Rachel Fee, 31, and her civil partner Nyomi Fee, 28, deny killing their son Liam in a house near Glenrothes on 22 March 2014.
The women also deny locking another boy in a cage and tying a third to a chair in a room with rats and snakes.
The trial, which is expected to last for between four and six weeks, at the High Court in Livingston continues.
The couple, originally from Ryton, Tyne and Wear, deny committing the offences at the home they shared near Glenrothes between 12 January 2012 and 22 March 2014.
Both women are charged with assaulting Liam by repeatedly inflicting blunt force trauma to his head and body between 12 January 2012 and 14 March 2014.
They are accused of murdering him by inflicting similar blunt force injuries between 5 and 22 March 2014.
They are also charged with wilfully ill-treating, neglecting and abandoning Liam in a manner likely to cause him unnecessary suffering or injury to health between January and March 2014 leaving him in a darkened room without physical or mental stimulation, giving him medicine to make him sleep and failing to provide and seek appropriate, timely and adequate medical aid for him when he was injured.
They further deny attempting to defeat the ends of justice following Liam's death by delaying contacting the emergency services and falsely claiming during a 999 call - and later to police, friends and family - another boy was responsible for his death.
The Crown also alleges that prior to the arrival of police and paramedics on 22 March, they forced the hand of a boy they blamed into the dead child's mouth.
The women face cruelty and neglect charges against all three boys and the indictment includes allegations that they deprived them of food and threatened them with violence.
One of the boys allegedly had a cage of rats put on his head and the other was alleged to have been tied up in a room where rats and snakes were kept.
Two women have gone on trial accused of murdering a two-year-old boy in Fife and blaming the killing on another boy.