Thomas, who is a transgender woman, won the 500-yard freestyle Thursday night in 4 minutes, 37.32 seconds, a Blodgett Pool record and her best time since the Zippy Invitational in December.
Thomas was among three Penn swimmers in the final, with teammate Catherine Buroker finishing seven seconds behind in second place and Anna Kalandadze placing fourth.
Buroker and Kalandadze applauded as Thomas was awarded her medal. Following the ceremony, the three Quakers posed for pictures on the podium, Thomas holding an "Ivy 2022 Champion" sign.
Thomas entered the night as the top seed after winning her morning heat with a time of 4:41.19. She closed her Day 2 slate by swimming the second leg of Penn's 200 freestyle relay that placed fourth. She is scheduled to swim the 200 freestyle and either the 1,650 or 100 freestyle later this week.
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On Wednesday, Thomas was part of Penn's 800 free relay that finished third.
Penn senior Andie Myers, who competes in the freestyle and butterfly, wore a facemask with a transgender flag Thursday to show support for Thomas.
"I want everyone at this meet to know that I support her," Myers said. "She's worked for all of this and she's given up so much to transition and to be authentically herself. I think it's really important and I think it's really brave what she's doing today."
Princeton's Ellie Marquardt, the 500 freestyle champion in 2020, finished third Thursday.
No swimmers were made available to media after the races.
Also among the newly minted conference champions Thursday was Yale's Iszac Henig, who won the 50 freestyle. Henig, who is a transgender man, won in 21.93 seconds, breaking his own pool record set earlier Thursday in preliminaries. He returned to the pool Thursday night to help Yale set a meet record in the 200 freestyle relay. The Bulldogs finished in 1:29.66.
Thomas' success has brought national attention to the issue of transgender athletes, garnering criticism and praise. Several of Thomas' teammates have spoken out anonymously, both in support of Thomas and criticizing her inclusion on the women's team. Thomas was a member of the Penn men's team for three seasons.
On Feb. 3, three-time swimming Olympic gold medalist Nancy Hogshead-Makar sent an unsigned letter on behalf of 16 Penn swimmers and their families asking the Ivy League not to advocate for Thomas' inclusion this postseason. On Feb. 10, more than 300 members of the swimming community -- including representatives of each of the Power 5 conferences, five of Thomas' current teammates (including Myers) and Tokyo Games silver medalist Erica Sullivan -- signed an open letter published by Athlete Ally supporting Thomas.
Thomas returns to the pool Friday for the 200 freestyle.
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