Plumage evolution in relation to light environment in a novel clade of Neotropical tanagers

Molecular Phylogenetics and Evolution

Volumn 66, Issue 1, 2013, Pages 112-125

  Shultz, Allison J ^a,b   Burns, Kevin J ^a  

^a SAN DIEGO STATE UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

Hemispingus; Light environment; Plumage coloration; Polyphyly; Poospiza; Thlypopsis

Indexed keywords

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; DNA SEQUENCE; ECOSYSTEM; EVOLUTION; FEATHER; GENETICS; LIGHT; PHENOTYPE; PHYLOGENY; PIGMENTATION; SONGBIRD; SOUTH AMERICA; STATISTICAL MODEL;

ANIMALS; BAYES THEOREM; BIOLOGICAL EVOLUTION; ECOSYSTEM; FEATHERS; LIGHT; LIKELIHOOD FUNCTIONS; MODELS, BIOLOGICAL; PASSERIFORMES; PHENOTYPE; PHYLOGENY; PIGMENTATION; SEQUENCE ANALYSIS, DNA; SOUTH AMERICA;

AVES; EMBERIZINAE; HEMISPINGUS; POOSPIZA; THLYPOPSIS;

EID: 84870255084     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.09.011     Document Type: Article

References (101)

1. Akaike H. Information theory and an extension of the maximum likelihood principle. Second International Symposium on Information Theory 1973, 267-281. Akademiai Kiado, Budapest. B.N. Petrov, F. Csaki (Eds.).
2. Armenta J.K., Dunn P.O., Whittingham L.A. Effects of specimen age on plumage color. Auk 2008, 125:803-808.
3. Assis C.P., Raposo M.A., Parrini R. Validação de Poospiza cabanisi Bonaparte, 1850 (Passeriformes: Emberizidae). Rev. Bras. Ornitol. 2007, 15:103-112.
4. Badyaev A.V. Altitudinal variation in sexual dimorphism: a new pattern and alternative hypotheses. Behav. Ecol. 1997, 8:675.
5. Badyaev A.V. Covariation between life history and sexually selected traits: an example with cardueline finches. Oikos 1997, 80:128-138.
6. Barker F.K., Barrowclough G.F., Groth J.G. A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data. Proc. Roy. Soc. Lond. Ser. B: Biol. Sci. 2002, 269:295-308.
7. Barker, F.K., Burns, K.J., Klicka, J. Lanyon, S.M., Lovette, I.J., submitted for publication. Going to extremes: contrasting rates of diversification in a recent radiation of New World passerine birds. Sys. Biol.
8. Barker F.K., Cibois A., Schikler P., Feinstein J., Cracraft J. Phylogeny and diversification of the largest avian radiation. PNAS 2004, 101:11040-11045.
9. 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.
10. Blake E.R., Hocking P. Two new species of tanager from Peru. Wilson Bull. 1974, 86:321-324.
11. Bledsoe A.H. Nuclear DNA evolution and phylogeny of the New World nine-primaried oscines. Auk 1988, 105:504-515.
12. Brandley M.C., Leache A.D., Warren D.L., McGuire J.A. Are unequal clade priors problematic for Bayesian phylogenetics?. Syst. Biol. 2006, 55:138-146.
13. 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.
14. Burnham, K.P., Anderson, D.R., 2002. Model Selection and Multimodel Inference. A Practical Information-theoretic Approach. Springer, New York.
15. Burns K.J. Molecular systematics of tanagers (Thraupinae): Evolution and biogeography of a diverse radiation of Neotropical birds. Mol. Phylogen. Evol. 1997, 8:334-348.
16. Burns K.J., Naoki K. Molecular phylogenetics and biogeography of Neotropical tanagers in the genus Tangara. Mol. Phylogen. Evol. 2004, 32:838-854.
17. Burns K.J., Racicot R.A. Molecular phylogenetics of a clade of lowland tanagers: implications for avian participation in the great American interchange. Auk 2009, 126:635-648.
18. Burns K.J., Shultz A.J. Widespread cryptic dichromatism and ultraviolet reflectance in the largest radiation of Neotropical songbirds: implications of accounting for avian vision in the study of plumage evolution. Auk 2012, 129:211-221.
19. 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.
20. 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.
21. Butler M.A., King A.A. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. Am. Nat. 2004, 164:683-695.
22. Campagna L., Geale K., Handford P., Lijtmaer D.A., Tubaro P.L., Lougheed S.C. A molecular phylogeny of the Sierra-Finches (Phrygilus, Passeriformes): extreme polyphyly in a group of Andean specialists. Mol. Phylogen. Evol. 2011, 61:521-533.
23. Clements, J.F., Schulenberg, T.S., Iliff, M.J., Sullivan, B.L., Wood, C.L., 2011. The Clements Checklist of Birds of the World: Version 6.6. http://www.birds.cornell.edu/clementschecklist/downloadable-clements-checklist.
24. Derryberry E.P., Claramut S., Derryberry G., Chesser R.T., Cracraft J., Aleixo A., Pérez-Emán J.L., Remsen J.V., Brumfield R.T. Lineage diversification and morphological evolution in a large-scale continental radiation: the Neotropical ovenbirds and woodcreepers (Aves: Furnariidae). Evolution 2011, 65:2973-2986.
25. Doucet S.M., Hill G.E. Do museum specimens accurately represent wild birds? A case study of carotenoid, melanin, and structural colours in long-tailed manakins Chiroxiphia linearis. J. Avian Biol. 2009, 40:146-156.
26. Doucet S.M., Mennill D.J., Hill G.E. The evolution of signal design in manakin plumage ornaments. Am. Nat. 2007, 169:S62-S80.
27. Eaton M.D. Human vision fails to distinguish widespread sexual dichromatism among sexually "monochromatic" birds. PNAS 2005, 102:10942-10946.
28. Eaton M.D., Lanyon S.M. The ubiquity of avian ultraviolet plumage reflectance. Proc. Roy. Soc. Lond. Ser. B: Biol. Sci. 2003, 270:1721-1726.
29. Endler J.A. The color of light in forests and its implications. Ecol. Monogr. 1993, 63:2-27.
30. Endler J.A., Thery M. Interacting effects of lek placement, display behavior, ambient light, and color patterns in three neotropical forest-dwelling birds. Am. Nat. 1996, 148:421-452.
31. Felsenstein J. Phylogenies and the comparative method. Am. Nat. 1985, 125:1-15.
32. Fjeldså J. Biogeographic patterns and evolution of the avifauna of relict high-altitude woodlands of the Andes. Steenstrupia 1992, 18:9-62.
33. Fjeldså J., Rahbek C. Diversification of tanagers, a species rich bird group, from lowlands to montane regions of South America. Integr. Comp. Biol. 2006, 46:72-81.
34. García-Moreno J., Fjeldså J. Phylogenetic relationships among Hemispingus tanagers. Ornitol. Neotrop. 2003, 14:363-370.
35. García-Moreno J., Ohlson J., Fjeldså J. MtDNA sequences support monophyly of Hemispingus tanagers. Mol. Phylogen. Evol. 2001, 21:424-435.
36. Gomez D., Théry M. Influence of ambient light on the evolution of colour signals: comparative analysis of a Neotropical rainforest bird community. Ecol. Lett. 2004, 7:279-284.
37. Goméz D., Théry M. Simultaneous crypsis and conspicuousness in color patterns: comparative analysis of a Neotropical rainforest bird community. Am. Nat. 2007, 169:S42-S61.
38. Hansen T.F., Martins E.P. Translating between microevolutionary process and macroevolutionary patterns: the correlation structure of interspecific data. Evolution 1996, 50:1404-1417.
39. Hart N.S. Variations in cone photoreceptor abundance and the visual ecology of birds. J. Comp. Physiol. A 2001, 187:685-697.
40. Hart N.S., Partridge J.C., Cuthill I.C., Bennett A.T.D. Visual pigments, oil droplets, ocular media and cone photoreceptor distribution in two species of passerine bird: the blue tit (Parus caeruleus L.) and the blackbird (Turdus merula L.). J. Comp. Physiol. A 2000, 186:375-387.
41. Hausmann F., Arnold K.E., Marshall N.J., Owens I.P.F. Ultraviolet signals in birds are special. Proc. Roy. Soc. Lond. Ser. B: Biol. Sci. 2003, 270:61-67.
42. Heindl M., Winkler H. Interacting effects of ambient light and plumage color patterns in displaying Wire-tailed Manakins (Aves, Pipridae). Behav. Ecol. Sociobiol. 2003, 53:153-162.
43. Heindl M., Winkler H. Vertical lek placement of forest-dwelling manakin species (Aves, Pipridae) is associated with vertical gradients of ambient light. Biol. J. Linn. Soc. 2003, 80:647-658.
44. Hellmayr, C.E., 1938. Catalog of Birds of the Americas and the Adjacent Islands. Field Mus. of Nat. Hist. Publ. Zool., Series 13, Part XI.
45. Hilty, S., 2011. Family Thraupidae (Tanagers). In: Hoyo, J.D., Elliott, A., Christie, D.A. (Eds.), Handbook of the Birds of the World, vol. 16. Tanagers to New World Blackbirds. Lynx Edicions, Barcelona, pp. 46-329.
46. Huelsenbeck J.P., Ronquist F. MrBayes: a program for the Bayesian inference of phylogeny. Bioinformatics 2001, 17:754-755.
47. Isler M.L., Isler P.R. The Tanagers: Natural History, Distribution, and Identification 1999, Smithsonian Institution Press, Washington, DC.
48. Jaramillo, A., 2011a. Donacospiza albifrons, Long-tailed Reed Finch. In: del Hoyo, J., Elliott, A., Christie, D.A. (Eds.), Handbook of the Birds of the World, vol. 16. Tanagers to New World Blackbirds. Lynx Edicions, Barcelona, p. 616.
49. Jaramillo A. Poospiza nigrorufa, Black-and-rufous Warbling-finch. Tanagers to New World Blackbirds 2011, vol. 16:624-625. Lynx Edicions, Barcelona. J. del Hoyo, A. Elliott, D.A. Christie (Eds.).
50. Kass R.E., Raftery A.E. Bayes factors. J. Am. Stat. Assoc. 1995, 90:773-795.
51. King, A.A., Butler, M.A., 2009. Ouch: Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses (R package). http://ouch.r-forge.r-project.org.
52. Klicka J., Johnson K.P., Lanyon S.M. New World nine-primaried oscine relationships: constructing a mitochondrial DNA framework. Auk 2000, 117:321-336.
53. Klicka J., Burns K.J., Spellman G.M. Defining a monophyletic Cardinalini: a molecular perspective. Mol. Phylogen. Evol. 2007, 45:1014-1032.
54. Larkin M.A. ClustalW and ClustalX version 2.0. Bioinformatics 2007, 23:2947-2948.
55. Lougheed S.C., Freeland J.R., Handford P., Boag P.T. A molecular phylogeny of warbling-finches (Poospiza): paraphyly in a neotropical emberizid genus. Mol. Phylogen. Evol. 2000, 17:367-378.
56. Lovette I.J., Bermingham E. What is a wood-warbler? Molecular characterization of a monophyletic Parulidae. Auk 2002, 119:695-714.
57. Lowery G.H., Tallman D.H. A new genus and species of nine-primaried oscine of uncertain affinities from Peru. Auk 1976, 93:415-428.
58. Maddison, W.P., Maddison, D.R., 2010. Mesquite: A Modular System for Evolutionary Analysis. 2.74. http://mesquiteproject.org.
59. Marchetti K. Dark habitats and bright birds illustrate the role of the environment in species divergence. Nature 1993, 362:149-152.
60. Marshall D.C. Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees. Syst. Biol. 2010, 59:108-117.
61. Martin T.E., Badyaev A.V. Sexual dichromatism in birds: importance of nest predation and nest location for females versus males. Evolution 1996, 50:2454-2460.
62. Mauck W.M., Burns K.J. Phylogeny, biogeography, and recurrent evolution of divergent bill types in the nectar-stealing flowerpiercers (Thraupini: Diglossa and Diglossopis). Biol. J. Linn. Soc. 2009, 98:14-28.
63. 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.
64. McNaught M.K., Owens I.P.F. Interspecific variation in plumage colour among birds: species recognition or light environment?. J. Evol. Biol. 2002, 15:505-514.
65. McNett G.D., Marchetti K. Ultraviolet degradation in carotenoid patches: live versus museum specimens of wood warblers (Parulidae). Auk 2005, 122:793-802.
66. Miller, M., Holder, M., Vos, R., Midford, P., Liebowitz, T., Chan, L., Hoover, P., Warnow, T., 2009. The CIPRES Portal. http://www.phylo.org/sub_sections/portal.
67. Mundy N.I., Unitt P., Woodruff D.S. Skin from feet of museum specimens as a non-destructive source of DNA for avian genotyping. Auk 1997, 114:126-129.
68. Nylander J.A.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.
69. Paradis E., Claude J., Strimmer K. Ape: analyses of phylogenetics and evolution in R language. Bioinformatics 2004, 20:289-290.
70. Parker T.A., Stotz D.F., Fitzpatrick J.W. Ecological and distributional databases for neotropical birds. Neotropical Birds: Ecology and Conservation 1996, University of Chicago Press, Chicago. D. Stotz, T. Parker, J. Fitzpatrick, D. Moskovits (Eds.).
71. Paynter, R.A., Storer, R.W., 1970. In: Paynter Jr., R.A. (Ed.), Subfamilies Emberizinae, Catamblyrhynchinae, Cardinalinae, Thraupinae, and Tersininae. Check-list of Birds of the World, vol. 13. Museum of Comparative Zoology, Cambridge, MA.
72. Posada D. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253.
73. R Core Development Team, 2010. R: A Language and Environment for Statistical Computing. http://www.R-project.org/.
74. Rambaut, A., Drummond, A.J., 2007. TRACER. 1.5. (last accessed 09.09.12). http://beast.bio.ed.ac.uk/Tracer.
75. Remsen J.V. The "Coerebidae": a polyphyletic taxon that dramatizes historical over-emphasis on bill shape as a taxonomic character. J. Avian Biol. 2003, 34:321-323.
76. Remsen, J.V.J., Cadena, C.D., Jaramillo, A., Nores, M., Pacheco, J.F., Pérez-Emán, J.L., Robbins, M.B., Stiles, F.G., Stotz, D.F., Zimmer, K.J. Version 24 April 2012. A Classification of the Bird Species of South America. American Ornithologists' Union. http://www.museum.lsu.edu/~Remsen/SACCBaseline.html.
77. Ridgely R.S., Tudor G. The Birds of South America 1989, vol. I. University of Texas Press, Austin, The oscine passerines.
78. Ridgely R.S., Tudor G. Field Guide to the Songbirds of South America 2009, University of Texas Press, Austin.
79. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572.
80. Sanderson M.J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 2002, 19:101-109.
81. Sanderson, M.J., 2004. r8s v. 1.70. http://loco.biosci.arizona.edu/r8s/.
82. Sato A., Tichy H., O'Huigin C., Grant P.R., Grant B.R., Klein J. On the origin of Darwin's finches. Mol. Biol. Evol. 2001, 18:299-311.
83. Schluter D., Price T., Mooers A.Ø., Ludwig D. Likelihood of ancestor states in adaptive radiation. Evolution 1997, 51:1699-1711.
84. Sedano R.E., Burns K.J. Are the Northern Andes a species pump for Neotropical birds? Phylogenetics and biogeography of a clade of Neotropical tanagers (Aves: Thraupini). J. Biogeogr. 2010, 37:325-343.
85. Shultz, A.J., Rudy, J.C., 2011. Rtetracolorspace: Avian Tetrahedral Color Space (R package). http://code.google.com/p/rtetracolorspace/.
86. Sibley C.G., Monroe B.L. Distribution and Taxonomy of the Birds of the World 1990, Yale University Press, New Haven, Connecticut.
87. Snell-Rood E.C., Badyaev A.V. Ecological gradient of sexual selection: elevation and song elaboration in finches. Oecologia 2008, 157:545-551.
88. Soler J.J., Moreno J. Evolution of sexual dichromatism in relation to nesting habits in European passerines: a test of Wallace's hypothesis. J. Evol. Biol. 2012, 25:1614-1622.
89. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
90. Stamatakis A., Hoover P., Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 2008, 57:758-771.
91. 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.
92. Sugiura N. Further analysis of the data by Akaike's information criterion and the finite corrections. Commun. Stat. Theor. Method 1978, A7:13-26.
93. Swofford, D.L., 2003. PAUP*Version 4.0b10: Phylogenetic Analysis using Parsimony (*and other methods), Sunderland, Massachusetts, Sinaur Associates.
94. Thery M. Effects of light environment on color communication. Bird Coloration 2006, Harvard University Press, Cambridge. G. Hill, K. McGraw (Eds.).
95. Tubaro P.L., Lijtmaer D.A., Lougheed S.C. Cryptic dichromatism and seasonal color variation in the Diademed Tanager. Condor 2005, 107:648-656.
96. Vorobyev M. Coloured oil droplets enhance colour discrimination. Proc. Roy. Soc. Lond. Ser. B: Biol. Sci. 2003, 270:1255-1261.
97. Vorobyev M., Osorio D., Bennett A.T.D., Marshall N.J., Cuthill I.C. Tetrachromacy, oil droplets and bird plumage colours. J. Comp. Physiol. A 1998, 183:621-633.
98. Wallace A. Darwinism: An Exposition of the Theory of Natural Selection with Some of its Applications 1889, Macmillan, London.
99. Weske J.S., Terborgh J.W. Hemispingus parodii, a new species of tanager from Peru. Wilson Bull. 1974, 86:97-103.
100. Wier J.T., Bermingham E., Schluter D. The great American biotic interchange in birds. PNAS 2009, 106:21737-21742.
101. Yuri T., Mindell D.P. Molecular phylogenetic analysis of Fringillidae, 'New World nine-primaried oscines' (Aves: Passeriformes). Mol. Phylogen. Evol. 2002, 23:229-243.