SUPPLEMENTARY INFORMATION

Diversification analyses: Table S. Sampling for diversification analyses Table S2. Summary statistics for diversification analyses Figure S. Effects of sampling fraction and phylogenetic uncertainty on diversification analyses. Posterior distributions accounting for sampling fraction, both sampling fraction and phylogenetic uncertainty, or neither for the three groups most sensitive to these effects (Striginae+Suriinae, Falconidae, Caprimulgidae) Supplementary Note: Effects of differences in sampling levels for CP and non-cp taxa on speciation and transition rates and tip branch length estimates. Phylogenies: Supplementary Methods: Detailed phylogenetic methods and key references for molecular phylogenetic data Table S3. Number of sites and accessions for each gene used in each family-level phylogeny Table S4. Number of sites, accessions and proportion of taxa with each gene for passerine phylogeny Table S5. List of genes for all phylogenies Table S6. Datamatrix summary statistics and node support Table S7. Proportion of tips and internal nodes with mitochondrial and nuclear genes for each phylogeny Figure S2. Genes contributing information across the depth of the passerine phylogeny Figures S3-S7. Phylogenies for the Accipitridae, Strigiformes, Caprimulgiformes, Falconidae and Galliformes. WWW.NATURE.COM/NATURE

Table S. Sampling for diversification analyses Group Sub-group Taxonomy Data Sampling fraction all CP Proportion CP all CP non-cp CP Accipitridae 250 53 0.2 78 43 0.69 0.8 Buteonines & Sea Eagles 7 7 0.24 68 7 0.94.00 Strigiformes 220 6 0.28 08 45 0.40 0.74 Striginae & Surniinae 74 59 0.34 92 44 0.42 0.75 Surniinae 39 2 0.3 23 8 0.56 0.67 Striginae 38 47 0.34 69 36 0.36 0.77 Caprimulgidae 92 2 0.23 57 5 0.59 0.7 Falconidae 65 9 0.4 50 9 0.73.00 Phasianidae 8 5 0.08 30 2 0.7 0.80 Taxonomy and sampling based on IOC 2.4 species. Data and sampling fraction show the absolute numbers and proportions of species in the molecular phylogenies used for diversification analyses. WWW.NATURE.COM/NATURE 2

Table S2. Summary statistics for diversification analyses. Tip branch lengths Phylogenetic BiSSE diversification analyses clustering Maximum Likelihood Bayesian MCMC Group Sub-group all/cp ratio MP steps Proportion reshuffles with MP steps CP λ/λ0 lnl p q0/ Proportion of steps q0 lnl p q0/ λ µ/λ λ/λ0 with λ λ0 q0/q0 Proportion of steps with q0 q0 q0/ λ µ/λ Accipitridae 0.88 30/43 0.00 2.7 9.49.3E-05 6.92 2.75 4.4E-07 0.95.4E-05 2.83 <0.000 6.8 <0.000.00 0.7 Buteonines+ Sea Eagles 0.63 2/7 0.023 3.96 9.99 7.8E-06 2.83 6.7 2.5E-04 0.69 2.9E-07 4.42 <0.000 2.39 <0.000 0.73 0.25 Strigiformes 0.84 26/45 0.002.36 0.56 0.290 5.46 0.05 7.3E-06 0.59 3.7E-07.57 0.0648 0.0 0.008 0.62 0.0 Striginae +Surniinae 0.82 25/44 0.020.97 2.5 0.0379 >>0 7.78 8.0E-05 0.64 7.7E-07.99 0.0453 4.42 0.0040 0.64 0.6 Surniinae 0.67 5/8 0.088 5.40 3.6 0.0072 >>0 3.5 0.020 0.64 6.6E-06 5. 0.0046 6.9 0.0025 0.78 0.36 Striginae 0.94 20/36 0.099 0.48 0.36 0.3992.6 0.64 0.2573 2.73.9E-08 0.38 0.908.39 0.2795 0.76.2 Caprimulgidae 0.86 2/5 0.85 4.58 5.04 0.005 >>0 5.32 0.00 0.75 2.5E07 3.84 0.38 9.5 0.03 0.69 0.4 Falconidae 0.62 9/9.000 3.9 0.55 0.5763 7.79 2.4 0.0386.93 5.3E07 2.03 0.2960 5.27 0.040 2.4 0.7 Phasianidae.9 /2 0.294 0.3 0.97 0.632 8.04 0.35 0.4057 4.7 9.3E05 0.38 0.8458 6.36 0.047 3.3 2.00 CP = Colour Polymorphic species = state, non-cp = state 0. Analyses use BEAST trees, calibrated to an arbitrary mean rate of 0.0, therefore absolute values of rate parameters are arbitrary and unique to each major group and should not be compared. Bayesian analyses (MCMC) use 50 BEAST sample trees with 000 step MCMC each (= pool of 50,000 steps). All other analyses use the BEAST median node height maximum clade credibility (MCC) tree. The MP steps column shows the observed number of maximum parsimony inferred changes for the CP state, with the maximum possible number of changes after the forward slash. The proportion of reshuffles with MP steps CP refers to the frequency that randomisations show greater than or equal clustering than observed. Phylogenetic clustering analyses were done in Mesquite using 000 randomisations. BiSSE diversification rate analyses using Diversitree 0.6- and 0.7-6, with sampling fraction. λ = speciation rate for state (CP), λ0 = speciation rate for state 0 (non-cp). Speciation rate ratio = λ/λ0. Transition away ratio = q0/q0 = ratio of transition rate from CP to non-cp, over the transition rate from non-cp to CP. lnl = log likelihood difference between optimal and equal speciation rate models. P = probability that equal rate model is worse fit, by ANOVA Pr(> Chi ) 6 vs 5 d.f. q0/λ is the ratio of the transition rate away from polymorphism to the speciation rate for the polymorphic state: these two rates are generally of similar magnitude (ratio close to one). CP µ/λ is the ratio of extinction rate µ to speciation rate λ for the colour polymorphic state. Ratios are substantially less than one (in all but two instances) indicating much higher speciation rate than extinction rate.

Figure S. Examples of the effect of accounting for sampling fraction and phylogenetic uncertainty in posterior distributions of BISSE speciation rate; lambda0 = monomorphic species, lambda = colour polymorphic species. Top: 20,000 step MCMC using BEAST median MCC tree with no sampling fraction; middle: applying sampling.f = known taxon sampling for each class (0,); bottom: pool of 000 steps for each of 50 BEAST sample trees (with sampling fraction). Diversitree 0.6-; exponetial prior /(2r); optimized step size (w); MCMC starting with ML parameter values. Number of species and sampling fraction in each category (0,): Falconidae 4/9, 0.73/.00; Striginae+Surniinae 48/44, 0.42/0.75; Caprimulgidae 42/5, 0.59/0.7. Sampling fraction mostly had a quantitative effect, weakening apparent significance level, increasing any bimodal trend in posterior distribution. Effect in Accipitridae and Phasianidae was negligible (not shown). Phylogenetic uncertainty had a negligible effect. Some analyses gave unstable results probably due to limited taxa and multi-modal likelihood surface, as seen in both Bayesian and ML methods (e.g. Falconidae). Although there may be limitations to the BiSSE method, results qualitatively match those tip branch length results (Table S2). Falconidae Striginae+Surniinae Caprimulgidae No sampling Sampling Sampling fraction and phylogenetic uncertainty

Supplementary Note In order to gauge the effect of the difference in sampling of CP and non CP species on relative speciation and transition rates we randomly sub-sampled the CP species to give equal CP and non CP species sampling fractions (Table S). We repeated this ten times each for the Acciptridae, Strigiformes, Caprimulgidae and Falconidae phylogenies, and calculated median parameter estimates from the MCMC samples and average tip branch lengths. In all cases, the trend is the same as for the more complete sampling but with greater variance due to the weakened sampling. For the Acciptridae, Strigiformes, Caprimulgidae and Falconidae respectively, the speciation ratios λi/λ0 are 3.2,.6, 4.5 and., the transition ratios q0/q0 are 8.0, 5.7,.9 and 5.8 and the tip branch length ratios CP/non CP are 0.88, 0.80; 0.82 and 0.59. WWW.NATURE.COM/NATURE 5

Supplementary Methods We used Hackett et al. 3 as the overall high level phylogenetic framework demarking major groups and suitable outgroups, and further within family nomenclature follows that used in the key references for molecular phylogenetic data and inference (listed below). We constructed species-level phylogenies for groups containing the highest proportions and/or absolute numbers of polymorphic species. These are the Accipitridae, Strigiformes, Caprimulgiformes, Falconidae and Galliformes. We then identified monophyletic, wellsampled, biologically and phylogenetically coherent groups within these phylogenies for diversification analyses. This resulted in the exclusion of certain clades within some of these groups due to their phylogenetic distinctiveness, poor sampling and/or because they contained few or no CP species. Thus, we restricted our diversification analyses to the clade containing the Striginae and Suriinae within the Strigiformes; to the Caprimulgidae within the Caprimulgiformes and to the Phasianidae within the Galliformes. We also constructed several very large phylogenies for the Passeriformes. Genes were chosen on the basis of the density of coverage and therefore datasets are by-andlarge combinations of previously published studies, listed in the key references below. Additional details are provided on the passerine data as these are more complex. Tables S3-5 provide information on genes and GenBank accessions used in the sequence alignments, while Tables S6-7 and Figure S2 provide summaries of node support, gene density and coverage across phylogenetic levels. Trees in newick format (with node support values) are proved as a supplementary text file, and the Accipitridae, Strigiformes, Caprimulgiformes, Falconidae and Galliformes trees shown in Figures S3-7. Sequences were aligned with Clustal programs 36, either desktop ClustalX or via the EMBL Clustal Portal (http://www.ebi.ac.uk/tools/msa/clustalw2). For all but some passerine dataset introns alignment was straightforward. For the more complex cases a three-stage strategy was used: a first alignment to identify sequences with large insertions and/or inversions, followed by a second alignment with iteration, and then subsequent deletion of some chaotic sections. Preliminary phylogenies for each gene-by-group alignment were done with RAxML 37 via the CIPRES Gateway for RAxML (http://www.phylo.org) to check for possibly mislabelled GenBank accessions. Alignments were then assembled into supermatrices e.g 22,33 to give nexus format datasets with the maximum possible number of IOC species for that particular WWW.NATURE.COM/NATURE 6

group. Again, RAxML trees (with fast bootstrapping) were produced to check for phylogenetic stability. In a few cases some taxa were then excluded due to inadequate data. Model and partition strategies were assessed by the second order AIC 38,39 via RAxML likelihood scores, and by BEAST.5.4 40 MCMC parameter stability using Tracer.5 40,4. A two-partition GTR-gamma model (one for mitochondrial genes and one for nuclear genes) was chosen as this structure provides for the major features of sequence evolution while linking what might otherwise be a disparate patchwork of data 42,43. Final relaxed-clock trees for the diversification analyses were produced by BEAST.5.4 40 using the uncorrelated lognormal model. No attempt was made to infer actual ages and all phylogenies were calibrated to an arbitrary mean rate of 0.0 to remove the confounding effect of uncertainty in absolute dates. Although this results in arbitrary absolute values of rate parameters unique to each major group, here we are only interested in relative speciation rates. The RAxML phylogenies were used as starting trees, with a Yule node height (speciation) prior, and the two-partition GTR-gamma model. Two 20 million step chains were run sampling every 000 steps and the data combined allowing for a 25% burnin, giving all parameter effective sample sizes greater than 200, and a final median node height maximum clade credibility (MCC) tree. In addition, a set of 00 trees were taken from the post burnin samples for assessing the effect of phylogenetic uncertainty. Trees were subsequently manipulated using PAUP 4.0b0 44 TreeEdit v.0a4-6 45 and FigTree.3. 40. Phylogenetic clustering was assessed by maximum parsimony (MP) steps for character state changes on the BEAST MCC tree, done in Mesquite using 000 randomizations (http://www.mesquiteproject.org). Across all groups the CP state is present in multiple lineages, appearing to be relatively scattered, although there is some signal of clustering in most groups (Table S2). Phylogenetic analysis of the passerines involved first accumulating all GenBank accessions for genes that appeared to have a large coverage of species or genera or families. Libraries of 25 genes were assembled amounting to some fifty thousand accessions totalling 4 Megabases of sequence, and alignments built for twenty thousand accessions of 6 Mb. This WWW.NATURE.COM/NATURE 7

followed the above general procedure of aligning and generating gene trees for datachecking, and also included building family- and genus- level trees as part of the process. The different gene and taxon level trees were checked against each other for consistency and unstable taxa identified to check the component genes. Owing to the massive scale of the species level phylogeny, the passerines were broken down into three sub-trees: sub-oscines (878 = 68% of IOC 2.4 species), lower oscines up to the Corvoidea (709, 66%), the Passeroidea and attendant lineages (254, 69%). These shared a common datamatrix of nuclear and 7 mitochondrial genes, a common framework of four family-level outgroups and complementary sets of family-level passerine lineages to enable linking of the sub-trees. Due to the size of these trees CIPRES RAxML was used to generate trees, employing the two-partition model and fast bootstrap method 37. Altogether the data were able to generate reasonable trees for 20/23 families, 34/255 genera, and 428/623 species (66.5%). Within the genus and species level trees >60% of nodes have bootstraps >70% (Table S6). Ultrametric versions (suitable for analysis of relative branch length) of this tree were then created using PATHd8 46 arbitrarily calibrated to a tree height of one. All trees are based on at least one nuclear gene as well as several mitochondrial genes with an average of more than 2.5 kilobases per taxon but a considerable proportion of missing data (Tables S3-6). In an incomplete supermatrix sister lineages must have some data in common: two lineages with sets of genes A and B respectively are directly linked by A B genes in common, and together they contribute A B genes to the next lineage down 22,33,43. Thus the phylogenetic data in a supermatrix accumulates through the depth of the tree. Table S7 and Figure S2 give a brief summary of this accumulation in the passerines. Individual species have a median of three genes in common linking them to the tree (with 78% having at least two genes), this rises to median 5 genes for genera (93%) and 0 genes for families (00%). Across all the different datasets most species have both mitochondrial and nuclear data and virtually all deeper nodes have mitochondrial and nuclear genes in common (Table S7). In the passerines 7% of species have cytochrome b and 67% have ND2 (Table S4). While only 6% percent of species have a nuclear gene, in the context of the phylogeny this adds up to 74% of genera having at least one mitochondrial and one nuclear gene in common, rising to 95% at the family level (Table S7). WWW.NATURE.COM/NATURE 8

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Key references for molecular phylogenetic data and inference Accipitridae Arshad, M., Gonzalez, J., El-Sayed, A. A., Osborne, T. & Wink, M. Phylogeny and phylogeography of critically endangered Gyps species based on nuclear and mitochondrial markers. J. Ornithol. 50, 49-430, doi:0.007/s0336-008-0359-x (2009). do Amaral, F. R. et al. Patterns and processes of diversification in a widespread and ecologically diverse avian group, the buteonine hawks (Aves, Accipitridae). Mol. Phyl. Evol. 53, 703-75, doi:0.06/j.ympev.2009.07.020 (2009). Gamauf, A. & Haring, E. Molecular phylogeny and biogeography of Honey-buzzards (genera Pernis and Henicopernis). J. Zool. Syst. Evol. Res. 42, 45-53 (2004). Griffiths, C. S., Barrowclough, G. F., Groth, J. G. & Mertz, L. A. Phylogeny, diversity, and classification of the Accipitridae based on DNA sequences of the RAG- exon. J. Avian Biol. 38, 587-602, doi:0./j.2007.0908-8857.0397.x (2007). Haring, E., Kvaloy, K., Gjershaug, J. O., Rov, N. & Gamauf, A. Convergent evolution and paraphyly of the hawk-eagles of the genus Spizaetus (Aves, Accipitridae) - phylogenetic analyses based on mitochondrial markers. J. Zool. Syst. Evol. Res. 45, 353-365, doi:0./j.439-0469.2007.0040.x (2007). Helbig, A. J., Kocum, A., Seibold, I. & Braun, M. J. A multi-gene phylogeny of aquiline eagles (Aves : Accipitriformes) reveals extensive paraphyly at the genus level. Mol. Phyl. Evol. 35, 47-64, doi:0.06/j.ympev.2004.0.003 (2005). Lerner, H. R. L. & Mindell, D. P. Phylogeny of eagles, Old World vultures, and other Accipitridae based on nuclear and mitochondrial DNA. Mol. Phyl. Evol. 37, 327-346, doi:0.06/j.ympev.2005.04.00 (2005). Lerner, H. R. L., Klaver, M. C. & Mindell, D. P. Molecular phylogenetics of the Buteonine birds of prey (Accipitridae). Auk 25, 304-35, doi:0.525/auk.2008.066 (2008). Riesing, M. J., Kruckenhauser, L., Gamauf, A. & Haring, E. Molecular phylogeny of the genus Buteo (Aves : Accipitridae) based on mitochondrial marker sequences. Mol. Phyl. Evol. 27, 328-342, doi:0.06/s055-7903(02)00450-5 (2003). Wink, M., Heidrich, P. & Fentzloff, C. A mtdna phylogeny of sea eagles (genus Haliaeetus) based on nucleotide sequences of the cytochrome 6-gene. Biochem. Syst.Ecol. 24, 783-79 (996). WWW.NATURE.COM/NATURE 0

Strigiformes Fuchs, J. et al. Tracing the colonization history of the Indian Ocean scops-owls (Strigiformes : Otus) with further insight into the spatio-temporal origin of the Malagasy avifauna. BMC Evol. Biol. 8, doi:970.86/47-248-8-97 (2008). Hull, J. M. et al. Range-wide genetic differentiation among North American great gray owls (Strix nebulosa) reveals a distinct lineage restricted to the Sierra Nevada, California. Mol. Phyl. Evol. 56, 22-22, doi:0.06/j.ympev.200.02.027 (200). Wink, M. & Heidrich, P. in Raptors at Risk (eds R.D. Chancellor & B.U. Meyburg) (WWGBP/Hancock House, 2000). Wink, M., El-Sayed, A. A., Sauer-Gurth, H. & Gonzalez, J. Molecular phylogeny of owls (Strigiformes) inferred from DNA sequences of the mitochondrial cytochrome b and the nuclear RAG- gene. Ardea 97, 58-59 (2009). Caprimulgiformes Barrowclough, G. F., Groth, J. G. & Mertz, L. A. The RAG- exon in the avian order Caprimulgiformes: Phylogeny, heterozygosity, and base composition. Mol. Phyl. Evol. 4, 238-248, doi:0.06/j.ympev.2006.05.03 (2006). Braun, M. J. & Huddleston, C. J. A molecular phylogenetic survey of caprimulgiform nightbirds illustrates the utility of non-coding sequences. Mol. Phyl. Evol. 53, 948-960, doi:0.06/j.ympev.2009.08.025 (2009). Dumbacher, J. P., Pratt, T. K. & Fleischer, R. C. Phylogeny of the owlet-nightjars (Aves : Aegothelidae) based on mitochondrial DNA sequence. Mol. Phyl. Evol. 29, 540-549, doi:0.06/s055-7903(03)0035-0 (2003). Han, K. L., Robbins, M. B. & Braun, M. J. A multi-gene estimate of phylogeny in the nightjars and nighthawks (Caprimulgidae). Mol. Phyl. Evol. 55, 443-453, doi:0.06/j.ympev.200.0.023 (200). Larsen, C., Speed, M., Harvey, N. & Noyes, H. A. A molecular phylogeny of the nightjars (Aves : Caprimulgidae) suggests extensive conservation of primitive morphological traits across multiple lineages. Mol. Phyl. Evol. 42, 789-796, doi:0.06/j.ympev.2006.0.005 (2007). WWW.NATURE.COM/NATURE

Falconidae El-Sayed, A. A., Gonzalez, J. & Wink, M. Phylogenetic relationships in diurnal raptors and putative allies: Evidence from mitochondrial DNA sequences, nuclear RAG- genes and genomic fingerprints. J. Ornithol. 47, 62-63 (2006). Fuchs, J., Chen, S., Johnson, J. A. & Mindell, D. P. Pliocene diversification within the South American Forest falcons (Falconidae: Micrastur). Mol. Phyl. Evol. 60, 398-407, doi:0.06/j.ympev.20.05.008 (20). Griffiths, C. S., Barrowclough, G. F., Groth, J. G. & Mertz, L. Phylogeny of the Falconidae (Aves): a comparison of the efficacy of morphological, mitochondrial, and nuclear data. Mol. Phyl. Evol. 32, 0-09, doi:0.06/j.ympev.2003..09 (2004). Groombridge, J. J. et al. A molecular phylogeny of African kestrels with reference to divergence across the Indian Ocean. Mol. Phyl. Evol. 25, 267-277 (2002). Nittinger, F., Haring, E., Pinsker, W., Wink, M. & Gamauf, A. Out of Africa? Phylogenetic relationships between Falco biarmicus and the other hierofalcons (Aves : Falconidae). J. Zool. Syst. Evol. Res. 43, 32-33, doi:0./j.439-0469.2005.00326.32-33 (2005). Galliformes Bao, X. K. et al. The phylogenetic position and speciation dynamics of the genus Perdix (Phasianidae, Galliformes). Mol. Phyl. Evol. 56, 840-847, doi:0.06/j.ympev.200.03.038 (200). Bonilla, A. J., Braun, E. L. & Kimball, R. T. Comparative molecular evolution and phylogenetic utility of 3 '-UTRs and introns in Galliformes. Mol. Phyl. Evol. 56, 536-542, doi:0.06/j.ympev.200.04.006 (200). Crowe, T. M. et al. Phylogenetics, biogeography and classification of, and character evolution in, gamebirds (Aves : Galliformes): effects of character exclusion, data partitioning and missing data. Cladistics 22, 495-532, doi:0./j.096-003.2006.0020.x (2006). Frank-Hoeflich, K. et al. Increased taxon and character sampling reveals novel intergeneric relationships in the Cracidae (Aves : Galliformes). J. Zool. Syst. Evol. Res. 45, 242-254, doi:0./j.439-0469.2007.00396.x (2007). WWW.NATURE.COM/NATURE 2

Kimball, R. T. & Braun, E. L. A multigene phylogeny of Galliformes supports a single origin of erectile ability in non-feathered facial traits. J. Avian Biol. 39, 438-445, doi:0./j.2008.0908-8857.04270.x (2008). Kriegs, J. O. et al. Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves : Galliformes). BMC Evol. Biol. 7, doi:900.86/47-248-7-90 (2007). Shen, Y. Y. et al. A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae. BMC Evol. Biol. 0, doi:320.86/47-248-0-32 (200). Passeriformes Barker, F. K., Barrowclough, G. F. & Groth, J. G. A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data. Proc. Roy. Soc. Lond. B 269, 295-308, doi:0.098/rspb.200.883 (2002). Barker, F. K., Cibois, A., Schikler, P., Feinstein, J. & Cracraft, J. Phylogeny and diversification of the largest avian radiation. Proc. Natl. Acad. Sci. USA 0, 040-045, doi:0.073/pnas.0408920 (2004). Beresford, P., Barker, F. K., Ryan, P. G. & Crowe, T. M. African endemics span the tree of songbirds (Passeri): molecular systematics of several evolutionary 'enigmas'. Proc. Roy. Soc. Lond. B 272, 849-858, doi:0.098/rspb.2004.2997 (2005). Ericson, P. G. P. & Johansson, U. S. Phylogeny of Passerida (Aves : Passeriformes) based on nuclear and mitochondrial sequence data. Mol. Phyl. Evol. 29, 26-38, doi:0.06/s055-7903(03)00067-8 (2003). Gardner, J. L., Trueman, J. W. H., Ebert, D., Joseph, L. & Magrath, R. D. Phylogeny and evolution of the Meliphagoidea, the largest radiation of Australasian songbirds. Mol. Phyl. Evol. 55, 087-02, doi:0.06/j.ympev.200.02.005 (200). Irestedt, M., Johansson, U. S., Parsons, T. J. & Ericson, P. G. P. Phylogeny of major lineages of suboscines (Passeriformes) analysed by nuclear DNA sequence data. J. Avian Biol. 32, 5-25 (200). Irestedt, M. & Ohlson, J. I. The division of the major songbird radiation into Passerida and 'core Corvoidea' (Aves : Passeriformes) - the species tree vs. gene trees. Zoologica Scripta 37, 305-33, doi:0./j.463-6409.2007.0032.x (2008). WWW.NATURE.COM/NATURE 3

Johansson, U. S., Fjeldsa, J. & Bowie, R. C. K. Phylogenetic relationships within Passerida (Aves : Passeriformes): A review and a new molecular phylogeny based on three nuclear intron markers. Mol. Phyl. Evol. 48, 858-876, doi:0.06/j.ympev.2008.05.029 (2008). Jonsson, K. A. & Fjeldsa, J. A phylogenetic supertree of oscine passerine birds (Aves : Passeri). Zool. Scripta 35, 49-86, doi:0./j.463-6409.2006.0022.x (2006). Jonsson, K. A., Fabre, P. H., Ricklefs, R. E. & Fjeldsa, J. Major global radiation of corvoid birds originated in the proto-papuan archipelago. Proc. Natl. Acad. Sci. USA 08, 2328-2333, doi:0.073/pnas.0895608 (20). Lovette, I. J. et al. A comprehensive multilocus phylogeny for the wood-warblers and a revised classification of the Parulidae (Ayes). Mol. Phyl. Evol. 57, 753-770, doi:0.06/j.ympev.200.07.08 (200). Sangster, G., Alstrom, P., Forsmark, E. & Olsson, U. Multi-locus phylogenetic analysis of Old World chats and flycatchers reveals extensive paraphyly at family, subfamily and genus level (Aves: Muscicapidae). Mol. Phyl. Evol. 57, 380-392, doi:0.06/j.ympev.200.07.008 (200). WWW.NATURE.COM/NATURE 4

Table S3. Number of sites and accessions for each gene used in each family-level phylogeny Group Gene Total Accipitridae RAG- BFib7 cytb ND6 2S ATPase COI Sites 2872 972 077 59 805 842 827 794 accessions 88 92 6 6 68 53 57 580 Strigiformes RAG- MYO TGFB2 cytb ND2 COI Sites 948 728 605 43 056 693 573 accessions 72 37 39 04 45 39 336 Caprimulgiformes RAG- v-myc GH cytb COI Sites 2872 288 290 43 693 886 accessions 35 76 65 87 22 285 Falconidae RAG- cytb COI ND2 Sites 2836 43 693 04 573 accessions 50 48 5 34 47 Galliformes BFib7 OvoG mtdna cytb ND2 Sites 95 469 732 46 044 20742 accessions 57 72 37 8 09 456 WWW.NATURE.COM/NATURE 5

Table S4. Number of sites, accessions and proportion of taxa with each gene for passerine phylogeny Gene sequence Genes Accessions Proportion of taxa in trees with gene Family Genus Species Sites Family Genus Species Nuclear RAG- 22 642 95 290 0.56 0.22 c-myc 78 92 229 53 0.62 0.7 0.06 c-mos 79 53 93 624 0.63 0.3 0.05 Zenk 60 00 20 224 0.48 0.09 0.03 RAG-2 05 463 574 55 0.84 0.4 0.4 bfib7 46 228 466 0 0.37 0.2 0. bfib5 79 45 836 675 0.63 0.36 0.2 MYO 689 438 787 0.89 0.6 0.35 ODC 0 52 0 895 0.8 0.46 0.27 TGFB2 47 56 442 633 0.38 0.4 0. GAPDH 7 464 823 466 0.57 0.4 0.2 Mitochondrial cytb 07 902 2950 43 0.86 0.79 0.7 ND2 0 87 2785 04 0.88 0.77 0.67 COI 74 478 302 3 0.59 0.42 0.3 ATPase 52 206 542 985 0.42 0.8 0.3 2S 77 285 590 94 0.62 0.25 0.4 ND3 68 309 99 35 0.54 0.27 0.22 6S 58 29 425 6 0.46 0.9 0. Total 445 7293 6659 7375 WWW.NATURE.COM/NATURE 6

Table S5. Genes used for phylogeny reconstruction Gene sequences code gene Nuclear RAG- Recombination activating protein c-myc Proto-oncogene protein, exon 3 c-mos Oocyte maturation factor Mos zenk Zinc finger protein (ZENK = EGR-), exon 2 RAG-2 Recombination activating protein 2 OvoG Ovomucoid gene, intron G v-myc Myelocytomatosis viral oncogene-like protein, exon 3 GH Growth hormone, intron 2 Bfib7 Beta-Fibrinogen intron 7 BFib5 Beta-Fibrinogen intron 5 MYO Myoglobin, intron 2 to intron 3 ODC Ornithine decarboxylase, intron 6 to intron 7 TGFB2 Transforming growth factor beta 2, intron 5 ALDOB Aldolase B fructose-bisphosphate GAPDH Glyceraldehyde-3-phosphate dehydrogenase, intron Mitochondrial cytb Cytochrome b ND2 NADH dehydrogenase subunit 2 COI Cytochrome oxidase subunit ATPase ATPase subunits 6, 8 ND6 NADH dehydrogenase subunit 6 ND3 NADH dehydrogenase subunit 6 2S 2S ribosomal RNA Genbank accession numbers available from authors on request. WWW.NATURE.COM/NATURE 7

Table S6. Datamatrix summary statistics and node support Phylogeny Genes Sites Accessions Total bases Taxa Av. length Missing data p- taxa Support mtdna nuclear ingroup outgroups >50 >70 >90 Accipitridae 5 2 794 580 64454 78 3 44 0.55 0.7 0.87/0.87 0.7/0.8 0.52/0.72 Strigiformes 3 3 573 336 28404 08 3 2559 0.5 0.49 0.83/0.93 0.67/0.79 0.44/0.69 Caprimulgiformes 2 3 886 285 375764 8 7 4270 0.48 0.65 0.85/0.93 0.67/0.85 0.52/0.76 Falconidae 3 573 47 8950 50 3 3576 0.37 0.77 0.82/0.87 0.74/0.77 0.62/0.7 Galliformes 3 2 20742 456 97652 97 4932 0.76 0.66 0.84/0.87 0.7/0.8 0.55/0.74 Passeriformes genera-level 7 7375 725 636223 34 4 5550 0.68 0.9 0.77 0.6 0.45 species-level 7 7375 5202 3376707 428 4 3233 0.8 0.67 0.77 0.63 0.47 Sites = alignment length; Total bases = defined nucleotide characters in matrix; Accessions = number of individual GenBank accessions; Av length = average number of bases per taxon; Missing data is proportion of states coded as? (=missing data); p-taxa = proportion of IOC 2.4 taxa in the dataset; Caprimulgiformes outgroups include Aerodramus and Hemiprocne; Galliformes data includes entire mtdna genome less control region; Support shows proportion of nodes with indicated RAxML fast bootstrap and/or BEAST posterior probability. WWW.NATURE.COM/NATURE 8

Table S7. Proportion of tips and internal nodes with mitochondrial and nuclear genes for each phylogeny Phylogeny Nuclear Mitochondrial Both Accipitridae 0.69 0.96 0.65 Strigiformes 0.77 0.75 Caprimulgiformes 0.87 0.87 Falconidae 0.94 0.94 Galliformes 0.42 0.4 Passeriformes Nuclear Mitochondrial Both Multiple both family taxon 0.95 0.95 0.85 contribute to node 0.97 common to node 0.95 0.95 0.84 genus taxon 0.8 0.95 0.76 0.52 contribute to node 0.93 0.92 0.83 common to node 0.79 0.95 0.74 0.5 species taxon 0.6 0.95 0.56 0.27 contribute to node 0.83 0.83 0.66 common to node 0.6 0.95 0.55 0.29 both = at least one nuclear and one mitochondrial gene multiple both = multiple nuclear and multiple mitochondrial genes contribute to node = proportion of internal nodes with genes contributing information common to node = proportion of internal nodes with genes in common WWW.NATURE.COM/NATURE 9

Figure S2. Minimum number of genes contributing information to nodes across phylogenetic depth of the passerine phylogeny WWW.NATURE.COM/NATURE 20

Figure S3. Accipitridae datamatrix BEAST median node height MCC tree with posterior probability values. CP species highlighted in orange; taxon label shows genus_species_mt and nuclear genes_cp status. Major sub-groups denoted. Outgroups in grey. Approximate percentage of species sampled shown for some major clades (notwithstanding phylogenetic uncertainty). 0.73 0.7 Pernine Kites 67% Buteo_oreophilus_nm 0.97 Buteo_buteo_n5m_p 0.38 Buteo_rufinus_n4m_p 0.52 Buteo_hemilasius_0n4m_p Buteo_refectus_0n3m Buteo_japonicus_n4m 0.44 Buteo_augur_0n4m_p 0.36 Buteo_rufofuscus_n4m_p Buteo_auguralis_0nm Buteo_brachypterus_0nm Buteo_regalis_n5m_p 0.94 Buteo_lagopus_n5m_p Buteo_albonotatus_0n5m 0.94 Buteo_ventralis_0nm_p Buteo_jamaicensis_2n5m_p Buteo_swainsoni_n5m_p Buteo_galapagoensis_0n5m Buteo_brachyurus_0n5m_p Buteo_albigula_n4m Buteo_solitarius_0n4m_p Buteo_platypterus_n5m_p Buteo_ridgwayi_0n4m 0.9 Buteo_lineatus_n5m Buteo_nitidus_2n5m Leucopternis_melanops_n4m Leucopternis_kuhli_n4m Leucopternis_semiplumbeus_n4m Leucopternis_occidentalis_n4m Leucopternis_albicollis_n4m Leucopternis_polionotus_n4m Geranoaetus_melanoleucus_2n5m Buteo_polyosoma_n5m_p Buteo_albicaudatus_n5m_p Buteo_leucorrhous_0n5m_p 0.96 Parabuteo_unicinctus_n5m 0.96 Buteo_magnirostris_2n5m Leucopternis_princeps_n4m Buteogallus_aequinoctialis_0n4m Buteogallus_anthracinus_2n5m Leucopternis_schistaceus_n4m Buteogallus_meridionalis_2n5m Leucopternis_lacernulatus_0n4m Harpyhaliaetus_coronatus_0n4m Harpyhaliaetus_solitarius_2n4m Buteogallus_urubitinga_n5m Leucopternis_plumbeus_n4m Buteonine Geranospiza_caerulescens_2n5m 0.92 Rostrhamus_sociabilis_2n5m Hawks 95% 0.93 Busarellus_nigricollis_n5m Ictinia_mississippiensis_0n5m Ictinia_plumbea_2n5m Butastur_indicus_0n2m 0.88 Butastur_teesa_nm Butastur_rufipennis_nm Haliaeetus_leucocephalus_2n5m 0.58 Haliaeetus_albicilla_n4m Haliaeetus_pelagicus_0n3m_p 0.92 Haliaeetus_leucoryphus_0nm Haliaeetus_sanfordi_0nm Haliaeetus_leucogaster_n2m Haliaeetus_vociferoides_nm Haliaeetus_vocifer_nm 0.9 Ichthyophaga_humilis_0nm Ichthyophaga_ichthyaetus_0nm Sea Eagles Milvus_migrans_0n3m 00% Milvus_milvus_nm Haliastur_sphenurus_nm Haliastur_indus_2nm Circus_cinereus_0nm 0.63 0.84 0.07 Circus_cyaneus_0n2m 0.04 Accipiter_tachiro_n0m_p Accipiter_imitator_n0m_p 0.73 0.34 Accipiter_novaehollandiae_n0m_p Circus_ranivorus_nm 0.44 Circus_aeruginosus_2n3m_p 0.43 Circus_buffoni_0nm_p Accipiter_bicolor_n2m_p 0.97 Accipiter_cooperii_n2m 0.75 0.94 Accipiter_gentilis_2n5m_p Accipiter_striatus_0n2m 0.76 Accipiter_rufiventris_nm 0.76 Accipiter_nisus_2n3m 0.96 Accipiter_erythronemius_0nm Accipiters & Harriers 32% Accipiter_gularis_0n2m 0.86 Accipiter_virgatus_0nm 0.76 Accipiter_cirrocephalus_nm Accipiter_soloensis_0nm Melierax_canorus_2nm 0.84 0.28 Melierax_poliopterus_0nm Accipiter_superciliosus_0n2m_p 0.55 Harpagus_bidentatus_n0m 0.32 Micronisus_gabar_nm_p 0.7 0.03 Urotriorchis_macrourus_0nm_p Accipiter_trivirgatus_0nm 0.45 Kaupifalco_monogrammicus_n2m Aquila_fasciata_2n3m Aquila_spilogaster_nm Aquila_verreauxii_2nm Aquila_gurneyi_0nm 0.56 Aquila_audax_nm Aquila_africana_0nm Aquila_chrysaetos_2n4m 0.74 Hieraaetus_morphnoides_2nm_p Hieraaetus_pennatus_2nm_p Hieraaetus_ayresii_nm_p Hieraaetus_wahlbergi_2nm_p Aquila_adalberti_nm 0.94 Aquila_heliaca_2n2m Aquila_rapax_2nm_p Aquila_nipalensis_2n2m Aquila_clanga_n2m_p 0.97 Aquila_pomarina_nm_p Ictinaetus_malayensis_nm Lophaetus_occipitalis_2nm Polemaetus_bellicosus_2nm Lophotriorchis_kienerii_0nm Spizaetus_ornatus_2nm Spizaetus_isidori_2nm Spizaetus_melanoleucus_2nm Spizaetus_tyrannus_2nm Booted Eagles 92% Nisaetus_bartelsi_0nm 0.95 Nisaetus_alboniger_0n4m Nisaetus_kelaarti_0nm 0.55 Nisaetus_nipalensis_2n4m Nisaetus_nanus_0nm Nisaetus_pinskeri_0nm 0.42 Nisaetus_cirrhatus_nm_p 0.72 0.45 Nisaetus_philippensis_nm Nisaetus_lanceolatus_0nm Stephanoaetus_coronatus_2nm Harpia_harpyja_2nm 0.79 Morphnus_guianensis_2nm_p 0.97 Harpyopsis_novaeguineae_2nm Macheiramphus_alcinus_n0m_p Gyps_fulvus_n3m 0.7 Gyps_rueppellii_2nm 0.7 Gyps_coprotheres_2nm 0.37 Gyps_tenuirostris_0nm 0.95 Gyps_indicus_nm Gyps_himalayensis_nm Gyps_bengalensis_2nm Gyps_africanus_2nm Necrosyrtes_monachus_2nm Torgos_tracheliotus_2nm Aegypius_monachus_2n2m Trigonoceps_occipitalis_nm Sarcogyps_calvus_2nm Vultures & Serpent Eagles 86% Circaetus_cinereus_nm 0.5 Circaetus_pectoralis_2nm 0.53 Circaetus_gallicus_n3m_p Circaetus_cinerascens_0nm Circaetus_fasciolatus_nm Spilornis_elgini_0nm 0.73 Dryotriorchis_spectabilis_0nm Terathopius_ecaudatus_2nm_p Pithecophaga_jefferyi_nm Spilornis_rufipectus_0nm 0.33 Spilornis_holospilus_0nm Spilornis_cheela_n3m Henicopernis_longicauda_0nm 0.92 Lophoictinia_isura_nm 0.5 Hamirostra_melanosternon_2nm Aviceda_subcristata_n0m 0.34 Pernis_celebensis_0nm 0.74 Pernis_ptilorhynchus_0nm_p 0.68 Pernis_apivorus_n3m_p Aviceda_cuculoides_0nm 0.28 Elanoides_forficatus_2n4m 0.5 Eutriorchis_astur_0nm 0.96 0.47 Polyboroides_typus_2nm Gypohierax_angolensis_2nm 0.94 Gypaetus_barbatus_nm Neophron_percnopterus_2n2m Leptodon_cayanensis_2nm_p Chondrohierax_uncinatus_nm_p Elanus_leucurus_n2m 0.64 Elanus_caeruleus_n0m Gampsonyx_swainsonii_n2m Pandion_haliaetus_2n5m Sagittarius_serpentarius_2n2m Cathartes_aura_n0m

Figure S4. Strigiformes datamatrix BEAST median node height MCC tree with posterior probability values. CP species highlighted in orange; taxon label shows genus_species_mt and nuclear genes_ CP status. Major sub-groups denoted. Outgroups in grey.approximate percentage of species sampled shown for some major clades (notwithstanding phylogenetic uncertainty). 0.63 Strigidae 50% 0.84 Surniinae 59% Striginae 50% Tytonidae 39% 33% 54% 0.95 46% 0.89 0.44 0.85 0.25 0.38 0.93 0.77 Strix_uralensis_n2m Strix_davidi_0nm Strix_aluco_3n2m_p 0.34 Strix_nebulosa_n3m 0.6 0.92 Strix_leptogrammica_0nm Strix_butleri_nm_p Strix_woodfordii_3n2m_p Strix_virgata_0nm_p 0.7 0.73 Strix_rufipes_n2m_p Strix_varia_0n2m Strix_occidentalis_3n2m Lophostrix_cristata_0nm_p Pulsatrix_koeniswaldiana_nm 0.97 Pulsatrix_perspicillata_nm Bubo_ascalaphus_nm Bubo_bubo_3n3m_p 0.85 Bubo_capensis_nm Bubo_africanus_nm_p Bubo_bengalensis_nm_p Bubo_virginianus_3n3m_p Bubo_magellanicus_0n2m Bubo_scandiacus_n2m Ketupa_ketupu_nm Ketupa_zeylonensis_nm Bubo_nipalensis_nm Bubo_lacteus_nm Megascops_guatemalae_0nm_p 0.29 0.26 Megascops_napensis_n0m Megascops_sanctaecatarinae_0nm_p 0.2 Megascops_kennicottii_3n3m_p 0.96 0.6 Megascops_asio_3n3m_p Megascops_watsonii_0nm_p 0.96 0.58 Megascops_atricapilla_nm_p 0.56 Megascops_roboratus_n2m_p Megascops_hoyi_2n3m_p 0.96 Megascops_petersoni_0nm Megascops_koepckeae_n2m 0.9 Megascops_choliba_n2m_p 0.94 Megascops_albogularis_0nm Megascops_trichopsis_0nm_p Megascops_flammeolus_n2m_p Asio_otus_3n3m Pseudoscops_clamator_n2m Asio_capensis_nm Asio_flammeus_2n2m Ptilopsis_granti_nm Ptilopsis_leucotis_2n2m Otus_mayottensis_2n2m 0.45 Otus_rutilus_2n2m_p 0.9 Otus_capnodes_2n2m_p Otus_insularis_2n2m Otus_moheliensis_2n2m_p 0.83 Otus_pauliani_2n2m_p 0.53 Otus_longicornis_2n2m Otus_mirus_2n2m Otus_elegans_0nm Otus_pembaensis_2n2m_p Otus_senegalensis_2n2m_p Otus_scops_3n3m_p Otus_brucei_nm_p Otus_spilocephalus_3n2m_p Otus_sunia_3n3m_p Otus_semitorques_0nm 0.86 0.68 Otus_megalotis_3n3m_p Mimizuku_gurneyi_0nm Otus_bakkamoena_3n2m_p Otus_lempiji_3n3m_p Otus_lettia_3n3m_p Otus_ireneae_2n2m_p Glaucidium_griseiceps_nm Glaucidium_brasilianum_n3m_p Glaucidium_nana_n2m_p 0.73 Glaucidium_peruanum_nm Glaucidium_hardyi_nm_p Glaucidium_jardinii_nm_p Glaucidium_bolivianum_nm_p Glaucidium_californicum_nm_p 0.97 Glaucidium_gnoma_3n2m_p Glaucidium_minutissimum_0nm Glaucidium_perlatum_nm Glaucidium_tephronotum_0nm 0.8 Glaucidium_passerinum_nm Glaucidium_cuculoides_2nm 0.43 Surnia_ulula_n2m Glaucidium_capense_0nm Athene_noctua_3n2m_p 0.87 Athene_brama_0nm Athene_cunicularia_3n2m Aegolius_harrisii_nm Aegolius_acadicus_3n3m Aegolius_funereus_n2m Micrathene_whitneyi_0n2m Ninox_squamipila_0nm 0.27 Ninox_rudolfi_nm 0.57 Ninox_boobook_n0m Ninox_novaeseelandiae_0n3m 0.69 0.87 Ninox_connivens_n2m Ninox_strenua_n2m 0.8 Ninox_rufa_n2m Ninox_philippensis_0n2m Ninox_scutulata_n2m Tyto_capensis_0n2m 0.82 Tyto_longimembris_nm Tyto_novaehollandiae_nm_p Tyto_glaucops_0nm Tyto_alba_3n3m Tyto_tenebricosa_n2m Phodilus_badius_3nm Colius_striatus_2n3m Leptosomus_discolor_3n2m Pandion_haliaetus_3n3m

Figure S5. Caprimulgiformes datamatrix BEAST median node height MCC tree with posterior probability values. CP species highlighted in orange; taxon label shows genus_species_mt and nuclear genes_cp status. Major sub-groups denoted. Outgroups in grey. Approximate percentage of species sampled shown for some major clades (notwithstanding phylogenetic uncertainty). 0.57 0.89 Caprimulgidae 62% 0.95 0.96 0.59 0.8 Podargidae 43% Steatornithidae 00% Aegothelidae 9% Apodiformes Nyctibiidae 00% 0.78 0.5 0.95 0.63 0.5 0.85 0.4 0.36 0.39 0.88 0.59 0.68 0.88 0.76 0.83 0.5 0.94 0.54 0.34 Caprimulgus_europaeus_3n2m Caprimulgus_rufigena_2nm Caprimulgus_fraenatus_0nm Caprimulgus_climacurus_3nm_p Caprimulgus_fossii_2nm_p Macrodipteryx_vexillarius_3nm Macrodipteryx_longipennis_2nm_p Caprimulgus_batesi_2nm Caprimulgus_inornatus_0nm_p Caprimulgus_manillensis_2nm Caprimulgus_indicus_2n2m Caprimulgus_macrurus_3nm Caprimulgus_madagascariensis_2nm_p Caprimulgus_poliocephalus_2nm Caprimulgus_pectoralis_2nm_p Caprimulgus_nigriscapularis_2nm_p Caprimulgus_affinis_3nm_p Caprimulgus_aegyptius_2nm Chordeiles_rupestris_2nm Chordeiles_acutipennis_3n2m Chordeiles_minor_2n2m_p Chordeiles_pusillus_2nm Podager_nacunda_3n2m Caprimulgus_rufus_2nm Caprimulgus_carolinensis_3n2m_p Caprimulgus_salvini_2nm Caprimulgus_ridgwayi_2nm Caprimulgus_vociferus_3n2m Caprimulgus_saturatus_2nm Phalaenoptilus_nuttallii_3n2m Nyctiphrynus_yucatanicus_2nm_p Nyctiphrynus_ocellatus_3nm_p Nyctiphrynus_mcleodii_3n2m_p Nyctiphrynus_rosenbergi_2nm Siphonorhis_brewsteri_2nm Hydropsalis_climacocerca_3nm Hydropsalis_torquata_2n2m Caprimulgus_cayennensis_2nm Caprimulgus_maculicaudus_3nm Caprimulgus_parvulus_3n2m Eleothreptus_anomalus_2n2m Caprimulgus_candicans_0nm Caprimulgus_longirostris_3nm_p Uropsalis_segmentata_3nm Uropsalis_lyra_2nm Caprimulgus_whitelyi_2nm Nyctidromus_albicollis_3n2m_p Caprimulgus_anthonyi_2nm Caprimulgus_nigrescens_2nm Nyctiprogne_leucopyga_3nm Lurocalis_semitorquatus_3nm Lurocalis_rufiventris_2nm Caprimulgus_enarratus_2nm Eurostopodus_macrotis_3nm Eurostopodus_argus_2nm Eurostopodus_mystacalis_2nm Eurostopodus_papuensis_2nm Podargus_strigoides_3n2m_p Podargus_papuensis_nm_p Podargus_ocellatus_nm_p Rigidipenna_inexpectata_0nm Batrachostomus_cornutus_0nm_p Batrachostomus_septimus_3nm_p Steatornis_caripensis_3nm Aegotheles_wallacii_0nm Aegotheles_albertisi_2nm_p Aegotheles_archboldi_0nm_p Aegotheles_bennettii_nm Aegotheles_cristatus_n2m_p Aegotheles_crinifrons_0nm_p Aegotheles_insignis_3nm_p Aegotheles_tatei_0nm Aegotheles_savesi_0nm Aegotheles_novaezealandiae_0nm Aerodramus_3n2m Hemiprocne_3nm Nyctibius_griseus_n2m_p Nyctibius_jamaicensis_nm_p Nyctibius_leucopterus_nm Nyctibius_maculosus_nm Nyctibius_grandis_3nm Nyctibius_aethereus_2nm Nyctibius_bracteatus_2nm Grus_3n2m Tauraco_3nm Pandion_2n2m Strix_2n2m Psittaciformes_2n2m

0.32 Figure S6. Falconidae datamatrix BEAST median node height MCC tree with posterior probability values. CP species highlighted in orange; taxon label shows genus_species_mt and nuclear genes_ CP status. Major sub-groups denoted. Outgroups in grey. Approximate percentage of species sampled shown for some major clades (notwithstanding phylogenetic uncertainty). 0.44 Falconinae 74% Herpetotherinae 00% 79% Falco_cherrug_nm_p Falco_biarmicus_nm 0.6 Falco_rusticolus_n2m_p Falco_jugger_nm Falco_subniger_nm Falco_pelegrinoides_nm Falco_peregrinus_n3m_p Falco_mexicanus_n2m 0.65 Falco_chicquera_nm 0.25 Falco_columbarius_n3m 0.3 0.25 Falco_berigora_nm_p Falco_sparverius_n3m_p 0.54 0.64 Falco_femoralis_n2m Falco_novaeseelandiae_nm Falco_subbuteo_n3m 0.28 Falco_cuvierii_nm 0.8 Falco_concolor_nm Falco_eleonorae_nm_p 0.95 Falco_longipennis_n2m 0.4 Falco_deiroleucus_nm Falco_dickinsoni_nm Falco_vespertinus_nm Falco_amurensis_n2m Falco_newtoni_0nm_p Falco_araeus_0nm Falco_tinnunculus_n3m 0.76 Falco_cenchroides_nm Falco_rupicoloides_nm Falco_punctatus_nm 0.89 Falco_naumanni_n2m Falco_zoniventris_nm Microhierax_caerulescens_n2m Microhierax_erythrogenys_0nm Polihierax_semitorquatus_n2m Milvago_chimachima_n2m Milvago_chimango_n2m Daptrius_ater_nm Phalcoboenus_megalopterus_n2m Phalcoboenus_australis_nm Ibycter_americanus_n2m Caracara_plancus_n3m Spiziapteryx_circumcincta_n2m Micrastur_mintoni_nm 0.65 Micrastur_ruficollis_nm_p Micrastur_gilvicollis_n2m Micrastur_plumbeus_nm Micrastur_semitorquatus_n2m_p Micrastur_mirandollei_nm Micrastur_buckleyi_nm Herpetotheres_cachinnans_n2m Pandionidae_n3m Psittacidae_n3m Corvidae_n3m

Lophura_hatinhensis_0nm Lophura_edwardsi_0nm 0.55 Lophura_swinhoii_2n2m Lophura_leucomelanos_0nm_p Figure S7. Galliformes datamatrix BEAST median node height 0.94 Lophura_nycthemera_2n3m MCC tree with posterior probability values. CP species Lophura_bulweri_0nm highlighted in orange; taxon label shows 0.5 Lophura_inornata_2n2m genus_species_mt and nuclear genes_cp status. Major Lophura_ignita_0n2m sub-groups denoted. Outgroups in grey. Approximate 0.87 0.97 Lophura_diardi_0nm percentage of species sampled shown for some major Lophura_erythrophthalma_0nm clades (notwithstanding phylogenetic uncertainty). Catreus_wallichii_2n2m Crossoptilon_mantchuricum_0nm Crossoptilon_auritum_0n2m Crossoptilon_harmani_0nm 0.86 Crossoptilon_crossoptilon_2n2m Chrysolophus_pictus_2n3m Chrysolophus_amherstiae_n3m Phasianus_versicolor_0n2m Phasianus_colchicus_2n3m Syrmaticus_humiae_n3m Syrmaticus_ellioti_2n3m 0.9 Syrmaticus_mikado_n2m Syrmaticus_reevesii_2n3m Syrmaticus_soemmerringii_0n2m Perdix_dauurica_0n3m Perdix_perdix_2n2m Perdix_hodgsoniae_0n2m 0.97 Rhizothera_longirostris_0nm Pucrasia_macrolopha_2n3m_p Lyrurus_tetrix_0n2m_p Lyrurus_mlokosiewiczi_0n2m Tetrao_urogallus_0n2m Tetrao_parvirostris_0n2m Falcipennis_falcipennis_0n2m Falcipennis_canadensis_2n2m_p 0.5 Tympanuchus_phasianellus_2n2m 0.97 Tympanuchus_cupido_0n2m Tympanuchus_pallidicinctus_0n2m 0.92 Dendragapus_obscurus_0n2m Centrocercus_urophasianus_0n2m Lagopus_muta_0n2m 0.57 Lagopus_lagopus_0n2m_p Lagopus_leucura_0n2m Bonasa_umbellus_0n2m_p Tetrastes_sewerzowi_0n2m Tetrastes_bonasia_0n3m Meleagris_gallopavo_2n3m Lophophorus_lhuysii_0n3m 0.26 Lophophorus_sclateri_0n2m Lophophorus_impejanus_2n2m_p Tetraophasis_obscurus_0n2m Tetraophasis_szechenyii_0n3m Tragopan_blythii_2n2m 0.95 Tragopan_satyra_0nm Tragopan_temminckii_2n3m Tragopan_caboti_0n2m Ithaginis_cruentus_n2m Scleroptila_africana_n2m 0.85 Scleroptila_levaillantoides_0n2m 0.79 0.66 Scleroptila_shelleyi_n2m Scleroptila_finschi_0n2m 0.36 0.45 Francolinus_pintadeanus_0nm 0.49 Scleroptila_levaillantii_n2m 0.3 Peliperdix_coqui_n2m Peliperdix_lathami_n2m 0.3 Francolinus_pondicerianus_n2m 0.84 0.64 Francolinus_gularis_0nm 0.55 Dendroperdix_sephaena_n2m Francolinus_francolinus_0nm Gallus_sonneratii_2n2m Gallus_gallus_2n3m Gallus_varius_2n3m Gallus_lafayetii_2n2m Bambusicola_fytchii_0n2m Bambusicola_thoracicus_2n3m Pavo_cristatus_2n2m Pavo_muticus_2n3m 0.96 Afropavo_congensis_2n2m Argusianus_argus_nm Rheinardia_ocellata_0nm Polyplectron_chalcurum_2n2m Polyplectron_bicalcaratum_2n3m Polyplectron_inopinatum_2n2m 0.89 Polyplectron_germaini_2n2m Polyplectron_katsumatae_0nm Polyplectron_schleiermacheri_nm 0.89 Polyplectron_malacense_2n2m Polyplectron_napoleonis_2n2m 0.38 Haematortyx_sanguiniceps_0nm Galloperdix_lunulata_0nm Pternistis_hildebrandti_0nm Pternistis_natalensis_n2m_p Pternistis_capensis_n2m Pternistis_adspersus_n2m Pternistis_griseostriatus_n2m 0.57 Pternistis_swainsonii_n2m Pternistis_leucoscepus_n2m Pternistis_afer_n2m Pternistis_bicalcaratus_0nm_p Pternistis_squamatus_n2m_p Pternistis_erckelii_0nm Pternistis_castaneicollis_0nm_p 0.96 Pternistis_hartlaubi_0nm_p Ammoperdix_heyi_0nm Perdicula_asiatica_0nm Phasianidae 72% Alectoris_magna_0n2m 0.74 0.9 Alectoris_philbyi_0nm Alectoris_graeca_0nm 0.9 Alectoris_rufa_2nm 0.49 Alectoris_chukar_2n3m 0.95 Alectoris_melanocephala_0nm Alectoris_barbara_0nm Tetraogallus_altaicus_0nm 0.55 Tetraogallus_caspius_0nm Tetraogallus_himalayensis_0n2m Tetraogallus_tibetanus_0n2m Coturnix_coturnix_0n2m 0.95 Coturnix_japonica_2n2m Coturnix_pectoralis_0nm Margaroperdix_madagarensis_0nm Coturnix_ypsilophora_0n2m Excalfactoria_chinensis_0n2m Arborophila_gingica_0nm 0.46 Arborophila_rufogularis_0nm 0.45 0.8 Arborophila_javanica_nm Arborophila_torqueola_0nm 0.46 0.9 Arborophila_rufipectus_0nm 0.88 Rollulus_rouloul_0nm Caloperdix_oculeus_0nm Xenoperdix_udzungwensis_nm Callipepla_douglasii_0n2m 0.4 Callipepla_squamata_0n2m Callipepla_gambelii_n2m Callipepla_californica_0n2m_p Odontophoridae 29% Colinus_cristatus_0nm Colinus_virginianus_2n2m Oreortyx_pictus_2n2m_p Cyrtonyx_montezumae_2n2m Ptilopachus_petrosus_n2m Ptilopachus_nahani_n2m Numididae 83% Guttera_plumifera_0nm Guttera_pucherani_2n2m 0.95 Acryllium_vulturinum_n3m 0.96 Agelastes_meleagrides_0nm Numida_meleagris_2n3m Pauxi_unicornis_0nm 0.97 0.44 Mitu_tuberosum_nm Mitu_salvini_0nm 0.9 Mitu_tomentosum_0nm 0.7 0.94 Mitu_mitu_0nm Pauxi_pauxi_2nm_p Nothocrax_urumutum_nm Crax_globulosa_0nm Crax_alector_0nm 0.45 Crax_fasciolata_0nm Crax_blumenbachii_nm 0.2 Crax_rubra_2n2m_p 0.34 Crax_alberti_0nm_p Crax_daubentoni_0nm Ortalis_guttata_0nm 0.39 0.2 Ortalis_cinereiceps_0nm 0.2 Ortalis_poliocephala_0nm 0.66 Ortalis_canicollis_nm 0.36 Ortalis_ruficauda_0nm 0.96 0.73 Ortalis_garrula_0nm Ortalis_vetula_2n2m 0.33 Ortalis_leucogastra_0nm Ortalis_motmot_0nm Oreophasis_derbianus_nm Pipile_cumanensis_0nm 0.55 Cracidae 69% Pipile_cujubi_0nm 0.39 Pipile_jacutinga_n0m 0.76 Aburria_aburri_nm Penelope_argyrotis_0nm 0.9 0.78 Penelope_superciliaris_0nm Penelope_montagnii_0nm 0.84 Penelope_jacquacu_0nm 0.79 Penelope_purpurascens_0nm 0.33 Chamaepetes_goudotii_nm 0.97 Chamaepetes_unicolor_0nm Penelope_obscura_n0m Penelopina_nigra_nm Megapodius_forsteni_0nm 0.94 Megapodius_freycinet_0n2m Megapodius_decollatus_0nm Megapodius_eremita_0n2m Megapodius_reinwardt_nm Megapodius_layardi_2n2m Megapodius_pritchardii_0nm Megapodius_cumingii_0nm Megapodius_tenimberensis_0nm Megapodidae 78% Eulipoa_wallacei_0nm Alectura_lathami_2n3m 0.9 Aepypodius_arfakianus_0nm Leipoa_ocellata_2n2m 0.62 Talegalla_fuscirostris_0nm Macrocephalon_maleo_0n2m Anas_n2m