#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on May 15, 2024; 18:14 GMT TreeBASE (cc) 1994-2008 Study reference: Choi Y., Beakes G., Glockling S., Kruse J., Nam B., Nigrelli L., Ploch S., Shin H., Shivas R.G., Telle S., Voglmayr H., & Thines M. 2015. Towards a universal barcode of oomycetes – a comparison of the cox1 and cox2 loci. Molecular Ecology Resources, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S16949] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=112; TAXLABELS 'Hyaloperonospora parasitica ex Capsell bursa-pastoris 2561' Peronospora_aestivalis_ex_Medicago_lupulina_0574 Peronospora_aestivalis_ex_Medicago_sativa_2640 Peronospora_agremones_ex_Papaver_agremone_0749 Peronospora_alchemilae_ex_Alchemila_vulgaris_agg._2653 Peronospora_alpicola_ex_Ranunculus_aconitifolius_2706 Peronospora_alsinearum_ex_Stellaria_media_1189 Peronospora_alta_ex_Plangago_major_0817 Peronospora_anagallidis_ex_Anagallis_foemina_0019 Peronospora_antirrini_ex_Misopates_orontium_2582 Peronospora_aparines_ex_Galium_aparine_0359 Peronospora_arborescens_ex_Papaver_rhoeas_0776 Peronospora_arenariae_ex_Moehringia_trinervia_0650 Peronospora_arthurii_ex_Oenothera_biennis_0737 Peronospora_belbahrii_ex_Ocimum_basilicum_0730 'Peronospora boni-henrici ex Chenopodium bonus-henricus 0177' Peronospora_bulbocapni_ex_Corydalis_cava_0240A Peronospora_calotheca_ex_Galium_odoratum_0376 Peronospora_campestris_ex_Arenaria_serpyllifolia_2658 'Peronospora cerastii-anomali ex Cearstium dubium 2665' 'Peronospora cerastii-brachypetali ex Cerastium brachypetalum 2664' Peronospora_chenopodii_ex_Chenopodium_hybridum_0190 'Peronospora chenopodii-polyspermi ex Chenopodium polyspermum 0202' Peronospora_chrysosplenii_ex_Chrysosplenium_alternifolium__0217 Peronospora_conglomerata_ex_Geranium_pusillum_0424 Peronospora_consolidae_ex_Consolida_regalis_0222 Peronospora_coronillae_ex_Securigera_varia_1122 Peronospora_corydalis_ex_Corydalis_solida_2670 'Peronospora corydalis-intermediae ex Corydalis intermedia 0250' Peronospora_cyparissiae_ex_Euphorbia_cyparissia_0308 Peronospora_debaryi_ex_Urtica_urens_1284 Peronospora_destructor_ex_Allium_cepa_0015 Peronospora_digitalidis_ex_Digitalis_purpurea_0272 Peronospora_dipsaci_ex_Dipsacus_fullonum_0277 Peronospora_echii_ex_Echium_vulgare_2674 Peronospora_effusa_ex_Spinacia_oleracea_2748 Peronospora_elscholtziae_ex_Elsholtzia_ciliata_2739 Peronospora_erodii_ex_Erodium_cicutarium_0302 Peronospora_ervi_ex_Vicia_hirsuta_1463 Peronospora_esulae_ex_Euphorbia_esula_0322 Peronospora_ficariae_ex_Ficaria_verna_0974 Peronospora_flava_ex_Linaria_vulgaris_0571 Peronospora_fulva_ex_Lathyrus_pratensis_0550 Peronospora_galii_ex_Galium_mollugo_2677 Peronospora_glechomae_ex_Glechoma_hederacea_0450 Peronospora_hiemalis_ex_Ranunculus_acris_0948A Peronospora_holostei_ex_Holosteum_umbellatum_0454 Peronospora_honckenyae_ex_Honckenya_peploides_2683 Peronospora_illyrica_ex_Ranunculus_illyricus_HV2076 Peronospora_knautiae_ex_Scabiosa_ochroleuca_1084B 'Peronospora kochiae-scopariae ex Bassia scoparia 0063' Peronospora_lamii_ex_Lamium_purpureum_0534 Peronospora_lapponica_ex_Euphrasia_stricta_0323 Peronospora_lepigoni_ex_Spergularia_rubra_1157 Peronospora_linariae_ex_Chaenorhinum_minus_2668 'Peronospora linariae-genistifoliae ex Linaria genistifolia 0560' Peronospora_lithospermi_ex_Lithospermum_arvense_2690 Peronospora_mayorii_ex_Vicia_cracca_2731 Peronospora_meconopsidis_ex_Meconopsis_cambrica_2556 'Peronospora melandrii-noctiflori ex Silene noctiflora 1126' Peronospora_meliloti_ex_Melilotus_albus_0593 Peronospora_minor_ex_Atriplex_patula_2662 Peronospora_myosotidis_ex_Myosotis_arvensis_0670 Peronospora_myosotidis_s.l._ex_Myosotis_sp._2741 Peronospora_oblatispora_ex_Potentilla_paradoxa_2743 Peronospora_obovata_ex_Spergula_arvensis_1135 Peronospora_offinis_ex_Fumaria_officinalis_0344 Peronospora_parva_ex_Stellaria_holostea_1180 Peronospora_paula_ex_Cerastium_semidecandrum_0129 Peronospora_perillae_ex_Perilla_frutescens_2742 Peronospora_phacae_ex_Astragalus_penduliflorus_2661 Peronospora_pisi_ex_Pisum_sativum_0798 Peronospora_polygoni_ex_Polygonum_aviculare_0906 'Peronospora polygoni-convolvuli ex Fallopia convolvulus 2529' 'Peronospora potentillae-anserinae ex Potentilla anserina 2750' 'Peronospora potentillae-reptantis ex Potentilla reptans 0929' 'Peronospora potentillae-sterilis ex Potentilla sterilis 0936' Peronospora_pulveracea_ex_Helleborus_foetidus_2681 Peronospora_radii_ex_Tripleurospermum_perforatum_1277 Peronospora_ranunculi_sl_ex_Ranunculus_repens_0995 'Peronospora ranunculi-sardoi ex Ranunculus sardous 1015' Peronospora_rubi_ex_Rubus_caesius_1021 'Peronospora salviae-plebeiae ex Salvia plebeia 2747' Peronospora_sanguisorbae_ex_Sanguisorba_officinalis_2714 Peronospora_saturejae_hortensis_ex_Satureja_hortensis_1069 Peronospora_saxifragae_ex_Saxifraga_granulata_1070 Peronospora_schachtii_ex_Beta_vulgaris_2737 Peronospora_scleranthi_ex_Scleranthus_annuus_1095 Peronospora_scutellariae_ex_Scutellaria_galericulata_1118 Peronospora_sepium_ex_Vicia_sepium_1479 Peronospora_sherardiae_ex_Sherardia_arvensis_1124 Peronospora_stachydis_ex_Stachys_palustris_1172 Peronospora_stigmaticola_ex_Mentha_aquatica__0630 Peronospora_symphyti_ex_Symphytum_tuberosum_2720 Peronospora_tabacina_ex_Nicotiana_tabacum Peronospora_teucrii_ex_Teucrium_botrys_1229 Peronospora_tomentosa_ex_Cerastium_glomeratum_2557 'Peronospora trifolii-hybridi ex Trifolium hybridum 2721' 'Peronospora trifolii-minoris ex Trifolium dubium 1245' 'Peronospora trifolii-pratensis ex Trifolium pratense 1255' 'Peronospora trifolii-repentis ex Trifolium repens 1261' Peronospora_trifoliorum_ex_Trifolium_medium_1254 Peronospora_trigonotidis_ex_Trigonotis_peduncularis_2749 Peronospora_valerianae_ex_Valeriana_officinalis_2723 Peronospora_valerianellae_ex_Valerianella_carinata_2724 Peronospora_variabilis_ex_Chenopodium_album_0162 Peronospora_verbasci_ex_Verbascum_nigrum_1300 Peronospora_verbenae_ex_Verbena_officinalis_2726 Peronospora_vernalis_ex_Spergula_morisonii_1140 Peronospora_viciae_ex_Vicia_sativa_2735 Peronospora_violacea_ex_Knautia_arvensis_0477 Peronospora_violae_ex_Viola_arvensis_1519 ; END; BEGIN TREES; TITLE Oomycetes_cox1_ME; LINK TAXA = Taxa; TREE Imported_tree_1 = [&R] ((((((((((((((((((((('Peronospora boni-henrici ex Chenopodium bonus-henricus 0177':0.02063718,Peronospora_minor_ex_Atriplex_patula_2662:0.02836277)0.6470:0.00391483,'Peronospora chenopodii-polyspermi ex Chenopodium polyspermum 0202':0.02204284)0.4390:0.00343913,Peronospora_chenopodii_ex_Chenopodium_hybridum_0190:0.02296979)0.1870:0.00367373,(Peronospora_bulbocapni_ex_Corydalis_cava_0240A:0.02806091,('Peronospora kochiae-scopariae ex Bassia scoparia 0063':0.04197809,Peronospora_arthurii_ex_Oenothera_biennis_0737:0.02115943)0.3820:0.00247299)0.1870:0.00244388)0.0180:3.7257E-4,('Peronospora polygoni-convolvuli ex Fallopia convolvulus 2529':0.0287316,Peronospora_tabacina_ex_Nicotiana_tabacum:0.02856378)0.1920:0.00289596)0.0020:0.00253173,((Peronospora_agremones_ex_Papaver_agremone_0749:0.00737686,Peronospora_arborescens_ex_Papaver_rhoeas_0776:0.00811754)1.0000:0.0293209,((Peronospora_antirrini_ex_Misopates_orontium_2582:0.0225859,Peronospora_linariae_ex_Chaenorhinum_minus_2668:0.01573962)0.9850:0.01557586,((Peronospora_cyparissiae_ex_Euphorbia_cyparissia_0308:0.00327582,Peronospora_esulae_ex_Euphorbia_esula_0322:-2.321E-4)1.0000:0.03599318,(Peronospora_debaryi_ex_Urtica_urens_1284:0.02822629,Peronospora_meconopsidis_ex_Meconopsis_cambrica_2556:0.03177636)0.4570:0.00283222)0.5160:0.00331099)0.3560:0.00327667)0.2390:0.00315824)0.0010:0.00161377,Peronospora_destructor_ex_Allium_cepa_0015:0.03100373)0.0010:0.00100122,((((Peronospora_obovata_ex_Spergula_arvensis_1135:0.00387543,Peronospora_lepigoni_ex_Spergularia_rubra_1157:6.9907E-4)0.8710:0.00442808,(Peronospora_schachtii_ex_Beta_vulgaris_2737:0.00721898,Peronospora_effusa_ex_Spinacia_oleracea_2748:0.00673154)0.4770:0.00100935)1.0000:0.02039724,(Peronospora_arenariae_ex_Moehringia_trinervia_0650:0.03250683,(Peronospora_campestris_ex_Arenaria_serpyllifolia_2658:0.02298546,'Peronospora cerastii-anomali ex Cearstium dubium 2665':0.03967854)0.4180:0.00220875)0.4840:0.00636564)0.1150:0.00231233,((((Peronospora_vernalis_ex_Spergula_morisonii_1140:0.01314784,Peronospora_alsinearum_ex_Stellaria_media_1189:0.01536032)0.9330:0.00932303,Peronospora_variabilis_ex_Chenopodium_album_0162:0.02599644)0.1700:0.00196065,Peronospora_polygoni_ex_Polygonum_aviculare_0906:0.02853215)0.0270:0.00179469,('Peronospora melandrii-noctiflori ex Silene noctiflora 1126':0.02223805,(Peronospora_tomentosa_ex_Cerastium_glomeratum_2557:0.02751155,(Peronospora_paula_ex_Cerastium_semidecandrum_0129:0.0233208,(Peronospora_scleranthi_ex_Scleranthus_annuus_1095:0.0,(Peronospora_parva_ex_Stellaria_holostea_1180:0.0,(Peronospora_honckenyae_ex_Honckenya_peploides_2683:0.0,'Peronospora cerastii-brachypetali ex Cerastium brachypetalum 2664':0.0)0.2280:0.0)0.1550:0.0)1.0000:0.01862244)0.7810:0.00549617)0.7190:0.00782612)0.0650:3.07E-4)0.0090:0.0011693)0.0000:0.00118074)0.0020:5.272E-4,(Peronospora_anagallidis_ex_Anagallis_foemina_0019:0.0198021,Peronospora_holostei_ex_Holosteum_umbellatum_0454:0.02540912)0.3530:0.00513694)0.0090:8.0443E-4,(((Peronospora_chrysosplenii_ex_Chrysosplenium_alternifolium__0217:0.00828594,Peronospora_saxifragae_ex_Saxifraga_granulata_1070:0.01704067)0.9990:0.02501293,(Peronospora_hiemalis_ex_Ranunculus_acris_0948A:0.02222733,Peronospora_ranunculi_sl_ex_Ranunculus_repens_0995:0.03391335)0.1870:0.00190538)0.0250:3.7154E-4,(Peronospora_ficariae_ex_Ficaria_verna_0974:0.023065,(('Peronospora ranunculi-sardoi ex Ranunculus sardous 1015':0.01847251,Peronospora_illyrica_ex_Ranunculus_illyricus_HV2076:0.0577883)0.2490:0.00230155,(Peronospora_pulveracea_ex_Helleborus_foetidus_2681:0.00164652,Peronospora_alpicola_ex_Ranunculus_aconitifolius_2706:-1.2775E-4)1.0000:0.02094506)0.1750:0.00300752)0.1610:9.0216E-4)0.0640:0.00420179)0.0530:0.00361938,Peronospora_consolidae_ex_Consolida_regalis_0222:0.02635663)0.0050:4.6138E-4,(Peronospora_alta_ex_Plangago_major_0817:0.06050774,(Peronospora_alchemilae_ex_Alchemila_vulgaris_agg._2653:0.01127078,(Peronospora_sanguisorbae_ex_Sanguisorba_officinalis_2714:0.00339148,('Peronospora potentillae-reptantis ex Potentilla reptans 0929':5.925E-4,(Peronospora_rubi_ex_Rubus_caesius_1021:0.0,'Peronospora potentillae-anserinae ex Potentilla anserina 2750':0.0)0.7740:9.2811E-4)0.9950:0.00351855)0.7540:0.00280309)0.9960:0.01533783)0.0250:0.00101077)0.0000:7.2333E-4,((Peronospora_dipsaci_ex_Dipsacus_fullonum_0277:0.02605364,Peronospora_phacae_ex_Astragalus_penduliflorus_2661:0.03675038)0.0920:6.0193E-4,(Peronospora_offinis_ex_Fumaria_officinalis_0344:0.03243239,('Peronospora corydalis-intermediae ex Corydalis intermedia 0250':0.0144268,Peronospora_corydalis_ex_Corydalis_solida_2670:0.01558432)1.0000:0.02653928)0.5800:0.00722765)0.0300:0.00314946)0.0020:0.00120573,(Peronospora_knautiae_ex_Scabiosa_ochroleuca_1084B:0.03102473,(Peronospora_lithospermi_ex_Lithospermum_arvense_2690:0.05139916,(Peronospora_sherardiae_ex_Sherardia_arvensis_1124:0.02450395,(Peronospora_aparines_ex_Galium_aparine_0359:0.02114002,(Peronospora_calotheca_ex_Galium_odoratum_0376:0.00256361,Peronospora_galii_ex_Galium_mollugo_2677:0.00354897)1.0000:0.01165644)0.9970:0.01287944)0.6890:0.00497291)0.2160:0.00252272)0.0210:0.0029727)0.0000:0.00130417,((((((Peronospora_glechomae_ex_Glechoma_hederacea_0450:0.01332969,'Peronospora salviae-plebeiae ex Salvia plebeia 2747':0.01197577)0.4460:8.1222E-4,Peronospora_elscholtziae_ex_Elsholtzia_ciliata_2739:0.01341446)0.4320:0.00113056,Peronospora_belbahrii_ex_Ocimum_basilicum_0730:0.01633159)0.9980:0.01619603,Peronospora_violae_ex_Viola_arvensis_1519:0.0279323)0.3840:0.00480219,(Peronospora_teucrii_ex_Teucrium_botrys_1229:0.04543793,Peronospora_perillae_ex_Perilla_frutescens_2742:0.02879595)0.5130:0.00624987)0.0390:0.00307948,((((Peronospora_digitalidis_ex_Digitalis_purpurea_0272:0.03706693,Peronospora_verbenae_ex_Verbena_officinalis_2726:0.02913764)0.6470:0.00404441,Peronospora_flava_ex_Linaria_vulgaris_0571:0.03136879)0.9800:0.0177686,Peronospora_verbasci_ex_Verbascum_nigrum_1300:0.02908132)0.4060:0.00601828,((((((Peronospora_mayorii_ex_Vicia_cracca_2731:0.00685256,Peronospora_viciae_ex_Vicia_sativa_2735:0.00712411)0.4420:0.00129847,Peronospora_pisi_ex_Pisum_sativum_0798:0.01127081)0.7790:0.00477404,Peronospora_sepium_ex_Vicia_sepium_1479:0.01535799)1.0000:0.02168905,Peronospora_fulva_ex_Lathyrus_pratensis_0550:0.03272067)0.9980:0.02374623,(Peronospora_ervi_ex_Vicia_hirsuta_1463:0.03796648,(Peronospora_myosotidis_ex_Myosotis_arvensis_0670:0.03792988,Peronospora_trigonotidis_ex_Trigonotis_peduncularis_2749:0.0506219)0.3960:0.0054674)0.0680:0.00109594)0.0120:0.00155363,((Peronospora_saturejae_hortensis_ex_Satureja_hortensis_1069:0.02973193,Peronospora_symphyti_ex_Symphytum_tuberosum_2720:0.04964069)0.1440:0.00352321,((Peronospora_lapponica_ex_Euphrasia_stricta_0323:0.0519642,Peronospora_myosotidis_s.l._ex_Myosotis_sp._2741:0.05481928)0.1660:0.00333952,((Peronospora_violacea_ex_Knautia_arvensis_0477:0.0283196,Peronospora_stigmaticola_ex_Mentha_aquatica__0630:0.0169058)0.3950:0.00265053,(Peronospora_radii_ex_Tripleurospermum_perforatum_1277:0.02685343,('Peronospora linariae-genistifoliae ex Linaria genistifolia 0560':0.02170342,Peronospora_scutellariae_ex_Scutellaria_galericulata_1118:0.01833395)0.4370:0.00196956)0.4600:0.00324955)0.3840:0.00377595)0.0560:0.00427112)0.0030:9.7275E-4)0.0000:8.6068E-4)0.0000:7.2827E-4)0.0000:3.0621E-4)0.0000:1.8962E-4,(((Peronospora_erodii_ex_Erodium_cicutarium_0302:0.02166921,Peronospora_conglomerata_ex_Geranium_pusillum_0424:0.01672044)0.9940:0.02044446,Peronospora_echii_ex_Echium_vulgare_2674:0.04239813)0.0500:9.2169E-4,(('Peronospora trifolii-repentis ex Trifolium repens 1261':0.01533435,'Peronospora trifolii-hybridi ex Trifolium hybridum 2721':0.00822877)0.9990:0.02176618,('Peronospora trifolii-minoris ex Trifolium dubium 1245':0.0182742,(Peronospora_trifoliorum_ex_Trifolium_medium_1254:0.02345692,'Peronospora trifolii-pratensis ex Trifolium pratense 1255':0.01342396)0.5140:0.00442251)0.4020:0.00176039)0.9940:0.01807496)0.0040:0.00132443)0.0000:0.00150459,(Peronospora_aestivalis_ex_Medicago_sativa_2640:0.03747344,(Peronospora_aestivalis_ex_Medicago_lupulina_0574:0.04378056,Peronospora_coronillae_ex_Securigera_varia_1122:0.03732417)0.4200:0.00670463)0.0850:0.00421774)0.0080:0.00267562,(Peronospora_meliloti_ex_Melilotus_albus_0593:0.04289947,('Peronospora potentillae-sterilis ex Potentilla sterilis 0936':0.04067082,Peronospora_oblatispora_ex_Potentilla_paradoxa_2743:0.0538833)0.2920:0.00338373)0.0920:0.00216816)0.0620:0.00192557,(Peronospora_valerianae_ex_Valeriana_officinalis_2723:0.0562472,Peronospora_valerianellae_ex_Valerianella_carinata_2724:0.03811614)0.3770:0.00692491)0.8290:0.01651495,(Peronospora_lamii_ex_Lamium_purpureum_0534:0.03696282,Peronospora_stachydis_ex_Stachys_palustris_1172:0.03841577)1.0000:0.04744879)0.0000:0.01682079,'Hyaloperonospora parasitica ex Capsell bursa-pastoris 2561':0.0440097); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr85358] END;