Henry Louis Gates Jr, who hosts the programme, had written to Sony USA CEO Michael Lynton last year seeking advice as he was troubled by Affleck's request to not include the ancestor in the show. The mails were eventually released by WikiLeaks.
Speaking for the first time on the issue, Affleck said he was embarrassed by the discovery.
"After an exhaustive search of my ancestry for 'Finding Your Roots' it was discovered that one of my distant relatives was an owner of slaves. I didn't want any television show about my family to include a guy who owned slaves. I was embarrassed. The very thought left a bad taste in my mouth," Affleck said in a statement.
"I regret my initial thoughts that the issue of slavery not be included in the story. We deserve neither credit nor blame for our ancestors and the degree of interest in this story suggests that we are, as a nation, still grappling with the terrible legacy of slavery.
"It is an examination well worth continuing. I am glad that my story, however indirectly, will contribute to that discussion. While I don't like that the guy is an ancestor, I am happy that aspect of our country's history is being talked about," the actor-director said.
Gates has defended his decision to ultimately skip the particular detail, saying he maintained editorial control on all his projects and in Affleck's case he went for what he felt was most interesting aspects of the actor's ancestry.
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