sign in sign up
<<
Home , Neoaves

● 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 sister 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: and ; IV: , , and ; V: , Swifts, , and allies; VI: Doves, , and ; VII: and . Other short codes including S: Shorebirds; CR: Cranes and Rails; TB: Turacos and Bustards; M: ; W: and allies; EHV: Eagles, , 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 V Charadrius_vociferus Picoides_pubescens Charadrius_vociferus VI+VII Phaethon_lepturus Columba_livia chlamydotis_undulata Mesites& 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 Pelecanus_crispus Tyto_alba Merops_Picoides_pubescensnubicus Egretta_garzetta Penguins Falco_peregrinus &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 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& 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 Tropicbirds Mousebirds Nightjars Doves Cariama 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 + non_monop +Darter+ 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 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 (<2 genes) Polyphyletic PG

yletic_Owl

h

non_monop

unsupported 50% supports

unsupported unsupported Figure S3. –continued. B, Topology distribution of the ML gene trees for the three focal edges using Prum et al. (2015) data. Upper panel: without constraint bootstrap support. Polyphyletic PG: species within or Galloanserae are not monophyletic. non_monophyletic_Owl: the two species of Owls used in Prum et al. (2015) are not monophyletic in some gene trees. Lower panel: under 50% bootstrap cutoff. rare resolutions: relationships shown in less than 2 gene trees. RF distribution between ML gene tree and species tree RF distribution among ML gene trees 600

Exons 400 6e+05 200 0 0e+00 30 40 50 60 70 80 0 20 40 60 80 80000 80 Introns 40000 40 0 0 30 40 50 60 70 30 40 50 60 70 600

UCEs 400 1000000 200 0 0 40 50 60 70 40 50 60 70 80 distance distance 1200 15 800 Prum data 10 5 400 0 0 100 150 200 250 150 200 250 300 distance distance

Figure S4. RF distances among ML gene trees or between ML gene tree and species tree. For Jarvis et al. (2014) Exons, Introns and UCEs, we use concatenated TENT tree as species tree. For Prum et al. (2015) data, we use the concatenated RAxML tree as species tree.

A Earliest Neoaves Hoatzin Sister Owls Sister 1.00 1.00 1.00 V V EHV III+V+VI+VII I+III+V M Cranes TB M+W Cuckoos S W 0.75 VI+VII 0.75 0.75 S+CR Doves VII II+III+S+CR Hoatzin I Nightjars 0.50 0.50 Plovers 0.50 ercentage P

0.25 0.25 0.25

0.00 0.00 0.00 EL EH IL IH UL UH EL EH IL IH UL UH EL EH IL IH UL UH comparison between gene sets (∑Ng) of lower and upper quartile of ΔGC90

B Earliest Neoaves Hoatzin Sister Owls Sister 1.00 1.00 1.00 V V EHV III+V+VI+VII I+III+V M Cranes TB M+W Cuckoos S W 0.75 VI+VII 0.75 0.75 S+CR Doves VII II+III+S+CR Hoatzin I Nightjars

ercentage 0.50 0.50 0.50

P Plovers

0.25 0.25 0.25

0.00 0.00 0.00 EL EH IL IH UL UH EL EH IL IH UL UH EL EH IL IH UL UH comparison between gene sets (∑Ng) of lower and upper quartile of tree lengths

Figure S5. Support comparison among different hypotheses using ∑Ng (sum of number of genes) between gene sets of the lower and upper quartiles of A: ∆GC90 (the GC difference between the 95 and 5 percentile GC-rich taxa) or B: tree lengths, for the three focal edges. (EL and EH: exons with lower or higher quartile ∆GC90/tree length, respectively; IL and IH: introns with lower or higher quartile ∆GC90/tree length, respectively; UL and UH: UCEs with lower or higher quartile ∆GC90/tree length. hypotheses codes are the same as in Figure S2.

Exon Intron UCE Earliest Neoaves Exons No. Introns No. UCEs No. VII 5VII 6 Sandgrouse 8 Cuckoos 5Bustards 5Doves 6 Bustards 4Doves 5Bustards 5 Earliest Non_Mono_PG Hoatzin 4 Sandgrouse 4VII 5 Neoaves Non_Mono_PG Non_Mono_PG Doves 4V 3Killdeer 4 Grebes 3Cuckoos 3Mesites 3 Mesites 3 Sunbittern 3III+Doves 3 Hummingbirds+Swifts 3Nightjars 2 Turacos 3 rare resolutions rare resolutions rare resolutions <2genes Sunbittern 3Hoatzin 2Hoatzin 3 Hoatzin + Killdeer 2 Hummingbirds+Swifts 2V 3 rare resolutions 338 rare resolutions 319 rare resolutions 305 Exon Intron UCE Hoazin's sister Exons No. Introns No. UCEs No. Killdeer (shorebirds) 29 Killdeer 32 Cranes 24 Sunbittern 26 Sunbittern 25 Cuckoos 24 Tropicbirds 22 Cranes 24 Sunbittern 23 Cranes 22 Tropicbirds 22 Killdeer 19 Hoatzin's Sister Turacos 20 Doves 21 Doves 16 rare resolutions Bustards 17 Cuckoos 17 Turacos 16 rare resolutions rare resolutions Cuckoos 15 Turacos 17 Tropicbirds 14 Doves 15 Bustards 15 Nightjars 13 13 VII 11 Mesites 13 Nightjars 10 Mesites 11 III 12 rare resolutions 208 rare resolutions 211 rare resolutions 184 Exon Intron UCE Owls' sister Exons No. Introns No. UCEs No. NW vultures 54 NW vultures 48 Eagles 48 Eagles 38 Eagles 37 NW vultures 47 Mousebirds 23 Seriemas 29 Mousebirds 29 Owls' Seriemas 23 EHV 29 EHV 27 Sister rare resolutions rare resolutions rare resolutions -roller 19 Mousebirds 28 Seriemas 22 EHV 19 Falcons 16 Cuckoo-roller 16 Falcons 16 Cuckoo-roller 14 Falcons 14 Trogons 13 Trogons 14 Trogons 10 Parrots 13 Hornbills 12 10 Hornbills 12 Woodpeckers 12 Parrots 10 rare resolutions 146 rare resolutions 135 rare resolutions 143

Figure S6. Topology distribution of the ML gene trees for the three focal edges using simulated data. We relax support cutoff to show potential topology distributions. rare resolutions: relationships shown in less than 2 gene trees. Non_Mono_PG: non-monophyletic Palaeognathae and Galloanserae. The right panel showed the top 10 resolutions for each focal edge based on each simulated data type.

0-1000bp 1000-2000bp

9838.Exon Neat align

9527.Exon Neat align

1424.Exon Mess align

Figure S7. Intragenic alignment comparisons from three exons with intragenic gene tree conflicts, we can see exon locus 1424 have messy alignment from 0-1000bp and the conflicts between the two segments might be corresponded to misalignment.