Gene tree correction guided by orthology

Abstract

BackgroundReconciled gene trees yield orthology and paralogy relationships between genes. This information may however contradict other information on orthology and paralogy provided by other footprints of evolution, such as conserved synteny.ResultsWe explore a way to include external information on orthology in the process of gene tree construction. Given an initial gene tree and a set of orthology constraints on pairs of genes or on clades, we give polynomial-time algorithms for producing a modified gene tree satisfying the set of constraints, that is as close as possible to the original one according to the Robinson-Foulds distance. We assess the validity of the modifications we propose by computing the likelihood ratio between initial and modified trees according to sequence alignments on Ensembl trees, showing that often the two trees are statistically equivalent.AvailabilitySoftware and data available upon request to the corresponding author.

ASTRAL-Pro: quartet-based species tree inference despite paralogy

“…Most importantly, in its current form, it can only handle binary trees, which reduces its ability to handle gene tree error [47]. While A-Pro is more robust to gene tree error than alternatives, combining it with co-estimation [3] and tree fixing [72][73][74][75][76][77] may further improve its accuracy. Future work should also explore ways to extend A-Pro so that it can handle polytomies in input gene trees.…”

Polytomy refinement for the correction of dubious duplications in gene trees

“…We generated 960 random instances with forests of sizes ranging between 5 and 100 (10 instances for each $5\le n\le 100$). We compared the output of Algorithm MinNADref with that of Algorithm MinDLref, given in (Lafond et al , 2012), which computes refinement minimizing the duplication+loss ( DL ) cost of reconciliation with the species tree. Both algorithms gave the exact same refinement for only 12 instances (1.25%).…”

Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications

“…Genome 460 organisation information still remains difficult to incorporate in gene phylogenies, largely due to the lack of well-supported evolutionary models (Chauve et al 2013) and the need for contiguous genome assemblies. The most notable effort to use extant synteny to correct gene trees in a general context showed mixed results (ParalogyCorrector within the RefineTree framework (Lafond et al 2013;Noutahi et al 2016)). However, we show here that in contexts 465…”

“…Second, we included the original, uncorrected trees from Ensembl Compara (Vilella et al 2009), which are phylogeny-reconciled 280 consensus trees build with the TreeBeST pipeline. Last, we tested ParalogyCorrector, the only other existing methodology that corrects gene trees using synteny information (Lafond et al 2013). To compute ParalogyCorrector trees, we provided our synteny-derived orthologies constraints along with the original Ensembl subtree.…”

“…However, synteny has never been used to systematically select amongst alternative gene tree topologies in the context of a known WGD event. To the best of our knowledge, only two gene tree building methods are able to leverage evidence from gene organisation to correct 85 orthology and paralogy relationships: SYNERGY, a Neighbor-Joining iterative tree building algorithm that is no longer available (Wapinski et al 2007), and ParalogyCorrector, which identifies and corrects gene trees inconsistent with synteny information (Lafond et al 2013).…”