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doi:10.1038/nature13687 Contents of Supplementary Text: Taxon sampling.......2-3 Mitochondrial DNA data collection......3 UCE data collection.... 3-4 Biogeographic areas.......4-5 Gene trees, divergence times, and ancestral area reconstruction.......5-7 Bayesian species delimitation.......7-8 Testing for simultaneous divergence......8-10 Ecological and historical variables...10-13 Phylogenetic generalized least-squares analyses. 14-17 Supplementary Tables 1 to 16......18-30 References 31-33 Supplementary Figures 1 to 28.34-61 WWW.NATURE.COM/NATURE 1

METHODS Taxon sampling We sampled 27 taxonomically diverse Neotropical bird lineages whose widespread distributions encompass lowland rainforests both east and west of the Andes (Fig. 1; Supplementary Figs. 1-27). The lineages we examined encompass both single, independently evolving species (and subspecies within them) and species complexes that include several closely related species (and subspecies within them). Because the alpha taxonomy of the lineages we examined is based on morphology, which can be an unreliable indicator of the amount of genetic differentiation, we use the term lineage to denote that both species and species complexes were examined in our analyses. We sampled the following lineages: Piaya cayana (Cuculidae), Trogon rufus (Trogonidae), Ramphastos species complex (Ramphastidae; data from 31,32), Pteroglossus species complex (Ramphastidae; data from 33), Pyrrhura (Psittacidae; data from 34), Brotogeris species complex (Psittacidae; data from 35), Pyrilia species complex (Psittacidae; data from 36), Cymbilaimus lineatus (Thamnophilidae), Myrmotherula axillaris (Thamnophilidae), Sclerurus mexicanus (Furnariidae), Dendrocincla fuliginosa (Furnariidae), Glyphorynchus spirurus (Furnariidae), Xenops minutus (Furnariidae), Automolus ochrolaemus (Furnariidae), Colonia colonus (Tyrannidae), Attila spadiceus (Tyrannidae), Querula purpurata (Cotingidae), Lepidothrix coronata (Pipridae), Tityra semifasciata (Tityridae), Schiffornis turdina (Tityridae), Microcerculus marginatus (Troglodytidae), Henicorhina leucosticta (Troglodytidae), Tangara cyanicollis (Thraupidae), Tangara gyrola (Thraupidae), Tersina viridis (Thraupidae), Cyanerpes caeruleus (Thraupidae), and Chlorophanes spiza (Thraupidae). We included closely related outgroup taxa for each lineage to identify the sister lineage(s). We included all available samples for each focal lineage that were deposited in the author s institutions. To supplement our geographic coverage of each lineage, we also obtained samples via genetic resource loans from other natural history museums (see acknowledgements) that have tissue collections. The large sample sizes in this study are the product of 30+ years of collecting expeditions in the Neotropics. Detailed locality information with geographic coordinates and museum tissue numbers are presented in Supplementary Table 17. This study was approved by the LSU Institutional Animal Care and Use Committee (IACUC protocol 09-001) and is in compliance with IACUC guidelines. Sampling bias.- To evaluate comparative phylogeographic patterns across the Neotropical lowlands we directed our sampling to widespread lowland lineages whose distributions encompass both sides of the Andes. Although an assemblage of largely co-distributed lineages was expected to show concordant histories under the traditional model of landscape change driving speciation, we found that idiosyncratic histories are the predominant pattern. It seems likely that lineages having smaller distributions, which are presumably subject to the same stochastic processes as lineages having larger distributions, would also exhibit similar discordance in their phylogeographic patterns. There are many explanations for why some WWW.NATURE.COM/NATURE 2

lineages could have small distributions, including local population extinctions, limited habitat or resource availability, and competition. The generality of our results needs to be tested in other organisms, but the strength of our sampling design is that we have extensive taxonomic coverage with dense population-level sampling. Speciation in birds. We assume in this study that the first stage of speciation occurs via the geographic isolation of populations (i.e. allopatry). This is based on the overwhelming evidence for the predominance of this geographic mode of speciation for birds 3,37-39, and the fact that, to the best of our knowledge, there are no cases of parapatric or sympatric speciation documented in Neotropical birds 40. In this study we examine how landscape features have interacted with species ecologies to create geographic isolation. Mitochondrial DNA data collection We extracted total DNA from ~ 25 mg of pectoral muscle tissue using the DNeasy Tissue Kit (Qiagen, Valencia, CA). We performed polymerase chain reaction (PCR) amplifications (25 µl) of the mitochondrial protein-coding cytochrome b (cyt b) gene, containing 2.5 µl template DNA (~50 ng), 1 µl each of the primers L14996 and H16064 41 (10 µm), 0.5 µl dntps (10 µm), 2.5 µl 10X with MgCl 2 reaction buffer, 0.1 Taq DNA polymerase (5 U/µL AmpliTaq; ABI, Foster City, CA), and 17.4 µl sterile ddh2o. The PCR temperature profile was an initial denaturation of 2 min at 94 C, followed by 35 cycles of 30 s at 94 C, 30 s at 45 50 C, and 1 min at 72 C, with a final extension of 5 min at 72 C. We purified double-stranded PCR products using 20% polyethylene glycol and then cyclesequenced using 1.75 µl 5X sequencing buffer (ABI), 1 µl sequencing primer (10 µm), 2.25 µl template, 0.35 µl Big Dye Terminator Cycle-Sequencing Kit (ver.3.1; ABI), and 1.65 µl sterile ddh2o. We cleaned reactions using Sephadex (G-50 fine) columns and we electrophoresed them on an ABI 3100 Genetic Analyzer. We manually assembled contigs for each individual using Sequencher (ver. 4.9; GeneCodes, Ann Arbor, MI), and we verified there were no stop codons in the coding region. Data collection of ultraconserved elements We analyzed orthologous and independently segregating nuclear loci published in a complementary study using massively parallel sequencing and sequence capture of ultraconserved elements (UCEs 42-45 ). This data set comprised five of the lineages in our mtdna data set: Cymbilaimus lineatus, Microcerculus marginatus, Xenops minutus, Querula purpurata, and Schiffornis turdina 46. These five taxa were selected so as to have exemplars of both rainforest understorey and canopy foraging strata. Also, the variability in mtdna gene tree height across the five taxa was representative of the variability observed across the 27- lineage data set. A complete description of the wet-lab protocol and bioinformatics used to assemble UCE data is available in Smith et al. 46. Each lineage included 4-8 individuals and WWW.NATURE.COM/NATURE 3

had samples on both sides of the Andes, across the Isthmus of Panama, and across the Amazon River. The final UCE data sets included 166 orthologous loci that were shared across all five lineages. Divergence time analyses using coalescent modeling with migration found that cross-andes divergence events occurred over the last few million years 46 : Cymbilaimus lineatus: 0.13 Ma (0.1-0.17); Xenops minutus: 2.50 Ma (2.22-2.82); Schiffornis turdina: 1.04 Ma (0.85-1.22); Querula purpurata: 0.19 Ma (0.16-0.22); Microcerculus marginatus: 1.51 Ma (1.11-1.90) (Supplementary Table 17). Divergence time estimates from UCE data tended to be more recent than mtdna time estimates as predicted by coalescent theory, because divergence times from gene trees are expected to pre-date estimates from species trees 47. Despite the expected disparity between estimates of divergence times from gene and species tree, the values from both data sets were highly correlated (R 2 =0.69, P < 001; Supplementary Table 17). The Andes were the only dispersal barrier for which we had sufficient UCE sampling to further assess patterns of simultaneous divergence. We reduced each data set by removing haplotypes that represented phylogeographic structure that occurred prior or after cross- Andean divergence in order for the data to conform to the two population model in msbayes. We then removed loci from the reduced data set that contained >50% of missing data. The final data sets consisted of 129-163 loci: (Cymbilaimus lineatus: number of loci = 148; max length = 823 bp; min length = 34 bp; avg. length = 274 bp; Microcerculus marginatus: number of loci =156; max length = 804 bp; min length = 78 bp; avg. length = 437 bp; Querula purpurata: number of loci =156; max length = 978 bp; min length = 99 bp; avg. length = 584 bp; Schiffornis turdina: number of loci =129; max length = 931 bp; min length = 96 bp; avg. length = 509 bp; Xenops minutus: number of loci =163; max length = 961 bp; min length = 82 bp; avg. length = 428 bp). Biogeographic areas To examine how dispersal barriers in the lowlands of Central and South America influence diversification, we focused our sampling on avian taxa that are distributed on either side of landscape features previously recognized as barriers to lowland organisms. The majority of the sampled individuals were from humid lowland forests adjacent to these barriers. Due to variation in the distributions of our study taxa, however, some lineages contained population samples in foothills or open areas outside the humid lowlands. We assigned each individual sample to one of the biogeographic areas described below, and used this information in analyses to reconstruct ancestral ranges and to identify phylogeographic breaks in gene trees. We used the general biogeographic areas proposed by Cracraft 48 and Haffer 49 and included additional areas that surround the core Amazonian biogeographic areas (Extended Data Fig. 1). The areas within Amazonia are largely delimited by the major tributaries of the Amazon River: Guiana east of the Negro River through the entire Guiana Shield, Imerí west of the Negro River to east of the Japurá River, Napo the lowlands west of the Japurá River south through the area west of the Huallaga River and north of the upper Amazon WWW.NATURE.COM/NATURE 4

River, the area east of the Huallaga River, south of the Amazon River, and west of the Madeira River, Rondônia the area east of the Madeira River and west of the Tapajós River, Tapajós the area east of the Tapajós River and west of the Xingu River, Xingu the region east of the Xingu River and west of the Tocantins River, Belém the area east of the upper Tocantins River, and the Atlantic Forest the humid forest along the Brazilian Atlantic coast. Within the region west of the Andes: Magdalena Magdalena valley in Colombia, including the Nechí and lower Cauca river basins, the Chocó the area east of the Panamanian canal zone through the Darién and south to the humid forest along the Ecuadorian coast, Central America the area west of the Panama canal zone to the Isthmus of Tehuantepec, and West of the Isthmus of Tehuantepec (West IoT) the lowland forest of the Gulf Coast, and Pacific coast of Mexico. To capture a more nuanced view of species distributions we assigned individuals to the following additional Neotropical areas: Andean Foothills the foothill humid forests along the eastern side of the Eastern cordillera of Colombia and the Mérida cordillera and adjacent to the Llanos; Catatumbo the southwest portion of the Maracaibo basin surrounded by Serranía de Perijá and Serranía de Motilones and the Mérida cordillera; Tumbes the tropical deciduous dry forests along the Pacific coast of southwestern Ecuador and northwestern Peru; Orinoco Delta the humid forests around the delta of the Orinoco River in Venezuela; Ilha Marajó in the mouth of the Amazon. The taxa Tangara cyanicollis (montane forests along the Andes and south central Amazonia), Ramphastos ambiguus (Eastern Andean foothills), Pyrrhura rhodocephala (Mérida cordillera), Pyrrhura hoffmanni (Chiriquí- Talamanca highlands), Pyrrhura orcesi (foothills of southwestern Ecuador), and Pyrrhura albipectus (Andean slopes of southeastern Ecuador) occur at higher elevations than the other species, so we included additional areas to reflect these differences: Western Andes the foothill and cloud forests of Pichincha, Ecuador; Tachira the foothill and cloud forests of Tachira, Venezuela; Southeast the foothill and cloud forests of La Paz and Cochabamba, Bolivia; Northwest: the foothill and cloud forests of San Martín and Cajamarca, Peru; Eastern Andean foothills foothill forests along the eastern flanks of the Andes from Bolivia to Ecuador. Gene trees, divergence times, and ancestral area reconstruction We generated gene trees and estimated divergence times using the program BEAST v.1.6.2 50 with an uncorrelated relaxed substitution rate based on an avian molecular clock 51 (lognormal distribution, mean = 105, SD = 0.1), a coalescent: constant-size prior for the tree prior (except for Ramphastos and Pteroglossus, we used a speciation: Yule process tree prior), and a GTR + Γ finite-sites substitution model. We ran the analysis for 50 million generations and sampled every 2,500 generations. BEAST analyses were validated by performing multiple independent runs. We assessed MCMC convergence and determined the burn-in by examining ESS values and likelihood plots in Tracer v. 1.5 52. We included sister species to ingroup taxa and in some cases we also included more distantly related outgroup taxa. Although our estimates are based on a single locus, comparisons of single versus WWW.NATURE.COM/NATURE 5

multilocus divergence time estimates in Neotropical birds indicate that temporal estimates based on mtdna accurately reflect relative patterns of differentiation 53,54. Because the mtdna time estimates are gene divergences opposed to species divergences the inferred species ages are likely overestimates and represent the maximum ages of species. Thus, it is unlikely that multilocus species ages would be inconsistent with our conclusion of recent origins of species diversity. For the tree presented in Fig 2., we used a data set consisting of the inferred species (n=142) from our species delimitation analyses and followed the same approach that we used for the single lineage BEAST analyses, except that we used external calibrations for some nodes and fixed certain relationships identified from previous multilocus phylogenetic studies. We specified the prior distribution for the node representing the last common ancestor for: parrots and passerines (78.4 Ma 28 ), Glyphorynchus spirurus and Dendrocincla fuliginosa (23 Ma 29 ), and Sclerurus mexicanus and the other furnariids (33 Ma 29). For each calibrated node prior we used a normal distribution with a standard deviation of 1.0 for the prior distribution. We used a Bayesian phylogeographic model 55 in BEAST to infer spatial patterns of diversification and identify the most probable geographic origin of each of the 27 lineages. The Bayesian phylogeographic model implements ancestral reconstruction of discrete states on time-calibrated phylogenies. Within each of the 27 lineages we assigned individuals to a biogeographic area based on the geographic locality of the sample. A full description of biogeographic areas is discussed in the Biogeographic areas section above. We used the same parameter and prior settings as in the BEAST divergence-time analyses except that we restricted this analysis to only ingroup taxa and implemented the Bayesian Stochastic Search Variable Selection 55 (BSSVS). For the location.clock.rate prior we used a uniform prior (0 1). We used this Bayesian phylogeographic model to estimate whether a lineage had its ancestral origin west or east of the Andes. We determined the ancestral origin for a lineage by identifying the root node area with the highest posterior probability. Using the Bayesian phylogeographic model, we found that the most probable area of origin for 14 lineages was east of the Andes in the Amazon Basin, and for 13 it was west of the Andes in the Chocó and Central American region (Supplementary Table 17). To confirm an effect of the landscape matrix on the genetic structuring of populations we compiled divergence times across five prominent biogeographic barriers (Fig. 1; Extended Data Figure 1): the Andes (west vs. east), the Isthmus of Panama (Chocó vs. Central America), the Negro River (Napo vs. Guiana), the upper Amazon River (Napo vs. ), and the Madeira River ( vs. Rondônia). We found that for each of the major biogeographic barriers (the Andes, Isthmus of Panama, or Amazonian rivers), 66 100% of the lineages exhibited phylogeographic breaks across them. Using the relative frequency of genetically undifferentiated populations across a barrier as a proxy of permeability, we found that the Andes (Supplementary Table 17; number of undifferentiated populations across barrier: n=0, disregarding single individuals that may represent incomplete lineage sorting or gene flow) were the least porous to dispersal, whereas Amazonian Rivers were the most permeable (n=17). WWW.NATURE.COM/NATURE 6

Bayesian species delimitation The current taxonomy likely represents an inaccurate estimate of the standing avian diversity in the tropics 56,57, because the alpha taxonomy of many groups requires formal revision using modern methods (e.g. 54). We accounted for a potential effect of taxonomic bias in this study by delimiting putative species, irrespective of current taxonomy, using genetic data in a coalescent framework. Because evolutionary persistence is one of the variables we examined in this study, it is vital that within-lineage species be identified under a common framework 58. We performed species delimitation analysis using the program bgmyc 59, a Bayesian implementation of the mixed Yule-coalescent model for species delimitation 60. We explored different coalescent, Yule, and threshold values, and recovered similar results. For data sets with fewer than 50 individuals we lowered the default threshold value (number of species). We used the maximum clade credibility tree for each lineage and ran the program 100,000 generations using the single.phy function, discarding the first 15,000 generations as the burnin. We performed MCMC diagnostics by checking likelihood plots of parameters and we ran each data set multiple times to assess the stability of the results. The program provides a posterior probability that two sequences belong to the same species, where a posterior probability of 1.0 between two sequences indicates there is a 100% probability that the two sequences belong to the same species and a posterior probability of between two sequences indicates there is zero chance that the two sequences belong to the same species. We used a conservative approach for species delimitation and we classified species as clusters in the gene tree that had posterior probabilities > 0.95 of belonging to the same species. The number of species inferred using Bayesian species delimitation ranged from 1-18 for each lineage (Supplementary Table 17; Supplementary Table 1). To evaluate the impact of sample size on bgmyc species delimitation, we performed sensitivity analyses in which species diversity within each of the 27 lineages was estimated with bgmyc after excluding a fixed percentage of individuals in six different treatments. In the first treatment, we pruned 10% of the individuals (i.e. tree tips) randomly from each lineage s phylogeny using the R package APE 61. For subsequent treatments, we successively increased the number of pruned individuals by an additional 10%, with the final treatment having 60% of its individuals removed. For each treatment we re-estimated species diversity using the previously described bgmyc approach (Supplementary Table 1; Extended Data Fig. 4). We then used t-tests to compare the distribution of species diversity estimated in the 27 lineages for all treatments. We found that the pruned data sets were not significantly different (two-tailed test) from the complete sampling distribution with up to 50% of the tips removed (Supplementary Table 2). The results were equivalent when we used a nonparametric K-S test instead of a t-test. Although there have been some recent refinements, the bulk of the current taxonomy of the study lineages was established in the 1800s by examination of phenotypic variation in museum study skins. Because taxonomists tended to assign a name to any geographic variant, the current taxonomy (species and subspecies within lineages) is undoubtedly an overestimate WWW.NATURE.COM/NATURE 7

of the number of species within each lineage. In contrast, because of its dependence on dense genetic sampling and our conservative threshold for accepting genetic clusters as species, the Bayesian delimitation method likely underestimates diversity. The true species diversity lies somewhere in between these extremes of diversity. Despite the potential for issues of underor over-estimating species diversity, the number of inferred species using bgmyc was highly correlated (R 2 = 0.77) with the number of described taxa (species and subspecies). This result suggests that the bgmyc analyses identified taxa that are diagnosable with genetics as well as morphological and vocal characters. It is likely that future taxonomic revisions will elevate many of these inferred species or subspecies within the 27 lineages to biological species status 56,57. For example, it has been proposed that the species Schiffornis turdina in our study be split into five separate biological species 62. For subsequent analysis, we treated all taxa within the 27 lineages as species. Testing for simultaneous divergence To estimate the temporal patterns of disparity in isolation across the dispersal barriers, we used a hierarchical approximate Bayesian computation approach (habc) that accounts for gene tree/population divergence disparity under the coalescent while allowing independence across species in demographic parameters. We used an implementation of habc in the software msbayes 63 and we analyzed the sequence data for multiple co-distributed population pairs jointly under a hierarchical divergence model. We tested for simultaneous divergence and estimated the number and relative ages of co-divergence pulses between pairs of neighboring regions divided by biogeographic dispersal barriers. We used summary statistics from msbayes to compare observed patterns in sequence diversity with data simulated under a model of ancestral populations splitting into two daughter populations (without subsequent migration) simultaneously for all species. Each simulation run involved (i) drawing a random value of Ψ (number of divergence events across all population pairs in a data set) from its discrete uniform hyperprior distribution; (ii) drawing divergence times τ,..., τ n for each of the n population-pairs conditional on this instance of Ψ (i.e. all species will have the same τ if Ψ=1 whereas each population-pair draws from the τ,..., τ Ψ possible times when Ψ>1 conditional on each of these Ψ times having at least one population splitting), (iii) drawing species-specific demographic parameters independently from shared prior distributions (independent of Ψ); (iv) simulating multispecies data given the randomly drawn hyperparameters as well as sample sizes, fragment lengths and known generation times for each species and (v) generating vectors of summary statistics from these simulated data sets. Posterior distributions for the hyperparameters of interest Ψ, shared τ (τ,..., τ Ψ ), and σ 2 / τ - were generated by first applying a rejection step using the Euclidian distance between vectors of observed and simulated summary statistics, followed by a method of weighted local linear regression for continuous parameters and weight logistical polychotomous regression for discrete parameters 64. Population divergence times (τ i ) for each of the 27 WWW.NATURE.COM/NATURE 8

lineages were scaled relative to their effective population sizes (N i ), i.e. t = τ i 2N i g, where g is the generation time in years. To report divergence times across co-diverging lineages in global coalescent time units (i.e. τ scaled by N generations) given that each lineage has different values of N i, each τ i was rescaled to the same global scale using the relationship τ = τ i θ i /b, where b is, the global scalar of q. For example, if a population pair had a small N i and large τ i (in units if 2 N i g), its globally expressed divergence time τ would be directly comparable to a population pair with an equal divergence in absolute time but with differing N i (and hence differing τ i ). Using single-locus data from multiple population-pairs results in a borrowing strength for improved parameter estimation 65-67, which is akin to increasing statistical power of single-species estimates of parameters by sampling greater numbers of unlinked genetic loci. The pattern and degree of dissynchrony in divergence times is captured by hyperparameters; Ψ, which quantifies the number of divergence times; σ 2 / τ, the index of dispersion quantifying normalized variability in divergence times; and the vector of codivergence times τ,..., τ Ψ conditional on Ψ. We assumed uniform prior distributions for all species-level parameters with upper bounds that are not greater than the maximum gene-tree divergence estimated from BEAST, such that the ABC sampler efficiently drew plausible population divergence times < gene-tree divergence times 67,68 to avoid downwardly biased estimates in Ψ 69. To further demonstrate that the priors were able to reproduce the main features of the observed data 66,70, we further obtained a graphical check using the first two principal components of the summary statistics calculated from 1,000 random draws from each prior. The hyperprior for the hyperparameter Ψ was discrete uniform and upwardly bound by n, the number of species-pairs in any particular analysis; Ψ = (1,n). Scaled effective population sizes for both ancestral populations (θ a ) and descendent pairs of daughter populations (θ 1 and θ 2 ) were allowed to vary independently. We performed habc analyses on both single locus mtdna data (Extended Data Fig. 2) and data from orthologous, independently segregating nuclear UCEs (Extended Data Fig. 3). We identified sister population-pairs from the BEAST mtdna gene trees across five biogeographic barriers: the Andes (n=29), the Isthmus of Panama (n=14), the Negro River (n=17), the upper Amazon River (n=14), and the Madeira River (n=14). We did not include sister populations-pairs that only had one sample on each side of the Andes. In some taxonpair comparisons we removed haplotypes representing phylogeographic structure occurring after divergence in order for the data to conform to the two-population model of msbayes. For the expanded data matrix of UCE data, we assembled a data set of five lineages and 129 163 UCEs: Cymbilaimus lineatus (n = 148), Xenops minutus (n = 163), Schiffornis turdina (n = 129), Querula purpurata (n = 155), and Microcerculus marginatus (n = 156). For the UCE matrix our sampling only permitted testing simultaneous divergence across the Andes. For each data set of population pairs split by a particular barrier, we initially ran a separate msbayes analysis with a discrete uniform prior on Ψ, with the prior Ψ values ranging WWW.NATURE.COM/NATURE 9

from 1 (simultaneous divergence) to the maximum number of divergences (Ψ= number of pairs) all being equally likely. Comparisons of the posterior probabilities of a synchronous pulse of divergence (σ 2 / τ < 1; M 1 ) and asynchronous divergence (σ 2 / τ > 1; M 2 ) were made with Bayes Factors (B(M 1, M 2 )), with values of B(M 1, M 2 ) < 1/10 and 1/10 < B(M 1, M 2 ) < 1/3 being interpreted as strong and moderate support for asynchronous divergence, respectively 71. For all calculations of Bayes factors, we used the ABC approximation B(M 1, M 2 ) = Pr(M 1 D)/Pr(M 2 D)/Pr(M 1 )/Pr(M 2 ), where the posteriors of the two models Pr(M 1 D) and Pr(M 2 D) are approximated from the set of 1,000 summary statistic vectors passing the final ABC filter. For the mtdna data sets we performed additional msbayes analyses conditional on all Ψ values having > 2 posterior probability in order to visually represent the uncertainty underlying the estimates of co-divergence pulse times. We used a rate of 2.1% sequence divergence per million years for analyses with mtdna 51 and 0.2% per million years for analyses with UCEs 46, and mean substitution-rate uniformity across species with a gamma-distributed rate variation across loci within species as in Huang et al. 63. We note that the results presented herein are not dependent on absolute molecular dates nor on the accuracy of this molecular clock calibration, but that DNA substitution rate variation across species could result in incorrectly rejecting a history of synchronous divergence. For the mtdna data, we used four summary statistic classes calculated across all population pairs that have previously been shown to capture information about co-divergence using simulations 65 : average pairwise diversity scaled per base-pair (π), average net diversity between populations scaled per base-pair (π net ), Wattersons s theta scaled per base-pair (θ W ; the number of segregating normalized for sample size) and δ, the denominator of equation 38 in Tajima 72 (Tajima s D), where S, the number of segregating sites is scaled per base-pair rather than per locus. For the UCE data, only one summary statistic class was used (π b ; average pairwise differences between populations) to accommodate loci that lacked polymorphism within populations. To allow this vector of summary statistics to be orderindependent we used the ranking scheme of Huang et al 63. Summary statistics of mtdna are in Supplementary Tables 3-7 and π b values from UCEs are available in Supplementary Table 17. Bayes factors for model comparisons are presented in the main text. Ecological and historical variables The total number of variables used in our phylogenetic generalized least-squares (PGLS) analyses was dictated by the sample sizes of the response variables. Our complete data set consisted of ~2500 samples from 27 independent lineages, but to avoid a potential correlation between divergence estimates extracted from the same phylogeny we binned divergence estimates into three independent classes of barriers: the Andes, Isthmus of Panama, and Amazonian Rivers. This reduced set of response variables limited the number of potential predictor variables that could be included in multivariate models. The diversity of ecological and historical variables that can be collected for Neotropical birds is relatively large. Published data sets describing species-specific diet, WWW.NATURE.COM/NATURE 10

habitat, relative abundance, distribution, elevational range, and range size are available 73. Morphological data that may reflect ecological differences, such as body size and wing shape, can be obtained from museum specimens. Additionally, variables that capture aspects of a lineage s evolutionary history, such as clade age, colonization time of an area, diversification rate, and ancestral area of origin, can be inferred from phylogenetic data. Because the number of potential predictor variables was larger than the sample sizes of the genetic metrics to be modeled, we selected two ecological and two historical variables that are known or predicted to influence genetic differentiation. The ecological variables we examined initially were foraging stratum, foraging guild, habitat breadth, maximum elevation, niche breadth, and hand-wing index from museum specimens. Previous work found that foraging stratum and foraging guild were correlated and that foraging stratum was a more significant predictor of genetic differentiation 11. Further, sample sizes of the differing foraging guilds were skewed, with only a few omnivores (frugivore: n=10, insectivore: n=12, and omnivore: n=5), so we did not retain this variable for further analysis. Previous work also found that classifying species by their presence in forest edge or várzea forest, maximum elevation, and the total numbers of preferred habitats were poor predictors of levels of genetic divergence across barriers 11. However, the lack of an apparent influence of habitat on genetic differentiation may be due to the use of categorical variables that provide a course approximation of habitat preference. To further evaluate the relationship between environmental preferences and genetic divergence, we included niche breadth, a continuous variable estimated from climatic suitability values of ecological niche models, as a second ecological variable. Abundance, another potentially important variable that distinguishes between species with large and small populations, was not included because the lineages used in this study all exhibit relatively high abundance. Therefore, the two ecological variables retained for all analyses were foraging stratum and niche breadth. The historical variables we examined were stem age, crown age, and area of ancestral geographic origin. Stem and crown age are proxies for how old a lineage is. Stem age is the age of the last common ancestor of an ingroup and its sister clade and crown age is the timing of the basal divergence within an ingroup 74. Stem ages are expected to be more biased by extinction, but capture the length of time between a last common ancestor and the diversification of a crown clade, which provides insight into lineage persistence across deeper time than crown age. Alternatively, crown ages at the phylogeographic-scale are more likely to be subject to uncertainties associated with lineage sorting and reflect patterns retained within an ingroup. We observed a similar pattern between species diversity and age regardless of whether we used crown or stem age (Supplementary Table 12). Additionally, for some of the lineages in our data set the crown age and the cross-andes divergence event were the same node in the gene tree. Thus, we opted for stem age instead of crown age as the estimate of lineage age. Assuming extinction rates are comparable among lineages and that diversification within lineages is density-independent, stem ages can be interpreted as a measure of evolutionary persistence. WWW.NATURE.COM/NATURE 11

We also included area of ancestral geographic origin because it allowed us to compare patterns between lineages that originated in an area and those that dispersed into an area. In summary, we selected two ecological (foraging stratum and niche breadth) and two historical (stem age and ancestral area of origin) variables for our phylogenetic generalized leastsquares analyses because these variables are predicted to influence genetic differentiation and because they adequately reflect ecological and evolutionary differences among lineages (Supplementary Table 8). A complete description of each variable is listed below. Foraging stratum We binned lineages into two foraging stratum categories: understorey and canopy (sensu 11). Understorey birds are species that typically forage from the ground through the midstorey and canopy birds typically forage from the midstorey to the canopy (sensu 73). The foraging stratum of species has been shown to influence genetic differentiation across biogeographic barriers 11, because species that inhabit the canopy of rainforests are typically better dispersers than species that inhabit the understorey. Thus, the prediction is that poor-dispersing understorey birds will exhibit higher genetic differentiation or older divergence times across biogeographic barriers in the Neotropical lowlands than more dispersive canopy species 11. We assigned 16 lineages to the canopy category and 11 to the understorey category. Niche breadth We generated ecological niche models (ENMs) for each of the 27 lineages using temperature and precipitation variables (Supplementary Figs. 1-27). To build an ENM for each lineage, we used latitude-longitude coordinates obtained from voucher specimens that had genetic samples. For lineages with smaller sample sizes, we supplemented locality records by including observational records from the xeno-canto (http://www.xeno-canto.org/) online database of bird songs. Lineage and sample: Piaya cayana (n=128), Trogon rufus (n=53), Ramphastos (n=107), Pteroglossus (n=89), Pyrrhura (n=75), Brotogeris (n=84), Pyrilia (n=75), Cymbilaimus lineatus (n=53), Myrmotherula axillaris (n=85), Sclerurus mexicanus (n=38), Dendrocincla fuliginosa (n=82), Glyphorynchus spirurus (n=95), Xenops minutus (n=91), Automolus ochrolaemus (n=62), Colonia colonus (n=41), Attila spadiceus (n=52), Querula purpurata (n=38), Lepidothrix coronata (n=45), Tityra semifasciata (n=65), Schiffornis turdina (n=77), Microcerculus marginatus (n=62), Henicorhina leucosticta (n=40), Tangara cyanicollis (n=40), Tangara gyrola (n=53), Tersina viridis (n=57), Cyanerpes caeruleus (n=53), and Chlorophanes spiza (n=50). We used the bioclimatic variables from the World-Clim data set (v. 1.4) with a resolution of 30 arc-seconds 75. Using the correlation analyses in ENMtools 76, we found that nine of the variables were highly correlated with other variables (R > 0.9); therefore, we used 10 of the 19 temperature and precipitation variables (BIO1, BIO2, BIO3, BIO5, BIO7, BIO12, BIO14, BIO15, BIO18, and BIO19). We generated ten replicate models for each taxon using the maximum entropy algorithm in Maxent 3.3.3 77. For each model 75% of the points were used for model training and 25% were used as test points. The area under the WWW.NATURE.COM/NATURE 12

receiver operating characteristic (ROC) curve was close to one, with the average AUC ranging 0.714-0.915 across the 27 lineages (Supplementary Table 17). We used the average ENM from the ten replicate models for each lineage to estimate niche breadth 78 in ENMtools 76. Niche breadth was based on the Maxent predictions of climate suitability for each lineage. Species with wider niche breadths may face lower ecological resistance in dispersing across the landscape and may have lower genetic differentiation across their ranges (e.g. 79). We assessed whether range size, a variable often correlated with metrics of species diversity (e.g. 80), was correlated with niche breadth by calculating the area (km 2 ) occupied by each bird lineage using digital range maps 81 in ArcGIS10. In some instances there were overlapping ranges among species within lineages (e.g. Brotogeris), so we summed the area of overlapping ranges. We found that niche breadth was correlated with lineage range size (R 2 = 0.62), demonstrating that the relationship between genetic divergence and range size was likely captured using niche breadth. From our estimates of niche breadth, we identified a wide variability in values across lineages, ranging from 0.29-0.68 (Supplementary Table 17). Lineage age - We used the BEAST maximum credibility trees to identify the divergence time of each ingroup from its sister group. This divergence time is referred to as the stem age, and represents the length of time in which a lineage has been evolving independently from its last common ancestor. Species diversity at a given area is predicted to increase with the time a clade has been in the area 21. However, the relationship between stem age and the timing of cross-barrier divergence has not been evaluated. Thus, older and younger lineages may show differing patterns of diversification across the landscape because a lineage may have had more time for diversification. Ancestral geographic origin - We classified lineages as having their ancestral geographic origin in the lowlands west or east of the Andes based on the results from the BEAST phylogeographic modeling (see Gene trees, divergence times, and ancestral area reconstruction section) that provided a probability for geographic location of the root state. The influence of ancestral origins on patterns of genetic differentiation has not been fully explored. However, diversification rates have been shown to increase after lineages have colonized regions, such as the Andes 82 or across Wallace s line 83. Lineages that originated east of the Andes may show different patterns than lineages that originated west of the Andes. River - In the PGLS analyses examining divergence levels across Amazonian rivers, we included a River variable to correct for potential differences among the rivers (the Amazon, Negro, and Madeira Rivers) included in the model. The amount of gene flow across each river likely varies and divergence-time patterns may vary among riverine barriers. Thus, by treating the barrier that each divergence time was estimated across as a variable, we were able to account for among-river variability in temporal patterns. WWW.NATURE.COM/NATURE 13

Phylogenetic comparative analysis of species diversity and cross-barrier divergence levels We tested whether the observed variation in species diversity and cross- barrier divergence times could be attributed to species ecology and history. We employed a phylogenetic generalized least-squares (PGLS) analysis to evaluate the effect of two ecological and two historical variables on two metrics of genetic differentiation: 1) a speciesdiversity metric (presented in the main text), and 2) a genetic divergence metric of the level of differentiation across major dispersal barriers (not presented in main text): the Andes, the Isthmus of Panama, the upper Amazon River, the Negro River, and the Madeira River. The divergence metric allowed us to assess the effects of history and ecology on specific dispersal barriers. For the divergence metric we assessed three independent models that examined the effect of historical and ecological variables on genetic divergence levels across 1) the Andes (m 1 ), 2) the Isthmus of Panama (m 2 ), and 3) three Amazonian rivers (m 3 ). Sample sizes are provided in Supplementary Table 8. For the species-diversity metric, we ran a model that examined the effect of historical and ecological variables on the overall number of species in each lineage (m 4 ) using bgmyc species. All variables are discussed in detail in the Ecological and historical variables section of the Methods. In all models, we treated predictor variables as fixed effects and we accounted for the statistical non-independence of lineage data by including a phylogenetic correction. We performed PGLS analyses using the caper package 84 in the R programming language 85. The phylogenetic signal in the data is controlled by the parameters lambda, kappa, and delta. We optimized the value for lambda using maximum likelihood and we kept the default values for kappa (1.0) and delta (1.0). We performed both univariate and multivariate tests allowing us to assess relationships between a single variable and to identify the relative significance of each variable. We built two divergence data sets for the Isthmus of Panama and Amazonian rivers models, one that included only divergence times between sorted populations on each side of the barrier, and a second data set that included unsorted populations across barriers that had divergence times estimated to be zero. The Andes data set did not contain divergence times estimated to be zero. For the multivariate models, we included two ecological variables (foraging stratum and niche breadth) and two historical variables (ancestral origin and lineage age) that are predicted to influence genetic differentiation. We also included a term rivers to account for variation across rivers in the response variable in the model m 3. We performed preliminary analyses that examined the fit of the data to a model with and without square root and log conversions to the data. In cases where the conversion reduced the residual variance of a model, we converted variables in the final models. For models m 1 -m 3, we log transformed the cross-barrier divergence times and lineage age. For model m 4, we square root converted species diversity. For the stem age estimates in m 4 and the cross barrier divergence times in m 1 -m 3 we ran additional models using the time estimated from the low and high 95% HPD to assess how robust patterns were to uncertainty in molecular dating. Raw data used in these analyses are available in WWW.NATURE.COM/NATURE 14

Supplementary Table 17. Differences between sample sizes between the PGLS analyses and habc analyses are attributed inadequate sample sizes for population genetic summary statistics or our inability to identify node age in a gene tree. We built phylogenies in BEAST using the settings described in the divergence time section of the methods for models m 1 -m 4. For each model, we built a phylogeny with the appropriate number of tips to match the number of observations of species diversity and cross-barrier divergence levels. For preliminary analyses, we used 100 trees from the posterior distribution as input in the PGLS analyses. We found that phylogenetic uncertainty in the posterior distribution of trees had minimal influence on our model parameter estimates (results not shown); therefore we report model results from runs using a single tree. For multivariate models, we estimated Akaike information criterion (AICc) scores with a correction for sample size for models containing a complete list of variables and the AICc score for each model without each of the predictor variables. We assessed the relative importance of each variable by calculating Δ AICc = AICc a - AICc f, where Δ AICc is the change in AICc between the model without a particular predictor variable (AICc a ) and the full model (AICc f ). Models with a Δ AICc > 2 are deemed to be significantly different than the full model. For some of our multivariate models, we had a low sample size, which may decrease their power to accurately detect significant effects 86. To assess potential biases caused by low sample sizes in the multivariate models, we compared the results between the univariate and multivariate models (Table 1; Supplementary Tables 9-12). Overall, we obtained similar parameter estimates for most variables using both types of models (Table 1; Supplementary Tables 9-12), indicating that the relationship between the response and predictor variables was detectable with low sample sizes. In the species diversity model (m 4 ), however, Ancestral Origin was significant (α = 5) in the univariate model (Supplementary Table 12), but not in the multivariate model (Table 1). Influences of sample size and species-diversity on PGLS analyses To evaluate whether the differential sample sizes between understorey and canopy lineages biased our results, we conducted additional analyses on species diversity estimates from the pruned data sets in which 10-60% of the individuals were removed randomly (Extended Data Fig. 4; Supplementary Table 1). To examine how the pruning treatments influenced the relative importance of each predictor variable, we performed PGLS analyses for the model examining species diversity on each treatment. We found that lineage age and foraging stratum remained significant predictor variables with up to 30% and 50%, respectively, of the individuals removed randomly (Supplementary Table 16). We also ran the model with the low and high value of the 95% HPD to examine whether the uncertainty surrounding stem age influenced the results. We recovered the same pattern, with a few exceptions, that stem age and foraging stratum were significant variables when we used the low and high values of the 95% HPD (Supplementary Table 16). Based on our collective results, the diversity-lineage age relationship is robust to species diversity estimates with up WWW.NATURE.COM/NATURE 15

to 30% of the samples being randomly removed and the uncertainty surrounding stem age. Foraging stratum remained significant with up to 50% of the individuals in each data set being randomly pruned. Influence of undifferentiated populations across barriers Divergence times were extracted from lineages that had differentiated across barriers; however, there were taxa that were not genetically diverged across these same barriers. We explored how these undifferentiated taxa influenced our model interpretations by running additional analyses that included these taxa by setting their divergence times to zero. There were undifferentiated populations across the Isthmus of Panama and Amazonian rivers, but not across the Andes. For these models, we changed estimates of divergence time of 0 to 0.1 in order to log-transform the values. In the Isthmus of Panama model (m 2 ), we obtained overall similar results between the models with and without zero divergence times (Supplementary Table 14). The only significant difference was that when the 95% HPD high for cross-isthmus divergences was used ancestral origin changed from 11.4624 (Supplementary Table 14a, Δ AICc C) to 0.2148 (Supplementary Table 14b, Δ AICc C). In the Amazonian rivers model (m 3 ), ancestral origin also became not significant when zero divergence times were included (Supplementary Table 15), but stem age became significant for the mean (Supplementary Table 15b, Δ AICc A=2.9226) and 95% HPD high value (Supplementary Table 15b, Δ AICc C=3.8067). The lack of significance of Ancestral Origin in the Amazonian river model (m 3 ) with zero divergences is likely attributable to recent dispersal events across rivers in taxa that originated in Amazonia. Effects of ecology and evolutionary history on diversification Overall, we obtained similar parameter estimates for the majority of variables, using either the univariate or multivariate model (Table 1; Supplementary Tables 9-11 A & B; Supplementary Table 12) showing there were significant effects of individual histories and ecologies on the timing of diversification in most models. The only model that had no significant effects was the cross-andes divergence model (m 1 ), which measured the effect of the least permeable dispersal barrier, the Andes Mountains (Supplementary Table 9). This result suggests that our estimate of dispersal ability and the scale of the historical variables we included had no detectable influence on the timing of cross-andes divergence. Lineage age did show a positive, albeit non-significant, relationship with cross-andes divergence, which would suggest that the dispersal across the Andes was a function of how long a lineage has been in the landscape. Given the results of our cross-andes divergence model comparisons, however, the non-significance of any of the variables suggests that diversification across the Andes is most consistent with stochastic processes. We found that lineage age (Δ AICc A-C =6.4665-7.1862; Supplementary Table 14) had a significant positive effect in the model assessing genetic divergence across the Isthmus of Panama, and that geographic region of origin (Δ AICc A-C = 11.4624-11.9199; Supplementary Table 14; Supplementary Fig. 28) was also significant. Ecologically, foraging stratum significantly influenced the timing of WWW.NATURE.COM/NATURE 16

divergence across Amazonian rivers (foraging stratum, Δ AICc A-C =8.2501-1460; Supplementary Table 15), as did the region of ancestral origin (Δ AICc A-C = 8.0215-9.6711; Supplementary Table 15; Supplementary Fig. 28). Niche breadth was not a significant effect in any of the models assessing cross-barrier divergences (Supplementary Tables13-15). In sum these results suggest that divergence across barriers is determined by stochasticity, the amount of time a taxon is in the landscape, its geographic origin, and/or its dispersal ability. As discussed in the main text, species diversity, as defined by coalescent analyses within the 27 lineages, was predicted by lineage age (Supplementary Table 16). This pattern was robust to the uncertainty surrounding stem age and the random pruning of tips from the data sets (Supplementary Table 16). Ecologically, we found that foraging stratum (Supplementary Table 16) had a significant effect on species diversity, with lineages restricted to the forest understorey containing significantly higher species diversity than canopy lineages (Table 1, Foraging Stratum Understorey, coefficient= 0.5188, P = 178). The higher diversity in understorey birds than canopy birds appears not to be attributable to differences in range sizes because we tested for a significant difference in range size between understorey and canopy lineages and the test was not significant (two-sided Student s t-test: t = 1.6250; P = 0.1191). Niche breadth was not identified as a significant effect in the species diversity model (Supplementary Table 16). WWW.NATURE.COM/NATURE 17

Supplementary Table 1 List of lineages with number of described taxa (species and subspecies), number of inferred species with complete and pruned data sets, and total number of individuals in each data set. Number of Number of described taxa 87 species from bgmyc Sample size Lineage Foraging Stratum (species & subspecies) Complete sampling 10% pruned 20% pruned 30% pruned 40% pruned 50% pruned 60% pruned n Attila spadiceus Canopy 12 2 2 2 2 2 2 3 108 Brotogeris Canopy 17 6 7 6 6 6 5 5 54 Chlorophanes spiza Canopy 7 2 2 3 2 2 2 2 72 Colonia colonus Canopy 5 3 3 3 3 3 2 2 18 Cyanerpes caeruleus Canopy 5 1 1 1 1 1 1 2 39 Cymbilaimus lineatus Canopy 3 2 2 2 2 2 2 2 48 Piaya cayana Canopy 14 4 4 3 4 3 4 3 49 Pteroglossus Canopy 23 7 4 3 5 3 4 3 52 Pyrilia Canopy 9 6 7 7 6 5 3 6 29 Pyrrhura Canopy 48 18 15 4 4 2 2 3 81 Querula purpurata Canopy 1 2 2 2 2 2 2 2 49 Ramphastos Canopy 17 7 8 6 6 6 5 4 35 Tangara cyanicollis Canopy 7 2 2 2 2 2 2 2 47 Tangara gyrola Canopy 9 3 3 3 3 3 3 2 90 Tersina viridis Canopy 3 2 2 2 2 2 2 2 27 Tityra semifasciata Canopy 9 3 3 3 3 3 3 2 52 Average 11.81 4.38 4.19 3.25 3.31 2.94 2.75 2.81 53.13 Std. Dev. 11.34 4.13 3.56 1.69 1.66 1.48 1.18 1.22 23.99 WWW.NATURE.COM/NATURE 18

(continued) Lineage Foraging Stratum Number of described taxa (species & subspecies) Number of species from bgmyc Complete sampling 10% pruned 20% pruned 30% pruned 40% pruned 50% pruned 60% pruned Sample size n Automolus ochrolaemus Understorey 8 5 5 4 5 4 3 3 166 Dendrocincla fuliginosa Understorey 14 7 7 6 5 5 3 3 239 Glyphorynchus spirurus Understorey 13 11 11 11 11 11 11 11 337 Henicorhina leucosticta Understorey 12 4 3 4 4 5 4 3 44 Lepidothrix coronata Understorey 8 6 4 4 4 3 4 4 90 Microcerculus marginatus Understorey 6 7 7 7 4 7 4 4 100 Myrmotherula axillaris Understorey 6 3 3 3 3 3 2 2 230 Schiffornis turdina Understorey 14 7 8 8 8 7 8 6 209 Sclerurus mexicanus Understorey 7 6 5 6 7 4 9 3 63 Trogon rufus Understorey 6 8 7 9 3 4 4 2 37 Xenops minutus Understorey 10 8 8 9 8 8 8 8 218 Average 9.45 6.55 6.18 6.45 5.64 5.55 5.45 4.45 157.55 Std. Dev. 3.27 2.16 2.44 2.58 2.54 2.46 2.98 2.81 97.31 WWW.NATURE.COM/NATURE 19

Supplementary Table 2 Sensitivity analyses showing the impact of sample size on the number of species estimated in bgmyc. In each treatment the number of estimated bgmyc species using all samples was compared to the number of species estimated from data sets with a % of randomly pruned individuals. The number of observations was 27 for all tests. Shown are the P values for one and two-tailed tests. Treatment df t value P (one-tail) P (two-tail) 10% pruned 51.1 0.4674 0.3211 0.6422 20% pruned 46.6 1.0179 0.157 0.314 30% pruned 43.7 1.4045 836 0.1672 40% pruned 43.4 1.7173 465 931 50% pruned 45.1 1.8575 349 698 60% pruned 41.5 2.3803 110 220 Supplementary Table 3 Lineages with a phylogeographic break across the Andes used to test simultaneous vicariance in habc analysis, with samples sizes in each area and summary statistics scaled by per base-pair. Population-pair Sample Size (west/east) π θ W πνετ δ Attila spadiceus 45/40 0398 074 0496 3052 Automolus ochrolaemus A 20/56 198 1539 4071 4349 Automolus ochrolaemus B 8/24 1076 0944 2262 2925 Brotogeris 6/18 2082 1597 4414 3558 Chlorophanes spiza 3/45 0245 0928 0273 3141 Colonia colonus 5/3 2552 2415 3349 2735 Cymbilaimus lineatus 9/7 0703 0713 0638 2089 Dendrocincla fuliginosa 17/38 1394 1165 2332 3482 Glyphorynchus spirurus 28/9 0628 0951 0405 3029 Henicorhina leucosticta 4/9 2183 179 2743 3064 Lepidothrix coronata 13/7 2197 1528 3668 3303 Microcerculus marginatus 3/18 1114 1339 2386 3135 Myrmotherula axillaris 24/26 0911 0899 0917 3112 Piaya cayana 17/20 1505 1033 2525 3139 Pteroglossus 2/3 4183 3714 355 2149 Pyrilia A 2/3 3943 3294 6038 2018 Pyrilia B 3/6 4058 3397 6874 3523 Pyrrhura A 3/7 1014 0796 0827 1790 Pyrrhura B 2/13 0622 0874 1218 2260 Querula purpurata 9/39 0541 0631 0703 2586 Schiffornis turdina A 11/17 2535 1683 4547 3799 WWW.NATURE.COM/NATURE 20

Schiffornis turdina B 30/8 1052 0907 2461 2972 Sclerurus mexicanus 7/10 2487 1762 4265 3370 Tangara cyanicollis 12/13 102 0691 1705 2357 Tangara gyrola 13/21 0596 0973 1424 2705 Tersina viridis 2/20 2138 1395 3805 3611 Tityra semifasciata 3/18 036 0553 0861 2008 Trogon rufus 13/7 3154 2013 6064 3799 Xenops minutus 13/14 3593 2216 6271 4330 π = average pairwise genetic distance among DNA sequences sampled θ W = the number of segregating sites normalized for sample size πνετ = net average pairwise differences between populations δ =the denominator of equation 38 in Tajima 72, where S, the number of segregating sites is scaled per base-pair rather than per locus Phylogenetic position of A and B taxa are shown on corresponding gene trees Supplementary Table 4 Lineages with a phylogeographic break across the Isthmus of Panama used to test simultaneous vicariance, with samples sizes in each area and summary statistics scaled by per base-pair. Sample Size Population-pair (Central America/ Chocó) π θ W πνετ δ Brotogeris 3/6* 213 165 401 2430 Henicorhina leucosticta 8/7 0.1269 0.2284 683 0.12595 Glyphorynchus spirurus 20/5 036 030 077 1919 Lepidothrix coronata 5/8 040 040 032 1431 Microcerculus marginatus 3/11 185 174 475 3110 Myrmotherula axillaris 10/8 024 032 018 1459 Pyrrhura 2/2 142 118 206 0787 Querula purpurata 4/4 008 006 015 0414 Schiffornis turdina 6/24 021 033 028 1703 Sclerurus mexicanus 6/13 459 321 944 4742 Tangara gyrola 13/19 037 055 040 2219 Tityra semifasciata 3/27 040 053 140 2149 Trogon rufus 2/13 158 190 534 3346 Xenops minutus 27/14 164 107 231 3277 * Samples are from the Tumbes region π = average pairwise genetic distance among DNA sequences sampled θ W = the number of segregating sites normalized for sample size πνετ = net average pairwise differences between populations δ = the denominator of equation 38 in Tajima 72, where S, the number of segregating sites is scaled per base-pair rather than per locus WWW.NATURE.COM/NATURE 21

Supplementary Table 5 Lineages with a phylogeographic break across the Amazon River used to test simultaneous vicariance, with samples sizes in each area and summary statistics scaled by per base-pair. Taxon-pair Sample Size (Napo/ ) π θ W πνετ δ Brotogeris 4/4 0523 0395 0792 1095 Chlorophanes spiza 12/7 0224 0559 0013 1960 Cyanerpes caeruleus 4/5 0503 0574 0156 1428 Cymbilaimus lineatus 6/13 1111 1254 0236 2943 Dendrocicnla fuliginosa 6/7 2861 1814 5143 3085 Glyphorynchus spirurus 6/35 1847 1941 4943 4449 Lepidothrix coronata 19/37 2153 1881 2203 4602 Querula purpurata 4/11 0235 0271 0400 1256 Schiffornis turdina 13/16 1181 1061 1647 3035 Sclerurus mexicanus 5/8 0886 0631 1426 1809 Tangara gyrola 4/16 0479 0696 0041 2222 Tersina viridis 2/7 0405 0507 0109 1341 Trogon rufus 4/5 1639 1607 1273 2400 Xenops minutus 14/34 0885 1133 0856 3472 π = average pairwise genetic distance among DNA sequences sampled θ W = the number of segregating sites normalized for sample size πνετ = net average pairwise differences between populations δ = the denominator of equation 38 in Tajima 72, where S, the number of segregating sites is scaled per base-pair rather than per locus Phylogenetic position of A and B taxa are shown on corresponding gene trees Supplementary Table 6 Lineages with a phylogeographic break across the Negro River used to test simultaneous vicariance, with samples sizes in each area and summary statistics scaled by per base-pair. Sample Size Taxon-pair (Napo/Guiana) π θ W πνετ δ Attila spadiceus 13/2 0104 0210 0007 1104 Automolus ochrolaemus 5/7 0308 0301 0113 1204 Brotogeris 4/18 0820 0868 1454 2555 Chlorophanes spiza 10/18 0174 0498 0005 2075 Colonia colonus 2/2 5339 5488 0000 1763 Cyanerpes caeruleus 4/18 0660 0943 0201 2663 Cymbilaimus lineatus 3/4 1459 1084 2435 1642 Dendrocincla fuliginosa 7/2 0073 0122 0022 0655 WWW.NATURE.COM/NATURE 22

Glyphorynchus spirurus 34/106 2561 2794 4490 6319 Henicorhina leucosticta 9/15 1888 1514 2917 3464 Lepidothrix coronata 22/5 2491 2158 2183 4271 Pyrrhura 2/3 0078 0094 0049 0333 Querula purpurata 11/11 0387 0404 0233 1739 Schiffornis turdina 6/65 1574 3083 8922 6128 Sclerurus mexicanus 4/9 1610 1218 3237 2522 Tersina viridis 2/4 0381 0431 0081 0893 Trogon rufus 4/7 1462 1347 2049 2454 π = average pairwise genetic distance among DNA sequences sampled θ W = the number of segregating sites normalized for sample size πνετ = net average pairwise differences between populations δ = the denominator of equation 38 in Tajima 72, where S, the number of segregating sites is scaled per base-pair rather than per locus Supplementary Table 7 Lineages with a phylogeographic break across the Madeira River used to test simultaneous vicariance, with samples sizes in each area and summary statistics scaled by per base-pair. Taxon-pair Sample Size (/ Rondônia) π θ W π ΝΕΤ δ Attila spadiceus 17/8 0109 0310 0023 1577 Automolus ochrolaemus 45/23 0998 1135 1588 3672 Chlorophanes spiza 8/5 0256 0469 0024 1558 Cyanerpes caeruleus 6/4 1793 2973 0729 3496 Dendrocincla fuliginosa 23/32 2659 1803 0455 4492 Glyphorynchus spirurus 8/11 2913 2124 5489 3226 Microcerculus marginatus 21/10 1067 0818 1858 2703 Piaya cayana 8/11 0654 0966 0624 2580 Pyrilia 2/3 0948 1011 0849 1101 Pyrrhura 2/2 2775 2511 2840 1164 Schiffornis turdina 16/34 1615 1143 3291 3512 Tangara gyrola 16/4 0716 0843 0827 2447 Tersina viridis 6/7 0323 0413 0021 1462 Tityra semifasciata 11/4 0129 0245 0035 1192 π = average pairwise genetic distance among DNA sequences sampled θ W = the number of segregating sites normalized for sample size πνετ = net average pairwise differences between populations δ = the denominator of equation 38 in Tajima 72, where S, the number of segregating sites is scaled per base-pair rather than per locus WWW.NATURE.COM/NATURE 23

Supplementary Table 8 Phylogenetic generalized least-squares analyses (PGLS) parameters used to examine divergence levels and number of species in Neotropical forest birds. Model Response variable Predictor variables in full model divergence levels m 1 Cross-Andes divergence times (n= 33) ancestral origin, foraging stratum, niche breadth, lineage age m 2 Cross-Isthmus of Panama divergence ancestral origin, foraging stratum, niche breadth, lineage age times (n = 18; n = 21) m 3 Cross-Amazonian Rivers divergence ancestral origin, foraging stratum, niche breadth, lineage age, river, times (n = 31; n = 48) number of species m 4 Species diversity (n = 27) ancestral origin, foraging stratum, niche breadth, lineage age Shown are the response and predictor variables for the full phylogenetic generalized least-squares analyses (m 1 m 4 ) used to examine divergence levels and number of species for the 27 bird lineages. Models m 1 m 3 assessed the relationship between predictor variables and divergence times extracted from the timecalibrated gene trees. We accounted for the statistical non-independence of data by including a phylogenetic correction in each model. Divergence times across each barrier were modeled independently: m 1 cross-andes divergence levels, m 2 cross-isthmus of Panama divergence levels, and m 3 cross-amazonian river divergence levels. n 1 = sample size excluding 0 divergence times; n 2 sample size including 0 divergence times. Model m 4 examined the relationship between predictor variables and species diversity. The number of species in each of the 27 lineages was inferred by a coalescent-based Bayesian species delimitation method 59 as the overall total number of species or described taxa within each lineage (m 4 ). A complete description of each predictor variable is available in the Ecological and historical variables section of the Methods. WWW.NATURE.COM/NATURE 24

Supplementary Table 9 Phylogenetic generalized least-squares analyses examining the effects of historical and ecological variables on divergence times across the Andes. a) Results from univariate models Effect Estimate Standard Error t value P AICc Lineage Age 0.3917 0.2325 1.6848 0.1021 74.5852 Foraging Stratum 956 0.2728 0.3504 0.7284 77.3460 Ancestral Origin 0.2776 0.2595 1.0699 0.2929 76.3235 Niche Breadth 0.1022 1.3470 759 0.9400 77.4704 Output of each univariate model: Lineage Age - Adjusted R 2 : 543; f (df): 2.839 (1, 31) ; P = 0.1021; n= 33. Foraging Stratum - Adjusted R 2 : -282; f (df): 0.1228 (1, 31) ; P = 0.7284; n= 33. Ancestral Origin - Adjusted R 2 : 045; f (df): 1.145 (1, 31) ; P = 0.2929; n= 33. Niche Breadth - Adjusted R 2 : -321; f (df): 056 (1, 31) ; P = 0.94; n= 33. b) Result from multivariate model Effect Estimate Standard Error t value P (Intercept) -0.6887 0.8507-0.8095 0.4250 Lineage Age 0.4727 0.2531 1.8679 723 Foraging Stratum 326 0.2859 0.1141 0.9100 Ancestral Origin 0.4030 0.2766 1.4574 0.1561 Niche Breadth 0.1234 1.5321 806 0.9364 Output is from full model and the Δ AICc refers to the change in AICc when each predictor variable was removed from the full model. Lineage age is in units of millions of years. Full model AICc = 79.7969; Adjusted R 2 : 327; f (df): 1.27 (4, 28) ; P = 0.3052; n= 33. Lambda ML - ; lower bound - 0, P = 1; upper bound 1.00, P < 001. Model output for Foraging Stratum and Ancestral Origin correspond to the comparison of the reference level (Foraging Stratum Understorey; Ancestral Origin East of the Andes) for each categorical variable WWW.NATURE.COM/NATURE 25

Supplementary Table 10 Phylogenetic generalized least-squares analyses examining the effect of historical and ecological variables on genetic divergence levels across the Isthmus of Panama. a) Results from univariate models without zero divergence times Effect Estimate Standard Error t value P AICc Lineage Age 1.0390 0.4045 2.5683 206 49.6329 Foraging Stratum 0.3472 0.5097 0.6811 0.5056 55.1222 Ancestral Origin 1.1081 0.3665 3.0233 081 47.5878 Niche Breadth 1.1731 2.3519 0.4988 0.6247 55.4418 Output of each univariate model: Lineage Age - Adjusted R 2 : 0.2477; f (df): 6.596 (2, 16) ; P = 008; n= 18. Foraging Stratum - Adjusted R 2 : -326; f (df): 0.4639 (2, 16) ; P = 0.637; n= 18. Ancestral Origin - Adjusted R 2 : 0.3238; f (df): 9.14 (2, 16) ; P = 023; n= 18. Niche Breadth - Adjusted R 2 : -462; f (df): 0.2488 (2, 16) ; P = 0.7827; n= 18. b) Result from multivariate model without zero divergence times Effect Estimate Standard Error t value P (Intercept) -3.5796 0.8959-3.9954 015 Lineage Age 1.1162 0.2893 3.8587 020 Foraging Stratum 0.1021 0.3249 0.3143 0.7583 Ancestral Origin 1.3669 0.2839 4.6514 005 Niche Breadth 1.7687 1.5694 1.1270 0.2801 c) Result from multivariate model with zero divergence times included Effect Estimate Standard Error t value P (Intercept) -4.6611 1.3823-3.3720 039 Lineage Age 1.3039 0.4023 3.2408 051 Foraging Stratum 0.5756 0.4647 1.2385 0.2334 Ancestral Origin 1.0317 0.4016 2.5694 206 Niche Breadth 2.8832 2.2276 1.2943 0.2139 Output is from full model and the Δ AICc refers to the change in AICc when each predictor variable was removed from the full model. Lineage age is in units of millions of years. a) Full model (without zero divergences) AICc =42.1344; Adjusted R 2 : 0.6563; f (df): 9.019 (5, 13) ; P = 007; n= 18. Lambda ML - ; lower bound - 0, P = 1; upper bound 1.00, P = 038. b) Full model (with zero divergences) AICc = 64.0856; Adjusted R 2 : 0.4344; f (df): 4.84 (5, 16) ; P = 129; n= 21. Lambda ML - 0.330; lower bound - 0, P = 0.4672; upper bound 1.00, P = 0.1007. Model output for Foraging Stratum and Ancestral Origin correspond to the comparison of the reference level (Foraging Stratum Understorey; Ancestral Origin East of the Andes) for each categorical variable. WWW.NATURE.COM/NATURE 26

Supplementary Table 11 Phylogenetic generalized least-squares analyses examining the effect of historical and ecological variables on divergence times across Amazonian rivers. a) Results from univariate models without zero divergence times. Effect Estimate Standard Error t value P AICc Lineage Age 0.2460 0.3070 0.8013 0.4295 68.7123 Foraging Stratum 0.8994 0.2305 3.902 005 58.6586 Ancestral Origin -0.5985 0.2569-2.3296 27 64.0406 River - Negro 0.2994 0.2395 1.2502 0.2216 67.8280 River - Amazon -0.2145 0.2660-0.8062 0.4269 Niche Breadth -1.2053 1.5704-0.7675 0.449 68.7740 Output of each univariate model: Lineage Age - Adjusted R 2 : -121; f (df): 0.6421 (1, 29) ; P = 0.4295; n= 33. Foraging Stratum - Adjusted R 2 : 0.3217; f (df): 15.23 (1, 29) ; P = 005; n= 33. Ancestral Origin - Adjusted R 2 : 0.1286; f (df): 5.427 (1, 29) ; P = 27; n= 33. River - Adjusted R 2 : 0.1; f (df): 2.668 (2, 28) ; P = 870; n= 33. Niche Breadth - Adjusted R 2 : -139; f (df): 0.5891 (1, 29) ; P = 0.449; n= 33. b) Result from multivariate model without zero divergence times Effect Estimate Standard Error t value P (Intercept) 0.4330 0.7227 0.5992 0.5547 Lineage Age 0.1347 0.2103 0.6404 0.5280 Foraging Stratum 0.7926 0.2028 3.9087 007 Ancestral Origin -0.6898 0.2046-3.3714 025 River - Negro 0.1027 0.2293 0.4479 0.6582 River - Amazon -0.4627 0.2616-1.7687 897 Niche Breadth -1.4871 1.1693-1.2718 0.2156 c) Result from multivariate model with zero divergence times Effect Estimate Standard Error t value P (Intercept) -0.7686 1.1297-0.6804 0.5001 Lineage Age 0.6734 0.2782 2.4211 200 Foraging Stratum 1.4317 0.2861 5.0048 <001 Ancestral Origin -0.2812 0.3115-0.9029 0.3719 River - Negro 0.2200 0.3246 0.6777 0.5018 River - Amazon -0.5625 0.3342-1.6833 999 Niche -3.3690 1.7869-1.8854 665 Output is from full model and the Δ AICc refers to the change in AICc when each predictor variable was removed from the full model. Lineage age is in units of millions of years. b) Full model (without zero divergences) AICc = 57.0086; Adjusted R 2 : 0.5122; f (df): 6.251 (6, 24) ; P = 005; n= 31. Lambda ML - ; lower bound - 0, P = 1; upper bound 1.00, P < 001. c) Full model (with zero divergences) AICc = 132.8105; Adjusted R 2 : 0.5536; f (df): 10.71 (6, 41) ; P < 001; n= 48. Lambda ML - ; lower bound - 0, P = 1; upper bound 1.00, P < 001. Model output for Foraging Stratum, Ancestral WWW.NATURE.COM/NATURE 27

Origin, and River correspond to the comparison of the reference level (Foraging Stratum Understorey; Ancestral Origin East of the Andes; River Madeira) for each categorical variable. Supplementary Table 12 Univariate phylogenetic generalized least-squares analyses examining the effects of historical and ecological variables on species diversity. Effect Estimate Standard Error t value P AICc Lineage Crown Age 0.2477 599 4.1322 004 48.4397 Lineage Stem Age 0.1426 292 4.8861 <001 44.3954 Foraging Stratum 0.6357 0.2701 2.3539 267 50.8017 Ancestral Origin -0.5031 0.2059-2.4435 219 50.549 Niche Breadth -793 1.2631-628 0.9504 56.1602 Output of each univariate model: Lineage Crown Age - Adjusted R 2 0.3821; F s (df) : 17.08 (1, 25) ; P = 004; n= 27. Lineage Stem Age - Adjusted R 2 : 0.468; f (df): 23.87 (1, 25) ; P = 5.005e-05; n= 27. Foraging Stratum - Adjusted R 2 : 0.1487; f (df): 5.541 (1, 25); P = 267; n= 27. Ancestral Origin - Adjusted R 2 : 0.1605; f (df): 5.971 (1, 25) ; P = 219; n= 27. Niche Breadth - Adjusted R 2 : -398; f (df): 040 (1, 25) ; P = 0.9504; n= 27. Lineage age is in units of millions of years. Supplementary Table 13 Relative importance of each predictor variable determined with Δ AICc values from the phylogenetic generalized least-squares analyses assessing divergences across the Andes. Ancestral Origin Foraging Stratum Niche Breadth Lineage Age Δ AICc A -0.3809-2.7783-2.7860 1.0816 Δ AICc B -1.1886-2.2094-2.7915-0.3745 Δ AICc C 1.8880-2.7621-2.2287-987 Shown are models using cross Andes divergences as the response variable. Variable importance was measured by Δ AICc, which is the change in AICc when the predictor variable is removed from the full model. Δ AIC values > 2 are considered significant. Reported are Δ AICc scores in which mean (Δ AICc A), low (Δ AICc B) or high (Δ AICc C) 95% HPD cross Andes divergence was used. AICc scores for full models using mean, the low 95% HPD, and the high 95% HPD, respectively: 79.7969, 92.0685, 76.9737. Lineage Age is stem age. WWW.NATURE.COM/NATURE 28

Supplementary Table 14 Relative importance of each predictor variable determined with Δ AICc values from the phylogenetic generalized least-squares analyses assessing divergences across the Isthmus of Panama. a) Model comparisons without zero divergence times Ancestral Origin Foraging Stratum Niche Breadth Lineage Age Δ AICc A 13.7156-3.7868-2.2451 8.5055 Δ AICc B 13.5445-3.7363-2.6658 8.2753 Δ AICc C 13.3236-3.8180-2.1881 8.1927 b) Model comparisons with zero divergence times included Ancestral Origin Foraging Stratum Niche Breadth Stem Age Δ AICc A 3.7433-2.0258-1.4744 6.4914 Δ AICc B 8.8970-1.7535-1.2001 7.4605 Δ AICc C 1.2274-2.2250-1.8434 5.4432 Shown are models using cross Andes divergences as the response variable. Variable importance was measured by Δ AICc, which is the change in AICc when the predictor variable is removed from the full model. Δ AIC values > 2 are considered significant. Reported are Δ AICc scores in which mean (Δ AICc A), low (Δ AICc B) or high (Δ AICc C) 95% HPD cross Andes divergence was used. AICc scores for full models using mean, the low 95% HPD, and the high 95% HPD, respectively: a) Full model without zero divergence times: 42.1344, 48.0538, 40.2236; b) Full model with zero divergence times: 64.0856, 59.8406, 68.9057. Lineage Age is stem age. Supplementary Table 15 Relative importance of each predictor variable determined with Δ AICc values from the phylogenetic generalized least-squares analyses assessing divergences across Amazonian rivers. a) Model comparisons without zero divergence times Ancestral Origin Foraging Stratum Niche Breadth Stem Age River Δ AICc A 8.6493 9.4058-1.3476-2.8443 0.5731 Δ AICc B 9.6711 1460-1.2158-3.0597-0.5047 Δ AICc C 8.0215 8.2501-1.3890-2.7984 1.5659 b) Model comparisons with zero divergence times included Ancestral Origin Foraging Stratum Niche Breadth Stem Age River Δ AICc A -1.8062 9.3190 1.2398 2.9226 1.7316 Δ AICc B 0.5782 13.4094 1.5677 1.1055 2.6313 Δ AICc C -2.4823 7.7313 1.0098 3.8067 1.4867 Shown are models using cross Andes divergences as the response variable. Variable importance was measured by Δ AICc, which is the change in AICc when the predictor variable is removed from the full model. Δ AIC values > 2 are considered significant. Reported are Δ AICc scores in which mean (Δ AICc A), low (Δ AICc B) or high (Δ AICc C) 95% HPD cross Andes divergence was used. AICc scores for full models using mean, the low 95% HPD, and the high 95% HPD, WWW.NATURE.COM/NATURE 29

respectively: a) Full model without zero divergence times: 57.0086, 67.5593, 51.5928; b) Full model with zero divergence times: 133.5591, 117.0998, 145.3611. Lineage Age is stem age. Supplementary Table 16 Relative importance of each predictor variable determined with Δ AIC values from the phylogenetic generalized least-squares analyses assessing diversity. Data set Δ AIC Ancestral Origin Foraging Stratum Niche Breadth Stem Age Full Δ AICc A -1.9546 4.0122-1.9595 6.9586 Δ AICc B -1.6645 2.8719-1.6710 12.1708 Δ AICc C -2.2471 4.1784-2.6307 3.0659 10% pruned Δ AICc A -2.3370 3.8452-0.7117 6.0261 Δ AICc B -2.1630 2.6436-0.2495 9.9617 Δ AICc C -2.5318 4.3561-1.3133 2.5947 20% pruned Δ AICc A -2.9949 14.7324-0.8372 5.9602 Δ AICc B -2.9914 13.9077-0.5571 8.8632 Δ AICc C -2.9368 16.1837-0.6135 5.2660 30% pruned Δ AICc A -2.2903 7.8654 0.5107 3.7659 Δ AICc B -2.2162 7.0030 0.8195 5.7766 Δ AICc C -2.4034 7.1533 0.9896 2.1080 40% pruned Δ AICc A -2.8091 11.1890-0.3828-1.0755 Δ AICc B -2.8206 10.3410-0.3256-0.1421 Δ AICc C -2.8683 11.9767-0.2610-1.0967 50% pruned Δ AICc A -3.0389 9.9027-0.1020 0.3388 Δ AICc B -3.0389 8.5128 265 1.6970 Δ AICc C -3.0290 10.9465 494 0.7021 60% pruned Δ AICc A -2.0499 1.9926-2.1203-0.8841 Δ AICc B -2.0244 1.3488-2.0945-0.1799 Δ AICc C -2.2160 2.7264-2.0592-0.7147 Shown are models using either bgmyc species from all the samples (full) and the randomly pruned bgmyc species data sets (10%-60%). Variable importance was measured by Δ AIC, which is the change in AIC when the predictor variable is removed from the full model. Δ AIC values > 2 are considered significant. Reported are Δ AIC scores in which mean (Δ AICc A), low (Δ AICc B) or high (Δ AICc C) 95% HPD stem age was used as the predictor variable. AIC scores for full models using mean, the low 95% HPD, and the high 95% HPD, respectively: Full: 43.7365, 38.5242, 47.6291; 10% Pruned: 42.7542, 38.8186, 46.1856; 20% pruned: 33.5380, 30.6350, 34.2322; 30% pruned: 31.9908, 29.9802, 33.6487 ; 40% pruned: 36.1306, 35.1972, 36.1517; 50% pruned: 38.8414, 37.4833, 38.4782; 60% pruned: 38.3087, 37.6046, 38.1394. WWW.NATURE.COM/NATURE 30

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imeri_4ml688amazonasven napo_lsumzb2843loretope guiana_lsumzb55279suriname guiana_usnm14105kusadguy rondonia_fmnh389961rondoniabra inambari_lsumzb9413pandobo inambari_ufac437acrebra inambari_ufac1978acrebra rondonia_lsumzb12575santacrbo napo_lsumzb42724loretope huallaga_lsumzb5419sanmartpe guiana_usnm19091kopinangvillageguy inambari_mvz169640madredediospe guiana_65775sipaliwinisur guiana_lsumzb48372guy inambari_lsumzb10639ucayalipe guiana_5ml687amazonasven guiana_usnm16000essequiguy inambari_sil044amazonasbra guiana_1ml709amazonasven guiana_lsumzb45851suriname2003 rondonia_lsumzb12619santacrbo inambari_lsumzb10613ucaype guiana_lsumzb65776sipaliwinisur guiana_usnm22289upptakguy foothills_2ml516monagasven guiana_usnm22320uppertakutuguy inambari_ufac418acrebra inambari_mvz169642madresdiospe isla_maya039parabra rondonia_amana46parabra xingu_usnm6994parabr inambari_pime068parabra inambari_lsumzb9353pandobo inambari_ku466madrediospe napo_ku878loretoper guiana_3ml929bolivarven inambari_lsumzb21231lapazbo rondonia_pime036parabra inambari_lsumzb9506pandobo napo_lsumzb2913loretope rondonia_lsumzb15008santacrbo guiana_usnm10787northwestguy rondonia_fpr080amazonasbra inambari_cuj006bra guiana_usnm5026essequiboguy guiana_usnm19048kopvillguy inambari_lsumzb1013lapazbo inambari_lsumzb42434loretope huallaga_lsumzb5429sanmartpe napo_jap137amazonasbra napo_fmnh457497amazonasbra rondonia_lsumzb12532santacrbo rondonia_lsumzb12599santacrbo choco_lsumzb26882panamapa central_lsumzb28779colonpa central_lsumzb28208chiriqpa choco_lsumzb2238darienpa central_uwbm77019panamapan central_uwbm70059laluznic central_mbmjmd220panamapan central_mbmjk04143veraguaspan central_lsumzb60798honduras central_lsumzb55049honduras central_mbmjk04107pan choco_lsumzb28398panamapa mexico_mzfcb2153campechemex foothill_att.spad_iavh14179_casanareco magdalena_att_spad_andesbt592 magdalena_att.spad_iavh13307_caldasco magdalena_att_spad_andesbt2215 magdalena_att_spad_andesbt2216 mexico_ku2185campechemex mexico_mzfc2185campechemex central_uwbm56335laluznic central_mbmgms1017veraguaspan choco_lsumzb29986esmec central_uwbm70012laluznic central_usnm1279bocasdeltoropa central_usnm5364chiriquipan central_uwbm56336laluznic central_mbmjmd100 central_usnm1918bocasdeltoropan choco_att.spad_iavh12502_valleco central_72079puntarenascr central_lsumzb46698veragpa central_usnm5326chiriquipan central_usnm1797bocasdeltoropan central_lsumzb60697honduras mexico_ku551quintanaroomx mexico_ku2150campechemex mexico_ku530quintanaroomx mexico_ku1937campechemex mexico_ku1976campechemx central_lsumzb8802toledobe mexico_mzfcb532quermex mexico_fmnh393989veracruzmx central_mbmbrb913yucatanmex mexico_mzfcb2168campechemex mexico_mzfc493oaxacamex mexico_uwbm81460sinaloamex mexico_mzfcomvp689oaxmex mexico_mzfc690oaxacamex mexico_fmnh394278oaxacamex mexico_fmnh394276oaxacamex mexico_mzfc1029oaxacamex mexico_mbmjk07159oaxacamex mexico_fmnh394277oaxacamx Attila_torridus_LSUMZB7849_ElOroEC Attila_citriniventris_LSUMZB4852_LoretoPE Attila_citriniventris_KU1020_LoretoPE Attila_citriniventris_KU985 Attila_bolivianus_LSUMZB13074_SantaCruzBOL Attila_cinnamomeus_LSUMZB7301_LoretoPE Ramphotrigon_ruficauda_DQ294527 Myiarchus_swainsoni_DQ294512 Colonia_colonus_UWBM70302 imeri_4ml688amazonasven napo_lsumzb2843loretope guiana_lsumzb55279suriname guiana_usnm14105kusadguy rondonia_fmnh389961rondoniabra inambari_lsumzb9413pandobo inambari_ufac437acrebra inambari_ufac1978acrebra rondonia_lsumzb12575santacrbo napo_lsumzb42724loretope huallaga_lsumzb5419sanmartpe guiana_usnm19091kopinangvillageguy inambari_mvz169640madredediospe guiana_65775sipaliwinisur guiana_lsumzb48372guy inambari_lsumzb10639ucayalipe guiana_5ml687amazonasven guiana_usnm16000essequiguy inambari_sil044amazonasbra guiana_1ml709amazonasven guiana_lsumzb45851suriname2003 rondonia_lsumzb12619santacrbo inambari_lsumzb10613ucaype guiana_lsumzb65776sipaliwinisur guiana_usnm22289upptakguy foothills_2ml516monagasven guiana_usnm22320uppertakutuguy inambari_ufac418acrebra inambari_mvz169642madresdiospe isla_maya039parabra rondonia_amana46parabra xingu_usnm6994parabr inambari_pime068parabra inambari_lsumzb9353pandobo inambari_ku466madrediospe napo_ku878loretoper guiana_3ml929bolivarven inambari_lsumzb21231lapazbo rondonia_pime036parabra inambari_lsumzb9506pandobo napo_lsumzb2913loretope rondonia_lsumzb15008santacrbo guiana_usnm10787northwestguy rondonia_fpr080amazonasbra inambari_cuj006bra guiana_usnm5026essequiboguy guiana_usnm19048kopvillguy inambari_lsumzb1013lapazbo inambari_lsumzb42434loretope huallaga_lsumzb5429sanmartpe napo_jap137amazonasbra napo_fmnh457497amazonasbra rondonia_lsumzb12532santacrbo rondonia_lsumzb12599santacrbo choco_lsumzb26882panamapa central_lsumzb28779colonpa central_lsumzb28208chiriqpa choco_lsumzb2238darienpa central_uwbm77019panamapan central_uwbm70059laluznic central_mbmjmd220panamapan central_mbmjk04143veraguaspan central_lsumzb60798honduras central_lsumzb55049honduras central_mbmjk04107pan choco_lsumzb28398panamapa mexico_mzfcb2153campechemex foothill_att.spad_iavh14179_casanareco magdalena_att_spad_andesbt592 magdalena_att.spad_iavh13307_caldasco magdalena_att_spad_andesbt2215 magdalena_att_spad_andesbt2216 mexico_ku2185campechemex mexico_mzfc2185campechemex central_uwbm56335laluznic central_mbmgms1017veraguaspan choco_lsumzb29986esmec central_uwbm70012laluznic central_usnm1279bocasdeltoropa central_usnm5364chiriquipan central_uwbm56336laluznic central_mbmjmd100 central_usnm1918bocasdeltoropan choco_att.spad_iavh12502_valleco central_72079puntarenascr central_lsumzb46698veragpa central_usnm5326chiriquipan central_usnm1797bocasdeltoropan central_lsumzb60697honduras mexico_ku551quintanaroomx mexico_ku2150campechemex mexico_ku530quintanaroomx mexico_ku1937campechemex mexico_ku1976campechemx central_lsumzb8802toledobe mexico_mzfcb532quermex mexico_fmnh393989veracruzmx central_mbmbrb913yucatanmex mexico_mzfcb2168campechemex mexico_mzfc493oaxacamex mexico_uwbm81460sinaloamex mexico_mzfcomvp689oaxmex mexico_mzfc690oaxacamex mexico_fmnh394278oaxacamex mexico_fmnh394276oaxacamex mexico_mzfc1029oaxacamex mexico_mbmjk07159oaxacamex mexico_fmnh394277oaxacamx Attila_torridus_LSUMZB7849_ElOroEC Attila_citriniventris_LSUMZB4852_LoretoPE Attila_citriniventris_KU1020_LoretoPE Attila_citriniventris_KU985 Attila_bolivianus_LSUMZB13074_SantaCruzBOL Attila_cinnamomeus_LSUMZB7301_LoretoPE doi:10.1038/nature13687 Supplementary Figures Attila spadiceus Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Canopy Ancestral Origin: West of Andes Time-calibrated gene tree with Napo Guiana Rondonia Time-calibrated gene tree showing BGMYC species with 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 Andean foothills Central America Chocó Magdalena Central America, West IoT West IoT 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 Supplementary Figure 1 Range map, ENM, time-calibrated gene trees and delimited species for Attila spadiceus. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 34

inambari_fmnh433312cuscoper huallaga_lsu46009sanmartpe inambari_lsu11164ucaype inambari_fmnh433308cuscoper inambari_lsu10655ucaype inambari_ufac084acrebra inambari_ufac103acrebra inambari_fmnh391104lapazbo inambari_lsu31359rondbr inambari_lsu11048ucaype inambari_esec097acrebra inambari_fld433313cuzcope inambari_lsu40504loretope inambari_esec121acrebra huallaga_lsu46133sanmartpe inambari_2063pascoper inambari_8921pandobol inambari_lsu40554loretope inambari_lsu39944loretope inambari_ufac924acrebra inambari_ku18542cuscoper inambari_2027pascoper inambari_fmnh391105lapazbol inambari_ufac060acrebra rondonia_6785benibol inambari_lsu9255pandobo inambari_lsu22633lapazbo inambari_lsu22841lapazbo inambari_lsu22733lapazbo inambari_ku18566cuscoper inambari_ufac506acrebra inambari_esec115acrebra inambari_ufac012acrebra inambari_lsu22613lapazbo inambari_esec210acrebra inambari_lsu11187ucaype inambari_fmnh433310madredediosper inambari_lsu11244ucaype inambari_10514ucayaliper inambari_cuj159amazonasbra inambari_5123loretoper inambari_esec077acrebra inambari_lsu10864ucaype inambari_lsu8952pandobo inambari_fld433309madresdiospe inambari_fld433311cuzcope inambari_fmnh433311cuscoper rondonia_lsu18244santacruzbo rondonia_lsu18161santacruzbo rondonia_14484santacruzbol rondonia_lsu18225santacruzbo rondonia_mpds480rondoniabra rondonia_13829santacruzbol rondonia_18550santacruzbol rondonia_lsu18444santacruzbo rondonia_lsu14655santacruzbo rondonia_lsu18522santacruzbo rondonia_lsu18197santacruzbo rondonia_lsu12537santacruzbo rondonia_12375santacruzbol rondonia_lsu12479santacruzbo rondonia_15160santacruzbol rondonia_mar188amazonasbra rondonia_mar174amazonasbra rondonia_mar166amazonasbra rondonia_56655 rondonia_fpr049amazonasbra rondonia_op074rondoniabol rondonia_lsu36699rondbr rondonia_mar189amazonasbra rondonia_mar036amazonasbra choco_lsu2241darienpa choco_lsu26528colonpa magdalena_aut_ochr_andesbt521 magdalena_aut_ochr_andesbt1312 choco_bar15332panpa choco_lsu26537colonpa choco_ansp3436manabiec choco_ansp4306esmec guiana_usnmb11894upperessequiboguy guiana_48396kopinangvillageguy guiana_fmnh391345amapabra guiana_amnh14626amazbr guiana_usnm12761guy guiana_cn252parabra guiana_usnm10423sipuriverguy guiana_cn651parabra guiana_cn650parabra guiana_usnm4187berbiceguy guiana_usnm12563guy guiana_amz518amazonasbra guiana_cn777parabra guiana_usn11935wuppessrivguy guiana_usnmb22310uppertakutuguy guiana_sil060amazonasbra guiana_lsu48382kopvillguy guiana_orx056parabra guiana_usnmb11495upperessequiboguy guiana_usnm11390upperessequivoguy guiana_usnmb11694upperessequiboguy guiana_usnm11630upperessequivoguy guiana_fld389199roraimbr guiana_usnmb11857upperessequiboguy guiana_usnm4185berbiceguy guiana_cn031parabra guiana_usnm14298kakoriverguy guiana_orx046parabra guiana_cn051parabra guiana_usnmb12776parabaraguy guiana_usnmb22212uppertakutuguy guiana_ansp5716guy guiana_usnmb22318uppertakutuguy guiana_usnmb22305uppertakutuguy guiana_usnm9415baramitaguy guiana_lsu48411kopvillguy guiana_usnmb9680northwestdistrictguy guiana_usn14589barimarivguy guiana_amnh2950bolivarvz guiana_ku5272guy guiana_usnm9513baramitaguy guiana_usnmb9544barimaguy napo_fld457890amazbr napo_jap549amazonasbra imeri_aut.ochr_iavh14533_amazonasco imeri_aut.ochr_iavh14569_amazonasco napo_4234loretoper imeri_aut.ochr_iavh11229_co guiana_aut.ochr_iavh12853_vichadaco imeri_aut.ochr_iavh11217_co napo_lsu4264loretope guiana_aut.ochr_iavh14393_vichadaco imeri_aut.ochr_iavh11206_co guiana_aut.ochr_iavh14413_vichadaco guiana_amnh14519amazbr guiana_amnh12394amazvz guiana_amz409amazonasbra napo_lsu4159loretope napo_ansp5854sucuec napo_lsu4353loretope napo_ansp5956sucuec guiana_amnh12688amazvz guiana_amnh12407amazvz mexico_mzfyach400chiapmex mexico_mzfcyach238chiapasmex central_lsu3774toledobel mexico_mzfyach368chiapmex central_lsu8766toledobel mexico_mzfyach354chiapmex mexico_fld343240veracruzmex mexico_mzfcyach72chipasmex mexico_mzfchima175oaxmex mexico_fld393900veracruzmex mexico_fld343241veracruzmex mexico_mzfchima027oaxmex mexico_mzfomvp562oaxmex mexico_fld393901veracruzmex central_bar4376laluznic central_uwbm70060laluznic central_mbmdab1242laluznic central_lsu16279limoncr central_usnmb1990bocasdeltoropan central_lsu51424bocasdeltoropa central_mbmjmd874chiriquipan central_72080puntarenascr central_mbmjmd867chiriquipan Automolus.leucophthalmus_AY590048 Hyloctistes.subulatus_GQ140085 Hylocryptus.rubiginosus_11736 inambari_fmnh433312cuscoper huallaga_lsu46009sanmartpe inambari_lsu11164ucaype inambari_fmnh433308cuscoper inambari_lsu10655ucaype inambari_ufac084acrebra inambari_ufac103acrebra inambari_fmnh391104lapazbo inambari_lsu31359rondbr inambari_lsu11048ucaype inambari_esec097acrebra inambari_fld433313cuzcope inambari_lsu40504loretope inambari_esec121acrebra huallaga_lsu46133sanmartpe inambari_2063pascoper inambari_8921pandobol inambari_lsu40554loretope inambari_lsu39944loretope inambari_ufac924acrebra inambari_ku18542cuscoper inambari_2027pascoper inambari_fmnh391105lapazbol inambari_ufac060acrebra rondonia_6785benibol inambari_lsu9255pandobo inambari_lsu22633lapazbo inambari_lsu22841lapazbo inambari_lsu22733lapazbo inambari_ku18566cuscoper inambari_ufac506acrebra inambari_esec115acrebra inambari_ufac012acrebra inambari_lsu22613lapazbo inambari_esec210acrebra inambari_lsu11187ucaype inambari_fmnh433310madredediosper inambari_lsu11244ucaype inambari_10514ucayaliper inambari_cuj159amazonasbra inambari_5123loretoper inambari_esec077acrebra inambari_lsu10864ucaype inambari_lsu8952pandobo inambari_fld433309madresdiospe inambari_fld433311cuzcope inambari_fmnh433311cuscoper rondonia_lsu18244santacruzbo rondonia_lsu18161santacruzbo rondonia_14484santacruzbol rondonia_lsu18225santacruzbo rondonia_mpds480rondoniabra rondonia_13829santacruzbol rondonia_18550santacruzbol rondonia_lsu18444santacruzbo rondonia_lsu14655santacruzbo rondonia_lsu18522santacruzbo rondonia_lsu18197santacruzbo rondonia_lsu12537santacruzbo rondonia_12375santacruzbol rondonia_lsu12479santacruzbo rondonia_15160santacruzbol rondonia_mar188amazonasbra rondonia_mar174amazonasbra rondonia_mar166amazonasbra rondonia_56655 rondonia_fpr049amazonasbra rondonia_op074rondoniabol rondonia_lsu36699rondbr rondonia_mar189amazonasbra rondonia_mar036amazonasbra choco_lsu2241darienpa choco_lsu26528colonpa magdalena_aut_ochr_andesbt521 magdalena_aut_ochr_andesbt1312 choco_bar15332panpa choco_lsu26537colonpa choco_ansp3436manabiec choco_ansp4306esmec guiana_usnmb11894upperessequiboguy guiana_48396kopinangvillageguy guiana_fmnh391345amapabra guiana_amnh14626amazbr guiana_usnm12761guy guiana_cn252parabra guiana_usnm10423sipuriverguy guiana_cn651parabra guiana_cn650parabra guiana_usnm4187berbiceguy guiana_usnm12563guy guiana_amz518amazonasbra guiana_cn777parabra guiana_usn11935wuppessrivguy guiana_usnmb22310uppertakutuguy guiana_sil060amazonasbra guiana_lsu48382kopvillguy guiana_orx056parabra guiana_usnmb11495upperessequiboguy guiana_usnm11390upperessequivoguy guiana_usnmb11694upperessequiboguy guiana_usnm11630upperessequivoguy guiana_fld389199roraimbr guiana_usnmb11857upperessequiboguy guiana_usnm4185berbiceguy guiana_cn031parabra guiana_usnm14298kakoriverguy guiana_orx046parabra guiana_cn051parabra guiana_usnmb12776parabaraguy guiana_usnmb22212uppertakutuguy guiana_ansp5716guy guiana_usnmb22318uppertakutuguy guiana_usnmb22305uppertakutuguy guiana_usnm9415baramitaguy guiana_lsu48411kopvillguy guiana_usnmb9680northwestdistrictguy guiana_usn14589barimarivguy guiana_amnh2950bolivarvz guiana_ku5272guy guiana_usnm9513baramitaguy guiana_usnmb9544barimaguy napo_fld457890amazbr napo_jap549amazonasbra imeri_aut.ochr_iavh14533_amazonasco imeri_aut.ochr_iavh14569_amazonasco napo_4234loretoper imeri_aut.ochr_iavh11229_co guiana_aut.ochr_iavh12853_vichadaco imeri_aut.ochr_iavh11217_co napo_lsu4264loretope guiana_aut.ochr_iavh14393_vichadaco imeri_aut.ochr_iavh11206_co guiana_aut.ochr_iavh14413_vichadaco guiana_amnh14519amazbr guiana_amnh12394amazvz guiana_amz409amazonasbra napo_lsu4159loretope napo_ansp5854sucuec napo_lsu4353loretope napo_ansp5956sucuec guiana_amnh12688amazvz guiana_amnh12407amazvz mexico_mzfyach400chiapmex mexico_mzfcyach238chiapasmex central_lsu3774toledobel mexico_mzfyach368chiapmex central_lsu8766toledobel mexico_mzfyach354chiapmex mexico_fld343240veracruzmex mexico_mzfcyach72chipasmex mexico_mzfchima175oaxmex mexico_fld393900veracruzmex mexico_fld343241veracruzmex mexico_mzfchima027oaxmex mexico_mzfomvp562oaxmex mexico_fld393901veracruzmex central_bar4376laluznic central_uwbm70060laluznic central_mbmdab1242laluznic central_lsu16279limoncr central_usnmb1990bocasdeltoropan central_lsu51424bocasdeltoropa central_mbmjmd874chiriquipan central_72080puntarenascr central_mbmjmd867chiriquipan Automolus.leucophthalmus_AY590048 Hyloctistes.subulatus_GQ140085 Hylocryptus.rubiginosus_11736 doi:10.1038/nature13687 Automolus ochrolaemus Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Canopy Ancestral Origin: West of Andes Time-calibrated gene tree with outgroup A B Rondonia Choco, Magdalena Guiana Napo, Imeri, Guiana Time-calibrated gene tree showing BGMYC species with outgroup West of IoT, Central America Central America 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 Supplementary Figure 2 Range map, ENM, time-calibrated gene trees and delimited species for Automolus ochrolaemus. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). Nodes labeled A and B refer to multiple cross-andes divergence events used in the msbayes analysis. WWW.NATURE.COM/NATURE 35

Brotogeris Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Canopy Ancestral Origin: East of Andes Time-calibrated gene tree with tapajos_fj652892_bcr_b7029 rondonia_fj652893_bcr_mpeg58248 tapajos_fj652889_bcr_b7095 tapajos_fj652891_bcr_b7002 tapajos_fj652890_bcr_b7096 tapajos_fj652888_bcr_lgema2948 guiana_fj652880_bcr_b11427 guiana_fj652881_bcr_b12727 rondonia_fj652887_bcr_fmnh389686 inambari_fj652894_bcr_mpeg56993 rondonia_fj652886_bcr_fmnh389685 rondonia_fj652885_bcr_fmnh389684 guiana_fj652884_bcr_b12730 guiana_fj652879_bcr_ku1262 guiana_fj652876_bcr_ansp7778 guiana_fj652878_bcr_ansp7791 guina_fj652882_bcr_b11598 guiana_fj652883_bcr_b9732 napo_fj652868_bcy_ansp1640 napo_fj652869_bcy_ansp2647 napo_fj652867_bcy_ansp1490 napo_fj652870_bcy_ansp4873 inambari_fj652872_bcy_mpegesec109 inambari_fj652871_bcy_mpegesec028 inambari_fj652866_bcy_lgema2064 inambari_fj652875_bcy_b9534 tumbes_fj652862_bp_ansp1782 tumbes_fj652864_bp_ansp3493 tumbes_fj652863_bp_ansp1809 tumbes_fj652861_bp_ansp1733 tumbes_fj652860_bp_ansp1730 tumbes_fj652865_bp_ansp3547 central_fj652904_bj_69042 central_fj652905_bj_70139 central_fj652903_bj_b1543 isla_fj652851_bv_lgema1595 guiana_fj652850_bv_lgema1592 isla_fj652852_bv_lgema1596 isla_fj652853_bv_mpeg08493 inambari_fj652854_bv_b7252 rondonia_fj652856_bc_b37539 atlantic_fj652858_bc_ku3631 rondonia_fj652859_bc_wbm71475 atlantic_fj652857_bc_lgema5486 atlantic_fj652849_bt_fmnh399117 atlantic_fj652848_bt_lgema5366 inambari_fj652902_bs_mpeg20588 inambari_fj652901_bs_mpeg58038 inambari_fj652896_bs_mpeg58358 inambari_fj652900_bs_mpeg58037 inambari_fj652898_bs_mpeg58828 inambari_fj652897_bs_mpeg58359 inambari_fj652895_bs_lgema2060 inambari_fj652899_bs_b7287 Myiopsitta_AF370779 Myiopsitta_AF370778 EF517629_Pionus_sordidus Tapajos Guiana Rondonia Guiana Napo Tumbes Central America Guiana, Ilha Marajó, Rondonia, Atlantic Atlantic Time-calibrated gene tree showing BGMYC species with tapajos_fj652892_bcr_b7029 rondonia_fj652893_bcr_mpeg58248 tapajos_fj652889_bcr_b7095 tapajos_fj652891_bcr_b7002 tapajos_fj652890_bcr_b7096 tapajos_fj652888_bcr_lgema2948 guiana_fj652880_bcr_b11427 guiana_fj652881_bcr_b12727 rondonia_fj652887_bcr_fmnh389686 inambari_fj652894_bcr_mpeg56993 rondonia_fj652886_bcr_fmnh389685 rondonia_fj652885_bcr_fmnh389684 guiana_fj652884_bcr_b12730 guiana_fj652879_bcr_ku1262 guiana_fj652876_bcr_ansp7778 guiana_fj652878_bcr_ansp7791 guina_fj652882_bcr_b11598 guiana_fj652883_bcr_b9732 napo_fj652868_bcy_ansp1640 napo_fj652869_bcy_ansp2647 napo_fj652867_bcy_ansp1490 napo_fj652870_bcy_ansp4873 inambari_fj652872_bcy_mpegesec109 inambari_fj652871_bcy_mpegesec028 inambari_fj652866_bcy_lgema2064 inambari_fj652875_bcy_b9534 tumbes_fj652862_bp_ansp1782 tumbes_fj652864_bp_ansp3493 tumbes_fj652863_bp_ansp1809 tumbes_fj652861_bp_ansp1733 tumbes_fj652860_bp_ansp1730 tumbes_fj652865_bp_ansp3547 central_fj652904_bj_69042 central_fj652905_bj_70139 central_fj652903_bj_b1543 isla_fj652851_bv_lgema1595 guiana_fj652850_bv_lgema1592 isla_fj652852_bv_lgema1596 isla_fj652853_bv_mpeg08493 inambari_fj652854_bv_b7252 rondonia_fj652856_bc_b37539 atlantic_fj652858_bc_ku3631 rondonia_fj652859_bc_wbm71475 atlantic_fj652857_bc_lgema5486 atlantic_fj652849_bt_fmnh399117 atlantic_fj652848_bt_lgema5366 inambari_fj652902_bs_mpeg20588 inambari_fj652901_bs_mpeg58038 inambari_fj652896_bs_mpeg58358 inambari_fj652900_bs_mpeg58037 inambari_fj652898_bs_mpeg58828 inambari_fj652897_bs_mpeg58359 inambari_fj652895_bs_lgema2060 inambari_fj652899_bs_b7287 Myiopsitta_AF370779 Myiopsitta_AF370778 12.011.019.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 12.011.019.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 Supplementary Figure 3 Range map, ENM, time-calibrated gene trees and delimited species for Brotogeris. Ingroup includes all biological species in Brotogeris: B. tirica, B. versicolurus, B. chiriri, B. sanctithomae, B. pyrrhoptera, B. jugularis, B. cyanoptera,and B. chrysoptera. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 36

guiana_ansp21441potarosiparuniguy huallaga_lsumz42349loretoper napo_2696loretoper guiana_48357guy guiana_lsumz48389guy inambari_27495loretoper inambari_lsumz9048pandobol guiana_cn438parabra guiana_usnmb19128kopinangvillageguy napo_jap051amazonasbra inambari_22857lapazbol guiana_ansp21619potarosiparuniguy guiana_ansp21622potarosiparuniguy guiana_usnmb4291berbiceguy huallaga_lsumz42292loretoper napo_lsumz2727loretoper central_72165sanjosecr central_71963puntarenascr guiana_usnmb19238kopinangvillageguy guiana_ku1270iwokramareserveguy tapajos_cn338parabra guiana_cn503parabra rondonia_lsumz12296santacruzbol rondonia_12328santacruzbol rondonia_lsumz12339santacruzbol rondonia_lsumz12486santacruzbol trinidad_gu215293laslapistri inambari_lsumz28014loretoper guiana_usnmb14385kakoriverguy huallaga_lsumz5431sanmartinper choco_ansp2453esmeraldasecu napo_7030loretoper huallaga_lsumz42539loretoper guiana_usnmb14370kakoriverguy guiana_ansp21615potarosiparuniguy napo_lsumz2861loretoper guiana_usnmb5175cuyuniguy inambari_lsumz22731lapazbol napo_2838loretoper guiana_usnmb14369kakoriverguy guiana_usnmb14224lindenguy guiana_usnmb19094kopinangvillageguy foothills_6ml1371barinasven guiana_ku1397iwokramareserveguy napo_lsumz2783loretoper napo_2845loretoper xingu_ppbio235parabra inambari_lsumz27666loretoper napo_2966loretoper inambari_28016loretoper inambari_27558loretoper huallaga_42570loretoper rondonia_18302santacruzbol guiana_usnmb4289upperdemeraraguy guiana_ansp26377potarosiparuniguy central_usnmb295bocasdeltoropan central_usnmb537bocasdeltoropan central_usnmb536bocasdeltoropan central_mbmdab1008laluznic central_uwbm69945laluznic central_mbmgms158laceibahon central_lsumz16555colonpan central_usnmb1243bocasdeltoropan central_uwbm56021laluznic central_gu215292laceibahon central_uwbm70037laluznic central_mbmdab1186laluznic central_usnmb469bocasdeltoropan choco_lsumz2131darienpan magdalena_chl.spiz_icn30199_antioquiaco choco_lsumz2226darienpan magdalena_chl.spiz_icn32556_cundinamarcaco Iridophanes_pulcherrima Coryphospingus_pileatus_FJ799870 Schistochlamys_melanopis_AY383102 guiana_ansp21441potarosiparuniguy huallaga_lsumz42349loretoper napo_2696loretoper guiana_48357guy guiana_lsumz48389guy inambari_27495loretoper inambari_lsumz9048pandobol guiana_cn438parabra guiana_usnmb19128kopinangvillageguy napo_jap051amazonasbra inambari_22857lapazbol guiana_ansp21619potarosiparuniguy guiana_ansp21622potarosiparuniguy guiana_usnmb4291berbiceguy huallaga_lsumz42292loretoper napo_lsumz2727loretoper central_72165sanjosecr central_71963puntarenascr guiana_usnmb19238kopinangvillageguy guiana_ku1270iwokramareserveguy tapajos_cn338parabra guiana_cn503parabra rondonia_lsumz12296santacruzbol rondonia_12328santacruzbol rondonia_lsumz12339santacruzbol rondonia_lsumz12486santacruzbol trinidad_gu215293laslapistri inambari_lsumz28014loretoper guiana_usnmb14385kakoriverguy huallaga_lsumz5431sanmartinper choco_ansp2453esmeraldasecu napo_7030loretoper huallaga_lsumz42539loretoper guiana_usnmb14370kakoriverguy guiana_ansp21615potarosiparuniguy napo_lsumz2861loretoper guiana_usnmb5175cuyuniguy inambari_lsumz22731lapazbol napo_2838loretoper guiana_usnmb14369kakoriverguy guiana_usnmb14224lindenguy guiana_usnmb19094kopinangvillageguy foothills_6ml1371barinasven guiana_ku1397iwokramareserveguy napo_lsumz2783loretoper napo_2845loretoper xingu_ppbio235parabra inambari_lsumz27666loretoper napo_2966loretoper inambari_28016loretoper inambari_27558loretoper huallaga_42570loretoper rondonia_18302santacruzbol guiana_usnmb4289upperdemeraraguy guiana_ansp26377potarosiparuniguy central_usnmb295bocasdeltoropan central_usnmb537bocasdeltoropan central_usnmb536bocasdeltoropan central_mbmdab1008laluznic central_uwbm69945laluznic central_mbmgms158laceibahon central_lsumz16555colonpan central_usnmb1243bocasdeltoropan central_uwbm56021laluznic central_gu215292laceibahon central_uwbm70037laluznic central_mbmdab1186laluznic central_usnmb469bocasdeltoropan choco_lsumz2131darienpan magdalena_chl.spiz_icn30199_antioquiaco choco_lsumz2226darienpan magdalena_chl.spiz_icn32556_cundinamarcaco Iridophanes_pulcherrima Coryphospingus_pileatus_FJ799870 doi:10.1038/nature13687 Chlorophanes spiza Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Canopy Ancestral Origin: West of Andes Time-calibrated gene tree with Guiana Rondonia Napo Xingu Huallaga Trinidad Chocó Central America Foothills Central America Chocó, Magdalena Time-calibrated gene tree showing BGMYC species with outgroup 7.0 6.0 5.0 4.0 3.0 2.0 1.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 Supplementary Figure 4 Range map, ENM, time-calibrated gene trees and delimited species for Chlorophanes spiza. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 37

huallaga_lsumz43993sanmartinper inambari_lsumz954lapazbol inambari_lsumz10676ucayaliper inambari_dq294494fmnh323355madredediosper inambari_ku21521punoper atlantic_ku3640itapuapar napo_lsumz5941moronaecu inambari_ku21560punoper atlantic_uwbm70302misionesarg atlantic_ku3657itapuapar central_mbm18304veraguaspan central_usnmb279bocasdeltoropan central_mbmgms1191colonpan central_lsumz28471colonpan choco_lsumz11941esmeraldasecu napo_lsumz5945moronaecu guiana_mpds0432roraimabra guiana_usnmb9288northwestdistrictguy Sublegatus_modestus_AF447623 Empidonax_flavescens_AF447599 doi:10.1038/nature13687 Colonia colonus Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Canopy Ancestral Origin: East of Andes Time-calibrated gene tree with Huallaga Napo Atlantic Time-calibrated gene tree showing BGMYC species with outgroup huallaga_lsumz43993sanmartinper inambari_lsumz954lapazbol inambari_lsumz10676ucayaliper inambari_dq294494fmnh323355madredediosper inambari_ku21521punoper atlantic_ku3640itapuapar napo_lsumz5941moronaecu inambari_ku21560punoper atlantic_uwbm70302misionesarg atlantic_ku3657itapuapar Chocó Central America central_mbm18304veraguaspan central_usnmb279bocasdeltoropan central_mbmgms1191colonpan central_lsumz28471colonpan Napo, Guiana choco_lsumz11941esmeraldasecu napo_lsumz5945moronaecu guiana_mpds0432roraimabra guiana_usnmb9288northwestdistrictguy Sublegatus_modestus_AF447623 11.0 1 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 11.0 1 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 Supplementary Figure 5 Range map, ENM, time-calibrated gene trees and delimited species for Colonia colonus. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 38

rondonia_amana42parabra inambari_9049pandobol rondonia_amana40parabra inambari_amz519amazonasbra huallaga_42532loretoper guiana_lsumzb7554amazonasven inambari_ufac1982acrebra rondonia_12906santacruzbol guiana_nsp21530kabocalliguy guiana_usnmb11703upperessequiboguy inambari_1983pascoper foothills_8ml1207barinasven guiana_amz205amazonasbra inambari_puc219amazonasbra inambari_ufac1070acrebra guiana_usnmb23643cuyunimazaruniguy napo_lsumzb2730loretoper huallaga_lsumzb5404sanmartinper napo_43042loretoper napo_cyan.cae_icn34292_amazonasco guiana_ansp21531potarosiparuniguy guiana_ku5795ebarimariverguy guiana_usnmb23627cuyunimazaruniguy guiana_usnmb23650cuyunimazaruniguy guiana_usnmb23630cuyunimazaruniguy trinidad_gu215298simlatri guiana_ansp21825potarosiparuniguy guiana_ansp21681onverwagtguy guiana_usnmb15680mountroraimaguy guiana_usnmb23695cuyunimazaruniguy guiana_usnmb23614cuyunimazaruniguy guiana_usnmb5124cuyunimazaruniguy guiana_usnmb9500northwestdistrictguy guiana_usnmb5251essequiboguy guiana_ansp21402potarosiparuniguy magdalena_cyan.cae_icn37290_cordobaco magdalena_cyan.cae_icn36721_antioquiaco choco_lsumzb11825esmeraldasecu magdalena_cyan.cae_icn37289_cordobaco Cyanerpes_nitidus_GU215303 Cyanerpes_nitidus_AY190167 Cyanerpes_cyaneus_GU215299 Cyanerpes_cyaneus_GU215300 Cyanerpes_cyaneus_EF529958 Cyanerpes_cyaneus_FJ799873 Cyanerpes_cyaneus_GU215301 Tersina_viridis_USNM11711 Schistochlamys_melanopsis_AF006250 rondonia_amana42parabra inambari_9049pandobol rondonia_amana40parabra inambari_amz519amazonasbra huallaga_42532loretoper guiana_lsumzb7554amazonasven inambari_ufac1982acrebra rondonia_12906santacruzbol guiana_nsp21530kabocalliguy guiana_usnmb11703upperessequiboguy inambari_1983pascoper foothills_8ml1207barinasven guiana_amz205amazonasbra inambari_puc219amazonasbra inambari_ufac1070acrebra guiana_usnmb23643cuyunimazaruniguy napo_lsumzb2730loretoper huallaga_lsumzb5404sanmartinper napo_43042loretoper napo_cyan.cae_icn34292_amazonasco guiana_ansp21531potarosiparuniguy guiana_ku5795ebarimariverguy guiana_usnmb23627cuyunimazaruniguy guiana_usnmb23650cuyunimazaruniguy guiana_usnmb23630cuyunimazaruniguy trinidad_gu215298simlatri guiana_ansp21825potarosiparuniguy guiana_ansp21681onverwagtguy guiana_usnmb15680mountroraimaguy guiana_usnmb23695cuyunimazaruniguy guiana_usnmb23614cuyunimazaruniguy guiana_usnmb5124cuyunimazaruniguy guiana_usnmb9500northwestdistrictguy guiana_usnmb5251essequiboguy guiana_ansp21402potarosiparuniguy magdalena_cyan.cae_icn37290_cordobaco magdalena_cyan.cae_icn36721_antioquiaco choco_lsumzb11825esmeraldasecu magdalena_cyan.cae_icn37289_cordobaco Cyanerpes_nitidus_GU215303 Cyanerpes_nitidus_AY190167 doi:10.1038/nature13687 Cyanerpes caeruleus Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Canopy Ancestral Origin: East of Andes Time-calibrated gene tree with Rondonia Andean Foothills Guiana Napo Huallaga Time-calibrated gene tree showing BGMYC species with Guiana Trinidad Chocó, Magdalena 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 Supplementary Figure 6 Range map, ENM, time-calibrated gene trees and delimited species for Cyanerpes caeruleus. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 39

Cymbilaimus lineatus Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Canopy Ancestral Origin: East of Andes Time-calibrated gene tree with 1 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 central_gu215221bocasdeltoropan central_28749colonpan central_usnmb406bocasdeltoropan central_28582colonpan choco_ansp4686esmeraldasecu central_28750colonpan choco_46622darienpan choco_28690panamapan choco_2252darienpan choco_2205darienpan inambari_27958loretoper inambari_40200loretoper inambari_27679loretoper napo_ansp2641moronaecu napo_ansp1630moronaecu inambari_27594loretoper inambari_40476loretoper napo_jap458amazonasbra napo_jap443amazonasbra napo_jap457amazonasbra napo_4157loretoper napo_6890loretoper guiana_9fm40bolivarven imeri_cym.lin_icn33084_guainiaco imeri_amz170amazonasbra imeri_jap631amazonasbra inambari_cuj176acrebra inambari_4633loretoper inambari_11156ucayaliper xingu_ppbio018parabra xingu_ppbio108parabra rondonia_18168santacruzbol tapajos_br163161parabra tapajos_br163116parabra tapajos_wm382parabra inambari_puc209amazonasbra inambari_1129lapazbol inambari_puc114amazonasbra inambari_puc115amazonasbra inambari_esec212acrebra guiana_usnmb11881upessriverguy guiana_usnmb22078uppertakutoguy guiana_usnmb5127cuyuniguy guiana_usnmb9149barimaguy guiana_usnmb5125cuyuniguy guiana_cn394parapara guiana_cn1174parabra guiana_usnmb22134uppertakutoguy Taraba_major_FJ899315 Batara_cinerea_EF639939 Frederickena_unduligera_EF030316 Chocó Central America Napo Napo Imeri, Guiana Xingu Rondonia Tapajos Guiana Time-calibrated gene tree showing BGMYC species with outgroup 1 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 central_gu215221bocasdeltoropan central_28749colonpan central_usnmb406bocasdeltoropan central_28582colonpan choco_ansp4686esmeraldasecu central_28750colonpan choco_46622darienpan choco_28690panamapan choco_2252darienpan choco_2205darienpan inambari_27958loretoper inambari_40200loretoper inambari_27679loretoper napo_ansp2641moronaecu napo_ansp1630moronaecu inambari_27594loretoper inambari_40476loretoper napo_jap458amazonasbra napo_jap443amazonasbra napo_jap457amazonasbra napo_4157loretoper napo_6890loretoper guiana_9fm40bolivarven imeri_cym.lin_icn33084_guainiaco imeri_amz170amazonasbra imeri_jap631amazonasbra inambari_cuj176acrebra inambari_4633loretoper inambari_11156ucayaliper xingu_ppbio018parabra xingu_ppbio108parabra rondonia_18168santacruzbol tapajos_br163161parabra tapajos_br163116parabra tapajos_wm382parabra inambari_puc209amazonasbra inambari_1129lapazbol inambari_puc114amazonasbra inambari_puc115amazonasbra inambari_esec212acrebra guiana_usnmb11881upperessequiboriverguy guiana_usnmb22078uppertakutoguy guiana_usnmb5127cuyuniguy guiana_usnmb9149barimaguy guiana_usnmb5125cuyuniguy guiana_cn394parapara guiana_cn1174parabra guiana_usnmb22134uppertakutoguy Taraba_major_FJ899315 Supplementary Figure 7 Range map, ENM, time-calibrated gene trees and delimited species for Cymbilaimus lineatus. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 40

rondonia_mpds748amazonasbra napo_jap136amazonasbra napo_jap355amazonasbra rondonia_mpds6168amazonasbra imeri_amz153amazonasbra napo_jap526amazonasbra napo_jap391amazonasbra inambari_puc065amazonasbra inambari_lsumz10499ucayali PER inambari_lsumz11175ucayali PER inambari_puc185amazonasbra inambari_lsumz27822loretoper inambari_lsumz10694ucayali PER napo_jap155amazonasbra napo_ku834loretoper inambari_40188loretoper inambari_10651ucayali PER napo_gu215179napoecu huallaga_lsumz5438sanmartinper napo_lsumz6059moronaecu imeri_amz309amazonasbra guiana_mpds03768roraimabra napo_ku1008loretoper rondonia_12698santacruzbol huallaga_42362loretoper imeri_28ml716amazonasven imeri_den.ful_iavh14562_amazonasco napo_jap583amazonasbra inambari_ufac1125acrebra napo_jap096amazonasbra imeri_den.ful_iavh14377_vichadaco inambari_35705amazonasbra imeri_amz068amazonasbra imeri_amz113amazonasbra imeri_amz355amazonasbra imeri_amz319amazonasbra imeri_amz320amazonasbra huallaga_lsumz5478sanmartinper napo_jap303amazonasbra rondonia_amz468amazonasbra rondonia_amz448amazonasbra imeri_den.ful_iavh14400_vichadaco rondonia_amz506amazonasbra rondonia_amz436amazonasbra rondonia_amz451amazonasbra inambari_10799ucayali PER napo_35739amazonasbra inambari_cuj160amazonasbra inambari_27632loretoper inambari_27510loretoper inambari_27496loretobra foothills_31jpl335tachiraven foothills_25ic426mirandaven foothills_12ic1079barinasven foothills_den.ful_iavh14795_ar aucac O foothills_29ml1393barinasven foothills_75o7n0349laraven foothills_10ic970falconven foothills_14ic170barinasven orinocodelta_19ic83deltaamacuroven orinocodelta_24ic1488deltaamacuroven orinocodelta_21ic1515deltaamacuroven trinidad_gu215182simlatri trinidad_lsumz35978tri foothills_27ml519monagasven trinidad_lsumz35961tri trinidad_lsumz35951tri foothills_15ic178barinasven foothills_33ypl154tachiraven catatumbo_den_ful_andesbt 1430 foothills_73jp491yaracuyven foothills_32kcc172tachiraven foothills_30jpl326tachiraven catatumbo_den_ful_andesbt 1545 foothills_34ypl175tachiraven foothills_13ic1086barinasven foothills_26ic702deltaamacuroven foothills_22ml558sucreven foothills_18ic448mirandaven foothills_17ic423mirandaven choco_usnmb8803panamapan central_41624bocaspa central_dq364135bocasdeltoropan choco_gu215180strijtw744darienpan choco_52931darienpa magdalena_den.ful_iavh15248_sucreco magdalena_den.ful_iavh13106_sucreco magdalena_den.ful_iavh15137_sucreco choco_lsumz11754esmeraldasecu choco_1356darienpan central_usnmb5425chiriquipan choco_26888panamapan choco_lsumz26510colonpan choco_lsumz12096pichinchaecu choco_46570darienpan central_usnmb282bocasdeltoropan central_usnmb345bocasdeltoropan choco_26556colonpan magdalena_den.ful_iavh12010_caldascco magdalena_den.ful_iavh13107_sucreco magdalena_den.ful_iavh13282_caldasco choco_lsumz11927esmeraldasecu central_dendrocinclaanabatinagu215176ku536mex guiana_usnmb19028kopinangvillageguy guiana_usnmb5149essequiboguy guiana_usnmb12664parabaraguy guiana_usnmb14222lindenguy guiana_cn052parabra guiana_usnmb14312makwai maguy guiana_usnmb5193cuyunimazaruni GUY guiana_48314guy guiana_ku5780ebarimariverguy guiana_usnmb5035essequiboguy guiana_usnmb12774parabaraguy guiana_usnmb19036kopinangvillageguy guiana_orx089parabra guiana_usnmb11867upperessequiboguy guiana_cn056parabra guiana_sil015amazonasbra guiana_usnmb5192cuyunimazaruni GUY guiana_cn1070parabra guiana_55361sipallwinisur guiana_55317sipallwinisur guiana_cn324parabra guiana_usnmb5150cuyunimazaruni GUY guiana_usnmb14299makwai maguy guiana_usnmb14322makwai maguy guiana_usnmb14248lindenguy guiana_65787sipallwinisur guiana_sil058amazonasbra guiana_tro008parabra guiana_cn036parabra guiana_ku5752ebarimariverguy guiana_cn957parabra guiana_74ml1100bolivarven guiana_cn1116parabra guiana_usnmb11458upperessequiboguy guiana_usnm_b9550_barima_waini GUY guiana_usnmb4416berbiceguy guiana_cn240parabra guiana_usnmb14255eastdemeraraguy guiana_usnm_b9586_barima_waini GUY 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rondonia_amana10parabra rondonia_fpr072amazonasbr A atlantic_dq364139fmnh399178alagoasbra atlantic_gu215177fmnh399181alagoasbra Dendrocincla_homochroa_GU215183_PanamaPAN Dendrocincla_homochroa_DQ364138_M434035_SAL Dendrocincla_merula_GU215184_FM 389810_RondoniaBR A Dendrocincla_merula_AY442986 doi:10.1038/nature13687 Dendrocincla fuliginosa and D. anabatina Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Understory Ancestral Origin: East of Andes Time-calibrated gene tree with 5.0 4.0 3.0 2.0 1.0 Napo, Imeri Guiana Rondonia Andean Foothills, Catatumbo, Orinoco Delta Central America, Chocó, Magdalena Central America Guiana Xingu Xingu, Tapajos, Ilha Marajó, Belem Xingu, Tapajos, Rondonia, Rondonia, Xingu Rondonia Atlantic Time-calibrated gene tree showing BGMYC species with 5.0 4.0 3.0 2.0 1.0 Supplementary Figure 8 Range map, ENM, time-calibrated gene trees and delimited species for Dendrocincla fuliginosa. Ingroup includes D. fuliginosa and D. anabatina. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 41

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napo_jap071amazonasbra napo_jap357amazonasbra napo_jap435amazonasbra napo_jap003amazonasbra napo_jap392amazonasbra foothills_glyp_spir_andesbt1226 foothills_glyp_spir_andesbt797 napo_gly.spir_iavh10999_co napo_2921loretoper napo_fj899302lsumz4549 napo_4516loretoper napo_7103loretoper huallaga_fj899298lsumz7227 inambari_40344loretoper huallaga_fj899300lsumz7233 napo_7117loretoper napo_7191loretoper huallaga_fj899299lsumz7234 napo_2901loretoper inambari_ufac1009acrebra inambari_pnsd182acrebra napo_7365loretoper napo_7364loretoper inambari_10875ucayali PER inambari_10740ucayali PER inambari_ufac373acrebra inambari_10563ucayali PER inambari_cuj065amazonasbra inambari_ufac468acrebra inambari_ufac1876acrebra inambari_ufac1136acrebra inambari_ufac1048acrebra inambari_cuj070amazonasbra inambari_10605ucayali PER inambari_fj899306lsumz11131 inambari_ufac1137acrebra inambari_ufac375acrebra inambari_ufac1861acrebra inambari_ufac458acrebra inambari_40267loretoper huallaga_42485loretoper inambari_40176loretoper inambari_27512loretoper inambari_27492loretoper inambari_40625loretoper inambari_27623loretoper inambari_2042 inambari_40124loretoper inambari_2056pascoper inambari_27432loretoper inambari_27698loretoper inambari_40293loretoper huallaga_5515sanmartinper huallaga_42194loretoper huallaga_423830loretoper huallaga_42242loretoper huallaga_42237loretoper huallaga_42257loretoper inambari_27515loretoper huallaga_42630loretoper inambari_40486loretoper napo_3266loretoper napo_5973moronasantiagoecu napo_5993moronasantiagoecu napo_fj899305lsumz5967 inambari_ku979loretoper inambari_ku1009loretoper napo_5995moronasantiagoecu napo_3212loretoper napo_3249loretoper napo_2976loretoper inambari_puc011amazonasbra inambari_puc015amazonasbra inambari_puc010amazonasbra inambari_puc017amazonasbra inambari_ufac234acrebra inambari_ufac172acrebra inambari_31344rondoniabra inambari_ufac328acrebra inambari_8836pandobol inambari_ufac342acrebra inambari_31336rondoniabra inambari_esec102acrebra inambari_21192madredediosper inambari_8943pandobol inambari_9065pandobol inambari_esec252acrebra inambari_9115pandobol inambari_9157pandobol inambari_esec266acrebra inambari_22617lapazbol inambari_fj899301lsumz22619 inambari_22842lapazbol Dendrocincla.fuliginosa_10499 Xiphorhynchus_fuscus_EF190580 doi:10.1038/nature13687 Glyphorynchus spirurus Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Understory Ancestral Origin: East of Andes Time-calibrated gene tree with Guiana Rondonia Tapajos Xingu, Tapajos, Belem, Atlantic Rondonia Central America, Chocó Guiana/Imeri Napo, Andean Foothills, Huallaga, Napo, Huallaga Napo, Time-calibrated gene tree showing BGMYC species with 13.012.011.01 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 13.012.011.01 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 Supplementary Figure 9 Range map, ENM, time-calibrated gene trees and delimited species for Glyphorynchus spirurus. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 42

Henicorhina leucosticta Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Understory Ancestral Origin: West of Andes Time-calibrated gene tree with 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 guiana_usnmb11411upperesseuiboguy guiana_lsumzb55342sipaliwinisur guiana_lsumzb55339sipaliwinisur guiana_lsumzb55323sipaliwinisur guiana_usnmb9764barimaguy guiana_cn700parabra guiana_usnmb9424barimaguy guiana_usnmb5088cuyunimazaruniguy guiana_usnmb5237cuyunimazaruniguy guiana_usnmb19059kopinangguy guiana_77ml1078bolivarven guiana_lsumzb48436guy foothills_76ml1079barinasven guiana_usnmb5074cuyunimazaruniguy guiana_cn672bra napo_lsumzb43060loretoper napo_lsumzb42803loretoper napo_ansp2482moronaecu napo_lsumzb6019moronaec napo_ansp2653moronaecu napo_ansp2630moronaecu huallaga_lsumzb5391sanmartinper napo_ku814loretoper napo_ku847loretoper choco_lsumzb2236darienpan choco_lsumzb2097darienpan choco_46617darienpan choco_lsumzb1357darienpan central_lsumzb28632panamapan central_lsumzb41623bocasdeltoropan central_lsumzb28784colonpan central_dq415709limoncr central_lsumzb35756cartagocr central_lsumzb8744toledobel central_lsumzb8762toledobel mexico_ay352530fmnh343285mex choco_lsumzb11868esmeraldasecu choco_11739esmeraldasecu choco_ansp2396esmeraldasecu choco_ansp2426esmeraldasecu choco_lsumz12005esmeraldasecu choco_11869esmeraldasecu choco_11756esmeraldasecu choco_lsumzb11738esmeraldasecu LSUMZB28281_ChiriquiPAN_leucophrys Henicorhina_leucophrys_LSUMZB16049_HerediaCR Henicorhina_leucophrys_DQ415708_PichinchaECU Pheugopedius_nigricapillus_DQ415701 Pheugopedius_leucopogon_DQ415693 Guiana Andean Foothills Napo Huallaga Chocó Central America West IoT Chocó Time-calibrated gene tree showing BGMYC species with 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 guiana_usnmb11411upperesseuiboguy guiana_lsumzb55342sipaliwinisur guiana_lsumzb55339sipaliwinisur guiana_lsumzb55323sipaliwinisur guiana_usnmb9764barimaguy guiana_cn700parabra guiana_usnmb9424barimaguy guiana_usnmb5088cuyunimazaruniguy guiana_usnmb5237cuyunimazaruniguy guiana_usnmb19059kopinangguy guiana_77ml1078bolivarven guiana_lsumzb48436guy guiana_76ml1079barinasven guiana_usnmb5074cuyunimazaruniguy guiana_cn672bra napo_lsumzb43060loretoper napo_lsumzb42803loretoper napo_ansp2482moronaecu napo_lsumzb6019moronaec napo_ansp2653moronaecu napo_ansp2630moronaecu huallaga_lsumzb5391sanmartinper napo_ku814loretoper napo_ku847loretoper choco_lsumzb2236darienpan choco_lsumzb2097darienpan choco_46617darienpan choco_lsumzb1357darienpan central_lsumzb28632panamapan central_lsumzb41623bocasdeltoropan central_lsumzb28784colonpan central_dq415709limoncr central_lsumzb35756cartagocr central_lsumzb8744toledobel central_lsumzb8762toledobel mexico_ay352530fmnh343285mex choco_lsumzb11868esmeraldasecu choco_11739esmeraldasecu choco_ansp2396esmeraldasecu choco_ansp2426esmeraldasecu choco_lsumz12005esmeraldasecu choco_11869esmeraldasecu choco_11756esmeraldasecu choco_lsumzb11738esmeraldasecu LSUMZB28281_ChiriquiPAN_leucophrys Henicorhina_leucophrys_LSUMZB16049_HerediaCR Henicorhina_leucophrys_DQ415708_PichinchaECU Supplementary Figure 10 Range map, ENM, time-calibrated gene trees and delimited species for Henicorhina leucosticta. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 43

inambari_10744ucayaliper inambari_10607ucayaliper inambari_ufac1977acrebra inambari_10504ucayaliper inambari_11023ucayaliper inambari_11070ucayaliper inambari_11116ucayaliper inambari_ufac1134acrebra inambari_lsumz10492ucayaliper inambari_ufac457acrebra inambari_ufac453acrebra inambari_ufac2008acrebra inambari_11087ucayaliper inambari_10583ucayaliper inambari_4634loretoper inambari_4674loretoper inambari_4719loretoper inambari_5015loretoper inambari_4742loretope inambari_4637loretoper inambari_ufac1138acrebra inambari_ufac1127acrebra inambari_pnsd025acrebra inambari_ufac521acrebra inambari_lsumz27832loretoper huallaga_5394sanmartinper huallaga_5450sanmartinper huallaga_5487sanmartinper napo_jap001amazonasbra inambari_cuj002amazonasbra inambari_cuj038amazonasbra inambari_puc062bra inambari_9125pandobol inambari_9170pandobol inambari_901lapazbol rondonia_lsumz31333rondoniabra inambari_9269pandobol inambari_8837pandobol inambari_ufac327acrebra napo_jap342amazonasbra napo_jap343amazonasbra napo_jap028amazonasbra napo_jap335amazonasbra napo_jap330amazonasbra napo_jap007amazonasbra napo_jap026amazonasbra napo_jap016amazonasbra napo_ansp5859sucumbiosecu napo_2891loretoper napo_lsumz2836loretoper napo_2742loretoper napo_4313loretoper napo_4545loretoper inambari_4770loretoper napo_6994loretoper napo_7347loretoper napo_103257loretoper napo_3232loretoper napo_ku1013loretoper napo_3014loretoper napo_3105loretoper napo_ku1014loretoper napo_3116loretoper napo_ansp2490moronaecu napo_3265loretoper napo_103258loretoper central_16121puntarenascr central_71960puntarenascr central_71936puntarenascr central_16128puntarenascr central_71931puntarenascr central_16077puntarenascr central_16107puntarenascr choco_28720panamapan choco_28460panamapan choco_2215darienpan choco_ansp2140esmeraldasecu guiana_39ml942bolivarven guiana_7380amazonasven imeri_jap673amazonasbra imeri_jap619amazonasbra guiana_35fm27bolivarven Lepidothrix_nattereri_EF633407 Lepidothrix_iris_EF633417 Pipra_mentalis_DQ294491 Dixiphia_pipra_AY352534 inambari_10744ucayaliper inambari_10607ucayaliper inambari_ufac1977acrebra inambari_10504ucayaliper inambari_11023ucayaliper inambari_11070ucayaliper inambari_11116ucayaliper inambari_ufac1134acrebra inambari_lsumz10492ucayaliper inambari_ufac457acrebra inambari_ufac453acrebra inambari_ufac2008acrebra inambari_11087ucayaliper inambari_10583ucayaliper inambari_4634loretoper inambari_4674loretoper inambari_4719loretoper inambari_5015loretoper inambari_4742loretope inambari_4637loretoper inambari_ufac1138acrebra inambari_ufac1127acrebra inambari_pnsd025acrebra inambari_ufac521acrebra inambari_lsumz27832loretoper huallaga_5394sanmartinper huallaga_5450sanmartinper huallaga_5487sanmartinper napo_jap001amazonasbra inambari_cuj002amazonasbra inambari_cuj038amazonasbra inambari_puc062bra inambari_9125pandobol inambari_9170pandobol inambari_901lapazbol rondonia_lsumz31333rondoniabra inambari_9269pandobol inambari_8837pandobol inambari_ufac327acrebra napo_jap342amazonasbra napo_jap343amazonasbra napo_jap028amazonasbra napo_jap335amazonasbra napo_jap330amazonasbra napo_jap007amazonasbra napo_jap026amazonasbra napo_jap016amazonasbra napo_ansp5859sucumbiosecu napo_2891loretoper napo_lsumz2836loretoper napo_2742loretoper napo_4313loretoper napo_4545loretoper inambari_4770loretoper napo_6994loretoper napo_7347loretoper napo_103257loretoper napo_3232loretoper napo_ku1013loretoper napo_3014loretoper napo_3105loretoper napo_ku1014loretoper napo_3116loretoper napo_ansp2490moronaecu napo_3265loretoper napo_103258loretoper central_16121puntarenascr central_71960puntarenascr central_71936puntarenascr central_16128puntarenascr central_71931puntarenascr central_16077puntarenascr central_16107puntarenascr choco_28720panamapan choco_28460panamapan choco_2215darienpan choco_ansp2140esmeraldasecu guiana_39ml942bolivarven guiana_7380amazonasven imeri_jap673amazonasbra imeri_jap619amazonasbra guiana_35fm27bolivarven Lepidothrix_nattereri_EF633407 Lepidothrix_iris_EF633417 doi:10.1038/nature13687 Lepidothrix coronata Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Understory Ancestral Origin: East of Andes Time-calibrated gene tree with 1 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 inambari_cuj011amazonasbra inambari_11066ucayaliper inambari_9080pandobol inambari_9177pandobol choco_28731panamapan central_16103puntarenascr guiana_36ml947bolivarven guiana_37ml978bolivarven Napo Hullaga, Rondonia Napo Central America Chocó Guiana, Imeri Time-calibrated gene tree showing BGMYC species with 1 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 inambari_cuj011amazonasbra inambari_11066ucayaliper inambari_9080pandobol inambari_9177pandobol choco_28731panamapan central_16103puntarenascr guiana_36ml947bolivarven guiana_37ml978bolivarven Supplementary Figure 11 Range map, ENM, time-calibrated gene trees and delimited species for Lepidothrix coronata. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 44

rondonia_fpr036amazonasbra tapajos_35296parabra rondonia_fpr042amazonasbra rondonia_fmnhjh014ay612516matogrossobra rondonia_amana26parabra rondonia_fmnhjh124ay612514matogrossobra rondonia_fmnhjh260ay612515matogrossobra rondonia_fmnhjh052ay612513matogrossobra rondonia_fmnhjh376ay612511matogrossobra rondonia_fmnhjh395ay612512matogrossobra rondonia_op087rondoniabra rondonia_mar127aamazonasbra rondonia_op088rondoniabra rondonia_36744rondoniabra rondonia_36712rondoniabra rondonia_36713rondoniabra rondonia_op119rondoniabra rondonia_36711rondoniabra xingu_uhe438parabra xingu_ppbio173parabra xingu_ppbio309parabra xingu_uhe468parabra isla_maya053parabra xingu_ppbio215parabra xingu_ppbio289parabra isla_maya051parabra xingu_ppbio051parabra tapajos_br163203parabra tapajos_br163204parabra tapajos_br163205parabra tapajos_pime105parabra rondonia_flja031parabra inambari_lsumz9146pandobo inambari_lsumz10697ucayaliper inambari_4675loretoper inambari_10751ucayaliper inambari_ufac1451acrebra inambari_9308pandobol inambari_esec201acrebra inambari_10638ucayaliper inambari_8883pandobol inambari_ufac584acrebra inambari_9127pandobol inambari_esec232acrebra inambari_esec200acrebra rondonia_lsumz106784benibol inambari_lsumz11053ucayaliper inambari_lsumz1092lapazbo inambari_1139lapazbol inambari_rur047amazonasbra inambari_rur089amazonasbra inambari_rur048amazonasbra inambari_puc256amazonasbra inambari_puc182amazonasbra inambari_cuj183amazonasbra inambari_cuj127amazonasbra inambari_lsumz4734loretoper napo_ansp2518moronaecu napo_40824loretoper napo_lsumz42842loretoper napo_42759loretoper inambari_27847loretoper napo_ku924 napo_ansp1556moronaecu huallaga_5393sanmartinper napo_2821loretoper napo_2725loretoper napo_lsumz7077loretoper napo_lsumz2513loretoper napo_lsumz4459loretoper napo_2662loretoper napo_lsumz2640loretoper napo_ku844loretoper napo_ku886 napo_micr_mar_andesbt1257 foothills_micr_mar_andesbt791 foothills_27n0168ven andes_jm1039ven catatumbo_micr_mar_andesbt1408 catatumbo_micr_mar_andesbt1427 foothills_17n096ven magdalena_micr_mar_andesbt2219 choco_ansp2408esmeraldasecu choco_ansp2248esmeraldasecu choco_lsumz11839esmeraldasecu choco_lsumz2290darienpan central_lsumz28555colonpan choco_uwbm76917panamapan choco_uwbm76843panamapan central_usnm1333bocasdeltoropan central_usnm1406bocasdeltoropan choco_uwbm76950panamapan choco_uwbm76910panamapan choco_uwbm76891panamapan choco_uwbm77044panamapan central_lsumz28551colonpan central_usnmb1426chiriquipan central_usnmb1563chiriquipan central_16131puntarenascr Salpinctes_obsoletus_AY352537 Thryophilus_rufalbus_DQ415705 rondonia_fpr036amazonasbra tapajos_35296parabra rondonia_fpr042amazonasbra rondonia_fmnhjh014ay612516matogrossobra rondonia_amana26parabra rondonia_fmnhjh124ay612514matogrossobra rondonia_fmnhjh260ay612515matogrossobra rondonia_fmnhjh052ay612513matogrossobra rondonia_fmnhjh376ay612511matogrossobra rondonia_fmnhjh395ay612512matogrossobra rondonia_op087rondoniabra rondonia_mar127aamazonasbra rondonia_op088rondoniabra rondonia_36744rondoniabra rondonia_36712rondoniabra rondonia_36713rondoniabra rondonia_op119rondoniabra rondonia_36711rondoniabra xingu_uhe438parabra xingu_ppbio173parabra xingu_ppbio309parabra xingu_uhe468parabra isla_maya053parabra xingu_ppbio215parabra xingu_ppbio289parabra isla_maya051parabra xingu_ppbio051parabra tapajos_br163203parabra tapajos_br163204parabra tapajos_br163205parabra tapajos_pime105parabra rondonia_flja031parabra inambari_lsumz9146pandobo inambari_lsumz10697ucayaliper inambari_4675loretoper inambari_10751ucayaliper inambari_ufac1451acrebra inambari_9308pandobol inambari_esec201acrebra inambari_10638ucayaliper inambari_8883pandobol inambari_ufac584acrebra inambari_9127pandobol inambari_esec232acrebra inambari_esec200acrebra rondonia_lsumz106784benibol inambari_lsumz11053ucayaliper inambari_lsumz1092lapazbo inambari_1139lapazbol inambari_rur047amazonasbra inambari_rur089amazonasbra inambari_rur048amazonasbra inambari_puc256amazonasbra inambari_puc182amazonasbra inambari_cuj183amazonasbra inambari_cuj127amazonasbra inambari_lsumz4734loretoper napo_ansp2518moronaecu napo_40824loretoper napo_lsumz42842loretoper napo_42759loretoper inambari_27847loretoper napo_ku924 napo_ansp1556moronaecu huallaga_5393sanmartinper napo_2821loretoper napo_2725loretoper napo_lsumz7077loretoper napo_lsumz2513loretoper napo_lsumz4459loretoper napo_2662loretoper napo_lsumz2640loretoper napo_ku844loretoper napo_ku886 napo_micr_mar_andesbt1257 foothills_micr_mar_andesbt791 foothills_27n0168ven andes_jm1039ven catatumbo_micr_mar_andesbt1408 catatumbo_micr_mar_andesbt1427 foothills_17n096ven magdalena_micr_mar_andesbt2219 choco_ansp2408esmeraldasecu choco_ansp2248esmeraldasecu choco_lsumz11839esmeraldasecu choco_lsumz2290darienpan central_lsumz28555colonpan choco_uwbm76917panamapan choco_uwbm76843panamapan central_usnm1333bocasdeltoropan central_usnm1406bocasdeltoropan choco_uwbm76950panamapan choco_uwbm76910panamapan choco_uwbm76891panamapan choco_uwbm77044panamapan central_lsumz28551colonpan central_usnmb1426chiriquipan central_usnmb1563chiriquipan central_16131puntarenascr Salpinctes_obsoletus_AY352537 Thryophilus_rufalbus_DQ415705 doi:10.1038/nature13687 Microcerculus marginatus Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Understory Ancestral Origin: West of Andes Time-calibrated gene tree with Tapajos Rondonia Tapajos, Rondonia, Ilha Marajó, Xingu Rondonia Time-calibrated gene tree showing BGMYC species with Napo,, Huallaga, Andean Foothills Magdalena, Andean Foothills, Andes, Catatumbo Chocó Chocó, Central America Central America 1 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 1 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 Supplementary Figure 12 Range map, ENM, time-calibrated gene trees and delimited species for Microcerculus marginatus. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 45

rondonia_ded191_parabra rondonia_amana74_parabra tapajos_lsumz35374_parabra rondonia_ded224_parabra tapajos_ded310_matogrossobra rondonia_mpds640_amazonasbra tapajos_pime133_parabra rondonia_ded225_parabra tapajos_ded239_matogrossobra rondonia_fpr011_amazonasbra tapajos_ded304_matogrossobra tapajos_ded263_matogrossobra rondonia_ded195_parabra rondonia_14985_santacruzbol tapajos_tm037_parabra rondonia_lsumz15145_santacruzbol tapajos_ded252_matogrossobra rondonia_mpds639_amazonasbra tapajos_uhe563_parabra tapajos_ded247_matogrossobra rondonia_12823_santacruzbol rondonia_mpds642_amazonasbra tapajos_br163091_parabra rondonia_mpds641_amazonasbra rondonia_mar168_amazonasbra rondonia_lsumz18408_santacruzbol tapajos_ded312_matogrossobra rondonia_12865_santacruzbol rondonia_lsumz14916_santacruzbol tapajos_mt002_matogrossobra rondonia_lsumz12700_santacruzbol rondonia_fpr017_amazonasbra rondonia_fpr032_amazonasbra rondonia_flja075_parabra rondonia_jrt136_parabra tapajos_pime132_mattogrossobra rondonia_12280_santacruzbol tapajos_ded243_matogrossobra rondonia_12478_santacruzbol rondonia_14931_santacruzbol isla_marj078_parabra xingu_ppbio232_parabra isla_maya004_parabra isla_marj074_parabra isla_maya005_parabra xingu_bmp006_parabra belem_mlv163_parabra isla_marj151_parabra isla_maya015_parabra isla_marj075_parabra belem_mlv162_parabra tapajos_uhe481_parabra tapajos_uhe482_parabra rondonia_ded217_parabra tapajos_bmp003_parabra tapajos_fta021_parabra tapajos_bmp058_parabra napo_ku772_loretope napo_42373_loretoper huallaga_42243_loretoper huallaga_42342_loretoper napo_ku754_loretope napo_42833_loretoper huallaga_lsumz42520_loretoper huallaga_lsumz5468_sanmartinper napo_42972_loretoper napo_myrm.axil_iavh12779_vi chadaco napo_myrm.axil_iavh12790_vi chadaco napo_lsumz42872_loretoper napo_myrm.axill _IAvH11357_C O napo_myrm.axil_iavh8309_caquetac O napo_jap153_amazonasbra napo_jap117_amazonasbra imeri_amz116_amazonasbra imeri_amz275_amazonasbra napo_jap567_amazonasbra 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rondonia_14985_santacruzbol tapajos_tm037_parabra rondonia_lsumz15145_santacruzbol tapajos_ded252_matogrossobra rondonia_mpds639_amazonasbra tapajos_uhe563_parabra tapajos_ded247_matogrossobra rondonia_12823_santacruzbol rondonia_mpds642_amazonasbra tapajos_br163091_parabra rondonia_mpds641_amazonasbra rondonia_mar168_amazonasbra rondonia_lsumz18408_santacruzbol tapajos_ded312_matogrossobra rondonia_12865_santacruzbol rondonia_lsumz14916_santacruzbol tapajos_mt002_matogrossobra rondonia_lsumz12700_santacruzbol rondonia_fpr017_amazonasbra rondonia_fpr032_amazonasbra rondonia_flja075_parabra rondonia_jrt136_parabra tapajos_pime132_mattogrossobra rondonia_12280_santacruzbol tapajos_ded243_matogrossobra rondonia_12478_santacruzbol rondonia_14931_santacruzbol isla_marj078_parabra xingu_ppbio232_parabra isla_maya004_parabra isla_marj074_parabra isla_maya005_parabra xingu_bmp006_parabra belem_mlv163_parabra isla_marj151_parabra isla_maya015_parabra isla_marj075_parabra belem_mlv162_parabra tapajos_uhe481_parabra tapajos_uhe482_parabra rondonia_ded217_parabra tapajos_bmp003_parabra tapajos_fta021_parabra tapajos_bmp058_parabra napo_ku772_loretope napo_42373_loretoper huallaga_42243_loretoper huallaga_42342_loretoper napo_ku754_loretope napo_42833_loretoper huallaga_lsumz42520_loretoper huallaga_lsumz5468_sanmartinper napo_42972_loretoper napo_myrm.axil_iavh12779_vi chadaco napo_myrm.axil_iavh12790_vi chadaco napo_lsumz42872_loretoper napo_myrm.axill _IAvH11357_C O napo_myrm.axil_iavh8309_caquetac O napo_jap153_amazonasbra napo_jap117_amazonasbra imeri_amz116_amazonasbra imeri_amz275_amazonasbra napo_jap567_amazonasbra napo_jap113_amazonasbra imeri_amz094_amazonasbra imeri_amz117_amazonasbra imeri_amz022_amazonasbra napo_lsumz4319_loretoper napo_jap133_amazonasbra napo_jap116_amazonasbra napo_lsumz7051_loretoper napo_lsumz2512_loretoper inambari_lsumz27895_loretoper napo_myrm.axil_iavh14595_amazonasco napo_lsumz2644_loretoper choco_gu215257_darienpan choco_lsumz46580_darienpan choco_mbmgms1779_panamapan choco_lsumz46545_darienpan choco_gu215258_darienpan choco_lsumz2298_darienpan choco_mbmgms1837_panamapan choco_ansp2271_esmeraldasecu choco_ansp2115_esmeraldasecu choco_uwbm76973_panamapan choco_mbmgms982_panamapan choco_mbmgms965_panamapan central_gu215256_coclepan choco_mbmjk0695_panamapan central_usnm1122_bocasdeltoropan central_usnm1104_bocasdeltoropan central_usnm1166_bocasdeltoropan central_usnm_b1192_bocasdeltoropan central_usnm1099_bocasdeltoropan choco_lsumz26541_colonpan central_usnm_b1840_bocasdeltoropan central_usnm356_bocasdeltoropan central_usnm_b1828_bocasdeltoropan central_usnm_b1824_bocasdeltoropan guiana_usnm_b5233_cuyuni_mazar uniguy guiana_usnm_b4419_berbiceguy guiana_ku1188_iwokramaguy guiana_usnm_b11436_gunnslandingguy guiana_usnm_b12796_parabarasavannahguy guiana_usnm_b14368_makwai masavannahguy guiana_usnm_b9645_barima_waini GUY guiana_dpn33_parabra guiana_cn608_parabra guiana_cn1202_parabra guiana_usnm_b11683_upperessequiboguy guiana_usnm_b22061_upperessequiboguy guiana_usnm_b11739_upperessequiboguy guiana_usnm_b14622_barimari ver GUY guiana_cn1231_parabra guiana_usnm_b14316_makuripaisavannahguy guiana_usnm_b9137_barima_waini GUY guiana_lsumz55297_sur guiana_usnm_b9121_barima_waini GUY guiana_usnm_b14181_kamariafallsguy guiana_lsumz55309_sur guiana_usnm_b11435_gunnslandingguy guiana_usnm_b9114_barima_waini GUY guiana_55209_sipaliwinisur guiana_55324_sipaliwinisur guiana_usnm_b14670_barimari ver GUY guiana_usnm_b14321_makwai masavannahguy guiana_usnm_b10729_acarimountainsguy guiana_ku1205_iwokramaguy guiana_usnm_b4415_berbiceguy orinocodelta_71ic72_deltaamacuroven guiana_cn599_parabra guiana_usnm_b11714_upperessequiboguy orinocodelta_70ic71_deltaamacuroven guiana_55328_sipaliwinisur guiana_usnm_b11009_gunnslandingguy guiana_usnm_b22073_upperessequiboguy guiana_usnm9224_barimawainiguy guiana_usnm_b9244_barima_waini GUY guiana_usnm_b9622_northwestguy guiana_usnm10378_sipuriverguy guiana_usnm_b5234_essequiboguy guiana_usnm_b11571_gunnslandingguy guiana_usnm_b9607_barima_waini GUY guiana_dpn25_parabra guiana_cn1051_parabra guiana_cn1017_parabra guiana_cn1154_parabra guiana_cn1016_parabra guiana_cn497_parabra guiana_usnm_b11480_gunnslandingguy guiana_usnm12766_parabarasavannahguy guiana_cn350_parabra guiana_mpds0104_roraimabra guiana_usnm10419_sipuriverguy trinidad_gu215260_simlatri guiana_cn1201_parabra guiana_usnm_b11557_gunnslandingguy imeri_amz463_amazonasbra guiana_usnm_b9628_northwestguy guiana_cn114_parabra guiana_lsumz45832_sur trinidad_lsumz35969_tri guiana_20322_amazonasbra guiana_usnm_b11471_gunnslandingguy guiana_mpds0138_roraimabra guiana_usnm_b22287_upperessequiboguy guiana_mpds0146_roraimabra guiana_usnm_b11684_upperessequiboguy guiana_usnm_b11519_gunnslandingguy guiana_usnm_b11558_gunnslandingguy guiana_usnm_b10420_sipurivergu Y guiana_usnm_b11466_gunnslandingguy guiana_mpds0103_roraimabra guiana_mpds0028_roraimabra guiana_cn084_parabra atlantic_ef639972_pernambucobra inambari_ufac1928_acrebra inambari_lsumz11239_ucayaliper inambari_lsumz6808_benibol inambari_esec244_acrebra inambari_esec222_acrebra inambari_ufac933_acrebra inambari_lsumz9126_pandobol inambari_ufac116_acrebra inambari_puc184_amazonasbra inambari_puc205_amazonasbra inambari_ufac494_acrebra inambari_9436_pandobol inambari_11163_ucayali PER inambari_ufac1498_acrebra inambari_pnsd022_acrebra inambari_ufac1062_acrebra inambari_ufac1955_acrebra inambari_gu215259_madredediosper inambari_ufac384_acrebra inambari_ufac057_acrebra inambari_ufac549_acrebra inambari_lsumz1031_lapazbol inambari_esec279_acrebra inambari_puc212_amazonasbra inambari_ufac394_acrebra inambari_ku629_madredediosper inambari_lsumz8902_pandobol inambari_lsumz27479_loretoper inambari_11241_ucayali PER inambari_11055_ucayali PER inambari_lsumz11101_ucayaliper inambari_pnsd178_acrebra inambari_ufac0987_acrebra inambari_10882_ucayali PER inambari_lsumz10507_ucayaliper huallaga_46043_sanmartinper huallaga_46020_sanmartinper huallaga_46179_sanmartinper huallaga_46050_sanmartinper napo_lsumz46040_sanmartinper huallaga_lsumz46192_sanmartinper HM637168_Myrmotherula_longipennis EF639946_Formicivora_rufa EF030336_Thamnophilus_ruficapillus doi:10.1038/nature13687 Myrmotherula axillaris Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Understory Ancestral Origin: East of Andes Time-calibrated gene tree with Tapajos Rondonia Xingu Belem Ilha Marajó Napo, Hullaga, Chocó, Central America Guiana Atlantic Huallaga Time-calibrated gene tree showing BGMYC species with outgroup 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 Supplementary Figure 13 Range map, ENM, time-calibrated gene trees and delimited species for Myrmotherula axillaris. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 46

Piaya cayana Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Canopy Ancestral Origin: West of Andes Time-calibrated gene tree with 1 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 guiana_usnm18938kopinangriverguy rondonia_lsumz37524santacrbo rondonia_lsumz36770santacrbo napo_jap506amazonasbra guiana_usnm11565uppessequiboguy rondonia_14956santacruzbol rondonia_lsumz12469santacrbo guiana_usnm13692lindenguy guiana_usnm13170lindenguy rondonia_uwbm77353bol rondonia_lsumz35624santacrbo rondonia_mpds654amazonasbra rondonia_lsumz18359santacrbo rondonia_14529santacruzbol guiana_usnm13940kusadmountguy rondonia_15093santacruzbol atlantic_uwbm54434corrientesarg rondonia_lsumz12390santacrbo guiana_usnm9686barimawainiguy guiana_41jp287bolivarven inambari_ku18609cuscoper inambari_puc148amazonasbra inambari_ufac1242acrebra inambari_935lapazbol inambari_ufac567acrebra inambari_ufac138acrebra inambari_8843pandobol atlantic_uwbm70751corrientesarg atlantic_usnm5974misionesarg inambari_lsumz4718loretope central_71978puntarenascr central_lsumz16044herediacr central_uwbm69422lasplazulasnic central_uwbm68992casitanic central_uwbm69015chinandeganic central_71998limoncr central_16043herediacr central_uwbm69198lasplazulasnic central_uwbm69257casitanic central_ku2082campechemex central_ku4951morazansal central_ku2204campechemex central_usnm327bocasdeltoropan central_lsumz28579colonpa central_usnm1963bocasdeltoropan choco_lsumz28413panamapa choco_lsumz28412panamapa choco_lsumz12177pichec Piaya_melanogaster_AF168111 Piaya_minuta_LSUMZ15136 Coccyzus_erythropthalmus_AF082048 Napo Guiana Atlantic Rondonia Atlantic Central America Chocó Chocó Time-calibrated gene tree showing BGMYC species with outgroup 1 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 guiana_usnm18938kopinangriverguy rondonia_lsumz37524santacrbo rondonia_lsumz36770santacrbo napo_jap506amazonasbra guiana_usnm11565upperessequiboguy rondonia_14956santacruzbol rondonia_lsumz12469santacrbo guiana_usnm13692lindenguy guiana_usnm13170lindenguy rondonia_uwbm77353bol rondonia_lsumz35624santacrbo rondonia_mpds654amazonasbra rondonia_lsumz18359santacrbo rondonia_14529santacruzbol guiana_usnm13940kusadmountguy rondonia_15093santacruzbol atlantic_uwbm54434corrientesarg rondonia_lsumz12390santacrbo guiana_usnm9686barimawainiguy guiana_41jp287bolivarven inambari_ku18609cuscoper inambari_puc148amazonasbra inambari_ufac1242acrebra inambari_935lapazbol inambari_ufac567acrebra inambari_ufac138acrebra inambari_8843pandobol atlantic_uwbm70751corrientesarg atlantic_usnm5974misionesarg inambari_lsumz4718loretope central_71978puntarenascr central_lsumz16044herediacr central_uwbm69422lasplazulasnic central_uwbm68992casitanic central_uwbm69015chinandeganic central_71998limoncr central_16043herediacr central_uwbm69198lasplazulasnic central_uwbm69257casitanic central_ku2082campechemex central_ku4951morazansal central_ku2204campechemex central_usnm327bocasdeltoropan central_lsumz28579colonpa central_usnm1963bocasdeltoropan choco_lsumz28413panamapa choco_lsumz28412panamapa choco_lsumz12177pichec Piaya_melanogaster_AF168111 Supplementary Figure 14 Range map, ENM, time-calibrated gene trees and delimited species for Piaya cayana. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 47

Pteroglossus Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Canopy Ancestral Origin: East of Andes Time-calibrated gene tree with choco_ay661384_psa2403 choco_hq424063_b11783 choco_hq424066_b100021 choco_ay661378_per3582 central_ay661385_pto16076 central_hq424058_b16075 AY560621_Pteroglossus_torquatus central_ay661386_pto3778 central_hq424064_b28584 inambari_ay661382_pma726 inamabri_hq424050_b8991 inamabri_hq424049_b40614 inambari_ay661379_pfl4478 AY940810_Pteroglossus_flavirostris imeri_hq424047_fmnh456647 imeri_hq424048_fmnh456648 imeri_hq424046_fmnh456643 imeri_hq424045_fmnh456642 tapajos_hq424052_b35533 rondonia_ay661376_pbt21 xingu_hq424051_fmnh456656 inambari_ay661375_pbe4950 tapajos_hq424053_b35532 belem_hq424043_b35547 xingu_hq424042_fmnh456655 guiana_hq424044_b09755 guiana_ay661374_par7570 choco_ay661383_ppl5734 napo_hq424062_b7112 AF123520_Pteroglossus_castanostis tapajos_hq424054_b35266 rondonia_ay661377_pct18 rondonia_hq424055_b37611 inamabri_hq424056_b27624 imeri_hq424057_fmnh456651 AY279304_Pteroglossus_inscriptus inamabri_hq424059_b39983 napo_hq424060_fmnh456652 rondonia_ay661381_pin39 inambari_ay959827_b8819 napo_ay661380_pin1601 tapajos_hq424061_b35444 AF123519_Pteroglossus_inscriptis guiana_hq424065_b20231 guiana_ay661387_pvi8451 AY560618_Bailonius_bailloni AY560620_Pteroglossus_bitorquatus AF100551_Pteroglossus_beauharnaesii Chocó Central America Central America Imeri Napo Tapajos, Xingu, Rondonia, Tapajos Xingu, Belem Guiana Napo, Chocó Imeri Guiana Rondonia Napo, Tapajos,, Rondonia Guiana Atlantic Southern Amazon Southwest Amazon Time-calibrated gene tree showing BGMYC species with choco_ay661384_psa2403 choco_hq424063_b11783 choco_hq424066_b100021 choco_ay661378_per3582 central_ay661385_pto16076 central_hq424058_b16075 AY560621_Pteroglossus_torquatus central_ay661386_pto3778 central_hq424064_b28584 inambari_ay661382_pma726 inamabri_hq424050_b8991 inamabri_hq424049_b40614 inambari_ay661379_pfl4478 AY940810_Pteroglossus_flavirostris imeri_hq424047_fmnh456647 imeri_hq424048_fmnh456648 imeri_hq424046_fmnh456643 imeri_hq424045_fmnh456642 tapajos_hq424052_b35533 rondonia_ay661376_pbt21 xingu_hq424051_fmnh456656 inambari_ay661375_pbe4950 tapajos_hq424053_b35532 belem_hq424043_b35547 xingu_hq424042_fmnh456655 guiana_hq424044_b09755 guiana_ay661374_par7570 choco_ay661383_ppl5734 napo_hq424062_b7112 AF123520_Pteroglossus_castanostis tapajos_hq424054_b35266 rondonia_ay661377_pct18 rondonia_hq424055_b37611 inamabri_hq424056_b27624 imeri_hq424057_fmnh456651 AY279304_Pteroglossus_inscriptus inamabri_hq424059_b39983 napo_hq424060_fmnh456652 rondonia_ay661381_pin39 inambari_ay959827_b8819 napo_ay661380_pin1601 tapajos_hq424061_b35444 AF123519_Pteroglossus_inscriptis guiana_hq424065_b20231 guiana_ay661387_pvi8451 AY560618_Bailonius_bailloni AY560620_Pteroglossus_bitorquatus AF100551_Pteroglossus_beauharnaesii 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 Supplementary Figure 15 Range map, ENM, time-calibrated gene trees and delimited species for Pteroglossus. Ingroup includes all biological species in Pteroglossus: P. azara, viridis, inscriptus, P. bitorquatus, P. aracari, P. castanotis, P. pluricinctus, P. torquatus, P. frantzii, P. beauharnaesii, and P. bailloni. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 48

Pyrilia Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Canopy Ancestral Origin: West of Andes Time-calibrated gene tree with outgroup tapajos_ay669412_pv_amnh429164 xingu_ay669410_pv_nmnhb6905 tapajos_ay669411_pv_mpega4955 xingu_ay669409_pv_nmnhb6888 tapajos_ay669413_pv_amnh288269 tapajos_ay669405_pa_lgema2944 tapajos_ay669408_pa_lgema3668 Tapajos Xingu Time-calibrated gene tree showing BGMYC species with outgroup tapajos_ay669412_pv_amnh429164 xingu_ay669410_pv_nmnhb6905 tapajos_ay669411_pv_mpega4955 xingu_ay669409_pv_nmnhb6888 tapajos_ay669413_pv_amnh288269 tapajos_ay669405_pa_lgema2944 tapajos_ay669408_pa_lgema3668 tapajos_ay669406_pa_lgema2943 tapajos_ay669406_pa_lgema2943 tapajos_ay669407_pa_lgema2949 tapajos_ay669407_pa_lgema2949 guiana_ay669414_pc_ansp7638 guiana_ay669414_pc_ansp7638 guiana_ay669416_pc_ansp7587 guiana_ay669416_pc_ansp7587 guiana_ay669415_pc_nmbhb09175 guiana_ay669417_pc_fmnh389173 Guiana guiana_ay669415_pc_nmbhb09175 guiana_ay669417_pc_fmnh389173 guiana_ay669418_pc_nmnhb11726 guiana_ay669418_pc_nmnhb11726 guiana_ay669419_pc_nmnhb10779 guiana_ay669419_pc_nmnhb10779 rondonia_ay669424_pb_fmnh389693 rondonia_ay669424_pb_fmnh389693 B A rondonia_ay669422_pb_fmnh389691 rondonia_ay669421_pb_fmnh38960 inambari_ay669423_pb_b10823 inambari_ay669420_pb_b9596 choco_ay669425_pp_amnh475573 choco_ay669426_pp_amnh133049 Rondonia Chocó rondonia_ay669422_pb_fmnh389691 rondonia_ay669421_pb_fmnh38960 inambari_ay669423_pb_b10823 inambari_ay669420_pb_b9596 choco_ay669425_pp_amnh475573 choco_ay669426_pp_amnh133049 choco_ay669430_pco_b2185 choco_ay669431_pco_b2201 choco_ay669429_pco_b26852 central_ay669433_ph_ansp5769 central_ay669432_ph_ansp5770 Chocó Central America choco_ay669430_pco_b2185 choco_ay669431_pco_b2201 choco_ay669429_pco_b26852 central_ay669433_ph_ansp5769 central_ay669432_ph_ansp5770 choco_ay669428_ppu_b1449 choco_ay669427_ppu_b1448 Chocó choco_ay669428_ppu_b1449 choco_ay669427_ppu_b1448 AY669443_Hapalopsitta_amazonina AY669443_Hapalopsitta_amazonina 11.0 1 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 11.0 1 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 Supplementary Figure 16 Range map, ENM, time-calibrated gene trees and delimited species for Pyrilia. Ingroup includes all biological species in Pyrilia: P. haematotis, P. pulchra, P. pyrilia, P. barrabandi, P. caica, P. aurantiocephala, and P. vulturina. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). Nodes labeled A and B refer to multiple cross-andes divergence events used in the msbayes analysis. WWW.NATURE.COM/NATURE 49

rondonia_ay751593_ps_b12781 tapajos_ay751614_pa_b06897 rondonia_ay751613_ps_lgema2934 tapajos_ay751615_pa_b07027 rondonia_ay751607_ps_fmnh389694 tapajos_ay751616_pa_b07033 rondonia_ay751594_ps_b12782 tapajos_ay751610_ps_lgema2930 tapajos_ay751611_ps_lgema2931 tapajos_ay751612_ps_lgema2933 rondonia_ay751608_ps_fmnh389695 rondonia_ay751609_ps_fmnh389696 rondonia_ay751606_ps_lgema4976 natlantic_ay751630_pg_lgema3915 natlantic_ay751631_pg_lgema3916 natlantic_ay751629_pg_lgema3914 atlantic_ay751633_pl_lgema3922 natlantic_ay751628_pg_lgema1070 natlantic_ay751627_pg_lgema1069 atlantic_ay751634_pl_lgema3923 atlantic_ay751632_pl_legma3921 atlantic_ay751618_ppf_lgema3913 atlantic_ay751617_ppf_lgema3912 atlantic_ay751619_ppf_lgema4041 atlantic_ay751621_ppf_lgema4045 atlantic_ay751620_ppf_lgema4044 central_ay751598_pei_ansp5758 central_ay751599_pei_ansp5759 inambari_ay751588_pr_b10847 inambari_ay751586_pr_b10802 inambari_ay751589_pr_b10849 inambari_ay751585_pr_fmnh397723 inambari_ay751592_pr_b11282 inambari_ay751587_pr_b10804 inambari_ay751590_pr_b11085 inambari_ay751597_pr_b27648 inambari_ay751591_pr_b11281 napo_ay751583_ppe_usp5085 inambari_ay751584_pr_b27652 napo_ay751582_ppe_usp5084 inambari_ay751595_pr_b27438 inambari_ay751596_pr_b27441 guiana_ay751605_ppi_b10944 guiana_ay751604_ppi_b10941 guiana_ay751600_ppi_fmnh395728 guiana_ay751603_ppi_b09631 guiana_ay669400_ppi_b09287 guiana_ay751601_ppi_ku1196 guiana_ay751602_ppi_ku1198 ven_ay751623_pem_lgema3514 ven_ay751626_pem_lgema4248 ven_ay751625_pem_lgema4247 ven_ay751622_pem_lgema3513 ven_ay751624_pem_lgema3515 natlantic_ay751658_pcr_lgema2230 natlantic_ay751657_pcr_lgema2228 guiana_ay751650_pme_amnhsc889 guiana_ay751648_pme_amnhsc759 napo_ay751639_pa_ansp4439 guiana_ay751649_pme_amnhsc888 napo_ay751640_pa_ansp4490 choco_fj899163_pmel_b11845 napo_fj899162_pmel_b6946 choco_fj899161_pmel_b29972 napo_ay751651_pme_ansp5111 napo_ay751652_pme_ansp5112 tumbes_ay751635_po_b7803 tumbes_ay751636_po_b7818 central_ay751654_ph_b05447 central_ay751653_ph_b05272 merida_ay751637_prh_lgema3871 merida_ay751638_prh_lgema3872 inambari_ay751655_pru_ku1525 rondonia_ay751656_pru_ku653 tapajos_ay751645_pl_b07028 tapajos_ay751644_pl_b07007 tapajos_ay751646_pp_lgema848 tapajos_ay751647_pp_lgema860 rondonia_ay751641_pmo_amnhcjv140 rondonia_ay751642_pmo_ku1526 atlantic_ay751643_pf_b25884 DQ143297_Rhynchopsi_pachyrhyncha rondonia_ay751593_ps_b12781 tapajos_ay751614_pa_b06897 rondonia_ay751613_ps_lgema2934 tapajos_ay751615_pa_b07027 rondonia_ay751607_ps_fmnh389694 tapajos_ay751616_pa_b07033 rondonia_ay751594_ps_b12782 tapajos_ay751610_ps_lgema2930 tapajos_ay751611_ps_lgema2931 tapajos_ay751612_ps_lgema2933 rondonia_ay751608_ps_fmnh389695 rondonia_ay751609_ps_fmnh389696 rondonia_ay751606_ps_lgema4976 natlantic_ay751630_pg_lgema3915 natlantic_ay751631_pg_lgema3916 natlantic_ay751629_pg_lgema3914 atlantic_ay751633_pl_lgema3922 natlantic_ay751628_pg_lgema1070 natlantic_ay751627_pg_lgema1069 atlantic_ay751634_pl_lgema3923 atlantic_ay751632_pl_legma3921 atlantic_ay751618_ppf_lgema3913 atlantic_ay751617_ppf_lgema3912 atlantic_ay751619_ppf_lgema4041 atlantic_ay751621_ppf_lgema4045 atlantic_ay751620_ppf_lgema4044 central_ay751598_pei_ansp5758 central_ay751599_pei_ansp5759 inambari_ay751588_pr_b10847 inambari_ay751586_pr_b10802 inambari_ay751589_pr_b10849 inambari_ay751585_pr_fmnh397723 inambari_ay751592_pr_b11282 inambari_ay751587_pr_b10804 inambari_ay751590_pr_b11085 inambari_ay751597_pr_b27648 inambari_ay751591_pr_b11281 napo_ay751583_ppe_usp5085 inambari_ay751584_pr_b27652 napo_ay751582_ppe_usp5084 inambari_ay751595_pr_b27438 inambari_ay751596_pr_b27441 guiana_ay751605_ppi_b10944 guiana_ay751604_ppi_b10941 guiana_ay751600_ppi_fmnh395728 guiana_ay751603_ppi_b09631 guiana_ay669400_ppi_b09287 guiana_ay751601_ppi_ku1196 guiana_ay751602_ppi_ku1198 ven_ay751623_pem_lgema3514 ven_ay751626_pem_lgema4248 ven_ay751625_pem_lgema4247 ven_ay751622_pem_lgema3513 ven_ay751624_pem_lgema3515 natlantic_ay751658_pcr_lgema2230 natlantic_ay751657_pcr_lgema2228 guiana_ay751650_pme_amnhsc889 guiana_ay751648_pme_amnhsc759 napo_ay751639_pa_ansp4439 guiana_ay751649_pme_amnhsc888 napo_ay751640_pa_ansp4490 choco_fj899163_pmel_b11845 napo_fj899162_pmel_b6946 choco_fj899161_pmel_b29972 napo_ay751651_pme_ansp5111 napo_ay751652_pme_ansp5112 tumbes_ay751635_po_b7803 tumbes_ay751636_po_b7818 central_ay751654_ph_b05447 central_ay751653_ph_b05272 merida_ay751637_prh_lgema3871 merida_ay751638_prh_lgema3872 inambari_ay751655_pru_ku1525 rondonia_ay751656_pru_ku653 tapajos_ay751645_pl_b07028 tapajos_ay751644_pl_b07007 tapajos_ay751646_pp_lgema848 tapajos_ay751647_pp_lgema860 rondonia_ay751641_pmo_amnhcjv140 rondonia_ay751642_pmo_ku1526 atlantic_ay751643_pf_b25884 DQ143297_Rhynchopsi_pachyrhyncha doi:10.1038/nature13687 Pyrrhura Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Canopy Ancestral Origin: East of Andes Time-calibrated gene tree with outgroup Tapajos Guiana Rondonia North Atlantic, Atlantic Atlantic Central America Napo Guiana Venezuela North Atlantic Guiana, Napo Napo, Chocó Tumbes Central America Merida Rondonia, Tapajos Tapajos Rondonia Atlantic Time-calibrated gene tree showing BGMYC species with outgroup 17.5 15.0 12.5 1 7.5 5.0 2.5 17.5 15.0 12.5 1 7.5 5.0 2.5 Supplementary Figure 17 Range map, ENM, time-calibrated gene trees and delimited species for Pyrrhura. Ingroup includes all biological species in Pyrrhura: P. roseifrons, P. eisenmanni, P. picta, P. amazonum, P. pfrimeri, P. emma, P. griseipectus, P. leucotis, P. orcesi, P. rhodocephala, P. albipectus, P. molinae, P. frontalis, P. lepida, P. perlata, P. melanura, P. rupicola, and P. cruentata. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). Nodes labeled A and B refer to multiple cross-andes divergence events used in the msbayes analysis. WWW.NATURE.COM/NATURE 50

Querula purpurata Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Canopy Ancestral Origin: West of Andes Time-calibrated gene tree with inambari_ufac1813acrebra inambari_ufac189acrebra inambari_103546loretoper inambari_40407loretoper napo_jap512amazonasbra napo_jap595amazonasbra inambari_ufac1728acrebra guiana_usnm13637lindenguy napo_2823loretoper napo_2824loretoper guiana_usnm4486berbiceguy guiana_usnm4490berbiceguy guiana_cn476parabra guiana_usnm13159lindenguy guiana_usnm13161lindenguy guiana_usnm9436barimaguy guiana_usnm4491berbiceguy guiana_usnm13160lindenguy belem_35548parabra guiana_usnm9426nwdistguy inambari_42632loretoper inambari_5511sanmartinper guiana_usnm13162lindenguy napo_4375loretoper inambari_27975loretoper inambari_27363loretoper inambari_42317loretoper inambari_42318loretoper inambari_42391loretoper napo_jap338amazonasbra inambari_ku1419madredediosper napo_jap429amazonasbra inambari_9648pandobol napo_jap337amazonasbra napo_2785loretoper inambari_9495pandobol napo_jap250amazonasbra inambari_ufac188acrebra napo_2542loretoper central_usnm326bocasdeltoropan central_usnm492bocasdeltoropan central_usnm1955bocasdeltoropan central_usnm351bocasdeltoropan central_28529colonpan choco_ansp4628esmeraldasecu central_28604colonpan choco_51410darienpan central_28536colonpan choco_2217darienpan Perissocephalus_tricolor_DQ470506 Cephalopterus_ornatus_DQ470494 Pyroderus_scutatus Tapajos Guiana Rondonia Belem Central America Chocó Time-calibrated gene tree showing BGMYC species with inambari_ufac1813acrebra inambari_ufac189acrebra inambari_103546loretoper inambari_40407loretoper napo_jap512amazonasbra napo_jap595amazonasbra inambari_ufac1728acrebra guiana_usnm13637lindenguy napo_2823loretoper napo_2824loretoper guiana_usnm4486berbiceguy guiana_usnm4490berbiceguy guiana_cn476parabra guiana_usnm13159lindenguy guiana_usnm13161lindenguy guiana_usnm9436barimaguy guiana_usnm4491berbiceguy guiana_usnm13160lindenguy belem_35548parabra guiana_usnm9426nwdistguy inambari_42632loretoper inambari_5511sanmartinper guiana_usnm13162lindenguy napo_4375loretoper inambari_27975loretoper inambari_27363loretoper inambari_42317loretoper inambari_42318loretoper inambari_42391loretoper napo_jap338amazonasbra inambari_ku1419madredediosper napo_jap429amazonasbra inambari_9648pandobol napo_jap337amazonasbra napo_2785loretoper inambari_9495pandobol napo_jap250amazonasbra inambari_ufac188acrebra napo_2542loretoper central_usnm326bocasdeltoropan central_usnm492bocasdeltoropan central_usnm1955bocasdeltoropan central_usnm351bocasdeltoropan central_28529colonpan choco_ansp4628esmeraldasecu central_28604colonpan choco_51410darienpan central_28536colonpan choco_2217darienpan Perissocephalus_tricolor_DQ470506 Cephalopterus_ornatus_DQ470494 Pyroderus_scutatus 6.0 5.0 4.0 3.0 2.0 1.0 6.0 5.0 4.0 3.0 2.0 1.0 Supplementary Figure 18 Range map, ENM, time-calibrated gene trees and delimited species for Querula purpurata. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 51

Ramphastos Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Canopy Ancestral Origin: East of Andes Time-calibrated gene tree with napo_ay959841_ansp4465 choco_ay959839_b11712 choco_ay959840_b2309 inambari_gq457998_b35666 inambari_ay959849_b9392 guiana_ay959850_b1356 inambari_ay959847_b27691 Chocó, Napo, Belem, Guiana Time-calibrated gene tree showing BGMYC species with napo_ay959841_ansp4465 choco_ay959839_b11712 choco_ay959840_b2309 inambari_gq457998_b35666 inambari_ay959849_b9392 guiana_ay959850_b1356 inambari_ay959847_b27691 belem_ay959848_b35550 belem_ay959848_b35550 inambari_gq457997_b35665 inambari_gq457997_b35665 rondonia_gq457988_b38206 atlantic_gq457987_r265 atlantic_gq457986_r264 Atlantic, Rondonia rondonia_gq457988_b38206 atlantic_gq457987_r265 atlantic_gq457986_r264 atlantic_ay959842_b282 atlantic_gq457985_r210 central_ay959846_b28577 central_jf424518_ku2060c central_ay959845_b2007 choco_ay959843_b12175 choco_ay959844_b34977 atlantic_ay959837_b35555 atlantic_gq457989_r213 magdalena_gq457992_fmnh352027 magdalena_gq457990_fmnh190822 Atlantic Central America Chocó Atlantic Magdalena atlantic_ay959842_b282 atlantic_gq457985_r210 central_ay959846_b28577 central_jf424518_ku2060c central_ay959845_b2007 choco_ay959843_b12175 choco_ay959844_b34977 atlantic_ay959837_b35555 atlantic_gq457989_r213 magdalena_gq457992_fmnh352027 magdalena_gq457990_fmnh190822 magdalena_gq457991_fmnh190823 magdalena_gq457991_fmnh190823 guiana_ay959835_b1237 tapajos_ay959836_b35638 tapajos_gq457993_b35646 napo_ay959833_b7192 napo_ay959832_b2860 inambari_ay959834_b924 inambari_gq457995_b35721 rondonia_gq457994_b35652 rondonia_ay959831_b35586 belem_gq457996_b35668 Tapajos Guiana Rondonia Belem guiana_ay959835_b1237 tapajos_ay959836_b35638 tapajos_gq457993_b35646 napo_ay959833_b7192 napo_ay959832_b2860 inambari_ay959834_b924 inambari_gq457995_b35721 rondonia_gq457994_b35652 rondonia_ay959831_b35586 belem_gq457996_b35668 belem_ay959838_b35667 belem_ay959838_b35667 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 Supplementary Figure 19 Range map, ENM, time-calibrated gene trees and delimited species for Ramphastos. Ingroup includes all biological species in Ramphastos: R. sulfuratus, R. brevis, R. vitellinus, R. dicolorus, R. ambiguus, R. tucanus, and R. toco. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 52

rondonia_18133santacruzbol rondonia_14881santacruzbol rondonia_36675rondoniabra rondonia_12631santacruzbol rondonia_12807santacruzbol rondonia_18387santacruzbol rondonia_15370santacruzbol rondonia_13931santacruzbol rondonia_13832santacruzbol rondonia_12367santacruzbol rondonia_14551santacruzbol rondonia_lsumns13831ef458563santacruzbol rondonia_12305santacruzbol rondonia_13899santacruzbol rondonia_36739rondoniabra rondonia_13884santacruzbol rondonia_lsumns36666ef458564rondoniabra rondonia_13007santacruzbol rondonia_15090santacruzbol rondonia_15253santacruzbol rondonia_14455santacruzbol rondonia_mtma006matogrossobra rondonia_14919santacruzbol rondonia_12311santacruzbol rondonia_14538santacruzbol rondonia_12299santacruzbol rondonia_18107santacruzbol rondonia_14779santacruzbol rondonia_12447santacruzbol rondonia_14888santacruzbol rondonia_14469santacruzbol rondonia_12670santacruzbol rondonia_36730rondoniabra rondonia_15243santacruzbol rondonia_15247santacruzbol rondonia_15246santacruzbol xingu_mpds709amazonasbr A rondonia_mpds649amazonasbra rondonia_fpr012amazonasbr A guiana_pime076parabra guiana_fpr109bra rondonia_fpr067amazonasbr A xingu_fmnh391539ef458559parabr A inambari_fmnh322499ef458560cuzcoper xingu_maya040parabra rondonia_mop094parabra xingu_fmnh391540ef458561parabr A tapajos_br163006parabra rondonia_br163072parabra xingu_mt009matogrossobra tapajos_br163013parabra xingu_peg006parabra napo_4163loretoper inambari_4676loretoper napo_4175loretoper napo_7119loretoper imeri_amz161amazonasbra napo_4321loretoper guiana_lsumzb7550ef458553amazonasven napo_7087loretoper napo_4179loretoper napo_lsumzb2552ef458554loretoper napo_schif.turd_iavh11195_c O napo_ansp5792ef458555sucumbiosecu imeri_jap816amazonasbra napo_jap770amazonasbra imeri_amz514amazonasbra napo_schif.turd_iavh11033_c O huallaga_42453loretoper napo_42928loretoper huallaga_42548loretoper inambari_1038lapazbol inambari_1015lapazbol inambari_22701lapazbol inambari_1087lapazbol inambari_904lapazbol inambari_22835lapazbol inambari_lsumzb1984ef458557pascoper inambari_ku18445cuscoper inambari_lsumzb9545ef458558pandobol inambari_ku18518cuscoper inambari_1173lapazbol inambari_22740lapazbol inambari_4680loretoper inambari_4732loretoper guiana_cuj181amazonasbra inambari_cuj187amazonasbra inambari_9588pandobol inambari_4703loretoper choco_lsumzb1358darienpan choco_9884darienpan choco_lsumns2261ef458566darienpa choco_29571pan choco_lsumns1352ef458565darienpan choco_52925darienpan choco_mbmjmd208panamapan choco_28393panamapan choco_lsumns9883ef458568panamapan choco_lsumzb9882panamapan choco_2114darienpan choco_2103darienpan central_lsumzb9885ef458544chiriquipan central_usnmb5302chiriquipan central_usnmb5353chiriquipan central_lsumzb9887ef458545coclepan choco_28339panamapan central_mbmgms1112coclepan central_9888coclepan central_usnmb5498chiriquipan central_28371panamapan central_usnmb1487chiriquipan choco_schif.turd_iavh3166_chococo central_lsumzb28373panamapan central_mzfc10543ef458542quintanamex central_ku2115campechemex central_usnmb1476chiriquipan central_lsumzb60632hon central_60706atlantidahon central_usnmb5457chiriquipan central_ku2198campechemex central_usnmb5392chiriquipan central_lsumzb9886chiriquipan central_mzfc14589ef458540chiapasmex central_lsumzb16118ef458546puntaarenascr central_usnmb1421chiriquipan central_mzfc14587ef458541chiapasmex choco_ansp2230ef458547esmeraldasecu choco_lsumzb11820ef458548esmeraldasecu choco_11759esmeraldasecu choco_lsumzb11889esmeral dasec U choco_30009esmeraldasecu choco_ansp3531ef458549azuayec U napo_6140moronaecu napo_ansp4450ef458550zamoraec U huallaga_lsumzb5543ef458551sanmartinper napo_lsumzb6028moronaecu napo_6043moronaecu inambari_27769loretoper inambari_27903loretoper napo_ansp5100ef458552sucumbiosecu guiana_usnmb14399piruruguy guiana_usnmb5153cuyunimazaruni GUY guiana_usnmb5133essequioguy guiana_usnmb5137cuyunimazaruni GUY guiana_usnmb14671washikur ari ver GUY 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guiana_sil019amazonasbra guiana_sil034amazonasbra guiana_sil025amazonasbra guiana_usnmb14631washikur ari ver GUY guiana_usnmb15757mountroraimaguy guiana_42ml1037bolivarven guiana_usnm5097essequiboguy guiana_usnmb14357makwai masavannahguy guiana_fmnh391537ef458538amapabra guiana_cn865parabra guiana_65791sipaliwinisur guiana_cn866parabra guiana_cn376parabra guiana_cn366parabra guiana_cn882parabra tapajos_cn846parabra guiana_cn1306parabra guiana_cn922parabra guiana_cn456parabra guiana_cn367parabra guiana_fmnh391536ef458539amapabra guiana_cn390parabra guiana_65803sipaliwinisur guiana_cn313parabra guiana_cn1305parabra guiana_usnmb22267upperessequiboguy guiana_cn413parabra guiana_usnmb22213upperessequiboguy guiana_usnmb11492gunnslandingguy guiana_cn082parabra guiana_cn457parabra atlantic_schiffornisvirescensaf 453816 rondonia_18133santacruzbol rondonia_14881santacruzbol rondonia_36675rondoniabra rondonia_12631santacruzbol rondonia_12807santacruzbol rondonia_18387santacruzbol rondonia_15370santacruzbol rondonia_13931santacruzbol rondonia_13832santacruzbol rondonia_12367santacruzbol rondonia_14551santacruzbol rondonia_lsumns13831ef458563santacruzbol rondonia_12305santacruzbol rondonia_13899santacruzbol rondonia_36739rondoniabra rondonia_13884santacruzbol rondonia_lsumns36666ef458564rondoniabra rondonia_13007santacruzbol rondonia_15090santacruzbol rondonia_15253santacruzbol rondonia_14455santacruzbol rondonia_mtma006matogrossobra rondonia_14919santacruzbol rondonia_12311santacruzbol rondonia_14538santacruzbol rondonia_12299santacruzbol rondonia_18107santacruzbol rondonia_14779santacruzbol rondonia_12447santacruzbol rondonia_14888santacruzbol rondonia_14469santacruzbol rondonia_12670santacruzbol rondonia_36730rondoniabra rondonia_15243santacruzbol rondonia_15247santacruzbol rondonia_15246santacruzbol xingu_mpds709amazonasbr A rondonia_mpds649amazonasbra rondonia_fpr012amazonasbr A guiana_pime076parabra guiana_fpr109bra rondonia_fpr067amazonasbr A xingu_fmnh391539ef458559parabr A inambari_fmnh322499ef458560cuzcoper xingu_maya040parabra rondonia_mop094parabra xingu_fmnh391540ef458561parabr A tapajos_br163006parabra rondonia_br163072parabra xingu_mt009matogrossobra tapajos_br163013parabra xingu_peg006parabra napo_4163loretoper inambari_4676loretoper napo_4175loretoper napo_7119loretoper imeri_amz161amazonasbra napo_4321loretoper guiana_lsumzb7550ef458553amazonasven napo_7087loretoper napo_4179loretoper napo_lsumzb2552ef458554loretoper napo_schif.turd_iavh11195_c O napo_ansp5792ef458555sucumbiosecu imeri_jap816amazonasbra napo_jap770amazonasbra imeri_amz514amazonasbra napo_schif.turd_iavh11033_c O huallaga_42453loretoper napo_42928loretoper huallaga_42548loretoper inambari_1038lapazbol inambari_1015lapazbol inambari_22701lapazbol inambari_1087lapazbol inambari_904lapazbol inambari_22835lapazbol inambari_lsumzb1984ef458557pascoper inambari_ku18445cuscoper inambari_lsumzb9545ef458558pandobol inambari_ku18518cuscoper inambari_1173lapazbol inambari_22740lapazbol inambari_4680loretoper inambari_4732loretoper guiana_cuj181amazonasbra inambari_cuj187amazonasbra inambari_9588pandobol inambari_4703loretoper choco_lsumzb1358darienpan choco_9884darienpan choco_lsumns2261ef458566darienpa choco_29571pan choco_lsumns1352ef458565darienpan choco_52925darienpan choco_mbmjmd208panamapan choco_28393panamapan choco_lsumns9883ef458568panamapan choco_lsumzb9882panamapan choco_2114darienpan choco_2103darienpan central_lsumzb9885ef458544chiriquipan central_usnmb5302chiriquipan central_usnmb5353chiriquipan central_lsumzb9887ef458545coclepan choco_28339panamapan central_mbmgms1112coclepan central_9888coclepan central_usnmb5498chiriquipan central_28371panamapan central_usnmb1487chiriquipan choco_schif.turd_iavh3166_chococo central_lsumzb28373panamapan central_mzfc10543ef458542quintanamex central_ku2115campechemex central_usnmb1476chiriquipan central_lsumzb60632hon central_60706atlantidahon central_usnmb5457chiriquipan central_ku2198campechemex central_usnmb5392chiriquipan central_lsumzb9886chiriquipan central_mzfc14589ef458540chiapasmex central_lsumzb16118ef458546puntaarenascr central_usnmb1421chiriquipan central_mzfc14587ef458541chiapasmex choco_ansp2230ef458547esmeraldasecu choco_lsumzb11820ef458548esmeraldasecu choco_11759esmeraldasecu choco_lsumzb11889esmeral dasec U choco_30009esmeraldasecu choco_ansp3531ef458549azuayec U napo_6140moronaecu napo_ansp4450ef458550zamoraec U huallaga_lsumzb5543ef458551sanmartinper napo_lsumzb6028moronaecu napo_6043moronaecu inambari_27769loretoper inambari_27903loretoper napo_ansp5100ef458552sucumbiosecu guiana_usnmb14399piruruguy guiana_usnmb5153cuyunimazaruni GUY guiana_usnmb5133essequioguy guiana_usnmb5137cuyunimazaruni GUY guiana_usnmb14671washikur ari ver GUY guiana_usnmb19195kopinangvillageguy guiana_usnmb14310makwai masavannahguy guiana_usnmb19176kopinangvillageguy guiana_usnmb19079kopinangvillageguy guiana_43ml1027bolivarven guiana_usnmb14302makwai masavannahguy guiana_55343sipaliwinisur guiana_usnmb14323makwai masavannahguy guiana_usnmb19031kopinangvillageguy guiana_usnmb9265barimawainigu Y guiana_usnmb5157essequiboguy guiana_usnmb14492piruruguy guiana_ku1265ef458531guy guiana_ku5793ef458532guy guiana_usnmb14623washikur ari ver GUY guiana_ku3937ef458533guy guiana_usnmb10438sipurivereguy guiana_usnmb22151upperessequiboguy guiana_usnm10460sipuriverguy guiana_usnmb11440gunnslandingguy belem_cn113parabra guiana_usnmb11441gunnslandingguy guiana_amnhrop164ef458537bolivarven guiana_usnmb11625upperessequiboguy guiana_usnmb22268upperessequiboguy guiana_usnmb22256upperessequiboguy guiana_cn019parabra guiana_sil066amazonasbra inambari_lsumzb20362ef458536amazonasbra guiana_usnm10470sipuriverguy guiana_usnmb11389gunnslandingguy guiana_usnm11592guy guiana_sil019amazonasbra guiana_sil034amazonasbra guiana_sil025amazonasbra guiana_usnmb14631washikur ari ver GUY guiana_usnmb15757mountroraimaguy guiana_42ml1037bolivarven guiana_usnm5097essequiboguy guiana_usnmb14357makwai masavannahguy guiana_fmnh391537ef458538amapabra guiana_cn865parabra guiana_65791sipaliwinisur guiana_cn866parabra guiana_cn376parabra guiana_cn366parabra guiana_cn882parabra tapajos_cn846parabra guiana_cn1306parabra guiana_cn922parabra guiana_cn456parabra guiana_cn367parabra guiana_fmnh391536ef458539amapabra guiana_cn390parabra guiana_65803sipaliwinisur guiana_cn313parabra guiana_cn1305parabra guiana_usnmb22267upperessequiboguy guiana_cn413parabra guiana_usnmb22213upperessequiboguy guiana_usnmb11492gunnslandingguy guiana_cn082parabra guiana_cn457parabra atlantic_schiffornisvirescensaf 453816 doi:10.1038/nature13687 Schiffornis turdina Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Understory Ancestral Origin: East of Andes Time-calibrated gene tree with A B Rondonia Guiana Xingu, Tapajos, Rondonia Napo, Guiana, Huallaga, Guiana Chocó Central America, Chocó Napo,, Huallaga Guiana Time-calibrated gene tree showing BGMYC species with 1 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 1 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 Supplementary Figure 20 Range map, ENM, time-calibrated gene trees and delimited species for Schiffornis turdina. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). Nodes labeled A and B refer to multiple cross-andes divergence events used in the msbayes analysis. WWW.NATURE.COM/NATURE 53

Sclerurus mexicanus Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Understory Ancestral Origin: West of Andes Time-calibrated gene tree with outgroup inambari_9565pandobol inambari_8897pandobol inambari_mpeg58883acrebra rondonia_op096rondoniabra rondonia_36721rondoniabra inambari_inpa339rondoniabra tapajos_uhe073parabra tapajos_br163068parabra xingu_mpeg8398parabra tapajos_mt062matograssobra tapajos_mt061matograssobra xingu_ppbio198parabra xingu_ppbio277parabra belem_mlv153parabra guiana_cn889parabra guiana_20395amazonasbra guiana_cn869parabra guiana_usnm4485berbiceguy guiana_cn279parabra guiana_cn174parabra guiana_usnm5155essequiboguy guiana_cn451parabra guiana_amnhrop108bolivarven guiana_usnm5077cuyunimazaruniguy inambari_fmnh321714cuscoper inambari_986lapazbol inambari_fmnh433369cuscoper inambari_1078lapazbol inambari_58406punoper rondonia_6765benibol inambari_40524loretoper napo_5452sanmartinper inambari_1991pascoper napo_ansp4454zamoraecu napo_ansp4877napoecu napo_6980loretoper inambari_28035loretoper napo_ku949loretoper andes_iavhbt2445vallecol andes_iavhbt2444vallecol andes_sclmexandesbt2024 andes_12146pichinchaecu andes_amc1270tachiraven andes_iavhbt115nortedesantandercol andes_sclmexandesbt784 choco_ansp2410esmeraldasecu choco_11813esmeraldasecu choco_11742esmeraldasecu central_usnm5317chiriquipan central_16042herediacr central_usnm5540chiriquipan central_72105cartagocr central_35755cartagocr central_usnm5459chiriquipan central_35770cartagocr central_72631cr central_usnm5325chiriquipan central_mbm14943veraguaspan central_usnm1464chiriquipan central_usnm5363chiriquipan central_1366darienpan central_mbm10648quetzaltenangogua central_mbm10649quetzaltenangogua Sclerurus_caudacutus_9654 Sclerurus_scansor_25912 Automolus_rubiginosus_2650 Dendrocolaptes_certhia_ANSP7732 Tapajos Xingu, Belem Rondonia Guiana Napo Andes Chocó Central America Central America Time-calibrated gene tree showing BGMYC species with inambari_9565pandobol inambari_8897pandobol inambari_mpeg58883acrebra rondonia_op096rondoniabra rondonia_36721rondoniabra inambari_inpa339rondoniabra tapajos_uhe073parabra tapajos_br163068parabra xingu_mpeg8398parabra tapajos_mt062matograssobra tapajos_mt061matograssobra xingu_ppbio198parabra xingu_ppbio277parabra belem_mlv153parabra guiana_cn889parabra guiana_20395amazonasbra guiana_cn869parabra guiana_usnm4485berbiceguy guiana_cn279parabra guiana_cn174parabra guiana_usnm5155essequiboguy guiana_cn451parabra guiana_amnhrop108bolivarven guiana_usnm5077cuyunimazaruniguy inambari_fmnh321714cuscoper inambari_986lapazbol inambari_fmnh433369cuscoper inambari_1078lapazbol inambari_58406punoper rondonia_6765benibol inambari_40524loretoper napo_5452sanmartinper inambari_1991pascoper napo_ansp4454zamoraecu napo_ansp4877napoecu napo_6980loretoper inambari_28035loretoper napo_ku949loretoper andes_iavhbt2445vallecol andes_iavhbt2444vallecol andes_sclmexandesbt2024 andes_12146pichinchaecu andes_amc1270tachiraven andes_iavhbt115nortedesantandercol andes_sclmexandesbt784 choco_ansp2410esmeraldasecu choco_11813esmeraldasecu choco_11742esmeraldasecu central_usnm5317chiriquipan central_16042herediacr central_usnm5540chiriquipan central_72105cartagocr central_35755cartagocr central_usnm5459chiriquipan central_35770cartagocr central_72631cr central_usnm5325chiriquipan central_mbm14943veraguaspan central_usnm1464chiriquipan central_usnm5363chiriquipan central_1366darienpan central_mbm10648quetzaltenangogua central_mbm10649quetzaltenangogua Sclerurus_caudacutus_9654 Sclerurus_scansor_25912 18.0 17.0 16.0 15.0 14.0 13.0 12.0 11.0 1 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 18.0 17.0 16.0 15.0 14.0 13.0 12.0 11.0 1 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 Supplementary Figure 21 Range map, ENM, time-calibrated gene trees and delimited species for Sclerurus mexicanus. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions; locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 54

Tangara cyanicollis Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Canopy Ancestral Origin: East of Andes Time-calibrated gene tree with tachira_45jm655tachiraven tachira_48jm668tachiraven tachira_jpl343tachiraven tachira_47jm667tachiraven tachira_52ml1195barinasven tachira_44jm638tachiraven magdalena ANDESBT262 tachira_kcc154tachiraven tachira_kcc269tachiraven tachira_kcc156tachiraven tachira_jpl338tachiraven tachira_50jm759laraven tachira_49jm756laraven tachira_51jm802laraven tachira_46jm660tachiraven northwest_34845cajamarcaper northwest_5613sanmartinper magdalena_andesbt2211 northwest_44348sanmartinper northwest_33030cajamarcaper northwest_33160cajamarcaper southwest_22724lapazbol southwest_22768lapazbol southwest_38927cochabambabol southwest_uwbm77400cocbol southwest_39065cochabambabol southwest_39204cochabambabol rondonia_15204santacruzbol rondonia_15101santacruzbol rondonia_15097santacruzbol rondonia_15351santacruzbol rondonia_14522santacruzbol rondonia_15352santacruzbol rondonia_18102santacruzbol rondonia_14423santacruzbol westtrans_34862pichinchaecu westtrans_34867pinchinchaecu westtrans_34866pinchinchaecu westtrans_35010pichinchaecu westtrans_34904pichinchaec westtrans_34903pichinchaecu westtrans_35017pichinchaecu westtrans_35016pichinchaecu westtrans_34905pichinchaecu westtrans_34902pichinchaecu westtrans_34901pichinchaecu Tangara_larvata_AY383138 Tangara_nigrocincta_AY383143 Tangara_preciosa_EU647994 Time-calibrated gene tree showing BGMYC species with outgroup tachira_45jm655tachiraven tachira_48jm668tachiraven tachira_jpl343tachiraven tachira_47jm667tachiraven tachira_52ml1195barinasven tachira_44jm638tachiraven magdalena_andesbt262 tachira_kcc154tachiraven tachira_kcc269tachiraven tachira_kcc156tachiraven tachira_jpl338tachiraven tachira_50jm759laraven tachira_49jm756laraven tachira_51jm802laraven tachira_46jm660tachiraven northwest_34845cajamarcaper northwest_5613sanmartinper magdalena_andesbt2211 northwest_44348sanmartinper northwest_33030cajamarcaper northwest_33160cajamarcaper southwest_22724lapazbol southwest_22768lapazbol southwest_38927cochbol southwest_uwbm77400cochbol southwest_39065cochabambabol southwest_39204cochabambabol rondonia_15204santacruzbol rondonia_15101santacruzbol rondonia_15097santacruzbol rondonia_15351santacruzbol rondonia_14522santacruzbol rondonia_15352santacruzbol rondonia_18102santacruzbol rondonia_14423santacruzbol westtrans_34862pichinchaecu westtrans_34867pinchinchaecu westtrans_34866pinchinchaecu westtrans_35010pichinchaecu westtrans_34904pichinchaec westtrans_34903pichinchaecu westtrans_35017pichinchaecu westtrans_35016pichinchaecu westtrans_34905pichinchaecu westtrans_34902pichinchaecu westtrans_34901pichinchaecu Tangara_larvata_AY383138 5.0 4.0 3.0 2.0 1.0 5.0 4.0 3.0 2.0 1.0 Tangara_xanthogastra_AY383162 Tachira Magdalena Northwest Andes, Magdalena Southwest Andes Rondonia Rondonia Western Andes Supplementary Figure 22 Range map, ENM, time-calibrated gene trees and delimited species for Tangara cyanicollis. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 55

napo_lsumz6838loretoper napo_lsumz5397sanmartinper inambari_lsumz28002loretoper napo_lsumz34925napoecu inambari_40025loretoper inambari_40244loretoper inambari_40846loretoper inambari_lsumz27563loretoper inambari_40164loretoper foothills_53ml1265barinasven foothills_andesbt1416 foothills_andesbt1398 foothills_andesbt1215 inambari_lsumz28004loretoper napo_ansp2677moronaecu trinidad_gu215362simlatri inambari_lsumz11150ucayaliper inambari_lsumz11294ucayaliper inambari_lsumz936lapazbol inambari_lsumz22706lapazbol inambari_934lapazbol inambari_fmnh433876cuscoper inambari_fmnh433877cuscoper inambari_lsumz6793benibol inambari_22850lapazbol guiana_usnm15829mountroraimaguy guiana_usnm10630acarimountainsguy guiana_lsumz45852suriname guiana_usnm19155kopinangvillageguy guiana_usnm9316barimawainiguy guiana_usnm15838mountroraimaguy guiana_usnm15864mountroraimaguy guiana_usnm15828mountroraimaguy guiana_ansp21289potarosiparuniguy guiana_45852sur guiana_usnm15930mountroraimaguy guiana_usnm10665acarimountainsguy guiana_ansp21624potarosiparuniguy guiana_usnm18996kopinangvillageguy guiana_usnm10610acarimountainsguy guiana_usnmb10638acarimountainsguy guiana_usnm19202kopinangvillageguy guiana_ku3977mountroraimaguy guiana_cn782parabra rondonia_lsumz13020santacruzbol rondonia_lsumz12295santacruzbol tapajos_lsumz35277parabra rondonia_mt028matogrossobra rondonia_14862santacruzbol central_mbmgms1031veraguaspan central_35789cartagocr central_26854colonpan central_26584colonpan central_lsumz35788cartagocr choco_mbmjk0497panamapan central_lsumz28351panamapan central_lsumz26862colonpan choco_lsumz2149darienpan central_72119cartagocr central_lsumz35757cartagocr central_35805cartagocr central_35802cartagocr central_35787cartagocr central_lsumz16008herediacr central_lsumz35748cartagocr central_35803cartagocr central_lsumz27281cartagocr central_71973puntarenascr central_72161sanjosecr choco_mbmjmd640panamapan choco_lsumz34886pichinchaecu choco_ansp26413esmeraldasecu choco_35008pichinchaecu choco_34906pichinchaecu choco_12085pichinchaecu choco_lsumz34869pichinchaecu choco_34907pichinchaecu choco_35009pichinchaecu choco_ansp4337esmeraldasecu choco_34871pichinchaecu choco_34908pichinchaecu choco_lsumz34861pichinchaecu magdalena_tan_gyr_andesbt531 magdalena_jpl470huilacol magdalena_tan_gyr_andesbt530 lavinia.ansp17083_esmeraldasecu lavinia.ansp17082_esmeraldasecu lavinia.ansp17108_esmeraldasecu lavinia.ansp17252_esmeraldasecu Tangara_lavinia_AY383139 Tangara_cyanocephala_AY383118 Tangara_seledon_AY383154 Tangara_mexicana_AY383141 napo_lsumz6838loretoper napo_lsumz5397sanmartinper inambari_lsumz28002loretoper napo_lsumz34925napoecu inambari_40025loretoper inambari_40244loretoper inambari_40846loretoper inambari_lsumz27563loretoper inambari_40164loretoper foothills_53ml1265barinasven foothills_andesbt1416 foothills_andesbt1398 foothills_andesbt1215 inambari_lsumz28004loretoper napo_ansp2677moronaecu trinidad_gu215362simlatri inambari_lsumz11150ucayaliper inambari_lsumz11294ucayaliper inambari_lsumz936lapazbol inambari_lsumz22706lapazbol inambari_934lapazbol inambari_fmnh433876cuscoper inambari_fmnh433877cuscoper inambari_lsumz6793benibol inambari_22850lapazbol guiana_usnm15829mountroraimaguy guiana_usnm10630acarimountainsguy guiana_lsumz45852suriname guiana_usnm19155kopinangvillageguy guiana_usnm9316barimawainiguy guiana_usnm15838mountroraimaguy guiana_usnm15864mountroraimaguy guiana_usnm15828mountroraimaguy guiana_ansp21289potarosiparuniguy guiana_45852sur guiana_usnm15930mountroraimaguy guiana_usnm10665acarimountainsguy guiana_ansp21624potarosiparuniguy guiana_usnm18996kopinangvillageguy guiana_usnm10610acarimountainsguy guiana_usnmb10638acarimountainsguy guiana_usnm19202kopinangvillageguy guiana_ku3977mountroraimaguy guiana_cn782parabra rondonia_lsumz13020santacruzbol rondonia_lsumz12295santacruzbol tapajos_lsumz35277parabra rondonia_mt028matogrossobra rondonia_14862santacruzbol central_mbmgms1031veraguaspan central_35789cartagocr central_26854colonpan central_26584colonpan central_lsumz35788cartagocr choco_mbmjk0497panamapan choco_lsumz28351panamapan central_lsumz26862colonpan choco_lsumz2149darienpan central_72119cartagocr central_lsumz35757cartagocr central_35805cartagocr central_35802cartagocr central_35787cartagocr central_lsumz16008herediacr central_lsumz35748cartagocr central_35803cartagocr central_lsumz27281cartagocr central_71973puntarenascr central_72161sanjosecr choco_mbmjmd640panamapan choco_lsumz34886pichinchaecu choco_ansp26413esmeraldasecu choco_35008pichinchaecu choco_34906pichinchaecu choco_12085pichinchaecu choco_lsumz34869pichinchaecu choco_34907pichinchaecu choco_35009pichinchaecu choco_ansp4337esmeraldasecu choco_34871pichinchaecu choco_34908pichinchaecu choco_lsumz34861pichinchaecu magdalena_tan_gyr_andesbt531 magdalena_jpl470huilacol magdalena_tan_gyr_andesbt530 lavinia.ansp17083_esmeraldasecu lavinia.ansp17082_esmeraldasecu lavinia.ansp17108_esmeraldasecu lavinia.ansp17252_esmeraldasecu Tangara_lavinia_AY383139 doi:10.1038/nature13687 Tangara gyrola Distribution Map and Sampling Localities Ecological Niche Model Foraging Stratum: Canopy Ancestral Origin: East of Andes Time-calibrated gene tree with inambari_40012loretoper napo_4258loretoper rondonia_lsumz12604santacruzbol rondonia_14492santacruzbol choco_34872pichinchaecu choco_lsumz34911pichinchaecu Napo, Andean Foothills Trinidad Guiana Rondonia, Tapajos Central America Chocó Chocó Magdalena Time-calibrated gene tree showing BGMYC species with inambari_40012loretoper napo_4258loretoper rondonia_lsumz12604santacruzbol rondonia_14492santacruzbol choco_34872pichinchaecu choco_lsumz34911pichinchaecu 6.0 5.0 4.0 3.0 2.0 1.0 6.0 5.0 4.0 3.0 2.0 1.0 Supplementary Figure 23 Range map, ENM, time-calibrated gene trees and delimited species for Tangara gyrola. Range map (natureserv.org) showing approximate geographic distribution of each lineage with sampling localities as black circles (upper left). Ecological niche model (ENM) indicating areas with suitable climatic conditions from 0 (clear) to 1.0 (red); locality records used to construct the ENM appear as black circles (upper right). Time-calibrated gene tree showing geographic clades (bottom left). Time-calibrated gene tree with clades collapsed to show species delimited using bgmyc (bottom right). WWW.NATURE.COM/NATURE 56