There could be errors in the genomic studies as well. Furthermore, I wonder if these yeasts are all just so very closely related that it's like splitting hairs. Like for years we've been saying WLP001 and 1056 were the same, when in fact they are not super closely related, but by their RESULTS... perhaps "close enough for most intents & purposes" !?
One of the reasons I don't take those too seriously.
Same. Functional resemblance is the only thing of consequence AFAIC, rather than genetic resemblance. For example, the "Chico" strains all have a similar flavor profile to me (except for US-05 with that dang apricot), regardless of how they cluster on the phylogenetic tree. I will always consider WLP001 and 1056 to be the same because they are the same functionally IMO, a little drift notwithstanding, if not genetically.
Viewed from another perspective, the position of a strain on the tree does not seem to be a good predictor of its fermentation characteristics. In some cases functional and genetic similarity are congruent, e.g. WY2112 and WLP810, but in other cases they are not, e.g. WLP029 and WY2565 or A15 and 34/70.