Species are not defined by simply the number of genes they possess. But variations in the number of genes from isolate to isolate (let's say a species of yeast that has been isolated from a beer, vs a yeast isolated from the skin of a grape) can be caused by gene gain or gene loss. A common rule of thumb is that DNA is an expensive molecule to harbor because it must be maintained, replicated, and repaired. This is energetically expensive. Therefore, it is in the best interest of the organism to have only the genes necessary for its lifestyle. If the cost of maintaining a gene is more expensive than the benefit it confers, the gene will likely be lost.
For a yeast that has been cultured for generations upon generations in a very stable and predictable environment such as a beer culture, genes involved in antagonizing other species of yeast, surviving under variable oxygen levels, resistance to antimicrobials secreted by competing organisms, etc, are no longer necessary. Therefore, these genes may be lost over generations simply because they are not selected for.
Conversely, a yeast that is exposed to the elements and other competing organisms regularly, such as the grape yeast, must deal with variable temperatures, other yeast or bacterial isolates, chemicals such as pesticides, and different levels of humidity. Because of the immense environmental variation that this yeast must survive through, it is likely that they have more genes than would the beer culture due to selective pressures.
