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Title: 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 genome, 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:originof a gene from outside the sampled species tree andrearrangementof gene syntenic regions. 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 to handle uncertainty in gene tree topologies. 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.  more » « less
Award ID(s):
2231150
PAR ID:
10539019
Author(s) / Creator(s):
; ; ; ; ;
Publisher / Repository:
BMC
Date Published:
Journal Name:
BMC Bioinformatics
Volume:
22
Issue:
S10
ISSN:
1471-2105
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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