Within a single species you can often see differentiation in terms of preferred ecological niches. Yeast for bread is not usually the same strain as yeast for brewing beer, even though they are the same species. They compared ~150 different strains of S. cerevisiae and clustered them by the presence of SNPs to determine "categories", and found some that strongly clustered in modern beer brewing, some that clustered together with wine and additional beer strains, sections for Asia- or West Africa-derived strains, and a "mixed" section with bread yeast, some wines, and some other spirits.

The ancient yeast clustered squarely within one of the two beer-brewing groups, suggesting it may be a precursor to these modern beer species.

So it's not just the presence of the these DNAs they are looking at; they are using functional genomics to determine the biological role these specific species may have had.