Appendix References used for constructing the phylogenetic tree

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Appendix 1. References used for constructing the phylogenetic tree






























Non-passerine families

Passerine families


Barhoum, D. N. & Burns, K. J. 2002 Phylogenetic relationships of the Wrentit based on mitochondrial cytochrome b sequences. Condor 104, 740-749.

Barker, F. K. 2004 Monophyly and relationships of wrens (Aves : Troglodytidae): a congruence analysis of heterogeneous mitochondrial and nuclear DNA sequence data. Mol. Phylo. Evol. 31, 486-504.

Benz, B. W., Robbins, M. B. & Peterson, A. T. 2006 Evolutionary history of woodpeckers and allies (Aves : Picidae): Placing key taxa on the phylogenetic tree. Mol. Phylo. Evol. 40, 389-399.

Bridge, E. S., Jones, A. W. & Baker, A. J. 2005 A phylogenetic framework for the terns (Sternini) inferred from mtDNA sequences: implications for taxonomy and plumage evolution. Mol. Phylo. Evol. 35, 459-469.

Canales-del Castillo, R., Klicka, J., Favela, S. & González-Rojas, J. I. 2010 Molecular phylogenetic analysis of an endangered Mexican sparrow: Spizella wortheni. Molecular Phylogenetics and Evolution 57, 1319-1322.

Carson, R. J. & Spicer, G. S. 2003 A phylogenetic analysis of the emberizid sparrows based on three mitochondrial genes. Mol. Phylo. Evol. 29, 43-57.

Cicero, C. & Johnson, N. K. 2002 Phylogeny and character evolution in the Empidonax group of tyrant flycatchers (Aves : Tyrannidae): A test of W. E. Lanyon's hypothesis using mtDNA sequences. Mol. Phylo. Evol. 22, 289-302.

Donne-Gousse, C., Laudet, V. & Hanni, C. 2002 A molecular phylogeny of Anseriformes based on mitochondrial DNA analysis. Mol. Phylo. Evol. 23, 339-356.

Griffiths, C. S., Barrowclough, G. F., Groth, J. G. & Mertz, L. 2004 Phylogeny of the Falconidae (Aves): a comparison of the efficacy of morphological, mitochondrial, and nuclear data. Mol. Phylo. Evol. 32, 101-109.

Griffiths, C. S., Barrowclough, G. F., Groth, J. G. & Mertz, L. A. 2007 Phylogeny, diversity, and classification of the Accipitridae based on DNA sequences of the RAG-1 exon. J. Avian Biol. 38, 587-602.

Hackett, S. J., Kimball, R. T., Reddy, S., Bowie, R. C. K., Braun, E. L., Braun, M. J., Chojnowski, J. L., Cox, W. A., Han, K. L., Harshman, J., Huddleston, C. J., Marks, B. D., Miglia, K. J., Moore, W. S., Sheldon, F. H., Steadman, D. W., Witt, C. C. & Yuri, T. 2008 A phylogenomic study of birds reveals their evolutionary history. Science 320, 1763-1768.

Han, K.-L., Robbins, M. B. & Braun, M. J. 2010 A multi-gene estimate of phylogeny in the nightjars and nighthawks (Caprimulgidae). Molecular Phylogenetics and Evolution 55, 443-453.

Helbig, A. J., Seibold, I., Bednarek, W., Brüning, H., Gaucher, P., Ristow, D., Scharlau, W., Schmidl, D. & Wink, M. 1994 Phylogenetic relationships among falcon species (genus Falco) according to DNA sequence variation of the cytochrome b gene. In Raptor conservation today (ed. B.-U. Meyburg & R. D. Chancellor), pp. 593-599: The Pica Press.

Jacobsen, F., Friedman, N. R. & Omland, K. E. 2010 Congruence between nuclear and mitochondrial DNA: Combination of multiple nuclear introns resolves a well-supported phylogeny of New World orioles (Icterus). Molecular Phylogenetics and Evolution 56, 419-427.

Johnson, K. P. & Clayton, D. H. 2000 Nuclear and mitochondrial genes contain similar phylogenetic signal for pigeons and doves (Aves: Columbiformes). Mol. Phylo. Evol. 14, 141-151.

Johnson, K. P., De Kort, S., Dinwoodey, K., Mateman, A. C., Ten Cate, C., Lessells, C. M. & Clayton, D. H. 2001 A molecular phylogeny of the dove genera Streptopelia and Columba. Auk 118, 874-887.

Johnson, K. P. & Sorenson, M. D. 1999 Phylogeny and biogeography of dabbling ducks (genus : Anas): a comparison of molecular and morphological evidence. Auk 116, 792-805.

Johnson, N. K. & Cicero, C. 2002 The role of ecologic diversification in sibling speciation of Empidonax flycatchers (Tyrannidae): Multigene evidence from mtDNA. Mol. Ecol. 11, 2065-2081.

Jonsson, K. A. & Fjeldsa, J. 2006 A phylogenetic supertree of oscine passerine birds (Aves : Passeri). Zool. Scr 35, 149-186.

Kennedy, M., Gray, R. D. & Spencer, H. G. 2000 The phylogenetic relationships of the shags and cormorants: Can sequence data resolve a disagreement between behavior and morphology? Mol. Phylo. Evol. 17, 345-359.

Klicka, J., Burns, K. & Spellman, G. M. 2007 Defining a monophyletic cardinalini: A molecular perspective. Mol. Phylo. Evol. 45, 1014-1032.

Klicka, J., Voelker, G. & Spellman, G. M. 2005 A molecular phylogenetic analysis of the "true thrushes" (Aves : Turdinae). Mol. Phylo. Evol. 34, 486-500.

Klicka, J., Zink, R. M. & Winker, K. 2003 Longspurs and snow buntings: phylogeny and biogeography of a high-latitude clade (Calcarius). Mol. Phylo. Evol. 26, 165-175.

Lerner, H. R. L., Klaver, M. C. & Mindell, D. P. 2008 Molecular phylogenetics of the Buteonine birds of prey (Accipitridae). Auk 125, 304-315.

Lerner, H. R. L. & Mindell, D. P. 2005 Phylogeny of eagles, Old World vultures, and other Accipitridae based on nuclear and mitochondrial DNA. Mol. Phylo. Evol. 37, 327-346.

Livezey, B. C. 1997 A phylogenetic analysis of basal Anseriformes, the fossil Presbyornis, and the interordinal relationships of waterfowl. Zool. J. Linn. Soc. 121, 361-428.

Livezey, B. C. 1998 A phylogenetic analysis of the Gruiformes (Aves) based on morphological characters, with an emphasis on the rails (Rallidae). Phil. Trans. R. Soc. Lond. B. Biol. Sci. 353, 2077-2151.

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. 2010 A comprehensive multilocus phylogeny for the wood-warblers and a revised classification of the Parulidae (Aves). Molecular Phylogenetics and Evolution 57, 753-770.

Lovette, I. J. & Rubenstein, D. R. 2007 A comprehensive molecular phylogeny of the starlings (Aves: Sturnidae) and mockingbirds (Aves: Mimidae): Congruent mtDNA and nuclear trees for a cosmopolitan avian radiation. Molecular Phylogenetics and Evolution 44, 1031-1056.

Lüpold, S., Linz, G. & Birkhead, T. R. 2009 Sperm design and variation in the New World blackbirds (Icteridae). Behav. Ecol. & Sociobiol. 63, 899-909.

McCraken, K. G. & Sheldon, F. H. 1998 Molecular and osteological heron phylogenies- Sources of incongruence. Auk 115, 127-141.

McGuire, J. A., Witt, C. C., Remsen, J. V., Dudley, R. & Altshuler, D. L. 2009 A higher-level taxonomy for hummingbirds. J. Ornithol 150, 155-165.

Murray, B. W., McGillivray, W. B., Barlow, J. C., Beech, R. N. & Strobeck, C. 1994 The use of cytochrome b sequence variation in estimation of phylogeny in the Vireonidae. Condor 96, 1037-1054.

Nguembock, B., Fjeldså, J., Couloux, A. & Pasquet, E. 2009 Molecular phylogeny of Carduelinae (Aves, Passeriformes, Fringillidae) proves polyphyletic origin of the genera Serinus and Carduelis and suggests redefined generic limits. Molecular Phylogenetics and Evolution 51, 169-181.

Ohlson, J., Fjeldsa, J. & Ericson, P. G. P. 2008 Tyrant flycatchers coming out in the open: phylogeny and ecological radiation of Tyrannidae (Aves, Passeriformes). Zool. Scr 37, 315-335.

Pons, J. M., Hassanin, A. & Crochet, P. A. 2005 Phylogenetic relationships within the Laridae (Charadriiformes : Aves) inferred from mitochondrial markers. Mol. Phylo. Evol. 37, 686-699.

Riesing, M. G., Kruckenhauser, L., Gamauf, A. & Haring, E. 2003 Molecular phylogeny of the genus Buteo (Aves: Accipitridae) based on mitochondrial marker sequences. Mol. Phylo. Evol. 27, 328-342.

Sheldon, F. H. & Slikas, B. 1997 Advances in Ciconiiform Systematics 1976-1996. Col. Waterbirds 20, 106-114.

Sheldon, F. H., Whittingham, L. A., Moyle, R. G., Slikas, B. & Winkler, D. W. 2005 Phylogeny of swallows (Aves: Hirundinidae) estimated from nuclear and mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 35, 254-270.

Thomas, G. H., Wills, M. A. & Szekely, T. 2004 A supertree approach to shorebird phylogeny - art. no. 28. BMC Evol. Biol 4, 24.

Thomassen, H. A., den Tex, R. J., de Bakker, M. A. G. & Povel, G. D. E. 2005 Phylogenetic relationships amongst swifts and swiftlets: A multi locus approach. Mol. Phylo. Evol. 37, 264-277.

Van der Meij, M. A. A., de Bakker, M. A. G. & Bout, R. G. 2005 Phylogenetic relationships of finches and allies based on nuclear and mitochondrial DNA. Mol. Phylo. Evol. 34, 97-105.

Voelker, G. & Klicka, J. 2008 Systematics of Zoothera thrushes, and a synthesis of true thrush molecular systematic relationships. Molecular Phylogenetics and Evolution 49, 377-381.

Weibel, A. C. & Moore, W. S. 2005 Plumage convergence in Picoides woodpeckers based on a molecular phylogeny, with emphasis on convergence in Downy and Hairy woodpeckers. Condor 107, 797-809.

Wink, M., El-Sayed, A. A., Sauer-Gurth, H. & Gonzalez, J. 2009 Molecular phylogeny of owls (Strigiformes) inferred from DNA sequences of the mitochondrial cytochrome b and the nuclear RAG-1 gene. Ardea 97, 581-591.

Yuri, T. & Mindell, D. P. 2002 Molecular phylogenetic analysis of Fringillidae, "New World nine-primaried oscines" (Aves : Passeriformes). Mol. Phylo. Evol. 23, 229-243.

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