The Lost City of the Monkey God

by Douglas Preston

What Strong realized right away was that these were not Maya cities: The Maya built with stone, while this region had been extensively settled by a separate, sophisticated culture that built great earthen mounds. This was an entirely new culture. Even as Strong’s work showed definitively that Mosquitia was not part of the Maya realm, however, his discoveries raised more questions than they answered. Who were these people, where had they come from, and why had all record of them vanished until now? How in the world did they manage to live and farm in such a hostile jungle environment? What was their relationship to their powerful Mayan neighbors? The earthworks posed another enigma: Did these mounds hide buried buildings or tombs, or were they constructed for some other reason?

Even as he uncovered many other ancient wonders, Strong continued to hear stories of the greatest ruin of them all, the White City, which he dismissed as a “lovely legend.” While sitting on the banks of the Río Tinto in Mosquitia, an informant told Strong the following story, which he recorded in his journal, under an entry entitled “The Forbidden City.” The lost city, he wrote, lies on the shores of a lake deep in the mountains to the north, its white ramparts surrounded by groves of orange, lemon, and banana trees. But if one partakes of the forbidden fruit, he will be lost in the hills forever. “So goes the tale,” Strong wrote, “but it would be better to do as an informant’s father did, follow the river until it becomes a mere trickle among dark rocks and woods and then have to turn back. The city would still be there that way. Like the ‘Ciudad Blanco’—the ‘forbidden fruit’ will probably long remain a lure to the curious.”

There are two major reasons why Honduras had such a difficult time getting back on its feet after the storm. The first was the land-tenure system it inherited from Spain, in which a small number of extremely wealthy families ended up controlling most of the land. But even more debilitating was the country’s unhealthy relationship with the United States, whose shortsighted policies and business interests had kept the country politically unstable for more than a century. From the time of its independence in 1821 to the present, Honduras has suffered through a tumultuous history that includes close to 300 civil wars, rebellions, coups, and unplanned changes in government.

In 1885, Boston entrepreneur Andrew Preston* and a partner formed the Boston Fruit Company, with the idea of using fast steamships, rather than sail, to get bananas to market before they spoiled. It was a success: Inexpensive, delicious bananas took the country by storm. By the turn of the century Boston Fruit, which was later merged into the United Fruit Company, had carved out forty thousand acres of banana plantations along the northern coastline of Honduras, becoming the largest employer in the country. This was the beginning of a long and destructive relationship between American banana companies and the country of Honduras, earning it the pejorative nickname “Banana Republic.” United Fruit and the other fruit companies that soon followed became infamous for their political and tax machinations, engineered coups, bribery, and exploitation of workers. They strangled the country’s evolution and cultivated a corrupt and extreme form of crony capitalism, in which they subverted the government to their own ends.

And then, in that same discouraging year, Elkins read an article in Archaeology magazine entitled “Lasers in the Jungle.” The article described a powerful technology called lidar, or Light Detection and Ranging, which had just been used to map the Maya city of Caracol, in Belize. The lidar mapping of Caracol was a watershed moment in archaeology. The article electrified him: He realized he might finally have the tool he needed to locate Ciudad Blanca.

Explorers had discovered Caracol in the 1930s and realized it was one of the largest cities in the Maya realm. The article told the story of how, in the 1980s, the husband and wife team of Arlen and Diane Chase had begun the daunting project of mapping Caracol and its environs. For twenty-five years, the Chases and teams of assistants and students tramped through the rainforest, recording and measuring every wall, rock, cave, terrace, road, tomb, and structure they could find. By 2009 they had created some of the most detailed maps ever made of a Maya city. But over the years of work, the Chases felt continually frustrated. The city was enormous, and they always had the uneasy sense there was a great deal they weren’t finding, due to the thickness of the jungle and the struggle and dangers of mapping in such an environment. “We cut paths with machetes,” they wrote, “scramble through thick underbrush, and wonder what we might be missing.” They longed for a better way to map the city without, they said, “spending another twenty-five years in the field.” And so they turned to a new tool: lidar. Although lidar had been used for mapping the moon’s surface and doing large-scale terrestrial charting, only in the previous decade had it gained the resolution necessary to resolve fine-scale archaeological features. It had been used to map the ruins of Copán after the hurricane, but that was about the extent of its use in Central America. The Chases joined forces with NASA and the Na...

NCALM owned a small Cessna Skymaster that had had its guts ripped out to carry a big green box containing the million-dollar lidar machine. A pilot trained in lidar missions flew the aircraft from Houston to Belize, where he was joined by three mapping engineers. The team flew five missions over Caracol and its environs, scanning the rainforest with lasers, a process that took a little over a week. When the images came back, the Chases were floored. “Seemingly without effort,” they wrote, “the system produced a detailed view of nearly eighty square miles—only 13 percent of which had previously been mapped—revealing topography, ancient structures, causeways, and agricultural terraces,” as well as caves, terracing, buildings, tombs—tens of thousands of archaeological features that their ground-mapping had missed. In five days, lidar had accomplished seven times more ...

Jared Diamond, in his book Collapse, argues that the destruction of Copán was caused by environmental degradation combined with royal neglect and incompetence. Beginning around AD 650, the rulers of Copán engaged in a building spree, erecting gorgeous temples and monuments that glorified themselves and their deeds. As is typical of Maya inscriptions, not a single one at Copán mentions a commoner. Working folk had to build all those buildings. Farmers had to feed all those laborers along with the holy lords and nobles. This type of class division usually works when everyone believes they are part of a system, with each person occupying a valued place in society and contributing to the vital ceremonies that maintain the cosmic order. In Maya culture, the holy lords had a responsibility to keep the cosmos in order and appease the gods through ceremonies and rituals. The commoners were willing to support this privileged class as long as they kept up their end of the bargain with effective rituals. But after 650, deforestation, erosion, and soil exhaustion began reducing crop yields. The working classes, the farmers and monument builders, may have suffered increasing hunger and disease, even as the rulers hogged an ever-larger share of resources. The society was heading for a crisis.

Diamond writes: “We have to wonder why the kings and nobles failed to recognize and solve these seemingly obvious problems undermining their society. Their attention was evidently focused on their short-term concerns of enriching themselves, waging wars, erecting monuments, competing with each other, and extracting enough food from the peasants to support all those activities.” (If this sounds familiar, I would note that archaeology is thick with cautionary tales that speak directly to the twenty-first century.) Other archaeologists say this conclusion is too simple, and that the holy lords did indeed see things were going awry. They tried to solve these problems with solutions that had worked in centuries past: increased building projects (a jobs program) and more raiding (resource acquisition), both of which involved moving workers from outlying farms into the city. But this time the old solutions failed. The ill-advised building projects speeded up the deforestation that was already reducing rainfall, and it accelerated soil loss, erosion, and the silting of precious farmland and rivers.

A series of droughts between AD 760 and 800 seem to have been the trigger for famine that hit the common people disproportionately hard. It was the last straw for a society teetering on the edge of alienation and conflict. Here was proof the holy lords were not delivering on their social promises. All building projects halted; the last inscription found in the city dates to 822; and around 850, the royal palace burned. The city never recovered. Some people died of disease and starvation, but the majority of the peasant and artisan classes appear to have simply walked away. Over the centuries the region experienced a relentless population decline, and b...

From AD 400 to 800, during the rise of Copán, small settlements in Mosquitia sprang up and grew at a modest rate. But when Copán fell apart, the civilization in Mosquitia experienced the opposite: a tremendous flowering. By AD 1000, even as most of the Maya cities had been left to the monkeys and birds, the ancient inhabitants of Mosquitia were building their own cities, which were starting to look vaguely Maya in layout, with plazas, elevated platforms, earthworks, geometric mounds, and earthen pyramids. This is also when they seem to have adopted the Mesoamerican ball game. How were these ancient people of the Mosquitia rainforest able to settle and thrive in a snake- and disease-ridden jungle, an area far more challenging than most lands settled by the Maya? What was their relationship to their powerful neighbors, and what allowed them to flourish even as Copán was crumbling? In other words, how did they survive what the Maya couldn’t—and what eventually brought them down? While the Maya are the most studied of ancient cultures in the Americas, the people of Mosquitia have been among the least—a question mark embodied by the legend of the White City. This culture is so little...

Most intriguingly, around the time of the fall of Copán, the people of Mosquitia began to adopt aspects of Maya culture. The simplest and most convincing theory about how Maya influence flowed into Mosquitia has it that when Copán was struck with famine and unrest, some of the original Chibcha people of Copán simply packed up and left, seeking refuge in Mosquitia where they had linguistic ties and possibly even relatives. We know that most of the population of Copán walked away; Mosquitia was probably one destination. Some archaeologists take this further: They think that during the chaos of the Maya collapse, a group of warriors marched over from Copán and seized control of Mosquitia. As proof they cite the fact that, when the early Spanish arrived in Honduras, they found tribes of Nahua/Aztec-speaking Indians in Honduras southwest of Mosquitia who may have been a remnant of one such invasive group. (Others think those tribes were descended from Aztec traders, not invaders.)

One of the most intriguing theories about why Mosquitia began to look Maya involves what archaeologists call the “esoteric knowledge” model. In many societies, the elites rule over the common people and get them to do what they want by displaying their sanctity and holiness. This ruling class of priests and lords awe the populace with arcane rituals and ceremonies using secret knowledge. The priests claim, and of course themselves believe, that they are performing rites that are essential to appease the gods and gain divine favor for everyone’s benefit—to avert disaster, sickness, and defeat in battle, while encouraging fertility, rainfall, and bountiful crops. In Mesoamerica and probably also in Mosquitia, these rituals were dramatic and involved human sacrifice. Those noble lords with access to the “ultimate truths” leveraged that knowledge to control the masses, avoid physical labor, and amass wealth for themselves.* Part of the allure and prestige of esoteric knowledge, the theory goes, is its association with distant and exotic lands—in this case, the lands of the Maya. The “Mayanization” of Mosquitia, therefore, may not have required an invasion; it might instead have been a method for local elites to gain and hold supremacy over the common folk.

While the valley is spectacularly isolated now, in its heyday it was a center of trade and commerce. “When you’re here today,” Chris said, “you feel so disconnected. It’s a wilderness, and it’s hard to imagine you’re even in the twenty-first century. But in the past, it wasn’t isolated at all. It was in the midst of an intense network of human interaction.” Situated in a fortress-like valley, the city of T1 would have been a highly defensible place of retreat, something akin to a medieval castle that was normally a bustling center of trade but, if threatened, could raise its drawbridge, arm the battlements, and defend itself from attack. Because of this, T1 might have been part of a strategic zone of control in pre-Columbian times, possibly an anchor that defended the interior from invaders coming inland from the coast. It may also have been a bulwark against attacks from the Maya realm. And then, around 1500, this culture collapsed. But unlike the Maya, who experienced a multitiered collapse, with various city-states declining at different times, the Mosquitia civilization vanished everywhere all at once—in a sudden, civilization-wide catastrophe. “We have only a glimpse of this great culture,” said Oscar Neil, “before it vanished in the forest.”

The myths of the White City, the City of the Monkey God, a Casa Blanca or Kaha Kamasa, have a similar arc: There was once a great city in the mountains struck down by a series of catastrophes, after which the people decided the gods were angry and left, leaving behind their possessions. Thereafter it was shunned as a cursed place, forbidden, visiting death on those who dared enter. A legend, certainly, but legends are frequently based on the truth, and this one, so persistent and long-lasting, is no exception. To dig the truth out of the myth, we have to go back in time, to the discovery of the New World by Europeans. In October of 1493, Columbus set sail on his second voyage to the New World. This expedition was very different from the first. That one, with three ships, had been a voyage of exploration: This one was primarily aimed at subjugation, colonization, and conversion. Columbus’s enormous flotilla on that second voyage consisted of seventeen ships carrying fifteen hundred men and thousands of head of livestock, including horses, cattle, dogs, cats, chickens, and pigs. But on board those ships was something far more threatening than soldiers with steel arms and armor, priests with crosses, and animals that would disrupt the New World ecology. Columbus and his men unwittingly carried microscopic pathogens, to which the people of the New World had never been exposed and against which they had no genetic resistance. The New World was like a vast, tinder-dry forest wai...

Epidemiologists generally agree that smallpox is the cruelest disease ever to afflict the human race. In the century before it was eradicated in the 1970s, it killed more than half a billion people and left millions of others horribly scarred and blind. It inflicts unbearable suffering, both physical and psychological. It usually starts like the flu, with headache, fever, and body aches; and then it breaks out as a sore throat that soon spreads into a body rash. As the disease develops over the subsequent week, the victim often experiences frightful hallucinatory dreams and is racked by a mysterious sensation of existential horror. The rash turns into spots that swell into papules, and then fluid-filled pustules that cover the entire body, including the soles of the feet. These pustules sometimes merge, and the outer layer of skin becomes detached from the body. In the most deadly variety of smallpox, the hemorrhagic form, called the bloody pox or black pox, the skin turns a deep purple or takes on a charred look, and comes off in sheets. The victim often “bleeds out,” blood pouring from every orifice in the body. It is extremely contagious. Unlike most other viruses, smallpox can survive and remain virulent for months or years outside the body in clothing, blankets, and sickrooms.

The Indians were in abject terror of it. It was like nothing they had ever experienced before. The history of the Conquest contains many Spanish eyewitness accounts attesting to the horrors of the pandemic. “It was a dreadful illness,” wrote one friar, “and many people died of it. No one could walk; they could only lie stretched out on their beds. No one could move, not even able to turn their heads. One could not lie face down, or lie on the back, nor turn from one side to another. When they did move, they screamed in pain… Many died from it, but many died only of hunger. There were deaths from starvation, for they had no one left to care for them.” These epidemics of disease weakened Indian military resistance, and in many instances it aided the Spanish in their conquest. But overall, the Spanish (and Columbus personally) were deeply dismayed by the vast die-offs; the deaths of so many Indians interfered with their slaving businesses, killed their servants, and emptied their plantations and mines of forced labor. When smallpox arrived, the Indians often responded with panic and flight, abandoning towns and cities, leaving behind the sick and dead. And while the Spanish were less susceptible to these epidemics, they were not immune, and many also died in the general conflagration. Epidemics cleared out huge swaths of the New World even before Europeans got there. There are numerous accounts of European explorers arriving in a village for the first time, only to find every...

Historians once marveled at how Cortés, with his army of five hundred soldiers, defeated the Aztec empire of over a million people. Various ideas have been advanced: that the Spanish had crucial technological advantages in horses, swords, crossbows, cannon, and armor; that the Spanish had superior tactics honed by centuries of fighting the Moors; that the Indians held back, fearful the Spanish were gods; and that the Aztecs’ subjugation and misrule of surrounding chiefdoms had created conditions ripe for revolt. All this is true. But the real conquistador was smallpox. Cortés and his troops occupied the Aztec capital city of Tenochtitlan (the future Mexico City) in 1519, but this cannot be counted as a conquest: The uneasy Aztec emperor, Moctezuma, invited Cortés into the city, unsure if he were god or man. Eight months later, after Moctezuma was murdered under murky circumstances (perhaps by the Spanish, perhaps by his own people), the Indians rose up and handily drove the Spanish from the city, in the so-called Noche Triste, the “Night of Sorrows.” In this crushing rout, many Spanish soldiers either were killed or drowned as they fled the island on which the city was built, be...

At the same time that smallpox was ravaging Mexico, it burned southward into the Maya realm before the Spanish arrived. While the Maya cities were no longer inhabited, the Maya people were spread out over the region and were still known for their fierceness and military prowess. The contagion paved the way for the conquest of Guatemala four years later by one of Cortés’s captains. In the ten years following the first outbreak of smallpox in the New World, the disease had stretched deep into South America. The pandemics also felled several of the great pre-Columbian kingdoms in North America. From 1539 to 1541, explorer Hernando de Soto passed through a powerful and flourishing chiefdom called Coosa, which occupied territory encompassing parts of Tennessee, Georgia, and Alabama, and had a population of perhaps 50,000 people. But twenty years later, by the time the next European came through, Coosa had been almost entirely abandoned, the landscape littered with empty houses, the once-abundant gardens overgrown with thistles and weeds. In the Mississippi R...

The fall of Tenochtitlan, the general collapse of native populations everywhere, and the continuing waves of pandemics allowed the Spanish to quickly crush Indian resistance throughout most of Central America. Compare this to the Spanish conquest of the Philippines, which occurred at the same time. The Spanish were just as ruthless there, but the conquest was not aided by disease: Filipinos were resistant to Old World diseases, and the islands experienced no mass die-offs or population crashes. As a result, the Spanish were forced to accommodate and adjust to coexistence with the indigenous people of the Philippines, who remained strong and retained their languages and cultures. Once the Spanish left, the Iberian influence largely faded away, along with the Spanish language, which is today spoken by few.

As it turned out, one of the answers to the mystery of the White City had been lying before us the whole time: The various myths of Ciudad Blanca, its abandonment and cursed nature, probably originated in this grim history. Viewed in the light of these pandemics, the White City legends are a fairly straightforward description of a city (or several) swept by disease and abandoned by its people—a place that, furthermore, may have remained a hot zone for some time afterward. We have few accounts giving the native point of view of these pandemics. One of the most moving is a rare contemporary eyewitness description, called the Book of Chilam Balam of Chumayel, which recalls the two worlds, before and after contact. It was written by an Indian in the Yucatec Mayan language: There was then no sickness; they had no aching bones; they had then no high fever; they had then no smallpox; no stomach pains; no consumption… At that time people stood erect. But then the teules [foreigners] arrived and everything fell apart. They brought fear, and they came to wither the flowers.

Leishmaniasis has a long and terrible history with human beings, stretching back as far as human records exist and causing suffering and death for thousands of years. A few years ago, a hundred-million-year-old piece of Burmese amber was found to have trapped a sand fly that had sucked the blood of a reptile, most likely a dinosaur. Inside this sand fly, scientists discovered leishmania parasites, and in its proboscis, or sucking tube, they found reptilian blood cells mingled with the same parasites. Even dinosaurs got leishmaniasis. Leishmania has probably been around since the final breakup of the primordial continent known as Pangaea. As these ancient landmasses eventually drifted apart to become the Old and New Worlds, the populations of that sand fly ancestor were separated and continued to evolve independently, eventually giving rise to the two basic strains of the disease in the Old World and the New. At some point the disease made the leap from reptiles to mammals. (Modern reptiles still get leish, and there has been a medical debate over whether reptilian leish can be transmitted to humans; the answer is probably not.) Unlike many diseases that afflict human beings, leish was global from the very outset, and it was dreaded by our ancient ancestors in both hemispheres. Archaeologists have found leish parasites in Egyptian mummies dating back five thousand years, and in Peruvian mummies going back three thousand years. A description of leish appears in one of the ea...

Leishmaniasis comes in three main varieties, each with distinct symptoms. The most common form is cutaneous (i.e., skin) leishmaniasis, which is found in many parts of the Old World, especially Africa, India, and the Middle East. It is also widespread in Mexico and Central and South America, and it recently popped up in Texas and Oklahoma. Some US troops returning from Iraq and Afghanistan contracted cutaneous leish during their deployments and nicknamed it the Baghdad boil. This kind of leish starts as a sore at the location of the bite, which grows into a weeping lesion. If left alone, it usually goes away, leaving only an ugly scar. It can usually be treated by burning, freezing, or surgically removing the ulcer. In visceral leishmaniasis, the second type—also from the Old World—the parasite invades the body’s internal organs, particularly the liver, spleen, and bone marrow. It is sometimes known as black fever, because it often turns its victim’s skin black. This variety is deadly; without treatment it is always fatal. But treatment of visceral leish is quick and reliable, requiring a single infusion of an antibiotic drug that yields a cure rate of about 95 percent. Most of the deaths in the world from leish are caused by the visceral form, among poor children who don’t have access to treatment. The final form of leish is the mucocutaneous or mucosal variety, the major New World form of the disease. It starts as a skin sore like the cutaneous kind. Months or years late...

Acute fear of the disease may have even driven human settlement patterns in South America. The archaeologist James Kus, a retired professor at California State University, Fresno, believes that the Inca site of Machu Picchu may have been chosen, in part, because of the prevalence of mucosal leish. “The Incas were paranoid about leishmaniasis,” he told me. The sand fly that transmits leish can’t live at higher altitudes, but it is widespread in the lowland areas where the Inca grew coca, a sacred crop. Machu Picchu lies at just the right altitude: too high for leish, but not too high for coca; at Machu Picchu the king and ...

When the Spanish conquistadors arrived in South America in the sixteenth century, they were horrified at the facial deformities they saw among native people in the lowlands of the Andes, especially among the coca growers. The Spanish thought they were looking at a form of leprosy and called the disease lepra blanca, “white leprosy.” Over the years, mucosal leish has acquired many nicknames in Latin America: tapir nose, hoarse voice, spongy wound, big canker. Mucosal leish didn’t exist in the Old World. But the even deadlier visceral form, the kind that invades the internal organs, had long plagued the Indian subcontinent. It first gained the attention of Western medicine as the British extended their empire into India. Eighteenth-century writers described it as “kala-azar” or “black fever.” Visceral leish easily spreads from person to person via the bite of sand flies, using human beings as its primary reservoir...

The British also noted the cutaneous form of the disease in India and the Near East and gave it various names: Aleppo evil, Jericho button, Delhi boil, Oriental sore. But doctors did not recognize a connection between the two strains until 1901. William Boog Leishman, a doctor from Glasgow who was a general in the British Army, was posted in the town of Dum Dum, near Calcutta, where one of his soldiers fell ill with a fever and a swollen spleen. After the man died, Leishman looked at thin sections of the man’s spleen under the microscope and, using a new staining method, discovered tiny round bodies in the cells—the leishmania parasite. Leishman called it Dum Dum fever. A few weeks after Leisham published his discovery, another British doctor, named Charles Donovan, also stationed in India, independently reported the results of his own research. He, too, had spied the offending parasite, and between the two of them the disease “leishmaniasis” was identified. Leishman got the dubious honor of having the disease named after him, while Donovan was gifted with the species’ name: Leishmania donovani. Doctors figured out in 1911 that it was transmitted by the sand fly, and later they ...

When the news of our mini-epidemic began to spread among members of the expedition, accompanied by gruesome photos of weeping ulcers, it was hard not to think about the centuries-old legend and its oft-cited “curse of the monkey god.” All those flowers we chopped down! Gallows humor aside, though, many of us were privately aghast at having walked so blithely into that hot zone, and then having congratulated ourselves, prematurely, for emerging from the jungle unscathed. The jokes petered out quickly in the face of this dramatic disease, which had the potential to alter the course of each of our lives. This was deadly serious.

When our team members were diagnosed, biopsies were taken from our lesions and sent to another lab at NIH, called the Molecular Parasitology Section, where the lab’s director, Michael Grigg, had originally identified the parasite as L. braziliensis by sequencing part of its genome. I called up Grigg to find out if he had found out anything unusual. “The type of leish you have was very hard to grow,” he recalled. In fact, like some difficult strains, it wouldn’t grow at all. He smeared tissue samples from our biopsies on blood agar plates, but the parasites refused to multiply. Because of that, his lab wasn’t able to tease enough parasites clear of human tissue to sequence the entire genome at the time—there was too much human DNA mucking up the works. Instead, he explained, they initially sequenced one gene or marker: a characteristic one that reveals the species. That marker matched braziliensis. But later, Grigg sequenced five markers—which he described as “five little windows into the parasite.” He got a big surprise. In two “windows” he found genetic sequences different from any known species of leish. In another window, he found that the DNA resembled another species called L. panamensis, an equally bad mucosal strain. But that gene also had a couple of mutations. Our parasite, he said, might have been a hybrid between panamensis and braziliensis, in which the two species mingled in a sand fly gut, mated, and produced hybrid offspring. That hybrid was then isolated an...

When humans first walked into the Americas over the Bering Land Bridge fifteen to twenty thousand years ago,* our species existed everywhere as small, wandering bands of hunter-gatherers. There were no cities, no towns, no farming or animal husbandry. We were spread out and moving all the time, only rarely encountering other groups. The low population densities prevented most potential diseases from gaining a foothold. People suffered from parasites and infections, but they did not get most of the diseases so familiar in recent human history—measles, chicken pox, colds, the flu, smallpox, tuberculosis, yellow fever, and bubonic plague, to name only a few. In the last ten thousand years, as human population densities increased, disease moved into center stage of human affairs. Pandemics changed the very arc of human history. Despite our dazzling technology, we are still very much at the mercy of pathogens, old and new. In his groundbreaking book Guns, Germs, and Steel, biologist Jared Diamond poses the question: Why did Old World diseases devastate the New World and not the other way around? Why did disease move in only one direction?* The answer lies in how the lives of Old World and New World people diverged after that cross-continental migration more than fifteen thousand years ago.

Humans do not usually catch infectious diseases from animals; pathogens tend to confine their nasty work to a single species or genus. (Leishmaniasis is a striking exception.) But microbes mutate all the time. Once in a while, an animal pathogen will change in such a way that it suddenly infects a person. When people in the Near East first domesticated cattle from a type of wild ox called an aurochs, a mutation in the cowpox virus allowed it to jump into humans—and smallpox was born. Rinderpest in cattle migrated to people and became measles. Tuberculosis probably originated in cattle, influenza in birds and pigs, whooping cough in pigs or dogs, and malaria in chickens and ducks. The same process goes on today: Ebola probably jumped to humans from bats, while HIV crashed into our species from monkeys and chimpanzees.

Alongside the domestication of animals, humans in the Old World began settling down in villages, towns, and cities. People lived together in much denser numbers than before. Cities, with their bustle, trade, filth, and close quarters, created a marvelous home for pathogens and an ideal staging ground for epidemics. So when diseases migrated from livestock to people, epidemics broke out. Those diseases found plenty of human fuel, racing from town to town and country to country and even crossing the oceans on board ships. Biologists call these “crowd diseases” because that’s exactly what they need to propagate and evolve. Epidemics periodically swept through European settlements, killing the susceptible and sparing the robust, culling the gene pool. As always, children were the majority of the victims. Almost no disease is 100 percent fatal: Some victims always survive. The survivors tended to have genes that helped them resist the disease a little better, and they passed that resistance on to their children. Over thousands of years and countless deaths, people in the Old World gradually built up a genetic resistance to many brutal epidemic diseases.

The genes that resist disease can only spread in a population through the pitiless lottery of natural selection. People with weaker immune systems (children especially) must die, while the stronger live, in order for a population to gain widespread resistance. A staggering amount of suffering and death over thousands of years went into building European (and African and Asian) resistance to crowd diseases. One biologist told me that what probably saved many indigenous Indian cultures from complete extinction were the mass rapes of native women by European men; many of the babies from those rapes inherited European genetic resistance to disease. (The scientist, after telling me this horrifying theory, said, “For God’s sake don’t attach my name to that idea.”)

In the New World, these many thousands of years of anguish and death were compressed into a window from 1494 to around 1650. The mass murder by pathogen happened in that one cruel century and a half, and it struck at precisely the worst moment, when the population of the New World had recently coalesced into big cities and reached the levels of density necessary for those epidemics to spread furiously. It was a perfect storm of infection.

What would a 90 percent mortality rate mean to the survivors and their society? The Black Death in Europe at its worst carried off 30 to 60 percent of the population. That was devastating enough. But the mortality rate wasn’t high enough to destroy European civilization. A 90 percent mortality rate is high enough: It does not just kill people; it annihilates societies; it destroys languages, religions, histories, and cultures. It chokes off the transmission of knowledge from one generation to the next. The survivors are deprived of that vital human connection to their past; they are robbed of their stories, their music and dance, their spiritual practices and beliefs—they are stripped of their very identity.

The overall mortality rate in this wave of epidemics was indeed about 90 percent. To put that statistic into personal terms, make a list of the nineteen people closest to you: All but one will die. (This of course counts you also as a survivor.) Think what it would be like for you, as it was for the author of the Cakchiquel manuscript, to watch all these people die—your children, parents, grandparents, brothers and sisters, your friends, your community leaders and spiritual authorities. What would it do to you to see them perish in the most agonizing, humiliating, and terrifying ways possible? Imagine the breakdown of every pillar of your society; imagine the wasteland left behind, the towns and cities abandoned, the fields overgrown, the houses and streets strewn with the unburied dead; imagine the wealth rendered worthless, the stench, the flies, the scavenging animals, the loneliness and silence. Enlarge this scenario beyond towns and cities; enlarge it beyond kingdoms and civilizations; enlarge it beyond even continents—until it embraces half the planet. This inferno of contagion destroyed thousands of societies and millions of people, from Alaska to Tierra del Fuego, from California to New England, from the Amazon rainforest to the tundra of Hudson Bay. It is what destroyed T1, the City of the Jaguar, and the ancient people of Mosquitia. This is the sort of thing that writers of postapocalyptic fiction put themselves to imagining, the stuff of our greatest news-cycle ...

It is tempting to argue that if Europeans hadn’t arrived in the New World, these deadly pandemics would not have happened. But the meeting of the Old World and the New was inevitable. If Europeans hadn’t carried disease to the New World, Asians or Africans would have; or New World mariners would have eventually reached the Old. No matter what, disaster would have ensued. This was a monstrous geographic accident waiting to happen. This was a time bomb that had been ticking for fifteen thousand years—counting down to that fateful moment when a ship with sick passengers finally set sail across the wide ocean. This is in no way an apologia for genocide. Still, the catastrophe was largely a natural event, a mindless biological imperative, a vast migration of dumb pathogens from one side of the planet to the other.

It seems that leishmaniasis, a disease that has troubled the human race since time immemorial, has in the twenty-first century come into its own. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases at the NIH, told our team bluntly that, by going into the jungle and getting leishmaniasis, “You got a really cold jolt of what it’s like for the bottom billion people on earth.” We were, he said, confronted in a very dramatic way with what many people have to live with their entire lives. If there’s a silver lining to our ordeal, he told us, “it’s that you’ll now be telling your story, calling attention to what is a very prevalent, very serious disease.”

Global warming has opened the southern door of the United States not just to leish but to many other diseases. The big ones now entering our country include Zika, West Nile virus, chikungunya, and dengue fever. Even diseases like cholera, Ebola, Lyme, babesiosis, and bubonic plague will potentially infect more people as global warming accelerates.

The world’s last great pandemic was the Spanish flu outbreak in 1918 that killed a hundred million people—about 5 percent of the world’s population. If a pandemic like that were to happen again, it would spread faster and might be impossible to contain. According to the Bill & Melinda Gates Foundation, in such a pandemic “the death toll could reach 360 million”—even with the full deployment of vaccines and powerful modern drugs. The Gates Foundation estimated that the pandemic would also devastate the world financially, precipitating a three-trillion-dollar economic collapse. This is not scaremongering: Most epidemiologists believe such a pandemic will eventually happen.

Archaeology contains many cautionary tales for us to ponder in the twenty-first century, not just about disease but also about human success and failure. It teaches us lessons in environmental degradation, income inequality, war, violence, class division, exploitation, social upheaval, and religious fanaticism. But archaeology also teaches us how cultures have thrived and endured, overcoming the challenges of the environment and the darker side of human nature. It shows us how people adapted, lived their lives, and found fulfillment and meaning under fantastically diverse conditions. It tracks both the failures and the successes. It tells us how cultures faced difficulty and challenge, sometimes in successful ways and sometimes in ways that, while successful at first, sowed the seeds of eventual collapse. The Maya created a vibrant and brilliant society that, in the end, failed to adjust to a changing environment and the needs of its people; so did the Roman Empire and the ancient Khmer, to pluck civilizations randomly out of the hat. But the people of the City of the Jaguar did adapt to the challenges of the rainforest, and they continued to thrive in one of the harshest environments on the planet, transforming it into a beautiful garden—until their abrupt demise.

I can recall the very moment when we stumbled over the cache and I first saw that jaguar head coming out of the ground. Gleaming with rain, it rose up snarling, as if struggling to escape the earth. It was an image that spoke directly to me across the centuries—forging an immediate, emotive connection to these vanished people. What had been theoretical for me became real: This spirited image had been created by people who were confident, accomplished, and formidable. Standing in the gloom among the ancient mounds, I could almost feel the presence of the invisible dead. At its zenith, the people of the city of T1, the City of the Jaguar, must have felt nearly invulnerable in their valley redoubt ringed by mountains. What power could overthrow their mighty gods and potent rituals? But the unseen invader ghosted in and visited upon them a destruction that was a...

No civilization has survived forever. All move toward dissolution, one after the other, like waves of the sea falling upon the shore. None, including...