As stated earlier, genes that are made from scratch are identified by comparing closely related species and finding spots where there is a gene in one species that is missing in another. Scientists must also be able to tell that this new gene sprang from the DNA that was already there.
A great example of one of these genes is the BSC4 gene from baker's yeast. To see why BSC4 almost certainly formed from the DNA that was already in some ancestral yeast from long ago, it helps to understand what a gene looks like. And how one is put together.
T's are replaced with U's
because RNA has U instead of T.
Click here for why that might be.
A gene is really the set of instructions for making a protein. That protein then goes on to do a specific job in a cell.
These instructions are written with just four letters: A, G, C, and T. All the words in the instructions are three letters long meaning that the DNA language consists of the 64 different three letter words to the right.
One of these words, ATG, tells the cell to start making a protein at that ATG. Three different words, TAG, TGA, and TAA, tell the cell that a gene ends there. This is pretty much all there is to a gene.
Note the "pretty much." There have to be 50 or 100 three letter words between the start and stop codons (as genetic words are called). And they have to spell out something useful. And the cell has to know that the ATG that starts the whole thing off is a gene and not just a random ATG (they are obviously common).
A key step, though, is to get an ATG at one end, a TAG, TGA, or TAA at the other and 50-100 codons in between. Once you have that, natural selection can start to work on the gene and its protein so something useful is made.
The BSC4 gene is an excellent place to start to understand how many changes need to happen to get the ball rolling on new gene formation. Here is the sequence of the new yeast gene in its entirety:
As you can see, it starts with an ATG and ends with a TGA and has no TAG's, TGA's or TAA's in between. It is a nice sized, perfectly well behaved gene.
Here is what that same stretch of DNA looks like in a related yeast:
The five trouble spots have been highlighted in blue, lower case letters. Just changing one letter in each of these five words turns this DNA sequence into a gene. Not the same gene but a stretch of DNA that can evolve into a useful protein. And this is exactly what has happened in this case.
BSC4 is an important protein in baker's yeast. Scientists think that it helps the yeast fix its broken DNA. And they know that if you get rid of it under certain conditions, the yeast dies.
So this looks to be a definite case where a gene has appeared where there wasn't one before. The 60 in this study are not so clear cut because the scientists don't have as high quality data that cells read and use these genes in a human cell. But scientists will now get to work seeing which bits of DNA are actually genes.
BSC4 Region from Four Different Yeast Species
This image is taken from here. It has been included for people who want to delve more deeply into the DNA of all four yeast species to see the sorts of changes that have happened over time. The gray shaded boxes are DNA letters shared by all four yeast species at that position. Enjoy!