Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

PLoS Genet. 2016 Mar 7;12(3):e1005896. doi: 10.1371/journal.pgen.1005896. eCollection 2016 Mar.

Abstract

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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computer Simulation
  • Evolution, Molecular*
  • Gene Transfer, Horizontal*
  • Likelihood Functions
  • Models, Genetic
  • Phylogeny*

Grants and funding

This work was supported by the National Science Foundation with grants:(http://www.nsf.gov) DEB 0936214 and DEB 1354793 to CA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.