Six-year-old Alesha was found dead in woodland last summer on the Isle of Bute. She had been spending a summer break with her dad and grandparents at their home.
A 16-year-old boy, who cannot be named because of his age, denies taking her from her bed before raping and murdering her on July 2 last year.
He has lodged a special defence blaming Toni McLachlan for her death.
Glasgow High Court today heard Alesha was raped before she was murdered.
Pathologist Dr John Williams said her injuries "were beyond anything he has examined before in his profession."
He noted 117 injuries on her body and said it was possible some of her injuries could have been inflicted after her death.
Dr Williams told the court Alesha was alive for part of the time while being sexually assaulted.
FORCEFUL PRESSURE TO HER NECK AND FACE
He said the six-year-old, who was three foot nine inches tall, died "as a result of significant forceful pressure to her neck and face…the inflicted trauma is consistent with manual gripping of the neck and face with hand(s), in other words, smothering."
The pathologist said her feet were uninjured, suggesting she'd been carried to the scene.
Giving evidence yesterday Ms McLachlan denied having sex with the teenager accused of killing Alesha and planting evidence to frame him.
She told the court: "She knew I loved her and that's what I'm trying to keep in my head just now."
Brian McConnachie, QC, for the defence, claimed Ms McLachlan had been in a sexual relationship with the boy until early last year, and had had sex with him using a condom on the night Alesha went missing.
Mr McConnachie accused Ms McLachlan of going into Alesha's room, taking her to the woods, attacking her and planting the accused's semen from the condom before murdering her.
The trial continues.
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