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Wood from the vessel was found during excavations for a car park and has now been dated to around 1773.
The wood is thought to come from a forest in Philadelphia.
Scientists believe the ship is a Hudson River Sloop, designed by the Dutch to carry passengers and cargo over shallow water.
The site where it was found was filled in around 1818 when the Manhattan shoreline was expanded.
The Dutch first settled the southern tip of Manhattan as New Amsterdam in the early 17th century.
It was renamed New York in 1665 after the English seized control.