Shanann's body was found in a shallow grave near an oil tank, according to court documents filed in Weld County and obtained by ABC News.
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The daughters' bodies were found inside oil and gas tanks that were mostly full, according to a motion filed Thursday by the district attorney.
In another document, Chris' defense team requests that their own DNA expert be present for the autopsy when DNA swabs were taken from the girls' necks.
According to documents, the bodies had been submerged in oil for four days
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Documents say that forensic scientist Richard Eikelenboom, an expert hired by Watts' defense team, advised that even though the bodies had been in the tanks for several days, DNA would still be present. The motion requests that the hands and nails of the mother should also be sampled.
"It does not seem clear that the coroner, pathologist, or anyone working on behalf of the prosecution team in autopsy plan to take swabs of the necks of the two decedent children," the document states.
According to the motion, the autopsies should have been completed Friday, Aug. 17.
The causes of death were not immediately clear, but a recommendation from Eikelenboom stated, "I have a lot of experience taking samples from dead bodies getting good results after strangulation. The hands of the children should be sampled as well."
ABC7 News contributed to this report.