Specifically, Don Steven McDougal has been charged with capital murder of a person equal to more than 10 years old but less than 15 years old.
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McDougal was already in custody on an unrelated aggravated assault with a deadly weapon charge.
On Tuesday, crews found the Texas girl's body, not long after declaring the search area a crime scene.
According to Texas Department of Public Safety Lt. Craig Cummings, the crime scene included an area around US-59 and the Trinity River Bridge in Livingston, Texas.
During an afternoon press conference, officials said they had the Trinity River Authority lower water levels to find the girl's body.
"My heart aches with the news, and I express my deepest sympathies and condolences," said Polk County Sheriff Byron Lyons as he announced the tragic discovery.
Lyons did not disclose the condition of Audrii's body, which the Harris County Institute of Forensic Sciences received for an autopsy.
On Tuesday night, the community held a private prayer vigil at the Livingston VFW Post.
"She was really important to the community of Livingston," Elizabeth Kobes said afterward. "It's just heartbreaking."
Audrii had been missing since Thursday, Feb. 15, when, according to authorities, she did not make it to her school bus that morning.
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McDougal was first named as a primary person of interest in the case before officials labeled him a suspect.
McDougal was said to be a friend of Audrii's father, who was also allowed to live in a trailer behind their Livingston house.
According to Lyons, McDougal admitted to leaving the house with Audrii the morning she disappeared but would not tell investigators what happened next.
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"We believe there is enough evidence," Lyons said during Tuesday's press conference.
Newly obtained criminal records show McDougal was indicted on attempted indecency with a child nearly 17 years ago in Brazoria County, which, according to legal analyst Anthony Osso Jr., would have required him to register as a sex offender. However, McDougal pleaded down to child enticement in 2008. The charge does not require sex offender registration.
According to records, on March 31, 2007, McDougal "attempted to remove (a child's) pants after getting in bed with her."
Additionally, according to online records, McDougal has a criminal history that goes back two decades and includes more than a dozen arrests.
Our sister station, KTRK, also learned on Tuesday that McDougal was seen at a mechanic shop near Highway 59 in Livingston the day Audrii went missing. Workers at the shop told KTRK off camera that McDougal was there trying to get a part for his blue Chevy Suburban, adding that he was filthy, covered in dirt and acting suspicious.
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Following Audrii's disappearance, Lyons said McDougal agreed to take investigators to several locations, including the Livingston Dam, where investigators discovered what they believe to be the girl's backpack.
Authorities were being very cautious with the information McDougal gave them, Lyons said, stressing at the time that McDougal had not confessed to anything concerning Audrii's disappearance.
McDougal has been in the Polk County Jail on an unrelated aggravated assault charge. He was taken into custody around 11 p.m. on Friday. Video obtained by KTRK shows him talking to officers outside a shopping plaza before that arrest.