Bayesian-weighted triplet and quartet methods for species tree inference
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Abstract: Inference of the evolutionary histories of species, commonly represented by a species tree, is complicated by the divergent evolutionary history of different parts of the genome. Different loci on the genome can have different histories from the underlying species tree (and each other) due to processes such as incomplete lineage sorting (ILS), gene duplication and loss, and horizontal gene transfer. The multispecies coalescent is a commonly used model for performing inference on species and gene trees in the presence of ILS. This paper introduces Lily-T and Lily-Q, two new methods for species tree inference under the multispecies coalescent. We then compare them to two frequently used methods, SVDQuartets and ASTRAL, using simulated and empirical data. Both methods generally showed improvement over SVDQuartets, and Lily-Q was superior to Lily-T for most simulation settings. The comparison to ASTRAL was more mixed - Lily-Q tended to be better than ASTRAL when the length of recombination-free loci was short, when the coalescent population parameter { heta} was small, or when the internal branch lengths were longer.
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Cited in
(8)- Comparing methods for species tree estimation with gene duplication and loss
- Species tree estimation under joint modeling of coalescence and duplication: sample complexity of quartet methods
- Site pattern probabilities under the multispecies coalescent and a relaxed molecular clock: theory and applications
- On the effect of intralocus recombination on triplet-based species tree estimation
- Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent
- Fast and accurate species trees from weighted internode distances
- Hypothesis tests for phylogenetic quartets, with applications to coalescent-based species tree inference
- Analytic solutions for three taxon ML trees with variable rates across sites
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