The man had bite marks on much of his body, and some were major.
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"To the legs and arms, they appear to be minor, but to the face and neck area, they appear to be significant wounds," said Madera Police Detective mark Trukki.
The banks of the river are a place many homeless people live. Many have dogs as pets.
Officers say the dog suspected of fatally injuring the victim was the only threatening one at the scene. After it advanced toward officers and was shot and killed, the dog was also taken away to be swabbed for evidence.
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Investigators say the man who died didn't have an ID on him, and his face was unrecognizable because of the trauma.
"He had several tattoos on his person, so we're going to have the coroner help us identify the person positively, but right now, we don't have confirmation on his identity," Trukki said.
Officers didn't see any other obvious injuries on the man. They will retrace his final steps to find out when he was last seen alive.
At this point, it does not appear the man was dead for long before he was found. An autopsy is set for Tuesday.