Molecular Phylogenetics and the Diversification of Hummingbirds

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1 Current Biology, Volume 24 Supplemental Information Molecular Phylogenetics and the Diversification of Hummingbirds Jimmy A. McGuire, Christopher C. Witt, J. V. Remsen, Jr., Ammon Corl, Daniel L. Rabosky, Douglas L. Altshuler, and Robert Dudley

2 Outgroups Topazes 0.79 Hermits Hummingbird / Swift Split Mangoes Brilliants Coquettes Patagona Mtn. Gems Bees Emeralds 65.5 U Paleocene Oligocene Eocene Miocene 20 Pliocene 10 Pl. 0 Ma Fig. S1. Time-calibrated phylogenetic estimate for hummingbirds and outgroup species, Related to Figure 1. The tree is derived a BEAST MCMC analysis of a concatenated 6-gene (5-locus) data set. Numbers at nodes reflect posterior probabilities less than 1.0. Asterisks denote nodes with 100% posterior probability support. The first page is the backbone tree for all hummingbirds with species-level detail presented on the following pages.

3 Topazes Hermits Florisuga fusca LSUMZ B16936 Florisuga mellivora LSUMZ B9646 Topaza pella NMNH b5205 Topaza pella LSUMZ B35362 Topaza pyra LSUMZ B42167 Topaza pyra LSUMZ B42323 Topaza pyra LSUMZ B42387 Topaza pyra LSUMZ B42522 Eutoxeres condamini LSUMZ B8094 Eutoxeres aquila LSUMZ B2110 Ramphodon naevius ZMC Glaucis aeneus NMNH b368 Glaucis hirsutus LSUMZ B28468 Threnetes leucurus LSUMZ B2673 Threnetes ruckeri LSUMZ B28170 Phaethornis hispidus LSUMZ B18351 Phaethornis hispidus LSUMZ B18142 Phaethornis syrmatophorus LSUMZ B12138 Phaethornis syrmatophorus Jaime sequence Phaethornis syrmatophorus LSUMZ B33578 Phaethornis syrmatophorus LSUMZ B33737 Phaethornis mexicanus JK07_110 Phaethornis mexicanus JK07_108 Phaethornis longirostris LSUMZ B28503 Phaethornis longirostris NMNH b310 Phaethornis yaruqui LSUMZ B7812 Phaethornis guy JLPV 35 Phaethornis guy LSUMZ B28342 Phaethornis guy LSUMZ B35966 Phaethornis malaris LSUMZ B27511 Phaethornis superciliosus FMNH Phaethornis superciliosus FMNH Phaethornis superciliosus AMNH DOT4284 Phaethornis superciliosus ANSP Phaethornis superciliosus LSUMZ B48308 Phaethornis superciliosus ANSP Phaethornis superciliosus LSUMZ B48364 Phaethornis superciliosus AMNH DOT2979 Phaethornis subochraceus LSUMZ B6544 Phaethornis eurynome FMNH Phaethornis pretrei LSUMZ B14702 Phaethornis augusti UMMZ t604 Phaethornis bourcieri LSUMZ B11104 Phaethornis bourcieri LSUMZ B11017 Phaethornis bourcieri LSUMZ B10629 Phaethornis bourcieri LSUMZ B10502 Phaethornis koepckeae LSUMZ B5479 Phaethornis koepckeae LSUMZ B5398 Phaethornis philippii LSUMZ B9280 Phaethornis philippii LSUMZ B9020 Phaethornis philippii LSUMZ B8868 Phaethornis anthophilus UMMZ t594 Phaethornis rupurumii IAVHB 4463 Phaethornis rupurumii LSUMZ B20240 Phaethoris longuemareus LSUMZ B35952 Phaethornis nattereri LSUMZ B12859 Phaethornis atrimentalis LSUMZ B1969 Phaethornis ruber FMNH Phaethornis ruber FMNH Phaethornis ruber LSUMZ B9481 Phaethornis striigularis LSUMZ B28411 Phaethornis striigularis LSUMZ B28790 Phaethornis striigularis LSUMZ B28518 Phaethornis griseogularis AMNH PEP1971 Phaethornis griseogularis LSUMZ B5571 Phaethornis griseogularis LSUMZ B44650

4 Mangoes Doryfera johannae LSUMZ B1728 Doryfera ludovicae LSUMZ B1802 Doryfera ludovicae LSUMZ B8000 Schistes geoffroyi LSUMZ B6300 Colibri serrirostris LSUMZ B14576 Colibri coruscans LSUMZ B6310 Colibri delphinae LSUMZ B5403 Colibri sp. LSUMZ B49711 Colibri thalassinus LSUMZ B28263 Heliactin bilophus LSUMZ B14845 Androdon aequatorialis LSUMZ B1402 Heliothryx auritus LSUMZ B6913 Heliothryx barroti LSUMZ B12039 Polytmus guainumbi LSUMZ B6691 Polytmus theresiae NMNH b10307 Polytmus milleri AMNH PRS476 Avocettula recurvirostris FMNH Chrysolampis mosquitus LSUMZ B35902 Chrysolampis mosquitus NMNH b12236 Anthracothorax mango MVZ Anthracothorax mango MVZ Anthracothorax mango STRI JAAMA2 Anthracothorax mango STRI JAAMA1 Anthracothorax nigricollis LSUMZ B9552 Anthracothorax viridigula FMNH Anthracothorax prevostii NMNH b360 Anthracothorax veraguensis NMNH b1347 Anthracothorax dominicus LSUMZ B11318 Anthracothorax viridis LSUMZ B11519 Eulampis holosericeus NMNH b2121 Eulampis jugularis STRI svej46 Eulampis jugularis STRI maej412 Eulampis jugularis STRI doej413 Brilliants Haplophaedia aureliae LSUMZ B32971 Haplophaedia lugens LSUMZ B30032 Eriocnemis glaucopoides UWBM Lodiggesia mirabilis LSUMZ B44698 Eriocnemis mosquera LSUMZ B6335 Eriocnemis nigrivestis ZMC Eriocnemis vestita LSUMZ B324 Eriocnemis aline LSUMZ B1805 Eriocnemis luciani LSUMZ B6337 Eriocnemis derbyi ANSP Eriocnemis cupreoventris JPLV 30 Eriocnemis cupreoventris JPLV 2558 Lafresnaya lafresnayi LSUMZ B32576 Lafresnaya lafresnayi LSUMZ B32771 Aglaeactis cupripennis LSUMZ B6304 Aglaeactis pamela LSUMZ B Aglaeactis castelnaudii NK Aglaeactis castelnaudii LSUMZ B8215 Pterophanes cyanopterus LSUMZ B1296 Ensifera ensifera LSUMZ B8224 Boissonneaua jardini ANSP Boissonneaua flavescens LSUMZ B12099 Boissonneaua mathewsii LSUMZ B8130 Urosticte ruficrissa JPLV 2325 Urosticte benjamini LSUMZ B5546 Ocreatus underwoodii JPLV 39 Ocreatus underwoodii LSUMZ Urochroa bougueri ZMC Heliodoxa schreibersii LSUMZ B5440 Heliodoxa xanthogonys LSUMZ B7415 Heliodoxa branickii LSUMZ B1996 Heliodoxa gularis LSUMZ B5428 Heliodoxa aurescens LSUMZ B6789 Clytolaema rubricauda FMNH Heliodoxa rubinoides LSUMZ B1651 Heliodoxa imperatrix LSUMZ B12088 Heliodoxa leadbeateri LSUMZ B6036 Heliodoxa jacula LSUMZ B11940 Heliodoxa jacula LSUMZ B16037 Coeligena prunellei JPLV 42 Coeligena wilsoni LSUMZ B7858 Coeligena coeligena LSUMZ B8015 Coeligena coeligena JAVH 5334 Coeligena coeligena JAVH 1216 Coeligena coeligena JAVH 1950 Coeligena torquata inca AMNH DOT2599 Coeligena torquata inca AMNH DOT2598 Coeligena torquata LSUMZ B6230 Coeligena torquata JPLV 58 Coeligena torquata AVHB 4633 Coeligena violifer LSUMZ B8200 Coeligena iris LSUMZ B31770 Coeligena phalerata JPLV 485 Coeligena bonapartei AVHB 4188 Coeligena helianthea JPLV 2504 Coeligena bonapartei JPLV 2271 Coeligena lutetia LSUMZ B340 Coeligena lutetiae AVHB 1915 Coeligena orina PCPR 1 Coeligena orina JPLV 5169 Coeligena orina PCPR 3

5 Coquettes Sephanoides fernandensis MR 622 Sephanoides fernandensis MR 620 Sephanoides sephaniodes MR 629 Sephanoides sephaniodes Jose 1 Sephanoides sephaniodes AMNH 1126 Sephanoides sephaniodes MR 613 Sephanoides sephaniodes MR 626 Lophornis pavoninus KU 6045 Lophornis delattrei LSUMZ B22644 Lophornis chalybeus LSUMZ B9399 Discosura longicauda NMNH b5265 Discosura conversii LSUMZ B16064 Discosura popelairii LSUMZ B5950 Discosura langsdorfii LSUMZ B9633 Phlogophilus hemileucurus LSUMZ B5999 Phlogophilus harterti KU Phlogophilus harterti KU Heliangelus regalis LSUMZ B5532 Heliangelus strophianus LSUMZ B6296 Heliangelus amethysticollis LSUMZ B6246 Heliangelus amethysticollis LSUMZ B33890 Heliangelus exortis ANSP Heliangelus viola LSUMZ B32370 Heliangelus exortis JPLV 40 Heliangelus micraster LSUMZ B34698 Heliangelus micraster LSUMZ B31990 Heliangelus micraster ANSP 5013 Heliangelus exortis ANSP Adelomyia melanogenys LSUMZ B8025 Adelomyia melanogenys maculata Valqui 681 Adelomyia melanogenys maculata Valqui 656 Heliangelus zusii ANSP Taphrolesbia griseiventris LSUMZ B10388 Aglaiocercus kingii LSUMZ B8017 Aglaiocercus coelestis LSUMZ B7813 Sappho sparganurus LSUMZ B1195 Ramphomicron microrhynchum LSUMZ B8376 Lesbia nuna LSUMZ B3615 Lesbia victoriae ZMC Oreotrochilus estella LSUMZ B Oreotrochilus estella MR 649 Oreotrochilus chimborazo ZMC Oreotrochilus estella stolzmanni ANSP Oreotrochilus estella stolzmanni ANSP Oreotrochilus melanogaster LSUMZ B2077 Polyonymus caroli Valqui 680 Polyonymus caroli LSUMZ B15503 Opisthoprora euryptera ZMC Chalcostigma herrani LSUMZ 6277 Chalcostigma ruficeps LSUMZ 1293 Chalcostigma olivaceum LSUMZ Chalcostigma olivaceum LSUMZ Oreonympha nobilis FMNH Chalcostigma stanleyi MSB:Bird:27151 Oxypogon guerinii ZMC Metallura phoebe LSUMZ Metallura tyrianthina LSUMZ 6272 Metallura aeneocauda LSUMZ 1236 Metallura odomae LSUMZ 353 Metallura williami LSUMZ 5939 Metallura baroni ZMC Metallura theresiae LSUMZ 3534 Metallura eupogon LSUMZ 8293 Metallura eupogon Jaime

6 Mtn. Gems Lamprolaima rhami LSUMZ B22001 Eugenes fulgens LSUMZ B28291 Eugenes fulgens LSUMZ B9964 Panterpe insignis LSUMZ B16264 Heliomaster constantii UWBM DAB 1903 Heliomaster longirostris LSUMZ B18268 Heliomaster furcifer LSUMZ B6709 Heliomaster squamosus FMNH Lampornis hemileucurus LSUMZ B16006 Lampornis hemileucurus LSUMZ B26428 Lampornis clemenciae LSUMZ B10119 Lampornis amethystinus FMNH Lampornis sybillae UWBM DAB 1362 Lampornis viridipallens LSUMZ B19268 Lampornis castaneoventris cinereicauda LSUMZ B19791 Lampornis castaneoventris castaneoventris LSUMZ B28257 Lampornis calolaemus LSUMZ B28257 Tilmatura dupontii KU 8188 Calliphlox amethystina NMNH b10703 Thaumastura cora LSUMZ B14278 Myrmia micrura LSUMZ B5233 Myrtis fanny LSUMZ B3592 Rhodopis vesper Jose 2 Rhodopis vesper LSUMZ B14277 Eulidia yarrellii Wouter Chaetocercus bombus LSUMZ B5225 Microstilbon burmeisteri ZMC Chaetocercus mulsant LSUMZ B6301 Calliphlox bryantae LSUMZ B28180 Calliphlox mitchellii LSUMZ B12194 Calliphlox mitchellii LSUMZ B2310 Calothorax lucifer LSUMZ B43113 Doricha eliza UNAM b590 Doricha eliza KU 4435 Archilochus alexandri LSUMZ B21848 Archilochus colubris LSUMZ B5270 Calliphlox evelynae LSUMZ B58890 Calliphlox evelynae LSUMZ B59204 Mellisuga minima MVZ Mellisuga minima STRI JAMM11 Mellisuga minima MVZ Calypte anna LSUMZ B24864 Calypte costae CJC 210 Calypte costae LSUMZ B21595 Atthis heloisa FMNH Atthis heloisa UNAM OVMP 1041 Selasphorus ardens JK Selasphorus ardens LSUMZ B52914 Selasphorus scintilla LSUMZ B16266 Selasphorus ardens LSUMZ B52915 Selasphorus ardens LSUMZ B52913 Selasphorus flammula LSUMZ B28269 Selasphorus flammula LSUMZ B19883 Selasphorus flammula LSUMZ B19794 Selasphorus flammula LSUMZ B28313 Selasphorus flammula LSUMZ B28253 Selasphorus flammula LSUMZ B28260 Selasphorus flammula LSUMZ B19847 Selasphorus flammula LSUMZ B9952 Selasphorus flammula LSUMZ B28246 Selasphorus flammula LSUMZ B16222 Selasphorus platycercus LSUMZ B23428 Selasphorus rufus MVZ Selasphorus calliope MVZ Selasphorus calliope MVZ Selasphorus calliope MVZ Selasphorus calliope LSUMZ B26272 Selasphorus calliope LSUMZ B16854 Selasphorus calliope LSUMZ B23775 Selasphorus sasin LSUMZ B33988 Selasphorus sasin MVZ Selasphorus sasin MVZ Selasphorus sasin MVZ Selasphorus sasin MVZ Selasphorus sasin LSUMZ B43117 Selasphorus sasin LSUMZ B43116 Selasphorus sasin MVZ Selasphorus sasin MVZ Bees

7 Cynanthus sordidus LSUMZ B22004 Emeralds Cynanthus sordidus LSUMZ B22005 Chlorostilbon ricordii ANSP 5570 Chlorostilbon swainsonii AMNH NKK 1017 Chlorostilbon maugaeus LSUMZ B11520 Cyanophaia bicolor STRI MACB11 Cyanophaia bicolor STRI DOCB17 Cynanthus latirostris LSUMZ B33304 Cynanthus latirostris doubledayi JK Chlorostilbon canivetii salvini JK Chlorostilbon canivetii UWBM DAB 1591 Chlorostilbon mellisugus LSUMZ B9450 Chlorostilbon lucidus pucherani FMNH Chlorostilbon lucidus pucherani FMNH Chlorostilbon lucidus lucidus LSUMZ B18889 Chlorostilbon lucidus lucidus LSUMZ B31514 Chlorostilbon poortmani JPLV 4198 Chlorostilbon assimilis LSUMZ B46483 Chlorostilbon assimilis LSUMZ B46655 Chlorostilbon melanorhynchus LSUMZ B6327 Chlorostilbon melanorhynchus JLPV 36 Hylocharis xantusii LSUMZ B3794 Hylocharis leucotislsumz B22003 Campylopterus rufus FMNH Campylopterus excellens FMNH Campylopterus excellens UNAM 554 Klais guimeti LSUMZ B6168 Abeillia abeillei LSUMZ B22002 Orthorhyncus cristatus LSUMZ B11526 Stephanoxis lalandi LSUMZ B25958 Anthocephala floriceps Juan i1253 Anthocephala floriceps Juan i1269 Campylopterus villaviscensio LSUMZ B5588 Campylopterus ensipennis CE 115 Campylopterus ensipennis CE 117 Campylopterus falcatus Juan i4641 Campylopterus falcatus IAVHP 77 Campylopterus largipennis LSUMZ B4474 Campylopterus duidae LSUMZ B7743 Campylopterus hyperythrus FMNH Campylopterus rufus FMNH Campylopterus hemileucurus LSUMZ B26474 Microchera albocoronata LSUMZ B35764 Elvira chionura LSUMZ B26446 Elvira cupreiceps LSUMZ B16066 Goethalsia bella LSUMZ B2111 Goldmania violiceps LSUMZ B28405 Thalurania ridgwayi FMNH b225 Thalurania ridgwayi FMNH b312 Thalurania ridgwayi FMNH b305 Eupherusa poliocerca LSUMZ B21999 Eupherusa cyanophrys LSUMZ B21997 Eupherusa eximia LSUMZ B21998 Eupherusa nigriventris LSUMZ B16055 Chalybura urochrysia LSUMZ B28467 Chalybura buffonii LSUMZ B26911 Thalurania glaucopis FMNH Thalurania watertonii FMNH Thalurania furcata LSUMZ B22683 Thalurania furcata LSUMZ B3518 Thalurania furcata LSUMZ B4756 Thalurania furcata LSUMZ B2807 Thalurania colombica colombica LSUMZ B1142 Thalurania colombica fannyae LSUMZ B7867 Thalurania colombica fannyae LSUMZ B11728 Thalurania colombica colombica LSUMZ B11793 Phaeochroa cuvierii LSUMZ B26913 Leucippus fallax STRI VELFA2 Leucippus fallax STRI LFA6 Leucippus taczanowskii LSUMZ B33447 Leucippus baeri LSUMZ B35232 Taphrospilus hypostictus LSUMZ B5465 Eupetomena macroura LSUMZ B15299 Aphantochroa cirrochloris FMNH Leucippus chlorocercus LSUMZ B7264 Trochilus polytmus STRIJ ATP08 Trochilus polytmus STRI JATP07 Trochilus scitulus MVZ Trochilus scitulus MVZ Trochilus polytmus MVZ Trochilus scitulus FMNH Amazilia viridifrons wagneri UNAM OMVP730 Amazilia violiceps UNAM 828 Amazilia viridifrons UNAM OMVP684 Amazilia cyanocephala LSUMZ B19260 Amazilia saucerrottei hoffmanni FMNH Amazilia beryllina FMNH Amazilia cyanura UWBM DAB1441 Amazilia edward LSUMZ B2303 Amazilia saucerrottei JPLV34 Amazilia saucerrottei JPLV60 Amazilia castaneiventris OC Amazilia tobaci LSUMZ B35895 Amazilia tobaci AMNH 2796 Amazilia viridigaster LSUMZ B7490 Amazilia viridigaster LSUMZ B7587 Amazilia rutila UWBM DAB1054 Amazilia yucatanensis LSUMZ B4090 Amazilia tzacatl handleyi NMNH b1010 Amazilia tzacatl LSUMZ B16538 Amazilia amazilia LSUMZ B14263 Amazilia franciae LSUMZ B12063 Lepidopyga goudoti JCC Chrysuronia oenone LSUMZ B5381 Amazilia versicolor FMNH Amazilia versicolor LSUMZ B15313 Lepidopyga coeruleogularis LSUMZ B29053 Lepidopyga coeruleogularis LSUMZ B46528 Hylocharis grayi ANSP 5064 Amazilia brevirostris chionopectus LSUMZ B35896 Amazilia brevirostris NMNH b11307 Amazilia leucogaster ANSP 8392 Leucochloris albicollis FMNH Amazilia fimbriata LSUMZ B5956 Amazilia lactea LSUMZ 9484 Hylocharis sapphirina LSUMZ B12912 Hylocharis chrysura LSUMZ B1503 Amazilia chionogaster LSUMZ B17165 Amazilia viridicauda LSUMZ B8136 Amazilia viridicauda LSUMZ B8158 Amazilia rosenbergi ZMC Amazilia decora LSUMZ B10024 Amazilia amabilis LSUMZ B28483 Amazilia candida KU MBR4474 Amazilia candida UNAM PUE102 Hylocharis eliciae LSUMZ B16074 Hylocharis cyanus LSUMZ B9547 Juliamyia julie LSUMZ B16556 Juliamyia julie LSUMZ B28497 Chlorestes notatus LSUMZ B35953 Chlorestes notatus LSUMZ B4558 Chlorestes notatus FMNH

8 Fig. S2 Time-calibrated phylogenetic estimate for hummingbirds and outgroup species based on a BEAST MCMC analysis of a concatenated 6-gene (5-locus) data set, Related to Figure 1. Bars at nodes reflect 95% credibility intervals of age estimates Corvus frugilegus Myrmotherula brachyura NMNH b12607 Coturnix chinensis Gallus gallus Podargus strigoides LSUMZ B6435 Caprimulgus longirostris LSUMZ B32361 Nyctibius bracteatus LSUMZ B4509 Steatornis caripensis LSUMZ B32579 Aegotheles insignis KU 5081 Chaetura pelagica LSUMZ B3346 Aeronautes saxatalis GM42600 Aerodramus vanikorensis NMNH b04039 Aerodramus salangana Streptoprocne zonaris NMNH b13064 Hemiprocne mystacea UWBM Florisuga mellivora LSUMZ B9646 Florisuga fusca LSUMZ B16936 Topaza pyra LSUMZ B42522 Topaza pyra LSUMZ B42323 Topaza pyra LSUMZ B42387 Topaza pyra LSUMZ B42167 Topaza pella LSUMZ B35362 Topaza pella NMNH b5205 Eutoxeres aquila LSUMZ B2110 Eutoxeres condamini LSUMZ B8094 Ramphodon naevius ZMC Threnetes ruckeri LSUMZ B28170 Threnetes leucurus LSUMZ B2673 Glaucis aeneus NMNH b368 Glaucis hirsutus LSUMZ B28468 Phaethornis anthophilus UMMZ t594 Phaethornis rupurumii LSUMZ B20240 Phaethornis rupurumii iavhb 4463 Phaethornis longuemareus LSUMZ B35952 Phaethornis nattereri LSUMZ B12859 Phaethornis griseogularis AMNH PEP 1971 Phaethornis griseogularis LSUMZ B44650 Phaethornis griseogularis LSUMZ B5571 Phaethornis striigularis LSUMZ B28411 Phaethornis striigularis LSUMZ B28790 Phaethornis striigularis LSUMZ B28518 Phaethornis ruber FMNH Phaethornis ruber LSUMZ B9481 Phaethornis ruber FMNH Phaethornis atrimentalis LSUMZ B1969 Phaethornis bourcieri LSUMZ B10502 Phaethornis bourcieri LSUMZ B10629 Phaethornis bourcieri LSUMZ B11104 Phaethornis bourcieri LSUMZ B11017 Phaethornis philippii LSUMZ B9280 Phaethornis philippii LSUMZ B9020 Phaethornis philippii LSUMZ B8868 Phaethornis koepckeae LSUMZ B5479 Phaethornis koepckeae LSUMZ B5398 Phaethornis eurynome FMNH Phaethornis subochraceus LSUMZ B6544 Phaethornis augusti UMMZ t604 Phaethornis pretrei LSUMZ B14702 Phaethornis malaris LSUMZ B27511 Phaethornis superciliosus AMNH DOT4284 Phaethornis superciliosus ANSP Phaethornis superciliosus LSUMZ B48308 Phaethornis superciliosus LSUMZ B48364 Phaethornis superciliosus AMNH DOT 2979 Phaethornis superciliosus ANSP Phaethornis superciliosus FMNH Phaethornis superciliosus FMNH Phaethornis yaruqui LSUMZ B7812 Phaethornis guy JLPV 35 Phaethornis guy LSUMZ B28342 Phaethornis guy LSUMZ B35966 Phaethornis mexicanus JK07_110 Phaethornis mexicanus JK07_108 Phaethornis longirostris NMNH b310 Phaethornis longirostris LSUMZ B28503 Phaethornis syrmatophorus LSUMZ B33737 Phaethornis syrmatophorus LSUMZ B33578 Phaethornis syrmatophorus Jaime Phaethornis syrmatophorus LSUMZ B12138 Phaethornis hispidus LSUMZ B18351 Phaethornis hispidus LSUMZ B18142 Doryfera johannae LSUMZ B1728 Doryfera ludovicae LSUMZ B8000 Doryfera ludovicae LSUMZ B1802 Schistes geoffroyi LSUMZ B6300 Colibri serrirostris LSUMZ B14576 Colibri coruscans LSUMZ B6310 Colibri delphinae LSUMZ B5403 Colibri sp. LSUMZ B49711 Colibri thalassinus LSUMZ B28263 Androdon aequatorialis LSUMZ B1402 Heliothryx auritus LSUMZ B6913 Heliothryx barroti LSUMZ B12039 Heliactin bilophus LSUMZ B14845 Polytmus guainumbi LSUMZ B6691 Polytmus milleri AMNH PRS 476 Polytmus theresiae NMNH Avocettula recurvirostris FMNH Chrysolampis mosquitus NMNH Chrysolampis mosquitus LSUMZ B35902 Anthracothorax mango MVZ Anthracothorax mango MVZ Anthracothorax mango STRI JAAMA1 Anthracothorax mango STRI JAAMA2 Anthracothorax viridigula FMNH Anthracothorax prevostii NMNH b360 Anthracothorax veraguensis NMNH B1347 Anthracothorax nigricollis LSUMZ B9552 Anthracothorax dominicus LSUMZ B11318 Anthracothorax viridis LSUMZ B11519 Eulampis jugularis STRI SVEJ46 Eulampis jugularis STRI MAEJ412 Eulampis jugularis STRI DOEJ413 Eulampis holosericeus NMNH 2121 Haplophaedia aureliae LSUMZ B32971 Haplophaedia lugens LSUMZ B30032 Eriocnemis aline LSUMZ B1805 Eriocnemis luciani LSUMZ B6337 Eriocnemis derbyi ANSP Eriocnemis cupreoventris JPLV30 Eriocnemis cupreoventris Juan i2558 Lodiggesia mirabilis LSUMZ B44698 Eriocnemis glaucopoides UWBM Eriocnemis vestita LSUMZ B324 Eriocnemis nigrivestis ZMC Eriocnemis mosquera LSUMZ B6335 Lafresnaya lafresnayi LSUMZ B32771 Lafresnaya lafresnayi LSUMZ B32576 Aglaeactis pamela LSUMZ B Aglaeactis castelnaudii NK Aglaeactis castelnaudii LSUMZ B8215 Aglaeactis cupripennis LSUMZ B6304 Urochroa bougueri ZMC Heliodoxa leadbeateri LSUMZ B6036 Heliodoxa jacula LSUMZ B16037 Heliodoxa jacula LSUMZ B11940 Heliodoxa imperatrix LSUMZ B12088 Heliodoxa rubinoides LSUMZ B1651 Clytolaema rubricauda FMNH Heliodoxa aurescens LSUMZ B6789 Heliodoxa gularis LSUMZ B5428 Heliodoxa branickii LSUMZ B1996 Heliodoxa xanthogonys LSUMZ B7415 Heliodoxa schreibersii LSUMZ B5440 Pterophanes cyanopterus LSUMZ B1296 Ensifera ensifera LSUMZ B8224 Boissonneaua jardini ANSP Boissonneaua flavescens LSUMZ B12099 Boissonneaua mathewsii LSUMZ B8130 Urosticte ruficrissa Juan i2325 Urosticte benjamani LSUMZ B5546 Ocreatus underwoodii LSUMZ B22594 Ocreatus underwoodii jplv39 Coeligena prunellei Juan42 Coeligena coeligena LSUMZ B8015 Coeligena coeligena IAVH 1950 Coeligena coeligena IAVH 1216 Coeligena coeligena IAVH 5334 Coeligena wilsoni LSUMZ B7858 Coeligena violifer LSUMZ B8200 Coeligena iris LSUMZ B31770 Coeligena bonapartei IAVHB 4188 Coeligena bonapartei Juan i2271 Coeligena helianthea Juan 2504 Coeligena orina PCPR3 Coeligena orina Juan i5169 Coeligena orina PCPR1 Coeligena lutetiae iavhb1915 Coeligena lutetia LSUMZ B340 Coeligena phalerata Juan i485 Coeligena torquata LSUMZ B6230 Coeligena torquata JPLV58 Coeligena torquata avhb i4633 Coeligena torquata inca AMNH DOT 2598 Coeligena torquata inca AMNH DOT 2599 Sephanoides sephaniodes Jose1 Sephanoides sephaniodes AMNH 1126 Sephanoides sephaniodes MR626 Sephanoides sephanoides MR613 Sephanoides sephaniodes MR629 Sephanoides fernandensis MR620 Sephanoides fernandensis MR622 Lophornis delattrei LSUMZ B22644 Lophornis chalybeus LSUMZ B9399 Lophornis pavoninus KU 6045 Discosura longicauda NMNH b5265 Discosura langsdorfii LSUMZ B9633 Discosura popelairii LSUMZ B5950 Discosura conversii LSUMZ B16064 Phlogophilus harterti KU Phlogophilus harterti KU Phlogophilus hemileucurus LSUMZ B5999 Heliangelus regalis LSUMZ B5532 Heliangelus strophianus LSUMZ B6296 Heliangelus amethysticollis LSUMZ B33890 Heliangelus amethysticollis LSUMZ B6246 Heliangelus exortis JVLP40 Heliangelus micraster LSUMZ B34698 Heliangelus micraster LSUMZ B31990 Heliangelus micraster ANSP 5013 Heliangelus exortis ANSP Heliangelus exortis ANSP Heliangelus viola LSUMZ B32370 Adelomyia melanogenys maculata Valqui 681 Adelomyia melanogenys maculata Valqui 656 Adelomyia melanogenys LSUMZ B8025 Agliocercus kingii LSUMZ B8017 Aglaiocercus coelestis LSUMZ B7813 Taphrolesbia griseiventris LSUMZ B10388 Heliangelus zusii ANSP Sappho sparganurus LSUMZ B1195 Lesbia nuna LSUMZ B3615 Lesbia victoriae ZMC Ramphomicron microrhynchum LSUMZ B8376 Oreotrochilus estella stolzmanni ANSP Oreotrochilus melanogaster LSUMZ B2077 Oreotrochilus estella stolzmanni ANSP Oreotrochilus chimborazo ZMC Oreotrochilus estella MR649 Oreotrochilus estella LSUMZ B Polyonymus caroli Valqui680 Polyonymus caroli LSUMZ B15503 Opisthoprora euryptera ZMC Chalcostigma herrani LSUMZ B6277 Chalcostigma olivaceum LSUMZ B Chalcostigma olivaceum LSUMZ B Chalcostigma ruficeps LSUMZ B1293 Chalcostigma stanleyi MSB:Bird:27151 Oxypogon guerini ZMC Oreonympha nobilis FMNH Metallura phoebe LSUMZ B Metallura tyrianthina LSUMZ B6272 Metallura odomae LSUMZ B353 Metallura baroni ZMC Metallura williami LSUMZ B5939 Metallura theresiae LSUMZ B3534 Metallura eupogon LSUMZ B8293 Metallura eupogon Jaime Metallura aeneocauda LSUMZ B1236 Patagona gigas LSUMZ B7903 Patagona gigas LSUMZ B6303 Heliomaster squamosus FMNH Heliomaster furcifer LSUMZ B6709 Heliomaster longirostris LSUMZ B18268 Heliomaster constantii UWBM DAB1903 Panterpe insignis LSUMZ B16264 Eugenes fulgens LSUMZ B9964 Eugenes fulgens LSUMZ B28291 Lamprolaima rhami LSUMZ B22001 Lampornis hemileucus LSUMZ B26428 Lampornis hemileucus LSUMZ B16006 Lampornis clemenciae LSUMZ B10119 Lampornis castaneoventris LSUMZ B28257 Lampornis calolaemus LSUMZ B28169 Lampornis castaneoventris cinereicauda LSUMZ B19791 Lampornis viridipallens LSUMZ B19268 Lampornis sybillae UWBM DAB1362 Lampornis amethystinus FMNH Tilmatura dupontii KU 8188 Calliphlox amethystina NMNH b10703 Rhodopis vesper Jose2 Rhodopis vesper LSUMZ B14277 Myrmia micrura LSUMZ B5233 Thaumastura cora LSUMZ B14278 Myrtis fanny LSUMZ B3592 Eulidia yarrellii Wouter Chaetocercus bombus LSUMZ B5225 Chaetocercus mulsant LSUMZ B6301 Microstilbon burmeisteri ZMC Calliphlox bryantae LSUMZ B28180 Calliphlox mitchellii LSUMZ B2310 Calliphlox mitchellii LSUMZ B12194 Doricha eliza KU 4435 Doricha eliza UNAM b590 Calothorax lucifer LSUMZ B43113 Archilochus alexandri LSUMZ B21848 Archilochus colubris LSUMZ B5270 Mellisuga minima MVZ Mellisuga minima MVZ Mellisuga minima STRI JAMM11 Calliphlox evelynae LSUMZ B58890 Calliphlox evelynae LSUMZ B59204 Calypte costae CJC 210 Calypte costae LSUMZ B21595 Calypte anna LSUMZ B24864 Selasphorus ardens LSUMZ B52913 Selasphorus ardens LSUMZ B52915 Selasphorus scintilla LSUMZ B16266 Selasphorus ardens JK07_522 Selasphorus ardens LSUMZ B52914 Selasphorus flammula LSUMZ B19847 Selasphorus flammula LSUMZ B28313 Selasphorus flammula LSUMZ B28253 Selasphorus flammula LSUMZ B19794 Selasphorus flammula LSUMZ B28260 Selasphorus flammula LSUMZ B28246 Selasphorus flammula LSUMZ B16222 Selasphorus flammula LSUMZ B9952 Selasphorus flammula LSUMZ B19883 Selasphorus flammula LSUMZ B28269 Atthis heloisa UNAM OVMP 1041 Atthis heloisa FMNH Selasphorus platycercus LSUMZ B23428 Selasphorus rufus MVZ Selasphorus calliope LSUMZ B26272 Selasphorus calliope LSUMZ B23775 Selasphorus calliope LSUMZ B16854 Selasphorus calliope MVZ Selasphorus calliope MVZ Selasphorus calliope MVZ Selasphorus sasin MVZ Selasphorus sasin MVZ Selasphorus sasin LSUMZ B43116 Selasphorus sasin LSUMZ B43117 Selasphorus sasin MVZ Selasphorus sasin MVZ Selasphorus sasin MVZ Selasphorus sasin MVZ Selasphorus sasin LSUMZ B33988 Hylocharis leucotis LSUMZ B22003 Hylocharis xantusii LSUMZ B3794 Campylopterus rufus FMNH Campylopterus excellens FMNH Campylopterus excellens UNAM 554 Anthocephalus floriceps Juan i1253 Anthocephalus floriceps Juan i1269 Stephanoxis lalandi LSUMZ B25958 Orthorhyncus cristatus LSUMZ B11526 Abeillia abeillei LSUMZ B22002 Klais guimeti LSUMZ B6168 Campylopterus hemileucurus LSUMZ B26474 Campylopterus rufus FMNH Campylopterus hyperythrus FMNH Campylopterus duidae LSUMZ B7443 Campylopterus falcatus IAVHP 77 Campylopterus falcatus Juan i4641 Campylopterus ensipennis CE117 Campylopterus ensipennis CE115 Campylopterus villaviscensio LSUMZ B5588 Campylopterus largipennis LSUMZ B4474 Chlorostilbon swainsonii AMNH NKK 1017 Chlorostilbon maugaeus LSUMZ B11520 Chlorostilbon ricordii ANSP 5570 Cyanophaia bicolor STRI DOCB17 Cyanophaia bicolor STRI MACB11 Cynanthus latirostris doubledayi JK04_339 Chlorostilbon canivetii salvini JK00_048 Chlorostilbon canivetii UWBM DAB1591 Cynanthus latirostris LSUMZ B33304 Chlorostilbon assimilis LSUMZ B46483 Chlorostilbon assimilis LSUMZ B46655 Chlorostilbon melanorhynchus Juan 36 Chlorostilbon melanorhynchus LSUMZ B6327 Chlorostilbon poortmani Juan i4198 Chlorostilbon lucidus pucherani FMNH Chlorostilbon lucidus pucherani FMNH Chlorostilbon lucidus lucidus LSUMZ B18899 Chlorostilbon lucidus lucidus LSUMZ B31514 Chlorostilbon mellisugus LSUMZ B9450 Cynanthus sordidus LSUMZ B22004 Cynanthus sordidus LSUMZ B22005 Chalybura buffonii LSUMZ B26911 Chalybura urochrysia LSUMZ B28467 Thalurania furcata LSUMZ B22683 Thalurania furcata LSUMZ B3518 Thalurania furcata LSUMZ B4756 Thalurania colombica LSUMZ B1142 Thalurania colombica LSUMZ B11728 Thalurania colombica LSUMZ B11793 Thalurania colombica hypochlora LSUMZ B7867 Thalurania furcata LSUMZ B2807 Thalurania watertonii FMNH Thalurania glaucopis FMNH Eupherusa eximia LSUMZ B21998 Eupherusa nigriventris LSUMZ B16055 Eupherusa poliocerca LSUMZ B21999 Eupherusa cyanophrys LSUMZ B21997 Thalurania ridgwayi FMNH b305 Thalurania ridgwayi FMNH b312 Thalurania ridgwayi FMNH b225 Goethalsia bella LSUMZ B2111 Goldmania violiceps LSUMZ B28405 Microchera albocoronata LSUMZ B35764 Elvira cupreiceps LSUMZ B16066 Elvira chionura LSUMZ B26446 Leucippus fallax STRI VELFA2 Leucippus fallax STRI LFA6 Phaeochroa cuvierii LSUMZ B26913 Aphantochroa cirrochloris FMNH Eupetomena macroura LSUMZ B15299 Taphrospilus hypostictus LSUMZ B5465 Leucippus baeri LSUMZ B5232 Leucippus taczanowskii LSUMZ B33447 Leucippus chlorocercus LSUMZ B7264 Trochilus polytmus STRI JATP07 Trochilus polytmus STRI JATP08 Trochilus polytmus MVZ Trochilus polytmus MVZ Troch scitulus FMNH Trochilus polytmus MVZ Amazilia viridifrons wagneri UNAM OMVP730 Amazilia viridifrons UNAM OMVP684 Amazilia violiceps UNAM 828 Amazilia cyanura UWBM DAB1441 Amazilia beryllina FMNH Amazilia.saucerrottei hoffmanni FMNH Amazilia cyanocephala LSUMZ B19260 Amazilia tobaci LSUMZ B35895 Amazilia viridigaster LSUMZ B7587 Amazilia viridigaster LSUMZ B7490 Amazilia tobaci AMNH 2796 Amazilia castaneiventris oc Amazilia saucerrottei JVLP34 Amazilia saucerrottei JVLP60 Amazilia edward LSUMZ B2303 Amazilia yucatanensis LSUMZ B4090 Amazilia tzacatl LSUMZ B16538 Amazilia tzacatl handleyi NMNH b1010 Amazilia rutila UWBM DAB1054 Chrysuronia oenone LSUMZ B5381 Lepidopyga goudoti jcc Amazilia versicolor LSUMZ B15313 Amazilia versicolor FMNH Amazilia brevirostris chionopectus LSUMZ B35896 Amazilia leucogaster ANSP 8392 Amazilia brevirostris NMNH b11307 Hylocharis grayi ANSP 5064 Lepidopyga coeruleogularis LSUMZ B46528 Lepidopyga coeruleogularis LSUMZ B29053 Amazilia franciae LSUMZ B12063 Amazilia amazilia LSUMZ B14263 Amazilia candida KU MBR 4474 Amazilia candida UNAM PUE102 Hylocharis cyanus rostrata LSUMZ B9547 Chlorestes notatus FMNH Chlorestes notatus LSUMZ B4558 Chlorestes notatus LSUMZ B35953 Juliamyia julie LSUMZ B28497 Juliamyia julie LSUMZ B16556 Hylocharis eliciae LSUMZ B16074 Amazilia decora LSUMZ B Amazilia amabilis LSUMZ B28483 Amazilia rosenbergi ZMC Leucochloris albicollis FMNH Amazilia viridicauda LSUMZ B8158 Amazilia viridicauda LSUMZ B8136 Amazilia chionogaster LSUMZ B17165 Hylocharis sapphirina LSUMZ B12912 Hylocharis chrysura LSUMZ B1503 Amazilia lactea LSUMZ B9484 Amazilia fimbriata LSUMZ B5956 Millions of years ago

9 Non-Andes Emeralds Andes Bees Mtn. Gems Patagona Coquettes Brilliants Mangoes Hermits Topazes Miocene Pliocene Pleis Ma Fig. S3 Time-calibrated phylogenetic tree with ancestral state reconstructions of Andean vs. non-andean occurrence. Color-coded bars at the tips of the tree indicate the contemporary Andean occurrence data for the corresponding species. Color-coded pie diagrams at each node indicate the proportion of the maximum likelihood supporting alternative reconstructed character states.

10 all hummingbirds Extant Species Hermits Topazes Mangoes Andean Clade Mtn. Gems Bees Emeralds Time Before Present (Ma) 0 Fig. S4 Lineage-through-time (LTT) plots for all hummingbirds and for six primary clades. For the purposes of this analysis, Hermits and Topazes were plotted together, as were Coquettes and Brilliants (the Andean Clade ). In the inset, the hummingbird LTT is plotted along with confidence intervals assuming a pure-birth process, with color-coded confidence intervals. Net diversification rates are indicated adjacent to each color-coded LTT plot.

11 Speciation (Red) & Extinction (Blue) Rates/My Time Before Present (Ma) Fig. S5 BAMM plots showing overall pattern of speciation and extinction with credibility intervals.

12 Table S1 Clade-specific mean speciation (λ), mean extinction (µ), and carrying-capacity (K) estimates obtained for the principal clades of hummingbirds using DDD. Clade λ µ K contemporary species Bees Mountain Gems Emeralds Patagona 1 Coquettes Brilliants Mangoes Hermits Topazes Total

13 Table S2 Data partitions, substitution models, and substitution rate calibrations. Partition Model Substitution Rate (mean) Substitution Rate (SD) trna HKY+I ND2 position 1 GTR+I+G ND2 position 2 GTR+I+G ND2 position 3 GTR+I+G AK1 GTR+G BFib GTR+G ND4 position 1 GTR+I+G ND4 position 2 GTR+I+G ND4 position 3 GTR+I+G ODC GTR+I+G MUSK GTR+I+G NA NA

14 Supplemental Experimental Procedures Taxonomic Sampling and DNA Sequence Data. We include 15 outgroup species spanning four avian orders: five swifts (Apodidae: Aerodramus salangana, A. vanikorensis, Aeronautes saxatalis, Chaetura pelagica, Streptoprocne zonaris); one treeswift (Hemiprocnidae: Hemiprocne mystacea); one owlet-nightjar (Aegothelidae: Aegotheles insignis); four caprimulgiforms (Caprimulgus longirostris [Caprimulgidae], Nyctibius bracteatus [Nyctibiidae], Podargus strigoides [Podargidae], and Steatornis caripensis [Steatornithidae]; two galliforms: Coturnix chinensis and Gallus gallus; and two passeriforms: Corvus frugilegus and Myrmotherula brachyura). For ingroup taxa and most of our outgroup species, we collected 6461 alignment positions of DNA sequence data representing six genes (four nuclear and two mitochondrial plus flanking trnas). The nuclear genes include intron 7 of beta fibrinogen (FGB), intron 5 of the adenylate kinase gene (AK1), a segment of the ornithine decarboxylase gene extending from the end of exon 6 to the beginning of exon 8 (ODC), and a segment of the Z-linked muscle skeletal receptor tyrosine gene including parts of exons 4 and 5 and the intervening intron (MUSK). The mitochondrial gene sequences include the complete NADH dehydrogenase subunit 2 (ND2), approximately half of NADH dehydrogenase subunit 4 (ND4), and trnas flanking each of these protein-coding genes. Several FGB sequences (for the outgroup species A. vanikorensis, S. zonaris, P. strigoides, A. insignis, C. longirostris, S. caripensis, and H. mystacea) were provided by the Early Bird Tree of Life project (1). The AK1 sequence for A. insignis, the ND2 and ND4 sequences for Coturnix, and all Gallus sequences were obtained from GenBank. DNA Sequence Data Collection and Alignment. DNA was isolated using standard phenol-chloroform extraction, a sodium-chloride extraction protocol, or using Qiagen DNeasy extraction kits following standard protocols. Amplification of target sequences was performed using the polymerase chain reaction with the primer sets identified in Table S1. Amplified PCR products were gel-purified on Sephadex columns (Princeton Separations) or purified using shrimp phosphatase and exonuclease (exosapit). A subset of nuclear gene sequences was cloned prior to sequencing using TopoTA cloning kits (Invitrogen) because sequence length polymorphisms prevented us from obtaining clean sequences. However, most purified PCR products were sequenced directly using Big Dye Terminator sequencing reaction mix following the manufacturer s protocols (Applied Biosystems). Cycle-sequencing products were visualized on either an ABI 377, ABI 3700, or ABI 3730 automated sequencer (Applied Biosystems). All new DNA sequences generated for this study were deposited in GenBank (accession numbers XXX-XXX [to be added prior to publication]). DNA alignments of the intron sequences were performed initially using the alignment program Muscle version 3.6 (2) and adjusted manually. The AK1,

15 BFib, and trna sequences include a number of indels, some of which could not be aligned with confidence, and these regions were consequently excluded from further analysis. Heterozygous sites were scored using ambiguity codes and positions contributing to length polymorphisms were excluded from analysis. Phylogenetic Analyses. Time-calibrated Bayesian phylogenetic analyses were performed using BEAST v1.7.1 (3). We identified the best-fitting data partitioning strategy, as well as nucleotide substitution models for each data partition, using the Akaike Information Criterion (AIC; ref. 4; see ref. 5 for justification), as implemented in ModelTest 3.06 [6]. The 11 partitions and their corresponding nucleotide substitution models implemented in our analyses are listed in Table S2. Divergence times were estimated using an uncorrelated lognormal (UCLN) relaxed clock model, and a Birth-Death speciation tree prior. We calibrated our divergence-dating analyses using substitution rate priors (rather than fossil calibrations) using the rate estimates generated for Hawaiian honeycreepers [7], which allowed for the incorporation of separate normally distributed substitution rate calibration priors for our trnas, the three ND2 and ND4 codon positions, and for AK1, Bfib, and ODC (see Table S2 for mean substitution rates and standard deviations for each partition). The only locus for which we had no substitution rate prior was MUSK. We also performed divergence-dating analyses using fossil and island-age calibrations. Mayr [8] argued for a sister group relationship between Apodidae and the fossil Scaniacypselus to the exclusion of Hemiprocnidae, allowing us to put a minimum date on this node of 49 ma (we used a lognormal distribution with a mean of 0.01 my, an offset of 49.0 ma, and a standard deviation of 1.0). We also used information from Stuessy et al. [9] on the age of the Juan Fernandez Islands to date the common ancestor of Sephanoides. The best estimate for the age of Masatierra is ma. There is an older estimate of ma for Santa Clara, but the authors discount this age because of the large uncertainty around the estimate. Stuessy et al. indicate that this is a hot spot system with westward movement, but the ages of the submerged seamounts suggest that perhaps a 6 ma old seamount was land positive at a time that Masatierra was also land positive, but that there was an interval before that when it is pretty certain that no islands could have been emergent. Given this information, we calibrated this node with a lognormal distribution with a mean of 5.0 ma and a standard deviation of 0.2. We actually ran analyses under a diversity of standard deviations and with a variety of distribution shapes around the 49 ma age of Apodidae + Hemiprocnidae and 5.0 ma age of the Juan Fernandez Islands and all returned similar very old ages for the split between hummingbirds and swifts and for crown group hummingbirds. Typical estimates obtained from these analyses are 70.8 Ma the common ancestor of swifts and hummingbirds and 38.6 ma for the crown group of hummingbirds. We reject these estimates in favor of those obtained using multiple simultaneously-employed substitution rate calibrations. BEAST analyses were run four times to minimize the chance of becoming trapped on local optima,

16 with each run consisting of 1 X 10 8 generations. Burn-in was assessed via inspection of trace plots and ESS scores for parameter estimates using the program Tracer, version 1.5 ( Trees and log files from the four analyses were then combined using LogCombiner, version ( The maximum clade credibility (MCC) tree was summarized from the joint distribution of trees using TreeAnnotator, version ( and the mean and 95% credibility intervals of divergence time estimates were visualized using FigTree, version 1.40 ( Diversification Analyses using BAMM. BAMM relaxes the assumption of timehomogeneous diversification that underlies alternative approaches such as the MEDUSA model (10). BAMM incorporates incomplete taxon sampling directly into likelihood calculations; we assumed that our tree contained 86.0% of hummingbird species. We performed multiple BAMM runs on the MCC hummingbird phylogeny, with 10 million generations of Markov Chain Monte Carlo (MCMC) sampling per run and sampling evolutionary parameters every 1000 generations. We assessed convergence of BAMM runs by computing effective sample sizes of log-likelihoods, numbers of processes, and evolutionary rate parameters using the CODA library for R; all parameters had effective sample sizes > 500. We reconstructed marginal distributions of net diversification rates for each branch in the MCC hummingbird phylogeny using the posterior distribution of evolutionary parameters sampled using the reversible jump MCMC algorithm in BAMM. Finally, we reconstructed rate-through-time curves for eight major clades of hummingbirds from the joint posterior density of parameters simulated with BAMM. Supplemental References 1. Hackett SJ, et al. (2008) A phylogenomic study of birds reveals their evolutionary history Science 320(5884): Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics 5: Drummond, A.J., Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, Akaike, H. (1973). Information theory and an extension of the maximum likelihood principle. In Second International Symposium on Information Theory, Petrov, B.N., Csaki, B.F., eds. (Budapest: Akademiai Kiado), pp Posada, D., and Buckley, T.R. (2004). Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53, Posada, D., Crandall, K.A. (1998). MODELTEST: Testing the model of DNA substitution. Bioinformatics 14, Lerner, H.R.L., Meyer, M., James, H.F., Hofreiter, M., and Fleischer, R.C. (2011). Multilocus resolution of phylogeny and timescale in the extant adaptive radiation of Hawaiian honeycreepers. Curr. Biol. 21,

17 8. Mayr, G. (2003). Phylogeny of early Tertiary swifts and hummingbirds (Aves: Apodiformes). Auk 120, Stuessy, T.F., Foland, K.A., Sutter, J.F., Sanders, R.W., and Silva O., M. (1984). Botanical and geological significance of Potassium-Argon dates from the Juan Fernández Islands. Science 225, Alfaro ME, et al. (2009) Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates Proc Natl Acad Sci USA 106(32):