Table S1: Locality codes, identification, voucher number, institution and locality of the samples used LC C1 C2 C2 C2 C2 C2 C3 C3 C3 C4 C5 C6 C6 C6 C7 C8 C8 C8 C8 C9 C9 C10 N1 N2 N3 N4 N5 O1 O1 O1 O1 O2 L1 L1 L2 L2 L2 L3 L4 L5 L6 L7 L7 L8 V1 V1 V1 V2 V2 V3 V4 B1 I1 I1 I2 I2 D1 D2 D2 D2 D3 D4 Taxon P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. crepitans P. c. napensis P. c. napensis P. c. napensis P. c. napensis P. c. napensis P. l. ochroptera P. l. ochroptera P. l. ochroptera P. l. ochroptera P. l. ochroptera P. l. leucoptera P. l. leucoptera P. l. leucoptera P. l. leucoptera P. l. leucoptera P. l. leucoptera P. l. leucoptera P. l. leucoptera P. l. leucoptera P. l. leucoptera P. l. leucoptera P. l. leucoptera P. v. viridis P. v. viridis P. v. viridis P. v. viridis P. v. viridis P. v. viridis P. v. viridis P. v. obscura P. v. interjecta P. v. interjecta P. v. interjecta P. v. interjecta P. v. dextralis P. v. dextralis P. v. dextralis P. v. dextralis P. v. dextralis P. v. dextralis Voucher 1253 B10666 B10667 B10673 B10730 B10786 43640# 43641# 43642# 43715# 56259# 858SC B7513 B7553 64956 65336 65337 65338 65339 65724 65725 66388 257106# 460076# 310155# 434049# 62396 59309 59310 59311 59312 62395 21 93 58820 A8649 58821 B10733 B9498 60089 60090 56974 56975 61975 389701 389702 389703 B36685 B36686 58655 58403# 32376# 48495# 48496# 61659 61660 58592# 51283 51281 51284 285705# MNA4326 Institution KUMNH NMNH NMNH NMNH NMNH NMNH MPEG MPEG MPEG MPEG MPEG AMNH LSUMNS LSUMNS MPEG MPEG MPEG MPEG MPEG MPEG MPEG MPEG AMNH AMNH AMNH AMNH MPEG MPEG MPEG MPEG MPEG MPEG USP USP MPEG MPEG MPEG LSUMNS LSUMNS MPEG MPEG MPEG MPEG MPEG FMNH FMNH FMNH LSUMNS LSUMNS MPEG MPEG MPEG MPEG MPEG MPEG MPEG MPEG MPEG MPEG MPEG AMNH USP Locality Guyana, Iwokrama Reserve, Kurupukari, Guyana, Acari Mountains, North Side Guyana, Acari Mountains, North Side Guyana, Acari Mountains, North Side, Guyana, Acari Mountains, North Side, Guyana, Acari Mountains, North Side, Brazil, Amazonas, Balbina, Rio Uatumã Brazil, Amazonas, Balbina, Rio Uatumã Brazil, Amazonas, Balbina, Rio Uatumã Brazil, Pará, Rio Trombetas Brazil, Roraima, Caracaraí, Rio Branco, left bank Venezuela, Amazonas, Rio Baria Venezuela, Amazonas, Rio Baria Venezuela, Amazonas, Rio Baria, Brazil, Pará, Óbidos, Flota do Trombetas Brazil, Pará, Alenquer, ESEC Grão Pará Brazil, Pará, Alenquer, ESEC Grão Pará Brazil, Pará, Alenquer, ESEC Grão Pará Brazil, Pará, Alenquer, ESEC Grão Pará Brazil, Pará, Oriximináã, Serra do Acarí Brazil, Pará, Oriximináã, Serra do Acarí Brazil, Pará, Almeirim, Rio Parú Ecuador, Lagartococha Colombia, Mt Macarena Brazil, Amazonas, Mt Curicuriari, Rio Negro Brazil, Amazonas, Umarituba, Rio Negro Brazil, Amazonas, Japurá, Rio Acanauaí Brazil, Amazonas, Barcelos, Rio Quiuini Brazil, Amazonas, Barcelos, Rio Quiuini Brazil, Amazonas, Barcelos, Rio Quiuini Brazil, Amazonas, Barcelos, Rio Quiuini Brazil, Amazonas, Maraã, Lago Cumapi Brazil, Rondônia, Porto Velho, EE Antônio Mujica Nava Brazil, Rondônia, Porto Velho, EE Antônio Mujica Nava Brazil, Acre, Assis Brasil, ESEC do Rio Acre Brazil, Acre, Assis Brasil, ESEC do Rio Acre Brazil, Acre, Assis Brasil, ESEC do Rio Acre Peru, Ucayali, Pucallpa, Rio Shesha Bolivia, Pando, Nicolas Suarez Brazil, Amazonas, RDS Cujubim, Rio Jutaí Brazil, Amazonas, RDS Cujubim, Rio Jutaí Brazil, Amazonas, Rio Urucú, Coari Brazil, Amazonas, Rio Urucú, Coari Brazil, Acre, Porto Walter, Colônia Dois Portos Brazil, Rondônia, Cachoeira de Nazaré Brazil, Rondônia, Cachoeira de Nazaré Brazil, Rondônia, Cachoeira de Nazaré Brazil, Rondônia, Guajará-Mirim, Rio Ouro Preto Brazil, Rondônia, Guajará-Mirim, Rio Ouro Preto Brazil, Amazonas, Humaitá, Madeira River Brazil, Amazonas, Itaituba, Tapajós River, left bank Brazil, Pará, Ourém, Rio Guamá Brazil, Pará, Santana do Araguaia Brazil, Pará, Santana do Araguaia Brazil, Pará, Caxiuanã Brazil, Pará, Caxiuanã Brazil, Pará, Serra do Cachimbo Brazil, Mato Grosso, Alta Floresta, Rio Cristalino Brazil, Mato Grosso, Alta Floresta, Rio Cristalino Brazil, Mato Grosso, Alta Floresta, Rio Cristalino Brazil, Pará, Caxiricatuba, Rio Tapajós, right bank Brazil, Mato Grosso, Paranaíta, Rio Teles Pires left bank GenBank cytb, ND2, Fib7 Table S2: RAG 2 sequences obtained for this study and GenBank accession numbers Taxon Struthio camelus Anas platyrhynchus Anseranas semipalmatus Gallus gallus Talegalla Anhinga anhinga Phalacrocorax urile Morus serrator Fregata magnificens Pygoscelis antarctica Spheniscus humboldti Amaurornis phoenicurus Gallicrex cinerea Rallina fasciata Porphyrio porphyrio Fulica americana Gallinula chloropus Porzana carolina Rallus limicola Heliornis fulica Aramus guarauna Grus canadensis Psophia viridis Psophia crepitans Voucher # or Field number PRS1636 JJW110 PRS1635 number to be supplied number to be supplied JJW335 JP1472 AM-LAB1219 PRS190 PAC1011 PAC1010 PRS710 PRS704 PRS658 PRS536 PAC495 PRS937 PAC426 PAC687 JJW340 PRS1380 PAC513 B36686 B7553 Institution AMNH AMNH AMNH AMNH AMNH AMNH AMNH AMNH AMNH AMNH AMNH AMNH AMNH AMNH AMNH AMNH AMNH AMNH AMNH AMNH AMNH AMNH AMNH AMNH GenBank Accession Table S3: Primers used for amplification and sequencing Gene Primer Sequence 5’ – 3’ Cyt b CBL45PS CAACAACTCCCTAATCGACCT CBH640PS GGGATTTTATCGCAGTTGGAT CBL546PS TACATTTCCTCCTCCCTTTCAT CBH1074PS GGATCAGGAGGGTGGTGAAGTAGG Cyt b CBL45PS CAACAACTCCCTAATCGACCT (skins) CBH1 GCCTCGGCCGATGTGCAGGTAG CBL2 CGGCTGACTAATCCGYAACCTAC CBH2 GAGAATAGGTTGGTAATGACTGTGG CBL3 CCGCCTTCGTAGGTTACGTACTACC CBH3 GGATTTTATCGCAGTTGGATGTGATGCC CBL4 CCTCACCTTCCTACACGAATCTGG CBH4 GAGCGTAGGATGGCGTATGC CBL5 GACCCAGAAAACTTCACCCCAGC CBH5 CAGAATAGRAGTTGGGAGAGGGG CBL6 CTAATCCTCCTTCTAATCCCCTTCC CBH1074PS CCTACTTCACCACCCTCCTGATCC ND2 MetB CGAAAATGATGGTTTAACCCCTTCC H5766P GGATGAGAAGGCTAGGATTTTGCG L5602 GATTCCCAGAAGTTCTTCAAGG H6313 CTCTTATTTAAGGCTTTGAAGGC TrpC CGGACTTTAGCAGAAACTAAGAG ND2 MetB CGAAAATGATGGTTTAACCCCTTCC (skins) ND2H1 GGACTAGTGCTGAGGCGGTGGC ND2L2 GCCATCGAAGCTGCAGTCAAATAC ND2H2 CCGCCCTGCTACTGGCTACAGTAA ND2L3 CCACTTCTGATTCCCAGAAGTCCTCC ND2H3 CCCACCTAGGCTGAATAACCATCATC ND2L4 CCCGCAAAATCCTAGCCTTCTC ND2H4 GTGGCTATGATTGTGGCTGCTGG ND2L5 CTAGCAGGCCTTCCCCCCTTAAC ND2H5 GGCAGATAGGGAGGTGGAGATGGC ND2L6 TCACACTCCCACCAAACTCCACAAACC TrpC CGGACTTTAGCAGAAACTAAGAG Fib7 FIB-BI7U GGAGAAAACAGGACAATGACAATTCAC FIB-BI7L TCCCCAGTAGTATCTGCCATTAGGGTT RAG2 R2-1 TCTTTTTTGGGCAGAAGGGATG R2-41 TCTACATTTTGGGAGGCCATTC R2-22 ACGCTCATGCTTTTTCCC R2-42 CAGGTCACAGCTGGGCTG R2-16 GACCCAGGTGTTAATGTC Reference This study This study This study This study This study This study This study This study This study This study This study This study This study This study This study This study 1 This study 2 3 1 1 This study This study This study This study This study This study This study This study This study This study 1 4 4 5 This study 5 This study 5 1. Eberhard, J.R. & Bermingham, E. 2004 Phylogeny and biogeography of the Amazona ochrocephala (Aves; Psittacidae) complex. Auk 121, 318-332. 2 Ribas, C.C., Gaban-Lima, R., Miyaki, C.Y. & Cracraft, J. 2005 Historical biogeography and diversification within the Neotropical parrot genus Pionopsitta (Aves: Psittacidae). J Biogeog 32, 1409-1427 3 Sorenson, M.D., Ast, J.C., Dimcheff, E.D., Yuri, T. & Mindell, D.P. 1999 Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Mol Phylogenet Evol 12, 105-114. 4 Prychitko, T.M. & Moore, W.S. 1997 The utility of DNA sequences of an intron from the b-fibrinogen gene in phylogenetic analysis of woodpeckers (Aves: Picidae). Mol Phylogenet Evol 8, 193-204. 5 Barker, F.K., Cibois, A., Schikler, P., Feinstein, J. & Cracraft, J. 2004 Phylogeny and diversification of the largest avian radiation. Proc Natl Acad Sci USA 101, 11040-11045. Table S4- Fossils used for calibration of the molecular clock. Stem group means that the fossil taxon is outside the clade including modern representatives of the lineage, while crown group means it is inside. All fossils represent minimum ages. The only maximum bound was applied to the stem Neoaves, which was constrained between 85 and 100 mya. Taxon Stem Fregatidae Stem Sphenisciformes Crown Anseriformes Stem Neoaves MYA 53 60 66 100-85 Calibration BEAST Uniform Prior Uniform Prior Uniform Prior Uniform Prior Calibration r8s Minimum age Minimum age Minimum age Maximum and Minimum bounds Reference 1, 2 3 4 see text 1 Olson, S.L. 1977 A Lower Eocene frigatebird from the Green River Formation of Wyoming (Pelecaniformes, Fregatidae) Smithsonian Contributions to Paleobiology, 35, 1–33. 2 Olson, S.L. & Matsuoka, H. 2005 New specimens of the early Eocene frigatebird Limnofregata (Pelecaniformes: Fregatidae), with the description of a new species. Zootaxa 1046, 1-15. 3 Clarke, J.A., Ksepka, D.T., Stucchi, M., Urbina, M., Gianini, N., Bertelli, S., Narváez, Y. & Boyd, C.A. 2007 Paleogene equatorial penguins challenge the proposed relationship between biogeography, diversity, and Cenozoic climate change. Proc. Nat, Acad. Sci. USA 104, 11545-11550. 4 Clarke, J.A., Tambussi, C.P., Noriega, J.I., Erickson, G.M. & Ketcham, R.A. 2005 Definitive fossil evidence for the extant avian radiation in the Cretaceous. Nature, 433, 305-308. Table S5: Mitochondrial DNA nucleotide diversity, Tajima's D, Fu's Fs, and Ramos Onsins and Rozas R2 statistics for the main clades within Psophia N Ha π (%) Tajima's D Fu's Fs R2 MtDNA (cytb + ND2) obs. P obs. P obs. P crepitans 22 12 0.079±0.019 -2.3 0.001* -8.659 0.001* 0.055 0.001* napensis 5 5 0.315±0.078 0.804 0.727 -0.964 0.279 0.209 0.417 ochroptera 5 4 0.098±0.025 0.273 0.732 -1.012 0.358 0.194 0.140 leucoptera 12 9 0.097±0.018 -1.809 0.025* -6.569 0.002* 0.073 0.001* viridis 7 6 0.450±0.104 -0.377 0.363 -0.006 0.415 0.180 0.454 dexralis 6 2 0.067±0.043 -1.132 0.129 0.952 0.777 0.373 1.000 interjecta 4 2 0.025±0.013 N: Number of individuals, Ha: Number of haplotypes, * significant values Table S6: Mismatch distribution analysis and dating of population expansions for P. crepitans and P. leucoptera. Dates of expansion (years ago) τ µ=0.0067a µ=0.0092b µ=0.01c MtDNA N SSD Ragg (alpha=0.1) u=8.18E-5 u=1.12E-4 u=1.22E-4 0.011 0.10 1.977 12,084 8,825 8,102 P. leucoptera 12 (P=0.45) (P=0.34) (0.86-3.04) (5,257-18,582) (3,839-13,571) (3,524-12,459) 0.002 0.031 1.719 10.507 7,674 7.045 P. crepitans 22 (P=0.90) (P=0.91) (0.51-3.02) (3,117-18,460) (2,277-13,482) (2,090-12,377) a. rate obtained applying the age for the basal split within Psophia from the RAG2 PL analysis b. rate obtained applying the age for the basal split within Psophia from the RAG2 Bayesian analysis c. rate obtained from the literature, corresponding to 2% sequence divergence per million years
Download
