An international team contributed to the research, which compared the DNA sequences of 35 modern people living on islands off the coast of New Guinea with DNA drawn from two early human species: Denisovans, whose remains were found in Siberia, and Neandertals, first discovered in Germany.

“Substantial amounts of Neandertal and Denisovan DNA can now be robustly identified in the genomes of present-day Melanesians, allowing new insights into human evolutionary history,” they write. “As genome-scale data from worldwide populations continues to accumulate, a nearly complete catalog of surviving archaic lineages may soon be within reach.”

Andrew Merriwether, a molecular anthropologist at Binghamton University, collected the modern-day blood samples used in the study about 15 years ago in Melanesia. This is the first time full genomes from those samples have been sequenced.

“I’m surprised that these Neandertal and Denisovan genomes made it out to this remote place,” he says. “We know people have been there for at least 48,000 years because we find human remains that go back that far, but no one has ever been able to connect them to any other place. When you compare most of their genome sequences, they don’t cluster with any other group. They’ve been there and been isolated for a very, very long time.”

Earlier studies have revealed some genetic overlap (about 2 percent) between Neandertals and non-African populations and little or no Neandertal and Denisovan ancestry among Africans. This new research suggests Neandertals and modern human ancestors intersected at least three times. It also found an overlap of between 1.9 and 3.4 percent in the genetic codes of Denisovans and modern-day Melanesians.

Skepticism about the new findings is entirely appropriate, says Merriwether, who specializes in reconstructing the past using samples from contemporary populations and ancient DNA from the archaeological record.

“Ancient DNA is always damaged and broken into small pieces,” he explains. “You only need one molecule of modern DNA to outperform all the ancient DNA.”

An independent laboratory did the sequencing of Merriwether’s samples. That, combined with a powerful new statistical technique that was used in the analysis, finally convinced him that the genetic similarities were real.

The cost and time involved in sequencing a full human genome has dropped dramatically. The first, completed in 2003, took 13 years and cost about $2.7 million. Today, it’s possible to sequence a sample in days for thousands of dollars. Still, this type of research still poses significant challenges.

The human genome contains about 3 billion “letters,” and ancient samples are difficult to work with. When people die, their DNA starts breaking down immediately, Merriwether notes, and it isn’t repaired anymore. Normally, a person’s DNA is fixed thousands of times a minute. Bacteria and fungi contaminate most DNA samples taken from human remains, he says, making up as much as 97 percent of the DNA that’s recovered.

Even collecting the modern samples wasn’t a simple task.

Merriwether and longtime collaborator Jonathan Friedlaender of Temple University obtained blood samples throughout the Bismarck Archipelago in the late 1990s and early 2000s. They traveled with George Koki of the Institute for Medical Research in Papua New Guinea and Heather Norton, then a student at Penn State and now a faculty member at the University of Cincinnati.

“It’s challenging to reach these places,” Merriwether says. “They’re volcanic islands with mountains. It’s also the most linguistically diverse place on Earth.”

How diverse? People in this region speak some 800 languages. A common trading language (Tok Pisin) that’s a mix of Polynesian and English helped make it possible for the anthropologists to communicate with residents.

Because malaria is so prevalent in the region, there are many clinics set up to test and treat people. That also meant Merriwether and his colleagues usually weren’t the first people asking residents of these islands for blood samples.

Studies like this one may enable scientists to answer big questions about human migrations and evolution thousands of years ago.

Merriwether is particularly fascinated by the Denisovan DNA fragments found in the Melanesian genomes. How did ancient humans travel — and cross the ocean — to get to Melanesia and when and where did the Denisovan DNA enter our gene pool? Sequencing of additional DNA samples found in Asia may one day help to answer those questions.

“Most people know back a few generations, maybe five generations,” Merriwether says, “but where did we come from before that? That’s what we want to find out.”

The study’s authors are based at Binghamton University, the University of Washington, the University of Ferrara in Italy, the Max Planck Institute for Evolutionary Anthropology in Germany, the University of Cincinnati, the Coriell Institute for Medical Research, the Institute for Medical Research in Papua New Guinea and Temple University.

This perspective comes from a study of ancient DNA carried out by an international research team. Rolf Quam, a Binghamton University anthropologist, was a co-author of the study led by Anders Götherström at Uppsala University and Love Dalén at the Swedish Museum of Natural History, and published in the journal Molecular Biology and Evolution.

“The Neandertals are our closest fossil relatives and abundant evidence of their lifeways and skeletal remains has been found at many sites across Europe and western Asia,” said Quam, assistant professor of anthropology. “Until modern humans arrived on the scene, it was widely thought that Europe had been populated by a relatively stable Neandertal population for hundreds of thousands of years. Our research suggests otherwise and, in light of these new results, this long-held theory now faces scrutiny.”

Focusing on mitochondrial DNA sequences from 13 Neandertal individuals, including a new sequence from the site of Valdegoba cave in northern Spain, the research team found some surprising results. When they started looking at the DNA, a clear pattern emerged. Neandertal individuals from Western Europe that were older than 50,000 years and individuals from sites in western Asia and the Middle East showed a high degree of genetic variation, on par with what might be expected from a species that had been abundant in an area for a long period of time. In fact, the amount of genetic variation was similar to what characterizes modern humans as a species. In contrast, Neandertal individuals from Western Europe that were younger than 50,000 years show an extremely reduced amount of genetic variation, less even than the present-day population of remote Iceland.

These results suggest that Western European Neandertals went through a demographic crisis, a population bottleneck that severely reduced their numbers, leaving Western Europe largely empty of humans for a period of time. The demographic crisis seems to coincide with a period of extreme cold in Western Europe. Subsequently, this region was repopulated by a small group of individuals from a surrounding area. The geographic origin of this source population is not clear, but it may be possible to pinpoint it further with additional study.

“The fact that Neandertals in Western Europe were nearly extinct, but then recovered long before they came into contact with modern humans came as a complete surprise to us,” said Dalén, associate professor at the Swedish Museum of Natural History in Stockholm. “This indicates that the Neandertals may have been more sensitive to the dramatic climate changes that took place in the last Ice Age than was previously thought.”

Quam concurs and suggests that this discovery calls for a major rethinking of the idea of cold adaptation in Neandertals.

“At the very least, this tells us that without the aid of material culture or technology, there is a limit to our biological adaptation,” Quam said. “It may very well have been the case that the European Neandertal populations were already demographically stressed when modern humans showed up on the scene.”

The results presented in the study are based entirely on degraded ancient DNA, and the analyses have therefore required advanced laboratory and computational methods. The research team includes statisticians, experts on modern DNA sequencing and paleoanthropologists from Sweden, Denmark, Spain and the United States.

“This is just the latest example of how studies of ancient DNA are providing new insights into an important and previously unknown part of Neandertal history,” Quam said. “Ancient DNA is complementary to anthropological studies focusing on the bony anatomy of the skeleton, and these kinds of results are only possible with ancient DNA studies. It’s exciting to think about what will turn up next.”