Damion Comager, 23, was ordered held without bail during the brief court appearance in the Bronx.
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He is charged with murder and manslaughter in the death of his infant daughter, Genevieve.
In phone conversations with his parents, Comager allegedly told them that he shook the crying baby on May 14.
Authorities say that after it happened, Comager dressed the infant in clothes and put her in a stroller as to not draw suspicion as he rolled her to the Major Deegan Expressway, where he dumped the remains May 14 -- two weeks before they were found Sunday night.
Comager has three active arrest warrants in Colorado for assault, failure to appear and a probation violation, it was revealed.
He is alleged to have fled to France to avoid the charges, where he met his girlfriend and co-defendant Ivana Paolozzi.
The 20-year-old Paolozzi, the victim's mother, was expected to appear in court on Wednesday afternoon on charges of helping him dispose of the body.
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When reporters previously spoke to Comager after his arrest, he told them, "I love my daughter." When asked if he shook the baby, he said, "it was a mistake."
A GoFundMe page has been set up by a family friend seeking donations to help pay for Genevieve's funeral.
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