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They made the discovery while exploring volcanic rocks on the island which they thought were volcanic flow deposit.
When they analysed the rock they discovered it contained rare minerals from outer space - vanadium-rich and niobium-rich osbornite, which have never been reported on earth.
The minerals have, however, been collected by Nasa’s Stardust Comet Sample Return Mission as space dust in the wake of the Wild 2 comet.
A second site, seven kilometres away, proved to be a two-meter-thick layer of ejecta - material ejected from a crater - with the same strange mineralogy.
At the first site, at An Carnach on the Strathaird Peninsula, the geologists zeroed in on a meter-thick layer at the base of a 60-million-year-old lava flow which they thought was an ignimbrite (a volcanic flow deposit).
Dr Andrew Beard of the Earth and Planetary Sciences Department at Birkbeck, University of London, was one of the co lead-authors of the paper.
He said: “When we discovered what it was we were very surprised and it was a bit of a shock because we were not expecting that.
“We initially considered it to be volcanic rock so it was a bit of a shock when we realised what we had found.”
Dr Beard said it was worth the arduous trek to the first site which was in a recess at An Carnach.
He said: “It took us about two hours to get to the site. we could see in the distance that there was a recess at the base of the cliff and if you get a recess it usually shows there is a different type of rock there.
“We persevered across horrendous terrain and crawled up the slope to the recess.”
The researchers pin the impact to sometime between 60 million and 61.4 million years ago.
Lead co-author Dr Simon Drake, an associate lecturer in geology at Birkbeck, University of London, said it was hard work crossing the boggy terrain to reach the site.
He said: “We were sinking in up to our thighs. I distinctly recall saying to Andy Beard, ‘this had better be worth it’. It was worth it.”
The team published their discovery in Geology this week.
The second site was south west of Broadford.
Researchers said the discovery is the first meteorite impact described within the British Paleogene Igneous Province (BPIP) and raises questions about the impact and its possible connection to Paleogene volcanic activity across the North Atlantic.
Dr Drake has collected samples from another site on Skye that also yield strange mineralogy, including another mineral strikingly similar to one found in comet dust.