Reconstruction of time-consistent species trees

TL;DR

This paper presents a cubic-time algorithm to determine if a time-consistent species tree can be reconstructed from event-labeled gene trees that include speciation, duplication, and horizontal gene transfer events.

Contribution

It introduces an efficient algorithm for reconstructing species trees from complex gene trees with multiple evolutionary events, even when the species tree is initially unknown.

Findings

Algorithm runs in cubic time

Can construct species tree if it exists

Applicable to gene trees with multiple event types

Abstract

The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The question then arises as whether inferred event-labeled gene trees are "biologically feasible" which is the case if one can find a species tree with which the gene tree can be reconciled in a time-consistent way. In this contribution, we consider event-labeled gene trees that contain speciation, duplication as well as horizontal gene transfer and we assume that the species tree is unknown. We provide a cubic-time algorithm to decide whether a "time-consistent" binary species for a given event-labeled gene tree exists and, in the affirmative case, to construct the species tree within the same time-complexity.