Tuesday afternoon, those remains were confirmed to be that of missing 8-year-old Sophia Mason.
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Authorities said last week that Sophia had been missing for a month.
The investigation started Friday when Hayward Police in northern California contacted the Merced Police Department.
Investigators had Samantha Johnson, Sophia's mother, in custody related to a child abuse case from last year
Melanie Verlatti says her cousin Samantha Johnson was troubled, and would often leave her daughter Sophia in the care of her mom and aunt.
"Just a typical little girl giggling, happy, dancing - loved the park, loved singing, loved being with other kids," Verlatti said.
Verlatti says her family last saw Sophia in December, and the last time she was in school was even before that.
"I think the last time she was in school was in October of this last year and she hadn't been since," Verlatti said.
Child found dead inside Merced home is missing girl: Authorities
"Speaking with the investigators, they were very concerned on the whereabouts of Sophia Mason," said Merced Police Department Lt. Joseph Perez.
Hayward Police gave Merced Police an address on Barclay Way to check out connected to Dhante Jackson, Johnson's boyfriend.
It was there where investigators found Sophia's remains.
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"Detectives did canvass the neighborhood talked to some of the witnesses and neighbors. You know, most of the people that lived in the neighborhood rarely saw anybody coming to and from the house -- most of the people thought the house was just abandoned," said Lt. Perez.
Investigators say Jackson was renting the home but was rarely there because he worked in the Bay Area.
They believe Jackson went on the run when he heard about the investigation.
Police say he's wanted for Sophia's murder.
Johnson was booked into the Merced County Jail on murder charges late Tuesday afternoon.
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Investigators are not sharing details about what they believe happened to 8-year-old Sophia or how long she may have been at that Merced home.
A memorial stands outside the house where Sophia's body was found.
Bright balloons, and fluffy stuffed animals. Just a few of the things family says Sophia loved in her short life.
"I don't even know that I have the words. I'm more than disappointed; I'm angry. I'm heartbroken. I don't understand why," Verlatti said.
Anyone with information on Jackson's whereabouts is asked to contact Merced Police Detective John Pinnegar at 209-388-7712 or by email at pinnegarj@cityofmerced.org.
You can also call the anonymous tip line at 209-385-4725 with information.
You can also report an anonymous tip by clicking here.