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Exons, Introns [Upper Panel, Left to Right] and Uces [Lower Panel]) in Jarvis Et Al ● 40 R = 0.39 , p < 2.2e−16 ● ● ● ● ● ● ● ●● ● ●● ● ●● ● ● ●● ● ● ● ● ● ● ●● ● ● ● ● ●●● ●● ● ●● ● ● ● ● ●● ●●● ●●●●● ●●● ●● ● ●● ● ● ●●●●●● ●●● ●●●●●●●●● ●●●● ● ●● ● ●●●●●●●●●●●●●●●● ●●●●●●●●●●●●● ● ● ●● ● ● ● ● 30 ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●● ● ● ● ● ● ● ● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ● ●●● ●●● ● ●● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●● ●● ● ● ●● ●●● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●● ● ● ● ● ●● ● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●● ●●●● ● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●● ● ●● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●● ● ●● ●●● ● ● ● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ● ●●● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●● ● ●●● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●● ● ● ● ●● ● ● supporting nodes 20 ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●● ●●●● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●● ●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●● ●●●●● ●● ●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ● ● ● ● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ● ● ● ●●●●●●●●●●●●●●●● ●● ●●●●●●●●●●●●●●● ● ● ●●●●●●●● ●● ●● 10 ●●●●● ●● ● ● 0 5000 10000 15000 alignment length Figure S1. the correlation between supporting node numbers and the alignment length for each dataset (Exons, Introns [upper panel, left to right] and UCEs [lower panel]) in Jarvis et al. (2014). Earliest Neoaves Hoatzin sister Owls sister 1. VI+VII 1. I+III+V 1. M+W 2. V 2. I 2. W 3. VII 3. S+CR 3. EHV 4. III+V+VI+VII 4. V 4. M 5. Doves 5. S Others Others 6. TB 7. II+III+S+CR Others 1500 Exon 1000 500 1000 1500 2000 0 0 1000 2000 Intron 200 400 0 0 200 400 600 0 300 600 0 500 UCE 1000 1500 2000 400 800 1200 500 2000 0 04008001200 0 12 34 5 1234 567 1234 Best supported Constraints Best supported Constraints Best supported Constraints Figure S2: The consistency of the ML gene topology with its best supported constraint. The most genes presented a different ML topology for the focal edge other than its best supporting constraints or any other testing constraints. The Greek numbers (bolded) correspond to the “magnificent seven” of Reddy et al. (2017), including I: “core” Landbirds; II: “core” Waterbirds; III: Sunbittern and Tropicbirds; IV: Cuckoos, Bustards, and Turacos; V: Nightjars, Swifts, Hummingbirds, and allies; VI: Doves, Mesites, and Sandgrouse; VII: Flamingos and Grebes. Other short codes including S: Shorebirds; CR: Cranes and Rails; TB: Turacos and Bustards; M: Mousebirds; W: Woodpeckers and allies; EHV: Eagles, Hawks, and New world Vultures. Exon Intron UCE Hummingbirds&Swifts VII Columba_livia Pterocles_gutturalis VII Cuculus_canorus Cuculus_canorus Balearica_regulorum A Balearica_regulorum Columba_livia VI+VII Chlamydotis_macqueenii pterocles_guturalis Pterocles_gutturalis Cuculus_canorus Chlamydotis_macqueenii Mesitornis_unicolor Mesitornis_unicolor unsupported Mesitornis_unicolor Tauraco_erythrolophus Earliest Neoaves Parrots V Charadrius_vociferus Picoides_pubescens Charadrius_vociferus VI+VII Phaethon_lepturus Columba_livia chlamydotis_undulata Mesites&Sandgrouses Eurypyga_helias Antrostomus_carolinensis Phaethon_lepturus unsupported Ophisthocomus_hoazin Ophisthocomus_hoazin Phaethon_lepturus Colius_striatus caprimugus_carolinensis Balearica_regulorum Colius_striatus Hummingbirds&Swifts Passeriformes Gavia_stellata Charadrius_vociferus Core landbird (I) Tauraco_erythrolophus Core waterbird (II) V Falco_peregrinus Buceros_rhinoceros Parrots Eurypyga_helias Mesites&Sandgrouse Gavia_stellata Falco_peregrinus Picoides_pubescens unsupported Merops_nubicus Passeriformes III Tyto_alba Tyto_alba Calypte_anna Apaloderma_vittatum Phalacrocorax_carbo Cariama_cristata Leptosomus_discolor Cathartes_aura Apaloderma_vittatum Cariama_cristata Chaetura_pelagica Dove&VII VII Phalacrocorax_carbo Buceros_rhinoceros Eagles Pelecanus_crispus PLeptosoodiceps_cmus_discolorristatus CathaNipponia_nipponrtes_aura FulmaEgretta_garrus_glacialiszetta VI+VII 50% supports rare resolutions found in < 10 genes rare resolutions rare resolutions found in < 10 genes found in < 10 genes Eurypyga_helias Hoatzin missing Charadrius_vociferus Hoatzin missing Eurypyga_helias Charadrius_vociferus Balearica_regulorum Charadrius_vociferus Balearica_regulorum Tauraco_erythrolophus Phaethon_lepturus chlamydotis_undulata Pterocles_gutturalis Chlamydotis_macqueenii Eurypyga_helias Columba_livia Hoatzin sister Columba_livia Antrostomus_carolinensis Columba_livia Tauraco_erythrolophus Chlamydotis_macqueenii unsupported unsupported Cuculus_canorus Phaethon_lepturus Cuculus_canorus Gavia_stellata Tauraco_erythrolophus Phaethon_lepturus unsupported Balearica_regulorum Mesitornis_unicolor Mesitornis_unicolor VII Falco_peregrinus Gavia_stellata Apaloderma_vittatum Pterocles_gutturalis caprimugus_carolinensis Gavia_stellata Hmmingbirds&Swifts Egretta_garzetta pterocles_guturalis Antrostomus_carolinensis Leptosomus_discolor All other Neoaves Phalacrocorax_carbo Mesitornis_unicolor III Cariama_cristata Cuculus_canorus VII Colius_striatus Phoenicopterus_ruber V VII Buceros_rhinoceros Core Waterbird (II)−Gavia_stellata Hummingbirds&Swifts Nipponia_nippon Tyto_alba Phalacrocorax_carbo 50% supports Colius_striatus Colius_striatus Eagles Cariama_cristata Podiceps_cristatus Fulmarus_glacialis Fulmarus_glacialis Apaloderma_vittatum Cathartes_aura Penguins Pelecanus_crispus Tyto_alba Merops_Picoides_pubescensnubicus Egretta_garzetta Penguins Falco_peregrinus Hummingbird&Swifts Eagles AlPl arrotsother Neoaves Leptosomus_discolor Calypte_annaPasseriformes Buceros_rhinoceros rare resolutions CathaNipponia_nipponrtes_aura ParrotsPicoides_pubescens rare resolutions PPodiceps_celecaPasseG (iii)nrus_ciforristatusmesrispus rare resolutions found in < 10 genes MesiteB (V)s&Sandgrouse found in < 10 genes found in < 10 genes Eagles Colius_striatus Owl missing Falco_peregrinus Owl missing Colius_striatus Leptosomus_discolor Eagles Eagles Cariama_cristata Cariama_cristata Apaloderma_vittatum Cariama_cristata Owls sister Cathartes_aura Leptosomus_discolor Falco_peregrinus Colius_striatus Falco_peregrinus Parrots Cathartes_aura Buceros_rhinoceros Apaloderma_vittatum Phaethon_lepturus Eagles&New World Vultures unsupported Antrostomus_carolinensis Leptosomus_discolor Cathartes_aura Balearica_regulorum unsupported Merops_nubicus Merops_nubicus Eurypyga_helias Parrots Charadrius_vociferus Woodpeckers&allies Picoides_pubescens Chlamydotis_macqueenii Pterocles_gutturalis Apaloderma_vittatum Parrots unsupported Mesitornis_unicolor Ophisthocomus_hoazin Passeriformes Buceros_rhinoceros Gavia_stellata Picoides_pubescens Tauraco_erythrolophus Buceros_rhinoceros Passeriformes Cuculus_canorus Charadrius_vociferus Balearica_regulorum Picoides_pubescens chlamydotis_undulata Passeriformes Columba_livia Eurypyga_helias Phalacrocorax_carbo pterocles_guturalis Podiceps_cristatus Egretta_garzetta Ophisthocomus_hoazin Fulmarus_glacialis Cuculus_canorus 50% supports Pelecanus_crispus Chaetura_pelagica Tauraco_erythrolophus Nipponia_nippon PhoenicopteAll other Neorus_avesruber Hummingbirds&Swifts Hummingbirds&Swifts Mesitornis_unicolor Eagles & New World Vultures Charadrius_vociferus caprimugus_carolinensis All other Neoaves Phaethon_lepturus Columba_livia Gavia_stellata WWoodpecoodpeckerkers&s&Bee−eaterallies s&Hornbills Eagles & New World Vultures rare resolutions rare resolutions rare resolutions found in < 10 genes found in < 10 genes found in < 10 genes Figure S3. A, Topology distribution of the ML gene trees for the three focal edges using Jarvis et al. (2014) data. unsupported: relationships shown less than 50% UFBS (ultrafast bootstrap support, we use lower support cutoff to show potential topology distributions). Situations are even worse for 95% UFBS cutoff (not shown). rare resolutions: relationships shown in less than 10 gene trees. Hoatzin missing or Owl missing: Hoatzin or Owl is missing in the gene trees. B Earliest Neoaves Hoatzin sister Owls sister New_world_vultures (condors) Sandgrouse Hoatzin missing Bustards Nightjars Cuckoo_roller Doves Bustards Falcons Polyphyletic PG Hawks+Eagles (without condors) Sunbitten Rails+Sungrebe+Trumpeter+Cranes Tropicbirds Turacos Bustards Sunbitten Coraciiformes Tropicbirds Mousebirds Nightjars Doves Cariama Trogons Trogons Frogmouth Penguins Sandgrouse Common_potoo Falcons Nightjars Frogmouths Cuckoos Oilbirds Owlet_nightjar+Treeswifts+hummingbirds+swifts yletic_Owl Turacos h Cuckoos Rails+Sungrebe+Trumpeter+Cranes Passeriformes Common_Loon Trogons Mesites Flamingo+Grebe Storks non_monop Boobies+Darter+Cormorant rare resolutions (<2 genes) Cuckoos Cuckoos+Bustards All trees Mesites Mousebirds Hoatzin Penguins Common_potoo Frigatebirds Tropicbirds Cuckoos+Passeriformes Owlet_nightjar Cariama Hornbills Common_Loon Storks Mousebirds Common_potoo Flamingo+Grebe Shorebirds rare resolutions (<2 genes) Frigatebirds Parrots Falcons Herons Pelicans Barred_owl rare resolutions (<2 genes) Northern_storm_petrel All_Neoaves Treeswifts+hummingbirds+swifts Cuckoo_roller Sandgrouse+Bustards rare resolutions (<2 genes) Doves All_Neoaves rare resolutions (<2 genes) Hoatzin missing rare resolutions
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