The evolution of the spindlin gene in birds: Sequence analysis of an intron of the spindlin W and Z gene reveals four major divisions of the Psittaciformes

Molecular Phylogenetics and Evolution

Volumn 36, Issue 3, 2005, Pages 706-721

  De Kloet, Rolf S ^a   De Kloet, Siwo R ^a  

^a Animal Genetics Inc   (United States)

Author keywords

Indel; Intron; Phylogeny; Psittaciformes; Spindlin gene; W chromosome; Z chromosome

Indexed keywords

AVIAN PROTEIN; CELL CYCLE PROTEIN; MICROTUBULE ASSOCIATED PROTEIN; PHOSPHOPROTEIN; SPINDLIN;

ANIMAL; ARTICLE; CHROMOSOME; CLASSIFICATION; FEMALE; GENETICS; INTRON; MALE; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PSITTACINE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEXUAL DEVELOPMENT;

ANIMALS; AVIAN PROTEINS; BASE SEQUENCE; CELL CYCLE PROTEINS; CHROMOSOMES; EVOLUTION, MOLECULAR; FEMALE; INTRONS; MALE; MICROTUBULE-ASSOCIATED PROTEINS; MOLECULAR SEQUENCE DATA; PHOSPHOPROTEINS; PHYLOGENY; PSITTACIFORMES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEX CHARACTERISTICS;

AMAZONA; ARA; ARATINGA; AVES; CORACOPSIS VASA; LORIIDAE; LORIUS; MELOPSITTACUS UNDULATUS; NESTOR MERIDIONALIS; NESTOR NOTABILIS; PSITTACIDAE; PSITTACIFORMES; PSITTACUS ERITHACUS; PSITTRICHAS FULGIDUS; STRIGOPS HABROPTILUS;

EID: 23744439860     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2005.03.013     Document Type: Article

References (84)

1. F.K. Barker, G.F. Barrowclough, and J.D. Groth A phylogenetics hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data Proc. R. Soc. Lond. B Biol. Sci. 269 2002 295 305
2. W.M. Barnes PCR amplification of up to 35-kb DNA with high fidelity and high yield from lambda bacteriophage templates Proc. Natl. Acad. Sci. USA 91 1994 2216 2220
3. J.P. Birt, V.L. Friesen, J.M. Green, W.A. Montevecchi, and W.S. Davidson Cytochrome-b sequence variation among parrots Hereditas 117 1992 67 72
4. J.-R. Boisserie, F. Lihoreau, and M. Brunet The position of Hippopotamidae within Cetartiodactyla Proc. Natl. Acad. Sci. USA 102 2005 1537 1542
5. Brereton, J.L., 1953. Evolution within the Psittaciformes. In: Proceedings of the XIII International Ornithological Congress.
6. D.M. Brown, and C.A. Toft Molecular systematics and biogeography of the cockatoos (Psittaciformes: Cacatuini) Auk 116 1999 141 157
7. R. Chakrabarti, and C.E. Schutt The enhancement of PCR amplification by low molecular weight amides Nucleic Acids Res. 29 2001 2377 2381
8. L. Christides, L.R. Schodde, D.D. Shaw, and S.F. Maynes Relationships among the Australian-New Guinean parrots, lorikeets and Cockatoos (Aves: Psittaciformes): protein evidence Condor 93 1991 302 317
9. L. Christides, D.D. Shaw, and R. Schodde Chromosomal evolution in parrots, lorikeets and cockatoos (Aves: Psittaciformes) Hereditas 114 1991 47 56
10. N.J. Collar Family Psittacidae (Parrots) J. del Hoyo A. Elliott J. Sargatal Handbook of the birds of the world vol. 4 1998 Lynx Edicions Barcelona 280 477
11. A. Cooper, and D. Penny Mass survival of birds across the Cretaceous-Tertiary boundary: molecular evidence Science 275 1997 1109 1113
12. J. Cracraft Continental drift, paleoaclimatology and the evolution and biogeography of birds J. Zool. 169 1973 455 545
13. J. Cracraft Avian evolution, Gondwana biogeography and the Cretaceous-Tertiary mass extinction event Proc. R. Soc. Lond. B Biol. Sci. 268 2001 459 469
14. S.R. de Kloet Loss of the gene for the alpha subunit of ATP synthase (ATP5W1) from the W chromosome of the African grey parrot (Psittacus erithacus) J. Mol. Evol. 53 2001 135 143
15. S.R. de Kloet Molecular sex identification of tinamous with PCR using primers derived from the spindlin gene Mol. Ecol. Notes 1 2002 273 275
16. R.S. de Kloet, and S.R. de Kloet Evolution of the spindlin gene in birds: independent cessation of the recombination of sex chromosomes at the spindlin gene in neognathous birds and tinamous, a palaeognathous avian family Genetica 119 2003 333 342
17. E. de Kloet, and S.R. de Kloet Analysis of the beak and feather disease viral genome indicates the existence of several genotypes which have a complex psittacine host specificity Arch.Virol. 149 2004 2393 2412
18. G.J. Dyke, and G. Mayr Did parrots exist in the cretaceous period? Nature 399 1999 317 318
19. P.G.P. Ericson, U.S. Johansson, and T.J. Parsons Major divisions of oscines revealed byb insertions in the nuclear gene c-myc: a novel gene in avian phylogenetics Auk 117 2000 1077 1086
20. P.G.P. Ericson, L. Christides, A. Cooper, M. Irestedt, J. Jackson, U.S. Johansson, and J.A. Norman A Gondwanan origin of passerine birds supported by DNA sequences of the endemic New Zealand wrens Proc. R. Soc. Lond. B Biol. Sci. 269 2002 235 241
21. P.G.P. Ericson, M. Irestedt, and U.S. Johansson Evolution, biogeography, and patterns of diversification in passerine birds J. Avian Biol. 24 2003 3 15
22. A.E. Fidler, S. Kuhn, and E. Gwinner Convergent evolution of strigiform and caprimulgiform dark-activity is supported by phylogenetics analysis using the arylalkylamine N-acetyltransferase (Aanat) gene Mol. Phylogenet. Evol. 33 2004 908 921
23. J.M. Fornshaw Parrots of the world 1973 TFH Publications Neptune, New Jersey, USA
24. J. Garcia-Moreno, and D.P. Mindell Rooting a phylogeny with homologous genes on opposite sex chromosomes (Gametologs): a case study among avian CHD Mol. Biol. Evol. 17 2000 1826 1832
25. G. Giribet, and W.C. Wheeler On gaps Mol. Phylogenet. Evol. 13 1999 132 143
26. D. Graur, and W. Martin Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision Trends Genet. 20 2004 80 86
27. J.J. Groombridge, C.G. Jones, R.A. Nichols, M. Carlton, and M.W. Bruford Molecular phylogeny and morphological change in the Psittacula parakeets Mol. Phylogenet. Evol. 31 2004 96 108
28. S. Gustincich, G. Manfioletti, G. Del Sal, C. Scheider, and P.C. Carnici A fast method for high-quality genomic DNA extraction from whole human blood Biotechniques 11 1991 298 302
29. L.-J. Handley, H. Ceplitis, and H. Ellegren Evolutionary strata on the chicken Z chromosome: implications for sex chromosome evolution Genetics 167 2004 367 376
30. Harrison, G.L. (Abby), McLenachan, P.A., Philips, M.J. Slack, K.E. Cooper A., Penny, D., 2004. Four new avian mitochondrial genomes help get to basic evolutionary questions in the Late Cretaceous. Mol. Biol. Evol. 21, 974-983.
31. M. Hasegawa, K.Y. Kishino, and T. Yano Dating the human-ape splitting by a molecular clock of mitochondrial DNA J. Mol. Evol. 22 1985 160 174
32. S.B. Hedges, and S. Kumar Precision of molecular time estimates Trends Genet. 20 2004 242 247
33. B.L. Hoppe, B.M. Conti-Tronconi, and R.M. Horton Gel-loading dyes compatible with PCR Biotechniques 12 1992 679 680
34. W. Henke, K. Herdel, K. Jung, D. Schnorr, and S.A. Loening Betaine improves the PCR amplification of GC-rich DNA sequences Nucleic Acids Res. 25 1997 3957 3958
35. J.P. Huelsenbeck, B. Larget, and D. Swofford A compound Poison process for relaxing the molecular clock Genetics 154 2000 1879 1892
36. Y. Itoh, T. Hori, H. Saitoh, and S. Mizuno Chicken spindlin genes on W and Z chromosomes: transcriptional expression of both genes and dynamic behaviour of spindlin in interphase and mitotic cells Chrom. Res. 9 2001 283 299
37. A. Kawakita, T. Sota, J.S. Ascher, Ito M, H. Tanaka, and M. Kato Evolution and phylogenetic utility of alignment gaps within intron sequences of three nuclear genes in bumble bees (Bombus) Mol. Biol. Evol. 20 2003 87 92
38. P.R.J. Leeton, L. Christides, M. Westerman, and W.E. Boles Molecular phylogenetic affinities of the night parrot (Geopsittacus occidentalis) and the ground parrot (Pezoporus wallicus) Auk 111 1994 833 843
39. Q. Liu, E.C. Thorland, and S.S. Sommers Inhibition of PCR amplification by a point mutation downstream of a primer Biotechniques 22 1997 296 298
40. B.C. Livezey, and R.L. Zusi Higher-order phylogenetics of modern Aves based on comparative anatomy Neth. J. Zool. 51 2001 179 209
41. T. Maniatis, E.F. Fritsch, and J. Sambrook Molecular cloning; a laboratory manual 1983 Cold Spring Harbour Laboratory Cold Spring Harbour, New York
42. J. Mariaux, and M.J. Braun A molecular phylogenetic survey of the nightjars and allies (Caprimulgiformes) with special emphasis on the potoos (Nyctibiidae) Mol. Phylogenet. Evol. 6 1996 228 244
43. G. Mayr On the osteology and phylogenetic affinities of the Pseudasturidae-Lower Eocene stem-group representatives of parrots (Aves, Psittaciformes) Zool. J. Linn. Soc. 136 2002 715 729
44. G. Mayr Osteological evidence for paraphyly of the avian order Caprimulgiformes (nightjars and allies) J. Ornithol. 143 2002 82 97
45. G. Mayr, and M. Daniels Eocene parrots from Messel (Hessen, Germany) and the London Clay of Walton-on-the-Naze (Essex, England) Senck. Leth. 78 1998 157 177
46. G. Mayr, and U.B. Gohlich A new parrot from the Miocene of Germany, with comments of the variation of hypotarsus morphology in some Psittaciformes Belg. J. Zool. 134 2004 47 54
47. G. Mayr, A. Manegold, and U.S. Joahnsson Monophyletic groups within "higher land birds"-comparison of morphological and molecular data J. Zool. Syst. Evol. Res. 41 2003 233 248
48. L. McConlogue, M.A.D. Brow, and M.A. Innis Structure independent DNA amplification by PCR using 7-deaza-2′-deoxyguanosine Nucleic Acids Res. 16 1988 9869
49. S. McLoughlin The breakup history of Gondwana and it's impact on pre Cenozoic floristic provincialism Aust. J. Bot. 49 2001 271 300
50. M. Menossi, N. Cremonese, L.G. Maron, and P. Arruda Making colony PCR easier by adding gel-loading buffer to the amplification reaction Biotechniques 28 2000 424 426
51. S. Mita, R.C. Rizzuto, T. Moraes, S. Shanske, E. Arnaudo, G.M. Fabrizi, Y.S. Koga, S. DiMauro, and E.A. Schon Recombination vi flanking direct repeats is a major cause for large scale deletions of human mitochondrial DNA Nucleic Acids Res. 18 1990 561 567
52. C.Y. Miyaki, S.R. Matiolo, T. Burke, and A. Wajntal Parrot evolution and palaeographical events: mitochondrial DNA evidence Mol. Biol. Evol. 15 1998 544 551
53. J. Mlikovsky A new parrot (Aves: Psittacidae) from the early Miocene of the Czech republic Acta Soc. Zool. Bohem. 62 1998 335 341
54. M. Nikaido, P.R. Rooney, and N. Okada Phylogenetic relationships among the cetartiodactyls based on insertions of short and long interspersed elements: Hippopotamuses are the closest relatives of whales Proc. Natl. Acad. Sci. USA 96 1999 10261 10266
55. B. Oh, S.Y. Hwang, D. Solter, and B.B. Knowles Spindlin, a major maternal transcript expressed in the mouse during the transition from oocyte to embryo Development 124 1997 493 503
56. J.R. Ovenden, A.G. McKinlay, and R.H. Crozier Systematics and mitochondrial genome evolution of Australian rosellas (Aves: Platycercidae) Mol. Biol. Evol. 4 1987 526 543
57. S. Poe, and A.L. Chubb Birds in a bush: five genes indicate explosive evolution of avian orders Evolution 58 2004 404 415
58. D. Pomp, and F.J. Madrano Organic solvents as facilitators of polymerase chain reaction Biotechniques 10 1991 58 59
59. T.M. Prychitko, and W.S. Moore The utility of DNA sequences of an intron from the β-fibrinogen gene in phylogenetics analysis of woodpeckers (Aves: Picidae) Mol. Phylogenet. Evol. 8 1997 193 204
60. T.M. Prychitko, and W.S. Moore Comparative evolution of the mitochondrial cytochrome b gene and nuclear β-fibrinogen intron 7 in woodpeckers Mol. Biol. Evol. 17 2000 1101 1111
61. T.M. Prychitko, and W.S. Moore Alignment and phylogenetic analysis of β-fibrinogen intron 7 sequences among avian orders reveal conserved regions within the intron Mol. Biol. Evol. 20 2003 762 771
62. A. Rambaut, and L. Bromham Estimating divergence times from molecular sequences Mol. Biol. Evol. 15 1998 442 448
63. C.C. Ribas, and C.Y. Miyaki Molecular systematics in Aratinga parakeets: species limits and historical biogeography in the "solstitalis" group, and the systematic position of Nandayus nenday Mol. Phylogenet. Evol. 30 2003 663 675
64. A. Rokas, and P.W.H. Holland Rare genomic changes as a tool for phylogenetics Trends Ecol. Evol. 15 2000 454 459
65. M.A. Russello, and G. Amato A molecular phylogeny of Amazona: implications for Neotropical parrot biogeography, taxonomy, and conservation Mol. Phylogenet. Evol. 30 2004 421 477
66. N. Saitoh, and S. Ueda Evolutionary rates of insertion and deletion in noncoding nucleotide sequences of primates Mol. Biol. Evol. 11 1994 504 512
67. F. Sanger, S. Nicklen, and A.R. Coulson DNA sequencing with chain terminating inhibitors Proc. Natl. Acad. Sci. USA 74 1977 5463 5467
68. C.G. Sibley, and J. Ahlquist Phylogeny and classification of birds. A study in molecular evolution 1990 Yale University Press New Haven, London
69. M.P. Simmons, and H. Ochoterena Gaps as characters in sequence based phylogenetic analysis Syst. Biol. 49 2000 369 381
70. G.A. Smith Systematics of parrots Ibis 117 1975 18 68
71. G.A. Smith Biochemical systematics of parrots Aust. J. Zool. 32 1984 363 377
72. J.R. Smith, J.D. Carpten, M.S. Brownstein, S. Ghosh, V. Kagnuson, D.A. Gilbert, J.M. Trent, and F.S. Collins An approach to genotypical errors caused by non-templated nucleotide addition by Taq DNA polymerase Genome Res. 5 1995 312 317
73. T.K. Smith, C.M. Long, B. Bowman, and M.M. Manos Using co solvents to enhance PCR amplification Amplifications 5 1990 16 17
74. P.S. Soltis, D.E. Soltis, V. Savolainen, P.R. Crane, and T.G. Barraclough rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils Proc. Natl. Acad. Sci. USA 99 2002 4430 4433
75. T.A. Stidham A lower jaw from a Cretaceous parrot Nature 396 1998 29 30
76. H.M. Sundstrom, T. Webster, and H. Ellegren Molecular evolutionary analysis of avian and primate sex chromosome sequences Genetics 164 2003 259 268
77. Swofford, D.L., 1998. PAUP: phylogenetic analysis using parsimony. Version 4.0 b2. Sinauer, Sunderland, MA, USA.
78. J.D. Thompson, T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins The ClustalX interface: flexible strategies for multiple sequence alignment aide by quality analysis tools Nucleic Acids Res. 25 1997 4876 4882
79. M.A.M. Van Dijk, E. Paradis, F. Catzeflis, and W.W. de Jong The virtues of gaps: Xenarthran (Edentate) monophyly supported by a unique deletion in α-crystallin Syst. Biol. 48 1999 94 106
80. P.S. Walsh, D.A. Metzger, and R. Higuchi Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material Biotechniques 10 1991 506 513
81. A. Wetmore Descriptions of additional fossil birds from the Miocene of Nebraska Am. Mus. Novitates 211 1925 1 5
82. C.Y. Yan, and L.W. Kroenke A plate tectonic reconstruction of the southwest Pacific 0-100 Ma Proc. Ocean Drill. Prog. Sci. Res. 130 1993 697 709
83. N.D. Young, and J. Healy Gapcoder automates the use of indel characters in phylogenetic analysis BMC Bioinformatics 4 2003 6
84. L.I. Zon, M.D. Durfman, and S.H. Orkin The polymerase chain reaction miniprep Biotechniques 7 1991 696 698