July 14, 2008

Mystery Mushroom: Evolutionary Theory in Action

You might remember that a few days ago I collected some mystery mushrooms that I couldn’t identify based solely on macroscopic and microscopic characteristics. This morning, I got my rDNA sequences back and I’m happy to report that I have now been able to identify the fungus based on molecular characters. This is evolutionary theory put to practical application. Waddya know, this evolution stuff really works!

Here’s my final phylogenetic tree (although I could have collapsed the weakly-supported nodes if I'd wanted):

I produced this by matching my sequence against highly similar sequences in BLAST. I aligned these using MAFFT and then cleaned up the alignment in MacClade. The cladogram shown is a neighbor-joining tree created in MAFFT with branch lengths proportionate to phylogenetic distance. Bootstrap support is shown at all nodes and is the result of 500 replications. The taxon highlighted in red is my mystery mushroom and the clade containing its closest relatives is outlined in green.

As you can see, the unknown mushroom is clearly of the genus Gymnopus and is closest to, but not identical with, Gymnopus brunneigracilis. It may be that the mystery mushroom has not been sequenced before or I might need more characters to correctly identify it to species. Nonetheless, I do now know its genus and a photograph of one of its close relatives, G. luxurians, bears a striking resemblance. Moreover, the morphology and growth habits of G. luxurians are extremely similar to those of the mushroom I collected.

Imagine for a moment that this wasn’t a mushroom I found growing in wood chips. If this had been a mysterious fungus growing out of Aunt Tilly’s ear, I would have used the exact same techniques to diagnose our (thankfully) pretend parasite. None of this would have been possible without the principles of evolutionary theory, which informed every step of the process.

Of course, if you would like to try to identify the source of my sequence without resorting to evolutionary theory, by all means feel free. Here’s a link to the actual sequence from the fungus. I would be very interested in hearing all about how you made sense of it without involving mutations or knowing the genus and its relationship to other genera sharing a common ancestor.

Or, if you feel like trying your hand at this sort of thing, you can see pretty much the same things that I saw on the way to this result by using the links provided. If you don't feel like buying a copy of MacClade, you can substitute the freeware program BioEdit. It's all evolutionary theory in action embodied in software that makes life a lot easier than it used to be in the days of dot-plots and slide rules!

Sphere: Related Content