Laura Coward, 47, appeared in court via closed-circuit television in the town of Didsbury, about 100 kilometres northwest of Calgary.
Coward, with shoulder-length blond hair and wearing a black sweatshirt, answered "yes" tearfully when asked if she could hear the judge. She could be heard sobbing again when she was told the murder charge was replacing initial charges from last week of abducting the girl in violation of a court order, break and enter and theft.
Coward was arrested on Tuesday near Sundre when she was found standing outside the vehicle in which her dead daughter, Amber Lucius, was discovered.
Coward's next court appearance has been set for Oct. 6 in Calgary.
Amber's father, Duane Lucius, issued a statement that said a funeral for his daughter would be held later this week.
He urged parents not to take their children for granted and to make time to "have fun" with them because they could be taken from them at any time.
"I am devastated by the tragic loss of my innocent, sweet and lovely daughter," he said. "My heart is broken. The time I had with Amber was cut short, but the time I had with her will always be the most special time of my life."
RCMP Insp. Garrett Woolsey said the medical examiner has not yet given police a cause or time of death, except that it was sometime between Aug. 31 when she was reported missing and Sept. 2 when her body was found.
Recent evidence indicates that the matter is a homicide, he told a news conference in Calgary.
More than 30 officers have been directly working on the "ongoing" investigation, he added.
"Homicide investigations involving children are the worst of crimes. Children are true innocents."
There was no Amber Alert issued when Amber was reported missing. That's something that is being looked into, said Woolsey.
"In this specific case, the RCMP is aware that question has come up and we have assigned a senior RCMP officer to review ... all the facts around the Amber Alert question that is out there right now."
Court documents describe a bitter divorce between Amber's parents and a custody tug-of-war over their daughter that continued up until the girl was found dead.
Her father alleged in a court affidavit when Coward filed for divorce in December 2007 that his wife wasn't the same after the birth of their daughter.
"She would anger easily and we would argue often," he said.
The couple separated in October 2007 after three years of marriage. Lucius, 44, worked construction and Coward had a job as an accountant.
She also had an older daughter from a previous marriage.
The pair initially shared joint custody of both girls, but the children primarily lived with Coward. The woman claimed in affidavits that her estranged husband often didn't take medication for his epilepsy and was prone to outbursts. She said she feared for her safety and the safety of the girls.
In several other affidavits, Lucius alleged his wife was using his epilepsy as an excuse to deny him visits with the children. He said he hadn't had a seizure since he was 18.
He also alleged that she refused to grant numerous court-ordered visits. He provided a doctor's assessment that Coward was excessively possessive and protective of Amber.
But a letter on the court file from a daycare operator in Vauxhall, Alta., described Coward as an "excellent mother'' and called Amber a "cheerful and friendly little girl.''
Affidavits in the court file contain allegations not necessarily proven in court.
In June 2013, a judge named Lucius as Amber's primary caregiver and she moved back to his parents' farm near Millet with him. Coward and the other child then moved to a nearby rural property to be closer to Amber.
Documents say RCMP were called several times to intervene in the couple's disputes.
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