From event-labeled gene trees to species trees

Abstract

BackgroundTree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x represents a speciation or a duplication. This problem appears in the context of analyzing orthology data.ResultsWe show that S is a species tree for T if and only if S displays all rooted triples of T that have three distinct species as their leaves and are rooted in a speciation vertex. A valid reconciliation map can then be found in polynomial time. Simulated data shows that the event-labeled gene trees convey a large amount of information on underlying species trees, even for a large percentage of losses.ConclusionsThe knowledge of event labels in a gene tree strongly constrains the possible species tree and, for a given species tree, also the possible reconciliation maps. Nevertheless, many degrees of freedom remain in the space of feasible solutions. In order to disambiguate the alternative solutions additional external constraints as well as optimization criteria could be employed.

Accurate prediction of orthologs in the presence of divergence after duplication

“…Methods of this type include notably LOFT (Van der Heijden et al, 2007) and COCO-CL (Jothi et al, 2006). Recently, a number of methods exploit a fundamental property of orthology graphs, in which vertices are genes and edges depict orthology: a graph G is a valid orthology graph if and only if it is P 4free (Hernandez-Rosales et al, 2012;Hellmuth et al, 2013;Lafond and El-Mabrouk, 2014;Hellmuth et al, 2015;Dondi et al, 2017a;Lafond et al, 2016;Jones et al, 2016;Dondi et al, 2017b), i.e. G has no path on 4 vertices without a shortcut.…”

Time-Consistent Reconciliation Maps and Forbidden Time Travel

“…Genes that share a common origin (homologs) can be classified into orthologs, paralogs, and xenologs depending whether they originated by a speciation, duplication or horizontal gene transfer (HGT) event [16,22]. Recent advances in mathematical phylogenetics [19,24] have shown that the knowledge of these event-relations (orthologs, paralogs and xenologs) suffices to construct event-labeled gene trees and, in some case, also a species tree [18,25,20].…”

On the consistency of orthology relationships

“…In the last years, the decision problems associated with these questions have been extensively studied, both when is full , i.e., involves a constraint for each pair of genes in V [7, 8], and when it is not [9]. …”

“…Hernandez-Rosales et al [7] showed that ( T , s ) is consistent with a species tree S if and only S displays all triplets in t r ( T , s ). In light of this result, Hellmuth et al [10] gave a framework for finding the DS-tree and species tree for which the maximum number of triplets are displayed, using Integer Linear Programming.…”

“…In light of this result, Hellmuth et al [10] gave a framework for finding the DS-tree and species tree for which the maximum number of triplets are displayed, using Integer Linear Programming. Lafond and El-Mabrouk [9] improved the result of [7] by showing that it is enough to consider only the triplets in t r ( T , s ) that have a speciation node as the root node and a duplication node as the other internal node. This can expressed in terms of the consistency of an orthology graph in the following way.…”