Inferring Pareto-optimal reconciliations across multiple event costs under the duplication-loss-coalescence model

• Main Authors: Ross Mawhorter, Nuo Liu, Ran Libeskind-Hadas, Yi-Chieh Wu
• Format: Article
• Language: English
• Published: BMC 2019-12-01
• Series: BMC Bioinformatics
• Subjects: Phylogenetics; Reconciliation; Coalescence; Incomplete lineage sorting; Gene duplication and loss; Pareto optimality
• Online Access: https://doi.org/10.1186/s12859-019-3206-6

Abstract Background Reconciliation methods are widely used to explain incongruence between a gene tree and species tree. However, the common approach of inferring maximum parsimony reconciliations (MPRs) relies on user-defined costs for each type of event, which can be difficult to estimate. Prior work has explored the relationship between event costs and maximum parsimony reconciliations in the duplication-loss and duplication-transfer-loss models, but no studies have addressed this relationship in the more complicated duplication-loss-coalescence model. Results We provide a fixed-parameter tractable algorithm for computing Pareto-optimal reconciliations and recording all events that arise in those reconciliations, along with their frequencies. We apply this method to a case study of 16 fungi to systematically characterize the complexity of MPR space across event costs and identify events supported across this space. Conclusion This work provides a new framework for studying the relationship between event costs and reconciliations that incorporates both macro-evolutionary events and population effects and is thus broadly applicable across eukaryotic species.