I have applied DNA genealogy in my quest to find my Fleming patrilineal immigrant to America. I have been in two large Y DNA studies over the past 20 years and studied other Fleming patrilineal lines and their Y DNA in order to sort out families of the same surname who lived in the same region in order to sort them out. Note that you will find that there is never a single Y DNA profile for a given surname. For my surname Fleming, I found at least 4 going back to early America that differed in haplogroup and markers completely, yet lived in the state of Georgia during the same period. So, among Fleming men who immigrated to America, there are several Y DNA genetic lines that make them no more related than a Smith to a Jones. This is for several reasons, but suffice it to say there is no single Y DNA profile for each surname.
Looking at data for hundreds of Fleming men tested, I was able to come to the following conclusions about Y DNA genealogy.
1. DNA doesn't lie. If the results are unexpected, you must seek alternative explanations.
2. If a test subject shares a common male ancestor within 15 or so generations, you will be in the same haplogroup and your markers will differ by no more than 3/67 or 4/111.
An example is this. I found two living male subjects who were direct patrilineal descendants of two brothers of my great x3 grandfather who was born in 1800. Each differed from me by only 1 marker out of 43 but 2/43 with each other. We all 3 had the same haplogroup, of course.
Another two important examples of unexpected findings are these:
1. I tested 2 living male direct patrilineal men who descended from two different sons of a brother (by historical records) of my Fleming great x4 grandfather. They matched each other but did not match me (not even close), but they did match other subjects with the surname of Waggoner. Obviously, we can assume he was likely fathered by a Waggoner male. I checked and there were Waggoner men living close by and interacting with my Fleming family according to documents. Nonetheless he functioned in every way as a part of my Fleming family.
2. I tested 3 living male direct patrilineal men who descended from three different sons of a brother (or cousin) of my great x3 grandfather Fleming. Again, they all matched each other but did not match ANY Fleming in the Fleming Y DNA database. Again, though treated as part of my family and given my surname, he was fathered by a non-Fleming man.
Finally, a number of subjects who have the surname of Fleming who I connect with historically and many that are likely related but not a documented relative show matching Y DNA results with me and other known Fleming men as expected. So, deciding if you are a patrilineal match is not a difficult observation to make.
So, it is clear that unless Y DNA is the same haplogroup and very very close in marker matching to others with your surname who are likely family members, they are not in your direct patrilineal line within 15 or so generations.
If haplogroups and surnames match but markers differ more than 3-4, you do share a common male ancestor in my opinion, but that ancestor likely lived in his home country during the pre-American period.
I hope sharing my years of experience looking a lots of data helps put this important subject into perspective for fellow genealogists. I will also add that I consulted several DNA experts along the way who helped inform my opinion and experience.