Reconciliation Revisited: Handling Multiple Optima When Reconciling with Duplication, Transfer, and Loss

Phylogenetic tree reconciliation is a powerful approach for inferring evolutionary events like gene duplication, horizontal gene transfer, and gene loss, which are fundamental to our understanding of molecular evolution. While Duplication-Loss (DL) reconciliation leads to a unique maximum-parsimony solution, Duplication-Transfer-Loss (DTL) reconciliation yields a multitude of optimal solutions, making it difficult the infer the true evolutionary history of the gene family.

Here, we present an effective, efficient, and scalable method for dealing with this fundamental problem in DTL reconciliation. Our approach works by sampling the space of optimal reconciliations uniformly at random and aggregating the results. We present an algorithm to efficiently sample the space of optimal reconciliations uniformly at random in

O

(

mn

2

) time, where

m

and

n

denote the number of genes and species, respectively. We use these samples to understand how different optimal reconciliations vary in their node mapping and event assignments, and to investigate the impact of varying event costs.