Hi! The DNA testing can be confusing, that's for sure! I'm not positive I understand your question, but thought I'd give you some basic info in hopes it might clarify things for you :) Please don't think I'm questioning your intelligence-just want to be as clear as possible and make it as easy to understand as I can.

The ydna test (paternal DNA test) only looks at the paternal line-that means it looks at your father's father's father's father, etc-no females (mothers, grandmothers, great grandmothers) are brought into this picture at all. If your ydna shows matches with other men of a different surname, you're absolutely right to question a paternal ancestor's paternity (in this case, your paternal great grandfather, I believe). Females cannot take the ydna test-men only pass their ydna to their male offspring.

The mtdna test only "looks" at your maternal line, meaning your mother's mother's mother's mother, etc. This test brings no males into the picture at all. Women, however, pass their mtdna to both their male and female children, meaning that men and women can have this test done, however an mtdna test will not establish paternity (because it brings no males into the picture). Mtdna is tricky and can reflect very deep ancestry. As an example, my mtdna test could match someone else's mtdna with ZERO differences-exact match-yet the common ancestor I share with the person I match could be as many as 50 generations back.

If I'm understanding you correctly, I don't think an mtdna test will be the answer to establish paternity.

If you're finding that your ydna test is matching other men, all who have the surname "Jones" for example, it is most likely that your great grandfather's "real father" was a man by the last name of Jones. There are still ways to figure out exactly who his true father may have been. If you'd like a little info on how you might be able to do that, feel free to contact me :)

I hope this helps at least a little bit. If it seems that I'm not understanding your question clearly, feel free to contact me as well-I still may be able to offer some suggestions.

Dawn