Discordance of species trees with their most likely gene trees: The case of five taxa

Systematic Biology

Volumn 57, Issue 1, 2008, Pages 131-140

  Rosenberg, Noah A ^a,b   Tao, Randa ^b  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Coalescence; Lineage sorting; Probability

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; PHYLOGENY; SPECIES DIFFERENTIATION;

GENETIC SPECIATION; MODELS, GENETIC; PHYLOGENY;

EID: 47749087905     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150801905535     Document Type: Article

References (19)

1. Aldous, D. J. 2001. Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today. Stat. Sci. 16:23-34. (Pubitemid 33632845)
2. Brown, J. K. M. 1994. Probabilities of evolutionary trees. Syst. Biol. 43:78-91. (Pubitemid 24979625)
3. Degnan, J. H. 2005. Gene tree distributions under the coalescent process. PhD thesis, University of New Mexico, Albuquerque.
4. Degnan, J. H. and N. A. Rosenberg. 2006. Discordance of species trees with their most likely gene trees. PLoS Genet. 2:762-768. (Pubitemid 43794324)
5. Degnan, J. H. and L. A. Salter. 2005. Gene tree distributions under the coalescent process. Evolution 59:24-37. (Pubitemid 40181296)
6. Harding, E. F. 1971. The probabilities of rooted tree-shapes generated by random bifurcation. Adv. Appl. Prob. 3:44-77.
7. Hein, J., M. H. Schierup, and C.Wiuf. 2005. Gene genealogies, variation and evolution. Oxford University Press, Oxford, UK.
8. Maddison,W. P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
9. Nichols, R. 2001. Gene trees and species trees are not the same. Trends Ecol. Evol. 16:358-364. (Pubitemid 32525776)
10. Nordborg, M. 2003. Coalescent theory. Pages 602-635. in Handbook of statistical genetics, 2nd ed. (D. J. Balding, M. Bishop, and C. Cannings, editors), Wiley, Chichester, UK.
11. Pamilo, P. and M. Nei. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5:568-583.
12. Rosenberg, N. A. 2002. The probability of topological concordance of gene trees and species trees. Theor. Popul. Biol. 61:225-247. (Pubitemid 38042804)
13. Rosenberg, N. A. 2006. The mean and variance of the numbers of r - pronged nodes and r-caterpillars in Yule-generated genealogical trees. Ann. Comb. 10:129-146. (Pubitemid 43954175)
14. Rosenberg, N. A. 2007. Counting coalescent histories. J. Comput. Biol. 14:360-377. (Pubitemid 46742190)
15. Sjödin, P., I. Kaj, S. Krone, M. Lascoux, and M. Nordborg. 2005. On the meaning and existence of an effective population size. Genetics 169:1061-1070. (Pubitemid 40404333)
16. Steel, M. and A. McKenzie. 2001. Properties of phylogenetic trees generated by Yule-type speciation models. Math. Biosci. 170:91-112. (Pubitemid 32230649)
17. Takahata, N. 1989. Gene genealogy in three related populations: Consistency probability between gene and population trees. Genetics 122:957-966.
18. Takahata, N. and M. Nei. 1985. Gene genealogy and variance of interpopulational nucleotide differences. Genetics 110:325-344. (Pubitemid 15116808)
19. Tavaré, S. 1984. Line-of-descent and genealogical processes, and their applications in population genetics models. Theor. Popul. Biol. 26:119-164.