My PhD thesis, available to download either as individual chapters (in which case you lose the references), or as a single (rather large) PDF file.
The original thesis also contains two appendices, which are the two papers I wrote with Rod Page in 2000 and 2001 (see publications page). On a similar note, several of the chapters match papers available from the publications page - chapters 3 and 4 are identical to the papers of the same name, but uglier, so you're probably better off downloading the papers. Chapter 2 is significantly different to the book chapter, so I recommend downloading the book chapter as soon as its available as a pdf.

Entire Text2.9 MbGet Pdf
Front Matter  Abstract, Table of Contents, etc.36 KbGet Pdf
Chapter 1  Introduction: Gene Family Evolution and Phylogeny460 KbGet Pdf
Chapter 2Tangled Tales from Multiple Markers : Reconciling conflict between phylogenies to build molecular supertrees      184 KbGet Pdf
Chapter 3Gene Tree Parsimony vs. Uninode Coding for Phylogenetic Reconstruction380 KbGet Pdf
Chapter 4Going Nuclear: Gene Family Evolution and Vertebrate Phylogeny Reconciled232 KbGet Pdf
Chapter 5Primate Gene Family Evolution: An integrated study of phylogeny and evolution by gene duplication408 KbGet Pdf
Chapter 6Imbalance of Human Gene Family Phylogenies216 KbGet Pdf
Chapter 7Interpreting the Pattern of Vertebrate Gene Family Evolution272 KbGet Pdf
Chapter 8Future Directions832 KbGet Pdf
Bibliography75 KbGet Pdf