora africana Dacryodes cuspidata Dodonaea viscosa Dysoxylum binectariferum Dysoxylum gaudichaudianum Ekebergia capensis Guarea bullata Guarea glabra Guarea grandifolia Guarea guidonia Guarea pterorhachis Guarea silvatica Harpullia arborea Heckeldora staudtii Khaya anthotheca Koelreuteria paniculata Lansium domesticum Leplaea thompsonii Malleastrum mandenense Melia azedarach Munronia pinnata Naregamia alata Neobeguea mahafalensis Nymania capensis accession HM850604 HM163957 AY128177 GQ248073 GQ248074 FM179922 EU720681 AY128178 AY128180 GQ434125 HQ415266 AY128181 FJ514608 AY128182 GQ248096 AY128183 EF489116 JF270710 FJ514671 EU720567 JX982143 AY128187 JF270756 JQ588338 AY128188 GQ982002 HM446695 JQ588347 FJ514658 GQ248130 AY128189 AY128190 EU720695 AY128191 KC627594 AY128192 EF489117 AY128195 JF922888 AY128196 AY128197 notes in genbank as Neobeguea sp. Pseudobersama mossambicensis Quassia amara Rhus thouarsii Ruagea pubescens Ruta graveolens Schmardaea microphylla Simarouba amara Simarouba glauca Spondias mombin Swietenia macrophylla Swietenia mahagoni Toona ciliata Toona sinensis Trichilia capitata Trichilia dregeana Trichilia emetica Trichilia glabra Trichilia pallida Trichilia prieureana Trichilia trifolia Turraea nilotica Turraea obtusifolia Turraea sericea Turraeanthus mannii Walsura tubulata Xanthoceras sorbifolium JX517407 AY128207 AY594484 AY128198 EF489055 AY128199 EU042898 EF489113 AY594480 EF489114 EU042835 JX518246 JN680328 JX518085 JF270976 AY128202 JQ588355 FJ514739 KC627568 JQ588368 JF270981 JF270982 AY128203 KC627513 AY128204 AY724339 rbcL taxon Acer pseudoplatanus Aegle marmelos Aglaia argentea Aglaia cucullata Aglaia elaeagnoidea Aglaia elliptica Aglaia korthalsii Aglaia odorata Aglaia odoratissima Aglaia sapindina Ailanthus altissima Allophylus cobbe Anthocarapa nitidula Aphanamixis polystachya Atalantia ceylanica Azadirachta indica Brucea mollis Cabralea canjerana Calodecaryia crassifolia Canarium album Capuronianthus mahafalensis Carapa guianensis Carapa procera Cedrela odorata Chisocheton cumingianus Chisocheton macrophyllus Cipadessa baccifera Citrus sinensis Cneorum tricoccon Commiphora africana Dacryodes cuspidata Dodonaea viscosa Dysoxylum alliaceum Dysoxylum arborescens Dysoxylum binectariferum Dysoxylum gaudichaudianum Ekebergia capensis Flindersia australis Guarea bullata Guarea costata Guarea glabra Guarea grandifolia Guarea guidonia Guarea pterorhachis accession HM849739 AF066811 JF738463 JF738768 AY128209 AY128210 GQ248542 FN599442 GQ248543 JF738380 AY128247 AY128248 DQ238056 AY128213 AF066812 AY128215 GQ436502 DQ238055 AY128216 FJ466626 AJ402935 AY128219 FJ038112 AJ402938 GQ248567 AY128221 AY128224 DQ864733 EU042977 JF265357 FJ037973 DQ978445 JF738802 JF738491 JX982144 AY128227 AJ402947 U38861 JQ592718 JQ625748 AY128229 GQ981750 GQ981751 JQ592716 notes in genbank as Pseudocarapa nitidula Guarea silvatica Harpullia arborea Harrisonia abyssinica Heckeldora staudtii Humbertioturraea labatii Khaya anthotheca Koelreuteria paniculata Lansium domesticum Lepidotrichilia volkensii Leplaea thompsonii Lovoa trichilioides Malleastrum mandenense Melia azedarach Munronia breviflora Munronia humilis Munronia pinnata Naregamia alata Nymania capensis Owenia vernicosa Pseudobersama mossambicensis Pseudocedrela kotschyi Pseudoclausena chrysogyne Quassia amara Quivisianthe papinae Reinwardtiodendron kinabaluense Ruagea pubescens Ruta graveolens Sandoricum koetjape Schmardaea microphylla Simarouba amara Simarouba glauca Spondias mombin Swietenia macrophylla Swietenia mahagoni Synoum glandulosum Toona sinensis Trichilia cipo Trichilia dregeana Trichilia emetica Trichilia glabra Trichilia pallida Trichilia prieureana Trichilia surinamensis Trichilia trifolia Turraea nilotica Turraea obtusifolia Turraea sericea FJ038158 AY724356 FR747835 AJ402959 DQ238058 AY128231 U39283 AY128232 DQ238061 KC628089 AY128233 DQ238062 EU042973 EU621670 EU621669 AY128236 DQ238059 AY128238 DQ238063 DQ238064 AH015484 DQ238065 EU043017 AY128239 DQ238054 DQ238057 AY128251 DQ238068 AY128240 EU043036 EU043037 JQ590140 AY128241 FN599465 AY128242 FN599468 FJ038114 JF265635 AY128244 JQ592742 FJ038116 KC627970 JQ626055 JQ592755 JF265640 JF265641 AY128245 in genbank as Humbertioturraea sp. in genbank as Lovoa swynnertonii Turraeanthus mannii Vavaea amicorum Walsura tubulata Xanthoceras sorbifolium Xylocarpus moluccensis KC628095 AH015483 AJ403017 AJ403019 DQ238071 rps16 taxon Aegle marmelos Aglaia archboldiana Aglaia argentea Aglaia australiensis Aglaia basiphylla Aglaia chittagonga Aglaia coriacea Aglaia crassinervia Aglaia cucullata Aglaia edulis Aglaia elaeagnoidea Aglaia elliptica Aglaia eximia Aglaia exstipulata Aglaia forbesii Aglaia glabrata Aglaia grandis Aglaia korthalsii Aglaia lawii Aglaia leucophylla Aglaia macrocarpa Aglaia meridionalis Aglaia odorata Aglaia odoratissima Aglaia oligophylla Aglaia pachyphylla Aglaia perviridis Aglaia rugulosa Aglaia samoensis Aglaia sapindina Aglaia sexipetala Aglaia silvestris Aglaia simplicifolia Aglaia spectabilis Aglaia tenuicaulis Aglaia teysmanniana Aglaia tomentosa Aphanamixis borneensis Aphanamixis polystachya Atalantia ceylanica Azadirachta indica Canarium album accession AY295268 AY695596 AY695597 AY695642 AY695599 AY695600 AY695601 AY695602 AY695643 AY695605 AY695608 AY695612 AY695613 AY695615 AY695618 AY695619 AY695620 AY695621 AY695645 AY695622 AY695647 AY695648 AY695623 AY695625 AY695626 AY695627 AY695628 AY695649 AY695629 AY695630 AY695603 AY695633 AY695632 AY695650 AY695636 AY695609 AY695638 AY695654 AY695655 AY295262 AY695664 AY635355 Carapa guianensis Cedrela fissilis Cneorum tricoccon Commiphora africana Dodonaea viscosa Flindersia australis Guarea glabra Guarea macrophylla Harrisonia abyssinica Melia azedarach Reinwardtiodendron cinereum Reinwardtiodendron kinabaluense Ruagea pubescens Ruta graveolens Toona ciliata EU853727 EU853729 FR747940 AY831941 AY594597 EF126610 AY695661 EU853744 FR747939 AY695665 AY695659 AY695660 AY695663 AY295249 EF126632 Internal transcribed spacer (ITS) from GenBank taxon Acer pseudoplatanus Acronychia oblongifolia Aegle marmelos Aglaia archboldiana Aglaia argentea Aglaia australiensis Aglaia basiphylla Aglaia chittagonga Aglaia coriacea Aglaia crassinervia Aglaia cucullata Aglaia edulis Aglaia elaeagnoidea Aglaia elliptica Aglaia eximia Aglaia exstipulata Aglaia forbesii Aglaia glabrata Aglaia grandis Aglaia korthalsii Aglaia lawii Aglaia leucophylla Aglaia macrocarpa Aglaia meridionalis Aglaia odorata Aglaia odoratissima Aglaia oligophylla Aglaia pachyphylla Aglaia perviridis Aglaia rugulosa Aglaia samoensis Aglaia sapindina Aglaia sexipetala Aglaia silvestris Aglaia simplicifolia Aglaia spectabilis Aglaia tenuicaulis Aglaia teysmanniana Aglaia tomentosa Aglaia vitiensis Allophylus arboreus Anthocarapa nitidula accession AF241500 EU493185 FJ434169 AY695524 AY695525 AY695571 AY695527 AY695528 EF491263 AY695530 AY695572 AY695533 AY695536 AY695540 AY695541 AY695543 AY695546 AY695547 AY695548 EF491264 AY695574 AY695550 AY695576 AY695577 AY695551 AY695553 AY695554 AY695555 AY695556 AY695578 AY695557 AY695558 AY695531 AY695561 AY695560 AY695579 AY695564 AY695537 AY695568 AY695569 EU720531 DQ861616 notes Aphanamixis borneensis Aphanamixis polystachya Astrotrichilia asterotricha Atalantia ceylanica Azadirachta indica Brucea javanica Brucea mollis Cabralea canjerana Calodecaryia crassifolia Canarium album Capuronianthus mahafalensis Carapa akuri Carapa alticola Carapa angustifolia Carapa batesii Carapa dinklagei Carapa grandiflora Carapa guianensis Carapa hygrophila Carapa littoralis Carapa llanocartii Carapa longipetala Carapa macrantha Carapa mangaravensis Carapa megistocarpa Carapa microcarpa Carapa nicaraguensis Carapa oreophila Carapa palustre Carapa parviflora Carapa procera Carapa surinamensis Carapa vasquezii Carapa velutina Carapa zemagoana Cedrela angustifolia Cedrela balansae Cedrela dugesii Cedrela fissilis Cedrela kuelapensis Cedrela molinensis Cedrela monroensis Cedrela montana Cedrela nebulosa Cedrela oaxacensis Cedrela odorata AY695583 AY695584 FJ518866 FJ434159 FJ518867 AY510155 FJ980360 DQ861617 DQ861631 DQ517524 FJ518868 FJ518885 FJ518883 FJ518869 FJ518870 FJ518871 FJ518872 FJ518873 FJ518874 FJ518887 FJ518881 FJ518884 FJ518875 FJ518888 FJ518876 FJ518877 FJ518878 FJ518886 FJ518889 FJ518879 FJ518880 FJ518891 FJ518882 FJ518892 FJ518890 FJ462479 FJ462474 FJ462483 FJ518893 FJ462470 FJ462465 FJ462486 FJ462481 FJ462461 FJ462482 DQ861606 in GenBank as Carapa sp. 10 in GenBank as Carapa sp. 5 in GenBank as Carapa sp. 22 in GenBank as Carapa sp. 2 in GenBank as Carapa sp. 6 in GenBank as Carapa sp. 24 in GenBank as Carapa sp. 20 in GenBank as Carapa sp. 26 in GenBank as Carapa sp. 3 in GenBank as Carapa sp. 27 Cedrela saltensis Cedrela salvadorensis Cedrela tonduzii Cedrela weberbaueri Chisocheton macrophyllus Chukrasia tabularis Cipadessa baccifera Citrus sinensis Cneorum tricoccon Commiphora africana Dacryodes cuspidata Dictamnus sp. Dodonaea viscosa Dysoxylum arborescens Dysoxylum binectariferum Dysoxylum gaudichaudianum Dysoxylum spectabile Ekebergia capensis Entandrophragma angolense Entandrophragma utile Flindersia australis Guarea anomala Guarea bijuga Guarea blanchetii Guarea bullata Guarea carapoides Guarea carinata Guarea caulobotrys Guarea chiricana Guarea cinnamomea Guarea costata Guarea cristata Guarea ecuadoriensis Guarea fissicalyx Guarea fistulosa Guarea gentryi Guarea glabra Guarea gomma Guarea gracilis Guarea grandifolia Guarea guentheri Guarea guidonia Guarea jamaicensis Guarea kunthiana Guarea luxii Guarea macrocalyx FJ462462 FJ462484 FJ462485 FJ462472 DQ861613 FJ518894 DQ861627 AB456127 GU178981 AF445873 FJ037797 FJ593176 EU720536 DQ499101 JX982145 DQ861619 DQ499100 DQ861623 FJ518895 FJ518896 HM116975 HE653770 HE653766 HE653726 HE653765 HE653730 HE653731 HE653746 HE653767 HE653732 HE653733 HE653734 HE653736 HE653737 HE653748 HE653764 AY695591 HE653738 HE653739 GQ982002 HE653740 HE653741 HE653759 HE653760 HE653769 HE653742 Guarea macrophylla Guarea michel moddei Guarea pendula Guarea persistens Guarea pterorhachis Guarea pubescens Guarea purusana Guarea pyriformis Guarea riparia Guarea silvatica Guarea sprucei Guarea subandina Guarea tafae malekui Guarea tonduzii Guarea velutina Guarea zepivae Harrisonia abyssinica Heckeldora staudtii Humbertioturraea labatii Khaya anthotheca Khaya ivorensis Khaya senegalensis Koelreuteria paniculata Lansium domesticum Lansium membranaceum Lepidotrichilia volkensii Lovoa trichilioides Malleastrum mandenense Mangifera foetida Melia azedarach Melicope paniculata Munronia breviflora Munronia humilis Munronia pinnata Naregamia alata Neobeguea mahafalensis Nymania capensis Pseudocedrela kotschyi Pseudoclausena chrysogyne Pterorhachis zenkeri Quivisianthe papinae Reinwardtiodendron cinereum Reinwardtiodendron humile Reinwardtiodendron kinabaluense Reinwardtiodendron kostermansii Rhus thouarsii HE653729 HE653745 HE653747 HE653749 HE653758 HE653750 HE653751 HE653752 HE653753 FJ037836 HE653754 HE653755 HE653743 HE653768 HE653756 HE653757 GU178980 AY695592 DQ861632 DQ861608 FJ518897 FJ518898 EU720548 AY695587 DQ861611 DQ861620 FJ518899 DQ861626 AB071680 FJ518900 EU493171 FJ194497 FJ194496 DQ861604 DQ861629 FJ518901 DQ861633 FJ518902 DQ861602 DQ861628 DQ861605 AY695588 DQ861612 AY695589 DQ861634 EF089150 in GenBank as Humbertioturraea sp. Ruagea pubescens Ruta graveolens Sandoricum koetjape Schmardaea microphylla Simarouba amara Sphaerosacme decandra Spondias mombin Swietenia macrophylla Synoum glandulosum Toona ciliata Toona sinensis Trichilia acuminata Trichilia aquifolia Trichilia breviflora Trichilia bullata Trichilia catigua Trichilia cipo Trichilia elegans Trichilia emetica Trichilia euneura Trichilia fasciculata Trichilia glabra Trichilia hirta Trichilia lecointei Trichilia lepidota Trichilia magnifoliola Trichilia minutiflora Trichilia multifoliola Trichilia pallens Trichilia pallida Trichilia pleeana Trichilia poeppigii Trichilia prieureana Trichilia primogenita Trichilia pseudostipularis Trichilia quadrijuga Trichilia ramalhoi Trichilia schomburgkii Trichilia silvatica Trichilia singularis Trichilia sp. 1 Trichilia sp. 2 Trichilia sp. 3 Trichilia sp. 4 Trichilia stellatotomentosa Trichilia surinamensis AY695593 FJ434146 DQ861600 FJ518904 DQ787413 AY695590 AF080064 FJ518905 DQ861618 FJ518906 FJ462490 LN833604 LN833607 LN833609 LN833610 LN833611 FJ037837 LN833614 EF136577 LN833615 LN833617 LN833619 LN833621 LN833622 LN833623 LN833624 LN833628 LN833633 LN833636 FJ037840 LN833638 LN833639 EF136576 LN833640 LN833641 LN833642 LN833643 LN833646 LN833648 LN833649 LN833606 LN833613 LN833651 LN833654 LN833650 FJ037839 Trichilia triacantha Trichilia trifolia Trichilia ulei Trichoscypha acuminata Turraea heterophylla Turraea sericea Vavaea amicorum Walsura tubulata Xanthoceras sorbifolium Xylocarpus moluccensis Zanthoxylum armatum LN833652 LN833653 LN833655 AY594389 EF136578 DQ861630 DQ861610 DQ861625 FJ375202 FJ518907 DQ016546 ycf1 newly sequenced taxon accession voucher (herbarium) Aglaia coriacea KR364498 Muellner 2032 (BRUN, K) Aglaia korthalsii KR364499 Muellner 2041 (BRUN, K) Cabralea canjerana KR364500 Wasum et al. 1196 (B, HVCS) Chisocheton macrophyllus KR364501 Chase 1309 (K) Chisocheton patens KR364502 S. Tingki SAN135706 (L) Dysoxylum alliaceum KR364503 Slik SWPRI-785 (L) Dysoxylum cyrtobotryum KR364504 Ambri & Arifin W795 (L) Dysoxylum gaudichaudianum KR364505 Chase 1312 (K) Dysoxylum rufescens KR364506 Balgooy 7020 (L) Guarea blanchetii KR364507 Jardim et al. 225 (K) Guarea cinnamomea KR364508 T.D. Pennington et al. 17417 (K) Guarea fistulosa KR364509 Revilla 3668 (K) Guarea pubescens KR364510 T.D. Pennington et al. 16514 (K) Guarea purusana KR364511 Cardiel & Caballal 139 (K) Guarea silvatica KR364512 Sothers & Silva 456 (K) Heckeldora jongkindii KR364513 Jongkind 8949 (WAG) Heckeldora leonensis KR364514 Jongkind 6473 (WAG) Heckeldora leptotricha KR364515 Wieringa 5805 (WAG) Heckeldora zenkeri KR364516 Breteler 15727 (WAG) Leplaea adenopunctata KR364517 Nimba Botanic Team WD473 (WAG) Leplaea cauliflora KR364518 Wieringa 6270 (WAG) Leplaea cedrata KR364519 Sosef 2709 (WAG) Leplaea laurentii KR364520 Koenen 66 (WAG) Leplaea mangenotiana KR364521 Jongkind 4479 (WAG) Leplaea mayombensis KR364522 van Valkenburg 2778 (WAG) Leplaea thompsonii KR364523 Breteler 15389 (WAG) Melia azedarach KR364524 Chase 2867 (K) Neoguarea glomerulata KR364525 Koenen 44 (WAG) Reinwardtiodendron humile KR364526 Trichon 641 (FHO) Ruagea tomentosa KR364527 Vargas et al. 4046 (K) Synoum glandulosum KR364528 Schodde 5101 (K) Trichilia monadelpha KR364529 Koenen 24 (WAG) Turraeanthus africanus KR364530 Jongkind 7937 (WAG) Turraeanthus longipes KR364531 Chatrou 564 (WAG) Turraeanthus mannii KR364532 D.W. Thomas 4832 (WAG) Internal transcribed spacer (ITS) newly sequenced taxon Astrotrichilia aff. parvifolia Chisocheton cumingianus Chisocheton patens Chisocheton polyandrus Dysoxylum alliaceum Dysoxylum bijugum Dysoxylum cyrtobotryum Dysoxylum rufescens Heckeldora jongkindii Heckeldora ledermannii Heckeldora leonensis Heckeldora leptotricha Heckeldora trifoliolata Heckeldora zenkeri Heynea trijuga Lepidotrichilia ambrensis Leplaea adenopunctata Leplaea cauliflora Leplaea cedrata Leplaea laurentii Leplaea mangenotiana Leplaea mayombensis Leplaea thompsonii Malleastrum rakotozafyi Neoguarea glomerulata Owenia acidula Ruagea insignis Ruagea tomentosa Soymida febrifuga Trichilia capitata Trichilia monadelpha Trichilia rubescens Turraea thouarsiana Turraeanthus africanus Turraeanthus longipes Turraeanthus mannii Vavaea papuana accession KR364533 KR364534 KR364535 KR364536 KR364537 KR364538 KR364539 KR364540 KR364541 KR364542 KR364543 KR364544 KR364545 KR364546 KR364547 KR364548 KR364549 KR364550 KR364551 KR364552 KR364553 KR364554 KR364555 KR364556 KR364557 KR364558 KR364559 KR364560 KR364561 KR364562 KR364563 KR364564 KR364565 KR364566 KR364567 KR364568 KR364569 voucher (herbarium) Birkinshaw 286 (WAG) Lamothe MEL28 (L) S. Tingki SAN135706 (L) Mabberley 1708 (L) Slik SWPRI-785 (L) Pat Curry 1552 (L) Ambri & Arifin W795 (L) Balgooy 7020 (L) Jongkind 8949 (WAG) Leeuwenberg 8813 (WAG) Jongkind 6473 (WAG) Wieringa 5805 (WAG) van Valkenburg 2715 (WAG) Breteler 15727 (WAG) Boyce 870 (WAG) Schatz 1499 (WAG) Nimba Botanic Team WD473 (WAG) Wieringa 6270 (WAG) Sosef 2709 (WAG) Koenen 66 (WAG) Jongkind 4479 (WAG) van Valkenburg 2778 (WAG) Breteler 15389 (WAG) Harder 1557 (WAG) Koenen 44 (WAG) G.J. Harden 97017 (WAG) Palacios 3346 (K) Vargas et al. 4046 (K) Meyer 193a (K) Torre & Correia 14202 (WAG) Koenen 24 (WAG) Wieringa 5892 (WAG) Lorence 4503 (WAG) Jongkind 7937 (WAG) Chatrou 564 (WAG) D.W. Thomas 4832 (WAG) Brass 25858 (K) Methods S1 Molecular laboratory methods DNA extraction, PCR and sequencing Plant tissue collected in the field was dried and stored in silica gel prior to DNA extraction (Chase & Hills, 1991). Total genomic DNA was extracted using either a modified cetyl trimethyl ammonium bromide (CTAB) method (Doyle & Doyle, 1987) or a modified protocol for the DNeasy Plant Mini Kit (QIAGEN). Polymerase chain reaction (PCR) amplification was then carried out. For the fragment including internal transcribed spacers 1 and 2, the 5.8S rRNA gene and parts of the flanking 18S and 26S rRNA genes, primers F1-ITS and R1-ITS (Muellner et al., 2005) and ITS-4 (White et al., 1990) were used. In a few cases, amplification was carried out in two pieces, with internal primers ITS-C and ITS- E (Blattner, 1999). A 50 μl reaction mix included 5 μl of 10x PCR buffer, 2 μl dNTP’s, 5 μl bovine serum albumine (BSA), 1.75 μl of both the forward and reverse primers, 0.4 μl of Taq-polymerase, 1 to 5 μl of template DNA (approximately 30120 ng) and a certain volume of MQ water to arrive at a total of 50 μl. The addition of BSA increased the amount of amplification product in most cases, while some reactions (probably due to low quality of template DNA) did not yield any product without adding BSA. After an initial denaturing step of 3 minutes at 95°C, 36 cycles were performed with a 1 min. 11 denaturing step at 94°C, 1 min. annealing at 58-69°C (dependent on primer combination) and 1 min. extension at 72°C, followed by a final extension step of 7 minutes at 72°C. For ycf1, primers were designed based on previously published sequences of Citrus sinensis (L.) Osbeck (Bausher et al., 2006) and a number of taxa from the related angiosperm orders Malvales, Brassicales and Myrtales. For amplification the following primers were used: ycf1-F (5’- CCC TTA CCA TAC TGA AAC GAC – 3’) and ycf1-R (5’- TCA CAA GCA TAT GTA TTT TAC -3’), with additional internal primers ycf1-intF (5’-GCA TTC CAA AGT AGC ACA AAT TC-3’) and ycf1-intR (5’- ATA TCA AAC GAG GAG CTT TGG -3’) for some accessions were DNA was obtained from herbarium samples. Reaction mixtures were the same as for ITS. The following PCR program was used: an initial denaturing step of 2 minutes at 94°C, 36 cycles a 1 min. denaturing step at 94°C, 1 min. annealing at 55-59°C (dependent on primer combination) and 2 min. extension at 72°C, followed by a final extension step of 7 minutes at 72°C. Amplification products were cleaned up using the MinElute PCR purification kit (QIAGEN), following the manufacturers' protocols. Cycle sequencing reactions were performed with the use of the BigDye Terminator Cycle sequencing kit, following the manufacturers' protocols. The same primers were used as for the amplification, with the exception that for the large ycf1 fragments (when internal primers were not used in amplification) the internal primer ycf1-int-seqR (5’- GCC AAT ATG GAA GCC TGG GTT G -3’) was used as well (see Fig. 3). Sequence assembly and alignment The products of the cycle sequencing reaction were processed in an ABI3100 capillary sequencer. Assembly and sequence editing were done using the Staden package (Staden, 1996). Initial alignments were obtained with MAFFT version 6.818 (Katoh & Toh, 2008). For the alignment of ITS the Q-INS-i algorithm was used and a consensus secondary structure was predicted with RNAalifold (Bernhart et al., 2008) and was compared with secondary structures of ITS as published by for Aglaia elaeagnoidea (A.Juss.) Benth. and Lansium parasiticum (Osbeck) K.C.Sahni & Bennet. We have searched for the conserved Angiosperm sequence motif GGCRY-(4 to 7n)-GYGYCAAGGAA in ITS1 and the GAATTGCAGAATTC motif in the 5.8S gene to check for possible pseudogenes (Feliner & Rosselló, 2007). A few sequences were excluded on the suspicion that they represented pseudogenes or were otherwise mix-ups in the lab: ITS sequences of Aphanamixis sumatrana (GenBank accession number: AY695585), Astrotrichilia sp. (DQ861621), Owenia vernicosa (DQ861622) and Pseudobersama mossambicensis (DQ861603) resulted in inferring relationships for these taxa that were incompatible with morphological evidence and with relationships inferred from plastid sequences. All alignments were checked and edited by eye using Mesquite version 2.74 (Maddison & Maddison, 2010). The ITS and combined chloroplast matrices were first analyzed separately with RAxML 8 (Stamatakis, 2014) and no well-supported incongruence was observed. The plastid phylogeny was generally poorly resolved and less densely sampled, so not much incongruence was expected. The matrices were combined, which led to a large amount of missing data for the plastid loci (Table S2), but no conflicting relationships were found between analyses of combined and individual loci, and the addition of plastid data improved resolution along the backbone of the phylogeny. References Bausher MG, Singh ND, Lee S-B, Jansen RK, Daniell H. 2006. The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms. BMC Plant Biology 6: 21. Bernhart S, Hofacker I, Will S, Gruber A, Stadler P. 2008. RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics 9: 474. Blattner FR. 1999. Direct amplification of the entire ITS region from poorly preserved plant material using recombinant PCR. BioTechniques 27: 1180–1186. Chase MW, Hills HH. 1991. Silica gel: an ideal material for field preservation of leaf samples for DNA studies. Taxon 40: 215–220. Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11–15. Feliner GN, Rosselló JA. 2007. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Molecular Phylogenetics and Evolution 44: 911–919. Katoh K, Toh H. 2008. Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 9: 286–298. Maddison WP, Maddison DR. 2010. Mesquite: A modular system for evolutionary analysis, version 2.74. http://mesquiteproject.org. Muellner AN, Samuel R, Chase MW, Pannell CM, Greger H. 2005. Aglaia (Meliaceae): an evaluation of taxonomic concepts based on DNA data and secondary metabolites. American Journal of Botany 92: 534–543. Staden R. 1996. The Staden sequence analysis package. Molecular Biotechnology 5: 233–241. Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313. White TJ, Bruns T, Lee S, Taylor J 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ eds. PCR protocols: a guide to methods and applications. San Diego, California: Academic Press, 315–322.