DrML: Probabilistic Modeling of Gene Duplications

DrML is a software program for inferring evolutionary scenarios from a gene tree and a species tree with speciation time estimates that is based on a general maximum likelihood model. The program implements novel algorithms that efficiently infer most likely scenarios of gene duplication and loss events. Our comparative studies suggest that the general maximum likelihood model provides more credible estimates than standard parsimony reconciliation, especially when speciation times differ significantly. DrML is an open source project written in Python, and along with an on-line manual and sample data sets publicly available.

[1]  G. Moore,et al.  Fitting the gene lineage into its species lineage , 1979 .

[2]  R. Page.  Maps between trees and cladistic analysis of historical associations among genes , 1994 .

[3]  Louxin Zhang,et al.  On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies , 1997, J. Comput. Biol..

[4]  R. Page.  Extracting species trees from complex gene trees: reconciled trees and vertebrate phylogeny. , 2000, Molecular phylogenetics and evolution.

[5]  A. Hughes,et al.  Gene duplication and the structure of eukaryotic genomes. , 2001, Genome research.

[6]  A. Hughes,et al.  Pattern and timing of gene duplication in animal genomes. , 2001, Genome research.

[7]  N. Okada,et al.  Natural selection of the rhodopsin gene during the adaptive radiation of East African Great Lakes cichlid fishes. , 2002, Molecular biology and evolution.

[8]  Roderic D. M. Page,et al.  Vertebrate Phylogenomics: Reconciled Trees and Gene Duplications , 2001, Pacific Symposium on Biocomputing.

[9]  Andrew P. Martin,et al.  Perils of paralogy: using HSP70 genes for inferring organismal phylogenies. , 2002, Systematic biology.

[10]  Bengt Sennblad,et al.  Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution , 2004, RECOMB.

[11]  R. Sturm,et al.  The marsupial MHC: The Tammar Wallaby, Macropus eugenii, contains an expressed DNA-like gene on chromosome 1 , 1994, Journal of Molecular Evolution.

[12]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[13]  Paola Bonizzoni,et al.  Reconciling a gene tree to a species tree under the duplication cost model , 2005, Theor. Comput. Sci..

[14]  R. Page,et al.  Rates and patterns of gene duplication and loss in the human genome , 2005, Proceedings of the Royal Society B: Biological Sciences.

[15]  Tao Liu,et al.  TreeFam: a curated database of phylogenetic trees of animal gene families , 2005, Nucleic Acids Res..

[16]  Jerzy Tiuryn,et al.  DLS-trees: A model of evolutionary scenarios , 2006, Theor. Comput. Sci..

[17]  Joel Dudley,et al.  TimeTree: a public knowledge-base of divergence times among organisms , 2006, Bioinform..

[18]  M. Sanderson,et al.  Inferring angiosperm phylogeny from EST data with widespread gene duplication , 2007, BMC Evolutionary Biology.

[19]  Jerzy Tiuryn,et al.  URec: a system for unrooted reconciliation , 2007, Bioinform..

[20]  Tao Liu,et al.  TreeFam: 2008 Update , 2007, Nucleic Acids Res..

[21]  Oliver Eulenstein,et al.  DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony , 2008, Bioinform..

[22]  Oliver Eulenstein,et al.  The multiple gene duplication problem revisited , 2008, ISMB.

[23]  O. Gascuel,et al.  Estimating maximum likelihood phylogenies with PhyML. , 2009, Methods in molecular biology.

[24]  J. Lagergren,et al.  Simultaneous Bayesian gene tree reconstruction and reconciliation analysis , 2009, Proceedings of the National Academy of Sciences.

[25]  Bengt Sennblad,et al.  The gene evolution model and computing its associated probabilities , 2009, JACM.

[26]  Cédric Chauve,et al.  Space of Gene/Species Trees Reconciliations and Parsimonious Models , 2009, J. Comput. Biol..

[27]  Oliver Eulenstein,et al.  Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants , 2009, J. Comput. Biol..

[28]  D. Liberles,et al.  Evolution after gene duplication , 2010 .

[29]  David Fernández-Baca,et al.  iGTP: A software package for large-scale gene tree parsimony analysis , 2010, BMC Bioinformatics.

[30]  R. Murphy,et al.  Rapid Evolution of the Mitochondrial Genome in Chalcidoid Wasps (Hymenoptera: Chalcidoidea) Driven by Parasitic Lifestyles , 2011, PloS one.

[31]  Albee Y. Ling,et al.  The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes , 2012, Science.

[32]  Riccardo Dondi,et al.  Minimum Leaf Removal for Reconciliation: Complexity and Algorithms , 2012, CPM.

[33]  Cédric Chauve,et al.  An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[34]  Oliver Eulenstein,et al.  Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence , 2012, BMC Bioinformatics.

[35]  Oliver Eulenstein,et al.  Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem , 2012, BMC Bioinformatics.