The upgraded charges of murder and neglect of a dependent were filed against Riley Choate, 39, and his ex-wife, Kimberly Kubina, 45, Tuesday.
The body of Christian Choate was found last week buried under a concrete slab. His sister, Christina Choate, 17, of Kentucky, told prosecutors that her father confined the boy to a dog cage for about a year before he died at 13. She also said that he was beaten frequently and the only time he was let out of the cage was to eat and go to the bathroom. The sister said that on April 4, 2009 the boy refused to eat and Choate became enraged, punched him with full force several times in the head, then threw him back into the cage.
According to prosecutors, "Riley would slap Christian very hard in the face a couple times a week and the beatings started to happen more as Riley and his wife Kim...got into disagreements and Riley took it out on Christian."
An autopsy report shows the boy died of blunt force trauma.
On Tuesday, Choate appeared in court and pleaded not guilty to the original charges -- moving a body from a death scene, altering a body and failure to report a body.
"Today we had an initial appearance on the original D felony charge that was filed...we entered a not-guilty plea on that," said Randy Godshalk, Choate's attorney. "People need to avoid rushing to judgment. We do not know all of the facts."
Godshalk said he would enter another a not-guilty plea on the murder charges.
Christina Choate said that her father forced her to remove her brother's dead body. Following the death, the family moved to Kentucky. She told authorities that when her father moved back to Indiana she felt safe enough to report the crime to her biological mother, Aimee Estrada.
Authorities said it was Estrada who alerted police with a 911 call after she learned of her son's death. She had reportedly not seen him for six years.
Estrada declined to comment but her father issued a statement saying, "Today's news of Riley Choate officially being charged with murder is the first steps of justice for Christian. It doesn't stop here. We will continue to ensure he doesn't get away with this. Christian, and no other child in the world, deserves to be a prisoner to a maniac, and ultimately murdered."
David Rice, a neighbor of Estrada, told ABC7 that she has lived in the community for 30 years.
"They have always been real good people. There's been no problems with them. We rarely heard anything from them," said Rice. "I feel sick. For somebody to do something like that to a kid, kids got it hard enough today. They don't need parents doing anything like that, let alone anybody else."
Prosecutors say the investigation is continuing and more people could face charges in the case.