The hunt for the couple was launched Friday when the Hall County Sheriff's Office tipped off Dothan police that Mathis and Oakes were staying at an apartment in the area, and that it was possible their son was dead.
Alabama authorities could not locate them until Monday, when they were tracked to an apartment in Bronson, Fla., about 25 miles southwest of Gainesville, Fla.
Mathis was shot four times as he tried to run from authorities outside the apartment complex and is stable at a Florida hospital, police said.
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He was allegedly armed with a handgun at the time of the shooting.
Once in custody, Mathis and Oakes provided investigators with information that led them back to the InTown Suites in Dothan.
“A search warrant was executed at that location and the body of 6-month-old Carlton James Oakes was recovered from the freezer,” police said.
Authorities believe Mathis and Oakes placed him there.
The Alabama Department of Forensic Science in Montgomery is investigating the cause of the child’s death, which is still unknown. Foul play is suspected.
The spokesman said authorities expect to file additional charges out of Houston County, Ala., once an autopsy is performed.
Mathis and Oakes are currently awaiting extradition to Alabama to face their charges. Their bonds are set at $15,000 each.
In addition to his charges in Alabama and Florida, Mathis is also a person of interest in a gas station robbery, Hall County sheriff’s deputies told Channel 2 Action News. He is wanted there for allegedly violating his probation, officials said.