WASHINGTON (AP) — The University of Pennsylvania on Tuesday modified a trio of school records set by transgender swimmer Lia Thomas and said it would apologize to female athletes “disadvantaged” by her participation on the women’s swimming team, part of a resolution of a federal civil rights case.

The U.S. Education Department and Penn announced the voluntary agreement of the high-profile case that focused on Thomas, who last competed for the Ivy League school in 2022, when she became the first openly transgender athlete to win an NCAA Division I title.

The department investigated Penn as part of the Trump administration’s broader attempt to remove transgender athletes from girls’ and women’s sports, concluding the university in Philadelphia had violated the rights of female athletes.

Under the agreement, Penn agreed to restore all individual Division I records and titles to female athletes who lost to Thomas and send a personalized apology letter to each of those swimmers, the Education Department said.

By Tuesday afternoon, the Penn website showed other athletes holding the school’s top times in Thomas’ events. The site was annotated with a note that read, “Competing under eligibility rules in effect at the time, Lia Thomas set program records in the 100, 200 and 500 freestyle during the 2021-22 season.”

“While Penn’s policies during the 2021-2022 swim season were in accordance with NCAA eligibility rules at the time, we acknowledge that some student-athletes were disadvantaged by these rules,” Penn President J. Larry Jameson said. “We recognize this and will apologize to those who experienced a competitive disadvantage or experienced anxiety because of the policies in effect at the time.”

Thomas did not respond to a request for comment sent to her representatives.

As part of the settlement, the university must also announce that it “will not allow males to compete in female athletic programs” and it must adopt “biology-based” definitions of male and female, the Education Department said.

In his statement, Jameson said Penn has always been in compliance with NCAA and Title IX rules as they were interpreted at the time, and that the university has never had its own policies around transgender athlete participation.

The school has followed changes to eligibility guidelines as they were issued earlier this year, he said. The NCAA changed its participation policy for transgender athletes in February, limiting competition in women’s sports to athletes who were assigned female at birth.

“Our commitment to ensuring a respectful and welcoming environment for all of our students is unwavering,” Jameson said. “At the same time, we must comply with federal requirements, including executive orders, and NCAA eligibility rules, so our teams and student-athletes may engage in competitive intercollegiate sports.”

Education Secretary Linda McMahon called it a victory for women and girls.

“The Department commends UPenn for rectifying its past harms against women and girls, and we will continue to fight relentlessly to restore Title IX’s proper application and enforce it to the fullest extent of the law,” McMahon said in a statement.

Former University of Kentucky swimmer Riley Gaines thanked President Donald Trump on social media and wrote of the settlement, “Are pigs flying?” Gaines has said she started her activism against transgender athletes competing in women’s sports after sharing a locker room with Thomas at the 2022 NCAA championships.

The Education Department opened its investigation in February and concluded in April that Penn had violated Title IX, a 1972 law forbidding sex discrimination in education. Such findings have almost always been resolved through voluntary agreements.

If Penn had fought the finding, the department could have moved to refer the case to the Justice Department or pursued a separate process to cut the school’s federal funding.

In February, the Education Department asked the NCAA and the National Federation of State High School Associations, or NFSHSA, to restore titles, awards and records it says have been “misappropriated by biological males competing in female categories.”

The most obvious target at the college level was in women’s swimming, where Thomas won the national title in the 500-yard freestyle in 2022.

The NCAA has updated its record books when recruiting and other violations have stripped titles from certain schools, but the organization, like the NFSHSA, has not responded to the federal government’s request and did not respond to emails seeking comment Tuesday. It was not clear how either would determine which events had a transgender athlete participating years later.