Matthew Nilo, 35, of Weehawken, was linked to the rapes through investigative forensic genealogy, which combines uses traditional DNA analysis on publicly available genealogy research and historical records, said Joe Bonavolonta, the special agent in charge of the Boston office of the FBI.
This technique was not available when the attacks were happening.
The alleged attacks happened in August and November 2007 and August and December 2008 in Charlestown, authorities said.
Nilo reportedly lived in Wisconsin, California, and New York before 2008.
According to his LinkedIn, Nilo worked as a cyber attorney for the Cowbell law firm in New York.
Cowbell said in a statement provided to various news outlets that Nilo passed the company's background check when he was hired in January, but he has been suspended pending further investigation following his arrest.
Nilo has been charged with three counts of aggravated rape, two counts of kidnapping, one charge of intent to rape, and one account of indecent assault and battery, the Boston Police Department announced.
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