San Angelo, Texas ? The more than 400 children taken from a ranch run by a polygamous sect will stay in state custody and be subject to genetic testing to sort out family relationships that have confounded welfare authorities, a judge ruled Friday.

State District Judge Barbara Walther heard 21 hours of testimony over two days before ruling that the children would be kept in custody while the state continues to investigate allegations of abuse stemming from the teachings of the Fundamentalist Church of Jesus Christ of Latter Day Saints.

“This is but the beginning,” Walther said.

Individual hearings will be set for the children over the next several weeks, and the judge will determine whether they are moved into permanent foster care or can be returned to their parents. All hearings must be held by June 5.

Walther also ordered that all 416 children and parents be given genetic tests. Child welfare officials say they’ve had difficulty determining how the children and adults are related because of evasive or changing answers.

A mobile genetic lab will take samples Monday at the main shelter where children are being kept; parents will be able to submit samples Tuesday in Eldorado, closer to the ranch.

The custody case is one of the largest and most convoluted in U.S. history. The ruling capped two days of marathon testimony that sometimes descended into chaos as hundreds of lawyers for the children and parents competed to defend their clients in two large rooms linked by a video feed.

Attorneys popped up with objections in a courtroom and nearby auditorium, then queued up down the aisle to cross-examine witnesses in a mass hearing that frustrated attorneys and stretched the small-town court system.

The April 3 raid on the Yearning For Zion Ranch was prompted by a call made to a family violence shelter, purportedly by a 16-year-old girl who said her 50-year-old husband beat and raped her. That girl has never been identified.