The pattern was chillingly similar in each attack. The assailant lured women into his car in downtown Boston, authorities say, and then drove them to a peninsula in Charlestown. There, he threatened them with weapons and raped them.
On Monday, a Suffolk County prosecutor said the similarities, as well as new DNA-based investigative techniques, helped police link a spate of unsolved sexual assaults from 2007 and 2008 to a New York lawyer, Matthew Nilo, 35, who was arrested last week at his New Jersey apartment building.
Nilo, wearing handcuffs and blue prison garb, pleaded not guilty to three rapes and a fourth attempted rape, as his fiancée watched expressionless and clutched rosary beads. After the hearing, Nilo’s lawyer, Joseph Cataldo, questioned the constitutionality of the DNA analysis that allegedly tied his client to the crimes, perhaps signaling a strategy for the defense.
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In the courtroom, Assistant District Attorney Lynn Feigenbaum laid out the most detailed accounts of the Charlestown rapes to date.
Two of the victims, Feigenbaum said, had been out at Boston bars when Nilo found them on separate nights in 2007. One of the women was looking for her car and Nilo offered to help, she said. The other, after leaving a high school reunion, mistook Nilo for a taxi driver. A third woman was panhandling in August 2008 when Nilo offered to give her money if she got in his car, Feigenbaum said.
Nilo allegedly drove all three women to Terminal Street in Charlestown, a short roadway surrounded by shipyards and parking lots, where Feigenbaum said he raped them.
Nilo allegedly attacked a fourth woman, who was jogging near Terminal Street and managed to escape after poking Nilo’s eyes, the prosecutor said.
Boston police investigated the four attacks when they occurred and determined they had been perpetrated by the same man, prosecutors said. But despite DNA evidence from sexual assault evidence collection kits, they were unable to identify a suspect. The cases went cold for nearly 15 years.
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Then, last year, police revisited the unsolved sexual assaults after receiving a $2.5 million federal grant to investigate cold cases that “present the greatest threat to public safety,” Boston police Deputy Superintendent Victor Evans said.
In October, the police asked the FBI to use “investigative genetic genealogy” techniques to help solve the case, according to Joseph Bonavolonta, the head of the FBI Boston office.
The techniques involve uploading an individual’s DNA profile to commercially available genealogy databases, such as GEDmatch or FamilyTree DNA, that consumers use to locate relatives. But investigators can use the results to find the family members of an unidentified suspect.
After employing that method in the Charlestown rape cases, investigators began surveilling Nilo in the New York area. Eventually, investigators collected DNA from drinking cups and utensils they watched Nilo use at a corporate event, prosecutors said.
When they analyzed the DNA, it matched the samples in the rape kits from the 2007 and 2008 assaults.
“Just last month, we received positive confirmation of Matthew Nilo’s identity,” Bonavolonta said last week.
But outside Suffolk County Courthouse on Monday, Cataldo, Nilo’s attorney, described the investigative techniques as “questionable.”
Specifically, he said it appeared law enforcement had not obtained a search warrant before collecting the DNA samples at the corporate event.
“My educated guess is there are no search warrants,” he said, adding that the lack of a warrant could present a point of vulnerability for prosecutors. “Obtaining DNA and analyzing it without a warrant based on probable cause, I posit that is unconstitutional,” he said.
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Nancy Gertner, a former federal judge and current professor at Harvard Law School, said the question of whether law enforcement needed search warrants will turn on the details of the corporate event. If it took place in a space open to the public and if Nilo had “abandoned” the cups and utensils, then a warrant was probably unnecessary.
“The general rule is you don’t have a reasonable expectation of privacy with respect to something you have abandoned,” she said.
A spokesperson for the Suffolk district attorney’s office, which is prosecuting the case, declined to comment in response to questions about the corporate event and the DNA collection.
A separate dispute could arise over the use of forensic genealogy, which has been decried by some civil rights advocates. But here too, Gertner said, legal precedents are fairly clear.
As long as the genealogical information accessed by law enforcement is available to the public, then any evidence derived from it should pass legal muster, she said.
In remarks last week, Bonavolonta said all genealogical information had been properly collected. “We only get what any other customer using a publicly accessible genealogical service would receive,” he said.
In court Monday, Feigenbaum, the prosecutor, described the attacks in harrowing detail.
After reaching Terminal Street with the first victim, on Aug. 18, 2007, Nilo told her “to shut up or he would kill her” and said he had a weapon, before raping her on a grassy area near train tracks, according to prosecutors.
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In the second attack, during the early morning hours of Thanksgiving 2007, the woman who had mistaken Nilo for a taxi driver protested after he drove past the address she had given him, Feigenbaum said. When they reached Terminal Street, he flashed a knife as he ordered her out of the car, and then knocked her to the ground and raped her, she said.
As Feigenbaum described the attacks, a young woman who identified herself as Nilo’s fiancée stared straight ahead and gripped the rosary beads and a cross in her fist.
The rape victims went to hospitals immediately after the attacks and underwent evidence collection exams, prosecutors said. The fourth woman, the jogger, turned over her clothes to the police, including a glove she had worn while poking the attacker’s eyes on Dec. 23, 2008. The DNA from the glove was “314 times more likely to belong to Matthew Nilo than any other male in the population,” according to a filing by prosecutors.
The victims described their attacker as a man in his twenties. One described him as having brown hair and light olive skin.
Nilo, a former North End resident, graduated from the University of WisconsinMadison in 2010. He is also a graduate of Boston Latin School, according to his LinkedIn profile and public records.
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Clerk Magistrate Edward Curley, who presided over the Monday hearing, set cash bail at $500,000 and ordered Nilo to surrender his passport and submit to GPS tracking prior to release. He also must stay away from the victims and from Terminal Street, unless accompanied by his lawyer.
At the end of the hearing, a court official led Nilo through a back door with his wrists cuffed in front of his waist.
Tonya Alanez of the Globe staff contributed to this report.
Mike Damiano can be reached at mike.damiano@globe.com. Travis Andersen can be reached at travis.andersen@globe.com.