Is homoplasy or lineage sorting the source of incongruent mtDNA and nuclear gene trees in the stiff-tailed ducks (Nomonyx-Oxyura)?

Systematic Biology

Volumn 54, Issue 1, 2005, Pages 35-55

  McCracken, Kevin G ^a   Sorenson, Michael D ^b  

^a UNIVERSITY OF ALASKA FAIRBANKS   (United States)

^b BOSTON UNIVERSITY   (United States)

Author keywords

Ancestral polymorphism; Homoplasy; Lineage sorting; Nomonyx; Oxyura; Oxyurinae; Stiff tailed ducks; Waterfowl

Indexed keywords

MITOCHONDRIAL DNA; PRIMER DNA;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; COMPARATIVE STUDY; DNA SEQUENCE; DUCK; GENETICS; GEOGRAPHY; HAPLOTYPE; HYBRIDIZATION; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPECIES DIFFERENCE; STATISTICAL MODEL;

ANIMALS; BASE SEQUENCE; CLASSIFICATION; DNA PRIMERS; DNA, MITOCHONDRIAL; DUCKS; EVOLUTION, MOLECULAR; GEOGRAPHY; HAPLOTYPES; HYBRIDIZATION, GENETIC; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; RESEARCH DESIGN; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 15944416738     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150590910249     Document Type: Article

References (54)

1. Adams, J., and E. R. Slavid. 1984. Cheek plumage in the Colombian ruddy duck Oxyura jamaicensis. Ibis 126:405-407.
2. Akaike, H. 1973. Information theory and an extension of the maximum likelihood principle. Pages 267-281 in Proceedings of Second International Symposium on Information Theory (B. N. Petrov and F. Csaki, eds.). Akademia Kiado, Budapest.
3. Avise, J. C. 1994. Molecular markers, natural history, and evolution. Chapman and Hall, New York.
4. Avise, J. C. 2000. Phylogeography: The history and formation of species. Harvard University Press, Cambridge, Massachusetts.
5. Avise, J. C., C. D. Ankney, and W. S. Nelson. 1990. Mitochondrial gene trees and the evolutionary relationship between mallard and black ducks. Evolution 44:109-1119.
6. Bremer, K. 1988. The limits of amino-acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803.
7. Clement M., D. Posada, K. A, Crandall. 2000. TCS: A computer program to estimate gene genealogies. Mol. Ecol. 9:1657-1660.
8. Crochet, P. A., and E. Desmerais. 2000. Slow rate of evolution in the mitochondrial control region of gulls (Aves: Laridae). Mol. Biol. Evol. 17:1797-1806.
9. Delacour, J., and E. Mayr. 1945. The family Anatidae. Wilson Bull. 56:3-55.
10. DeSalle, R., R. Absher, and G. Amato. 1994. Speciation and phylogenetic resolution. TREE 9:297-298.
11. Desjardins, P., and R. Morais. 1990. Sequence and gene organization of the chicken mitochondrial genome: A novel gene order in higher vertebrates. J. Mol. Biol. 212:599-634.
12. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
13. Fieldså, J. 1986. Color variation in the ruddy duck (Oxyura jamaicensis andina). Wilson Bull. 98:592-594.
14. Friesen, V. L, B. C. Congdon, H. E. Walsh, and T. P. Birt. 1997. Intron variation in marbled murrelets detected using analyses of single-stranded conformational polymorphisms. Mol. Ecol. 6:1047-1058.
15. Gladstein, D., and W. Wheeler. 2000. POY: Phylogeny reconstruction via direct optimization of DNA data, version 2.0. American Museum of Natural History, New York, New York.
16. Green, A. J., and B. Hughes. 1996. Action plan for the white-headed duck Oxyura leucocephala. Pages 119-146 in Globally threatened birds in Europe (B. Heredia, L. Rose, and M Painter, eds.). Council of Europe Publishing, Strasbourg, France.
17. Harshman, J. 1996. Phylogeny, evolutionary rates, and ducks. Ph.D. dissertation, University of Chicago, Chicago, Illinois.
18. Hasegawa, M. H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
19. Hoelzer, G. A., and D. J. Melnick. 1994. Patterns of speciation and limits to phylogenetic resolution. TREE 9:104-107.
20. Huelsenbeck, J. P., and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
21. Hughes, B., J. Criado, S. Delany, U. Gallo-Orsi, A. J. Green, M. Grussu, C. Perennou, and J. A. Torres. 1999. The status of the North American ruddy duck Oxyura jamaicensis in the Western Palearctic: Towards an action plan for eradication. Council of Europe Publication T-PVS/Birds (99) 9. Council of Europe Publishing, Strasbourg, France.
22. Johnsgard, P. A. 1965. Handbook of waterfowl behavior. Cornell Uni-versity Press, Ithaca, New York.
23. Johnsgard, P. A. 1978. Ducks, geese, and swans of the world University of Nebraska Press, Lincoln, Nebraska.
24. Johnsgard, P. A., and M. Carbonell. 1996. Ruddy ducks and other stifftails: Their behavior and biology. University of Oklahoma Press, Norman, Oklahoma.
25. Livezey, B. C. 1986. A phylogenetic analysis of recent anseriform genera using morphological characters. Auk 103:737-754.
26. Livezey, B. C. 1995. Phylogeny and comparative ecology of stifftailed ducks (Anatidae: Oxyurini). Wilson Bull. 107:214-234.
27. Livezey, B. C. 1997. A phylogenetic classification of waterfowl (Aves: Anseriformes), including selected fossil species. Ann. Carnegie Mus. 66:457-496.
28. Maddison, W. 1989. Reconstructing character evolution on polytomous cladograms. Cladistics 5:365-377.
29. Marshall, H. D., and A. J. Baker. 1997. Structural conservation and variation in the mitochondrial control region of fringilline finches (Fringilla spp.) and in the greenfinch (Carduelis chloris). Mol. Biol. Evol. 14:173-184.
30. McCracken, K. G., J. Harshman, D. A. McClellan, and A. D. Afton. 1999. Date set incongruence and correlated character evolution: An example of functional convergence in the hind-limbs of stifftail diving ducks. Syst. Biol. 48:683-714.
31. Moore, W. S. 1995. Inferring phylogenies from mtDNA variation: Mitochondrial gene trees versus nuclear-gene trees. Evolution 49:718-726.
32. Neigel, J. E., and J. C. Avise. 1986. Phylogenetic relationships of mitochondrial DNA under various demographic models of speciation. Pages 515-534 in Evolutionary processes and theory (E. Nevo and S. Karlin, eds.). Academic Press, New York.
33. O'hUigin, C., Y. Satta, N. Takahata, and J. Klein. 2002. Contribution of homoplasy and of ancestral polymorphism to the evolution of genes in Anthropoid primates. Mol. Biol. Evol. 19:1501-1513.
34. Pacheco, N. M., B. C. Congdon, and V. L. Friesen. 2002. The utility of nuclear introns for investigating hybridization and genetic introgression: A case study involving Brachyramphus murrelets. Conserv. Genet. 3:175-182.
35. Posada, D., and K. A. Crandall. 1998. Modeltest: Testing the model of DNA substitution. Bioinformatics 14:817-818.
36. Primmer, C. R., T. Borge, J. Lindell, and G. P. Sætre. 2002. Single-nucleotide polymorphism characterization in species with limited available sequence information: High nucleotide diversity revealed in the avian genome. Mol. Ecol. 11:603-612.
37. Quinn, T. W., and A. C. Wilson. 1993. Sequence evolution in and around the mitochondrial control region in birds. J. Mol. Evol. 37:417-425.
38. Raikow, R. J. 1970. Evolution of diving adaptations in the stiff-tailed ducks. Univ. Calif. Publ. Zool. 94:1-52.
39. Rambaut, A., and N. C. Crassly. 1997. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
40. Saitou, N., and M. Nei. 1986. The number of nucleotides required to determine the branching order of three species, with special reference to the human-chimpanzee-gorilla divergence. J. Mol. Evol. 24:189-204.
41. Shimodaira, H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51:492-508.
42. Sorenson, M. D. 1999. TreeRot, version 2. Boston University, Boston, Massachusetts.
43. Sorenson, M. D., J. C. Ast, D. E. Dimcheff, T. Yuri, and D. P. Mindell. 1999. Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Mol. Phylogenet. Evol. 12:105-114.
44. Sorenson, M. D., and R. C. Fleischer. 1996. Multiple independent transpositions of mitochondrial DNA control region sequences to the nucleus. Proc. Nat. Acad. Sci. USA 93:15239-15243.
45. Sorenson, M. D., and R. B. Payne. 2001. A single, ancient origin of obligate brood parasitism in African finches: Implications for host-parasite coevolution. Evolution 55:2550-2567.
46. Sorenson, M. D., and T. W. Quinn, T. W. 1998. Numts: A challenge for avian systematics and population biology. Auk 115:214-221.
47. Sraml, M., L. Christidis, S. Easteal, P. Horn, and C. Collet. 1996. Molecular relationships within Australian waterfowl (Anseriformes). Aust. J. Zool. 44:47-58.
48. Swofford, D. L. 1998. PAUP*: Phylogenetic analysis using parsimony (and other methods), version 4. Sinauer Associates, Sunderland, Massachusetts.
49. Tajima, F. 1983. Evolutionary relationships of DNA sequences in finite populations. Genetics 105:437-460.
50. Takahata, M. 1995. Mhc diversity and selection. Immunol. Rev. 143:225-247.
51. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties, and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
52. Todd, F. S. 1979. Waterfowl: Ducks, geese, and swans of the world. Sea World Press, Sand Diego, California.
53. Walsh, H. E., M. G. Kidd, T. Moum, and V. L. Friesen. 1999. Polytomies and the power of phylogenetic inference. Evolution 53:932-937.
54. Wheeler, W. C. 1996. Optimization alignment: The end of multiple sequence alignment in phylogenetics? Cladistics 12:1-9.