The first cheese was made thousands of years ago. Cheese makers developed new varieties often by discovering new molds. In France the traditional method for making Roquefort cheese, for example, starts with bringing loaves of bread into caves.

Penicillium roqueforti grows on cave walls, and before long it attacks the bread. The cheese makers retrieve the loaves and break off bits to transfer the mold to their curds.

The first cheese makers had no idea that they were collecting particular species of mold. It wasn’t until the early 1900s that scientists discovered the identities. Only then did it become possible for industrial cheese makers to select certain strains of mold grown in laboratories in order to produce cheese in factories.

Dr. Rodríguez de la Vega and his colleagues were curious to see how mold species changed once people began using them to make cheese. After all, wild species of Penicillium mold typically feed on decaying plant matter, not milk.

So the scientists sequenced the genomes of 10 species of Penicillium. Six of the species grow on milk — either because they are used to make cheese, or because they can contaminate cheese and spoil it. The other four are never found in cheese, including Penicillium rubens, the mold in which Alexander Fleming discovered the antibiotic penicillin in 1928.

The scientists then reconstructed the evolutionary tree of these molds. At the base was the common ancestor of all 10 species: a wild mold that lived millions of years ago. As its descendants diverged, their genes gradually changed and they adapted to new ways of living.

The scientists could still recognize similarities in these genes, but they also came across large chunks of DNA that looked out of place. These pieces of DNA weren’t present in the closest relatives of each mold species, but they were found in identical form in distantly related species.