Inferring Phylogenies Joseph Felsenstein
Phylogenies, or evolutionary trees, are the basic structures necessary to think clearly about differences between species, and to analyze those differences statistically. They have been around for over 140 years, but statistical, computational, and algorithmic work on them is barely 40 years old. In that time there have been great advances in understanding, but much remains to be done. It's a good time to summarize this work, while it is still compact enough for a single book to cover it. I have tried to cover the major methods for inferring phylogenies, at a level appropriate to a graduate course for biologists interested in using numerical methods. I have also tried to cover methods of statistical testing of phylogenies, as well as some methods for using phylogenies for making other inferences. The book assumes some calculus and an elementary command of matrix algebra.
Phylogenies are inferred with various kinds of data. I have concentrated on some of the central ones: discretely coded characters, molecular sequences, gene frequencies, and quantitative traits. There is also some coverage of restriction sites, RAPDs, and microsatellites. The reader may benefit from enough familiarity with molecular biology to understand the major features of molecular sequence data, ands some exposure to the theory of quantitative genetics. Other data types that are less widely used, such as DNA hybridization, are not covered. I estimate that there are about 3,000 papers on methods for inferring phylogenies. This book refers to a small friction of those, with less emphasis on studies that investigate behavior of methods on simulated data or real data. I hope that the reader will be able to find their way through this literature from these references, with creative use of computerized literature searches. From the Preface