Assessing Phylogenetic Relationships among Galliformes: A Multigene Phylogeny with Expanded Taxon Sampling in Phasianidae

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Wang, Ning ^a,b,c   Kimball, Rebecca T ^b   Braun, Edward L ^b   Liang, Bin ^c   Zhang, Zhengwang ^a  

^a BEIJING NORMAL UNIVERSITY   (China)

^b UNIVERSITY OF FLORIDA   (United States)

^c HAINAN NORMAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMMOPERDIX; ARTICLE; BOOTSTRAPPING; CALOPERDIX; DUCKS AND GEESE; EXCALFACTORIA; GALLIFORMES; GENE LOCUS; GENUS; INTRON; MARGAROPERDIX; MITOCHONDRION; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PARTRIDGE; PHYLOGENY; QUAIL; SAMPLING; SEQUENCE ANALYSIS; TAXON; TREE OF LIFE; UNCERTAINTY; UNINDEXED SEQUENCE;

ANIMALS; ANSERIFORMES; CELL NUCLEUS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GALLIFORMES; GENETIC SPECIATION; INTRONS; MITOCHONDRIA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

AMMOPERDIX; ANSERIFORMES; AVES; CALOPERDIX; EXCALFACTORIA; GALLIFORMES; MARGAROPERDIX; PHASIANIDAE;

EID: 84878569337     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0064312     Document Type: Article

References (86)

1. del Hoyo J, Elliott A, Sargatal J (Eds.) (1994) Handbook of the Birds of the World, Vol. 2. New World Vultures to Guineafowls. Lynx Edicions, Barcelona.
2. Brown WR, Hubbard SJ, Tickle C, Wilson SA, (2003) The chicken as a model for large-scale analysis of vertebrate gene function. Nature Rev Genet 4: 87-98.
3. Dimcheff DE, Krishnan M, Mindell DP, (2001) Evolution and characterization of tetraonine endogenous retrovirus: a new virus related to avian sarcoma and leukosis viruses. J Virol 75: 2002-2009.
4. Kimball RT, St.Mary CM, Braun EL (2011) A Macroevolutionary Perspective on Multiple Sexual Traits in the Phasianidae (Galliformes). Int J Evol Biol Doi:10.4061/2011/423938.
5. Crowe TM, Bowie RCK, Bloomer P, Mandiwana TG, Hedderson TAJ, et al. (2006) Phylogenetics, biogeography and classification of, and character evolution in, gamebirds (Aves: Galliformes): effects of character exclusion, data partitioning and missing data. Cladistics 22: 495-532.
6. Kimball RT, Braun EL, Ligon JD, Lucchini V, Randi E, (2001) A molecular phylogeny of the peacock-pheasants (Galliformes: Polyplectron spp.) indicates loss and reduction of ornamental traits and display behaviours. Biol J Linn Soc 73: 187-198.
7. Kolm N, Stein RW, Mooers AØ, Verspoor JJ, Cunningham EJA, (2007) Can sexual selection drive female life histories? A comparative study on galliform birds. J Evol Biol 20: 627-638.
8. Nadeau NJ, Burke T, Mundy NI, (2007) Evolution of an avian pigmentation gene correlates with a measure of sexual selection. Proc R Soc B 274: 1807-1813.
9. Lislevand T, Figuerola J, Székely T, (2009) Evolution of sexual size dimorphism in grouse and allies (Aves: Phasianidae) in relation to mating competition, fecundity demands and resource division. J Evol Biol 22: 1895-1905.
10. IUCN Red list of Threatened species Version 2012.1. Available: http://www.iucnredlist.org. Accessed 2013 April 17.
11. Mooers AO, Heard SB, Chrostowski E (2005) Evolutionary heritage as a metric for conservation: in Phylogeny and Conservation (A. Purvis, T.L. Brooks and J.L. Gittleman, eds.) Oxford University Press, Oxford. 120-138.
12. Minh BQ, Klaere S, von Haeseler A, (2009) Taxon selection under split diversity. Syst Biol 58: 586-594.
13. Hackett SJ, Kimball RT, Reddy S, Bowie RCK, Braun EL, et al. (2008) A phylogenomic study of birds reveals their evolutionary history. Science 320: 1763-1767.
14. Kimball RT, Braun EL, Zwartjes PW, Crowe TM, Ligon JD, (1999) A molecular phylogeny of the pheasants and partridges suggests that these lineages are not monophyletic. Mol Phylogenet Evol 11: 38-54.
15. Armstrong MH, Braun EL, Kimball RT, (2001) Phylogenetic utility of avian ovomucoid intron G: a comparison of nuclear and mitochondrial phylogenetics in Galliformes. Auk 118: 799-804.
16. Dyke GJ, Gulas BE, Crowe TM, (2003) Suprageneric relationships of galliform birds (Aves, Galliformes): a cladistic analysis of morphological characters. Zool J Linn Soc 137: 227-244.
17. Kimball RT, Braun EL, (2008) A multigene phylogeny of Galliformes supports a single origin of erectile ability in non-feathered facial traits. J Avian Biol 39: 438-445.
18. Sibley CG, Ahlquist JE (1990) Phylogeny and Classification of Birds: A Study in Molecular Evolution. New Haven: Yale University Press.
19. Akishinonomiya F, Miyake T, Takada M, Ohno S, Kondo N, (1995) The genetic link between the Chinese bamboo partridge (Bambusicola thoracica) and the chicken and junglefowls of the genus Gallus. Proc Natl Acad Sci USA 92: 11053-11056.
20. Johnsgard PA (1986) The Pheasants of the World. New York: Oxford University Press.
21. Johnsgard PA (1988) The Quails, Partridges, and Francolins of the World. Oxford: Oxford University Press.
22. Beebe CW, (1914) Preliminary pheasant studies. Zoologica 1: 261-285.
23. Verheyen R, (1956) Contribution a l'anatomie et a la systematique des Galliformes. Bull Inst Roy Sci Nat Belg 32: 1-24.
24. Delacour J (1977) The pheasants of the world, 2nd edn. Hindhead, UK: World Pheasant Association and Spur Publications.
25. Prager EM, Wilson AC, Osuga DT, Feeney RE, (1976) Evolution of flightless land birds on southern continents: transferrin comparison shows monophyletic origin of ratites. J Mol Evol 8: 283-294.
26. Jolles J, Schoentgen F, Jolles P, Wilson AC, (1976) Amino acid sequence and immunological properties of chachalaca egg white lysozymes. J Mol Evol 8: 59-78.
27. Gutierrez RJ, Zink RM, Yang SY, (1983) Genic variation, systematic, and biogeographic relationships of some galliform birds. Auk 100: 33-47.
28. Henderson JY, Moir AJ, Fothergill LA, Fothergill JE, (1981) Sequences of sixteen phosphoserine peptides from ovalbumins of eight species. Eur J Biochem 114: 439-450.
29. Helm-Bychowski KM, Wilson AC, (1986) Rates of nuclear DNA evolution in pheasant-like birds: Evidence from restriction maps. Proc Natl Acad Sci USA 83: 688-692.
30. Kaiser VB, Van Tuinen M, Ellegren H, (2007) Insertion events of CR1 retrotransposable elements elucidate the phylogenetic branching order in galliform birds. Mol Biol Evol 24: 338-347.
31. Kriegs JO, Matzke AJM, Churakov G, Kuritzin A, Mayr G, et al. (2007) Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes). BMC Evol Biol 7: 190.
32. Eo SH, Bininda-Emonds ORP, Carroll JP, (2009) Phylogenetic supertree of the fowls (Galloanserae, Aves). Zool Scripta 38: 465-481.
33. Sorenson MD, Ast JC, Dimcheff DE, Yuri T, Mindell DP, (1999) Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Mol Phylogenet Evol 12: 105-114.
34. Kimball RT, Braun EL, Bowie RCK, Braun MJ, Chojnowski JL, et al. (2009) A set of resources to amplify nuclear regions across the avian genome. Mol Phylogenet Evol 50: 654-660.
35. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
36. Ogden TH, Rosenberg MS, (2006) Multiple sequence alignment accuracy and phylogenetic inference. Syst Biol 55: 314-328.
37. Smythe AB, Sanderson MJ, Nadler SA, (2006) Nematode small subunit phylogeny correlates with alignment parameters. Syst Biol 55: 972-992.
38. Katoh K, Asimenos G, Toh H, (2009) Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol 537: 39-64.
39. Notredame C, Higgins DG, Heringa J, (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205-217.
40. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 32: 1792-1797.
41. Stamatakis A, (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
42. Robinson DF, Foulds LR, (1981) Comparison of phylogenetic trees. Math Biosci 53: 131-147.
43. Posada D, Crandall KA, (1998) Modeltest: Testing the model of DNA substitution. Bioinformatics 14: 817-818.
44. Swofford DL (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4. Sinauer Associates, Sunderland, MA.
45. Felsenstein J, (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
46. Ronquist F, Huelsenbeck JP, (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
47. Gelman A, Rubin D, (1992) Inference from iterative simulation using multiple sequences. Stat Sci 7: 457-511.
48. Rambaut A, Drummond AJ (2007) Tracer v1.4, Available: http://beast.bio.ed.ac.uk/Tracer. Accessed 2013 April 17.
49. Wilgenbusch JC, Warren DL, Swofford DL (2004) AWTY: A system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. Available: http://ceb.csit.fsu.edu/awty. Accessed 2013 April 17.
50. Liu L, Yu L, (2011) Estimating species trees from unrooted gene trees. Syst Biol 60: 661-667.
51. Liu L, Yu L, Pearl DK, Edwards SV, (2009) Estimating species phylogenies using coalescence times among sequences. Syst Biol 58: 468-477.
52. Shaw TI, Ruan Z, Glenn T, Liu L (2012) Webserver for Species Tree Reconstruction.
53. Xia X, Xie Z, Salemi M, Chen L, Wang Y, (2003) An index of substitution saturation and its application. Mol Phylogenet Evol 26: 1-7.
54. Prychitko TM, Moore WS, (2000) Comparative evolution of the mitochondrial cytochrome b gene and nuclear beta-fibrinogen intron 7 in woodpeckers. Mol Biol Evol 17: 1101-1111.
55. Kubatko LS, Degnan JH, (2007) Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst Biol 56: 17-24.
56. Mayr G, (2008) The fossil record of galliform birds: comments on Croweet al. (2006). Cladistics 24: 74-76.
57. Braun EL, Kimball RT, (2002) Examining basal avian divergences with mitochondrial sequences: model complexity, taxon sampling, and sequence length. Syst Biol 51: 614-625.
58. McGuire JA, Linkem CW, Koo MS, Hutchison DW, Lappin AK, et al. (2007) Mitochondrial introgression and incomplete lineage sorting through space and time: phylogenetics of crotaphytid lizards. Evolution 61: 2879-2897.
59. Cox WA, Kimball RT, Braun EL, (2007) Phylogenetic position of the New World quail (Odontophoridae): Eight nuclear loci and three mitochondrial regions contradict morphology and the Sibley-Ahlquist tapestry. Auk 124: 71-84.
60. Kruger D, Kapturska D, Fischer C, Daniel R, Wubet T, (2012) Diversity measures in environmental sequences are hightly dependent on alignment quality-data from ITS and new LSU primers targeing Basidiomycetes. PLoS One. 7: e32139.
61. Wang N, Braun EL, Kimball RT, (2012) Testing hypotheses about the sister group of the Passeriformes using an Independent 30-locus data set. Mol Biol Evol 29: 737-750.
62. Smith JV, Braun El, Kimball RT, (2013) Ratite non-monophyly: Independent evidence from 40 novel loci. Syst Biol 62: 35-49.
63. Chojnowski JL, Kimball RT, Braun EL, (2008) Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes. Gene 410: 89-96.
64. Bonilla AJ, Braun EL, Kimball RT, (2010) Comparative molecular evolution and phylogenetic utility of 3′-UTRs and introns in Galliformes. Mol Phylogenet Evol 56: 536-542.
65. Braun EL, Kimball RT, Han KL, Iuhasz-Velez NR, Bonilla AJ, et al. (2011) Homoplastic microinversions and the avian tree of life. BMC Evol Biol 11: 141-151.
66. Han KL, Braun EL, Kimball RT, Reddy S, Bowie RCK, et al. (2011) Are transposable element insertions homoplasy free?: An examination using the avian tree of life. Syst Biol 60: 375-86.
67. Liu Z, He L, Yuan H, Yue B, Li J, (2012) CR1 retroposons provide a new insight into the phylogeny of Phasianidae species (Aves: Galliformes). Gene 502: 125-132.
68. Lemmon AR, Brown JM, Stanger-Hall K, Lemmon EM, (2009) The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst Biol 58: 130-145.
69. Roure B, Baurain D, Philippe H, (2012) Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. Mol Biol Evol 30: 197-214.
70. Wetmore A, (1960) A classification for the birds of the world. Smithson Miscellaneous Collection 139: 1-37.
71. Hudson GE, Lanzillotti PJ, (1964) Muscles of the pectroal limb in galliform birds. Amer Midl Natur 71: 1-113.
72. Hudson GE, Parker RA, Berge JV, Lanzillotti PJ, (1966) A numerical analysis of the modifications of the appendicular muscles in various genera of gallinaceous birds. Amer Midl Natur 76: 1-73.
73. Pereira SL, Baker AJ, (2006) A molecular timescale for galliform birds accounting for uncertainty in time estimates and heterogeneity of rates of DNA substitutions across lineages and sites. Mol Phylogenet Evol 38: 499-509.
74. Stock AD, Bunch TD, (1982) The evolutionary implications of chromosome banding pattern homologies in the bird order Galliformes. Cytogenet Cell Genet 34: 136-148.
75. Crowe TM, (1988) Molecules vs. morphology in phylogenetics: A non-controversy. Trans R Soc South Afr 46: 317-334.
76. Randi E, Fusco G, Lorenzini R, Timothy MC, (1991) Phylogenetic relationships and rates of allozyme evolution with the Phasianidae. Biochem Syst Ecol 19: 213-221.
77. Kornegay JR, Kocher TD, Williams LA, Wilson AC, (1993) Pathways of lysozyme evolution inferred from the sequences of cytochrome b in birds. J Mol Evol 37: 367-379.
78. Cohen C, Wakeling JL, Mandiwana-Neudani TG, Sande E, Dranzoa C, et al. (2012) Phylogenetic affinities of evolutionary enigmatic African galliforms: the Stone Partridge Ptilopachus petrosus and Nahan's Francolin Francolinus nahani, and support for their sister relationship within New World quails. Ibis 154: 768-780.
79. Lucchini V, Randi E (1999) Molecular evolution of the mtDNA control-region in galliform birds. In: Adams, N.J., Slotow, R.H. (Eds.), Proceedings of the 22 International Ornithological Congress. Durban. Birdlife South Africa, Johannesburg, pp. 732-739.
80. Shen YY, Liang L, Sun YB, Yue BS, Yang XJ, et al. (2010) A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae. BMC Evol Biol 10: 132.
81. Dimcheff DE, Drovetski SV, Mindell DP, (2002) Phylogeny of Tetraoninae and other galliform birds using mitochondrial 12S and ND2 genes. Mol Phylogenet Evol 24: 203-215.
82. Smith EJ, Shi L, Tu Z, (2005) Gallus gallus agrecan gene-based phylogenetic analysis of selected avian groups. Genetica 124: 23-32.
83. Kan XZ, Yang JK, Li XF, Chen L, Lei ZP, et al. (2010) Phylogeny of major lineages of galliform birds (Aves: Galliformes) based on complete mitochondrial genomes. Genet Mol Res 9: 1625-1633.
84. Meng Y, Dai B, Ran JH, Li J, Yue BS, (2008) Phylogenetic position of the genus Tetraophasis (Aves, Galliformes, Phasianidae) as inferred from mitochondrial and nuclear sequences. Biochem Syst Ecol 36: 626-637.
85. Bao XK, Liu NF, Qu JY, Wang XL, An B, et al. (2010) The phylogenetic position and speciation dynamics of the genus Perdix (Phasianidae, Galliformes). Mol Phylogenet Evol 56: 840-847.
86. Bloomer P, Crowe TM, (1998) Francolin phylogenetics: molecular, morphobehavioral, and combined evidence. Mol Phylogenet Evol 9: 236-254.