- Email: [email protected]
Mathematical perspectives of phylogenetic inference
Update
480
TRENDS in Ecology and Evolution
References 1 McGrath, C.L. and Katz, L.A. (2004) Genome diversity in microbial eukaryotes. Trends Ecol. Evol. 19, 32–38 2 Boucher, Y. et al. (2003) Lateral gene transfer and the origins of prokaryotic groups. Annu. Rev. Genet. 37, 283–328 3 Ramesh, M.A. et al. (2005) A phylogenomic inventory of meiotic genes:
Vol.20 No.9 September 2005
evidence for sex in Giardia and an early eukaryotic origin of meiosis. Curr. Biol. 15, 185–191 4 Bonner, J.T. (1998) The origins of multicellularity. Integ. Biol. 1, 27–36 0169-5347/$ - see front matter Q 2005 Elsevier Ltd. All rights reserved. doi:10.1016/j.tree.2005.04.027
Mathematical perspectives of phylogenetic inference Mathematics of Evolution and Phylogeny edited by Olivier Gascuel. Oxford University Press, 2005. £45.00 hbk (416 pages) ISBN 0 19 856610 7
Charles Semple Biomathematics Research Centre, Department of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
In June 2003, Olivier Gascuel, together with several others, organized a workshop entitled ‘Mathematics of Evolution and Phylogeny’ at Institut Henri Poincare´ in Paris. In addition to being leading experts in their respective fields, a common theme among the invited speakers was that they all had a mathematical or statistical perspective on phylogenetic inference. As a follow-up to the workshop, and based on the material covered in their talks, each of the invited speakers was asked to write a compact summary of mathematical techniques and concepts currently used in phylogenetic inference. Mathematics of Evolution and Phylogeny is the amalgamation of these summaries. Beginning with an informative introduction by Gascuel, much of the material in this book is based on mathematical (mostly Markov and combinatorial) models of sequence and genome evolution. More particularly, subjects include approaches to phylogenetic inference based on distance, likelihood, Bayesian, gene-order, and mixture models; the statistical testing and inherent limitations of these inferences; comparative genomics (much of which is based on genome rearrangements); as well as Hadamard conjugation (a method for recovering the original parameters of certain models) and phylogenetic networks. Often, a book arising from a workshop is simply a diverse collection of research papers with each paper disguised as a chapter. With mathematical aspects of phylogenetic inference as the common thread, Mathematics of Evolution and Phylogeny is not such a collection. Yes, the material in each chapter is based around the authors’ own interests and so, unsurprisingly, much of the work presented is their own. However, in many cases, this work has a supporting role to the real purpose of each chapter, which is to provide a survey-styled introduction to some particular topic with mathematical substance. Corresponding author: Semple, C. ([email protected]).
www.sciencedirect.com
In addition to describing the mathematical techniques and concepts, each chapter with its numerous references follows a common pattern of historical notes, motivation and biological interpretation, and ends with a discussion containing directions for future research. Generally, the chapters are self-contained, but do assume that the reader has some familiarity with the basics of phylogenetics. One of the highlights of Mathematics of Evolution and Phylogeny is the chapters on comparative genomics and, in particular, the material on genome rearrangements. Included in these chapters is an excellent account of the pioneering work of Hannenhalli and Pevzner in the analysis of evolutionary genome rearrangements. One motivation for a book such as this is to capture the imagination of mathematicians and statisticians, enticing them into this area of applied mathematics. Consequently, many biologists might find Mathematics of Evolution and Phylogeny a bit daunting. However, for biologists not afraid of mathematical ‘chicken scratchings’, there are plenty of insightful and informative comments to be found. In recent years, there have been other books written on the mathematical aspects of phylogenetics, in particular [1] and [2]. Mathematics of Evolution and Phylogeny complements and adds to both of these in a positive way. It approaches topics such as distance methods for phylogenetic inference from a different point of view and includes topics such as phylogenetic networks, tandem duplication trees, and genome rearrangements that are not covered in detail by either [1] or [2]. Although it could not be used as a teaching text, Mathematics of Evolution and Phylogeny is a valuable research tool for postgraduate students and researchers wanting an in-depth, overall introduction of the topics that it covers. References 1 Felsenstein, J. (2004) Inferring Phylogenies, Sinauer Press 2 Semple, C. and Steel, M. (2003) Phylogenetics, Oxford University Press 0169-5347/$ - see front matter Q 2005 Elsevier Ltd. All rights reserved. doi:10.1016/j.tree.2005.04.028
480
TRENDS in Ecology and Evolution
References 1 McGrath, C.L. and Katz, L.A. (2004) Genome diversity in microbial eukaryotes. Trends Ecol. Evol. 19, 32–38 2 Boucher, Y. et al. (2003) Lateral gene transfer and the origins of prokaryotic groups. Annu. Rev. Genet. 37, 283–328 3 Ramesh, M.A. et al. (2005) A phylogenomic inventory of meiotic genes:
Vol.20 No.9 September 2005
evidence for sex in Giardia and an early eukaryotic origin of meiosis. Curr. Biol. 15, 185–191 4 Bonner, J.T. (1998) The origins of multicellularity. Integ. Biol. 1, 27–36 0169-5347/$ - see front matter Q 2005 Elsevier Ltd. All rights reserved. doi:10.1016/j.tree.2005.04.027
Mathematical perspectives of phylogenetic inference Mathematics of Evolution and Phylogeny edited by Olivier Gascuel. Oxford University Press, 2005. £45.00 hbk (416 pages) ISBN 0 19 856610 7
Charles Semple Biomathematics Research Centre, Department of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
In June 2003, Olivier Gascuel, together with several others, organized a workshop entitled ‘Mathematics of Evolution and Phylogeny’ at Institut Henri Poincare´ in Paris. In addition to being leading experts in their respective fields, a common theme among the invited speakers was that they all had a mathematical or statistical perspective on phylogenetic inference. As a follow-up to the workshop, and based on the material covered in their talks, each of the invited speakers was asked to write a compact summary of mathematical techniques and concepts currently used in phylogenetic inference. Mathematics of Evolution and Phylogeny is the amalgamation of these summaries. Beginning with an informative introduction by Gascuel, much of the material in this book is based on mathematical (mostly Markov and combinatorial) models of sequence and genome evolution. More particularly, subjects include approaches to phylogenetic inference based on distance, likelihood, Bayesian, gene-order, and mixture models; the statistical testing and inherent limitations of these inferences; comparative genomics (much of which is based on genome rearrangements); as well as Hadamard conjugation (a method for recovering the original parameters of certain models) and phylogenetic networks. Often, a book arising from a workshop is simply a diverse collection of research papers with each paper disguised as a chapter. With mathematical aspects of phylogenetic inference as the common thread, Mathematics of Evolution and Phylogeny is not such a collection. Yes, the material in each chapter is based around the authors’ own interests and so, unsurprisingly, much of the work presented is their own. However, in many cases, this work has a supporting role to the real purpose of each chapter, which is to provide a survey-styled introduction to some particular topic with mathematical substance. Corresponding author: Semple, C. ([email protected]).
www.sciencedirect.com
In addition to describing the mathematical techniques and concepts, each chapter with its numerous references follows a common pattern of historical notes, motivation and biological interpretation, and ends with a discussion containing directions for future research. Generally, the chapters are self-contained, but do assume that the reader has some familiarity with the basics of phylogenetics. One of the highlights of Mathematics of Evolution and Phylogeny is the chapters on comparative genomics and, in particular, the material on genome rearrangements. Included in these chapters is an excellent account of the pioneering work of Hannenhalli and Pevzner in the analysis of evolutionary genome rearrangements. One motivation for a book such as this is to capture the imagination of mathematicians and statisticians, enticing them into this area of applied mathematics. Consequently, many biologists might find Mathematics of Evolution and Phylogeny a bit daunting. However, for biologists not afraid of mathematical ‘chicken scratchings’, there are plenty of insightful and informative comments to be found. In recent years, there have been other books written on the mathematical aspects of phylogenetics, in particular [1] and [2]. Mathematics of Evolution and Phylogeny complements and adds to both of these in a positive way. It approaches topics such as distance methods for phylogenetic inference from a different point of view and includes topics such as phylogenetic networks, tandem duplication trees, and genome rearrangements that are not covered in detail by either [1] or [2]. Although it could not be used as a teaching text, Mathematics of Evolution and Phylogeny is a valuable research tool for postgraduate students and researchers wanting an in-depth, overall introduction of the topics that it covers. References 1 Felsenstein, J. (2004) Inferring Phylogenies, Sinauer Press 2 Semple, C. and Steel, M. (2003) Phylogenetics, Oxford University Press 0169-5347/$ - see front matter Q 2005 Elsevier Ltd. All rights reserved. doi:10.1016/j.tree.2005.04.028