Until recently, it was a little-known program to help Black and Latino students pursue business degrees.

But in January, conservative strategist Christopher Rufo flagged the program known as The PhD Project in social media posts that caught the attention of Republican politicians. The program is now at the center of a Trump administration campaign to root out diversity, equity and inclusion programs in higher education.

The U.S. Education Department last week said it was investigating dozens of universities for alleged racial discrimination, citing ties to the nonprofit organization. That followed a warning a month earlier that schools could lose federal money over “race-based preferences” in admissions, scholarships or any aspect of student life.

The investigations left some school leaders startled and confused, wondering what prompted the inquiries. Many scrambled to distance themselves from The PhD Project, which has aimed to help diversify the business world and higher education faculty.

The rollout of the investigations highlights the climate of fear and uncertainty in higher education, which President Donald Trump’s administration has begun policing for policies that run afoul of his agenda even as he moves to dismantle the Education Department.

There is a range of nonprofits that work to help minority groups advance in higher education but The PhD Project was not well known before Rufo began posting on X about its work with colleges, said Jonathan Fansmith, senior vice president of government relations at the American Council on Education, an association of college presidents.

“It’s not hard to draw some lines between that incident and why 45 institutions that were partners with The PhD Project are getting this investigation announced,” he said.

The 45 colleges under investigation for ties to the organization include public universities such as Arizona State, Ohio State and the University of California, Berkeley, along with private schools like Yale, Cornell, Duke and the Massachusetts Institute of Technology.

The Education Department sent letters to the universities informing them its Office for Civil Rights had received a complaint and they were under investigation for allegedly discriminating against students on the basis of race or ethnicity because of a past affiliation with The PhD Project. The letters set a March 31 deadline for information about their relationship with the nonprofit.

In a statement, the PhD Project said it aims to “create a broader talent pipeline” of business leaders. “This year, we have opened our membership application to anyone who shares that vision,” it said.

Public reaction from the universities’ leadership has been minimal and cautious, with most issuing brief statements saying they will cooperate with investigators and refusing further comment.

Colleges may see reason not to push back. The Trump administration has shown willingness to withhold federal funding over issues involving antisemitism allegations, diversity programs and transgender athletes. At Columbia University, under fire for its handling of pro-Palestinian protests, the administration pulled $400 million in federal money and threatened billions more if it does not comply with its demands.

“There is a concern that if one university steps up and fights this then that university will have all of their funding cut,” said Veena Dubal, general counsel for the American Association of University Professors. “They are being hindered not just by fear but a real collective action problem. None of these universities wants to be the next example.”

Some colleges moved swiftly to stop working with The PhD Project.

The University of Kentucky said it severed ties with the nonprofit on Monday. The University of Wyoming said in a statement that its college of business was affiliated with the group to develop its graduate student pipeline, but it plans to discontinue its membership.

The University of Nevada, Las Vegas issued a statement saying three professors participated in the program, but two no longer work at the university and a third was killed in a shooting on campus in 2023. Arizona State said its business school is not financially supporting The PhD Project this year and it told faculty in February the school would not support travel to the nonprofit’s conference.

Similar fallout came in Texas earlier this year, when Rufo began posting on X about the PhD Project.

“Texas A&M is sponsoring a trip to a DEI conference,” Rufo posted on Jan. 13. Rufo, a senior fellow at the Manhattan Institute, a conservative think tank, accused the university of “supporting racial segregation and breaking the law.”

The next day Republican Texas Gov. Greg Abbot posted on X that the university “president will soon be gone” unless he immediately “fixed” the matter. Texas A&M responded by withdrawing from the conference, and soon after at least eight other Texas public universities that had participated previously in The PhD Project’s conference also withdrew, the Texas Tribune reported.

Rufo has not responded to a request for comment.

Some of the schools under investigation raised questions about where the complaints against them originated.

Montana State University said it follows all state and federal laws and was “surprised” by the notice it received and “unaware of any complaint made internally with regards to The PhD Project.”

Six other colleges are being investigated for awarding “impermissible race-based scholarships,” the Education Department said. Additionally, the University of Minnesota is being investigated for allegedly operating a program that segregates students on the basis of race.

At the University of California, Berkeley, hundreds gathered Wednesday on the campus known for student protests. But this one was organized by faculty, who stood on the steps of Sproul Hall, known as the birthplace of the free speech movement in the 1960s.

“This is a fight that can be summed up in five words: Academic freedom is under assault,” Ula Taylor, a professor of African American studies, said to the crowd.

In a campus email Monday, Berkeley Chancellor Rich Lyons did not specifically mention the investigation targeting his school. But he described the federal government’s actions against higher education as a threat to the school’s core values.

“A Berkeley without academic freedom, without freedom of inquiry, without freedom of expression is simply not Berkeley,” Lyons said. “We will stand up for Berkeley’s values and defend them to the very best of our ability.”

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Associated Press writer Collin Binkley contributed to this report.

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