A mutation results in the formation of a new allele of a gene that is already present. So any new genes that form and support multicellular yeast are alleles of genes that were present in the single cellular ones...they just now have a new function.

What I was wondering was did the code for the propensity of multi-cellularity exist before or after the experiment started. Was there two traits or three traits that existed before the experiment started or did the mutations occur afterwards. That is why I said maybe it would had been better if they studied the genomes at each stage of the experiment to see what changes occurred. And even studied the singular cells a couple of generations down. My thought was there could point to a single cell 60 generations down and say hey look at this strain it mutated but that didn't cause multi-cellularity but look over here at this mutation (that differs from the ancestor cell) when this sequence started to appear that is when we first saw clumping etc. That's all. I guess I wanted more info than I saw in the article. The biggest concern it seem was that it appeared different but it didn't mention anything about the inner working of the DNA sequence.

The clumps would likely be yeast cells that stuck together after reproduction. One cell buds off another cell and the two stick together because there's a stickyness to the surface, even on normal yeasts. Through evolution, that trait (as well as some others) was encouraged.

For reasons due to biological selfishsness, it is unlikely that more advanced multicellularity (with specialized cells doing different tasks) would evolve between unrelated yeasts. F.ex if you are a part of a multicellular machinery and have to sacrifice your own ability to reproduce, that could only have a fitness benefit as long as you did it in order to increase the fitness of those closely related to you.

Biological selfishness is a heavy topic to get into with someone who has not studied biology, but it is a highly interesting subject and for most who don't know it, learning about it would surely change their lives or at least the way in which they percieve life. Yet again, I recommend Richard Dawkins' popular classic The Selfish Gene.