Machu Picchu, Lost Civilizations, and the Resolving Power of DNA Analysis

450px-peru_machu_picchu_sunrise“We are on our way to Machu Picchu”. These were the words to which I awoke on a warm July morning in 1984 as I struggled to make sense of where I was and regain my memory of the previous week. My family and I had come to Peru on a mission to learn more about the Incas, a civilization that I knew little about. We had spent two days in the coast-hugging capital city of Lima, seen much of the colonial architecture and even experienced the full force of a midnight earthquake (which because of sheer exhaustion I had slept right through). We had taken a plane down the coast in the hope of visiting the smaller city of Arequipa, but cloud cover had forced us to fly several hundred miles further south to a town called Tacna and take an overnight taxi ride to Arequipa through the Peruvian desert.

In the coolness of the desert air we arrived in Arequipa and crashed into our beds for what was left of the night. The following day, with little less than a couple of hours to soak in the colonial town, we left on an airplane bound for Cuzco- the ancient Inca capital high up in the Andean cordillera. “Totus Tuus”—it’s all yours—were the words engraved on one mountain side as we departed from Arequipa. Now, only two days after having arrived in Cuzco and having visited the nearby market town of Pizaq and farming terraces of Urubamba, we were bound for the climax of our trip—the Inca ruins of Machu Picchu.

We pulled out of Cuzco train station on an overcast morning and headed out north past the Urubamba river. We made frequent stops along the 50-mile stretch that separated Cuzco from Puente Ruinas- the village nearest to Machu Picchu. The carriages were comfortable albeit rudimentary. While we felt relatively relaxed there were rumors that trains like these had previously been targets for terrorist attacks.Fortunately this time the journey was uneventful. Upon arrival we took a bus up a steep mountain-side. Much of the talk was of the thin air that made breathing difficult for those of us who were not accustomed to the high altitude. Yet once at the top the sight that befell us was doubly breath-taking. With roofless houses and walled ruins crowded together amidst the terraced farmland, we knew that we had reached the pinnacle of our momentous trip.

The tour around the cloud-shrouded city told of a civilization that had once occupied this land but had fallen at the hands of merciless Spanish conquistadores many hundreds of years earlier. Discovered by the American archaeologist Hiram Bingham in 1911, Machu Picchu quickly gained the title of the long-sought-after, lost capital of the Inca empire. According to Daniel Eisenberg, much of what was found around these ruins was taken to a museum at Yale, in keeping with Bingham’s contract with the Peruvian government (1). TIME reporter Jeffrey Kluger described how Hiram Bingham was at once convinced that he had just found the remains of a sacred city: “the birthplace and final stronghold of the Incas, where virgins sought sanctuary and priests worshipped the sun god” (2).

Today archaeologists are making radical claims about the function of Machu Picchu. Some suggest, for example, that it might not have been anything more than a holiday retreat– “a 15th century Camp David” for the Inca emperor Pachacuti (2). The true identity remains a mystery largely because the Incas had no written language by which to document their activities. However, much of what has been found including skulls and early documents written by the Spanish points to Machu Picchu as having been some sort of vacationing resort (2).

As we set off late that afternoon on the last train to Cuzco, we began to ponder not only on the enigma of how Hiram Bingham had ever been able to find the Machu Picchu ruins but also on the more general question of how civilizations like those of the Incas had emerged, thrived and fallen at the mercy of unpredictable circumstances. The same question was rekindled in my mind almost a decade later when, during my time at the University of Strasbourg in France, I made my first trip to the Louvre museum in Paris and saw the fantastic displays of Roman remains, the accounts of scholarship of the ancient Greeks and the exquisite art of the Chinese dynasties.

In February of 2006, anthropologist Ken-Ichi Shinoda spear-headed a study to genetically characterize ancient DNA from corpses recovered by Hiram Bingham himself from around the Machu Picchu site (3). Using PCR-based amplification, mitochondrial DNA from these corpses was compared to that of individuals in extant Peruvian and Bolivian highland communities (3). Shinoda’s group discovered a “strong genetic affinity” between these highland groups and the Pre-Hispanic populations that had at one time served Machu Picchu.

More recent investigations have demonstrated the application of DNA extraction and STR amplification technologies–notably the Promega automated Maxwell® 16 System and PowerPlex® 16 System for the analysis of DNA in ancient samples (4). Future genetic studies may allow us to glean more information on the relatedness between existing and ancient populations. Furthermore the identification of paleodiseases in mummified remains could provide critical histological information on the health issues that may have contributed to the demise of civilizations such as the Incas (5).

  1. Daniel Eisenberg (1989) The Editor’s Column: Machu Picchu And Cuzco. Journal Of Hispanic Philology, 13, 97-101.
  2. Jeffrey Kluger (2003) Spiritual Retreat. TIME Magazine February 24, 46–7
  3. Shinoda,K-I. (2006) Mitochondrial DNA analysis of ancient Peruvian highlanders. American Journal Of Physical Anthropology 131, 98–107.
  4. Torres, F., Moraga, M. and Rios, J. (2009) Characterization Of Genetic Markers Of A Kawésqar Body And The Last Descendants Of The Same Ethnic Group. Profiles In DNA
  5. Rühli, F.J., Chhem,R.K., Boni, T. (2004) Diagnostic Paleoradiology Of Mummified Tissue, Interpretation And Pitfalls. Canadian Association of Radiologists Journal, 218–27.
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Robert Deyes

Robert has been a Technical Services Scientist at Promega for over 10 years. He also worked for two years as a Technical Advisor at the Paisley, Scotland facility of Life Technologies Inc. After earning his Masters in Medical Genetics from the University of Glasgow, he spent 18 months at the Université Louis Pasteur in Strasbourg, France where he did research into the molecular basis of the inherited disorder Spinal Muscular Atrophy. He also holds a BSc from the University of Portsmouth in England.

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