Abstract
BackgroundReconciliation 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.ResultsWe 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.ConclusionThis 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.
Highlights
Reconciliation methods are widely used to explain incongruence between a gene tree and species tree
Given G, S, and Le, an labeled coalescent tree (LCT) for G, S, Le is a tuple M, L, O, where M is a species map that maps each node of G to a node of S; L is a locus map that maps each node of G to a finite set of natural numbers, each representing a locus that has evolved within the gene family; and O is a partial order that orders gene tree nodes within the same species and locus (Fig. 1b)
In this work, we have presented an algorithm for understanding the relationship between event costs and maximum parsimony reconciliations under the DLC model
Summary
Reconciliation methods are widely used to explain incongruence between a gene tree and species tree. 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. Gene tree, a species tree, and an association between their More recently, several combined duplication-lossleaves, reconciliation methods explain the incongruence coalescence (DLC) models have been developed, which, as between the trees by postulating a sequence of evolution- the name implies, allow for duplication, loss, and coalesary events, with different evolutionary models allowing cence. While allows for horizontal gene transfers as well, and the multi- the models of Vernot et al [8] and Chan et al [9] are conspecies coalescent (MSC) model [5] allows for incomplete ceptually simpler, neither keep track of the inferred loci lineage sorting through deep coalescence. The of genes nor rely explicitly on the multispecies coalescent, limitations that prevent the models from capturing all possible evolutionary histories [10, 11]. (For a detailed comparison of these models, see Chan et al [9] and Du et al [11].) While it is possible to perform DLC
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