PoMo: An Allele Frequency-Based Approach for Species Tree Estimation. Incomplete lineage sorting can cause incongruencies of the overall species-level phylogenetic tree with the phylogenetic trees for individual genes or genomic segments. If these incongruencies are not accounted for, it is possible to incur several biases in species tree estimation. Here, we present a simple maximum likelihood approach that accounts for ancestral variation and incomplete lineage sorting. We use a POlymorphisms-aware phylogenetic MOdel (PoMo) that we have recently shown to efficiently estimate mutation rates and fixation biases from within and between-species variation data. We extend this model to perform efficient estimation of species trees. We test the performance of PoMo in several different scenarios of incomplete lineage sorting using simulations and compare it with existing methods both in accuracy and computational speed. In contrast to other approaches, our model does not use coalescent theory but is allele frequency based. We show that PoMo is well suited for genome-wide species tree estimation and that on such data it is more accurate than previous approaches.
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References in zbMATH (referenced in 7 articles )
Showing results 1 to 7 of 7.
- Borges, Rui; Kosiol, Carolin: Consistency and identifiability of the polymorphism-aware phylogenetic models (2020)
- Kamm, Jack; Terhorst, Jonathan; Durbin, Richard; Song, Yun S.: Efficiently inferring the demographic history of many populations with allele count data (2020)
- Burden, Conrad J.; Griffiths, Robert C.: The transition distribution of a sample from a Wright-Fisher diffusion with general small mutation rates (2019)
- Burden, Conrad J.; Griffiths, Robert C.: The stationary distribution of a sample from the Wright-Fisher diffusion model with general small mutation rates (2019)
- Speed, Maria Simonsen; Balding, David Joseph; Hobolth, Asger: A general framework for moment-based analysis of genetic data (2019)
- Schrempf, Dominik; Hobolth, Asger: An alternative derivation of the stationary distribution of the multivariate neutral Wright-Fisher model for low mutation rates with a view to mutation rate estimation from site frequency data (2017)
- Hobolth, Asger; Siren, Jukka: The multivariate Wright-Fisher process with mutation: moment-based analysis and inference using a hierarchical beta model (2016)