This is from our FAQ, which partially addresses your question:
What if I get back results I don't like, such as indications of a non-paternity event?
Non-paternity results did occur and they may be obvious through DNA testing when the result is being compared in a well-documented family.
There are several scenarios that fit into the category of non-paternity event. One, of course, is infidelity, while another common event was the unrecorded adoption. As there were many adult deaths on the frontier, children were frequently raised by relatives or friends, with the adoptive parents giving the child their own last name. Where infidelities or adoptions have long been rumored and now proven, there can be some satisfaction. Where an infidelity or adoption occurred in a well-documented family, identifying it helps in clarifying the DNA profile of descendants. Where the non-paternity event occurs in a family without extensive documentation, it can be very disruptive and prevent the participant from obtaining matches within the surname.
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In the end, you are relying on the paper trails of whoever is tested. A good researcher has kept his source material to make it easy to verify his family tree. You'd have to ask whoever you get tested for that person's research in order to judge it for yourself.
DNA testing does provide a major boon though - if there are other individuals in the database with matching DNA, you can do a search to find out. This may help you verify your paper trails to make sure that you actually are getting the results you expect:
How do I compare my results to other people?
Once your results are available, you'll be able to go into your personal page at FTDNA and do a search for yDNA matches. You'll always see all of the other results in your surname - and at that time, you'll be able to select a preference that allows you to compare against all others of all surnames who opt in to the FTDNA internal comparison. (When your results are back, we'll post them on your surname project’s Results page.)
You'll also be able to upload your results to Ysearch (FTDNA's public database - open to all) and see who you match there.
FTDNA will send you automated messages when you have a match (either with only your surname project members or to their internal "opted-in" database) - depending on your selectionhttp://www.worldfamilies.net/faqs.html#compareresults