The recently discovered mass grave of Irish railroad workers in Pennsylvania — at first believed to have been victims of a cholera outbreak — has taken a far-darker turn: Investigators at the site, known as Duffy's Cut, told IrishCentral that at least two of the skulls they have unearthed were found to have had blunt-force trauma inflicted on them at the time of death.

“When we removed the first skull, we found that there was actually a decent-sized hole at the rear, and when the physical anthropologist examined it, she (Janet Monge) was able to tell us that his fracture, this blunt-force trauma fracture, was inflicted 'perimortem' – right around the time of death,” Frank Watson told IrishCentral on Tuesday.

“Because this is the second skull that has shown perimortem blunt-force trauma, she is calling it suspicious, and for us it is a very strange turn of events that the first two skulls show signs of blunt-force trauma. “

The damage on the skulls recovered is significant. The first skull has a half by one-quarter-inch divot, while the second skull had much-more significant damage done to it. A blunt instrument opened a hole two square inches wide on the skull and the collateral damage to the skull spreads over  a four or five-inch area.

So, was it murder?

“I am always hesitant to say without further evidence, but most of the time traumatic blows to the head happen at the time of death,” said Janet Monge, Adjunct Associate Professor, Department of Anthropology, University of Pennsylvania, the anthropologist who examined the skulls taken from the Duffy’s Cut site.

Another factor that indicates the blow happened before death is the fact that the second skull was found intact in a coffin-like box, meaning that there was little chance that such a significant blow could have been inflicted post mortem

“I will say the one who has the hole in his skull would fit perfectly the end of a pickax head, but the anthropologist can’t make a full decision on that. We did also find an odd metallic item that was in there, and we are going to have some tests done on that too. We are not sure, but it might show some sign of a firearm being used,” continued Watson.

“If more evidence turns up of trauma among the rest of them, it sheds a totally different light on the story," Watson says.

Until the latest shocking developments, the story of the Irish immigrant workers, their journey to America and to the railroad site, and the discovery of their remains years later in a mass grave near Malvern, PA., has occupied most of the investigators' attention.

They have said that they want to identify every single man, and give him a proper burial in Ireland. Watson and his brother Bill, along with historians and archaeologists, are trying to find out what really happened to the Irishmen.

In 1832, 57 Irishmen from Counties Donegal, Tyrone, and Derry traveled to the United States on the John Stamp ship to find work on the railroads.

They headed to Pennsylvania and began work, but within six weeks they were all dead, apparently from cholera, and their bodies had been dumped in an unmarked grave along the railroad's path.

The partial remains of five of the Irishmen have now been found, four with skeletons partially recoverable. The five were found at the bottom of the pit, and were more than likely the first to die. The two men with traumatic skull injuries were among this group.

“What’s interesting is that there were coffins, which was very surprising to us, because the railroad file says that they were buried by the blacksmith, but now we also know that they were buried with some care,” continued Watson.

“These men were buried properly in terms of a traditional Irish understanding, with their head at the west and their feet at the east,” Watson noted. "This is of interest to us because it shows some care and concern for the dead.”

It also raises the possibility that the first of the men to die might have been buried by their fellow Irishmen, and not by the blacksmith, who likely would have simply thrown them in the grave.

But — if two of the first-buried men were murdered — who killed them, and why?

Watson said the first men might have been killed as a warning to their Irish compatriots to keep news of the growing cholera epidemic quiet.

“We know that when they found cholera in the shanty that they fled, and the doors were shut on them and they were forced back into the valley.” Their neighbors at the edge of the valley were members of the East Whiteland Horse Company, “a vigilante group” that might have inflicted violence on the sick Irishmen to keep them away.

There's even the possibility it was an act of compassion. “Was it a mercy killing? I don’t know” Watson ponders. “The blacksmith continued to work for the railroad afterward, but what we have in terms of his character is that he was basically a decent guy.”

The research team has already found two pre-Civil War bullets in the ruins of the shanty where the Irishmen lived. The shanty was burned to the ground after the last Irishman was buried, and railroad contractor Philip Duffy accused the blacksmith, Harris, of burning it down — destroying nearly all of the evidence that could have told more of the 57 men’s’ fate.

The mystery of Duffy's Cut — and its very unique place in Irish-American history — just keep on getting bigger. And far more ominous.