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Book reviews

“A highly effective volume ideal as textbook for an advanced undergraduate course or for seasoned biologists seeking deeper understanding of applying mathematical approaches to address fundamental questions in phylogeny and evolution. . . . In his latest book, Xia (Univ. of Ottawa) offers a treatment of phylogenetics deeply rooted in mathematical principles yet conversational in tone. Though the book is certainly best suited to an audience with background in mathematics and statistics, readers whose primary focus is molecular or evolutionary biology will find that chapter preambles offer an effective bridge between biological concepts and their mathematical treatment in phylogenetics. Xia’s frequent references to papers that use phylogenetic methods to resolve essential evolutionary questions also work to make the methods presented accessible to a broad readership. Though minimalist in presentation, Xia’s illustrations of concepts—including sequence alignment—successfully capture the essence of complex inference techniques. Moreover, rather than simply presenting mathematical expressions, Xia provides specific numeric examples, offering readers the opportunity to check their understanding by working through problems themselves. . . . Summing Up: Highly recommended. Upper-division undergraduates. Graduate students and faculty.”

CHOICE (publication of the Association of College and Research Libraries), review by D. P. Genereux, Broad Institute of Harvard University and Massachusetts Institute of Technology

“A nice job of presenting detailed worked analyses and of making strong connections to empirical settings, making it a useful reference for those wishing for a deeper description of these aspects. . . . Professor Xia has gone to considerable effort to provide examples that are based on empirical data, as well as worked details for the analyses performed on these data. These aspects of the book differ from many of the standard books on this topic, where toy examples and more abstract descriptions of the methodology are often provided instead.”

Systematic Biology, review by Laura Kubatko, Ohio State University, USA

“Gives the lay of the land in computing on DNA sequence data to reconstruct evolutionary history. The volume sensibly progresses from aligning raw sequences with one another to the models that describe their mutations and onwards to the construction of phylogenetic trees from these data, with the nuts and bolts of each method described and exemplified along the way. Professor Xia doesn’t shy away from challenging us; for example, where he treats the application of affine functions in alignment algorithms, he warns us that this is something ‘only a very good student can understand.‘ Yet his explanations are so concrete and laced with pseudocode and references to real-world implementations that they invite the reader to experiment and figure out what’s going on. The Primer is geared towards researchers who are familiar with the tools and methods of the field but who now, finally, want to know how they actually work and be able to implement them by themselves. For this audience, Xia’s work compares favorably where there is overlap in subject matter with Felsenstein’s Inferring Phylogenies. For example, where the Farris algorithm is described in prose by Felsenstein, Xia helpfully describes possible implementations (using bitmasks, as connoisseurs will understand). Along the way, the reader is treated to illustrative anecdotes and the occasional, charming Canadianism: the code samples in the book are provided in MAPLE, which, we are told, is ‘a beautiful Canadian product.‘ The same could be said about the Primer, and I wish it had been around when I was a graduate student.”

—Dr. Rutger Vos, Naturalis Biodiversity Center, The Netherlands

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