The most controversial fossil site in human evolution just got even more puzzling

Paleoanthropologist Lee Berger makes the awkward climb on the main thoroughfare through Rising Star Cave. (Robbie Shone/National Geographic via CNN Newsource)

Humanlike fossils have emerged from the deep and twisting caverns of the Rising Star cave system in South Africa over the past decade — and what they have revealed has rocked the field of human origins. Now, new findings on the sex of individuals whose remains were discovered there are giving researchers a fresh but perplexing perspective on this oddball human relative.

In 2015, scientists first described a tiny and puzzling species of hominin from an unusually rich cache of fossils found at a site known as Dinaledi Chamber within the cave system.

Despite having a brain not much bigger than a chimp, researchers hypothesized that Homo naledi, as the species was named, deliberately buried its dead in the confines of the cave. This act represented a sophisticated practice once regarded as uniquely human. Members of the species may even have engraved symbols on the rock walls, they reported.

The latest research adds another layer of mystery: Scientists have recovered ancient proteins from teeth representing 20 individuals found at the site and determined that all the teeth came from females.

“When these results came out, there were a lot of quite nervous scientists. This was not what we expected,” said Lee Berger, a paleoanthropologist and National Geographic explorer in residence, who has led excavations at the site and coauthored the latest research.

“Two labs ran this data,” Berger said. “We ran it through twice because we didn’t want it to be an internal error,” he added.

Molecular scientist Palesa Madupe led the research while working at the Globe Institute at the University of Copenhagen, which has pioneered the field of ancient protein research known as paleoproteomics.

Madupe, who now works as a postdoctoral researcher at the Max Planck Institute for Evolutionary Anthropology in Germany, investigated 23 samples of tooth enamel. Two of the teeth yielded no useful information, and two belonged to the same individual, making for a sample size of 20, the study reported.

To determine the sex of the remains, Madupe evaluated the samples for the male version of the protein amelogenin — which is only found on the male Y chromosome — but the biological marker was completely absent in each sample.

Among hominins and other mammals, females typically exhibit two X chromosomes and males carry an X and a Y chromosome. Because only males have a Y chromosome, finding the y-linked version of the amelogenin protein would have revealed that a tooth belonged to a male. The technique, while relatively new, has been widely deployed on ancient remains, including a 2-million-year-old fossils belonging to even earlier species of human relative. The Homo naledi remains were between 335,000 and 241,000 years old.

In hindsight, Berger said, he should have spotted sooner that the fossils appeared to be female. The adult fossils found in the Dinaledi Chamber had little variation in size, shape and other physical characteristics. Typically, some variation is expected between males and females, a phenomenon known as sexual dimorphism.

“When we described those hominins in 2015, we said they’re the least sexually dimorphic species of ancient hominid ever found,” Berger said.

“It’s one of the great scientific lessons that come out of this,” he added.

‘Why only female individuals?’

Why would only individuals of one sex be found at the site? Berger argues that it is an example of sex bias in mortuary practices. Homo naledi “buried its loved ones by rituals that separated them in death by sex and gender,” he said.

However, the study, which published in the scientific journal Cell on Wednesday, noted that the absence of male markers in the tested remains could be explained by an amelogenin-Y gene that may have mutated or have been deleted over time.

Enrico Cappellini, a senior author of the new study and a professor of paleoproteomics at the Globe Institute, University of Copenhagen, said the deletion of the entire gene had been observed in some living male humans and even in the DNA of a Neanderthal male.

He noted in a news release, however, that it would be very unlikely for the gene to have been deleted “among even half of the 20 individuals we studied or for an entire population.”

“Either scenario, namely the absence of Homo naledi males in the Rising Star cave system or a systematic deletion of their AMELY gene, is fascinating and would have deep implications for a better understanding of the biology and evolution of this species,” he added.

Ryan McRae, a paleoanthropologist at the Smithsonian National Museum of Natural History who was not involved in the work, said that the Rising Star site and Homo naledi are so “interesting and abnormal” that they would always inspire scientific and popular curiosity and intrigue.

“Even if this is a single sex accumulation as the authors suggest, it presents more questions than answers: Why only female individuals?

“We know where the bodies of the Homo naledi individuals ended up, but we do not know how they got there nor where or how they lived.”

Michael Petraglia, a professor at Griffith University in Brisbane, Australia, and director of the ARC Centre of Excellence for Transforming Human Origins Research, has long argued that there is insufficient evidence to support the idea that Homo naledi intentionally buried their dead and made rock art. Both behaviors would suggest advanced cognitive abilities.

The idea that this was the first known example of a sex-specific burial site was “more hyperbole,” he said. However, he had no reason to question the female sex determination, noting the authors from the University of Copenhagen “do scientifically rigorous work on proteomics.”

“With respect to their interpretation that female sex bias supports their interpretation of burial - all I would say is not so fast,” he said via email.

“It is entirely possible that Homo naledi, being a small-brained hominin, and similar to non-human primates, had groups with high female to male sex ratios, foraging in particular places on the landscape.”

For example, he said that female-only foraging groups occur among chimpanzees, and primatologists have observed that small parties, including females with offspring, sometimes use rock shelters or cave entrances for shade, refuge from heat or protection from rain.

Berger argues, however, that if Homo naledi led sex-segregated adult lives, he would expect to find baby boys at the site, which was not the case even though multiple children have been unearthed.

“I think that even our most detailed critic is just going to have to stop and think about this for a while because the chance of it being a natural occurrence is one in a million,” Berger said.

By Katie Hunt, CNN