Antoinette Davis is accused of human trafficking, prostitution and felony child abuse in her daughter's disappearance. Warrants say she provided her daughter with intent that the girl be held in sexual servitude.
Davis showed no emotion during a court appearance in Fayetteville Monday afternoon and she did not enter a plea to the charges.
Shaniya's body was found in an area bordered by Highway 87 south and Walker Road - just south of Sanford - during a second day of searching.
Fayetteville police spokesperson Theresa Chance said the body of a child was located about 100 feet off the road. The state medical examiner positively identified the body Tuesday afternoon.
Authorities are releasing few details about the findings or a cause of death.
Davis' father, Bradley Lockhart, spoke with reporters from the front porch of his home Tuesday afternoon. He asked everyone to remember his daughter, and to work to prevent a similar tragedy from happening again.
"My heart bleeds and hopes and prays that this community, this country can unite as one to possibly prevent something like this from happening again, to another special angel. I ask that everyone makes it a point not to ignore or look past a situation where a person, a child, or anybody might be in danger," he said.
Lockhart thanked all the law enforcement officers and volunteers who put in countless hours in the search for his daughter.
"It's not the result I wanted, or any father would want, but God has a greater calling for all of us," he said.
Through the grief, family and friends revealed to ABC11 Tuesday that they offered to take care of Shaniya Davis in October, but Lockhart declined.
"I believe he is 99 percent the reason this happened in the first place," family friend Timothy Allen said. "And he came to me and he was like I'm going to let Shaniya go stay with her mom basically she needs to learn how to be a mom."
The Allen's have taken care of Lockhart's 17-year-old daughter Cheyenne Lockhart after they say he kicked her out on the streets.
Myrna Allen says during a recent visit to her home she noticed scars on her arms and asked the 5-year-old what happened.
"She says 'cigarette' and then I said 'from where,' she said 'my momma's friends,' and I said 'they were burning you with butts,' and she said 'some times'," Myrna Allen said.
Lockhart's former father-in-law, Byron Coleman, offered to take care of Shaniya, but says he was turned down too.
"He put the child in that position," Coleman said. "He knew the mother was doing drugs there. He knew that people she associated with was drug people."
Lockhart called the allegations speculation and said he wasn't going to talk about it.
"This isn't about Brad or Antoinette or Mr. McNeill, this about Shaniya and the memory of a beautiful lady, a beautiful angel," he said.
If Lockhart wasn't worried about his daughter's safety at the time, his sister said she was.
"I worried about her just as if she was mine," Carey Lockhart-Davis said. "Antionette and I never really got along because I felt as if the way she neglected her children."
And Cheyenne Lockhart says her father wasn't in either of their lives that much.
"I understand he did love her, but he wasn't always in her life," she said. "She was raised by ex-girlfriends, another child's mother in Florida; I mean other people raised her."
Vigils honor Shaniya Davis
Meanwhile, those who searched for Shaniya Davis continue to grieve her death.
Tuesday night, they held another vigil where the little girl's body was found. Many say they are angry, but relieved.
"I'm just glad it's over, she's up in heaven," searcher Brian Dunlap said. "Everything's all right now."
The searchers wanted to hold the vigil at the scene on Walker Road Monday night, but couldn't because investigators were still there.
After authorities left, they moved candles and stuffed animals and handmade mementos to the site to honor the little girl.
Suspect in abduction arrested
Davis was last seen alive at a Comfort Suites hotel in Sanford last week - the same morning her mother reported her missing from her Fayetteville home. Police say a surveillance video from the hotel showed the child with 29-year-old Mario McNeill.
The area where police found the body is about seven miles from the hotel.
McNeill turned himself in Thursday night and police say he confessed to taking the 5-year-old. However, McNeill's attorney told reporters his client would plead not guilty.
McNeill remains in jail. Police have not announced any new charges in the girl's death.