Their legal battle over visitation rights and custody, carried out over the last seven years in Vermont and Virginia courts, received wide publicity because of the clashes over sexual orientation and religion, and because it raised questions about the rights of nonbiological parents in same-sex unions that are not recognized in many states.
Lisa Miller, the girl’s biological mother and a newly fervent Baptist, was championed by conservatives for her efforts to shield her daughter from homosexuality. A Vermont court had granted her primary custody of the daughter, Isabella Ruth Miller-Jenkins, after Ms. Miller split with her partner, Janet Jenkins, in 2003. But the court also declared Ms. Jenkins to be a legal parent with liberal visiting rights, and Ms. Miller, who had moved with the girl to Virginia, defied repeated orders to permit the visits.
The case took a turn in late 2009, as the Vermont family court, citing Ms. Miller’s noncompliance, shifted primary custody to Ms. Jenkins. Ms. Miller and Isabella, who is now 9, disappeared. A warrant was issued for Ms. Miller’s arrest, and they have not been heard from since.
According to an F.B.I. affidavit unsealed in Vermont on Thursday, the pastor, Timothy David Miller of Crossville, Tenn., helped arrange in September 2009 for Ms. Miller and Isabella to fly from Canada to Mexico and travel on to Nicaragua, where he worked as a missionary for Christian Aid Ministries. (The F.B.I. said it had no evidence that Mr. Miller and Lisa Miller were related.)
Ms. Miller and Isabella stayed in a beach house in Nicaragua that is owned by a conservative businessman with close ties to Liberty University, an evangelical school in Lynchburg, Va., and whose daughter works at the university’s law school, according to the affidavit.
Lawyers from Liberty, including the dean of the law school, Mathew D. Staver, represented Ms. Miller in court appeals on the custody issues. They argued without success that Ms. Jenkins had no parental rights and that laws in Virginia, which ban same-sex unions, should prevail over those in Vermont.
On Friday, Mr. Staver said the legal team has had no contact with Ms. Miller since the fall of 2009 and had always advised her to obey the law. He said he knew nothing about the accusations involving a law school office assistant, Victoria Hyden, and her father Philip Zodhiates, the beach house’s owner.
Mr. Zodhiates runs Response Unlimited, a Christian direct-mail company in Waynesboro, Va. He did not respond to requests for comment, but on Friday he told The Advocate magazine that the pair were not living at his house in Nicaragua and called the accusations “absurd.”
Ms. Miller and Ms. Jenkins were joined in a civil union in Vermont in 2000 and planned to raise a child together. Isabella was conceived by artificial insemination and born to Ms. Miller in 2002, with Ms. Jenkins present at the birth. But the parents’ relations soured over the following year. Ms. Miller moved with Isabella to Virginia, became deeply involved with a Baptist church and renounced homosexuality. A Vermont court dissolved the civil union but treated Ms. Jenkins as a full parent with visitation rights.
Over time, Ms. Miller began refusing to allow the required visits, among other things objecting that Ms. Jenkins’s “homosexual lifestyle” would offend Isabella’s religious beliefs. At one point, a court in Virginia, which does not recognize same-sex unions, agreed with Ms. Miller’s claim to be the sole legal parent, but the Virginia Supreme Court eventually confirmed that the Vermont rulings should prevail.
Last June, according to the Federal Bureau of Investigation affidavit, an unnamed person called one of Ms. Jenkins’s lawyers, Sarah Star, and told Ms. Star that the mother and daughter were hiding in Mr. Zodhiates’s Nicaraguan house. Much of the evidence in support of the criminal charges and other accusations, the affidavit said, was obtained through court-approved, covert searches of e-mail accounts, uncovering messages from Mr. Miller that appear to arrange the mother and daughter’s 2009 flight to Nicaragua and from Mr. Zodhiates arranging to send them supplies.
On Friday, Ms. Jenkins issued a statement through Gay & Lesbian Advocates & Defenders, a rights group in Boston that has also represented her in court.
“I know very little at this point, but I really hope that this means that Isabella is safe and well,” it said. “I am looking forward to having my daughter home safe with me very soon.”
The United States attorney for Vermont, Tristram Coffin, told the Rutland Herald newspaper that Mr. Miller had been arrested on Monday night in Virginia and was scheduled to appear in Federal District Court in Burlington on Monday. Officials declined to say whether others may be arrested or what measures they are taking to find Ms. Miller, who faces criminal charges, and Isabella, who under current rulings should be in the primary custody of Ms. Jenkins, with visitation rights for Ms. Miller.