Updated with Ben Affleck’s explanation:

PBS and WNET have launched an investigation into Henry Louis Gates Jr.’s decision to censor his celebrity-genealogy series Finding Your Roots after getting a request from one of its “megastar” subjects. PBS and WNET’s announcement today coincides with a report from PBS ombudsman Mike Getler, blasting Gates’ handling of the situation and PBS’ initial reaction.

“PBS and WNET are conducting an internal review led by our respective programming teams of the circumstances around the Finding Your Roots episode ‘Roots of Freedom,‘” the two public broadcasting entities said this afternoon.

The rannygazoo only came to light late last week when WikiLeaks released a searchable archive of LisaDeMoraesColumnhacked Sony emails. Among the eyebrow-raisers was an email exchange between Gates and Sony Entertainment CEO Michael Lynton in which Gates reveals that a “megastar” had asked that the discovery he is the descendant of a slave owner be stricken from the show. Gates acknowledges in the email that fulfilling the request “would be a violation of PBS rules, actually, even for Batman” and “would embarrass him and compromise our integrity” and that “once we open the door to censorship, we lose control of the brand.”

So far, Gates is batting 1,000.

But, instead of taking his concerns to PBS or WNET, which is the show’s producing station, Gates took them to Lynton. Gates explained it’s the first time one of his show’s “guests” has asked to edit anything out of a broadcast and that several previous “guests” had discovered they too were descendants of slave owners (including Ken Burns and Anderson Cooper) but they had not asked to censor or edit what the show discovered. But this guest, Gates noted, is a “megastar” and he asked Lynton “what do we do?”

Lynton advised taking it out if no one knew about the situation, but warned it would get tricky if word got out that Gates was editing material based on this kind of sensitivity.

The CEO was correct.

The episode featuring Ben Affleck aired October 14 on PBS. No reference to Affleck’s slave-owning ancestor was made. Finding Your Roots is financed, in part, according to Gates, by the Public Broadcasting Service and the Corporation for Public Broadcasting.

When the media got wind of Gates’ email exchange with Lynton while poring through the WikiLeaks cache late last week, Gates issued this statement:

The mission of Finding Your Roots is to find and share interesting stories from our celebrity guests’ ancestries and use those stories to unlock new ways to learn about our past. We are very grateful to all of our guests for allowing us into their personal lives and have told hundreds of stories in this series including many about slave ancestors—never shying away from chapters of a family’s past that might be unpleasant. Ultimately, I maintain editorial control on all of my projects and, with my producers, decide what will make for the most compelling program. In the case of Mr. Affleck — we focused on what we felt were the most interesting aspects of his ancestry—including a Revolutionary War ancestor, a 3rd great–grandfather who was an occult enthusiast, and his mother who marched for Civil Rights during the Freedom Summer of 1964.

It had the crackle of confederate money. So too did PBS’ initial statement:

It is clear from the [email] exchange how seriously Professor Gates takes editorial integrity. He has told us that after reviewing approximately ten hours of footage for the episode, he and his producers made an independent editorial judgment to choose the most compelling narrative. The range and depth of the stories on Finding Your Roots speak for themselves.

PBS now says it’s been investigating the situation since Saturday.

PBS’ ombudsman says WNET reps told him Gates’ team had made them aware they wanted to remove the slave-owner reference from the segment but positioned it as a redundancy concern, given the other profiles that already had dealt with slave-owning ancestors. WNET said it did not learn of Affleck’s request, or Gates’ email exchange with anyone at Sony, until the press began calling last Friday. PBS, meanwhile, says it knew nothing of the editing — or the Affleck kerfuffle or the Sony email exchange — until it too started hearing from press on Friday.

“Any serious program about genealogy, especially dealing with celebrities, cannot leave out a slave-owning ancestor,” PBS’ ombudsman scolded this afternoon. “It also seems clear from the emails that Gates knew the stakes involved in terms of PBS credibility yet went with the advice from the Sony executive to squelch the factoid about a slave-owning ancestor and try to keep it quiet.”

The emails, Getler concluded, “make clear that Gates understood the serious journalistic and credibility issues at stake and the risks should this become public” but did not inform PBS.

“As for PBS, they just struck me as asleep at the switch when this broke,” the ombudsman said. “It was pretty apparent from the leaked emails what had happened, and to put out a statement that said essentially nothing and very quickly looked pathetic, as if they were hiding something.

“So PBS, in my view, deserves all the articles and TV reports that have PBS in the headline. PBS invests a huge amount of responsibility, and faith, in those who produce programs for it. They need producers to bring to their attention critical issues, especially ones that may reflect poorly on what people expect of PBS or might damage their credibility.”

Late today, Affleck wrote on Facebook that he did not want a TV show about his family to include a person who owned slaves because “I was embarrassed” and “the very thought left a bad taste in my mouth.” He said he lobbied Gates “the same way I lobby directors about what takes of mine I think they should use,” explaining, “this is the collaborative creative process.” Affleck said he think it’s important to remember that PBS’s Finding Your Roots “isn’t a news program.”