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A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
Liang Liu1, Lili Yu, Scott V Edwards
1Department of Agriculture and Natural Resources, Delaware State University, Dover, DE 19901, USA. lliu@desu.edu
BMC Evolutionary Biology
|October 13, 2010
Summary
This study introduces Maximum Pseudo-likelihood for Estimating Species Trees (MP-EST), a novel method for robustly estimating species trees from gene trees. MP-EST provides statistically consistent results, even with limited data or gene flow, offering a faster alternative for phylogenetic analysis.
Area of Science:
- Phylogenetics and evolutionary biology
- Computational biology and bioinformatics
Background:
- Estimating species trees from gene trees is crucial in phylogenetics.
- Existing maximum likelihood methods under the coalescent model have limitations.
- A statistically sound maximum likelihood estimate for species trees does not exist.
Purpose of the Study:
- To develop a novel method for estimating species trees using a pseudo-likelihood function.
- To obtain maximum pseudo-likelihood estimates (MPE) for species tree topology and branch lengths.
- To address limitations in existing maximum likelihood approaches for species tree inference.
Main Methods:
- Developed a pseudo-likelihood function for species tree estimation under the coalescent model.
- Introduced the Maximum Pseudo-likelihood for Estimating Species Trees (MP-EST) method.
- Validated the method's statistical consistency and performance through simulations and a mammal dataset.
Main Results:
- The MPE of the species tree is statistically consistent as the number of genes increases.
- MP-EST accurately estimates species trees, even in the anomaly zone, with convergence to the true tree.
- Applied MP-EST to mammal data, yielding results consistent with Bayesian methods but with more robust support values.
Conclusions:
- MP-EST consistently estimates species tree topology and branch lengths in coalescent units.
- The method is robust to a small amount of horizontal gene transfer (HGT).
- MP-EST is computationally efficient for large gene datasets and moderate species numbers.
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