Maximum Parsimony Reconciliation in the DTLOR Model

BackgroundAnalyses of microbial evolution often use reconciliation methods. However, the standard duplication-transfer-loss (DTL) model does not account for the fact that species trees are often not fully sampled and thus, from the perspective of reconciliation, a gene family may enter the species tree from the outside. Moreover, within the species tree, genes are often rearranged, causing them to move to new syntenic "regions." ResultsWe extend the DTL model to account for two events that commonly arise in the evolution of microbes: evolution occurring outside the sampled species tree and changes in the syntenic regions of genes in the genome due to rearrangement. We describe an efficient algorithm for maximum parsimony reconciliation in this new DTLOR model and then show how it can be extended to account for non-binary gene trees. Finally, we describe preliminary experimental results from the integration of our algorithm into the existing xenoGI tool for reconstructing the histories of genomic islands in closely related bacteria. ConclusionsReconciliation in the DTLOR model can offer new insights into the evolution of microbes that is not currently possible under the DTL model.