The stepfather of a missing 12-year-old girl has been arrested on federal child molestation charges in connection with a sexual assault investigation involving her uncle.

Brooke Bennett's stepfather Ray A. Gagnon, 40, was in federal custody Tuesday on a charge of aggravated sexual assault on a minor, according to Vermont State Police.

The arrest is related to charges against Brooke's uncle, Michael Jacques, who was charged on Monday with sexually assaulting a young girl over a five-year period. The girl told police she had been enrolled in what police called a program for sex.

According to court papers, she told police that Jacques was to be her trainer in a "program for sex" and that she had met three men affiliated with the program.

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Girls in the program were warned that "the first (girl) who does it lives and the second gets her throat cut," according to an affidavit filed Monday at Vermont District Court for Orange County.

Col. James Baker, head of the state police, said authorities were considering all possibilities, including that the sex ring was a ruse Jacques created to intimidate the girl into having sex with him.

State police say Jacques, a registered sex offender, also is a "person of interest" in Brooke's disappearance.

The new charges and second arrest do not involve Brooke, who vanished last week, police said.

The Vermont U.S. Attorney's office said Gagnon, of San Antonio, Texas, will appear in court Wednesday to answer a charge of obstruction of justice. An arraignment originally scheduled for Tuesday was postponed. Gagnon is accused of destroying evidence in connection with the probe into Bennett's disappearance. If convicted, he could be sentenced to life in prison.

Brooke's father James Bennett told FOX News that Brooke's mother had been married to Gagnon after his marriage to her.

Bennett said Cassandra and Ray Gagnon separated about four years ago, but he wasn't sure whether the couple had divorced.

Brooke lived in Alabama with Gagnon and her mother for six years, Bennett said.

Police said Gagnon's arrest was related to the Sunday arrest of Jacques, 42. He pleaded not guilty Monday to a charge of aggravated sexual assault against the now-14-year-old girl over a five-year period, ending last month.

"This arrest is a result of Gagnon sexually assaulting another minor in the Royalton, Vermont, area during the summer of 2007," police said in a news release issued early Tuesday.

The alleged victim in the Jacques case, identified in court papers as "A.R.", told police Jacques was to be her trainer in a "program for sex." She said she had met three men affiliated with the program.

Jacques is being held for lack of $250,000 bail.

Police did not say when or where Gagnon was arrested, but he is being held at Vermont's Southern State Correctional Facility in Springfield.

The charges against Jacques — and now Gagnon — grew out of the investigation into the disappearance of Brooke, who was last seen at 9 a.m. June 25 when Jacques dropped her off at a convenience store in Randolph.

Store surveillance video shows the two leaving the store together and then Brooke going left out the door while Jacques goes right.

Brooke had told family she was to meet a friend to visit the friend's hospitalized relative. Police now believe that was a lie and Brooke intended to meet someone she'd met on the Internet.

Police have described their investigation into Brooke's disappearance as involving social networking Web sites.

The Associated Press contributed to this report.