Perfect Dark
In Perfect Dark, Jonathan is an agent for the Carrington Institute whose last name is revealed to be "Dark" during the "Duel" mission briefing on Special Agent difficulty. This possibly indicates that Jonathan is Joanna's brother, though the game contains no other references to his last name.

In Perfect Dark Zero, Jonathan is introduced at the end of mission 7 after saving Joanna from Chandra Sekhar. In this game, however, his last name is Steinberg.

Because Perfect Dark was made before Perfect Dark Zero, Jonathan may have been Joanna's brother at one point in the first game's development. The inclusion of his name as "Jonathan Dark" may also have been an oversight of the developers if this was later changed. It's likely that Jonathan's character was retconned and his last name to changed to Steinberg in Perfect Dark Zero to have no previous affiliation with Joanna.
Contributed by Kakariko Kid
A sister title for Perfect Dark was at one point planned called Velvet Dark. The title would've possibly starred Joanna Dark's sister, Velvet Dark, and was presumably for either the GameCube, or according to Gregg Mayles, possibly the Nintendo 64.
Contributed by KnowledgeBase