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In the miniseries "Children of Dune", Paul asks Alia and the Duncan ghola to investigate a body found outside the city. The body had its head and hands removed to preclude identification as

Lichna, daughter of Othyem - an identity assumed now by the Face Dancer Scytale.

It is mentioned by Liet Kynes in the first book that it's not possible to identify a Fremen merely by sight. Paul and his mother can do so, but presumably only because of their Bene Gesserit training. And even then, it is largely because of the deeper blue-on-blue eyes of the deep desert dwellers.

The person in question grew up in the city and was born after the events of Dune, so it's doubtful her body would have any other deep-desert indicators. It's been years since I've read the book, however, so I thought perhaps it expanded on this point some.

Given this fact, how was a headless corpse identified as Fremen?

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I can not find an absolute "this is how we know the body is a Fremen" reference, but in todays world we can do it by matching a human genome down to tribal affiliations (let alone familial ones)

Genetics is a well understood field in Herbert universe (the eugenics programs of the Bene Gesserit bloodlines, Bene Tleilaxu use genetic engineering to create humans with specific attributes and Leto II was manipulating the entire human populations breeding patterns to diversify the gene pool).

So it's only logical that the same sort of genome matching could be easily done in the Dune timeframe (214th Century).

This of course begs the question, why weren't they able to identify exactly who the body belonged to…

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Through advanced Bene Gesserit perception.

In the novel Dune Messiah, Alia investigates the body and sees things in a way that only a trained Bene Gesserit would see them, a level of perception that we mere mortals can barely fathom. Given the state of the body this presumably includes marks and callouses on the body, the pliability and colouration of the skin, the musculature of the legs and a thousand other minor snippets of information that even a skilled Suk doctor or cultural anthropologist would miss but which a Bene Gesserit would consider conclusive.

Alia crouched, resting elbows on knees, chin on fists, stared at the body on the dune—a few bones and some tattered flesh that once had been a young woman. The hands, the head, most of the upper torso were gone—eaten by the coriolis wind. The sand all around bore the tracks of her brother’s medics and questors. They were gone now, all excepting the mortuary attendants who stood to one side with Hayt, the ghola, waiting for her to finish her mysterious perusal of what had been written here.

Additionally we learn that some kind of chemical analysis has been done on the body. The results presumably indicate a level of spice suffusing the corpse's cells that wouldn't be seen outside of someone living on Dune.

The body had been discovered several hours earlier by a low-flying courier whose instruments had detected a faint water trace where none should be. His call had brought the experts. And they had learned—what? That this had been a woman of about twenty years, Fremen, addicted to semuta … and she had died here in the crucible of the desert from the effects of a subtle poison of Tleilaxu origin.

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What we know from Dune Messiah:

The woman killed was Lichna, the daughter of Otheym. Scytale murders her to assume her identity to get close to Paul. The reader knows this, but the characters in the story do not.

So first off, we know that genetic identification is impossible.

"We may never learn who it was died here," he said. "The head, the teeth are gone. The hands... Unlikely such a one had a genetic record somewhere to which her cells could be matched."

Also what she was wearing at the time of her murder wasn't particularly Fremen. She was not wearing a stillsuit, but a blue robe:

"We have the woman here," Farok said. "Do you wish to see her now?"

"I've seen her," Scytale said. "I've studied her with care. Where is she?"

Farok snapped his fingers.

The youth took up his rebec, drew the bow across it. Semuta music wailed from the strings. As though drawn by the sound, a young woman in a blue robe emerged from a doorway behind the musician. Narcotic dullness filled her eyes which were the total blue of the Ibad. She was a Fremen, addicted to the spice, and now caught by an offworld vice.

So with most of the major features missing (dental/cranial), and no genetic record, and nothing notably Fremen about any clothing or trinkets that could have been left where the body was dumped - how could anyone know if the body was Fremen?

Most likely, through Forensic Anthropology.

From that link:

Determination of Race from the Skeleton through Forensic Anthropological Methods.

FORDISC, a computer program developed at the University of Tennessee, is another metric technique reviewed that not only distinguishes Whites, Blacks, and Native Americans but also male Hispanics, Chinese, and Vietnamese. Platycnemia, femoral curvature and other morphological attributes of the post-cranial skeleton may be used in support of a racial determination; however, several investigators have turned to post-cranial elements not only to use in support of cranial findings but for use when cranial information is not available. As a result, several discriminant functions from measurements of the pelvis, femur, tibia or combinations of these elements have been developed. Accuracy for these techniques varies from 57% to 95%, depending on the sample and technique used. Other aspects of the femur, such as the diameter of the neck, height of the intercondylar notch and femoral curvature, have been measured for assessment of race.

So it is possible to read a partial skeleton for a racial "fingerprint" even with our technology today. I'd imagine it would be a simple matter for a Suk doctor to study the skeletal remains and note some unique Fremen features.

So that would have to be the answer, since bones were really all that was left at that point.

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