Malta’s earliest ancient inhabitants were inbred and shorter than their European counterparts, a new study suggests.  

An academic paper published earlier this month, saw scientists from Dublin’s Trinity College and other partners explore DNA from nine 5,000-year-old Maltese. 

The scientists studied genomes from the Neolithic human remains of the Xagħra stone circle cave burials discovered in Gozo.

In their paper, published in the scientific journal Current Biology earlier this month, the academics argue that these ancient Maltese missed out on genetic changes that were prevalent across Europe at the time. 

They suggest that this was the result of an absence of sea arrivals and is why Malta’s temple-building community declined towards the end of the third millennium BC.

Ggantija is a temple complex from the Neolithic period on the Mediterranean island of Gozo

Exploring Malta's ancient genetics

From nine human bone and tooth samples from the Late Neolithic Xagħra Circle excavation, three yielded excellent DNA content.

This, the paper reads is probably because of the “enhanced preservation” provided by the underground limestone cave burial complex, known as a hypogeum.

The three samples, known as Xagħra 5, 6, and 9, were analysed using shotgun sequencing. 

The resulting data showed "outlying homozygosity levels" - a telltale sign of a  historically restricted population size.  

A replica of the skirted female figure found shattered at the Xagħra Circle - a Neolithic funerary complex dating back to 3,000 BC. Photo: Shutterstock.

Inbreeding results from this genetic state which can increase the chances of offspring being affected by recessive traits, a marker of inbreeding.

The scientists examined whether these Neolithic Maltese showed what is known as shared ancestry within their genetic make-up. 

The second most inbreeding ever recorded

One of the samples, Xagħra 9, had the second most extreme levels of inbreeding DNA data yet reported from a prehistoric sample, the paper says.  

The level of hereditary inbreeding discovered in the sample was only exceeded within an individual discovered in an Irish passage tomb, who was identified as having been the result of first-degree inbreeding, either between siblings or through a parent-offspring pairing. 

The Xagħra 9 sample was found to be just on the periphery of this type of inbreeding, likely the result of “a complex combination of multiple inbreeding loops within his genealogy”. 

“Given the small size and relative isolation of Gozo island, it is possible that the inbreeding loops that gave rise to the Xagħra 9 genome are the result of both recent genealogical inbreeding and a historically small ancestral population size,” the paper reads.  

Ancient Maltese were isolated and shorter

The academics found that Malta’s ancient Neolithic people also shrank in stature around this time when compared to their other European contemporaries. The paper points to the possibility of food scarcity.  

The first settlements in Malta and Gozo, the paper reads, were Neolithic, dating from the sixth millennium BC. 

Throughout their history, these ancient Maltese showed signs of having been in touch with the outside world, such as through the discovery of a type of imported polished rock which does not form part of the Maltese geology. 

However, the presence of these imported artefacts faded from 3,600 BC around the time the island’s pottery and architecture started to show distinctive features.

The paper suggests that fewer arrivals of seafarers led to insularity in Malta and left its inhabitants out of new genetic trends that swept across the rest of Europe at the time.