But authorities declined to say whether they had found the body of Kelsey Berreth, 29, what led to the arrest of Patrick Michael Frazee and what motive there might be for Berreth's disappearance and slaying.
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Frazee, 32, was arrested at his home in the alpine town of Florissant on suspicion of murder and solicitation of murder, said Miles de Young, chief of police in neighboring Woodland Park, where Berreth lived.
"As you can tell from the arrest, sadly, we do not believe that Kelsey is still alive," De Young said.
Authorities also declined to elaborate on the solicitation of murder charge, how they believe Berreth was killed or any other aspect of the investigation.
Police have said Frazee was the last person to see Berreth alive. The couple shared a baby daughter but did not live together.
The disappearance of the young pilot mystified family and friends and led to national social media seeking any information on her whereabouts.
She was last seen at a grocery store near her home that's about two hours south of Denver and about 15 miles from Florissant, where Frazee lives.
Surveillance video showed her entering the store on Thanksgiving Day with what appears to be the couple's daughter in a baby carrier. Frazee had told police that the couple met that afternoon so he could pick up the child.
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De Young said the child is in protective custody and will be turned over to Berreth's family.
Police had urged Frazee to speak directly with investigators this week. His attorney, Jeremy Loew, had said his client was cooperating with investigators and had provided DNA samples.
Loew wasn't immediately available for comment Friday but planned to release a statement, his office said.
Authorities searched Frazee's cattle ranch and Berreth's townhome but declined to say what they found. De Young did say evidence suggests "the crime" occurred at Berreth's home and that her cellphone was found in Idaho. Investigators were working to recover it.
The cellphone is key. Police said the only signs of Berreth after Thanksgiving were some text messages and that location data suggested the phone by Nov. 25 was near Gooding, Idaho, 800 miles (1,290 kilometers) from her house.
Police started looking for Berreth on Dec. 2 after her mother, Cheryl, asked for a welfare check.
Investigators who went to Berreth's home found cinnamon rolls in the kitchen and both of her cars outside. De Young said the company where Berreth worked as a flight instructor, Doss Aviation, had accounted for all their planes and that police had no reason to believe she used someone else's plane for a flight.
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Frazee did not attend a Dec. 10 news conference where Cheryl Berreth made a plea for information about her daughter. His attorney said Frazee only learned of the event an hour before it began and would have attended with more notice.
"Mr. Frazee hopes and prays for Ms. Berreth's return," Loew said that day. "Mr. Frazee will continue to cooperate with law enforcement and continue to parent the child he shares with Ms. Berreth."
District Attorney Dan May says formal charges are pending and could take as long as 10 days to file. Frazee's arraignment has yet to be set, May said. He said the search and arrest affidavits will stay sealed for now.
"There are a lot of investigative leads that need to be done," May said.
Authorities said as many as 30 FBI agents are participating in the investigation in several states.
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