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GENE TREE DISTRIBUTIONS UNDER THE COALESCENT PROCESS
Abstract
Under the coalescent model for population divergence, lineage sorting can cause considerable variability in gene trees generated from any given species tree. In this paper, we derive a method for computing the distribution of gene tree topologies given a bifurcating species tree for trees with an arbitrary number of taxa in the case that there is one gene sampled per species. Applications for gene tree distributions include determining exact probabilities of topological equivalence between gene trees and species trees and inferring species trees from multiple datasets. In addition, we examine the shapes of gene tree distributions and their sensitivity to changes in branch lengths, species tree shape, and tree size. The method for computing gene tree distributions is implemented in the computer program COAL.
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Cites
Genome-scale approaches to resolving incongruence in molecular phylogenies.
Rokas, A., Williams, B. L., King, N., & Carroll, S. B. (2003) · Nature · doi:10.1038/nature02053 · Cited by 1,512
Cited by
Is a new and general theory of molecular systematics emerging?
Edwards, S. V. (2009) · Evolution · doi:10.1111/j.1558-5646.2008.00549.x · Cited by 1,040
Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N. A., & RoyChoudhury, A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss086 · Cited by 965
Isolation with Migration Models for More Than Two Populations
Hey, J. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msp296 · Cited by 894
Coalescent-based species delimitation in an integrative taxonomy
Fujita, M. K., Leaché, A. D., Burbrink, F. T., McGuire, J. A., & Moritz, C. (2012) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2012.04.012 · Cited by 893
Delimiting Species without Monophyletic Gene Trees
Knowles, L. L., & Carstens, B. C. (2007) · Systematic Biology · doi:10.1080/10635150701701091 · Cited by 788
Metadata
- Authors
- Degnan, J. H., & Salter, L. A.
- Venue
- Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2005-01
- Volume
- 59
- Issue
- 1
- Pages
- 24-37
- ISSN
- 0014-3820 (ISSN-L)
- 1558-5646
- OpenAlex
- W2172696783
- Cited by
- 379
- References
- 1
- FWCI
- 4.96
- Type
- journal article
- Language
- en
- Open access
- closed
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- Degnan, J. H., & Salter, L. A. (2005). GENE TREE DISTRIBUTIONS UNDER THE COALESCENT PROCESS. Evolution. https://doi.org/10.1111/j.0014-3820.2005.tb00891.x
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
