Here's a page that attempts to explain this. I can't vouch for it - and I'm not an expert anyway. What I take from it is that only FamilyTreeDNA's big-Y test can claim to identify your haplogroup in full (or pretty close, at least). Any test on a smaller set of markers gets an incomplete identification, and they then guess the full haplogroup label. And guesses - or estimates, to be more polite - can be different.
Thanks for giving us that magnificent analysis of haplogroups.
In it I found this remark: "Neither MyHeritage nor Ancestry provide Y or mitochondrial haplogroups."
This is a concern. Naming no names, we are being told on the one hand that we must use Ancestry, particularly as they have so many test results. And on the other hand we are told that Ancestry do not do Y or mitochrondrial hapslogroups.
So what are Ancestry good for? Never having used them, I can say confidently that they are good for closely related family members, perhaps up to third or fourth cousins. Ancestry's methods mean that they cannot provide information about distant relatives at all.
What FamilyTreeDNA is good for is long distant relationships. I have found through FTDNA's Big-Y test that a half seventh cousin and I have identical Y-DNA. So we are descended from a common ancestor, who we always knew and who was born in 1749. This means that all other true male-line descendants of this common ancestor with have the same Y-DNA. So we have found an eighth cousin to try this out and his sample went into testing a few days ago. If his Y-DNA is not the same, then one of his more recent male ancestors was not the man we think he was, but this is to be expected sometimes.
My understanding is that Ancestry cannot begin to provide information of this quality about long distant male (and female through mitochondrial testing) ancestry. Can this be added to the encouragement to buy into Anstry's limited DNA testing?