Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

• DOI: 10.1371/journal.pgen.1005896
• Publication Date: 2016-03-07T18:38:34Z
• Authors: Claudia Solís-Lemus; Cécile Ané
• Keywords: Coalescent theory; Computational phylogenetics; Lineage (genetic); Inheritance

Phylogenetic networks are necessary to represent the tree of life expanded by edges events such as horizontal gene transfers, hybridizations or flow. Not all species follow paradigm vertical inheritance their genetic material. While a great deal research has flourished into inference phylogenetic trees, statistical methods infer still limited and under development. The main disadvantage existing is lack scalability. Here, we present method from multi-locus data in pseudolikelihood framework. Our model accounts for incomplete lineage sorting through coalescent model, genes reticulation nodes network. Computation fast simple, it avoids burdensome calculation full likelihood which can be intractable with many species. Moreover, estimation at quartet-level added computational benefit that easily parallelizable. Simulation studies comparing our approach show much faster without compromising accuracy. We applied reconstruct evolutionary relationships among swordtails platyfishes (Xiphophorus: Poeciliidae), characterized widespread hybridizations.