300,000 years ago - around the same time that early modern humans emerged - a group of hominins belonging to the ancient species Homo naledi reached their final resting place deep inside the Rising Star Cave system in South Africa. A new protein analysis of their skeletons has just revealed a bizarre twist in this mysterious tale: they’re all female.
In 2013, while exploring the Rising Star Cave system in the Cradle of Humankind, South Africa, a pair of cavers came across a trove of hominin fossils unlike any that had been found before. These fossils were dated to 335,000-236,000 years ago and, in 2015, were described as a brand-new species, Homo naledi.
In 2016, at least three additional individuals were found in another chamber of the cave, but so far H. naledi remains haven’t been found anywhere else.
The discovery of H. naledi has prompted a lot more questions than it’s answered. Instead of filling in an ‘evolutionary gap’ on the hominin family tree, H. naledi represents an anatomically archaic species more similar to earlier hominins such as Australopithecus and H. habilis, despite living at the same time as the earliest modern humans (Homo sapiens).
How so many H. naledi remains ended up in a tight, difficult-to-access cave has also puzzled researchers. Some, including palaeoanthropologist Lee Berger, who named the species in 2015, argue that the bodies were deliberately carried and placed in the chamber. Others, however, discount claims of intentional burial and instead point to natural forces depositing the bodies together.
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Genetic clues
By extracting proteins from the tooth enamel of at least 20 individuals, a study recently published in the journal Cell has revealed that they all appear to be missing a Y chromosome - the genetic marker for males.
Berger, a co-author of the recent study, told Science that there’s an obvious explanation for this absence of males and an overrepresentation of females in Rising Star Cave: H. naledi must have engaged in “some cultural behaviour that separates males and females in their death rituals.”
This isn’t the first study to identify homogeneity amongst the individuals in Rising Star Cave. In their original 2015 description, Berger and colleagues noticed that the adult teeth varied little in size and shape. They suggested this may be a sign H. naledi lacked pronounced sexual dimorphism, like modern humans.
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Determining sex from teeth
Working with paleoproteomics specialists from the University of Copenhagen, Enrico Cappellini and Palesa Madupe, the lead author of the recent study Berger extracted proteins from the enamel of 23 teeth (representing at least 20 individuals) in an attempt to determine the sex of the fossils.
They applied a minimally destructive acid etching technique to extract protein fragments called peptides from the enamel. These peptide samples were then analysed for the presence of amelogenin y (AMELY) and amelogenin x (AMELX). Both sexes typically carry AMELX, but only males have AMELY.
Madupe carried out the majority of the acid etching work. After finding no presence of AMELY in the first four H. naledi teeth she analysed, she began to wonder whether she’d contaminated the sample with her own proteins. To rule this out, she asked her supervisor Cappellini and another male colleague to extract new samples. The results were the same: there was no AMELY anywhere in the samples.
A separate lab at the Max Planck Institute of Biochemistry in Martinsried, Germany, independently arrived at the same result.
“Given a sample set of 20 distinct individuals, and assuming a population sex ratio of 1:1, the odds of finding all female individuals are extremely low and represent 0.0000954%,” wrote the authors of the recent study. In other words, the odds of this happening by chance are less than one in one million.
For Berger, this adds further weight to his theory that H. naledi deliberately buried its dead in Rising Star Cave, and that it treated males and females differently. If confirmed, the burials would predate the next oldest (and first widely accepted) evidence of intentional burial by around 100,000 years. These buried remains belong to a female Neanderthal discovered in Tabun Cave, Israel.
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Separating culture from nature
There are still many researchers that disagree with Berger’s interpretations. They continue to raise questions about the taphonomy (the processes that take place from the moment of death through decomposition, burial, fossilisation, and eventual discovery), arguing Berger’s evidence for intentional burial is “heavily influenced by a presupposed narrative” and doesn’t stand up to statistical scrutiny.
However, there’s little debating the sex skew identified by the recent protein analyses. Instead, researchers have suggested alternative explanations and pointed to the founder effect as a potential cause of this skew.
This is a principle in population genetics where a small group of individuals breaks away from a larger parent population to establish a new, isolated colony. Because this small group carries only a fraction of the total gene pool, the new population has significantly reduced genetic variation.
Even though males lacking AMELY are exceedingly rare today, they might have been common in H. naledi if a male ancestor lost AMELY as a splinter population split from a larger parent population, reducing genetic diversity. Indeed, the analysis showed all the individuals found in Rising Star Cave had identical protein sequences, suggesting they were part of a small group.
According to Science, others have speculated the females of Rising Star Cave may have been hiding from H. naledi males or those from another species, or may have even “been part of some strange subterranean harem”.
How 20 H. naledi ended up deep inside Rising Star Cave, and why all of them may have been female, is still a mystery. Berger’s next goal is to find some males that might help shed some much needed light on this 300,000-year-old cold case.
Read the full findings here.
Top image: A fossil mandible of Homo naledi photographed during palaeoanthropological research in the Cradle of Humankind. Credit: Mathew Berger
