From the Cover: Island radiation on a continental scale: Exceptional rates of plant diversification after uplift of the Andes -- Hughes and Eastwood 103 (27): 10334 Data Supplement - HTML Page - index.htslp -- Proceedings of the National Academy of Sciences

Hughes and Eastwood. 10.1073/pnas.0601928103.

Supporting Information

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Supporting Figure 4
Supporting Figure 5
Supporting Table 1

Supporting Figure 4

Fig. 4. Phylogeny of Lupinus. Strict consensus of 184,229 equal-length trees. Length (L) = 1,289 steps, consistency index (CI) = 0.52, and retention index (RI) = 0.89 from parsimony analysis of the combined ITS and LEGCYCIA data sets. Bootstrap values >50% are shown below nodes. The parsimony tree is more densely sampled than the Bayesian tree (Fig. 5) because of the inclusion of multiple accessions of some species. Although somewhat less resolved, the parsimony tree is congruent with the Bayesian (Figs. 2 and 5). Full details for all accessions including GenBank accession numbers are provided in Table 1.

Supporting Figure 5

Fig. 5. Phylogeny of Lupinus. Fifty percent majority rule Bayesian tree of the combined ITS/LEGCYC1A data set. This is a fully annotated version of Fig. 2 with taxon names indicated on terminals and all posterior probabilities shown below nodes. Full details for all accessions including GenBank accession numbers are provided in Table 1.

Table 1. Accession data including voucher number, herbarium where deposited, locality where collected, and GenBank numbers

Species	Accession/voucher/herbarium	Location	GenBank accession no., ITS	GenBank accession no., LEGCYCIA
Genista tenera *	UBC Botanical Garden BG11^†	UBC Botanical Garden	AY338950	AY338924
Genista pilosa	Hughes C.E. 2340, FHO	Cornwall, UK	DQ524183	DQ529976
Genista umbellata	Hughes C.E. 1980, FHO	Malaga, Spain	DQ524184	DQ529783, DQ529784
Genista anglica	Hughes C.E. 2339, FHO	Cornwall, UK	DQ524181	DQ529977
Pterospartum tridentatum	Hughes C.E. 2338, FHO	Alentejo, Portugal	DQ524325	DQ529866
Retama monosperma	Hughes C.E. 2182, FHO	Algarve, Portugal	DQ524326	DQ529755
Spartium junceum	Hughes C.E. 2190, FHO	Algarve, Portugal	DQ524327	DQ529756
Stauracanthus genistoides	Hughes C.E. 2335, FHO	Algarve, Portugal	DQ524328	DQ529865
Lupinus albus *	Hughes C.E. 1970, FHO	Algarve, Portugal	DQ524191	DQ529787, DQ529788
Lupinus albus	USDA PI 170528	UBC Botanical Garden	AY338946	AY338920
Lupinus angustifolius *	Hughes C.E. 1972, FHO	Algarve, Portugal	DQ524192	DQ529978
Lupinus angustifolius	Hughes C.E. 1976, FHO	Sevilla, Spain	DQ524193	DQ529757, DQ529758
Lupinus hispanicus *	Pannell J.R. 1, FHO	Chaves, Portugal	DQ524236	DQ529780, DQ529781
Lupinus luteus *	Hughes C.E. 1973, FHO	Sevilla, Spain	DQ524249	DQ529782
Lupinus micranthus *	Hughes C.E. 1982, FHO	Malaga, Spain	DQ524252	DQ529813
Lupinus cosentinii *	USDA W6 17967	UBC Botanical Garden, BG8	AY338947	AY338921
Lupinus cosentinii	Hughes C.E. 1967, FHO	Algarve, Portugal	DQ524222	DQ529744
Lupinus digitatus *	USDA W6 11995	UBC Botanical Garden, BG9	AY338948	AY338922
Lupinus cumulicola *	Hughes C.E. 1983, FHO	Florida	DQ524226	DQ529745, DQ529746
Lupinus cumulicola	Hughes C.E. 1988, FHO	Florida	DQ524227	DQ529747, DQ529748
Lupinus villosus *	Hughes C.E. 1986, FHO	Florida	DQ524322	DQ529749, DQ529750
Lupinus villosus	Hughes C.E. 1987, FHO	Florida	DQ524323	DQ529751, DQ529752
Lupinus andersonii *	Lavin M. 0815985, MONT	Nevada	AY338934	AY338908
Lupinus argenteus	Spellenberg R. 13448, FHO, NMC	New Mexico	DQ524197	DQ529970, DQ529971
Lupinus argenteus	Lavin M. 0815982, MONT	Nevada	AY338931	AY338905
Lupinus argenteus	Lavin M. s.n., MONT	Montana	AY338936	AY338910
Lupinus argenteus *	Delgado & Lavin s.n., MEXU	Montana	AY338929	AY338903
Lupinus arboreus *	Spellenberg R. 13488, FHO, NMC	California	DQ524196	DQ529972, DQ529973
Lupinus arboreus	UBC Botanical Garden, UBC	British Columbia, Canada	AY338944	AY338918
Lupinus arboreus	Kenicer G. 120, FHO	California	DQ524195	DQ529897, DQ529898
Lupinus arboreus	Hughes, C.E. s.n.	Oxford, UK	DQ524194	DQ529753, DQ529754
Lupinus arizonicus *	USDA PI 577285	Arizona	DQ524198	DQ529968, DQ529969
Lupinus bicolor *	USDA PI 284713	California	DQ524209	DQ529962, DQ529963
Lupinus concinnus	Bailey C.D. 242, FHO, NMC	New Mexico	DQ524212	DQ529960, DQ529961
Lupinus concinnus *	Baker M. 10768, ASU	Arizona	DQ524214	DQ529958, DQ529959
Lupinus breweri	Lavin 7031, MONT	California	AY338938	AY338912
Lupinus breweri *	Lavin M. 0815983, MONT	Nevada	AY338932	AY338906
Lupinus microcarpus	Drummond C.D. 0331A02	California	DQ524228	DQ529956, DQ529957
Lupinus densiflorus	UBC Botanical Garden BG1	British Columbia, Canada	AY338940	AY338914
Lupinus densiflorus	UBC Botanical Garden BG2	British Columbia, Canada	AY338941	AY338915
Lupinus densiflorus	UBC Botanical Garden BG3	British Columbia, Canada	AY338942	AY338916
Lupinus densiflorus *	UBC Botanical Garden BG4	British Columbia, Canada	AY338943	AY338917
Lupinus grayi *	Lavin M. 7033, MONT	California	AY338939	AY338913
Lupinus havardii *	USDA DLEG 930123	Texas	DQ524233	DQ529948, DQ529949
Lupinus havardii	USDA DLEG 910433	Texas	DQ524232	DQ529950, DQ529951
Lupinus hirsutissimus *	USDA DLEG 920120	California	DQ524235	DQ529944, DQ529945
Lupinus hirsutissimus	S & S Seeds	California	DQ524234	DQ529946, DQ529947
Lupinus latifolius *	Baker M. 10938, ASU	Arizona	DQ524243	DQ529942, DQ529943
Lupinus lactus *	Spellenberg R.13415, FHO, NMC	New Mexico	DQ524240	DQ529979
Lupinus lepidus *	USDA PI 504439	USA	DQ524246	DQ529939
Lupinus lepidus	Lavin M. 0815984, MONT	Nevada	AY338933	AY338907
Lupinus odoratus *	Drummond C.D. 0311A01	California	DQ524276	DQ529930
Lupinus polyphyllus *	Lavin M. 0815981, MONT	Nevada	AY338930	AY338904
Lupinus polyphyllus	UBC Botanical Garden		AY338945	AY338919
Lupinus neomexicanus *	Spellenberg R.13422, FHO, NMC	New Mexico	DQ524274	DQ529931, DQ529932
Lupinus rivularis *	Lavin M. 7040, MONT	California	AY338937	AY338911
Lupinus sericeus *	Lavin s.n., MONT	Montana	AY338935	AY338909
Lupinus sierrae-blancae *	Spellenberg R.13409, FHO, NMC	New Mexico	DQ524298	DQ529920, DQ529921
Lupinus texensis *	USDA PI 577291	Texas	AY338949	AY338923
Lupinus texensis	S & S Seeds	Texas	DQ524316	DQ529918, DQ529919
Lupinus truncatus *	S & S Seeds	USA	DQ524318	DQ529916, DQ529917
Lupinus chamissonis *	Kenicer G. 121, FHO	California	DQ524217	DQ529895, DQ529896
Lupinus chamissonis	Kenicer G. 122, FHO	California	DQ524218	DQ529893, DQ529894
Lupinus sp. 1*	Hughes C.E. 2107, FHO, MEXU	Oaxaca, Mexico	DQ524308	DQ529807, DQ529808
Lupinus sp. 2*	Hughes C.E. 2117, FHO, MEXU	Oaxaca, Mexico	DQ524310	DQ529912, DQ529913
Lupinus sp. 1	Hughes C.E. 2118, FHO, MEXU	Oaxaca, Mexico	DQ524309	DQ529768, DQ529769
Lupinus sp. 3*	Hughes C.E. 2160, FHO, MEXU	Mexico, Mexico	DQ524311	DQ529909, DQ529910
Lupinus montanus *	Hughes C.E. 2174, FHO, MEXU	Veracruz, Mexico	DQ524259	DQ529809, DQ529810
Lupinus mutabilis *	Hughes C.E. 2009, FHO, MOL	Cajamarca, Peru	DQ524262	DQ529799, DQ529800
Lupinus mutabilis	Hughes C.E. 2291, FHO, LPB	Cochabamba, Bolivia	DQ524270	DQ529778, DQ529779
Lupinus piurensis *	Hughes C.E. 1997, FHO, MOL	Cajamarca, Peru	DQ524281	DQ529814, DQ529815
Lupinus piurensis	Eastwood R.J. 110, FHO, MOL	Cajamarca, Peru	DQ524282	DQ529891, DQ529892
Lupinus semperflorens	Hughes C.E. 2012, FHO, MOL	Cajamarca, Peru	DQ524293	DQ529801, DQ529802
Lupinus semperflorens	Hughes C.E. 2030, FHO, MOL	Amazonas, Peru	DQ524188	DQ529765
Lupinus solangorum	Hughes C.E. 2014, FHO, MOL	Cajamarca, Peru	DQ524294	DQ529803, DQ529804
Lupinus semperflorens *	Eastwood R.J. 219, FHO, QCNE	Loja, Ecuador	DQ524296	DQ529922, DQ529923
Lupinus semperflorens	Eastwood R.J. 220, FHO, QCNE	Loja, Ecuador	DQ524297	DQ529869, DQ529870
Lupinus mantaroensis *	Hughes C.E. 2000, FHO, MOL	Cajamarca, Peru	DQ524200	DQ529759, DQ529760
Lupinus sp. 4*	Hughes C.E. 2002, FHO, MOL	Cajamarca, Peru	DQ524299	DQ529795, DQ529796
Lupinus sp. 4	Hughes C.E. 2005, FHO, MOL	Cajamarca, Peru	DQ524189	DQ529785, DQ529786
Lupinus sp. 5*	Hughes C.E. 2004, FHO, MOL	Cajamarca, Peru	DQ524305	DQ529797, DQ529798
Lupinus aff. ramosissimus *	Hughes C.E. 2010, FHO, MOL	Cajamarca, Peru	DQ524289	DQ529761, DQ529762
Lupinus aff sarmentosus *	Hughes C.E. 2015, FHO, MOL	Cajamarca, Peru	DQ524187	DQ529805, DQ529806
Lupinus chachas *	Hughes C.E. 2027, FHO, MOL	Amazonas, Peru	DQ524216	DQ529763, DQ529764
Lupinus sp. 6*	Hughes C.E. 2037, FHO, MOL	Cajamarca, Peru	DQ524306	DQ529766, DQ529767
Lupinus weberbaueri *	Hughes C.E. 2233, FHO, MOL	Ancash, Peru	DQ524324	DQ529811, DQ529812
Lupinus ballianus	Hughes C.E. 2038, FHO, MOL	Ancash, Peru	DQ524201	DQ529914, DQ529915
Lupinus prostratus *	Hughes C.E. 2239, FHO, MOL	Ancash, Peru	DQ524286	DQ529791, DQ529792
Lupinus huaronensis	Hughes C.E. 2241, FHO, MOL	Ancash, Peru	DQ524237	DQ529770, DQ529771
Lupinus purosericeus *	Hughes C.E. 2248, FHO, MOL	Pasco, Peru	DQ524238	DQ529772, DQ529773
Lupinus bangii *	Hughes C.E. 2250, FHO, LPB	La Paz, Bolivia	DQ524256	DQ529911
Lupinus chrysanthus *	Hughes C.E. 2264, FHO, LPB	La Paz, Bolivia	DQ524220	DQ529793, DQ529794
Lupinus microphyllus	Hughes C.E. 2238, FHO, MOL	Ancash, Peru	DQ524254	DQ529789, DQ529790
Lupinus microphyllus *	Hughes C.E. 2272, FHO, LPB	Cochabamba, Bolivia	DQ524255	DQ529774, DQ529775
Lupinus pulvinaris *	Hughes C.E. 2273, FHO, LPB	Cochabamba, Bolivia	DQ524288	DQ529776, DQ529777
Lupinus tomentosus *	Hughes C.E. 2322, FHO, LPB	La Paz, Bolivia	DQ524317	DQ529905, DQ529906
Lupinus praestabilis *	Hughes C.E. 2353, FHO, MOL	Arequipa, Peru	DQ524285	DQ529822, DQ529823
Lupinus chrysanthus *	Hughes C.E. 2390, FHO, MOL	Apurimac, Peru	DQ524221	DQ529901, DQ529902
Lupinus bangii *	Hughes C.E. 2444, FHO, LPB	La Paz, Bolivia	DQ524208	DQ529826, DQ529827
Lupinus tominensis	Hughes C.E. 2294, FHO, LPB	Cochabamba, Bolivia	DQ524207	DQ529824, DQ529825
Lupinus aff. bangii	Hughes C.E. 2370, FHO, MOL	Puno, Peru	DQ524300	DQ529903, DQ529904
Lupinus subacaulis	Hughes C.E. 2319, FHO, LPB	Potosi, Bolivia	DQ524312	DQ529907, DQ529908
Lupinus sp. 9*	Eastwood R.J. 59, FHO, MOL	La Libertad, Peru	DQ524301	DQ529867, DQ529868
Lupinus lindleyanus *	Eastwood R.J. 141, FHO, MOL	Lima, Peru	DQ524247	DQ529889, DQ529890
Lupinus misticola *	Eastwood R.J. 144, FHO, MOL	Lima, Peru	DQ524257	DQ529887, DQ529888
Lupinus sp. 7*	Eastwood R.J. 168, FHO, QCNE	Imbabura, Ecuador	DQ524302	DQ529883, DQ529884
Lupinus sarmentosus	Eastwood R.J. 174, FHO, QCNE	Pichincha, Ecuador	DQ524291	DQ529881, DQ529882
Lupinus pubescens	Eastwood R.J. 176, FHO, QCNE	Pichincha, Ecuador	DQ524287	DQ529879, DQ529880
Lupinus arvensis *	Eastwood R.J. 188, FHO, QCNE	Bolivar, Ecuador	DQ524199	DQ529877, DQ529878
Lupinus nubigenus *	Eastwood R.J. 200, FHO, QCNE	Chimborazo, Ecuador	DQ524275	DQ529875, DQ529876
Lupinus sp. 8*	Eastwood R.J. 206, FHO, QCNE	Azuay, Ecuador	DQ524303	DQ529873, DQ529874
Lupinus huigrensis *	Eastwood R.J. 217, FHO, QCNE	Loja, Ecuador	DQ524304	DQ529871, DQ529872
Lupinus mollendoensis *	Weigend M. 97/703, USM	Arequipa, Peru	DQ524258	DQ529933, DQ529934
Lupinus tarapacensis *	Gardner M.F. 6296, FHO	Tarapaca, Chile	DQ524314	DQ529899, DQ529900
Lupinus microcarpus *	Darwin Chilean Initiative DCI 1513, FHO	Valparaiso, Chile	DQ524253	DQ529935, DQ529936
Lupinus bandelierae	Hughes C.E. 2301, FHO, LPB	Cochabamba, Bolivia	DQ524202	DQ529966, DQ529967
Lupinus bandelierae	Hughes C.E. 2310, FHO, LPB	Chuquisaca, Bolivia	DQ524203	DQ529820, DQ529821
Lupinus bandelierae	Hughes C.E. 2318, FHO, LPB	Potosi, Bolivia	DQ524204	DQ529861, DQ529862
Lupinus bandelierae *	Hughes C.E. 2321, FHO, LPB	La Paz, Bolivia	DQ524205	DQ529859, DQ529860
Lupinus bandelierae	Hughes C.E. 2327, FHO, LPB	La Paz, Bolivia	DQ524206	DQ529964, DQ529965
Lupinus albescens *	Hughes C.E. 2509, FHO, ICN	Rio Grande do Sul, Brasil	DQ524190	DQ529974, DQ529975
Lupinus bracteolaris *	Miotto S.T.S. & Pinheiro M.1810, ICN	Santa Catarina, Brasil	DQ524210	DQ529816, DQ529817
Lupinus bracteolaris	Miotto S.T.S. & Pinheiro M.1819, ICN	Rio Grande do Sul, Brasil	DQ524211	DQ529857, DQ529858
Lupinus crotalarioides *	Hughes C.E. 2481, FHO, UB	Distrito Federal, Brasil	DQ524223	DQ529863, DQ529864
Lupinus crotalarioides	Hughes C.E. 2482, FHO, UB	Goias, Brasil	DQ524224	DQ529855, DQ529856
Lupinus crotalarioides	Hughes C.E. 2483, FHO, UB	Goias, Brasil	DQ524225	DQ529853, DQ529854
Lupinus gibertianus *	Miotto S.T.S. & Pinheiro M.1835, ICN	Rio Grande do Sul, Brasil	DQ524229	DQ529851, DQ529852
Lupinus guaraniticus	Hughes C.E. 2488, FHO, ICN	Rio Grande do Sul, Brasil	DQ524230	DQ529954, DQ529955
Lupinus guaraniticus *	Kenicer G. s.n., E, FHO	Argentina	DQ524231	DQ529952, DQ529953
Lupinus lanatus *	Miotto S.T.S. & Pinheiro M. 1806, ICN	Rio Grande do Sul, Brasil	DQ524241	DQ529849, DQ529850
Lupinus lanatus	Miotto S.T.S. & Pinheiro M. 1837, ICN	Santa Catarina, Brasil	DQ524242	DQ529847, DQ529848
Lupinus linearis *	Miotto S.T.S. & Pinheiro M. 1798, ICN	Rio Grande do Sul, Brasil	DQ524248	DQ529828, DQ529829
Lupinus linearis	Miotto S.T.S. & Pinheiro M. 1813, ICN	Rio Grande do Sul, Brasil	DQ524239	DQ529846
Lupinus magnistipulatus *	Miotto S.T.S. & Pinheiro M. 1840, ICN	Rio Grande do Sul, Brasil	DQ524250	DQ529830, DQ529831
Lupinus magnistipulatus	Pinheiro M. 164, ICN	Rio Grande do Sul, Brasil	DQ524251	DQ529937, DQ529938
Lupinus multiflorus *	Miotto S.T.S. & Pinheiro M. 1825, ICN	Santa Catarina, Brasil	DQ524260	DQ529844, DQ529845
Lupinus paranensis *	Miotto S.T.S. & Pinheiro M. ind2_18, ICN	Rio Grande do Sul, Brasil	DQ524279	DQ529924, DQ529925
Lupinus paraguariensis	Hughes C.E. 2495, FHO, ICN	Rio Grande do Sul, Brasil	DQ524277	DQ529928, DQ529929
Lupinus paraguariensis *	Hughes C.E. 2496, FHO, ICN	Rio Grande do Sul, Brasil	DQ524278	DQ529926, DQ529927
Lupinus parvifolius *	Hughes C.E. 2480, FHO, UB	Minas Gerais, Brasil	DQ524280	DQ529836, DQ529837
Lupinus reitzii *	Miotto S.T.S. & Pinheiro M. 1846, ICN	Rio Grande do Sul, Brasil	DQ524290	DQ529832, DQ529833
Lupinus rubriflorus *	Miotto S.T.S. & Pinheiro M. 1838, ICN	Rio Grande do Sul, Brasil	DQ524292	DQ529842, DQ529843
Lupinus subsessilis *	Hughes C.E. 2479, FHO, UB	Goias, Brasil	DQ524313	DQ529840, DQ529841
Lupinus uleanus *	Miotto S.T.S. & Pinheiro M. 1848, ICN	Rio Grande do Sul, Brasil	DQ524319	DQ529838, DQ529839
Lupinus velutinus	Hughes C.E. 2477, FHO, UB	Distrito Federal, Brasil	DQ524320	DQ529834, DQ529835
Lupinus velutinus *	Hughes C.E. 2478, UB	Distrito Federal, Brasil	DQ524321	DQ529818, DQ529819

*Sequences included in Bayesian analysis.

^†Herbarium acronyms follow Index Herbariorum.