Since Then: The brother and sister grew up without knowing each other. Penny also didn't know Eloise, Daniel's mother. In 1996 though, Daniel encouraged Desmond to speak with Penny to anchor himself in time, and his advice helped the two make contact again in 2004. Penny first heard of Daniel through Desmond, and she accompanied Desmond to England in 2007 when he searched for Daniel's mother.
The two never met while alive. After death though, they knew each other, and Daniel correctly refered to her as his half-sister.
Origin: On the day Desmond was relieved of his duties as an apprenticed monk at the monastery, Desmond met Penelope picking up a shipment of wine.
Since Then: The two dated, and Penny moved in with him. After two years together, Desmond decided to marry her, but her father rejected his request. He bought a ring nonetheless, but the jewelers insistence that his destiny led elsewhere convinced him to break up with Penny. He joined the army and was dishonorably discharged, and Widmore gave Penny none of the letters Desmond wrote Penny. After his release, Desmond entered a race around the world, despite Penny's objections, and ended up on the Island, where a letter she had tucked into his book saved him from killing himself. Penny, meanwhile, searched the world for him, eventually uncovering the Island's location. Desmond became unstuck in time trying to escape the Island, and contacting Penny again saved him. Penny then managed to rescue him in her boat. The two married and had a son. The Island separated them once more, but Hurley later planned to send him home. In the afterlife, Desmond met Penny again, spurring his mission to wake up his friends. They later moved on together, along with their friends.
Origin: Widmore fathered Penny off-island while still the Others' leader. This contributed to their banishing him.
Since Then: The two appeared to have a rough relationship for some time. In 1996, Penny described a potential life of working under her father as a "miserable existence". Widmore tried to protect his daughter, discouraging Desmond from marrying her. Some months later, he gave Desmond her address so she could express her feelings herself, and during Desmond's time in prison, Widmore refused to forward his letters to her to prevent the relationship from resuming. Widmore and Penny appear to have shared some resources over the next few years. Soon after Penny's listening station located the island, Widmore was able to dispatch a freighter there. By the time Penny rescued the Oceanic 6, however, she realized how dangerous her father was, and she went into hiding to avoid him. Widmore, meanwhile, learned Ben planned to kill her, and he eventually approved of her hiding and her relationship with Desmond - if it kept her safe. Widmore's last act before dying was to talk to the Man in Black to try to save Penny from him.
Though they were father and daughter and appeared in seven of the same episodes, Penny and Charles Widmore never shared a scene.