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 Text
2.9 Mb
Front Matter
Abstract, Table of Contents, etc.
36 Kb
Chapter 1
Introduction: Gene Family Evolution and Phylogeny
460 Kb
Chapter 2
Tangled Tales from Multiple Markers : Reconciling conflict between phylogenies to build molecular supertrees
184 Kb
Chapter 3
Gene Tree Parsimony vs. Uninode Coding for Phylogenetic Reconstruction
380 Kb
Chapter 4
Going Nuclear: Gene Family Evolution and Vertebrate Phylogeny Reconciled
232 Kb
Chapter 5
Primate Gene Family Evolution: An integrated study of phylogeny and evolution by gene duplication
408 Kb
Chapter 6
Imbalance of Human Gene Family Phylogenies
216 Kb
Chapter 7
Interpreting the Pattern of Vertebrate Gene Family Evolution