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- 99 - 61 76 69 - - - - 53 52 - 84 - 93 - 58 - 51 - 52 63 99 - - - 61 Zephyranthes challensis Zephyranthes andina Habranthus andalgalensis Zephyranthes citrina Zephyranthes pulchella Zephyranthes macrosiphon Zephyranthes smallii Zephyranthes chlorosolen Zephyranthes candida Zephyranthes seubertii Zephyranthes puertoricensis Zephyranthes albiella Zephyranthes longistyla Famatina cisandina Famatina andina Rhodophiala phycelloides Rhodophiala aff. advena Rhodophiala advena Rhodophiala bagnoldii Rhodophiala tiltilensis Rhodophiala sp. Rhodophiala splendens2 Rhodophiala montana Rhodophiala araucana Rhodophiala ananuca2 Rhodophiala splendens1 Famatina herbertiana Zephyranthes treatiae Zephyranthes rosea Zephyranthes carinata Zephyranthes orellanae Zephyranthes morrisclintii Zephyranthes drummondii Zephyranthes clintiae Zephyranthes simpsonii Zephyranthes atamasco Habranthus immaculatus Haylockia americana Sprekelia howardii Phycella sp. Phycella aff. cyrtanthoides Phycella angustifolia Placea davidii Placea lutea Rhodolirium speciosum Phycella australis Famatina maulensis Placea aff. ornata Placea ornata Placea germainii Placea arzae Phycella scarlatina Rhodolirium montanum Rhodolirium andicola Rhodolirium laetum Traubia modesta Zephyranthes bifolia Habranthus sp. Habranthus robustus Habranthus brachyandrus Habranthus martinezii Habranthus tubispathus Habranthus pedunculosus Sprekelia formosissima Zephyranthes filifolia Zephyranthes mesochloa Rhodophiala bifida subsp. bifida Rhodophiala bifida subsp. granatiflora Eithea blumenavia Hippeastrum reticulatum Hippeastrum brasilianum Hippeastrum sp. Hippeastrum puniceum Hippeastrum parodii Hippeastrum evansiae Hippeastrum psittacinum Hippeastrum morelianum Hippeastrum striatum Hippeastrum papilio Hippeastrum traubii Zephyranthes cearensis Griffinia parviflora Griffinia espiritensis Lycoris radiata Griffinia hyacinthina Lycoris aurea Worsleya procera Pancratium canariense Cyrtanthus herrei Cyrtanthus carneus Cyrtanthus obliquus FIGURE S1. Single most-parsimonious tree derived from trnL(UAA) intron data set. Values above branches correspond to parsimony jackknife frequency difference (GC MP-JK) values > 50%. Clades subtending terminals in bold denote groups of identical sequences. “-“ = JK < 50%. 56 61 62 94 93 - 85 58 Habranthus sp. Habranthus robustus Zephyranthes bifolia Habranthus brachyandrus Habranthus martinezii Habranthus tubispathus Habranthus pedunculosus Sprekelia formosissima Zephyranthes filifolia Famatina herbertiana Famatina cisandina Famatina andina Rhodophiala phycelloides Rhodophiala aff. advena Rhodophiala advena Rhodophiala bagnoldii Rhodophiala tiltilensis Rhodophiala sp. Rhodophiala montana Rhodophiala araucana Rhodophiala ananuca2 Rhodophiala splendens1 Zephyranthes puertoricensis Zephyranthes albiella Zephyranthes citrina Zephyranthes pulchella Zephyranthes macrosiphon Zephyranthes smallii Zephyranthes chlorosolen Zephyranthes candida Zephyranthes seubertii Habranthus immaculatus Haylockia americana Hippeastrum sp. Hippeastrum puniceum Hippeastrum parodii Hippeastrum evansiae Hippeastrum traubii Hippeastrum psittacinum Hippeastrum morelianum Hippeastrum striatum Hippeastrum papilio Hippeastrum reticulatum Rhodophiala bifida subsp. bifida Rhodophiala bifida subsp. granatiflora Sprekelia howardii Zephyranthes challensis Zephyranthes andina Zephyranthes longistyla Zephyranthes mesochloa Zephyranthes cearensis Zephyranthes treatiae Zephyranthes rosea Zephyranthes carinata Zephyranthes orellanae Zephyranthes morrisclintii Zephyranthes drummondii Zephyranthes clintiae Zephyranthes simpsonii Zephyranthes atamasco Habranthus andalgalensis Eithea blumenavia Hippeastrum brasilianum Phycella scarlatina Phycella sp. Phycella aff. cyrtanthoides Phycella angustifolia Placea davidii Placea lutea Placea aff. ornata Placea ornata Placea germainii Placea arzae Rhodolirium speciosum Phycella australis Famatina maulensis Griffinia parviflora Griffinia espiritensis Griffinia hyacinthina Lycoris aurea Worsleya procera Rhodolirium montanum Rhodolirium andicola Rhodolirium laetum Traubia modesta Lycoris radiata Pancratium canariense Cyrtanthus herrei Cyrtanthus carneus Cyrtanthus obliquus FIGURE S2. Strict consensus tree of 17 most-parsimonious trees derived from trnL(UAA)-F(GAA) intergenic spacer data set. Values above branches correspond to parsimony jackknife frequency difference (GC MP-JK) values > 50%. Clades subtending terminals in bold denote groups of identical sequences. “-“ = JK < 50%. 61/64 85/88 62/63 85/90 62/68 99/99 99/* 75/82 84/87 61/67 52/58 62/67 61/80 70/74 */* 60/74 85/86 85/93 85/87 80/86 94/96 94/95 50/80 97/98 98/99 */* 85/90 98/98 99/* 84/94 97/99 62/67 99/* 56/77 -/62 -/76 */98 Zephyranthes challensis Zephyranthes andina Habranthus andalgalensis Zephyranthes citrina Zephyranthes candida Zephyranthes seubertii Zephyranthes smallii Zephyranthes pulchella Zephyranthes macrosiphon Zephyranthes chlorosolen Zephyranthes puertoricensis Zephyranthes albiella Zephyranthes treatiae Zephyranthes rosea Zephyranthes carinata Zephyranthes orellanae Zephyranthes morrisclintii Zephyranthes drummondii Zephyranthes clintiae Zephyranthes atamasco Zephyranthes simpsonii Eithea blumenavia Hippeastrum reticulatum Sprekelia howardii Zephyranthes mesochloa Zephyranthes cearensis Famatina cisandina Rhodophiala tiltilensis Rhodophiala splendens2 Rhodophiala araucana Rhodophiala sp. Rhodophiala montana Rhodophiala aff. advena Rhodophiala advena Rhodophiala ananuca1 Rhodophiala ananuca2 Rhodophiala bagnoldii Famatina herbertiana Zephyranthes longistyla Zephyranthes flavissima Habranthus pedunculosus Habranthus martinezii Habranthus tubispathus Habranthus sp. Habranthus robustus Habranthus brachyandrus Sprekelia formosissima Zephyranthes filifolia Zephyranthes bifolia Hippeastrum sp. Hippeastrum puniceum Hippeastrum parodii Hippeastrum evansiae Hippeastrum psittacinum Hippeastrum morelianum Hippeastrum striatum Hippeastrum papilio Hippeastrum traubii Rhodophiala bifida subsp. bifida Rhodophiala bifida subsp. granatiflora Hippeastrum brasilianum Habranthus immaculatus Haylockia americana Famatina maulensis Rhodolirium speciosum Phycella australis Phycella sp. Phycella angustifolia Phycella aff. cyrtanthoides Placea davidii Placea aff. ornata Placea ornata Placea germainii Placea lutea Phycella scarlatina Rhodolirium montanum Rhodolirium andicola Rhodolirium laetum Traubia modesta Outgroups FIGURE S3. Strict consensus of 4 most-parsimonious trees derived from 3’ycf1 data set. Values above branches correspond to parsimony jackknife frequency difference (GC MP-JK) values > 50%, followed by maximum-likelihood bootstrap absolute frequency (ML-BS) values > 50% for all nucleotide characters. Clades subtending terminals in bold denote groups of identical sequences. Outgroups are not shown.”*” = 100 JK or BS; “-“ = JK or BS < 50%. 54/59 55/76 77/76 85/86 61/63 55/57 55/56 74/88 61/85 57/65 60/62 63/73 98/99 61/63 61/64 61/64 52/67 94/96 62/71 94/97 97/99 86/88 Rhodophiala ananuca1 Rhodophiala ananuca2 Rhodophiala bagnoldii Rhodophiala phycelloides Rhodophiala aff. advena Rhodophiala advena Famatina herbertiana Famatina cisandina Rhodophiala tiltilensis Rhodophiala sp. Rhodophiala montana Famatina andina Rhodophiala splendens1 Rhodophiala splendens2 Rhodophiala araucana Zephyranthes treatiae Zephyranthes rosea Zephyranthes carinata Zephyranthes orellanae Zephyranthes morrisclintii Zephyranthes drummondii Zephyranthes clintiae Zephyranthes atamasco Zephyranthes simpsonii Zephyranthes puertoricensis Zephyranthes albiella Zephyranthes minima Zephyranthes candida Zephyranthes pulchella Zephyranthes citrina Zephyranthes seubertii Zephyranthes smallii Zephyranthes macrosiphon Zephyranthes chlorosolen Zephyranthes longistyla Habranthus andalgalensis Sprekelia howardii Zephyranthes challensis Zephyranthes andina Zephyranthes mesochloa Zephyranthes cearensis Habranthus martinezii Habranthus tubispathus Habranthus sp. Habranthus robustus Habranthus pedunculosus Habranthus brachyandrus Sprekelia formosissima Zephyranthes filifolia Zephyranthes bifolia Rhodophiala bifida subsp. bifida Rhodophiala bifida subsp. granatiflora Hippeastrum sp. Hippeastrum parodii Hippeastrum puniceum Hippeastrum evansiae Hippeastrum traubii Hippeastrum psittacinum Hippeastrum morelianum Hippeastrum striatum Hippeastrum papilio Habranthus immaculatus Haylockia americana Eithea blumenavia Hippeastrum reticulatum Hippeastrum brasilianum Phycella angustifolia Phycella aff. cyrtanthoides Placea davidii Placea aff. ornata Phycella sp. Phycella scarlatina Placea ornata Placea germainii Placea lutea Placea arzae Rhodolirium montanum Rhodolirium andicola Rhodolirium laetum Traubia modesta Outgroups FIGURE S4. Most-parsimonious tree derived from ndhF data set. Values above branches correspond to parsimony jackknife frequency difference (GC MP-JK) values > 50%, followed by maximum-likelihood bootstrap absolute frequency (ML-BS) values > 50% for all nucleotide characters. Clades subtending terminals in bold denote groups of identical sequences. Outgroups are not shown. “-“ = JK or BS < 50%. 61/66 62/64 99/74 94/70 83/87 57/61 -/63/64 86/88 99/77 97/82 60/61 94/95 92/90 */* 62/65 61/76 Zephyranthes citrina Zephyranthes pulchella Zephyranthes macrosiphon Zephyranthes smallii Zephyranthes chlorosolen Zephyranthes puertoricensis Zephyranthes albiella Zephyranthes candida Zephyranthes seubertii Zephyranthes challensis Zephyranthes andina Habranthus andalgalensis Zephyranthes longistyla Habranthus sp. Habranthus robustus Zephyranthes bifolia Habranthus brachyandrus Habranthus martinezii Habranthus tubispathus Habranthus pedunculosus Sprekelia formosissima Zephyranthes filifolia Zephyranthes mesochloa Hippeastrum sp. Hippeastrum puniceum Hippeastrum parodii Hippeastrum evansiae Hippeastrum traubii Hippeastrum psittacinum Hippeastrum morelianum Hippeastrum striatum Hippeastrum papilio Famatina cisandina Famatina andina Rhodophiala phycelloides Rhodophiala aff. advena Rhodophiala advena Rhodophiala bagnoldii Rhodophiala tiltilensis Rhodophiala sp. Rhodophiala montana Rhodophiala araucana Rhodophiala ananuca2 Famatina herbertiana Rhodophiala splendens2 Rhodophiala splendens1 Habranthus immaculatus Haylockia americana Sprekelia howardii Zephyranthes treatiae Zephyranthes rosea Zephyranthes carinata Zephyranthes orellanae Zephyranthes morrisclintii Zephyranthes drummondii Zephyranthes clintiae Zephyranthes simpsonii Zephyranthes atamasco Hippeastrum reticulatum Rhodophiala bifida subsp. granatiflora Rhodophiala bifida subsp. bifida Zephyranthes cearensis Eithea blumenavia Hippeastrum brasilianum Phycella sp. Phycella aff. cyrtanthoides Phycella angustifolia Placea davidii Placea aff. ornata Placea ornata Placea germainii Placea arzae Famatina maulensis Rhodolirium speciosum Phycella australis Phycella scarlatina Placea lutea Rhodolirium montanum Rhodolirium andicola Rhodolirium laetum Traubia modesta Griffinia parviflora Griffinia espiritensis Griffinia hyacinthina Worsleya procera Lycoris aurea Lycoris radiata Pancratium canariense Cyrtanthus herrei Cyrtanthus carneus Cyrtanthus obliquus FIGURE S5. Strict consensus tree of 11 most-parsimonious trees derived from trnL(UAA)-F(GAA) data set. Values above branches correspond to parsimony jackknife frequency difference (GC MP-JK) values > 50%, followed by maximum-likelihood bootstrap absolute frequency (ML-BS) values > 50% for all nucleotide characters. Clades subtending terminals in bold denote groups of identical sequences. ”*” = 100% JK or BS; “-“ = JK or BS < 50%. rtii Zephyranthes seubeida thes cand Zephyran lbiella nthes a Zephyra ensis rtoric es p ue ranth onii Zephy imps e hes s treatia o yrant sc es Zeph nth ma hyra es ata Zep h ant hyr Zep nth a hyr Zep ose es r Zephyranthes filifolia Zephyranthes longistyla Habranthu s andalgal Zeph ensis yran Habra thes C O R E-RHOD nthus mes H ochl abra OPHIAL Ha nthu tubispathu oa A s s ma bra rtine Spre nth zii k e l ia fo us Spre r pe RHO kelia h mosissim du owa a nc D rd ulo ZEPH OPHI ALA ii su Y R s AN TH BIFIDA ES Ha AN br DIN an AS th .L. us br ac hy Ha an dr Ha bran us br an thus thu sp sr . ob us tus a HYR ZEP HES ANT LL A Ha HY CE a rin cit es nth us yra ph lat a Ze cu an ma eric im us ia am th ck ylo AP an br AC E Ha PL navia blume Eithea anthes bifolia yr Zeph Zephyranthes cearensis -1 xas /Te xico 2 Me asTex co/ exi SM THE AN HYR ZEP ola dic m an nu m ta riu mon oli m od Rh liriu o od Rh Rh o Fa dol m iriu at m in s a m pe au cio lensum sis AL I PH DO E- R CO um lat u tic O RH m nu re ilia um bras r t m as pe stru Hip ppea Hi Rh od o Tra liriu ub m l ia m ae od tum est a root FIGURE S6. Hybridization network derived from strict consensus trees resulting from analyses of cpDNA1 and equivalent ITS matrix (89 terminals) collapsed at nodes with GC MP-JK and ML-BS < 90% (HybNet1). Outgroups are not shown. Blue lines denote reticulation nodes and black lines are tree nodes. Branch lengths have no direct meaning; they have been modified to make the diagram more easily readable. A es treatiae Zephyranthes albiella Zephyranthes pu ertoricensis Zephyranthes cand ida Zephyranth es seuberti i m tru as i ret a n ica er k oc am s tu yl ula Ha c ma im s hu nt bra Ha ia lat cu pp um Hi um str ea um an sili bra a col ndi um an nt mo ma m riu iriu dol oli od Rh is Rho ns Hab pe ule RHO Hip ma A na LL ati CE HY Fa m lis P A- um Spr eke ran Sprelia how thu keli ard Zeph s pe a fo ii yra dun rmo nth Zep culo siss es b hyr ant sus ima ifo hes lia fil a se nthes ro tra ios ifol ia Ze Ze Habra ph ph nthus yr yr brach ZE an an yand P H H a th th b Y Habr rus r RA ant es es ant hus NT m cit tub Habran hus robus HE es rin ZE i tus s thu oc P SM pat H s sp hus hl a ex YRA . oa ico N Ha bra /Te THE SM nth xa us s-1 ex ma ico rtin /Te ezi xa s-2 i Zephyra Zephyranth asco Zephyranthes simpsonii tam nthes a Zephyra PHIALA E AC us ec navia blume nsis Eithea eare hes c .L. yrant INA S Zeph AND THES FIDA YRAN A BI HIAL DOP sp PL m aa riu ZEPH oli M TRU EAS IPP longistyla Zephyranthes alensis andalg nthus Habra HODO R CORE- E-H R CO od ell yc Ph Rh Rh od oli riu m Trau bia laetu mo des m ta root FIGURE S7. Hybridization network derived from strict consensus trees resulting from analyses of cpDNA1 and equivalent ITS matrix (89 terminals) collapsed at nodes with GC MP-JK and ML-BS < 70% (HybNet3). Outgroups are not shown. Blue lines denote reticulation nodes and black lines are tree nodes. Branch lengths have no direct meaning; they have been modified to make the diagram more easily readable. Sprek elia h Ha br an um A ns rach yand rus H abra nt nthu hu s t Habr s rob ub a ustu isp nthus s at sp. hu s rant hus b bra Hab Ha la u ac na imm ica s er thu am an ia abr k c lo H s O -RH y Ha RE CO um str ea HIALA um an sili bra um aet ml sta de dic ola num mo an onta iriu mm ia ium dol oliriu olir LA HIA P DO pp Rho od ub Tra Rh Rhod a br Hi is m tu a Eith via na s S.L. me ensi r INA m blu ea s cea latu e u nth retic owar dii AND str ea ra hy pp LL CE HY P A- E AC ule s hu nt Ha th u Sp s pe re du ke n lia cu fo los rm us os iss im HES Hi p Ze M Zeph y Zep ranthes nth bifo hyr lia an es the me s fi so lifo ch lia loa ANT TRU EAS PL hy ra HYR IPP Ph y riu cell m aa sp us ec tr io al Fa sum is ma tin am a oli Ze p ZEP E-H od Zephyranthes citrina nthes rosea ae thes treati Zephyra Zephyran psonii Zephyranthes sim Zephyranth es atamasc o ZEPHYRANTH ES Mexico/Te xas-1 ZEPHYRANTHES Mexico /Texas-2 Zephyranthes candida Zephyranthes se ubertii pu hes rant lla thes albie s Zephyran si ricen erto hy Zep R CO Rh zii ne ti ar OP RHOD A BIFID root FIGURE S8. Hybridization network derived from strict consensus trees resulting from analyses of cpDNA2 and equivalent ITS matrix (87 terminals) collapsed at nodes with GC MP-JK and ML-BS < 70% (HybNet4). Outgroups are not shown. Blue lines denote reticulation nodes and black lines are tree nodes. Branch lengths have no direct meaning; they have been modified to make the diagram more easily readable. Rhodophiala bifida subsp. granatiflora Rhodophiala bifida subsp. granatiflora Rhodophiala bifida subsp. granatiflora Rhodophiala bifida subsp. granatiflora Rhodophiala bifida subsp. granatiflora Rhodophiala bifida subsp. granatiflora Rhodophiala bifida subsp. granatiflora Rhodophiala bifida subsp. granatiflora Unknown (Rhodophiala bifida subsp. granatiflora?) Eithea blumenavia 473 646 p = 6.97 E-3 Unknown (Hippeastrum cipoanum?) Famatina andina p = 1.78 E-4 Unknown (Hippeastrum cipoanum?) Rhodophiala advena p = 1.78 E-4 Unknown (Hippeastrum cipoanum?) Rhodophiala araucana p = 1.78 E-4 Unknown (Hippeastrum cipoanum?) Rhodophiala bagnoldii p = 1.78 E-4 Unknown (Hippeastrum cipoanum?) Rhodophiala montana p = 1.78 E-4 Unknown (Hippeastrum cipoanum?) Rhodophiala phycelloides p = 1.78 E-4 Unknown (Hippeastrum cipoanum?) Rhodophiala splendens p = 1.78 E-4 Unknown (Hippeastrum cipoanum?) Hippeastrum cipoanum 445 640 p = 9.61 E-3 Hippeastrum striatum FIGURE S9. Partial schematic plot of alignment of ITS across Clade B indicating the presence of two recombination events detected by RDP4. The recombinant sequences are labelled above the bars, putative major parents to the left, and minor parents to the right. The p-values are Bonferroni corrected for multiple comparisons. Putative recombination breakpoint positions in the recombinants are indicated for the first sequence of each event.
