Mathematical Primer of Molecular Phylogenetics

Xuhua Xia, PhD, has been a professor of biology at the University of Ottawa, Canada, since 2009. Prior to that, he was an assistant professor at the University of Hong Kong in 1996, and served in 2001 as a senior scientist and head of Bioinformatics Laboratory in the then-newly established HKU-Pasteur Research Centre.

"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

• 1. Introduction to Molecular Phylogenetics 2. Sequence Alignment 3. Nucleotide Substitution Models and Evolutionary Distances 4. Protein and Codon Substitution Models and their Evolutionary Distances 5. Substitution Rate Heterogeneity over Sites 6. Maximum Parsimony Method 7. Distance-Based Phylogenetic Methods 8. Maximum Likelihood in Molecular Phylogenetics 9. Comparative Methods 10. Appendix