Bayesian Estimation of Species Trees


DEB 743330 & 743616

On the Web:

Pearl Lab

Edwards Lab

Liu Lab


BEST References:

(ordered by date of publication)

Liu. Reconstructing posterior distributions of a species phylogeny using estimated gene tree distributions. Ph.D. Dissertation. The Ohio State University. 2006. (pdf).

Liu and Pearl. Species Trees from Gene Trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Systematic Biology, 56: 504-514, 2007. (pdf)

Edwards, Liu, and Pearl. High resolution species trees without concatenation. PNAS, 104:5936-5941, 2007. (pdf)

Edwards, Liu, and Pearl. High resolution species trees without concatenation: Supplemental Material. PNAS, 2007. (pdf)

Liu, Pearl, Brumfield, and Edwards. Estimating species trees using multiple allele data. Evolution,62:2080-2091, 2008 (pdf)

Liu. BEST: Bayesian estimation of species trees under the coalescent model.Bioinformatics, 24:2542-2543, 2008 (pdf)

Other Gene Tree versus Species Tree References:

(ordered by authors' name)

Akerborg, Sennblad, Arvestad, and Lagergren. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. PNAS, 106: 5714-5719, 2009. (pdf)

Brito and Edwards. Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica, 135: 439-455, 2009. (pdf)

Brumfield, Liu, Lum, and Edwards. Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae: Manacus) from multilocus sequence data. Systematic Biology, 57(5):719-731, 2008.(pdf)

Carstens and Knowles. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: An example from Melanoplus grasshoppers. Systematic Biology, 56:400-411, 2007. (pdf)

Degnan and Rosenberg. Discordance of species trees with their most likely gene trees. PLoS Genetics, 2: 762-768, 2006. (pdf)

Degnan and Salter. Gene tree distributions under the coalescent process. Evolution 59:24-37, 2005. (pdf)

Eckert and Carstens. Does gene flow destroy phylogenetic signal? The performance of three methods of estimating species phylogenies in the presence of gene flow. Molecular Phylogenetics and Evolution, 49: 832-842, 2008. (pdf)

Edwards. Is a new and general theory of molecular systematics emerging? Evolution 63:1-19, 2009.(pdf)

Edwards and Beerli. Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54:1839-1854, 2000. (pdf)

Hobolth, Christensen, Mailund, and Schierup. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a Coalescent Hidden Markov Model. PLoS Genetics, 3: 294-304, 2007. (pdf)

Hudson. Gene trees, species trees and the segregation of ancestral alleles. Genetics, 131:509-512, 1992. (pdf)

Kubatko, Carstens, and Knowles. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics, 25: 971-973, 2009. (pdf)

Kubatko and Degnan. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic Biology, 56:17-24, 2007. (pdf)

Maddison. Gene trees in species trees. Systematic Biology, 46:523-536, 1997. (pdf)

Maddison and Knowles. Inferring phylogeny despite incomplete lineage sorting. Systematic Biology, 55:21-30, 2006. (pdf)

Meng and Kubatko. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model. Theoretical Population Biology, 75: 35-45, 2009. (pdf)

Nichols. Gene trees and species trees are not the same. Trends in Ecology and Evolution, 16:358-364, 2001. (pdf)

Oliver. AUGIST: inferring species trees while accommodating gene tree uncertainty. Bioinformatics, 24: 2932-2933, 2008. (pdf)

Page. GeneTree: comparing gene and species phylogenies using reconciled trees. Bioinformatics, 14:819-820, 1998. (pdf)

Page and Charleston. From gene to organismal phylogeny: reconciled trees and the gene tree species tree problem. Molecular Phylogenetics and Evolution, 7:231-240, 1997. (pdf)

Pamilo and Nei. Relationships between gene trees and species trees. Molecular Biology and Evolution, 5:568-583, 1988. (pdf)

Rannala and Yang. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics, 164:1645-1656, 2003. (pdf)

Rosenberg. The probability of topological concordance of gene trees and species trees. Theoretical Population Biology, 61:225-247, 2002. (pdf)

Rosenberg and Tao. Discordance of species trees with their most likely gene trees: The case of five taxa. Systematic Biology, 57: 131-140, 2008. (pdf)

Slowinski, Knight, and Rooney. Inferring species trees from gene trees: a phylogenetic analysis of the elapidae (Serpentes) based on the amino acid sequences of venom proteins. Molecular Phylogenetics and Evolution, 8:349-362, 1997. (pdf)

Takahata. Gene genealogy in three related population: Consistency probability between gene and population trees. Genetics, 122:957-966, 1989. (pdf)

Than and Nakhleh. Species tree inference by Minimizing Deep Coalescences.PLOS Computational Biology, 5: issue 9, 2009. (pdf)