Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting
By Claudia R. Solís-Lemus, Cécile Ané. PLoS Genetics, 2015
481 citations recorded by the source corpus.
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their genetic material. While a great deal of research has flourished into the inference of phylogenetic trees, statistical methods to infer phylogenetic networks are still limited and under development. The main disadvantage of existing methods is a lack of scalability. Here, we present a statistical method to infer phylogenetic networks from multi-locus genetic data in a pseudolikelihood framework. Our model accounts for incomplete lineage sorting through the coalescent model, and for horizontal inheritance of genes through reticulation nodes in the network. Computation of the pseudolikelihood is fast and simple, and it avoids the burdensome calculation of the full likelihood which can be intractable with many species. Moreover, estimation at the quartet-level has the added computational benefit that it is easily parallelizable. Simulation studies comparing our method to a full likelihood approach show that our pseudolikelihood approach is much faster without compromising accuracy. We applied our method to reconstruct the evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), which is characterized by widespread hybridizations.
Subfields: Genetics, Molecular Biology, Paleontology
View Paper: https://www.semanticscholar.org/paper/e663b7aaf9bdd6e99b3817fd3dff3a00e116b070
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Citations in the corpus
- The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves (2016, background): “Alternatively, it remains to be tested whether existing phylogenetic network methods (e.g. Yu et al. 2013, 2014; Sol ıs-Lemus & An e 2016) can handle the aforementioned complexity of the Neoaves problem.”
- Inferring Phylogenetic Networks Using PhyloNet (2017, background): “Identifiability of phylogenetic networks and their associated parameters has been discussed, in a preliminary way, in some papers (Yu et al. 2012; Yu and Nakhleh 2015b; Solís-Lemus and Ané 2016).”