The partial skull of a young Homo naledi, an extinct species of hominin that lies within the Homo family tree but on a different branch to modern humans, has been discovered for the first time in a cave in South Africa.

The remains were found around 12 meters beyond the Dinaledi Chamber in the Rising Star cave system – a complex 2km-long network of passageways and the original site of discovery of the first Homo naledi remains in 2015. They are thought to belong to a child aged between four and six that died almost 250,000 years ago.

“Homo naledi remains one of the most enigmatic ancient human relatives ever discovered,” said Prof Lee Berger, project leader and Director of the Centre for Exploration of the Deep Human Journey at Wits University and an Explorer at Large for the National Geographic Society.

“It is clearly a primitive species, existing at a time when previously we thought only modern humans were in Africa. Its very presence at that time and in this place complexifies our understanding of who did what first concerning the invention of complex stone tool cultures and even ritual practices.”

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The researchers have named the skull Leti, which means ‘the lost one’ in Setswana - one of South Africa’s 11 official languages. It was reconstructed from 28 skull fragments and six teeth and joins almost 2,000 other individual fragments belonging to more than 20 Homo naledi individuals unearthed in the Rising Star cave system since its discovery in 2013.

“This makes this the richest site for fossil hominins on the continent of Africa and makes naledi one of the best-known ancient hominin species ever discovered,” said John Hawks, a biological anthropologist and lead author of a previous study on the fossil skeleton of a male naledi nicknamed “Neo” that was also found at the Rising Star cave.

Leti’s remains were discovered in a claustrophobically tight passage that measures just 15 by 80 centimetres long. Although the skull was found in many fragments, there are no obvious signs of injury, so the researchers are unable to speculate on how Leti died.

There are also no signs of damage from carnivores or scavengers and no evidence of the skull being washed into the narrow passage by flowing water. This makes it likely that other members of its species were involved in transporting it to such a remote location, the researchers say.

“The discovery of a single skull of a child, in such a remote location within the cave system adds mystery as to how these many remains came to be in these remote, dark spaces of the Rising Star Cave system,” said Berger. “It is just another riddle among many that surround this fascinating extinct human relative.”

The team now plan to continue to explore the cave system, and hope that any new discoveries will enable them to shed further light on whether these chambers are in fact a burial ground of Homo naledi, he added.