In less than two decades, beginning when Walker and Doolittle (1982) examined relationships among aquatic fungi based on RNA nucleotide sequence, comparative studies of nucleic acid variation have revolutionized evolutionary mycology. Although there is far more remaining to be done than has been done, the big picture of fungal evolution is coming into focus. In this chapter we combine a review of the main points found in the new phylogenetic trees of fungi with a look at the methods used to make the trees. The challenge is not just to learn the current trees, but to learn how they are made and evaluated. The concept of testing alternative evolutionary histories is as important as the new insights that have been gained on fungal evolution; specific trees will change as new data become available but the need to evaluate alternative trees will remain.

Phylogenetic patterns among fungi

To appreciate the phylogeny of fungi, it is necessary to consider them in relation to the rest of life on earth, which is believed to be a continuum beginning several billions of years (Gyr) ago and leading to the present. We will break the continuum into three levels, the ‘Big Picture’ of fungal evolution or how the organisms studied by mycologists relate to the rest of life, the four phyla that make the kingdom Fungi, and individual members of the four phyla.

Big picture of fungal evolution

The most basic question is, how are fungi related to other biota?