Ufuk Kocabaş spent his summers swimming, snorkeling and eventually diving around nearby Marmara Island, where his grandfather and other forebears plied the sea as sailors. At age 14, he stumbled upon his first shipwreck, littered with pieces of amphora — an ancient type of storage and transport container — and got an early lesson in proper archaeological practice. “I took some amphora fragments [from the ship] to my sister who was studying at university,” recalls Kocabaş, now head of the Istanbul University Conservation Department. “She told me I shouldn’t have taken them from the site, that I should have left them where they were. At the time, I thought this was stupid. It’s my amphora!”

After chiding him, Kocabaş’s sister helped him identify the type of amphora he found. It dated to the seventh century, and they passed the information they’d ascertained about the shipwreck to a museum. “It was an amazing experience,” Kocabaş says. “I started to read about shipwrecks then, and haven’t stopped since.”

There would be plenty more amphorae and sunken vessels in Kocabaş’s future. In 2005, shortly after receiving his doctorate in ancient history, he was tapped to help lead an urban archaeological excavation in his home city. The dig has revealed perhaps the world’s largest collection of Byzantine shipwrecks, along with rare burial structures, the bones of dozens of animal species and thousands of prehistoric human footprints. All told, 35,000 artifacts dating as far back as the Neolithic period — from ceramics to coins, combs to cooking utensils — have been uncovered, providing new insights into daily life, trading routes and the age of the city itself.

The thought of such riches being found underfoot is hard to imagine while crossing the broad expanse of concrete that now leads to the Yenikapı subway station in central Istanbul. About a third of a mile from the sea today, the unshaded spot is scorching in summer and surrounded by construction cranes and boxy low-rise apartment blocks cheaply built in the 1980s. But from the fourth to the 11th century, it was a flourishing commercial and military harbor, the largest of the early Byzantine period. Trading ships from as far away as Crimea, North Africa and the Balkans pulled into port carrying wine, ivory, leather, ceramics, grain, construction materials, even exotic animals, from one distant end of the empire to another. “The existence of the Port of Theodosius was known from written sources — from the writings of historians and voyagers — but we had no idea about its exact location or dimensions,” Kocabaş explains while sitting in his lab, a nondescript warehouse near the Yenikapı dig site.

The port’s whereabouts remained a mystery until work began in 2004 on a metro extension, including the new Yenikapı station, meant to ease congestion in a rapidly growing city infamous for its traffic jams. Instead of driving across one of two often-clogged bridges from the heavily residential Asian side of the city to the commercial centers of the European side, Istanbul commuters would be able to take the Marmaray rail tunnel under the waters of the Bosporus Strait. In a nod to the long history of the area around Yenikapı, a team from the Istanbul Archaeological Museums was brought in to conduct what was expected to be a short “salvage excavation” — a standard quick survey of a site about to be developed — before the station construction began. As with most other such projects, the transit tunnels themselves run too deep below ground to disrupt any archaeological remnants, which are usually found when tunneling to build station entrances and other ground-level access points. The Yenikapı station sits 65 feet below the surface, while the oldest remains at the site, dating from the Neolithic period, were found more than 20 feet below the current sea level. The shipwrecks were unearthed at depths between 2 and 17 feet.

“A former classmate of mine who was working at the museum called me after they began finding the first pieces of a wreck,” says Kocabaş, describing his initial visit to the site in 2005. “There was a piece of the wooden hull, some amphorae, pieces of an iron anchor, even lengths of rope.”

The team had found the long-lost port of Theodosius.

“They were thinking they would just find one or two shipwrecks, but I told them they would find more than 25 because the city and harbor were so important,” says Kocabaş. In the end, 37 wrecks were uncovered, including the first Byzantine galleys — slim, long warships — ever excavated, cargo-laden trading vessels and small sailing boats for local travel. All were remarkably well preserved below layers of silt deposited by a river that once ran through the area.

The site’s importance was undeniable, but the clock was ticking on the massive multibillion-dollar Marmaray-Metro infrastructure project. Kocabaş and the other archaeologists had to assemble large teams to work long hours on the 625,000-square-foot site — an area larger than 10 football fields. The conditions were often difficult. Water had to be pumped out of the dig site for three hours early each morning before the teams could get to work, and an atomized spray system misted the wooden artifacts with water 24 hours a day so they wouldn’t dry out and crack apart, suffering irreversible damage. “Normally, you spend two months in the summer on a dig, then go back to your university and work on your objects and drawings. We were working in the mud year round, from 8 a.m. up to midnight sometimes, with the engineers waiting and sometimes getting angry,” Kocabaş says. “We froze in the winter and sweltered in the summer. Three times, the city’s sewer system overflowed into the dig trench after a big rain, and we had to pump it clear again. You never want to see that.”

Describing the urban dig site as very “dynamic,” Kocabaş says his early educational background in mechanical engineering, his father’s profession, came in handy for devising new apparatuses to lift out parts of the ancient ships as they were uncovered. “We couldn’t use mechanical tools in the excavation area because there were so many artifacts. Everything had to be moved by hand, but the wood was so soft, you couldn’t even touch it,” he says, showing photos of the L-shaped brackets and Styrofoam supports he designed so the workers could move the waterlogged vessels without damaging them. On the high-tech side, the team employed a total station device — a tripod-mounted cameralike instrument used by surveyors and engineers to measure distance and angles. It captured up to 30,000 digital reference points on each in situ shipwreck to be assembled later into large-scale 3-D images.

Excavations were completed before the subway station’s grand opening in fall 2013, but work to document and analyze the finds continues under Kocabaş’s supervision at the Yenikapı Shipwrecks Project lab. Wooden timbers from the sunken ships are kept submerged in narrow rectangular tanks measuring some 10 to 30 feet long and housed inside the warehouse as well as in an adjacent lot. The timbers stay there, protected by the water until a lab tech is able to clean, photograph and digitally measure them, noting the size, shape and placement of every nail, tool mark or glob of pitch. Pieces ready for storage are impregnated with polyethylene glycol or melamine resin to prevent cracking. Smaller pieces are then dried in an oven while larger ones go into a 2.5-meter-long freeze-dryer/condenser that resembles an MRI machine and is housed in its own trailer on the lab grounds.

“A vacuum moves all the water from the wood to the condenser section, where it quickly turns to vapor to keep the wood from cracking under the high tension,” Kocabaş explains, proudly noting that the $80,000 device is the first of its kind used in Turkey. Similar equipment was used to preserve the largest Viking warship ever found after it was excavated from the banks of Denmark’s Roskilde fjord. “Texas A&M University is the birthplace of nautical archaeology, but even they didn’t have one like this when we got ours!” 

The archaeologist smiled just as broadly, if perhaps a bit more mischievously, when pointing out his two secret weapons to keep the timbers still in the tanks from being damaged by bacteria, fungi or insect larvae. “That’s Guardian, and that’s Death Angel,” he says, gesturing to two tiny fish swimming around one of the vats. “I took my son’s goldfish when he was away at our summer house and told him they had to be put to work. They clean everything.”

More than 10 years after the Yenikapı dig began, much remains to be done before the full significance of the finds is understood. “Each vessel will be a doctoral thesis in itself,” Kocabaş says, adding, “I am very happy with the excavation result, but will only get a good night’s sleep when we’ve exhibited the ships.” City officials recently selected designs for a museum, or “arkeopark,” to house the remains, but no timetable for such a project has yet been announced.

Mindful of both the historical significance of the dig and its impact on a high-profile urban transit project, Kocabaş has taken pains throughout the excavation to make it unusually accessible to the public, giving hundreds of lectures and welcoming visitors to the dig site and lab. Despite the added responsibilities and challenges, he recognizes that working on a transportation-linked excavation also provides opportunities archaeologists might not otherwise enjoy.

“We know there are Byzantine palaces all around [this part of Istanbul], but it’s not easy to excavate a historic, heavily populated area like this,” he says. “If it hadn’t been for the construction of these subway tunnels, we would have kept walking on top of the shipwrecks without any knowledge of them.”

A much older settlement

Archaeologists digging below Istanbul’s Yenikapı neighborhood uncovered more than a rich hoard of Byzantine shipwrecks. They also turned up evidence that the great city’s history is even older than previously thought — by nearly 6,000 years.

“Before the excavation, we believed that Byzantium [the precursor to Istanbul] had been established in the seventh century B.C. by Greek colonists,” says archaeologist Ufuk Kocabas. “But then under the [Byzantine] harbor, we found Neolithic remains, which was very surprising. Now we understand that this city’s history goes back to the Neolithic Age.”

Human remains found in the earlier layers are still undergoing analysis. But funerary urns, wooden burial structures and the remains of buildings found below the Port of Theodosius date back around 8,500 years, according to the Istanbul Archaeological Museums, which supervised the Yenikapı excavations. The most heralded finds at the site provide insight into Byzantine shipbuilding techniques and trade routes. But thousands of other discoveries are revealing new details about animal populations of the time and their use by humans, as well as the Neolithic-era movement of people through Anatolia and Thrace in Europe, Kocabas says: “There are many phases to this excavation. We’ll be studying [the results] for years.”

Garbage in, garbage out

Excavations in Rio de Janeiro being carried out since 2012 as part of construction of a new subway line are revealing new details about the daily lives of the former Brazilian aristocracy — through their garbage.

The treasure trove of 17th- to 19th-century trash has come to light as part of work on a metro extension that will link parts of Rio de Janeiro’s greater metro area with Barra da Tijuca, the main site of the 2016 Olympic Games.

The royal palace was about 1 kilometer away [from the Subway Line 4 dig site], and our research in the archives showed that the area had been a place for discarded trash, so we suspected that we had a big discovery to make,” says Cláudio Prado de Mello, director-president of the Institute of Historical and Archaeological Research of Rio de Janeiro. He has been leading the excavations in the Leopoldina neighborhood.

“But when we began to remove the initial layers of the soil, we started to find thousands and thousands of objects from the imperial and colonial period,” he says.

The 200,000-plus artifacts uncovered at the Leopoldina site so far include stoneware and glass bottles, some still filled with liquid; household ceramics; pipes; coins; remains of a leather shoe; and 15 bone and ivory toothbrushes, one inscribed in French with the words “His Majesty, the Emperor of Brazil.” It is believed to have belonged to Dom Pedro II — the country’s last monarch, ousted in a coup in 1889 — or another member of the royal family.

“Usually what is documented by writers about a state administration are the historical moments, not the daily life of the aristocracy,” Prado de Mello says. “Now we have the opportunity to find a part of the past that is normally forgotten.”

Bedlam beneath the streets

Crossrail, the $22.5 billion railway expansion that spans more than 60 miles, much of it through London’s center, has unearthed finds dating back nearly 70,000 years. But it was in March that archaeologists began excavating the project’s crown jewels — all 3,000 of them, give or take. The thousands of skeletons originally interred from the mid-16th through 18th centuries at the Bedlam burial ground are expected to provide researchers with unparalleled information about a formative time for London that included the English Civil Wars, Restoration, the last major plague outbreak and The Great London Fire of 1666.

“It’s unique in London’s history,” says Jay Carver, the lead project archaeologist for Crossrail. “It covers a period not represented in other finds on this scale.”

The Bedlam site will give researchers a glimpse into the lives of ordinary Londoners as the city transformed into a modern capital. But the team also hopes to uncover one or more of the famous figures believed buried there, including John Lilburne, who ran afoul of the Crown in the mid-17th century because of his progressive ideas about human rights.

“We don’t know if it will be possible to find him because many of the burials were anonymous, and there are about eight bodies per cubic meter — that is extremely dense,” says Carver. He added that his team is conducting the Bedlam excavations and research at an accelerated pace and plans to publish an open-access report by the end of 2016.

Layers beneath the Bedlam burial grounds include a Roman-era road and marshlands. Evidence of earlier wetlands is a common find in Crossrail digs — the Londoners of long ago traversed a much more watery world. Two wooden stakes found during excavations in east London, for example, are thought to have been part of a timber pathway used by hunters across the wetlands that covered the area 3,500 years ago.

Excavations for the new subway lines have also revealed a set of rudimentary ice skates dating back to Saxon or even Roman times: Cow bones were smoothed flat so they could be strapped to the feet to cross the frozen marshes of what is now central London. “People previously had no idea about the depth of history in these places where they’re living,” says Carver. Members of his team spend much of their time consulting historical records, borehole logs and other data to model what might be underfoot so they can dig as quickly and accurately as possible and keep the infrastructure work moving ahead smoothly.

All their advance research led to what Carver describes as a “needle in a haystack” find in 2011 in west London: a buried channel dating back 68,000 years, full of bones of the prehistoric reindeer, bison and other animals that had the run of the place during the Pleistocene period. “Revealing these really ancient landscapes is always extraordinary,” says Carver. “It’s London before London.”

First-century culture

When digging underneath Rome, it would be a surprise not to run across an ancient artifact or two. But excavation teams were still amazed by what they found below the heavily trafficked Piazza Venezia while building the Metro C line subway extension between 2007 and 2011. Archaeologists uncovered a two-story cultural center built during the reign of Emperor Hadrian nearly two millennia ago.

The partially preserved building’s three large halls were decorated with colorfully painted marble and used for cultural events, oratory and poetry contests. “Probably the most impressive single piece uncovered there is a section of seating with a marble balustrade, where people would watch the performances and listen to declamations,” says Darius Arya, a Rome-based archaeologist and executive director of the American Institute for Roman Culture. “The excavations show the structure’s whole life cycle — the damage done by earthquakes, the pillaging, the medieval structures built on top using parts of the original building.”

Another standout find during the digs — the “biggest archaeological investigation ever conducted on Roman soil,” according to the Rome Metro company — has been the discovery, announced in late 2014, of a large working farm close to the city’s ancient center. “You think of first-century Rome as being crowded and urban, but there was food being produced locally,” Arya says. “An abundant supply of peach pits was found at that site, so we know there were peach trees on that farm.” The ongoing archaeology work for Metro C has also revealed the remains — copper slag and ingots, as well as the holes dug for small furnaces — of a sixth-century metallurgical workshop, the largest known in Rome from its time period.

[This article originally appeared in print as "Peeling Back a City's Layers."]