Gene tree distributions under the coalescent process

Evolution

Volumn 59, Issue 1, 2005, Pages 24-37

  Degnan, James H ^a   Salter, Laura A ^a  

^a UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

Coalescence; Coalescent history; Lineage sorting; Maximum likelihood; Phylogenetics; Species tree

Indexed keywords

DIVERGENCE; PHYLOGENETICS;

EID: 13244292527     PISSN: 00143820     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.0014-3820.2005.tb00891.x     Document Type: Article

References (26)

1. Aldous, D. J. 2001. Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today. Stat. Sci. 16:23-34.
2. Feller, W. 1968. An introduction to probability theory and its application. Vol. I. 3rd ed. Wiley, New York.
3. Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Sunderland, MA.
4. Graham, R. L., D. E. Knuth, and O. Patshnik. 1994. Concrete mathematics. 2nd ed. Addison-Wesley, Boston, MA.
5. Hein, J. 1993. A heuristic method to reconstruct the history of sequences subject to recombination. J. Mol. Evol. 36:396-405.
6. Kingman, J. F. C. 1982. Exchangeability and the evolution of large populations. Pp. 97-112 in G. Koch and F. Spizzichino, eds. Exchangeability in probability and statistics. North-Holland, Amsterdam.
7. Knowles, L. L., and W. P. Maddison. 2002. Statistical phylogeography. Mol. Ecol. 11:2623-2635.
8. Maddison, W. P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
9. Pamilo, P., and M. Nei. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5(5):568-583.
10. Poe, S., and A. L. Chubb. 2004. Birds in a bush: five genes indicate explosive radiation of avian orders. Evolution 58:404-415.
11. Rannala, B., and Z. Yang. 2003. Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 164:1645-1656.
12. Robert, C., and G. Casella. 1999. Monte Carlo statistical methods. Springer, New York.
13. Rokas, A., B. Williams, N. King, and S. Carroll. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804.
14. Rosen, K. H. 1999. Discrete mathematics and its applications. 4th ed. WCB/McGraw-Hill, Boston, MA.
15. Rosenberg, N. A. 2002. The probability of topological concordance of gene trees and species trees. Theor. Popul. Biol. 61:225-247.
16. _. 2003. The shapes of neutral gene genealogies in two species: probabilities of monophyly, paraphyly, and polyphyly in a coalescent model. Evolution 57:1465-1477.
17. Sang, T., and Y. Zhong. 2000. Testing hybridization hypotheses based on incongruent gene trees. Syst. Biol. 49:422-434.
18. Syvanen, M. 1994. Horizontal gene transfer: evidence and possible consequences. Annu. Rev. Genet. 28:237-261.
19. Tajima, F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460.
20. Takahata, N. 1989. Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics 122:957-966.
21. Takahata, N., and M. Nei. 1985. Gene genealogy and variance of interpopulational nucleotide differences. Genetics 110:325-344.
22. Tavaré, S. 1984. Line-of-descent and genealogical processes, and their applications in population genetics models. Theor. Popul. Biol. 26:119-164.
23. Watterson, G. A. 1984. Lines of descent and the coalescent. Theor. Popul. Biol. 26:77-92.
24. Wu, C.-I. 1991. Inferences of species phylogeny in relation to segregation of ancient polymorphisms. Genetics 127:429-435.
25. Yang, Z. 2002. Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 162:1811-1823.
26. Yule, G. U. 1924. A mathematical theory of evolution based on the conclusions of Dr. J. C. Willis, F. R. S. Philos. Trans. R. Soc. Lond. B 213:21-87.