A phylogenetic tree, also known as a phylogeny, is a diagram that depicts the lines of evolutionary descent of different species, organisms, or genes from a common ancestor. Phylogenies are useful for organizing knowledge of biological diversity, for structuring classifications, and for providing insight into events that occurred during evolution. Furthermore, because these trees show descent from a common ancestor, and because much of the strongest evidence for evolution comes in the form of common ancestry, one must understand phylogenies in order to fully appreciate the overwhelming evidence supporting the theory of evolution.

Tree diagrams have been used in evolutionary biology since the time of Charles Darwin. Therefore, one might assume that, by now, most scientists would be exceedingly comfortable with "tree thinking"--reading and interpreting phylogenies. However, it turns out that the tree model of evolution is somewhat counterintuitive and easily misunderstood. This may be the reason why biologists have only in the last few decades come to develop a rigorous understanding of phylogenetic trees. This understanding allows present-day researchers to use phylogenies to visualize evolution, organize their knowledge of biodiversity, and structure and guide ongoing evolutionary research.

But what exactly is a phylogeny? Moreover, how should one read and interpret one of these diagrams? In an attempt to answer such questions, the following sections present a brief introduction to tree thinking. A more complete view of this subject can be developed by learning about how traits evolve along trees, how trees are reconstructed, and how trees are used to study various aspects of evolution.

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