MUSHROOM GENETICS and the TREE OF LIFE
First we'll get some technical details out of the way, and then we'll look at which mushrooms are actually related to each other and how they evolved that way.
Here is a review of the traditional biological classification system, where each level gets more and more specific from Kingdom, where you are talking about all of the Fungi on the planet, all the way to Species, where you have narrowed it down to one specific species of mushroom. (Remember the mnemonic "King Philip Comes Of Fairly Good Stock".)
At what level groups of organisms are classified is kind of arbitrarily chosen. There are only a few levels that we have created, yet there are a near-infinite variety of relationships between organisms. To classify mushrooms, we have basically taken hundreds of square pegs and tried to cram them into a dozen or so round holes. For instance, if you know that a group of mushrooms are all in the same family, that doesn't give you much detail about how they are related, just that they are somewhat related. Two groups of mushrooms in two different families does not necessarily imply that they are related to each other the same way that two other groups of mushrooms also in two different families are. Think of trying to classify all species into a genus and family, etc. like trying to project a globe onto a flat map. You can't do it, and at some point the true relationships will become distorted.
If you want to get a concise overview of the different shapes and styles of mushrooms in the world, you get a pretty good overview by looking at Classes and Orders. Going down to the Family level or lower is way too detailed for this overview, and going up to the Phylum level, you only get two groups that contain almost all of the fungi with large fruiting bodies.
In the Fungi kingdom, Phylum names always end in -MYCOTA. Class names always end in -MYCETES. Orders always end in -ALES. Families always end in -ACEAE. So when you see a name, you know what level it is. For instance, Agaricomycetes is the class of Agaric (gilled) mushrooms. Agaricaceae is a family.
We used to think that the simple crusts and blobs of jelly growing on pieces of wood, and the truffles growing underground represented primitive, early evolutionary stages of mushrooms, before the "cap and stem" types evolved and lifted out of the ground. Now we know that we were right about the crusts and jellies, but we were often wrong about the truffles! Regular type mushrooms are actually closing up and going underground, as explained here.
You might notice that most of the Truffles (and other gastroid fungi) are going to be conspicuously missing from this list! That is because mushrooms evolved to close up and go below ground many, many times, so you will find truffles in many different orders.
There are also many crust fungi in almost every order. It seems that every order started out with species of crusts before branching out and evolving in many different directions.
Classes: Tremellomycetes and Dacrymycetes. Most jelly fungi are in these two primitive classes. This shows us that most jellies are quite different from everything else. Most other Basidiomycota macrofungi are in the Agaricomycetes.
Class: Agaricomycetes (everything else)
Order: Auriculariales. Most other jellies, like tree ear, black witches butter, tooth jelly, and apricot jelly are here.
Order: Cantharellales. Chanterelles are here. Related are the toothed Hydnum and some of the clubs and corals!
Order: Sebacinales. Tremellodendropsis, one odd coral, is in this order. Or perhaps it's actually in the Auriculariales.
Some fungi in the preceding three orders share some primitive microscopic characteristics showing that this group likely formed first from the Tremellomycetes and Dacrymycetes (called the basal clades), and you can find soft jelly-like consistencies in all three orders.
Order: Geastrales. The earth stars.
Hysterangiales.Stinkhorns and trufflized stinkhorns are sometimes considered separate orders.
Order: Gomphales. False chanterelles like Gomphus (the Pig's Ear). Related are the Ramaria corals and some clubs!
These three preceding orders look quite different but are closely related.
Orders: Polyporales and Hymenochaetales. It turns out there are 2 orders of polypores. Most polypores and poroid crusts are split between these 2 orders. Many of the rusty coloured fleshed ones are the Hymenochaetales, not related to all the other polypores. Polypores and crusts are mixed in together in these orders. Some of these have gills! Some people separate out the Gloeophyllales from the Polyporales.
Order: Thelephorales. Some toothed mushrooms (Sarcodon, Hydnellum, Phellodon) and some "corals" (Thelephora). Also includes the Polyozellus blue chanterelle! Interestingly, these mushrooms are not related to the other tooth, coral and chanterelle mushrooms.
Order: Agaricales. The most popular order, containing most gilled mushrooms and most other possible forms as well. Includes some tough polypores with tubes and gills! Some clubs and corals are related to gilled mushrooms! Bird's nests and puffballs are not only related to gilled mushrooms, they're most related to the store bought mushroom genus Agaricus. More detail about this most interesting of orders will be given shortly.
Order: Russulales. Russula and the Lactarius milk caps get their own order because evolved independently from other gilled mushrooms! They are made up of spherical cells that can break in any direction. They do not "fray" with threads hanging all over the place when you tear them apart like most other mushrooms do. Some polypores are actually Russula relatives! (Albatrellus, Bondarzewia, Heterobasidion). Some tooth fungi are too. (Echinodontium, Auriscalpium, Hericium bear's head)
Order: Boletales. The boletes. Some gilled mushrooms are really Boletes! (Paxillus, Gomphidius, Chroogomphus, Hygrophoropsis, Phylloporus). Scleroderma earth balls are Boletes!
Order: Trechisporales. Order Atheliales. Order Corticiales. These three orders basically never evolved anything more complicated than a crust. They represent the unambitious couch potatoes of the fungi kingdom. Before all of this taxonomic work was done, every crust was referred to as "Corticioid".
PHYLUM ASCOMYCOTA - the other half of the mushroom kingdom. This is much simpler. There are no good macroscopic rules to tell the different orders in these classes apart, so we'll just talk about the class level. Whereas "basidios" most often fruit in fall with some occasionally fruiting in spring, the "ascos" contain many spring species.
Class: Pezizomycetes. These are the Morels, false Morels, the larger cups and many small cups too (usually the ones not growing on wood). The expensive truffles are found here.
Class: Leotiomycetes. These are the earth tongues (club shaped with a differentiated head). Also many tiny cups are related (usually the ones growing on wood). Some mycologists place the tiny cup Orbilia in its own class (Orbiliomycetes) as well as the earth tongue Trichoglossum and Geoglossum (Geoglossomycetes).
Class: Sordariomycetes. The flasks including Hypomyces, Xylaria, Cordyceps, etc., clubs and crusts whose surface is often pimpled.
There are many other classes and orders (and even Phyla!) that don't have much interesting in them. Either they don't make big fruiting bodies or they don't occur very much in the PNW, so I have omitted them. But there are a couple really weird exceptions.
The Taphrinomycetes parasites can only be noticed by the way they deform plants, like alder catkins. Black knot of cherry (Dothideomycetes), the deer truffle and Onygena (Eurotiomycetes) and the irregular earth tongue (Neolectomycetes) are also in separate Ascomycota classes not mentioned here. Neolecta's closest relative is a half yeast. It is very odd that they don't have many relatives that also make large fruiting bodies. Where are the missing link species?
You might even find truffles (and a few other odd things) that don't belong to either Phylum! (Zygomycota and Glomeromycota). And slime molds, often studied with the fungi, are actually not even in the fungal kingdom. Slime molds start off gooey and turn powdery.
Agaricales (Basidiomycota - Agaricomycetes)
The group most interesting to many people are the gilled mushrooms, because they show so much diversity. If you think about it, they represent only one lineage out of several dozen, and yet it seems like one half of the mushrooms you will find in the world will be from this one group. This may show signs of human bias towards a gilled mushroom being what most people consider a "real" mushroom. So let's talk about the gilled mushrooms in a little more detail.
Much of this organization comes from the paper Major clades of Agaricales: a multilocus phylogenetic overview, by Matheny et. al., Mycologia 98(6), 2006.
Basal clades - Some relatively primitive families of gilled mushrooms, containing many other forms, like crusts, clubs, and corals as well as a few gill-like mushrooms. Some examples are Pleurotus (Pleurotaceae), Plicatura and Plicaturopsis (Amylocorticiaceae?) Schizophyllum (Schizophyllaceae) and Fistulina.
Hygrophoroid clade - Relatives of the waxy caps include many other white spored mushrooms that don't look waxy at all. This also includes some club and coral fungi, like Clavaria, Clavulinopsis, Ramariopsis and Mucronella.
Marasmioid clade - contains many white spored genera. Also contains crusts (of course), polypores (Schizophyllum and Fistulina may belong here or in the basal clade) and cup shaped fungi. Besides this clade, the Marasmioid and the basal clades, there are no other crusts in the rest of these clades. It appears they evolved into more complex organisms and did not look back. Many of the other clades do, however, contain gastroid and truffle fungi.
Tricholomatoid/Entoloma clade - Previously thought to contain most white spored mushrooms, it is now restricted to Tricholoma, Clitocybe and relatives, Catathelasma, Leucopaxillus, the Lyophyllum family, and a few other miscellaneous genera. This clade also contains the Entolomataceae. It can be very difficult to determine which of the previous three clades your white spored mushroom is in.
Pluteoid/Amanita clade - Contains Pluteus, Volvopluteus and Volvariella, Melanoleuca, and Amanita.
Agaricoid clade - the most recently evolved clade, the brown spored and dark spored mushrooms (including some white spored mushrooms like Lepiota and Laccaria that subsequently lost their pigment). This is also where thick walled spores evolved to protect the spores while being eaten and allowing them to grow on dung. It is not yet clear how these mushrooms are organized, but here is a guess at groupings of related families in this clade.
Cortinariaceae - Cortinarius. Formerly with more genera than any other family in the Agaricoid clade, but now it stands alone.
Bolbitiaceae - Bolbitius and Conocybe.
Panaeolus is probably deserving of a separate family.
Strophariaceae - some in this family evolved especially dark spores with a purple tinge (Stropharia s.l, Hypholoma s.l., Deconica). Also in this family: Agrocybe, Pholiota, Kuehneromyces (and Galerina subg. Tubariopsis?). (If you think of the two above families as one big family then it doesn't matter who goes where).
Are you thoroughly confused yet? Have patience. The work is being done as we speak to attempt to sort this all out.