Douglas Owsley views the bones of Anne Calvert, wife of Colonial governor Philip Calvert. In the background on the other exam table are the remains of what is now known to be his son. (Michael S. Williamson/The Washington Post)

The surviving pieces of the baby’s skull are paper thin in places. There are holes in the cranium. And the infant has the classic “rosary bead” rib deformities of the ancient childhood disease rickets.

Some of the bones with the tiny skeleton on the Smithsonian lab table also show evidence of anemia. And the infant probably had scurvy, from a lack of vitamin C.

Much is known about the 6-month-old who died in Maryland 300 years ago and was buried in a small lead-covered coffin. Yet there is no record of the child’s death — or birth. No one knew for certain who the infant was. No one knew if the baby was a boy or girl.

Now, almost 26 years after the coffin was unearthed in St. Mary’s County, experts at the Smithsonian’s National Museum of Natural History have learned that the baby was a boy — and the offspring of an important colonial governor of Maryland, Philip Calvert.

The development is the latest in the long-running archaeological project at St. Mary’s City — once the capital of Maryland and now a community of the dead where scientists have been digging on and off since the 1930s.

Owsley, with the bones of Anne Calvert. (Michael S. Williamson/The Washington Post)

The discovery came about through new genetic testing done at Harvard Medical School at the request of the Smithsonian.

“We continue to get new insights,” said Henry M. Miller, director of research for Historic St. Mary’s City. “There’s still materials that haven’t been analyzed . . . [and] new methods that come up.”

The baby, whose full name still is not known, is one of hundreds of early Marylanders buried in a large field where the old city once stood, according to the Smithsonian and the Historic St. Mary’s City project.

“Who were they?” Miller said. “What could they tell us . . . about the nature of life in the early colonies of America?”

The Maryland colony was established at St. Mary’s in 1634, and the field was its cemetery almost from the beginning, said Silas Hurry, the project’s curator of collections.

The skull of Anne Calvert. (Michael S. Williamson/The Washington Post)

In this case, DNA from an ear bone of the baby was matched to DNA from a shin bone of Calvert, a political, legal and diplomatic figure in early Maryland.

His remains and those of his first wife, Anne, also in lead-covered coffins, were exhumed amid great fanfare, along with the baby’s, in the early 1990s from the site of a long-vanished Jesuit chapel.

Recently, Douglas Owsley, a Smithsonian physical anthropologist who has been studying the Chesapeake region’s early colonists, asked Harvard geneticist David Reich to examine the DNA of the Calverts and the anonymous baby.

And last year, Owsley flew to Boston, carrying bone specimens from the three individuals.

Reich, who specializes in analyzing ancient DNA, was able to get DNA from the bones of Philip Calvert and the baby, but not from Anne. She was probably not the baby’s mother anyhow: Indications were that she had died before the infant was born.

Reich said in a telephone interview that, after testing, he was able to tell that “the male adult and the child have a father-son relationship.”

Owsley said the discovery “continues to show how much can be learned from the human skeleton . . . [and] confirm connections that are not recorded in any history book.”

The Calverts were Colonial elite. Philip Calvert owned 3,900 acres of land. In the late 1670s, he built a spectacular house in St. Mary’s named St. Peters, Miller said.

The house had a wine cellar as well as a large library with books on astronomy, medicine and law.

Now gone, the house “was the size of the Governor’s Palace at Williamsburg,” Miller said. “At the time, it was the largest private home in Colonial America.”

The Calverts were buried in expensive wooden coffins encased in sheets of lead that were shipped from England in the late 1670s.

When the coffins were opened, scientists found the remains of an adult male, an adult female and the baby.

The man, in his 50s, was badly decomposed. He turned out to be Philip Calvert.

The remains of the baby showed that it had been very sick.

“I wasn’t sure if it was a little boy or a little girl, and suspected it was a little girl,” Owsley said in a recent interview. He wondered whether it was Philip Calvert’s child, but wasn’t certain.

Anne’s bones were well preserved, along with sprigs of the memorial herb rosemary, bits of a silk ribbon that may have been used to bind her wrists for burial — and much of her hair.

She was in her 60s. An examination showed that her right thigh bone had been badly broken at some point in her life. The gruesome break had not healed properly and had become infected, leaving a hole in the bone and shortening her right leg by three inches.

In addition, she had lost all but eight of her teeth, in part from scrubbing them with the 17th century’s version of toothpaste: a mix of vinegar and tobacco ash.

“The ash . . . is going to wear away the enamel,” Owsley said. “The vinegar is an acid, so it’s destroying the tooth surface.”

After Anne died in 1678 or 1679, Philip Calvert married a young local woman named Jane Sewell.

Miller said he thinks that the infant may have been their son.

Evidence suggests that the baby was probably born around November 1682, he said. Two months later, in January 1683, Calvert died, leaving Jane with “a big house . . . and a sick child,” he said.

After the baby’s birth, swaddling had probably blocked the infant’s exposure to sunlight, which led to a vitamin D deficiency and rickets, Owsley said.

Scurvy, from the vitamin C deficiency, often went along with rickets. And the anemia probably came from intentional bloodletting, which was done by physicians of that time to treat disorders, he said.

The baby died about three months after his father, in the spring of 1683, judging by the pine and oak pollen in the coffin.

A year or so later, Sewell, having lost her husband and perhaps her baby son, left Maryland and moved to England with relatives, bidding farewell to the three graves in the small brick chapel.

She never returned and never remarried, said Kari Bruwelheide, a Smithsonian anthropologist who worked on the project.

In 1695, the Maryland capital was moved to Annapolis. St. Mary’s City was abandoned. The wooden buildings crumbled. And the settlement became a ghost town in the Colonial wilderness.

The chapel was dismantled around 1710, and its site became a farm field with hundreds of unmarked graves of the old capital’s citizens.

“Some of them actually form lines, as though there’s rows in the cemetery,” Miller said. “We suspect there’s maybe [400] to 500 people buried here.”

Many of the graves were spotted using ground-penetrating radar.

Historic St. Mary’s, a Maryland state enterprise, began work at the site in 1988, Miller said, and after much study completed a reproduction of the old chapel in 2009.

Research showed that about 70 people had the honor of being buried under the chapel’s stone floor, including the three in the lead-shrouded coffins. None of the others has been exhumed, Miller said.

Today, the three empty coffins are back at the chapel where they were buried 300 years ago, and are visible through viewing glass.

The occupants, for the time being, will remain at the Smithsonian, where the experts hope to learn even more about the lives they led so long ago.