Print Email Facebook Twitter TriLoNet Title TriLoNet: Piecing Together Small Networks to Reconstruct Reticulate Evolutionary Histories Author Oldman, James (University of East Anglia) Wu, Taoyang (University of East Anglia) van Iersel, L.J.J. (TU Delft Discrete Mathematics and Optimization) Moulton, V.L. (University of East Anglia) Date 2016 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. Subject phylogenetic networkreticulate evolutionnetworks reconstructionsupernetwork To reference this document use: http://resolver.tudelft.nl/uuid:9eaec7cc-8c92-4af5-b8be-39b218342195 DOI https://doi.org/10.1093/molbev/msw068 Embargo date 2017-04-15 ISSN 0737-4038 Source Molecular Biology and Evolution, 33 (8), 2151-2162 Part of collection Institutional Repository Document type journal article Rights © 2016 James Oldman, Taoyang Wu, L.J.J. van Iersel, V.L. Moulton Files PDF 10236859.pdf 784.71 KB Close viewer /islandora/object/uuid:9eaec7cc-8c92-4af5-b8be-39b218342195/datastream/OBJ/view