In researching a Y-DNA haplogroup J2a cohanim lineage that leads to this profile of Rabbi Yitzchak HaKohen---and after reading about all the other Y-DNA lineages identified with this Shapira lineage (J1, G2, R1b etc.)---I further delved into sources and made what I think is a significant discovery.
To wit, that according to the rather authoritative Jacobi Papers (Vol. 4, pg 188, 16.3m & other cites), this Rabbi Yitzchak MARRIED the daughter of a Spira (Shapira)...name not specified. Therefore, it would appear that he added the adopted Shapira surname due to a famous father-in-law's lineage rather than it being his direct paternal lineage.
This would then make it quite plausible that male line descendants of Rabbi Yitzchak would have a different Y-DNA signature than other Shapira lineages. Thoughts and evidence to the contrary welcome...
Deb Katz
Volunteer Coordinator, J2a Levant Project at FTDNA
dnadeb@gmail.com