Prone to the sneezes of seasonal allergies? Beset by watery eyes of hay fever? Blame your Neanderthal genetics.

New research has found that many of us have leftover Neanderthal genes in our DNA that predispose us to allergies.

Two studies published Thursday in the American Journal of Human Genetics looked at what happened to our immune systems when our early Homo sapiens ancestors left Africa and began breeding with Neanderthals in Europe and Asia 50,000 years ago.

The researchers found that the DNA of the two species combined, leaving Homo sapiens with gene variations that increased our ability to ward off many infections. But inheriting these Neanderthal genes may have also left many of us more prone to allergies.

Studies have shown that around one to six per cent of modern Eurasian genomes were inherited from two ancient extinct human species: Neanderthals and Denisovans.

This new research found that the interbreeding affected the genes on some key proteins in our immune systems, called toll-like receptor or TLR genes. These immune receptors help to activate our immune response and elicit inflammatory and anti-microbial reactions.

The research comes from teams at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and the Pasteur Institute. Although they didn’t work together, both teams decided to search through human DNA collected by the 1,000 Genomes Project looking for genetic remnants of Neanderthals and Denisovans.

They were hoping to explore the evolution of a part of our immune system known as the “innate immune system.” (The innate immune system responds to pathogens in a generic way, as opposed to our adaptive or acquired immune system, which is made up of cells that have “learned” to react to particular invaders.)

Both teams identified three genes from the two extinct hominin groups that they say would have helped early Homo sapiens to survive the diseases they encountered as they moved across Europe and Asia, where Neanderthals had been living for millennia.

"Neanderthals… had lived in Europe and Western Asia for around 200,000 years before the arrival of modern humans,” senior author Janet Kelso said in a statement.

“They were likely well adapted to the local climate, foods, and pathogens. By interbreeding with these archaic humans, we modern humans gained these advantageous adaptations."

But at the same time, it seems these genetic changes also made the immune systems of some of us more prone to overreact to certain allergens, such as pollen, thus making us susceptible to environmental allergies.