A comprehensive species-level molecular phylogeny of the New World blackbirds (Icteridae)

Molecular Phylogenetics and Evolution

Volumn 71, Issue 1, 2014, Pages 94-112

  Powell, Alexis F L A ^a   Barker, F Keith ^a   Lanyon, Scott M ^a   Burns, Kevin J ^b   Klicka, John ^c   Lovette, Irby J ^d  

^a UNIVERSITY OF MINNESOTA   (United States)

^b SAN DIEGO STATE UNIVERSITY   (United States)

^c UNIVERSITY OF NEVADA   (United States)

^d Fuller Evolutionary Biology Program   (United States)

Author keywords

Blackbird; Classification; Icteridae; Phylogeny; Systematics; Taxonomy

Indexed keywords

ANIMAL; ARTICLE; BLACKBIRD; CLASSIFICATION; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; ICTERIDAE; MITOCHONDRIAL GENOME; PHYLOGENY; SONGBIRD; TAXONOMY;

BLACKBIRD; CLASSIFICATION; ICTERIDAE; PHYLOGENY; SYSTEMATICS; TAXONOMY;

ANIMALS; BASE COMPOSITION; GENOME, MITOCHONDRIAL; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SONGBIRDS;

EID: 84890104722     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2013.11.009     Document Type: Article

References (102)

1. Allen E.S., Omland K.E. Novel intron phylogeny supports plumage convergence in orioles (Icterus). Auk 2003, 120:961-969.
2. Alström P., Olsson U., Lei F., Wang H., Gao W., Sundberg P. Phylogeny and classification of the Old World Emberizinae (Aves, Passeriformes). Mol. Phylogenet. Evol. 2008, 47:960-973.
3. American Ornithologists' Union Check-list of North American Birds 1983, American Ornithologists' Union, Washington, DC. sixth ed.
4. Barker F.K., Barrowclough G.F., Groth J.G. A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data. Proc. R. Soc. Lond. B. Biol. Sci. 2002, 269:295-308.
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. Barker F.K., Vandergon A.J., Lanyon S.M. Assessment of species limits among yellow-breasted meadowlarks (Sturnella spp.) using mitochondrial and sex-linked markers. Auk 2008, 125:869-879.
7. Beecher W.J. Convergent evolution in the American orioles. Wilson Bull. 1950, 62:51-86.
8. Beecher W.J. Adaptations for food-getting in the American blackbirds. Auk 1951, 68:411-440.
9. Blake E.R. Family Icteridae: American Orioles and Blackbirds. Check-list of Birds of the World: a Continuation of the Work of James L. Peters 1968, 138-202. Museum of Comparative Zoology, Cambridge, Massachusetts. R.A. Paynter (Ed.).
10. Björklund M. Evolution, phylogeny, sexual dimorphism and mating system in the grackles (Quiscalus spp.: Icterinae). Evolution 1991, 45:608-621.
11. Burns K.J. Molecular systematics of tanagers (Thraupinae): evolution and biogeography of a diverse radiation of Neotropical birds. Mol. Phylogenet. Evol. 1997, 8:334-348.
12. Burns K.J., Hackett S.J., Klein N.K. Phylogenetic relationships and morphological diversity in Darwin's finches and their relatives. Evolution 2002, 56:1240-1252.
13. Burns K.J., Hackett S.J., Klein N.K. Phylogenetic relationships of Neotropical honeycreepers and the evolution of feeding morphology. J. Avian Biol. 2003, 34:360-370.
14. Cadena C.D., Cuervo A.M., Lanyon S.M. Phylogenetic relationships of the Red-bellied Grackle (Icteridae: Hypopyrrhus pyrohypogaster) inferred from mitochondrial DNA sequence data. Condor 2004, 106:664-670.
15. Cardiff S.W., Remsen J.V. Type specimens of birds in the Museum of Natural Sciences, Louisiana State University. Occas. Pap. Mus. Nat. Sci. 1994, 68:1-33.
16. Darriba D., Taboada G.L., Doallo R., Posada D. JModelTest 2: more models, new heuristics and parallel computing. Nat. Methods 2012, 9:772.
17. D'Horta F.M., Cardosa da Silva J.M., Ribas C.C. Species limits and hybridization zones in Icterus cayanensis-chrysocephalus group (Aves: Icteridae). Biol. J. Linnean Soc. 2008, 95:583-597.
18. The Howard and Moore Complete Checklist of the Birds of the World 2003, Princeton University Press, Princeton, New Jersey. E.C. Dickinson (Ed.).
19. 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.
20. Dufort M.J., Barker F.K. Range dynamics, rather than convergent selection, explain the mosaic distribution of red-winged blackbird phenotypes. Ecol. Evol. doi 2013, 10.1002/ece3.859.
21. Dugand A., Eisenmann E. Rediscovery of, and new data on, Molothrus armenti Cabanis. Auk 1983, 100:991-992.
22. Eaton M.D. A phylogenetic perspective on the evolution of chromatic ultraviolet plumage coloration in grackles and allies (Icteridae). Auk 2006, 123:211-234.
23. Eaton M.D., Soberón J., Peterson A.T. Phylogenetic perspective on ecological niche evolution in American blackbirds (Family Icteridae). Biol. J. Linnean Soc. 2008, 94:869-878.
24. Fraga R.M. A new generic name for the Solitary Cacique. Bull. Brit. Ornithol. Club 2005, 125:286-287.
25. Fraga R.M. Phylogeny and behavioral evolution in the family Icteridae. Ornitol. Neotrop. 2008, 19:61-71.
26. Fraga R.M. Family Icteridae (New World blackbirds). Tanagers to New World Blackbirds 2011, vol. 16:684-807. Lynx Edicions, Barcelona. J. del Hoyo, A. Elliott, D.A. Christie (Eds.).
27. Freeman S., Zink R.M. A phylogenetic study of the blackbirds based on variation in mitochondrial DNA restriction sites. Syst. Biol. 1995, 44:409-420.
28. Friedman N.R., Hofmann C.M., Kondo B., Omland K.E. Correlated evolution of migration and sexual dichromatism in the New World Orioles (Icterus). Evolution 2009, 63:3269-3274.
29. Friedman N.R., Kiere L.M., Omland K.E. Convergent gains of red carotenoid-based coloration in the New World blackbirds. Auk 2011, 128:678-687.
30. Friedman N.R., McGraw K.J., Omland K.E. Evolution of carotenoid pigmentation in caciques and meadowlarks (Icteridae): repeated gains of red plumage coloration by carotenoid C4-oxygenation. Evolution 2013, 10.1111/evo.12304.
31. Gill, F., Donsker, D. (Eds.), 2012. IOC World Bird Names (version 3.2). (accessed 08.12.12). http://www.worldbirdnames.org.
32. Gruber K.F., Voss R.S., Jansa S.A. Base-compositional heterogeneity in the RAG1 locus among Didelphid marsupials: implications for phylogenetic inference and the evolution of GC content. Syst. Biol. 2007, 56:83-96.
33. Hellmayr, C.E., 1937. Catalogue of Birds of the Americas and the Adjacent Islands. Part X. Icteridae. Field Museum of Natural History, Zoological Series 13.
34. Hofmann C.M., Cronin T.W., Omland K.E. Using spectral data to reconstruct evolutionary changes in coloration: carotenoid color evolution in New World orioles. Evolution 2006, 60:1680-1691.
35. Hofmann C.M., Cronin T.W., Omland K.E. Melanin coloration in New World orioles II: ancestral state reconstruction reveals lability in the use of carotenoids and phaeomelanins. J. Avian Biol. 2007, 38:172-181.
36. Hofmann C.M., Cronin T.W., Omland K.E. Evolution of sexual dichromatism. 1. Convergent losses of elaborate female coloration in New World orioles (Icterus spp). Auk 2008, 125:778-789.
37. Hofmann C.M., Cronin T.W., Omland K.E. Evolution of sexual dichromatism. 2. Carotenoids and melanins contribute to sexual dichromatism in New World orioles (Icterus spp.). Auk 2008, 125:790-795.
38. Irwin R.E. The evolution of plumage dichromatism in the New World blackbirds: social selection on female brightness?. Am. Nat. 1994, 144:890-907.
39. Jacobsen F., Friedman N.R., Omland K.E. Congruence between nuclear and mitochondrial DNA: Combination of multiple nuclear introns resolves a well-supported phylogeny of New World orioles (Icterus). Mol. Phylogenet. Evol. 2010, 56:419-427.
40. Jacobsen F., Omland K.E. Species tree inference in a recent radiation of orioles (Genus Icterus): Multiple markers and methods reveal cytonuclear discordance in the northern oriole group. Mol. Phylogenet. Evol. 2011, 61:460-469.
41. Jaramillo A., Burke P. New World Blackbirds: the Icterids 1999, Princeton University Press, Princeton, NJ.
42. Johnson K.P., Lanyon S.M. Molecular systematics of the grackles and allies, and the effect of additional sequence (cytochrome b and ND2). Auk 1999, 116:759-768.
43. Johnson K.P., Lanyon S.M. Evolutionary changes in color patches of blackbirds are associated with marsh nesting. Behav. Ecol. 2000, 11:515-519.
44. Klein N.K., Burns K.J., Hackett S.J., Griffiths C.S. Molecular phylogenetic relationships among the wood warblers (Parulidae) and historical biogeography in the Caribbean Basin. J. Caribbean Ornithol. 2004, 17:3-17.
45. Klicka J., Johnson K.P., Lanyon S.M. New World nine-primaried oscine relationships: constructing a mitochondrial DNA framework. Auk 2000, 117:321-336.
46. Klicka J., Burns K., Spellman G.M. Defining a monophyletic Cardinalini: a molecular perspective. Mol. Phylogenet. Evol. 2007, 45:1014-1032.
47. Kondo B., Omland K.E. Ancestral state reconstruction of migration: multistate analysis reveals rapid changes in New World orioles (Icterus spp.). Auk 2007, 124:410-419.
48. Lanfear R., Calcott B., Ho S.Y.W., Guindon S. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol. Biol. Evol. 2012, 29:1695-1701.
49. Lanyon S.M. Interspecific brood parasitism in blackbirds (Icterinae): a phylogenetic perspective. Science 1992, 255:77-79.
50. Lanyon S.M. Polyphyly of the blackbird genus Agelaius and the importance of assumptions of monophyly in comparative studies. Evolution 1994, 48:679-693.
51. Lanyon S.M., Omland K.E. A molecular phylogeny of the blackbirds (Icteridae): five lineages revealed by cytochrome-b sequence data. Auk 1999, 116:629-639.
52. Lovette I.J., Bermingham E. What is a wood-warbler? Molecular characterization of a monophyletic parulidae. Auk 2002, 119:695-714.
53. Lovette I.J., Bermingham E., Ricklefs R.E. Mitochondrial DNA phylogeography and the conservation of endangered Lesser Antillean Icterus orioles. Conserv. Biol. 2001, 13:1088-1096.
54. Lovette I.J., Pérez-Emán J.L., Sullivan J.P., Banks R.C., Fiorentino I., Córdoba- Córdoba S., Echeverry-Galvis M., Barker F.K., Burns K.J., Klicka J., Lanyon S.M., Bermingham E. A comprehensive multilocus phylogeny for the wood-warblers and a revised classification of the Parulidae (Aves). Mol. Phylogenet. Evol. 2010, 57:753-770.
55. Lowther P.E. New name for the Bolivian Blackbird. Bull. Brit. Ornithol. Club 2001, 121:280-281.
56. Lowther P.E., Fraga R., Schulenberg T.S., Lanyon S.M. Nomenclatural solution for a polyphyletic Agelaius. Bull. Brit. Ornithol. Club 2004, 124:171-175.
57. Marshall D.C. Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees. Syst. Biol. 2010, 59:108-117.
58. Mazzoni L.G., Esser D., de Carvalho Dutra E., Perillo A., Morais R. New records of the Forbes's Blackbird Curaeus forbesi (Sclater, 1886) in the state of Minas Gerais, with comments on its conservation. Rev. Brasil. Ornitol. 2012, 20:44-47.
59. Miller, M.A., Pfeiffer, W., Schwartz, T., 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proc. Gateway Computing Environments Workshop (GCE 2010), 14 November 2010, New Orleans, Louisiana. Institute of Electrical and Electronics Engineers, pp. 1-8.
60. Omland K.E., Lanyon S.M. Reconstructing plumage evolution in orioles (Icterus): repeated convergence and reversal in patterns. Evolution 2000, 54:2119-2133.
61. Omland K.E., Lanyon S.M., Fritz S.J. A molecular phylogeny of the New World orioles (Icterus): the importance of dense taxon sampling. Mol. Phylogenet. Evol. 1999, 12:224-239.
62. Orians G.H. Blackbirds of the Americas 1985, University of Washington Press, Seattle.
63. Parker T.A., Remsen J.V. Fifty-two Amazonian bird species new to Bolivia. Bull. Brit. Ornithol. Club 1987, 107:94-107.
64. Powell, A.F.L.A., 2012. Molecular Phylogenetics of the New World Blackbirds (Icteridae). Ph.D. dissertation, University of Minnesota, Minneapolis and St. Paul.
65. Powell A.F.L.A., Barker F.K., Lanyon S.M. A complete species-level phylogeny of the grackles (Quiscalus spp.), including the extinct Slender-billed Grackle, inferred from mitochondrial DNA. Condor 2008, 110:718-728.
66. 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.
67. Price J.J. Evolution and life-history correlates of female song in the New World blackbirds. Behav. Ecol. 2009, 20:967-977.
68. Price J.J., Friedman N.R., Omland K.E. Song and plumage evolution in the New World Orioles (Icterus) show similar lability and convergence in patterns. Evolution 2007, 61:850-863.
69. Price J.J., Lanyon S.M. A robust phylogeny of the oropendolas: polyphyly revealed by mitochondrial sequence data. Auk 2002, 119:335-348.
70. Price J.J., Lanyon S.M. Reconstructing the evolution of complex bird song in the oropendolas. Evolution 2002, 56:1514-1529.
71. Price J.J., Lanyon S.M. Patterns of song evolution and sexual selection in the oropendolas and caciques. Behav. Ecol. 2004, 15:485-497.
72. Price J.J., Lanyon S.M. Song and molecular data identify congruent but novel affinities of the Green Oropendola (Psarocolius viridis). Auk 2004, 121:224-229.
73. Price J.J., Lanyon S.M., Omland K.E. Losses of female song with changes from tropical to temperate breeding in the New World blackbirds. Proc. R. Soc. Lond. B. Biol. Sci. 2009, 276:1971-1980.
74. Price J.J., Whalen L.M. Plumage evolution in the oropendolas and caciques: different divergence rates in polygynous and monogamous taxa. Evolution 2009, 63:2985-2998.
75. Raikow R.J. Appendicular myology and relationships of the New World nine-primaried oscines (Aves: Passeriformes). Bull. Carnegie Mus. Nat. Hist. 1978, 7:1-43.
76. Rambaut, A., Drummond, A.J., 2009. Tracer v1.5. http://tree.bio.ed.ac.uk/software/tracer.
77. Remsen Jr., J.V., Cadena, C.D., Jaramillo, A., Nores, M., Pacheco, J.F., Pérez-Emán, J.F., Robbins, M.B., Stiles, F.G., Stotz, D.F., Zimmer, K.J., Version 7 December 2012. A Classification of the Bird Species of South America. American Ornithologists' Union. http://www.museum.lsu.edu/~Remsen/SACCBaseline.html.
78. Ridgway R. The birds of North and Middle America. Part II 1902, Bull. U.S. National Mus, No. 50.
79. 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.
80. Schwarz G. Estimating the dimension of a model. Ann. Stat. 1978, 6:461-464.
81. Sclater P.L. Catalogue of the Birds in the British Museum. Coerebidae, Tanagridae, and Icteridae 1886, vol. 11. British Museum, London.
82. Searcy W.A., Yasukawa K., Lanyon S.M. Evolution of polygyny in the ancestors of Red-Winged Blackbirds. Auk 1999, 116:5-19.
83. Shawkey M.D., Hauber M.E., Estep L.K., Hill G.E. Evolutionary transitions and mechanisms of matte and iridescent plumage coloration in grackles and allies (Icteridae). J. R. Soc. Interface 2006, 3:777-786.
84. Short L.L. Sympatry of red-breasted meadowlarks in Argentina, and the taxonomy of meadowlarks (Aves: Leistes, Pezites, and Sturnella). Am. Mus. Novitates 1968, 2349:30.
85. Short L.L., Parkes K.C. The status of Agelaius forbesi Sclater. Auk 1979, 96:179-183.
86. Sibley C.G., Monroe B.L. Distribution and Taxonomy of Birds of the World 1990, Yale University Press, New Haven, CT.
87. Sturge R.J., Jacobsen F., Rosensteel B.B., Neale R.J., Omland K.E. Colonization of South America from Caribbean islands confirmed by molecular phylogeny with increased taxon sampling. Condor 2009, 111:575-579.
88. Swofford, D.L., 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer, Sunderland, Massachusetts.
89. Thomson R.C., Shaffer H.B. Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles. Syst. Biol. 2010, 59:42-58.
90. Tordoff H.B. Relationships in the New World nine-primaried oscines. Auk 1954, 71:273-284.
91. van Perlo B. A Field Guide to the Birds of Brazil 2009, Oxford University Press, New York.
92. Webster M.S. Sexual dimorphism, mating system and body size in New World Blackbirds. Evolution 1992, 46:1621-1641.
93. Webster J.D. Skeletal characters and the genera of blackbirds (Icteridae). Condor 2003, 105:239-257.
94. Wiens J.J. Can incomplete taxa rescue phylogenetic analyses from long-branch attraction?. Syst. Biol. 2005, 54:731-742.
95. Wiens J.J. Missing data and the design of phylogenetic analyses. J. Biomed. Inform. 2006, 39:34-42.
96. Wiens J.J., Fetzner J.W., Parkinson C.L., Reeder T.W. Hylid frog phylogeny and sampling strategies for speciose clades. Syst. Biol. 2005, 54:719-748.
97. Wiens J.J., Moen D.S. Missing data and the accuracy of Bayesian phylogenetics. J. Syst. Evol. 2008, 46:307-314.
98. Wiens J.J., Morrill M.C. Missing data in phylogenetic analysis: reconciling results from simulations and empirical data. Syst. Biol. 2011, 60:719-731.
99. Wiens J.J., Tiu J. Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling. PLoS ONE 2012, 7(8):e42925.
100. Wilgenbusch, J.C., Warren, D.L., Swofford, D.L., 2004. AWTY: A System for Graphical Exploration of MCMC Convergence in Bayesian Phylogenetic Inference. http://ceb.csit.fsu.edu/awty.
101. Yuri T., Mindell D.P. Molecular phylogenetic analysis of Fringillidae, "New World nine-primaried oscines" (Aves: Passeriformes). Mol. Phylogenet. Evol. 2002, 23:229-243.
102. Zwickl, D.J., 2006. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets Under the Maximum Likelihood Criterion. Ph.D. dissertation, University of Texas at Austin.