Species tree estimation under joint modeling of coalescence and duplication: Sample complexity of quartet methods
Max Hill, Brandon Legried, Sébastien Roch
Abstract
We consider species tree estimation under a standard stochastic model of gene tree evolution that incorporates incomplete lineage sorting (as modeled by a coalescent process) and gene duplication and loss (as modeled by a branching process). Through a probabilistic analysis of the model, we derive sample complexity bounds for widely used quartet-based inference methods that highlight the effect of the duplication and loss rates in both subcritical and supercritical regimes.
Topics & Concepts
Coalescent theoryMathematicsCoalescence (physics)Branching processTree (set theory)InferenceGene duplicationApplied mathematicsAlgorithmStatisticsCombinatoricsComputer scienceGeneBiologyPhylogenetic treeArtificial intelligenceBiochemistryAstrobiologyGenomics and Phylogenetic StudiesGenetic diversity and population structure