title: TriLoNet: Piecing Together Small Networks to Reconstruct Reticulate Evolutionary Histories.
abstract: Phylogenetic networks are a generalization of evolutionary trees that can be used to represent reticulate processes such as hybridization and recombination. Here, we introduce a new approach called TriLoNet (Trinet Level- one Network algorithm) to construct such networks directly from sequence alignments which works by piecing together smaller phylogenetic networks. More specifically, using a bottom up approach similar to Neighbor-Joining, TriLoNet constructs level-1 networks (networks that are somewhat more general than trees) from smaller level-1 networks on three taxa. In simulations, we show that TriLoNet compares well with Lev1athan, a method for reconstructing level-1 networks from three-leaved trees. In particular, in simulations we find that Lev1athan tends to generate networks that overestimate the number of reticulate events as compared with those generated by TriLoNet. We also illustrate TriLoNet's applicability using simulated and real sequence data involving recombination, demonstrating that it has the potential to reconstruct informative reticulate evolutionary histories. TriLoNet has been implemented in JAVA and is freely available at https://www.uea.ac.uk/computing/TriLoNet.
authors.affiliation: School of Computing Sciences, University of East Anglia, Norwich, United Kingdom.
authors.forename: James
authors.initials: J
authors.lastname: Oldman
authors.affiliation: School of Computing Sciences, University of East Anglia, Norwich, United Kingdom.
authors.forename: Taoyang
authors.initials: T
authors.lastname: Wu
authors.affiliation: Delft Institute of Applied Mathematics, Delft University of Technology, Delft, The Netherlands.
authors.forename: Leo
authors.initials: L
authors.lastname: van Iersel
authors.affiliation: School of Computing Sciences, University of East Anglia, Norwich, United Kingdom vincent.moulton@cmp.uea.ac.uk.
authors.forename: Vincent
authors.initials: V
authors.lastname: Moulton
mesh_terms: D000465:Algorithms; D005075:Biological Evolution; D003198:Computer Simulation; D019143:Evolution, Molecular; D053263:Gene Regulatory Networks / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*
keywords: networks reconstruction; phylogenetic network; reticulate evolution; supernetwork.