A comprehensive multilocus phylogeny of the Neotropical cotingas (Cotingidae, Aves) with a comparative evolutionary analysis of breeding system and plumage dimorphism and a revised phylogenetic classification

Molecular Phylogenetics and Evolution

Volumn 81, Issue , 2014, Pages 120-136

  Berv, Jacob S ^a,b   Prum, Richard O ^a  

^a YALE UNIVERSITY   (United States)

^b Fuller Evolutionary Biology Program   (United States)

Author keywords

Bayesian inference; Monogamy; Phylogenetics; Polygyny; Sexual selection; Species tree

Indexed keywords

MITOCHONDRIAL DNA;

ANATOMY AND HISTOLOGY; ANIMAL; BAYES THEOREM; BREEDING; CELL NUCLEUS; CLASSIFICATION; DNA SEQUENCE; EVOLUTION; FEATHER; FEMALE; GENETICS; MALE; PHYLOGENY; SEXUAL DEVELOPMENT; SONGBIRD; STATISTICAL MODEL;

ANIMALS; BAYES THEOREM; BIOLOGICAL EVOLUTION; BREEDING; CELL NUCLEUS; DNA, MITOCHONDRIAL; FEATHERS; FEMALE; LIKELIHOOD FUNCTIONS; MALE; PASSERIFORMES; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SEX CHARACTERISTICS;

EID: 84908012234     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2014.09.001     Document Type: Article

References (88)

1. Akaike H. A new look at the statistical model identification. Autom. Contr., IEEE Transact. 1974, 19:716-723.
2. Ames, P.L., 1971. The Morphology of the Syrinx in Passerine Birds.
3. Avalos V.D.R. Biparental care and nestling success of the Swallow-tailed Cotinga in northwestern Bolivia. Wilson J. Ornithol. 2011, 123:251-258.
4. Barker F.K., Cibois A., Schikler P., Feinstein J., Cracraft J. Phylogeny and diversification of the largest avian radiation. Proc. Natl. Acad. Sci. USA 2004, 101:11040-11045.
5. Barker F.K., Burns K.J., Klicka J., Lanyon S.M., Lovette I.J. Going to extremes: contrasting rates of diversification in a recent radiation of new world passerine birds. Syst. Biol. 2013, 62:298-320.
6. Belmonte-Lopes R., Maurício G.N., Bornschein M.R. Description of the nest and egg of an Atlantic forest endemic, the Black-headed Berryeater, Carpornis melanocephala (Cotingidae). Wilson J. Ornithol. 2011, 123:819-822.
7. Brown J.M., Lemmon A.R. The importance of data partitioning and the utility of bayes factors in bayesian phylogenetics. Syst. Biol. 2007, 56:643-655.
8. Burton P.J.K. Structure and histology of the wattle in the White bellbird (Procnias alba). J. Zool. 1976, 178:285-293.
9. Clarke J.A., Tambussi C.P., Noriega J.I., Erickson G.M., Ketcham R.A. Definitive fossil evidence for the extant avian radiation in the Cretaceous. Nature 2005, 433:305-308.
10. Cuervo A.M., Salaman P.G.W., Donegan T.M., Ochoa J.M. A new species of piha (Cotingidae: Lipaugus) from the Cordillera Central of Colombia. Ibis 2001, 143:353-368.
11. Darwin C. The Descent of Man, and Selection in Relation to Sex 1871, John Murray, London.
12. Degnan J.H., Rosenberg N.A. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 2009, 24:332-340.
13. del Hoyo, J., Elliot, A., Christie, D.A., 2004. Handbook of the Birds of the World. Cotingas to Pipits and Wagtail. Handbook of the Birds of the World, vol. 9. Lynx Editions, Barcelona.
14. Drovetski S.V. Molecular phylogeny of grouse: individual and combined performance of W-linked, autosomal, and mitochondrial loci. Syst. Biol. 2002, 51:930-945.
15. Drummond, A.J., Ho, S.Y., Rawlence, N., Rambaut, A., 2007. A Rough Guide to BEAST 1.4. Edinburgh: University of Edinburgh.
16. Drummond A.J., Suchard M.A., Xie D., Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 2012, 29:1969-1973.
17. Edwards S.V., Liu L., Pearl D.K. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. 2007, 104:5936-5941.
18. Ferreira M.A., Suchard M.A. Bayesian analysis of elapsed times in continuous-time Markov chains. Can. J. Stat. 2008, 36:355-368.
19. Garrod A.H. On some anatomical characters which bear upon the major divisions of the passerine birds. Proc. Zool. Soc. Lond. 1876, 1876:506-519.
20. Gelman A., Rubin D.B. Inference from iterative simulation using multiple sequences. Stat. Sci. 1992, 457-472.
21. Heled J., Drummond A.J. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 2010, 27:570-580.
22. Hellmayr, C.E., 1929. Catalogue of birds of the Americas, Part 6. Oxyruncidae-Pipridae-Cotingidae-Rupicolidae-Phytotomidae. Publ. Field Mus. Nat. Hist., pp. 1-258.
23. Hennessey A.B. Species Rank of Phibalura (flavirostris) boliviana Based on Plumage, Soft Part Color, Vocalizations, and Seasonal Movements. Wilson J. Ornithol. 2011, 123:454-458.
24. Hovmöller R., Lacey Knowles L., Kubatko L.S. Effects of missing data on species tree estimation under the coalescent. Mol. Phylogenet. Evol. 2013, 69:1057-1062.
25. Irwin R.E. The evolution of plumage dichromatism in the new world blackbirds: social selection on female brightness. Am. Nat. 1994, 144:890-907.
26. Johansson U.S., Irestedt M., Parsons T.J., Ericson P.G.P. Basal phylogeny of the Tyrannoidea based on comparisons of cytochrome b and exons of nucelar c-myc and RAG-1 genes. Auk 2002, 119:984-995.
27. Kirwan G.M., Green G. Cotingas and Manakins 2012, Princeton University Press, Princeton, NJ.
28. Kroodsma D., Hamilton D., Sánchez J.E., Byers B.E., Fandiño-Mariño H., Stemple D.W., Trainer J.M., Powell G.V.N. Behavioral evidence for song learning in the suboscine bellbirds (Procnias spp.; Cotingidae). Wilson J. Ornithol. 2013, 125:1-14.
29. Kubatko L.S., Degnan J.H. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 2007, 56:17-24.
30. Küchler W. Anatomische untersuchungen an Phytotoma rara Mol. J. für Ornithol. 1936, 84:350-362.
31. Kumar S., Nei M., Dudley J., Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief. Bioinform. 2008, 9:299-306.
32. Lanfear R., Calcott B., Ho S.Y., Guindon S. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol. Biol. Evol. 2012, 29:1695-1701.
33. Lanyon S.M., Lanyon W.E. The systematic position of the Plantcutters, Phytotoma. Auk 1988, 106:422-432.
34. Leavitt J.R., Hiatt K.D., Whiting M.F., Song H. Searching for the optimal data partitioning strategy in mitochondrial phylogenomics: a phylogeny of Acridoidea (Insecta: Orthoptera: Caelifera) as a case study. Mol. Phylogenet. Evol. 2013, 67:494-508.
35. Lewis P.O. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 2001, 50:913-925.
36. Li C., Lu G., Orti G. Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci. Syst. Biol. 2008, 57:519-539.
37. Longrich N.R., Tokaryk T., Field D.J. Mass extinction of birds at the Cretaceous-Paleogene (K-Pg) boundary. Proc. Natl. Acad. Sci. 2011, 108:15253-15257.
38. Luo A., Qiao H., Zhang Y., Shi W., Ho S.Y., Xu W., Zhang A., Zhu C. Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets. BMC Evol. Biol. 2010, 10:242.
39. Maddison, W., Maddison, D., 2011. Mesquite: A Modular System for Evolutionary Analysis. Version 2.75. Mesquite website. http://mesquiteproject.org.
40. Mayr G. The age of the crown group of passerine birds and its evolutionary significance - molecular calibrations versus the fossil record. Syst. Biodivers. 2013, 11:7-13.
41. Mayr E., Phelps W.H. The origin of the bird fauna of the south Venezuelan highlands. Bull. Am. Museum Natur. History 1967, 136:269-328.
42. McGuire J.A., Witt C.C., Altshuler D.L., Remsen J.V. Phylogenetic systematics and biogeography of hummingbirds: bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy. Syst. Biol. 2007, 56:837-856.
43. Midtgård U. Patterns of the blood vascular system in the pelvic limb of birds. J. Zool. 1982, 196:545-567.
44. Miller, M.A., Pfeiffer, W., Schwartz, T., 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Gateway Computing Environments Workshop (GCE), 2010. IEEE, pp. 1-8.
45. Mooers A.O., Schluter D. Reconstructing ancestor states with maximum likelihood: support for one-and two-rate models. Syst. Biol. 1999, 48:623-633.
46. Nemeth E. Measuring the sound pressure level of the song of the screaming Piha Lipaugus Vociferans: one of the loudest birds in the world?. Bioacoustics 2004, 14:225-228.
47. Nylander J.A., Wilgenbusch J.C., Warren D.L., Swofford D.L. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 2008, 24:581-583.
48. Ödeen A., Håstad O. Complex distribution of avian color vision systems revealed by sequencing the SWS1 opsin from total DNA. Mol. Biol. Evol. 2003, 20:855-861.
49. Ohlson J.I., Prum R.O., Ericson P.G.P. A molecular phylogeny of the cotingas (Aves: Cotingidae). Mol. Phylogenet. Evol. 2007, 42:25-37.
50. Ohlson J.I., Irestedt M., Ericson P.G.P., Fjeldså J. Phylogeny and classification of the New World suboscines (Aves, Passeriformes). Zootaxa 2013, 3613:1-35.
51. Pagel M. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc. Roy. Soc. Lond. Ser. B: Biol. Sci. 1994, 255:37-45.
52. Pagel M. Inferring evolutionary processes from phylogenies. Zoolog. Scr. 1997, 26:331-348.
53. Papadopoulou A., Jones A.G., Hammond P.M., Vogler A.P. DNA taxonomy and phylogeography of beetles of the Falkland Islands (Islas Malvinas). Mol. Phylogenet. Evol. 2009, 53:935-947.
54. Posada D., Buckley T.R. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 2004, 53:793-808.
55. Poux C., Madsen O., Glos J., de Jong W., Vences M. Molecular phylogeny and divergence times of Malagasy tenrecs: influence of data partitioning and taxon sampling on dating analyses. BMC Evol. Biol. 2008, 8:102.
56. Powell A.F.L.A., Barker F.K., Lanyon S.M. Empirical evaluation of partitioning schemes for phylogenetic analyses of mitogenomic data: an avian case study. Mol. Phylogenet. Evol. 2013, 66:69-79.
57. Prum R.O. A test of the monophyly of the manakins (Pipridae) and of the cotingas (Cotingidae) based on morphology. Occasion. Papers Museum Zool. Univ. Michigan 1990, 723:1-44.
58. Prum R.O. Phylogenetic analysis of the evolution of alternative social behavior in the manakins (Aves: Pipridae). Evolution 1994, 1657-1675.
59. Prum R.O. Phylogenetic tests of alternative intersexual selection mechanisms: macroevolution of male traits in a polygynous clade (Aves: Pipridae). Am. Natur. Am. Natur. 1997, 149:668-692.
60. Prum R.O. A new genus for the Andean green pihas (Cotingidae). Ibis 2001, 143:307-309.
61. Prum R.O. The Lande-Kirkpatrick mechanism is the null model of evolution by intersexual selection: implications for meaning, honesty, and design in intersexual signals. Evolution 2010, 64:3085-3100.
62. Prum R.O., Lanyon W.E. Monophyly and phylogeny of the Schiffornis group (Tyrannoidea). Condor 1989, 91:444-461.
63. Prum R.O., Torres R.H. Structural colouration of avian skin: convergent evolution of coherently scattering dermal collagen arrays. J. Exp. Biol. 2003, 206:2409-2429.
64. Prum R.O., Torres R.H., Williamson S., Dyck J. Coherent light scattering by blue feather barbs. Nature 1998, 396:28-29.
65. Prum R.O., Torres R.H., Williamson S., Dyck J. Two-dimensional Fourier analysis of the spongy medullary keratin of structurally coloured feather barbs. Proc. Roy. Soc. Lond. B 1999, 266:13-22.
66. Prum R.O., Rice N.H., Mobley J.A., Dimmick W.W. A preliminary phylogenetic hypothesis for the cotingas (Cotingidae) based on mitochondrial DNA. Auk 2000, 117:236-241.
67. Prum R.O., LaFountain A.M., Berro J., Stoddard M.C., Frank H.A. Molecular diversity, metabolic transformation, and evolution of carotenoid feather pigments in cotingas (Aves: Cotingidae). J. Compar. Physiol. B 2012.
68. Rambaut, A., Drummond, A., 2009. Tracer. MCMC Trace Analysis Tool, Version 1.5. University of Oxford, UK. >. http://tree.bio.ed.ac.uk/software/tracer/%5D.
69. Ridgway R. The birds of North and Middle America, part 4. Bull. United States Natl. Museum 1907, 50:1-973.
70. Robbins M., Rosenberg G.H., Sornoza Molina F. A new species of cotinga (Cotingidae: Doliornis) from the ecuadorian Andes, with comments on plumage sequences in Doliornis and Ampelion. Auk 1994, 111:1-7.
71. Ronquist F., Teslenko M., van der Mark P., Ayres D.L., Darling A., Höhna S., Larget B., Liu L., Suchard M.A., Huelsenbeck J.P. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 2012, 61:539-542.
72. Saranathan V., Hamilton D., Powell G.V.N., Kroodsma D.E., Prum R.O. Genetic evidence support song learning in the three-wattled bellbird Procnias tricarunculata (Cotingidae). Mol. Ecol. 2007, 16:3689-3702.
73. Saranathan V., Forster J.D., Noh H., Liew S.F., Mochrie S.G.J., Cao H., Dufresne E.R., Prum R.O. Structure and optical function of amorphous photonic nanostructures from avian feather barbs: a comparative small angle X-ray scattering (SAXS) analysis of 229 bird species. J. R. Soc. Interface 2012, 9:2563-2580.
74. Schwarz G. Estimating the dimension of a model. Annals Stat. 1978, 6:461-464.
75. Snow D.W. Observations on the Purple-throated Fruit-crow in Guyuna. Living Bird 1971, 10:5-15.
76. Snow, D.W., 1973. The Classification of the Cotingidae (Aves). Breviora 409.
77. Snow D.W. Tityrinae, Pipridae, Cotingidae. Check-list of Birds of the World Museum of Comparative Zoology 1979, 229-308. Harvard Univ, Cambridge, Massachusetts. M.A. Traylor (Ed.).
78. Snow D.W. The Cotingas 1982, Cornell Univ. Press, Ithaca, N.Y.
79. Snow, D.W. 2004. Family cotingidae (Cotingidae). In: del Hoyo, J., Elliott, A., Christie, D.A. (Eds.). Handbook of the birds of the world. vol. 9. Cotingas to pipits and wagtails Lynx Edicions, Barcelona, Spain, pp. 32-108.
80. Song S., Liu L., Edwards S.V., Wu S. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc. Natl. Acad. Sci. 2012, 109:14942-14947.
81. Stamatakis, A., 2006a. Phylogenetic Models of Rate Heterogeneity: A high Performance Computing Perspective. Parallel and Distributed Processing Symposium, 2006. IPDPS 2006. 20th International. IEEE, 8 pp.
82. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
83. Stamatakis A., Hoover P., Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst. Biol. 2008, 57:758-771.
84. Stoddard M.C., Prum R.O. Evolution of avian plumage color in a tetrahedral color space: a phylogenetic analysis of new world buntings. Am. Nat. 2008, 171:755-776.
85. Tello J.G., Moyle R.G., Marchese D.J., Cracraft J. Phylogeny and phylogenetic classification of the tyrant flycatchers, cotingas, manakins, and their allies (Aves: Tyrannides). Cladistics 2009, 25:429-467.
86. Ward P.S., Brady S.G., Fisher B.L., Schultz T.R. Phylogeny and biogeography of dolichoderine ants: effects of data partitioning and relict taxa on historical inference. Syst. Biol. 2010, 59:342-362.
87. Wiens J.J., Sparreboom M., Arntzen J.W. Crest evolution in newts: implications for reconstruction methods, sexual selection, phenotypic plasticity and the origin of novelties. J. Evol. Biol. 2011, 24:2073-2086.
88. Wu C.-H., Suchard M.A., Drummond A.J. Bayesian selection of nucleotide substitution models and their site assignments. Mol. Biol. Evol. 2013, 30:669-688.