Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models.

BMC Bioinformatics
Mukul S BansalOliver Eulenstein

Abstract

Genomic data provide a wealth of new information for phylogenetic analysis. Yet making use of this data requires phylogenetic methods that can efficiently analyze extremely large data sets and account for processes of gene evolution, such as gene duplication and loss, incomplete lineage sorting (deep coalescence), or horizontal gene transfer, that cause incongruence among gene trees. One such approach is gene tree parsimony, which, given a set of gene trees, seeks a species tree that requires the smallest number of evolutionary events to explain the incongruence of the gene trees. However, the only existing algorithms for gene tree parsimony under the duplication-loss or deep coalescence reconciliation cost are prohibitively slow for large datasets. We describe novel algorithms for SPR and TBR based local search heuristics under the duplication-loss cost, and we show how they can be adapted for the deep coalescence cost. These algorithms improve upon the best existing algorithms for these problems by a factor of n, where n is the number of species in the collection of gene trees. We implemented our new SPR based local search algorithm for the duplication-loss cost and demonstrate the tremendous improvement in runtime and scalab...Continue Reading

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Citations

Jan 8, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Cuong V Than, Noah A Rosenberg
Feb 22, 2011·Nucleic Acids Research·Marina Marcet-Houben, Toni Gabaldón
Nov 8, 2012·Genome Research·Bastien BoussauVincent Daubin
Nov 26, 2010·BMC Bioinformatics·Ruchi ChaudharyOliver Eulenstein
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Jan 26, 2012·PloS One·Stefanie HartmannChristoph Bleidorn
Oct 18, 2013·Journal of Bioinformatics and Computational Biology·Wen-Chieh ChangOliver Eulenstein
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Pawel Gorecki, Oliver Eulenstein
Jan 1, 2014·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Paweł Górecki, Oliver Eulenstein
Jan 11, 2014·IEEE/ACM Transactions on Computational Biology and Bioinformatics·André WeheOliver Eulenstein
May 25, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Cuong V Than, Noah A Rosenberg
Dec 18, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Mukul S Bansal, Oliver Eulenstein
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Aug 10, 2017·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Pawel Gorecki, Oliver Eulenstein
Sep 5, 2020·Molecular Biology and Evolution·Chao ZhangSiavash Mirarab
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Oct 30, 2020·BMC Evolutionary Biology·Paweł GóreckiOliver Eulenstein
May 11, 2021·PloS One·Ayed A R Alanzi, James H Degnan

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Software Mentioned

GTP
Mesquite
DupLoss
Windows XP
RAxML
GeneTree

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