A forensic anthropologist told jurors in US District Court today how investigators painstakingly dug up the remains of four alleged victims of James “Whitey” Bulger in unmarked graves in Dorchester.

Ann Marie Mires, who worked with the state medical examiner’s office until 2009, testified in Bulger’s racketeering trial in Boston that on a cold Jan. 13, 2000, investigators began digging across from Florian Hall on Hallet Street and spent hours pulling the bones of two men and a woman from the frozen ground.

As a prosecutor displayed photos of skeletons recovered at the site, Mires identified them for jurors as the remains of Arthur “Bucky” Barrett, Deborah Hussey, and John McIntyre.

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Kevin Weeks, Bulger’s former protégé, testified Tuesday that he watched as Bulger killed Barrett, Hussey, and McIntyre in a South Boston home in the early 1980s. He said Stephen “The Rifleman” Flemmi pulled teeth from the victims to make them harder to identify, then they buried them in the basement of the home at 799 East Third St. When the house was about to be sold, Weeks said he, Bulger, and Flemmi exhumed the bodies and buried them on Halloween night 1985 at the Dorchester site.

During her testimony Wednesday morning, Mires said the remains of two of the bodies were disarticulated, supporting Weeks testimony that the bodies were removed from one site to another. She also said that garden lime was also at the scene. Weeks testified earlier that they used lime so that the bodies would decompose quicker.

Mires said that the skulls of Hussey, McIntyre and Barrett had damage to the jaw area, consistent with Weeks’s claim that their teeth were removed when they were killed to hamper identification by law enforcement.

Also today, Mires agreed that both Barrett and McIntyre had been shot in the head, and used a plastic skull to demonstrate for jurors the areas she had found damaged on their remains. Weeks testified that Bulger shot Barrett in 1983, and McIntyre the following year.

Weeks said Bulger and Flemmi strangled Hussey in 1985, but Mires said the injuries were not visible on her remains. Investigators determined her “cause of death was homicidal violence, ideology unknown.”

Weeks testified he saw Bulger on the ground with his legs wrapped around Hussey, choking her. He said Bulger’s ally, Stephen “The Rifleman” Flemmi thought Hussey was still alive, so he used a stick and a rope to strangle her some more.

Mires also testified that in September 2000, investigators recovered the remains of Paul McGonagle, who had vanished in November 1974, from a grave by the shoreline of Tenean Beach in Dorchester.

“We’re battling the elements, high tide is pretty much full on and we’re getting (water) seepage,” said Mires, describing the race to pull McGonagle’s remains from the grave as they uncovered his shoes and fragments of clothing.

Mires showed jurors a gold claddagh ring and faded shoes that were pulled from grave, along with McGonagle’s skeletal remains. She also identified bullet fragments found in McGonagle’s skull.

Former hitman-turned-government witness John Martorano testified earlier in the trial that he shot McGonagle in the head, and that Bulger participated in the slaying. The sweeping racketeering indictment alleges Bulger participate in 19 murders.

Mires, considered an expert witness, spent the morning describing for jurors how investigators approach a crime scene and a dig site. Also, she described the process in examining remains.

“The skeleton is like a road map, it allows us, anthropologists, to drive through the lifetime of an individual,” she said. In “archeology, you don’t know what you’re going to find, so it’s revealing itself as you go along.”

She also said that the bodies had been at the sites for some time. The bones pulled from the earth near Florian Hall started to take on the color of the soil. And roots started to grow in between the remains.

“There is a lot of root growing through this material, and it speaks to how long its been in the ground,” Mires said.

Weeks, now 57, led investigators to the grave site near Florian Hall after he began cooperating with authorities following his own racketeering indictment in 1999. By then, Bulger had already fled an earlier indictment in 1995, and spent 16 years on the run before his arrest in June, 2011.

Weeks cooperated with authorities and told of his crimes with Bulger. He spent five years in prison after pleading guilty to charges including aiding and abetting in five murders.