Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent
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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.
Recommendations
- Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites
- Identifiability and reconstructibility of species phylogenies under a modified coalescent
- Split probabilities and species tree inference under the multispecies coalescent model
- Determining species tree topologies from clade probabilities under the coalescent
- Maximum tree: a consistent estimator of the species tree
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Cited in
(25)- Distance-based species tree estimation under the coalescent: information-theoretic trade-off between number of loci and sequence length
- Split probabilities and species tree inference under the multispecies coalescent model
- On the number of non-equivalent ancestral configurations for matching gene trees and species trees
- Identifiability and reconstructibility of species phylogenies under a modified coalescent
- Identifying species network features from gene tree quartets under the coalescent model
- Determining species tree topologies from clade probabilities under the coalescent
- Computing the probability of gene trees concordant with the species tree in the multispecies coalescent
- Rates of convergence in the two-island and isolation-with-migration models
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- Species tree estimation under joint modeling of coalescence and duplication: sample complexity of quartet methods
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- Inconsistency of parsimony under the multispecies coalescent
- Inferring metric trees from weighted quartets via an intertaxon distance
- Hypothesis testing near singularities and boundaries
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