Fast coalescent-based computation of local branch support from quartet frequencies

2016/01/31 by Erfan Sayyari, Siavash Mirarab · 39 citations
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Chromosomal and Genetic Variations #Genetic diversity and population structure #Genomics and Phylogenetic Studies #q-bio.PE #q-bio.QM

paper · pdf · doi:10.1093/molbev/msw079

openalex publication_date 2016/04/15 · arxiv created 2016/05/08 · arxiv updated 2016/05/10 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01

Abstract

Species tree reconstruction is complicated by effects of Incomplete Lineage Sorting (ILS), commonly modeled by the multi-species coalescent model. While there has been substantial progress in developing methods that estimate a species tree given a collection of gene trees, less attention has been paid to fast and accurate methods of quantifying support. In this paper, we propose a fast algorithm to compute quartet-based support for each branch of a given species tree with regard to a given set of gene trees. We then show how the quartet support can be used in the context of the multi-species coalescent model to compute i) the local posterior probability that the branch is in the species tree and ii) the length of the branch in coalescent units. We evaluate the precision and recall of the local posterior probability on a wide set of simulated and biological data, and show that it has very high precision and improved recall compared to multi-locus bootstrapping. The estimated branch lengths are highly accurate when gene trees have little error, but are underestimated when gene tree estimation error increases. Computation of both branch length and local posterior probability is implemented as a new feature in ASTRAL.

Citations

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• Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
• A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
• Gene Trees in Species Trees

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