ACCORDING to the history books, the Madeira archipelago 600 kilometres west of Africa was discovered in 1419 when Portuguese mariners were blown off-course by a storm. In Roman times Pliny and Plutarch wrote about islands that might be Madeira, but there is no definite account of the islands, nor any signs of people, prior to the arrival of the Portuguese. The mice of Madeira Island, however, tell a different and unexpected story.
The mice are not native to the island and must have arrived on European ships. Genetically, they most closely resemble the mice of Portugal. However, some of their DNA has strong similarities to that of mice found in Scandinavia – a strong hint that Viking ships found Madeira long before the Portuguese. “It might have been a temporary occupation, or just a few boats landing for a short period of time,” says Jeremy Searle, an evolutionary biologist at the University of York in the UK and an author of the study (). “But the mice are telling us something that no artefact so far has told us.”
Madeira’s mice are not an isolated case. Like spies in the halls of history, our animal and plant companions hold lost secrets about our past. Through their genes we can trace the paths of ancient migrations and trade routes, and sometimes unpick the knot of successive waves of colonisation. Plants and animals can also help archaeologists date the origin of some of the major innovations of human culture, such as the first use of clothing and the beginning of high-density urban living. They can even help researchers glimpse the motives of ancient peoples as they laid the cornerstones of civilisation.
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For instance, anthropologists have long been fascinated by one of the greatest seagoing migrations ever undertaken – the colonisation thousands of years ago of the remote islands of the south Pacific. Where did these ancient colonists come from? Did they spread through Polynesia in a single, rapid sweep, or was it a gradual move undertaken in several waves? The most obvious way to answer questions like these would be to study the DNA of Polynesian people. If they carry genetic variants shared only with, say, natives of Taiwan, that would point to a likely origin for the migration.
Ancestral DNA
However, this kind of study is not as simple as it sounds. Any clear genetic patterns that may once have existed would have been blurred over the past few centuries, making comparisons among modern people uncertain. A better alternative would be to extract DNA from human remains that pre-date European contact, but such remains are relatively scarce and, understandably, most communities do not want the bones of their ancestors ground up to extract DNA.
“If people don’t want their ancestors to be studied, then you just don’t do it,” says Lisa Matisoo-Smith, a molecular anthropologist at the University of Auckland in New Zealand. “So I said, how can we get at this in another way?”
She knew that the early colonists did not travel alone in their canoes. They brought pigs, chickens, dogs and even rats along with them. Perhaps, she thought, these domestic animals held the answer: the relatedness of the animals on different islands should be similar to that of the humans who brought them.
The rats proved especially helpful. Unlike the European rat, the Pacific rat, Rattus exulans, dislikes water and would not have scuttled aboard a boat of its own volition. Instead, the colonists took them for food. “The rats on the islands today are the direct descendants of the rats that arrived with the pre-European human population,” Matisoo-Smith says. This means there has been no later genetic “blurring”, so she could simply study modern rats rather than searching out ancient rat DNA.
Matisoo-Smith and her colleagues collected rat tissue from islands throughout the Pacific as well as from mainland Asia, and sequenced a short part of their mitochondrial DNA. This revealed two separate lineages of rats: one type in the Philippines, New Guinea and other islands of the western Pacific; and another on the more remote islands further to the east. Such a pattern is unlikely to be the result of a single wave of human migration, so the researchers concluded that there must have been at least two separate waves of colonisation (.
Bone of contention
Similar genetic analyses of pigs, chickens and dogs – using ancient DNA to avoid the blurring caused by the extensive trade in these animals – has turned up evidence of even more intricate settlement patterns. “It’s not that people came once and then there’s isolation,” says Matisoo-Smith. “It’s a much more dynamic process. The Pacific really is a highway. Once you have people moving, and you have knowledge of the island world, then everybody’s going to take advantage of that.”
Last year, the team turned up a big surprise: a single chicken bone, taken from a pre-Columbian archaeological site in Chile and dated to about AD 1400, yielded DNA sequences identical to those of prehistoric chickens from Tonga and Samoa in the south Pacific. This is the strongest evidence yet that Pacific islanders’ journeys took them all the way to South America on at least one occasion ().
“A chicken bone has shown that the Polynesians got as far as South America”
It might not be time to rewrite the history books yet, though. “There’s only one bone, and there’s one sequence, and there’s one date, which is just old enough. I’m happy with the data, but they need more of it,” says Keith Dobney, a zooarchaeologist at Durham University in the UK.
The worry is that because so little DNA remains in ancient specimens – especially in the warm, damp tropics – attempts to sequence it can be ruined by contamination with modern DNA. “One has to be sure there’s no other explanation for the chicken DNA in the bone. It could be something as ridiculous as that the archaeologist who handled it had chicken for lunch that day,” says Tom Gilbert, a specialist in ancient DNA at the University of Copenhagen in Denmark.
Trade routes
With more samples, careful handling and the latest techniques, though, studies of ancient DNA can yield solid results. Several research groups have now used this technique to track human migrations (see “Follow that hedgehog”). Similar approaches can also be used to unravel ancient trade routes, for instance by tracing the weevils found in Roman granaries in England back to their roots in the Mediterranean, a study which Gary King at the University of York is now beginning. If the same genotypes of weevils also turn up in medieval English granaries, it will show that the English were producing and storing grain throughout the Dark Ages. If, on the other hand, medieval weevils are different, it will confirm the idea that there was a period when grain was produced and stored only sporadically, causing the original colonists to die out.
The use of genotypes to study ancient trade routes has already thrown up one surprise. Anders Götherström, an evolutionary geneticist at Uppsala University in Sweden, has found African cattle genotypes in Bronze Age archaeological sites in Spain. This suggests that, even thousands of years ago, trade across the Strait of Gibraltar was extensive enough to include live cattle ().
Before Götherström’s study, people had noticed the presence of African genotypes in Spanish cattle, but assumed that they had arrived with the conquering Moors in the 8th century. “Nobody expected it to be any earlier than that,” says Götherström. “As long as we were relying on modern cattle DNA, we made the wrong conclusion. When we go back in time, we can see when it really came. It was there during the Bronze Age.”
Our companion species can reveal even more subtle things about our history (see “Gorillas gave us crabs”). The human head louse, for example, lives only in scalp hair. A closely related subspecies, the body louse, lives only in clothing, and so must have evolved from the head louse sometime after early humans created a new niche for them by wearing clothing regularly. Assuming this did not take long, dating the divergence of the two louse subspecies should give us a rough idea of when clothing became commonplace.
Recent invention
To do this, Mark Stoneking and his colleagues at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, sequenced DNA fragments from 40 head and body lice, and counted the genetic differences between the two. They then compared this with the number of genetic differences between human and chimpanzee lice, which are assumed to have diverged when proto-humans and chimps went their separate ways about 6 million years ago. Based on this comparison, the researchers estimate that human head and body lice must have diverged about 72,000 years ago, suggesting that clothing is a relatively recent human invention ().
While this work shows that much can be learned simply by looking at how closely plant or animal populations are related, some researchers are delving deeper. The latest trend in the growing field of genetic archaeology is to look at variations in the genes for specific functions.
One of the best examples comes from a study of flax plants led by Robin Allaby, a molecular archaeobotanist at the University of Warwick in the UK. Flax is unusual among crop plants because it provides two products – oil from the seeds, and fibre. Archaeologists disagree on which came first, so Allaby decided to read the genes directly. He collected a wide variety of flax lines and sequenced portions of a gene called sad2, which plays a role in the production of unsaturated fatty acids in the seeds. From these sequences he was able to reconstruct the genetic history of flax, which revealed that the ancestral form of sad2 was similar to the form typical of modern oilseed flax. Variants typical of fibre flax only appear relatively recently, suggesting that ancient people domesticated flax for its oil, rather than its fibre ().
As this shows, focusing on particular genes can sometimes tell us more than conventional archaeological artefacts. Applying the same approach to domestic animals should reveal, for example, when ancient people first began breeding cattle for milk or meat, Götherström says. He is now looking at DNA extracted from bones and teeth found in horse graves in the hope of determining whether certain colours of horse had greater ceremonial value in ancient times.
And this is just the start. As we sequence the genomes of more and more organisms, we will get ever better at reading the genetic runes, and researchers like Götherström should be able to uncover many more stories hidden within DNA of our plant and animal companions. Undoubtedly there will be many more surprises to come.
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Follow that hedgehog
The DNA of our companion plants and animals has already testified to several human migrations:
- The Swedish island of Gotland in the Baltic Sea supported a flourishing culture 4500 years ago, but it was unclear where the settlers came from. Hedgehogs held the answer. The island’s hedgehogs were brought with the people who settled there, and their DNA matches that of animals from regions to the west, in Denmark and Sweden, says Anders Götherström of Uppsala University in Sweden.
- Wheat genotypes clearly show two migrations of wheat-farming people into Europe from the Near East: an earlier migration along the northern shore of the Mediterranean, and a later one along the Rhine and Danube rivers, according to studies by Robin Allaby of the University of Warwick in the UK and colleagues.
- The voles of the Orkney Islands north of Scotland are most akin to those on the Atlantic coasts of France and Spain. Moreover, Orkney voles are enormously diverse. “We have more variation in this tiny Orkney archipelago than in all of western Europe, which is completely the opposite to what you’d expect,” says Keith Dobney of the University of Durham in the UK. This suggests that the Orkneys must have had a thriving sea trade with Europe during neolithic times, he says, and that the islands’ voles retain genetic diversity that has since been lost elsewhere.
- There were two separate migrations of maize farmers southward from Central America, one along the Andes and another further east, according to studies by Allaby.
Gorillas gave us crabs
Lice and other parasites that live in close proximity to people can tell us much about our history. For instance, the human pubic louse is most closely related to the body louse of gorillas.
Genetic studies by David Reed of the University of Florida in Gainesville suggest the two diverged just 3 million years ago – much more recently than humans diverged from gorillas. If so, early humans and gorillas must have been in close contact until that time, perhaps sharing caves. “If these data are to be believed, we can put Australopithecus at the same place and the same time as gorillas,” says Reed. “That would teach us a lot about gorilla biology 3 million years ago that we have scant other evidence for.”
Reed has also found two distinct lineages of modern human head lice, whose genes indicate they diverged more than a million years ago. He concludes that one lineage must have evolved on a different ancestral human species, perhaps Homo erectus, and only relatively recently shifted to Homo sapiens. This suggests that modern humans must have lived side by side with at least one other human species a few tens of thousands of years ago, he says.
Reed has now begun picking lice from ancient Peruvian mummies to extract their DNA. If he can get enough, he hopes to use them to retrace the peopling of the Americas. He also hopes to look at bedbugs and other parasites. “When you have lots of parasites to look at, you’ll really get a picture of the evolution of the host,” he says.
