Who is Who in Phylogenetic Networks

Publications of Manolis Kellis     Order by:   Type | Year

Associated keywords

duplication explicit-network from-rooted-trees from-species-tree lateral-gene-transfer loss phylogenetic-network phylogeny polynomial Program-Angst Program-Mowgli Program-RANGER-DTL Program-Xscape reconstruction

2014

1 Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S. Bansal and Manolis Kellis. Pareto-optimal phylogenetic tree reconciliation. In ISMB14, Vol. 30:i87-i95 of BIO, 2014. Keywords: duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, polynomial, Program Xscape, reconstruction. Note: http://dx.doi.org/10.1093/bioinformatics/btu289.         Toggle abstract "Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a reconciliation of minimum total cost. It is generally understood that reconciliations are sensitive to event costs, but little is understood about the relationship between event costs and solutions. Moreover, choosing appropriate event costs is a notoriously difficult problem. Results: We address this problem by giving an efficient algorithm for computing Pareto-optimal sets of reconciliations, thus providing the first systematic method for understanding the relationship between event costs and reconciliations. This, in turn, results in new techniques for computing event support values and, for cophylogenetic analyses, performing robust statistical tests. We provide new software tools and demonstrate their use on a number of datasets from evolutionary genomic and cophylogenetic studies. © 2014 The Author. Published by Oxford University Press. All rights reserved."

2013

2 Mukul S. Bansal, Eric J. Alm and Manolis Kellis. Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss. In RECOMB13, Vol. 7821:1-13 of LNCS, springer, 2013. Keywords: duplication, from rooted trees, from species tree, loss, phylogenetic network, phylogeny, polynomial, Program RANGER-DTL, reconstruction. Note: http://people.csail.mit.edu/mukul/Bansal_RECOMB2013.pdf.         Toggle abstract "Phylogenetic tree reconciliation is a powerful approach for inferring evolutionary events like gene duplication, horizontal gene transfer, and gene loss, which are fundamental to our understanding of molecular evolution. While Duplication-Loss (DL) reconciliation leads to a unique maximum-parsimony solution, Duplication-Transfer-Loss (DTL) reconciliation yields a multitude of optimal solutions, making it difficult the infer the true evolutionary history of the gene family. Here, we present an effective, efficient, and scalable method for dealing with this fundamental problem in DTL reconciliation. Our approach works by sampling the space of optimal reconciliations uniformly at random and aggregating the results. We present an algorithm to efficiently sample the space of optimal reconciliations uniformly at random in O(mn 2) time, where m and n denote the number of genes and species, respectively. We use these samples to understand how different optimal reconciliations vary in their node mapping and event assignments, and to investigate the impact of varying event costs. © 2013 Springer-Verlag." 3 Mukul S. Bansal, Eric J. Alm and Manolis Kellis. Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss. In JCB, Vol. 20(10):738-754, 2013. Keywords: duplication, from rooted trees, from species tree, loss, phylogenetic network, phylogeny, Program RANGER-DTL, reconstruction. Note: http://www.engr.uconn.edu/~mukul/Bansal_JCB2013.pdf.         Toggle abstract "Phylogenetic tree reconciliation is a powerful approach for inferring evolutionary events like gene duplication, horizontal gene transfer, and gene loss, which are fundamental to our understanding of molecular evolution. While duplication-loss (DL) reconciliation leads to a unique maximum-parsimony solution, duplication-transfer-loss (DTL) reconciliation yields a multitude of optimal solutions, making it difficult to infer the true evolutionary history of the gene family. This problem is further exacerbated by the fact that different event cost assignments yield different sets of optimal reconciliations. Here, we present an effective, efficient, and scalable method for dealing with these fundamental problems in DTL reconciliation. Our approach works by sampling the space of optimal reconciliations uniformly at random and aggregating the results. We show that even gene trees with only a few dozen genes often have millions of optimal reconciliations and present an algorithm to efficiently sample the space of optimal reconciliations uniformly at random in O(mn 2) time per sample, where m and n denote the number of genes and species, respectively. We use these samples to understand how different optimal reconciliations vary in their node mappings and event assignments and to investigate the impact of varying event costs. We apply our method to a biological dataset of approximately 4700 gene trees from 100 taxa and observe that 93% of event assignments and 73% of mappings remain consistent across different multiple optima. Our analysis represents the first systematic investigation of the space of optimal DTL reconciliations and has many important implications for the study of gene family evolution. © 2013 Mary Ann Liebert, Inc."

2012

4 Mukul S. Bansal, Eric J. Alm and Manolis Kellis. Efficient Algorithms for the Reconciliation Problem with Gene Duplication, Horizontal Transfer, and Loss. In ISMB12, Vol. 28(12):i283-i291 of BIO, 2012. Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Angst, Program Mowgli, Program RANGER-DTL, reconstruction. Note: http://dx.doi.org/10.1093/bioinformatics/bts225.         Toggle abstract "Motivation: Gene family evolution is driven by evolutionary events such as speciation, gene duplication, horizontal gene transfer and gene loss, and inferring these events in the evolutionary history of a given gene family is a fundamental problem in comparative and evolutionary genomics with numerous important applications. Solving this problem requires the use of a reconciliation framework, where the input consists of a gene family phylogeny and the corresponding species phylogeny, and the goal is to reconcile the two by postulating speciation, gene duplication, horizontal gene transfer and gene loss events. This reconciliation problem is referred to as duplication-transfer-loss (DTL) reconciliation and has been extensively studied in the literature. Yet, even the fastest existing algorithms for DTL reconciliation are too slow for reconciling large gene families and for use in more sophisticated applications such as gene tree or species tree reconstruction.Results: We present two new algorithms for the DTL reconciliation problem that are dramatically faster than existing algorithms, both asymptotically and in practice. We also extend the standard DTL reconciliation model by considering distance-dependent transfer costs, which allow for more accurate reconciliation and give an efficient algorithm for DTL reconciliation under this extended model. We implemented our new algorithms and demonstrated up to 100 000-fold speed-up over existing methods, using both simulated and biological datasets. This dramatic improvement makes it possible to use DTL reconciliation for performing rigorous evolutionary analyses of large gene families and enables its use in advanced reconciliation-based gene and species tree reconstruction methods. © The Author(s) 2012. Published by Oxford University Press."