Analyses 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 genome, genes are often rearranged, causing them to move to new syntenic regions.
We extend the DTL model to account for two events that commonly arise in the evolution of microbes:
Reconciliation in the DTLOR model can offer new insights into the evolution of microbes that is not currently possible under the DTL model.