"We're fascinated with the kings and queens who lived at that time and anything that belonged to them," O'Regan said. "In these specimens we have something that was alive and probably presented to [the royals]."
Jeremy Ashbee, a former Tower of London curator, says the menagerie was the king's private collection and a sign that he enjoyed good relations with foreign monarchs, who presented him with exotic animals.
"Lions were particularly prized as the living emblems of the royal arms of England, much like modern mascots," Ashbee said.
Three lions have featured on the royal arms since the reign of King Henry II, the 12th-century English monarch. The national emblem remains popular today, decorating the jerseys of the English national soccer team.
The researchers say the site where the big cat skulls were found may also help reveal the medieval zoo's whereabouts within the Tower.
Though few physical traces of the menagerie remain, experts have previously pointed to written records of a semi-circular structure built by King Edward I in 1277 in an area that later became known as the Lion Tower.
"By the 16th century the menagerie was definitely in the Lion Tower, but nobody was really sure where it was before then," O'Regan said.
The lion skulls came from a part of the moat close to the Lion Tower. Researchers say it's possible the animals were dumped in the moat after they died.
"It would have been pretty damned smelly, and the carcasses would have floated around for a while as well before they sank," O'Regan said.
The captive lions had little room to roam. Excavations in 1999 revealed that one lion cage measured just 6.5 feet by 10 feet (2 meters by 3 meters). "A lion can be two and half meters [about eight feet] long," O'Regan noted.
The team estimates the two lions were three to four years old when they died.
Researchers say a high nitrogen content in their bones suggests the cats had a meat-rich diet. A record from the 15th century reveals Tower lions were fed sheep.
Other animals kept in the Tower were given less appropriate nourishment.
In his book The Tower Menagerie, Daniel Hahn recounts the strange case of an elephant given to King James I by his Spanish counterpart in 1623.
"Throughout his short but rather pleasant life this animal was given nothing to drink but wine, a gallon a day," the author wrote.
Meanwhile ostriches were thought to have a huge appetite for iron. One of them died in the Tower after being fed more than 80 nails.
By contrast "the lions were quite good at surviving," O'Regan said.
Even so, the team found one of the lions had an unusual abnormality where its spinal cord connected to its brain.
"This hole in the skull has been partially filled by bone, so there isn't as much room [for the spinal cord] as there should be," O'Regan said, referring to the lion remains.
The unknown condition might have made movement difficult for the animal.
The lion was radiocarbon dated to 1420 to 1480, a period during which the Chronicles of Londona history of the city written in the 15th centuryreports that all the lions at the Tower died.
The same abnormality has been found in a captive lion from the early 20th century.
"There are around 500 years between the Tower lion and the 1950s captive animal. And yet they both still show the same condition, suggesting that this is, or was, a condition that is persistent in captive lions," O'Regan added.
The team also analyzed the skulls of 19 dogs unearthed at the Tower. Dogs were often used to bait lions, tigers, bears, and other big mammals as part of bloody spectacles popular with the king and paying visitors.
The study is described in the current issue of the International Journal of Osteoarchaeology.
Ashbee, the former Tower of London curator, said, "The results of this research are of great significance for the history of the Tower."
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