Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees

Abstract

Motivation: Gene duplication (D), transfer (T), loss (L) and incomplete lineage sorting (I) are crucial to the evolution of gene families and the emergence of novel functions. The history of these events can be inferred via comparison of gene and species trees, a process called reconciliation, yet current reconciliation algorithms model only a subset of these evolutionary processes.Results: We present an algorithm to reconcile a binary gene tree with a nonbinary species tree under a DTLI parsimony criterion. This is the first reconciliation algorithm to capture all four evolutionary processes driving tree incongruence and the first to reconcile non-binary species trees with a transfer model. Our algorithm infers all optimal solutions and reports complete, temporally feasible event histories, giving the gene and species lineages in which each event occurred. It is fixed-parameter tractable, with polytime complexity when the maximum species outdegree is fixed. Application of our algorithms to prokaryotic and eukaryotic data show that use of an incomplete event model has substantial impact on the events inferred and resulting biological conclusions.Availability: Our algorithms have been implemented in Notung, a freely available phylogenetic reconciliation software package, available at http://www.cs.cmu.edu/~durand/Notung.Contact: mstolzer@andrew.cmu.edu

Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns

“…Branch support was assessed with the aLRT statistic . Gene losses and gains at each divergence node were reconciled using Notung software (Stolzer et al, 2012). The number of ancestral NBS genes at different divergence nodes was determined using monophyletic NBS lineages as described elsewhere (Shao et al, 2014).…”

Coordinated Functional Divergence of Genes after Genome Duplication in Arabidopsis thaliana

“…Gene tree-species tree reconciliation defines nodes in a gene tree as either "duplication" nodes or "speciation" nodes, depending on whether children nodes represent orthologs or paralogs. In addition, they report a relative age of gene duplication based on predictions of where duplications likely map on the species tree (Stolzer et al, 2012). After filtering out low-quality duplication nodes , we obtained duplication nodes in 3981 gene families, including 2350 of 2699 homoeologous gene pairs (Supplemental Data Set 4).…”

Robustness of the Parsimonious Reconciliation Method in Cophylogeny

“…A way to deal with this is to allow for solutions that may be biologically unfeasible, that is for solutions where some of the switches induce a contradictory time ordering for the internal nodes of the host tree. In this case, the problem can be solved in polynomial time [1,6,7,13,21]. In most situations, as shown in [6], among the many optimal solutions, some are time-feasible.…”

“…Many tree reconciliation algorithms exist, but only a few enumerate all solutions. The most commonly used are Notung [22], Jane 4 [5], and CoRe-Pa [13]. However, the first was designed for a gene/species context and imposes some restrictions on the costs that may be given to some of the events, while the last two provide for most instances only a proper subset of all the optimal solutions [6].…”