Timeline of
Ancient DNA
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1984
Ancient DNA research begins with genetic analysis of 140-year-old ancient zebra
The field of ancient DNA was launched in 1984 when Allan Wilson and his team at the University of California, Berkeley, retrieved two short sequences of mitochondrial DNA from a 140-year-old museum skin specimen from a quagga (Equus quagga). The quagga, a South African horse relative that became extinct late in the 19th century, was known by a unique pattern of stripes on the front part of its body. DNA analysis showed that quaggas were more closely related to zebras than to horses. From a technological standpoint, this analysis demonstrated that traces of DNA could be obtained from museum specimens.
Did you know? The name “quagga,” used by the Khoikhoi people, referred to any type of zebra found on the African Plains and was probably an attempt to imitate the animal’s call: “kwa-ha-ha.”
1985
Researchers look at 2,400-year-old Egyptian mummies to understand ancient DNA
Egyptians are famous for practicing mummification between 2600 BC and 400 AD. In 1985, Swedish biologist and ancient DNA trailblazer Svante Paabo analyzed 23 Egyptian mummies and detected DNA in two adults and an infant. Skin from the infant’s lower leg, approximately 2,400 years old, contained about 5% as much DNA as expected in fresh tissue. Amazingly, this ancient human DNA was well-enough preserved to be recovered, cloned, and sequenced.
Did you know? Ancient Egyptians mummified rams, gazelles, lions, hawks, fish, birds, dogs, and cats – lots and lots of cats!
1989
DNA analysis reveals closest living relatives to now-extinct Tasmanian tiger
The now- extinct Tasmanian tiger was a dog-like marsupial once widespread in Australia. From a bone sample collected in Tasmania before 1893, ancient DNA pioneers Allan Wilson and Svante Pääbo recovered short stretches of mitochondrial DNA with polymerase chain reaction (PCR) technology. A comparison with mitochondrial DNA from six types of living marsupials from South America and Australia showed that the Tasmanian tiger was closely related to current carnivorous Australian marsupials, such as the tiger quoll. It also demonstrated that DNA retrieval from museum specimens by PCR was a successful approach to studying extinct animals.
Did you know? The last Tasmanian tiger, called Benjamin, died in captivity on September 7, 1936 at Hobart Zoo after being left out in the cold.
1990
The best-selling novel Jurassic Park introduces ancient DNA technology to readers
This sci-fi thriller by Michael Crichton, along with Steven Spielberg’s blockbuster movie Jurassic Park (1993) introduced the public to the idea that extinct life could be resurrected by recovering and cloning ancient DNA. The thought that dinosaurs could be cloned from DNA retrieved from dinosaur-biting insects preserved in amber was contested in 2013. A team of researchers led by Terence Brown at the University of Manchester, UK, found no DNA in insects trapped in modern amber – indicating that previous claims that DNA could be successfully taken from insects fossilized in amber millions of years ago were false.
Did you know? Jurassic Park was the highest-grossing film at the time of its release and won three Academy Awards in 2006. Sequels include the Lost World: Jurassic Park (1997); Jurassic Park III (2001); and Jurassic World (2015).
1992
DNA from extinct giant birds recovered from 3,550 years old museum specimens
Moas were giant flightless birds that lived in New Zealand during the Pleistocene epoch (about 2,588,000 to 11,700 years ago). The largest moa species reached 12-feet high with neck extended and weighed about 500 pounds! All moas were extinct by 1400 A.D. due to overhunting and general habitat loss. In 1992, a team of international scientists led by Allan Wilson and Svante Pääbo sequenced short stretches of mitochondrial DNA from museum specimens of four moas dating as far back as 3,550 years ago. In 1992, this was the oldest DNA sequence ever recovered, and its analysis helped unravel the relationships between moas and living flightless birds such as ostriches and kiwis.
Did you know? The nine species of moas were the only true wingless birds, lacking even the residual wings present in all other wingless birds such as ostriches.
1994
DNA of tuberculosis found in 1,000-year-old pre-Columbian Peruvian mummy
In palaeomicrobiology, the DNA most frequently extracted is from the pathogen Mycobacterium tuberculosis, commonly known as tuberculosis or TB. TB has afflicted humans for at least 8,000 years. One of the first studies to extract pathogen DNA from archaeological specimens demonstrated M. tuberculosis DNA in a 1,000-year-old Peruvian mummy, proving that tuberculosis existed in pre-Columbian South America. The investigators used polymerase chain reaction (PCR) to amplify IS6110, a short DNA tag derived from the M. tuberculosis genome. IS6110 still remains a means for detecting M. tuberculosis DNA in ancient samples.
Did you know? Analysis of ancient M. tuberculosis DNA suggests that humans infected their livestock with TB during domestication, instead of the other way around as traditionally believed.
1994
First woolly mammoth DNA recovered from Siberian species
Woolly mammoths shook the ice-age tundras for millennia, living next to prehistoric humans. In 1994, Erika Hagelberg at the University of Cambridge, UK, and Matthias Höss at the Institute of Zoology, Germany, independently reported extracting DNA from Siberian mammoth bones 9,000 to 50,000 years old. In 1994, this was the oldest DNA ever recovered. The studies targeted mitochondrial and ribosomal sequences, respectively, because each cell contains many copies of both. In 2008, the woolly mammoth’s nuclear genome was reported – the first complete genome-wide sequence ever obtained from an extinct animal.
Did you know? Woolly Mammoths are famous for their extra-long tusks, which measured up to 15 feet on the biggest males.
1997
90 centuries and 300 generations later, DNA links British caveman to local teacher
Cheddar Man, considered Britain's oldest complete skeleton at 9,000 years old, was found in 1903 in Gough’s cave in Cheddar Gorge, Somerset, England. His remains are kept by the Natural History Museum in London. In 1996 Bryan Sykes, a documentary filmmaker researching a series on archaeology in Somerset, decided to test whether the Cheddar Man had any descendants in Somerset. A team of Oxford University researchers distributed DNA test kits to local Cheddar schools, and a mitochondrial DNA match was found to a local schoolteacher, Adrian Targett. In 2013, Australian and British descendants of Cheddar Man met for a unique family reunion in the cave where the Cheddar Man's skeleton once lay.
Did you know? Cheddar Man and his descendants are part of the world's oldest known family tree.
1997
First successful identification of ancient malaria DNA from human remains
Malaria affects the blood, liver, and spleen but leaves no marks in skeletal remains. Thus, the presence of malaria in ancient human remains can only be identified using immunological or molecular tools. This was the first study to demonstrate malarial infection by finding DNA from the infectious organism – Plasmodium falciparum – in the remains of a person who had died some time ago (in 1937). Since this study, scientists have extracted P. falciparum DNA from much older human samples, such as 1,500-year-old bones from Rome and mummified Egyptian remains.
Did you know? The study of traces of microbial DNA in ancient human remains contributes to the treatment of human disease and the development of forensic science.
1997
Scientists study ancient virus for answers to the deadly 1918 “Spanish flu” pandemic
The “Spanish” influenza of 1918-1919, which killed at least 20 million people, was the most deadly pandemic in human history. To understand the pandemic’s origins and unusual virulence, Thomas Fanning at the Armed Forces Institute of Pathology, Washington, DC, isolated viral RNA from the laboratory-prepared tissue of a 1918 flu victim. By sequencing RNA fragments from the influenza virus, they found the virus was an H1N1 strain that could infect humans and swine, but not birds. In 2005, Dr. Fanning’s team successfully reconstructed the complete 1918 influenza virus genome, advancing the development of new flu vaccines and treatments.
Did you know? The 1918 “Spanish” flu was especially deadly to people 20 to 40 years old, decreasing the average U.S. life span by a full 10 years.
1998
DNA from ground sloths’ fossilized dung reveals ecology of lost world
DNA in fossilized dung from a cave near Las Vegas has revealed the diet of long-extinct Shasta ground sloths. The hairy mammals become extinct about 11,000 years ago. Shaped a bit like giant anteaters, these sloths weighed around 400 pounds and only ate plants. Previous attempts to extract DNA from fossilized dung had failed, but Hendrik Poinar and Svante Pääbo at the Max-Planck Institute, Germany, treated the samples with an agent that broke chemical bonds and freed DNA for analysis. Plants commonly eaten by these sloths were capers and mustards, along with lilies, grasses, mints, and a member of the grape family.
Did you know? Another species of ground sloth, the gigantic Megatherium, weighed more than 5 tons and could be as much as 20 feet tall – larger than an African bull elephant.
2003
From teosinte to tortillas: Domestication of corn is revealed
Corn (Zea mays) was domesticated from Mexican wild grass teosinte 6,300 years ago. Traditionally, archaeologists have studied corn domestication based on the shape of corncobs found at archaeological sites. Ancient DNA technology now allows tracking how and when early farmers selected for other features. Using corn samples from Mexico and the U.S., Viviane Jaenicke-Despres and Svante Pääbo at the Max-Planck Institute, Germany, discovered that, by 4,400 years ago, farmers had considerably reduced corn’s natural genomic diversity. They selected variants for at least three genes influencing plant morphology and starch content in corn kernels.
Did you know? An ear of teosinte bears only five to 12 kernels; but thanks to selective breeding by generations of farmers, one ear of corn now contains more than 500!
2003
Ice cores from Siberia reveal DNA of ancient plants and animals
In this pioneering study, evolutionary biologist Eske Willerslev at the University of Copenhagen, Denmark, obtained five permafrost cores from Siberia ranging from 400,000 to 10,000 years old. Analysis revealed that sediments deposited in the cores contained DNA from at least 19 types of plants – including the oldest DNA sequences known at the time. The sediments also contained DNA sequences from megafauna (large animals) including horses, bison, and mammoths. This kind of DNA information helps scientists track the regional changes in types and diversity of plants and animals.
Did you know? An ice core taken from the right site can be used to reconstruct an uninterrupted and detailed climate record extending over hundreds of thousands of years.
2005
Scientists recover DNA from 40,000-year-old cave bears and their environment
Cave bears roamed Western Europe about 250,000 years ago and became extinct around 12,000 years ago. James Noonan and Edward Rubin at Berkeley National Laboratory, CA, extracted DNA from 40,000-year-old cave bear samples using a novel metagenomic approach. This technique avoids polymerase chain reaction (PCR), which selectively amplifies modern DNA contaminants over ancient sequences. After cloning all of the sample’s DNA in bulk, powerful computer analyses were used to identify the tiny fraction of ancient DNA in the mix. Six percent of the DNA recovered showed about 97% identity with DNA from modern brown bears – supporting the validity of metagenomics for recovering ancient DNA from complex samples.
Did you know? Cave bears lived in the same spaces coveted by prehistoric humans in Europe around 32,000 years ago.
2005
Paleoindians brought bottle gourds to Americas 10,000 years ago – or did they?
The bottle gourd (Lagenaria siceraria), an early-domesticated plant, was eaten and used to craft water containers. Native to Africa, the gourd was grown in Asia, Europe, and the Americas long before Columbus arrived. Scholars asked how the gourd reached America: Was it wild or domesticated when it arrived? Comparing DNA of ancient bottle gourds with modern Asian and African varieties, the Smithsonian’s David Erickson and collaborators concluded that Paleoindians brought gourds from Asia to the Americas about 10,000 years ago. Yet, a 2014 study of gourds’ chloroplast DNA indicates an African source. Still questions remain: How did the gourds reach Asia? And why are there few wild varieties?
Did you know? Among its many reported cultural uses, the gourds can be dried and used to smoke pipe tobacco.
2007
Ice-covered Greenland was a conifer forest half-a-million years ago
Ice and glaciers cover about 10% of the earth’s landmasses, limiting our ability to study these lands in the distant past. In this study, Eske Willerslev and his team at the University of Copenhagen, Denmark, extracted the oldest DNA recovered to date from the basal sections of deep ice cores in southern Greenland. When compared with DNA of modern animals and plants, these ancient DNA fragments revealed conifers such as alder, pine, spruce, and yew trees in Greenland’s past. The ice also contained DNA from beetles, flies, butterflies, and spiders. Dating indicated that the DNA was at least 450,000 years old – a result confirmed by several labs and techniques.
Did you know? Greenland, the world's largest island, is about 80% ice-capped, with an ice thickness of 1,500 meters on average.
2010
Fossilized eggshells yield well-preserved DNA – even in warm climates
Michael Bunce and graduate student Charlotte Oskam at Murdoch University, Western Australia, collected fragments of fossil eggshells from Australia, New Zealand, Madagascar, museum collections, and excavation sites. The shells included fragments from eggs of extinct moas (Pleistocene era), extinct elephant birds (Holocene era), as well as ducks, emu, and owl. Both mitochondrial and nuclear DNA were extracted successfully. Astonishingly, the moa eggshell had only 1/125 the bacterial contamination typical of fossil bone samples. The quality of DNA preservation pointed to fossil eggshells as excellent ancient DNA sources, even in warm climates.
Did you know? In 2013, a partially fossilized elephant-bird egg from Madagascar was sold by Christie's auction house for $101,813.
2010
Secrets of the Pharaohs: family tree of King Tutankhamen unveiled
Researchers performed genetic analyses on 11 royal Egyptian mummies from about 1400 BC – thought to be related to King Tutankhamen – and five more royal Egyptian mummies roughly a century older. They looked for indications of infectious disease, inherited disorders, and close blood relationships. King Tutankhamen’s parents were identified, and four mummies contained genes specific to Plasmodium falciparum – the oldest genetic proof of malaria in precisely dated mummies. Overall, a five-generation family tree, showing relationships between members of Tutankhamun’s immediate family, was unraveled.
Did You Know? King Tutankhamen inherited the throne of Egypt when he was only 8- or 9-years old and died 10 years later.
2010
Neanderthal genome yields insights into human evolution
When Homo sapiens spread from Africa to the Middle East about 60,000 years ago, Neanderthals already occupied that region. Did the two species ever meet? Svante Pääbo at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany sought answers from DNA in ancient bones. Neanderthal DNA is so close to that of H. sapiens, that one difficulty in sequencing was the possibility of contamination with modern people’s DNA. After limited success in the late 1990s, the Neanderthal Genome Project was launched in 2006, achieving an historic milestone in 2010 by publishing a draft genome sequence from 40,000-year-old Neanderthal samples. The data suggested some degree of interbreeding between the two species.
Did you know? Some modern humans are part Neanderthal. Research indicates that non-Africans living today have from 1 to 4 percent Neanderthal DNA in their genomes.
2010
Early Greenland settler “Inuk” has whole genome decoded
Genomics can yield knowledge about now-extinct cultures. The remains of 4,000-year-old “Inuk” – “Person” in Inuit languages – were found in Qeqertasussuk, Greenland. From four frozen hair strands, Morten Rasmussen and Eske Willerslev sequenced the genome of one of the earliest known inhabitants of the Arctic. Genetic evidence traced his lineage to Siberia around 5,500 years ago, as part of a previously unknown migration. The man probably had Type A+ blood, shovel-graded front teeth, and dry earwax typical of modern East Asians and Native Americans.
Did you know? Inuk was the ninth human to have their entire genome sequenced but unlike the previous eight, he had been deceased for millennia.
2011
Cave paintings show true colors of Stone Age horses
The famous spotted horses of the Pech-Merle Cave in France (dating back ~25,000 years) resemble the “leopard coat” of today’s horses. When Arne Ludwig of the Leibniz Institute for Zoo and Wildlife Research, Germany, and Michael Hofreiter of the University of York, UK, analyzed DNA from 31 prehistoric horses from Siberia, as well as Eastern and Western Europe (about 35,000 to 2,200 years ago), six had a genetic variant – named LP – corresponding to leopard-like spotting in modern horses. Moreover, of 10 Western European horses with lineage estimated at about 14,000 years old, four had the LP variant, suggesting that the paintings represent the animals’ true appearance.
Did you know? The 1,250 documented cave paintings of horses comprise about 30% of all animal illustrations in European Upper Paleolithic cave art.
2011
Black Death genome dug out from burials in a London plague cemetery
Yersinia pestis, a cause of the Black Death, wiped out nearly half of Europe’s population in the mid-1300s. Although Y. pestis is still around, infections are not as deadly or frequent as previously. Johannes Krause and his team at the University of Tübingen, Germany, recovered DNA from the skeletons of four 660-year-old plague victims buried in London’s East Smithfield Cemetery. When compared with modern Y. pestis, no genomic differences accounted for the lethal power of the Black Death. Researchers think its high mortality may be partially explained by the 14th century environment – where malnutrition, poor hygiene, and crowded housing were common.
Did you know? Y. pestis was carried by fleas that live primarily on rats and other rodents that were common in medieval cities.
2011
Fossilized fingertip in Siberia reveals missing human species, the Denisovans
The remains found in the remote Denisova cave in Siberia in 2008 were modest: a fingertip and two teeth. In 2011, scientists led by Svante Pääbo announced they had reconstructed an entire human genome from these fragments – discovering a lineage of ancient humans never known before. For the first time, a new group of extinct humans was defined just from DNA evidence and not from bone morphology. The Denisovans – dated in this study to about 80,000 years ago – share more genes with people from Papua New Guinea than any other modern population studied. This suggests that Denisovans and modern humans might have crossed paths in central Asia.
Did you know? The Denisova cave is the one spot on Earth that we know of where Neanderthals, Denisovans, and modern Homo sapiens all lived at some point.
2012
Ancient syphilis genome recovered from newborns deceased in the 16th-17th Century
Isolating syphilis (Treponema pallidum) DNA from ancient specimens has usually been very unsuccessful. Rafael Montiel at the Instituto Politécnico Nacional, Mexico, collaborated with Assumpció Malgosa in the Universitat Autònoma, Spain, and others to amplify T. pallidum DNA obtained from two newborns affected by syphilis from birth. These 16th-17th century individuals were the most ancient to date in which T. pallidum DNA was successfully detected. It’s likely that the preservation of T. pallidum DNA was favored by the bacteria’s rapid dissemination through the newborns’ immature skeletons.
Did you know? Scientists now believe that the crew of Christopher Columbus possibly brought syphilis back to Europe.
2012
Tyrolean Iceman mummy, “Ötzi,” has whole genome decoded
The shockingly well-preserved, frozen mummy of the Tyrolean Iceman, “Ötzi,” was discovered in 1991 in the Italian Alps. Genetic analyses of the 5,300-year-old Copper Age man began in 1994, recovering partial mitochondrial sequences, and culminated in 2012 with whole genome sequencing of a sample from his hipbone. Ötzi probably had brown eyes, Type O blood, and lactose intolerance. He was genetically predisposed to heart disease and suffered from Lyme disease. Other genetic studies focused on his last meal (red deer meat and, possibly, cereals) and his sheep’s lineage – inferred from DNA in hair shafts from his clothes.
Did you know? In 2013, researchers identified 19 living relatives of Ötzi among 3,700 people in the Tyrolean region.
2013
Medieval leprosy genome compared with modern strains
Leprosy results from infection with Mycobacterium leprae bacteria, and leads to nerve damage and mutilation. Leprosy, seen in Europe until the 16th century, is still common in the developing world. Johannes Krause at the University of Tübingen, Germany, obtained nearly complete genomes of M. leprae from 11th- to 14th-century European skeletal remains and recent biopsies worldwide. DNA from ancient M. leprae was astonishingly preserved, likely because the bacteria’s thick waxy cell wall protects DNA from environmental destruction. Sequence comparisons revealed little genomic changes among M. leprae strains during the past 1000 years, and showed that leprosy in the Americas originated in Europe.
Did you know? Armadillos, the only animals besides humans known to carry leprosy, can transmit the disease to humans.
2013
Mystery of Irish potato famine solved by DNA sequencing 170 years later
The fungus Phytophthora infestans (Irish potato famine of 1845-1849) caused one million deaths, up to two million refugees, and a century-long population decline in Ireland. Today, P. infestans remains a threat to potato production worldwide. In 2013, Thomas Gilbert and others at the University of Copenhagen sequenced five 19th-century European strains from archival herbariums – including the oldest-known European specimen (1845). Comparisons with modern strains illuminated the fungus’s migratory story and revealed P. infestans as an aggressive pathogen, mutating quickly to overcome fungicides and the breeding of resistant potato crops.
Did you know? Ireland’s disproportionate dependency on the Irish Lumper potato variety reduced genomic diversity of the crops and contributed to the devastation.
2013
Ancient medical kit in shipwreck reveals ingredients of Roman medicine
Archaeologists studying a merchant vessel sunk off the Tuscan coast around 120 BC found a surprise in 1998 – ancient medicinal pills the size of coins in tin boxes. Using next-generation DNA sequencing, Smithsonian scientists determined in 2011 that the pills contained crushed celery, onions, carrots, cabbage, alfalfa, chestnuts, radish, yarrow, parsley, nasturtium, hibiscus, and clay – probably to treat intestinal disorders. Dr. Alain Touwaide, Smithsonian’s National Museum of Natural History, says the remedies are documented in Ancient Greek medical texts, later modeled by Ancient Romans. These are the only known archaeological remains of ancient medicines.
Did you know? The Institute for the Preservation of Medical Traditions has the world's largest digital database of medical manuscripts.
2013
700,000-year-old horse genome shatters the age record for ancient DNA
A multinational team of scientists led by Ludovic Orlando and Eske Willerslev at the University of Copenhagen are analyzing the oldest genome ever sequenced, from a horse bone frozen in permafrost in the Yukon region of Canada. The specimen, dating 560,000-780,000 years old, is nearly 10 times older than the oldest full genome previously sequenced (a 120,000-year-old polar bear). The analysis used Single DNA Molecule Sequencing, in which a machine reads DNA directly without needing to amplify it. The ancient horse genome revealed that the common lineage of present-day horses, donkeys, and zebras arose 4.0-4.5 million years ago, twice as long ago as previously estimated.
Did you know? The Przewalski's horse is the only living wild horse species and is native to Mongolia in Central Asia.
2013
DNA in fossilized dental plaque traces human diet from Neolithic through modern times
Early humans had cavity-free teeth at the time they were consuming a low-starch diet. Christina Adler and Alan Cooper at the University of Adelaide in South Australia set to sequence the DNA from ancient dental plaque from Neolithic, Medieval, and Industrial revolution European skeletons. The farming and industrial revolutions – 10,000 and 150 years ago, respectively – had dramatic impacts on human tooth health, they found. As starches, processed sugar, and flour increased in the diet, the diversity of the bacteria in the mouth went down. Dangerous and unfriendly bacteria took hold, causing chronic diseases of the teeth, gums, and other body systems.
Did you know? Homo heidelbergensis Kabwe lived in Zambia 300,000 to 125,000 years ago and is one of the oldest humans known to have rampant tooth cavities.
2014
“Clovis Boy” DNA links ancient boy to American Indians and other Native peoples in the Americas
The 18-month-old’s bones discovered in Montana in 1968 are the only human remains ever found associated with the Clovis culture in the Americas. Whether the Clovis were the first people of the Americas, and the details of their migration routes, are hot research topics. The boy's genome shows that his lineage came from northeastern Asia, and that his people are direct ancestors of about 80% of Native Americans alive today. His genome also rules out any close affinity between Clovis and European people. This is in agreement with people migrating into the Americas about 15,000 years ago via a land bridge connecting what is now eastern Siberia with western Alaska.
Did you know? Clovis people crafted the “Clovis point,” a beautifully shaped projectile point found in northern Mexico, New Mexico, Texas, and many other portions of the United States.
2014
Genetic studies reveal kiwis are the closest living relatives of the huge elephant birds
Ratites are mostly flightless bird that include the African ostrich, South American rhea, Australian emu and cassowary, New Zealand kiwis and extinct moa, and Madagascar's extinct elephant bird. Alan Cooper at the Australian Centre for Ancient DNA analyzed elephant birds' mitochondrial DNA and found their closest living relatives were diminutive kiwis half a world away! As shown by this and other DNA research, ratites evolved from small birds that flew between continents about 50 million years ago, becoming large and flightless at least six independent times. This differs radically from the previous view that ratites evolved from a common large flightless ancestor.
Did you know? Convergent evolution produces similar traits in multiple lineages whose ancestors lacked the trait.