Bilardello, N. and L. Valdes (1998). Constructing phylogenies. The American Biology Teacher 60(5): 369-373.

This "How-To-Do-It" article addresses the mathematical properties of trees and other types of graphs. It discusses the elements of trees, minimum weight spanning trees, an rooted cubic trees. A molecular dataset and 6 classroom exercises are included.

Quote from source: A graph is a mathematical structure that is often used to show relations between elements of a set. These elements are depicted by points or vertices and can be labeled with symbols. If two elements are related, they are connected with a line called an edge.

Rudolph, J. L., & Stewart, J. (1998). Evolution and the nature of science: On the historical discord and its implications for education. Journal of Research in Science Teaching, 35(10), 1069-1089.

Quote from source: Research in the teaching and learning of evolutionary biology has revealed persistent difficulties in student understanding of fundamental Darwinian concepts. These difficulties may be traced, in part, to science instruction that is based on philosophical conceptions of science that are no longer viewed as adequately characterizing the diverse nature of scientific practice, especially in evolutionary biology. This mismatch between evolution as practiced and the nature of science as perceived by researchers and educators has a long history extending back to the publication of Darwin's theory of natural selection. An examination of how this theory was received by the scientific community of the time may provide insight into some of the difficulties that students have today in learning these important biological concepts...

This is a great simulation tool for helping students get started with the idea of independence of populations and divergence. Jon Herron at the University of Washington wrote this software to complement his textbook "Evolutionary Analysis". The site has nice teaching resources and introductory materials as well as the software. Runs on Mac and PC.

Quote from source: ForensicEA lets the user explore the logic of phylogeny reconstruction. The program creates populations of virus particles. The populations evolve by genetic drift. The user can sample and compare nucleotide sequences from the populations. Various simulations let the user collect and analyze data on: genetic drift within a single population; divergence of populations by drift; and variation among populations on a known phylogeny.

Gee, H. (1999). In search of deep time: Beyond the fossil record to a new history of life. New York: Free Press.

Gee, an editor at the journal Nature, describes the conceptual difficulty involved when reasoning about "deep time" and uses this as a base from which he examines the historical development of cladistics. It really helped me think about the ways we draw inferences from trees.

A classic, and very readable. The description of descent with modification accompanying the only figure in the book (a line drawing of branching and extinction) is interesting. You can read Darwin's description of the diagram in the "the probable effects..." section of Chapter 4 - Natural Selection. A reproduction of the tree diagram is available here.

The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during former years may represent the long succession of extinct species. At each period of growth all the growing twigs have tried to branch out on all sides, and to overtop and kill the surrounding twigs and branches, in the same manner as species and groups of species have at all times overmastered other species in the great battle for life. the limbs, divided into great branches, and these into lesser and lesser branches, were themselves once, when the tree was young, budding twigs, and this connection of the former and present buds by ramifying branches may well represent the classification of all extinct and living species in groups subordinate to groups.

This PowerPoint file by Tony Weisstein provides a nice overview of several important issues in phylogenetic analysis. It addresses the differences between evolutionary trees and phylograms, rooted and unrooted trees, and several tree building techniques.

As part of the Virtual Paleobotanical Laboratory at the Univeristy of California - Berkeley Museum of Paleontology this lab was designed by Nan Arens and others for an undergraduate course. It contains a significant introduction to phenetics and cladistics that uses a fair amount of technical vocabulary. The lab activity is built around specific plant specimens but the procedure could be modified to take advantage of local resources.

Quote from source: In this week's lab you will learn how to reconstruct evolutionary relationships. Biologists have experimented with a variety of methods for interpreting who is related to whom, however, many of these methods did not well reflect the process that we believe underlies evolutionary relationships. After reading about the evolution of the methods, you will try your skills on some living plants in the Mesozoic Garden opposite the T. rex, in the Atrium of VLSB.

This web based Java program written by David Joyce at Clark University is used to demonstrate and complement brief discussions of phylogeny, mutation, distance and reconstruction algorithms

Quote from source: These few pages describe the problem of reconstructing phylogenetic trees with the help of a Java applet. I wrote the applet to discover more about the java language and the API interface.

This essay discusses the nature of evolutionary biology as a historical science and how narrow definitions of science can appear to be in conflict with evolutionary inquiry. It also provides a historical overview of some of the methods used by scientists to investigate the past.

Quote from source: This article presents the argument that, contrary to creationists claims and public perception, a variety of methods are used in science and among those methods are some that enable scientists to understand the past.

This Mac application written by Andrew Rambaut and Mike Charleston from the University of Oxford allows you to reroot trees, rotate branches, and rearrange trees that are in the NEXUS format.

Quote from source: TreeEdit is an application for organizing, viewing and manipulating sets of phylogenetic trees. It is intended as a tool for preparing sets of trees for use in phylogenetics packages such as PAUP.