A partial skull found in Manot Cave in Israel's West Galilee province suggests Neanderthals and modern humans met and mated from 55,000 years ago – 10,000 years earlier than previously thought.

Modern Europeans get about 4% of their genes from Neanderthals, showing that at some point, the two species interbred. But when this happened has been a long-standing mystery.

The skull is the earliest evidence of modern humans co-habiting an area with Neanderthals.

Published in the journal Nature, palaeontologist Bruce Latimer said: "It has been suspected that modern man and Neanderthals were in the same place at the same time but we didn't have the physical evidence. Now we do have it in the new skull fossil."

The skull was found covered in minerals produced in the cave, allowing them to use dating techniques to put the cranium age at between 50,000 to 60,000 years old.

It contained a relatively small brain and features resemble modern man's skull – the occipital bun (a bony formation) on the back of the skull in particular. Neanderthals' bun appear like a "bony hot dog bun", with a grove down the middle, but in modern humans this is missing.

As the brow ridge is missing, the gender of the fossil is unknown. Researchers do not believe it is related to other sub-adult human teeth and bones found in the cave.

"This leads us to believe that there are likely more fossils in the cave where other bones associated with the skull might be found," said Mark Hans, chair of Cape Western Reserve University's Department of Orthodontics.

The Manot cave is in a region where Neanderthals lived for a period – possibly when ice sheets forced them into warmer areas.

The prehistoric cave is located along the only land route available for ancient humans to have travelled out of Africa and into the Middle East, Asia and Europe.

Latimer said: "Modern humans and Neanderthals likely encountered each other foraging for food."