Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies
AbstractPhylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the inability to resolve relationships is often shown as a (soft) polytomy. Both types of polytomies have been traditionally studied in the context of gene tree reconstruction from sequence data. However, polytomies in the species tree cannot be detected or ruled out without considering gene tree discordance. In this paper, we describe a statistical test based on properties of the multi-species coalescent model to test the null hypothesis that a branch in an estimated species tree should be replaced by a polytomy. On both simulated and biological datasets, we show that the null hypothesis is rejected for all but the shortest branches, and in most cases, it is retained for true polytomies. The test, available as part of the Accurate Species TRee ALgorithm (ASTRAL) package, can help systematists decide whether their datasets are sufficient to resolve specific relationships of interest. View Full-Text
Scifeed alert for new publicationsNever miss any articles matching your research from any publisher
- Get alerts for new papers matching your research
- Find out the new papers from selected authors
- Updated daily for 49'000+ journals and 6000+ publishers
- Define your Scifeed now
Sayyari, E.; Mirarab, S. Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies. Genes 2018, 9, 132.
Sayyari E, Mirarab S. Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies. Genes. 2018; 9(3):132.Chicago/Turabian Style
Sayyari, Erfan; Mirarab, Siavash. 2018. "Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies." Genes 9, no. 3: 132.
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.