The parasite, Plasmodium odocoilei, infects up to 25 per cent of white-tailed deer along the East Coast of US, researchers said.
Though white-tailed deer diseases have been heavily studied - scientist had not noticed that many have malaria parasites.
"It is a parasite that has been hidden in the most iconic game animal in the US. I just stumbled across it," said Ellen Martinsen from Smithsonian Conservation Biology Institute who led the study.
They discovered that the deer malaria is widespread - though 'cryptic,' because the parasites occur in very low levels in many of the infected deer.
Using sensitive molecular Polymerase Chain Reaction (PCR) techniques to understand the genetics, researchers confirmed a high prevalence of the disease - between eighteen and twenty-five per cent - in sites ranging from New York to West Virginia to Louisiana.
The data shows that the deer actually carry two genetic lineages of the malaria parasites - "probably different species," and that the two lineages are substantially different from each other, she said.
This divergence between the two forms of malaria was used by researchers as a kind of molecular clock.
"We can date the evolutionary split between those two lineages to 2.3 to 6 million years ago. Which probably means that when the ancient evolutionary ancestors to white-tailed deer travelled from Eurasia across the Bering Land Bridge to North America in the Miocene, some 4.2 to 5.7 million years ago - malaria came along for the ride," said Martinsen.
The findings were published in the journal Science Advances.
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