Reconciliation With Nonbinary Gene Trees Revisited

Abstract

By reconciling the phylogenetic tree of a gene family with the corresponding species tree, it is possible to infer lineage-specific duplications and losses with high confidence and hence annotate orthologs and paralogs. However, the currently available reconciliation methods for non-binary gene trees are too computationally expensive to be applied on a genomic level. Here, we present an O(m + n) algorithm to reconcile an arbitrary gene tree with its corresponding species tree, where m and n are the number of nodes in the gene and species trees respectively. The improvement is achieved through two innovations: a fast computation of compressed child-image subtrees, and efficient reconstruction of irreducible duplication histories. This method will be a valuable tool to genome-wide studies of the evolution of individual gene families.

Gene tree species tree reconciliation with gene conversion

“…The problem of reconciliation between a polytomous gene tree and a binary species tree minimizing the number of mutations (duplications + losses) is polynomial (Chang and Eulenstein 2006;Lafond et al 2012). In Zheng and Zhang (2017), O(|G| + |S|) algorithms for reconciling a nonbinary gene tree and a binary species tree in the duplication, loss, mutation, and deep coalescence models are given.…”