Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent
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Publication:658995
DOI10.1007/S00285-010-0355-7zbMATH Open1230.92033arXiv0912.4472OpenAlexW2067677292WikidataQ51677123 ScholiaQ51677123MaRDI QIDQ658995FDOQ658995
James H. Degnan, Elizabeth S. Allman, John A. Rhodes
Publication date: 9 February 2012
Published in: Journal of Mathematical Biology (Search for Journal in Brave)
Abstract: Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals -- each with many genes -- splitting into new populations or species. The coalescent process, which models ancestry of gene copies within populations, is often used to model the probability distribution of gene trees given a fixed species tree. This multispecies coalescent model provides a framework for phylogeneticists to infer species trees from gene trees using maximum likelihood or Bayesian approaches. Because the coalescent models a branching process over time, all trees are typically assumed to be rooted in this setting. Often, however, gene trees inferred by traditional phylogenetic methods are unrooted. We investigate probabilities of unrooted gene trees under the multispecies coalescent model. We show that when there are 4 species with one gene sampled per species, the distribution of unrooted gene tree topologies identifies the unrooted species tree topology and some, but not all, information in the species tree edges (branch lengths). The location of the root on the species tree is not identifiable in this situation. However, for 5 or more species with one gene sampled per species, we show that the distribution of unrooted gene tree topologies identifies the rooted species tree topology and all its internal branch lengths. The length of any pendent branch leading to a leaf of the species tree is also identifiable for any species from which more than one gene is sampled.
Full work available at URL: https://arxiv.org/abs/0912.4472
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Applications of statistics to biology and medical sciences; meta analysis (62P10) Problems related to evolution (92D15)
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Cited In (18)
- Identifying species network features from gene tree quartets under the coalescent model
- Linearization of the Kingman coalescent
- Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss
- The tree of blobs of a species network: identifiability under the coalescent
- Determining species tree topologies from clade probabilities under the coalescent
- Species tree estimation under joint modeling of coalescence and duplication: sample complexity of quartet methods
- Rates of convergence in the two-island and isolation-with-migration models
- The probability distribution of ranked gene trees on a species tree
- A stochastic Farris transform for genetic data under the multispecies coalescent with applications to data requirements
- Classes of explicit phylogenetic networks and their biological and mathematical significance
- Statistically consistent rooting of species trees under the multispecies coalescent model
- On the number of non-equivalent ancestral configurations for matching gene trees and species trees
- Anomalous networks under the multispecies coalescent: theory and prevalence
- Hypothesis testing near singularities and boundaries
- Identifying circular orders for blobs in phylogenetic networks
- Inferring metric trees from weighted quartets via an intertaxon distance
- Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites
- Split probabilities and species tree inference under the multispecies coalescent model
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