Modern humans once shared the Earth with a few other hominin lineages, the best known of which are Neanderthals. Living in Eurasia from a few hundred thousand years to roughly 30,000 years ago, Neanderthals’ muscular builds left them well adapted to the cold weather of the Pleistocene Epoch. Unlike modern humans, they had pronounced brow ridges and bulges at the back of their skulls, along with receding chins and broad noses. Despite their pop culture reputation for being brutish cavemen, Neanderthals actually had slightly larger brains than modern humans. Among other signs of intelligence, they purportedly used tools, buried their dead, controlled fire, created artwork and may have even built boats.

No one knows for sure why they died out. “There probably were never that many Neanderthals around,” said Ian Tattersall, a paleoanthropologist at the American Museum of Natural History, “and they were probably very vulnerable to extinction.” Some experts believe that modern humans either violently displaced them or indirectly outcompeted them upon moving out of Africa into Eurasia, whereas others hypothesize that climate change did them in or that they were absorbed into the modern human population due to interbreeding. The later of these theories received somewhat of a boost in 2010 when Pääbo and his team announced that about 1 percent to 4 percent of the DNA of non-Africans comes from Neanderthals. Most Africans, on the other hand, have no Neanderthal DNA, the scientists found.

A subsequent study, however, asserted that Neanderthals and modern humans rarely mated with each other, if ever, and that their similar genomes were simply the result of having a common ancestor. “We don’t know where, and we don’t know when, and we don’t know how often,” John Hawks, a paleoanthropologist at the University of Wisconsin at Madison, said in reference to interbreeding between Neanderthals and modern humans. Some scientists want to believe it was essentially an unrepeated “one-night stand,” he added, while others want to believe that “every time they met they couldn’t keep their hands off each other.”

For their latest paper, which came out Monday in the Proceedings of the National Academy of Sciences, Pääbo and his team partially sequenced the genome of an approximately 49,000-year-old Neanderthal from Spain and an approximately 44,000-year-old Neanderthal from Croatia. They then compared those specimens, along with a third Neanderthal from Siberia that was part of Pääbo’s original genome project, with the DNA of several modern humans. “You’re looking at data from these Neanderthals that is as good as looking at living people,” said Hawks, who is unaffiliated with the study. Comparisons were also made with the DNA of a Denisovan, another kind of ancient hominin known only from a single Siberian cave.

In addition to remarking on Neanderthals’ low genetic diversity, the study noted that they appeared to lack certain genes, such as those related to hyperactivity and aggressive behavior. The study cautioned, however, against jumping to conclusions on how those genes manifest themselves. “For example, if they affected activity or aggression levels, it is unclear whether they increased or decreased such traits,” the study said. Since the three Neanderthals analyzed did not live contemporaneously, the DNA sequences from more specimens should be taken as they become available, according to the study. Hawks concurred, saying that would allow us to find out if Neanderthal individuals “are different because one group replaced the other one, or are they different because they lived in different places.”