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

摘要

Phylogenetic tree reconciliation is a fundamental technique for studying the evolution of gene families. Given a gene tree, a species tree, and an association between their leaves, reconciliation methods explain the incongruence between the trees by postulating a sequence of evolutionary events, with different evolutionary models allowing for different types of events. For example, the duplication-loss (DL) model [ , ] allows for gene duplication and gene loss, the duplication-transfer-loss (DTL) model [ , ] allows for horizontal gene transfers as well, and the multispecies coalescent (MSC) model [ ] allows for incomplete lineage sorting through deep coalescence. However, the DL and DTL models do not model population effects, and the MSC model implicitly assumes that all genes are orthologs.