Determining species tree topologies from clade probabilities under the coalescent
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Publication:1786519
DOI10.1016/J.JTBI.2011.08.006zbMATH Open1397.92478arXiv1103.0375OpenAlexW2964076513WikidataQ39714325 ScholiaQ39714325MaRDI QIDQ1786519FDOQ1786519
Authors: Elizabeth S. Allman, James H. Degnan, John A. Rhodes 
Publication date: 24 September 2018
Published in: Journal of Theoretical Biology (Search for Journal in Brave)
Abstract: One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy consensus algorithm, which consecutively accepts the most probable clades compatible with previously accepted clades, can be used for this second stage, this method is known to be statistically inconsistent under the multispecies coalescent model. This raises the question of whether it is theoretically possible to reconstruct the species tree from known probabilities of clades on gene trees. We investigate clade probabilities arising from the multispecies coalescent model, with an eye toward identifying features of the species tree. Clades on gene trees with probability greater than 1/3 are shown to reflect clades on the species tree, while those with smaller probabilities may not. Linear invariants of clade probabilities are studied both computationally and theoretically, with certain linear invariants giving insight into the clade structure of the species tree. For species trees with generic edge lengths, these invariants can be used to identify the species tree topology. These theoretical results both confirm that clade probabilities contain full information on the species tree topology and suggest future directions of study for developing statistically consistent inference methods from clade frequencies on gene trees.
Full work available at URL: https://arxiv.org/abs/1103.0375
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Problems related to evolution (92D15) Trees (05C05) Taxonomy, cladistics, statistics in mathematical biology (92B10)
Cites Work
Cited In (19)
- Enumeration of coalescent histories for caterpillar species trees and \(p\)-pseudocaterpillar gene trees
- Coalescent histories for discordant gene trees and species trees
- Identifiability of phylogenetic parameters from \(k\)-mer data under the coalescent
- Identifying species network features from gene tree quartets under the coalescent model
- Identifiability and reconstructibility of species phylogenies under a modified coalescent
- The tree of blobs of a species network: identifiability under the coalescent
- Computing the probability of gene trees concordant with the species tree in the multispecies coalescent
- Statistically consistent rooting of species trees under the multispecies coalescent model
- Multiple merger gene genealogies in two species: monophyly, paraphyly, and polyphyly for two examples of lambda coalescents
- Species Tree Inference from Genomic Sequences Using the Log-Det Distance
- Consistency and inconsistency of consensus methods for inferring species trees from gene trees in the presence of ancestral population structure
- Maximum tree: a consistent estimator of the species tree
- Species-Driven Persistent Phylogeny
- Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites
- Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent
- Split probabilities and species tree inference under the multispecies coalescent model
- The reconstructed tree in the lineage-based model of protracted speciation
- Identifying a species tree subject to random lateral gene transfer
- The probability of topological concordance of gene trees and species trees.
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