How can I prove Joseph was John's Father ...

In reply to a query from Kerryn I wrote: Proof is an ideal which it is often very difficult to establish the further you go back, particularly with the poorer members of society.  What you need to do is to establish what the options are, and eliminate those which do not fit. This may well mean checking up on many people who turn out not to be close relatives. In some cases there will only be one "looks likely" alternative which falls well short of being positively proved. In such cases you have to treat it as a good working assumption - but always be on the lookout for further information to strengthen, or weaken, the support for your assumption. 

To see my response in Kerryn's case see DAWSON, Cheshunt, early 19th century

For a more general discussion see  How can you be certain about ...